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.AssociationResults; import java.lang.reflect.Type; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; public class BioentitysetApi { private ApiClient apiClient; public BioentitysetApi() { this(Configuration.getDefaultApiClient()); } public BioentitysetApi(ApiClient apiClient) { this.apiClient = apiClient; } public ApiClient getApiClient() { return apiClient; } public void setApiClient(ApiClient apiClient) { this.apiClient = apiClient; } /* Build call for getEntitySetAssociations */ private com.squareup.okhttp.Call getEntitySetAssociationsCall(String objectSlim, String objectCategory, List<String> subject, List<String> background, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // create path and map variables String localVarPath = "/bioentityset/associations/".replaceAll("\\{format\\}", "json"); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (objectSlim != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "object_slim", objectSlim)); if (objectCategory != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "object_category", objectCategory)); if (subject != null) localVarQueryParams.addAll(apiClient.parameterToPairs("multi", "subject", subject)); if (background != null) localVarQueryParams.addAll(apiClient.parameterToPairs("multi", "background", background)); 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 compact associations for a given input set * * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param objectCategory E.g. phenotype, function (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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> getEntitySetAssociations(String objectSlim, String objectCategory, List<String> subject, List<String> background) throws ApiException { ApiResponse<List<AssociationResults>> resp = getEntitySetAssociationsWithHttpInfo(objectSlim, objectCategory, subject, background); return resp.getData(); } /** * Returns compact associations for a given input set * * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param objectCategory E.g. phenotype, function (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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>> getEntitySetAssociationsWithHttpInfo(String objectSlim, String objectCategory, List<String> subject, List<String> background) throws ApiException { com.squareup.okhttp.Call call = getEntitySetAssociationsCall(objectSlim, objectCategory, subject, background, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns compact associations for a given input set (asynchronously) * * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param objectCategory E.g. phenotype, function (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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 getEntitySetAssociationsAsync(String objectSlim, String objectCategory, List<String> subject, List<String> background, 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 = getEntitySetAssociationsCall(objectSlim, objectCategory, subject, background, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getEntitySetGraphResource */ private com.squareup.okhttp.Call getEntitySetGraphResourceCall(String objectSlim, String objectCategory, List<String> subject, List<String> background, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // create path and map variables String localVarPath = "/bioentityset/graph/".replaceAll("\\{format\\}", "json"); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (objectSlim != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "object_slim", objectSlim)); if (objectCategory != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "object_category", objectCategory)); if (subject != null) localVarQueryParams.addAll(apiClient.parameterToPairs("multi", "subject", subject)); if (background != null) localVarQueryParams.addAll(apiClient.parameterToPairs("multi", "background", background)); 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 Graph object spanning all entities * * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param objectCategory E.g. phenotype, function (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getEntitySetGraphResource(String objectSlim, String objectCategory, List<String> subject, List<String> background) throws ApiException { getEntitySetGraphResourceWithHttpInfo(objectSlim, objectCategory, subject, background); } /** * TODO Graph object spanning all entities * * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param objectCategory E.g. phenotype, function (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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> getEntitySetGraphResourceWithHttpInfo(String objectSlim, String objectCategory, List<String> subject, List<String> background) throws ApiException { com.squareup.okhttp.Call call = getEntitySetGraphResourceCall(objectSlim, objectCategory, subject, background, null, null); return apiClient.execute(call); } /** * TODO Graph object spanning all entities (asynchronously) * * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param objectCategory E.g. phenotype, function (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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 getEntitySetGraphResourceAsync(String objectSlim, String objectCategory, List<String> subject, List<String> background, 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 = getEntitySetGraphResourceCall(objectSlim, objectCategory, subject, background, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getEntitySetHomologsDeprecated */ private com.squareup.okhttp.Call getEntitySetHomologsDeprecatedCall(String objectSlim, String objectCategory, List<String> subject, List<String> background, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // create path and map variables String localVarPath = "/bioentityset/DEPRECATEDhomologs/".replaceAll("\\{format\\}", "json"); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (objectSlim != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "object_slim", objectSlim)); if (objectCategory != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "object_category", objectCategory)); if (subject != null) localVarQueryParams.addAll(apiClient.parameterToPairs("multi", "subject", subject)); if (background != null) localVarQueryParams.addAll(apiClient.parameterToPairs("multi", "background", background)); 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 homology associations for a given input set of genes * * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param objectCategory E.g. phenotype, function (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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> getEntitySetHomologsDeprecated(String objectSlim, String objectCategory, List<String> subject, List<String> background) throws ApiException { ApiResponse<List<AssociationResults>> resp = getEntitySetHomologsDeprecatedWithHttpInfo(objectSlim, objectCategory, subject, background); return resp.getData(); } /** * Returns homology associations for a given input set of genes * * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param objectCategory E.g. phenotype, function (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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>> getEntitySetHomologsDeprecatedWithHttpInfo(String objectSlim, String objectCategory, List<String> subject, List<String> background) throws ApiException { com.squareup.okhttp.Call call = getEntitySetHomologsDeprecatedCall(objectSlim, objectCategory, subject, background, null, null); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); return apiClient.execute(call, localVarReturnType); } /** * Returns homology associations for a given input set of genes (asynchronously) * * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param objectCategory E.g. phenotype, function (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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 getEntitySetHomologsDeprecatedAsync(String objectSlim, String objectCategory, List<String> subject, List<String> background, 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 = getEntitySetHomologsDeprecatedCall(objectSlim, objectCategory, subject, background, progressListener, progressRequestListener); Type localVarReturnType = new TypeToken<List<AssociationResults>>() { }.getType(); apiClient.executeAsync(call, localVarReturnType, callback); return call; } /