Java tutorial
/** * BioLink API * API integration layer for linked biological objects. __Source:__ https://github.com/monarch-initiative/biolink-api/ * * OpenAPI spec version: 0.1 * * * NOTE: This class is auto generated by the swagger code generator program. * https://github.com/swagger-api/swagger-codegen.git * Do not edit the class manually. * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package io.swagger.client.api; import io.swagger.client.ApiCallback; import io.swagger.client.ApiClient; import io.swagger.client.ApiException; import io.swagger.client.ApiResponse; import io.swagger.client.Configuration; import io.swagger.client.Pair; import io.swagger.client.ProgressRequestBody; import io.swagger.client.ProgressResponseBody; import com.google.gson.reflect.TypeToken; import java.io.IOException; import io.swagger.client.model.Allele; import io.swagger.client.model.Association; import io.swagger.client.model.AssociationResults; import io.swagger.client.model.Gene; import io.swagger.client.model.BioObject; import io.swagger.client.model.Genotype; import io.swagger.client.model.NamedObject; import io.swagger.client.model.Substance; import java.lang.reflect.Type; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; public class BioentityApi { private ApiClient apiClient; public BioentityApi() { this(Configuration.getDefaultApiClient()); } public BioentityApi(ApiClient apiClient) { this.apiClient = apiClient; } public ApiClient getApiClient() { return apiClient; } public void setApiClient(ApiClient apiClient) { this.apiClient = apiClient; } /* Build call for getAlleleObject */ private com.squareup.okhttp.Call getAlleleObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getAlleleObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/allele/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns allele object * This is a composition of multiple smaller operations, including fetching allele metadata, plus allele associations TODO - should allele be subsumed into variant? * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Allele> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Allele> getAlleleObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Allele>> resp = getAlleleObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns allele object * This is a composition of multiple smaller operations, including fetching allele metadata, plus allele associations TODO - should allele be subsumed into variant? * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Allele>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Allele>> getAlleleObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getAlleleObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Allele>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns allele object (asynchronously) * This is a composition of multiple smaller operations, including fetching allele metadata, plus allele associations TODO - should allele be subsumed into variant? * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getAlleleObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Allele>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getAlleleObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Allele>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getAnatomyGeneAssociations */ private com.squareup.okhttp.Call getAnatomyGeneAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getAnatomyGeneAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/anatomy/{id}/genes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns associations between anatomical entity and genes * Typically encompasses genes expressed in a particular location. * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getAnatomyGeneAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getAnatomyGeneAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns associations between anatomical entity and genes * Typically encompasses genes expressed in a particular location. * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getAnatomyGeneAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getAnatomyGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns associations between anatomical entity and genes (asynchronously) * Typically encompasses genes expressed in a particular location. * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getAnatomyGeneAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getAnatomyGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getAnatomyObject */ private com.squareup.okhttp.Call getAnatomyObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getAnatomyObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/anatomy/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns anatomical entity * Anatomical entities span ranges from the subcellular (e.g. nucleus) through cells to tissues, organs and organ systems. * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getAnatomyObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getAnatomyObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * TODO Returns anatomical entity * Anatomical entities span ranges from the subcellular (e.g. nucleus) through cells to tissues, organs and organ systems. * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getAnatomyObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getAnatomyObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * TODO Returns anatomical entity (asynchronously) * Anatomical entities span ranges from the subcellular (e.g. nucleus) through cells to tissues, organs and organ systems. * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getAnatomyObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getAnatomyObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getAnatomyPhenotypeAssociations */ private com.squareup.okhttp.Call getAnatomyPhenotypeAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getAnatomyPhenotypeAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/anatomy/{id}/phenotypes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns associations between anatomical entity and phenotypes * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getAnatomyPhenotypeAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getAnatomyPhenotypeAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns associations between anatomical entity and phenotypes * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getAnatomyPhenotypeAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getAnatomyPhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns associations between anatomical entity and phenotypes (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getAnatomyPhenotypeAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getAnatomyPhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getDiseaseAnatomyAssociations */ private com.squareup.okhttp.Call getDiseaseAnatomyAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getDiseaseAnatomyAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/disease/{id}/anatomy/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns anatomical locations associated with a disease * For example, neurodegeneratibe disease located in nervous system. For cancer, this may include both site of original and end location. * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getDiseaseAnatomyAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getDiseaseAnatomyAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns anatomical locations associated with a disease * For example, neurodegeneratibe disease located in nervous system. For cancer, this may include both site of original and end location. * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getDiseaseAnatomyAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getDiseaseAnatomyAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns anatomical locations associated with a disease (asynchronously) * For example, neurodegeneratibe disease located in nervous system. For cancer, this may include both site of original and end location. * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getDiseaseAnatomyAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getDiseaseAnatomyAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getDiseaseFunctionAssociations */ private com.squareup.okhttp.Call getDiseaseFunctionAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getDiseaseFunctionAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/disease/{id}/function/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns biological functions associated with a disease * This may come from a combination of asserted knowledge (e.g. Fanconi Anemia affects DNA repair) or from data-driven approach (cf Translator) Results are typically represented as GO classes * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getDiseaseFunctionAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getDiseaseFunctionAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns biological functions associated with a disease * This may come from a combination of asserted knowledge (e.g. Fanconi Anemia affects DNA repair) or from data-driven approach (cf Translator) Results are typically represented as GO classes * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getDiseaseFunctionAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getDiseaseFunctionAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns biological functions associated with a disease (asynchronously) * This may come from a combination of asserted knowledge (e.g. Fanconi Anemia affects DNA repair) or from data-driven approach (cf Translator) Results are typically represented as GO classes * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getDiseaseFunctionAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getDiseaseFunctionAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getDiseaseGeneAssociations */ private com.squareup.okhttp.Call getDiseaseGeneAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getDiseaseGeneAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/disease/{id}/genes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns genes associated with a disease * * @param id CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getDiseaseGeneAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getDiseaseGeneAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns genes associated with a disease * * @param id CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getDiseaseGeneAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getDiseaseGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns genes associated with a disease (asynchronously) * * @param id CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getDiseaseGeneAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getDiseaseGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getDiseaseModelAssociations */ private com.squareup.okhttp.Call getDiseaseModelAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getDiseaseModelAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/disease/{id}/models/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns associations to models of the disease * In the association object returned, the subject will be the disease, and the object will be the model. The model may be a gene or genetic element. If the query disease is a general class, the association subject may be to a specific disease. In some cases the association will be *direct*, for example if a paper asserts a genotype is a model of a disease. In other cases, the association will be *indirect*, for example, chaining over orthology. In these cases the chain will be reflected in the *evidence graph* * TODO: provide hook into owlsim for dynamic computation of models by similarity * @param id CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getDiseaseModelAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getDiseaseModelAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns associations to models of the disease * In the association object returned, the subject will be the disease, and the object will be the model. The model may be a gene or genetic element. If the query disease is a general class, the association subject may be to a specific disease. In some cases the association will be *direct*, for example if a paper asserts a genotype is a model of a disease. In other cases, the association will be *indirect*, for example, chaining over orthology. In these cases the chain will be reflected in the *evidence graph* * TODO: provide hook into owlsim for dynamic computation of models by similarity * @param id CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getDiseaseModelAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getDiseaseModelAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns associations to models of the disease (asynchronously) * In the association object returned, the subject will be the disease, and the object will be the model. The model may be a gene or genetic element. If the query disease is a general class, the association subject may be to a specific disease. In some cases the association will be *direct*, for example if a paper asserts a genotype is a model of a disease. In other cases, the association will be *indirect*, for example, chaining over orthology. In these cases the chain will be reflected in the *evidence graph* * TODO: provide hook into owlsim for dynamic computation of models by similarity * @param id CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getDiseaseModelAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getDiseaseModelAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getDiseaseModelTaxonAssociations */ private com.squareup.okhttp.Call getDiseaseModelTaxonAssociationsCall(String taxon, String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'taxon' is set if (taxon == null) { throw new ApiException( "Missing the required parameter 'taxon' when calling getDiseaseModelTaxonAssociations(Async)"); } // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getDiseaseModelTaxonAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/disease/{id}/models/{taxon}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "taxon" + "\\}", apiClient.escapeString(taxon.toString())) .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Same as `/disease/<id>/models` but constrain models by taxon * * @param taxon CURIE of organism taxonomy class to constrain models, e.g NCBITaxon:6239 (C elegans). Higher level taxa may be used (required) * @param id CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getDiseaseModelTaxonAssociations(String taxon, String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getDiseaseModelTaxonAssociationsWithHttpInfo(taxon, id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Same as `/disease/<id>/models` but constrain models by taxon * * @param taxon CURIE of organism taxonomy class to constrain models, e.g NCBITaxon:6239 (C elegans). Higher level taxa may be used (required) * @param id CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getDiseaseModelTaxonAssociationsWithHttpInfo(String taxon, String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getDiseaseModelTaxonAssociationsCall(taxon, id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Same as `/disease/<id>/models` but constrain models by taxon (asynchronously) * * @param taxon CURIE of organism taxonomy class to constrain models, e.g NCBITaxon:6239 (C elegans). Higher level taxa may be used (required) * @param id CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getDiseaseModelTaxonAssociationsAsync(String taxon, String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getDiseaseModelTaxonAssociationsCall(taxon, id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getDiseaseObject */ private com.squareup.okhttp.Call getDiseaseObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getDiseaseObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/disease/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns disease object * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getDiseaseObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getDiseaseObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * TODO Returns disease object * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getDiseaseObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getDiseaseObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * TODO Returns disease object (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getDiseaseObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getDiseaseObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getDiseasePhenotypeAssociations */ private com.squareup.okhttp.Call getDiseasePhenotypeAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getDiseasePhenotypeAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/disease/{id}/phenotypes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns phenotypes associated with disease * * @param id CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getDiseasePhenotypeAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getDiseasePhenotypeAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns phenotypes associated with disease * * @param id CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getDiseasePhenotypeAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getDiseasePhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns phenotypes associated with disease (asynchronously) * * @param id CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getDiseasePhenotypeAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getDiseasePhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getDiseaseSubstanceAssociations */ private com.squareup.okhttp.Call getDiseaseSubstanceAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getDiseaseSubstanceAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/disease/{id}/substance/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns substances associated with a disease * e.g. drugs or small molecules used to treat * @param id CURIE identifier of disease, e.g. DOID:2841 (asthma). Equivalent IDs not yet supported (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getDiseaseSubstanceAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getDiseaseSubstanceAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * Returns substances associated with a disease * e.g. drugs or small molecules used to treat * @param id CURIE identifier of disease, e.g. DOID:2841 (asthma). Equivalent IDs not yet supported (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getDiseaseSubstanceAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getDiseaseSubstanceAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * Returns substances associated with a disease (asynchronously) * e.g. drugs or small molecules used to treat * @param id CURIE identifier of disease, e.g. DOID:2841 (asthma). Equivalent IDs not yet supported (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getDiseaseSubstanceAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getDiseaseSubstanceAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getDiseaseSubstanceAssociations_0 */ private com.squareup.okhttp.Call getDiseaseSubstanceAssociations_0Call(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getDiseaseSubstanceAssociations_0(Async)"); } // create path and map variables String localVarPath = "/bioentity/substance/{id}/treats/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns substances associated with a disease * e.g. drugs or small molecules used to treat * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getDiseaseSubstanceAssociations_0(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getDiseaseSubstanceAssociations_0WithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * Returns substances associated with a disease * e.g. drugs or small molecules used to treat * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getDiseaseSubstanceAssociations_0WithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getDiseaseSubstanceAssociations_0Call(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * Returns substances associated with a disease (asynchronously) * e.g. drugs or small molecules used to treat * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getDiseaseSubstanceAssociations_0Async(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getDiseaseSubstanceAssociations_0Call(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getEnvironmentObject */ private com.squareup.okhttp.Call getEnvironmentObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getEnvironmentObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/environment/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns environment entity * TODO consider renaming exposure * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getEnvironmentObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getEnvironmentObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * TODO Returns environment entity * TODO consider renaming exposure * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getEnvironmentObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getEnvironmentObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * TODO Returns environment entity (asynchronously) * TODO consider renaming exposure * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getEnvironmentObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getEnvironmentObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getEnvironmentPhenotypeAssociations */ private com.squareup.okhttp.Call getEnvironmentPhenotypeAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getEnvironmentPhenotypeAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/environment/{id}/phenotypes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns list of associations * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getEnvironmentPhenotypeAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getEnvironmentPhenotypeAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns list of associations * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getEnvironmentPhenotypeAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getEnvironmentPhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns list of associations (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getEnvironmentPhenotypeAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getEnvironmentPhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGeneExpressionAssociations */ private com.squareup.okhttp.Call getGeneExpressionAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getGeneExpressionAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/gene/{id}/expressed/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns expression events for a gene * * @param id CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getGeneExpressionAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getGeneExpressionAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns expression events for a gene * * @param id CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getGeneExpressionAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGeneExpressionAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns expression events for a gene (asynchronously) * * @param id CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGeneExpressionAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGeneExpressionAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGeneFunctionAssociations */ private com.squareup.okhttp.Call getGeneFunctionAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, String type, String homologTaxon, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getGeneFunctionAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/gene/{id}/function/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (type != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "type", type)); if (homologTaxon != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "homolog_taxon", homologTaxon)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns function associations for a gene * Note: currently this is implemented as a query to the GO solr instance. A smaller set of identifiers may be supported: - ZFIN e.g. ZFIN:ZDB-GENE-050417-357 - MGI e.g. MGI:1342287 - Use UniProt for human (TODO: map this) * @param id id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param type P, O or LDO (paralog, ortholog or least-diverged). (optional) * @param homologTaxon Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getGeneFunctionAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, String type, String homologTaxon, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getGeneFunctionAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, type, homologTaxon, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns function associations for a gene * Note: currently this is implemented as a query to the GO solr instance. A smaller set of identifiers may be supported: - ZFIN e.g. ZFIN:ZDB-GENE-050417-357 - MGI e.g. MGI:1342287 - Use UniProt for human (TODO: map this) * @param id id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param type P, O or LDO (paralog, ortholog or least-diverged). (optional) * @param homologTaxon Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getGeneFunctionAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, String type, String homologTaxon, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGeneFunctionAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, type, homologTaxon, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns function associations for a gene (asynchronously) * Note: currently this is implemented as a query to the GO solr instance. A smaller set of identifiers may be supported: - ZFIN e.g. ZFIN:ZDB-GENE-050417-357 - MGI e.g. MGI:1342287 - Use UniProt for human (TODO: map this) * @param id id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param type P, O or LDO (paralog, ortholog or least-diverged). (optional) * @param homologTaxon Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGeneFunctionAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, String type, String homologTaxon, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGeneFunctionAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, type, homologTaxon, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGeneHomologAssociations */ private com.squareup.okhttp.Call getGeneHomologAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, String type, String homologTaxon, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getGeneHomologAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/gene/{id}/homologs/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (type != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "type", type)); if (homologTaxon != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "homolog_taxon", homologTaxon)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns homologs for a gene * * @param id id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param type P, O or LDO (paralog, ortholog or least-diverged). (optional) * @param homologTaxon Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getGeneHomologAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, String type, String homologTaxon, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getGeneHomologAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, type, homologTaxon, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns homologs for a gene * * @param id id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param type P, O or LDO (paralog, ortholog or least-diverged). (optional) * @param homologTaxon Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getGeneHomologAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, String type, String homologTaxon, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGeneHomologAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, type, homologTaxon, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns homologs for a gene (asynchronously) * * @param id id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param type P, O or LDO (paralog, ortholog or least-diverged). (optional) * @param homologTaxon Taxon CURIE of homolog, e.g. NCBITaxon:9606. Can be intermediate note, includes inferred by default (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGeneHomologAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, String type, String homologTaxon, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGeneHomologAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, type, homologTaxon, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGeneInteractions */ private com.squareup.okhttp.Call getGeneInteractionsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getGeneInteractions(Async)"); } // create path and map variables String localVarPath = "/bioentity/gene/{id}/interactions/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns interactions for a gene * * @param id id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getGeneInteractions(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getGeneInteractionsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns interactions for a gene * * @param id id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getGeneInteractionsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGeneInteractionsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns interactions for a gene (asynchronously) * * @param id id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGeneInteractionsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGeneInteractionsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGeneObject */ private com.squareup.okhttp.Call getGeneObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getGeneObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/gene/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns gene object * * @param id id, e.g. NCBIGene:84570 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Gene> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Gene> getGeneObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Gene>> resp = getGeneObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns gene object * * @param id id, e.g. NCBIGene:84570 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Gene>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Gene>> getGeneObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGeneObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Gene>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns gene object (asynchronously) * * @param id id, e.g. NCBIGene:84570 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGeneObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Gene>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGeneObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Gene>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGenePhenotypeAssociations */ private com.squareup.okhttp.Call getGenePhenotypeAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getGenePhenotypeAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/gene/{id}/phenotypes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns phenotypes associated with gene * * @param id CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getGenePhenotypeAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getGenePhenotypeAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * Returns phenotypes associated with gene * * @param id CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getGenePhenotypeAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGenePhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * Returns phenotypes associated with gene (asynchronously) * * @param id CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGenePhenotypeAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGenePhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getGenePublicationList */ private com.squareup.okhttp.Call getGenePublicationListCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getGenePublicationList(Async)"); } // create path and map variables String localVarPath = "/bioentity/gene/{id}/pubs/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns expression events for a gene * * @param id CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getGenePublicationList(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getGenePublicationListWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns expression events for a gene * * @param id CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getGenePublicationListWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGenePublicationListCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns expression events for a gene (asynchronously) * * @param id CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGenePublicationListAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGenePublicationListCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGeneproductObject */ private com.squareup.okhttp.Call getGeneproductObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getGeneproductObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/geneproduct/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns gene product object * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getGeneproductObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getGeneproductObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * TODO Returns gene product object * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getGeneproductObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGeneproductObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * TODO Returns gene product object (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGeneproductObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGeneproductObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getGenericAssociations */ private com.squareup.okhttp.Call getGenericAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getGenericAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/{id}/associations/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns associations for an entity regardless of the type * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getGenericAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getGenericAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns associations for an entity regardless of the type * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getGenericAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGenericAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns associations for an entity regardless of the type (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGenericAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGenericAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGenericObject */ private com.squareup.okhttp.Call getGenericObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getGenericObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/{id}".replaceAll("\\{format\\}", "json").replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns object of any type * * @param id id, e.g. NCBIGene:84570 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<BioObject> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<BioObject> getGenericObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<BioObject>> resp = getGenericObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns object of any type * * @param id id, e.g. NCBIGene:84570 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<BioObject>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<BioObject>> getGenericObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGenericObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<BioObject>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns object of any type (asynchronously) * * @param id id, e.g. NCBIGene:84570 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGenericObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<BioObject>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGenericObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<BioObject>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGenotypeDiseaseAssociations */ private com.squareup.okhttp.Call getGenotypeDiseaseAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getGenotypeDiseaseAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/genotype/{id}/diseases/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns diseases associated with a genotype * * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286 (if non-human will return models) (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getGenotypeDiseaseAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getGenotypeDiseaseAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns diseases associated with a genotype * * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286 (if non-human will return models) (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getGenotypeDiseaseAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGenotypeDiseaseAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns diseases associated with a genotype (asynchronously) * * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286 (if non-human will return models) (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGenotypeDiseaseAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGenotypeDiseaseAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGenotypeGeneAssociations */ private com.squareup.okhttp.Call getGenotypeGeneAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getGenotypeGeneAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/genotype/{id}/genes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns genes associated with a genotype * * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getGenotypeGeneAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getGenotypeGeneAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns genes associated with a genotype * * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getGenotypeGeneAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGenotypeGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns genes associated with a genotype (asynchronously) * * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGenotypeGeneAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGenotypeGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGenotypeGenotypeAssociations */ private com.squareup.okhttp.Call getGenotypeGenotypeAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getGenotypeGenotypeAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/genotype/{id}/genotypes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns genotypes-genotype associations * Genotypes may be related to one another according to the GENO model * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getGenotypeGenotypeAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getGenotypeGenotypeAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns genotypes-genotype associations * Genotypes may be related to one another according to the GENO model * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getGenotypeGenotypeAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGenotypeGenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns genotypes-genotype associations (asynchronously) * Genotypes may be related to one another according to the GENO model * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGenotypeGenotypeAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGenotypeGenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGenotypeObject */ private com.squareup.okhttp.Call getGenotypeObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getGenotypeObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/genotype/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns genotype object * The genotype object will have the following association sets populated: * gene * phenotype * disease * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Genotype> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Genotype> getGenotypeObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Genotype>> resp = getGenotypeObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns genotype object * The genotype object will have the following association sets populated: * gene * phenotype * disease * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Genotype>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Genotype>> getGenotypeObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGenotypeObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Genotype>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns genotype object (asynchronously) * The genotype object will have the following association sets populated: * gene * phenotype * disease * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-6607 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGenotypeObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Genotype>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGenotypeObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Genotype>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGenotypePhenotypeAssociations */ private com.squareup.okhttp.Call getGenotypePhenotypeAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getGenotypePhenotypeAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/genotype/{id}/phenotypes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns phenotypes associated with a genotype * * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getGenotypePhenotypeAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getGenotypePhenotypeAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns phenotypes associated with a genotype * * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getGenotypePhenotypeAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGenotypePhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns phenotypes associated with a genotype (asynchronously) * * @param id CURIE identifier of genotype, e.g. ZFIN:ZDB-FISH-150901-4286 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGenotypePhenotypeAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGenotypePhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGotermGeneAssociations */ private com.squareup.okhttp.Call getGotermGeneAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getGotermGeneAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/goterm/{id}/genes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns associated phenotypes * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getGotermGeneAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getGotermGeneAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns associated phenotypes * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getGotermGeneAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGotermGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns associated phenotypes (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGotermGeneAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGotermGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getGotermObject */ private com.squareup.okhttp.Call getGotermObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getGotermObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/goterm/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns GO class object * * @param id GO class CURIE identifier, e.g GO:0016301 (kinase activity) (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getGotermObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getGotermObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * TODO Returns GO class object * * @param id GO class CURIE identifier, e.g GO:0016301 (kinase activity) (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getGotermObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGotermObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * TODO Returns GO class object (asynchronously) * * @param id GO class CURIE identifier, e.g GO:0016301 (kinase activity) (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGotermObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGotermObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getGotermPhenotypeAssociations */ private com.squareup.okhttp.Call getGotermPhenotypeAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getGotermPhenotypeAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/goterm/{id}/phenotype/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns associated phenotypes * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getGotermPhenotypeAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getGotermPhenotypeAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns associated phenotypes * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getGotermPhenotypeAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getGotermPhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns associated phenotypes (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getGotermPhenotypeAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getGotermPhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getLiteratureDiseaseAssociations */ private com.squareup.okhttp.Call getLiteratureDiseaseAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getLiteratureDiseaseAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/literature/{id}/diseases/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns associations between a lit entity and a disease * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getLiteratureDiseaseAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getLiteratureDiseaseAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns associations between a lit entity and a disease * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getLiteratureDiseaseAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getLiteratureDiseaseAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns associations between a lit entity and a disease (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getLiteratureDiseaseAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getLiteratureDiseaseAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getLiteratureGeneAssociations */ private com.squareup.okhttp.Call getLiteratureGeneAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getLiteratureGeneAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/literature/{id}/genes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns associations between a lit entity and a gene * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getLiteratureGeneAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getLiteratureGeneAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns associations between a lit entity and a gene * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getLiteratureGeneAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getLiteratureGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns associations between a lit entity and a gene (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getLiteratureGeneAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getLiteratureGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getLiteratureGenotypeAssociations */ private com.squareup.okhttp.Call getLiteratureGenotypeAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getLiteratureGenotypeAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/literature/{id}/genotypes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns associations between a lit entity and a genotype * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getLiteratureGenotypeAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getLiteratureGenotypeAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns associations between a lit entity and a genotype * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getLiteratureGenotypeAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getLiteratureGenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns associations between a lit entity and a genotype (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getLiteratureGenotypeAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getLiteratureGenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getParentObject */ private com.squareup.okhttp.Call getParentObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getParentObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/individual/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns individual * Individuals may typically encompass patients, but can be individuals of any species * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getParentObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getParentObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * TODO Returns individual * Individuals may typically encompass patients, but can be individuals of any species * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getParentObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getParentObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * TODO Returns individual (asynchronously) * Individuals may typically encompass patients, but can be individuals of any species * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getParentObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getParentObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getParentObject_0 */ private com.squareup.okhttp.Call getParentObject_0Call(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getParentObject_0(Async)"); } // create path and map variables String localVarPath = "/bioentity/investigation/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns investigation object * Investigations encompass clinical trials, molecular biology experiments or any kind of study * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getParentObject_0(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getParentObject_0WithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * TODO Returns investigation object * Investigations encompass clinical trials, molecular biology experiments or any kind of study * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getParentObject_0WithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getParentObject_0Call(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * TODO Returns investigation object (asynchronously) * Investigations encompass clinical trials, molecular biology experiments or any kind of study * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getParentObject_0Async(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getParentObject_0Call(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getPathwayGeneAssociations */ private com.squareup.okhttp.Call getPathwayGeneAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getPathwayGeneAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/pathway/{id}/genes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns list of genes associated with a pathway * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getPathwayGeneAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getPathwayGeneAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns list of genes associated with a pathway * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getPathwayGeneAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getPathwayGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns list of genes associated with a pathway (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getPathwayGeneAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getPathwayGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getPathwayObject */ private com.squareup.okhttp.Call getPathwayObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getPathwayObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/pathway/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns pathway object * * @param id CURIE any pathway element. May be a GO ID or a pathway database ID (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getPathwayObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getPathwayObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * TODO Returns pathway object * * @param id CURIE any pathway element. May be a GO ID or a pathway database ID (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getPathwayObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getPathwayObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * TODO Returns pathway object (asynchronously) * * @param id CURIE any pathway element. May be a GO ID or a pathway database ID (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getPathwayObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getPathwayObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getPathwayParticipantAssociations */ private com.squareup.okhttp.Call getPathwayParticipantAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getPathwayParticipantAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/pathway/{id}/participants/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns associations to participants (molecules, etc) for a pathway * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getPathwayParticipantAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getPathwayParticipantAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns associations to participants (molecules, etc) for a pathway * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getPathwayParticipantAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getPathwayParticipantAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns associations to participants (molecules, etc) for a pathway (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getPathwayParticipantAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getPathwayParticipantAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getPhenotypeAnatomyAssociations */ private com.squareup.okhttp.Call getPhenotypeAnatomyAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getPhenotypeAnatomyAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/phenotype/{id}/anatomy/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns anatomical entities associated with a phenotype * Example IDs: * ZP:0004204 * MP:0008521 abnormal Bowman membrane For example, *abnormal limb development* will map to *limb* * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<NamedObject> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<NamedObject> getPhenotypeAnatomyAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<NamedObject>> resp = getPhenotypeAnatomyAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns anatomical entities associated with a phenotype * Example IDs: * ZP:0004204 * MP:0008521 abnormal Bowman membrane For example, *abnormal limb development* will map to *limb* * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<NamedObject>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<NamedObject>> getPhenotypeAnatomyAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getPhenotypeAnatomyAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<NamedObject>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns anatomical entities associated with a phenotype (asynchronously) * Example IDs: * ZP:0004204 * MP:0008521 abnormal Bowman membrane For example, *abnormal limb development* will map to *limb* * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getPhenotypeAnatomyAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<NamedObject>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getPhenotypeAnatomyAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<NamedObject>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getPhenotypeFunctionAssociations */ private com.squareup.okhttp.Call getPhenotypeFunctionAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getPhenotypeFunctionAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/phenotype/{id}/function/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns biological functions associated with a Phenotype * This may come from a combination of asserted knowledge (e.g. abnormal levels of metabolite to corresponding GO activity) or from data-driven approach (cf Translator) Results are typically represented as GO classes * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getPhenotypeFunctionAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getPhenotypeFunctionAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns biological functions associated with a Phenotype * This may come from a combination of asserted knowledge (e.g. abnormal levels of metabolite to corresponding GO activity) or from data-driven approach (cf Translator) Results are typically represented as GO classes * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getPhenotypeFunctionAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getPhenotypeFunctionAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns biological functions associated with a Phenotype (asynchronously) * This may come from a combination of asserted knowledge (e.g. abnormal levels of metabolite to corresponding GO activity) or from data-driven approach (cf Translator) Results are typically represented as GO classes * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getPhenotypeFunctionAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getPhenotypeFunctionAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getPhenotypeGeneAssociations */ private com.squareup.okhttp.Call getPhenotypeGeneAssociationsCall(String taxid, String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'taxid' is set if (taxid == null) { throw new ApiException( "Missing the required parameter 'taxid' when calling getPhenotypeGeneAssociations(Async)"); } // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getPhenotypeGeneAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/phenotype/{id}/gene/{taxid}/ids".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "taxid" + "\\}", apiClient.escapeString(taxid.toString())) .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns gene ids for all genes for a particular phenotype in a taxon * For example, + NCBITaxon:10090 (mouse) * @param taxid Species or high level taxon grouping, e.g NCBITaxon:10090 (Mus musculus) (required) * @param id Pheno class CURIE identifier, e.g MP:0001569 (abnormal circulating bilirubin level) (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getPhenotypeGeneAssociations(String taxid, String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getPhenotypeGeneAssociationsWithHttpInfo(taxid, id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * Returns gene ids for all genes for a particular phenotype in a taxon * For example, + NCBITaxon:10090 (mouse) * @param taxid Species or high level taxon grouping, e.g NCBITaxon:10090 (Mus musculus) (required) * @param id Pheno class CURIE identifier, e.g MP:0001569 (abnormal circulating bilirubin level) (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getPhenotypeGeneAssociationsWithHttpInfo(String taxid, String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getPhenotypeGeneAssociationsCall(taxid, id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * Returns gene ids for all genes for a particular phenotype in a taxon (asynchronously) * For example, + NCBITaxon:10090 (mouse) * @param taxid Species or high level taxon grouping, e.g NCBITaxon:10090 (Mus musculus) (required) * @param id Pheno class CURIE identifier, e.g MP:0001569 (abnormal circulating bilirubin level) (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getPhenotypeGeneAssociationsAsync(String taxid, String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getPhenotypeGeneAssociationsCall(taxid, id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getPhenotypeGeneAssociations_0 */ private com.squareup.okhttp.Call getPhenotypeGeneAssociations_0Call(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getPhenotypeGeneAssociations_0(Async)"); } // create path and map variables String localVarPath = "/bioentity/phenotype/{id}/genes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns associated phenotypes * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getPhenotypeGeneAssociations_0(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getPhenotypeGeneAssociations_0WithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns associated phenotypes * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getPhenotypeGeneAssociations_0WithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getPhenotypeGeneAssociations_0Call(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns associated phenotypes (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getPhenotypeGeneAssociations_0Async(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getPhenotypeGeneAssociations_0Call(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getPhenotypeObject */ private com.squareup.okhttp.Call getPhenotypeObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getPhenotypeObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/phenotype/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns phenotype class object * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getPhenotypeObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getPhenotypeObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * TODO Returns phenotype class object * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getPhenotypeObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getPhenotypeObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * TODO Returns phenotype class object (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getPhenotypeObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getPhenotypeObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getPhenotypePhenotypeAssociations */ private com.squareup.okhttp.Call getPhenotypePhenotypeAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getPhenotypePhenotypeAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/phenotype/{id}/phenotype/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns associated phenotypes * Includes phenologs, as well as equivalent phenotypes in other species * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getPhenotypePhenotypeAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getPhenotypePhenotypeAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns associated phenotypes * Includes phenologs, as well as equivalent phenotypes in other species * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getPhenotypePhenotypeAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getPhenotypePhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns associated phenotypes (asynchronously) * Includes phenologs, as well as equivalent phenotypes in other species * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getPhenotypePhenotypeAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getPhenotypePhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getPubObject */ private com.squareup.okhttp.Call getPubObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getPubObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/literature/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns publication object * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getPubObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getPubObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * TODO Returns publication object * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getPubObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getPubObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * TODO Returns publication object (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getPubObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getPubObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getSequenceFeatureObject */ private com.squareup.okhttp.Call getSequenceFeatureObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getSequenceFeatureObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/sequence_feature/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns seqfeature * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getSequenceFeatureObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getSequenceFeatureObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * TODO Returns seqfeature * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getSequenceFeatureObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getSequenceFeatureObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * TODO Returns seqfeature (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getSequenceFeatureObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getSequenceFeatureObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getSubstanceExposures */ private com.squareup.okhttp.Call getSubstanceExposuresCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getSubstanceExposures(Async)"); } // create path and map variables String localVarPath = "/bioentity/substance/{id}/exposures/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns associations between a substance and related exposures * E.g. between pesticide and occupational exposure class * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getSubstanceExposures(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getSubstanceExposuresWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns associations between a substance and related exposures * E.g. between pesticide and occupational exposure class * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getSubstanceExposuresWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getSubstanceExposuresCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns associations between a substance and related exposures (asynchronously) * E.g. between pesticide and occupational exposure class * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getSubstanceExposuresAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getSubstanceExposuresCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getSubstanceInteractions */ private com.squareup.okhttp.Call getSubstanceInteractionsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getSubstanceInteractions(Async)"); } // create path and map variables String localVarPath = "/bioentity/substance/{id}/interactions/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns associations between given drug and interactions * Interactions can encompass drugs or environments * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getSubstanceInteractions(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getSubstanceInteractionsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns associations between given drug and interactions * Interactions can encompass drugs or environments * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getSubstanceInteractionsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getSubstanceInteractionsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns associations between given drug and interactions (asynchronously) * Interactions can encompass drugs or environments * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getSubstanceInteractionsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getSubstanceInteractionsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getSubstanceObject */ private com.squareup.okhttp.Call getSubstanceObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getSubstanceObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/substance/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns substance entity * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Substance> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Substance> getSubstanceObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Substance>> resp = getSubstanceObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns substance entity * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Substance>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Substance>> getSubstanceObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getSubstanceObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Substance>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns substance entity (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getSubstanceObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Substance>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getSubstanceObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Substance>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getSubstanceParticipantInAssociations */ private com.squareup.okhttp.Call getSubstanceParticipantInAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getSubstanceParticipantInAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/substance/{id}/participant_in/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns associations between an activity and process and the specified substance * Examples relationships: * substance is a metabolite of a process * substance is synthesized by a process * substance is modified by an activity * substance elicits a response program/pathway * substance is transported by activity or pathway For example, CHEBI:40036 (amitrole) * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getSubstanceParticipantInAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getSubstanceParticipantInAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns associations between an activity and process and the specified substance * Examples relationships: * substance is a metabolite of a process * substance is synthesized by a process * substance is modified by an activity * substance elicits a response program/pathway * substance is transported by activity or pathway For example, CHEBI:40036 (amitrole) * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getSubstanceParticipantInAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getSubstanceParticipantInAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns associations between an activity and process and the specified substance (asynchronously) * Examples relationships: * substance is a metabolite of a process * substance is synthesized by a process * substance is modified by an activity * substance elicits a response program/pathway * substance is transported by activity or pathway For example, CHEBI:40036 (amitrole) * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getSubstanceParticipantInAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getSubstanceParticipantInAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getSubstanceRelationships */ private com.squareup.okhttp.Call getSubstanceRelationshipsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getSubstanceRelationships(Async)"); } // create path and map variables String localVarPath = "/bioentity/substance/{id}/substances/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns associations between a substance and other substances * E.g. metabolite-of, tautomer-of, parent-of, ... * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getSubstanceRelationships(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getSubstanceRelationshipsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns associations between a substance and other substances * E.g. metabolite-of, tautomer-of, parent-of, ... * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getSubstanceRelationshipsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getSubstanceRelationshipsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns associations between a substance and other substances (asynchronously) * E.g. metabolite-of, tautomer-of, parent-of, ... * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getSubstanceRelationshipsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getSubstanceRelationshipsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getSubstanceRoleAssociations */ private com.squareup.okhttp.Call getSubstanceRoleAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getSubstanceRoleAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/substance/{id}/roles/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns associations between given drug and roles * Roles may be human-oriented (e.g. pesticide) or molecular (e.g. enzyme inhibitor) * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getSubstanceRoleAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getSubstanceRoleAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns associations between given drug and roles * Roles may be human-oriented (e.g. pesticide) or molecular (e.g. enzyme inhibitor) * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getSubstanceRoleAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getSubstanceRoleAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns associations between given drug and roles (asynchronously) * Roles may be human-oriented (e.g. pesticide) or molecular (e.g. enzyme inhibitor) * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getSubstanceRoleAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getSubstanceRoleAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getSubstanceTargetAssociations */ private com.squareup.okhttp.Call getSubstanceTargetAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getSubstanceTargetAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/substance/{id}/targets/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns associations between given drug and targets * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<Association> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<Association> getSubstanceTargetAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<Association>> resp = getSubstanceTargetAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * TODO Returns associations between given drug and targets * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<Association>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<Association>> getSubstanceTargetAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getSubstanceTargetAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * TODO Returns associations between given drug and targets (asynchronously) * * @param id (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getSubstanceTargetAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<Association>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getSubstanceTargetAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<Association>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getVariantGeneAssociations */ private com.squareup.okhttp.Call getVariantGeneAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getVariantGeneAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/variant/{id}/genes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns genes associated with a variant * * @param id CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getVariantGeneAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getVariantGeneAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns genes associated with a variant * * @param id CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getVariantGeneAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getVariantGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns genes associated with a variant (asynchronously) * * @param id CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getVariantGeneAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getVariantGeneAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getVariantGenotypeAssociations */ private com.squareup.okhttp.Call getVariantGenotypeAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getVariantGenotypeAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/variant/{id}/genotypes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns genotypes associated with a variant * * @param id CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getVariantGenotypeAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getVariantGenotypeAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns genotypes associated with a variant * * @param id CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getVariantGenotypeAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getVariantGenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns genotypes associated with a variant (asynchronously) * * @param id CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getVariantGenotypeAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getVariantGenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getVariantObject */ private com.squareup.okhttp.Call getVariantObjectCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException("Missing the required parameter 'id' when calling getVariantObject(Async)"); } // create path and map variables String localVarPath = "/bioentity/variant/{id}".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * TODO Returns sequence variant entity * * @param id CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getVariantObject(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { getVariantObjectWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); } /** * TODO Returns sequence variant entity * * @param id CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<Void> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<Void> getVariantObjectWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getVariantObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); return apiClient.execute(call); } /** * TODO Returns sequence variant entity (asynchronously) * * @param id CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getVariantObjectAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<Void> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getVariantObjectCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getVariantPhenotypeAssociations */ private com.squareup.okhttp.Call getVariantPhenotypeAssociationsCall(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'id' is set if (id == null) { throw new ApiException( "Missing the required parameter 'id' when calling getVariantPhenotypeAssociations(Async)"); } // create path and map variables String localVarPath = "/bioentity/variant/{id}/phenotypes/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "id" + "\\}", apiClient.escapeString(id.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (fetchObjects != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "fetch_objects", fetchObjects)); if (rows != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "rows", rows)); if (excludeAutomaticAssertions != null) localVarQueryParams.addAll( apiClient.parameterToPairs("", "exclude_automatic_assertions", excludeAutomaticAssertions)); if (unselectEvidence != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "unselect_evidence", unselectEvidence)); if (useCompactAssociations != null) localVarQueryParams .addAll(apiClient.parameterToPairs("", "use_compact_associations", useCompactAssociations)); Map<String, String> localVarHeaderParams = new HashMap<String, String>(); Map<String, Object> localVarFormParams = new HashMap<String, Object>(); final String[] localVarAccepts = { "application/json" }; final String localVarAccept = apiClient.selectHeaderAccept(localVarAccepts); if (localVarAccept != null) localVarHeaderParams.put("Accept", localVarAccept); final String[] localVarContentTypes = { "application/json" }; final String localVarContentType = apiClient.selectHeaderContentType(localVarContentTypes); localVarHeaderParams.put("Content-Type", localVarContentType); if (progressListener != null) { apiClient.getHttpClient().networkInterceptors().add(new com.squareup.okhttp.Interceptor() { @Override public com.squareup.okhttp.Response intercept(com.squareup.okhttp.Interceptor.Chain chain) throws IOException { com.squareup.okhttp.Response originalResponse = chain.proceed(chain.request()); return originalResponse.newBuilder() .body(new ProgressResponseBody(originalResponse.body(), progressListener)).build(); } }); } String[] localVarAuthNames = new String[] {}; return apiClient.buildCall(localVarPath, "GET", localVarQueryParams, localVarPostBody, localVarHeaderParams, localVarFormParams, localVarAuthNames, progressRequestListener); } /** * Returns phenotypes associated with a variant * * @param id CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return List<AssociationResults> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public List<AssociationResults> getVariantPhenotypeAssociations(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { ApiResponse<List<AssociationResults>> resp = getVariantPhenotypeAssociationsWithHttpInfo(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations); return resp.getData(); } /** * Returns phenotypes associated with a variant * * @param id CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @return ApiResponse<List<AssociationResults>> * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public ApiResponse<List<AssociationResults>> getVariantPhenotypeAssociationsWithHttpInfo(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations) throws ApiException { com.squareup.okhttp.Call call = getVariantPhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns phenotypes associated with a variant (asynchronously) * * @param id CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783 (required) * @param fetchObjects If true, returns a distinct set of association.objects (typically ontology terms). This appears at the top level of the results payload (optional, default to true) * @param rows number of rows (optional, default to 20) * @param excludeAutomaticAssertions If set, excludes associations that involve IEAs (ECO:0000501) (optional) * @param unselectEvidence If set, excludes evidence objects in response (optional) * @param useCompactAssociations If true, returns results in compact associations format (optional) * @param callback The callback to be executed when the API call finishes * @return The request call * @throws ApiException If fail to process the API call, e.g. serializing the request body object */ public com.squareup.okhttp.Call getVariantPhenotypeAssociationsAsync(String id, Boolean fetchObjects, Integer rows, Boolean excludeAutomaticAssertions, Boolean unselectEvidence, Boolean useCompactAssociations, final ApiCallback<List<AssociationResults>> callback) throws ApiException { ProgressResponseBody.ProgressListener progressListener = null; ProgressRequestBody.ProgressRequestListener progressRequestListener = null; if (callback != null) { progressListener = new ProgressResponseBody.ProgressListener() { @Override public void update(long bytesRead, long contentLength, boolean done) { callback.onDownloadProgress(bytesRead, contentLength, done); } }; progressRequestListener = new ProgressRequestBody.ProgressRequestListener() { @Override public void onRequestProgress(long bytesWritten, long contentLength, boolean done) { callback.onUploadProgress(bytesWritten, contentLength, done); } }; } com.squareup.okhttp.Call call = getVariantPhenotypeAssociationsCall(id, fetchObjects, rows, excludeAutomaticAssertions, unselectEvidence, useCompactAssociations, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } }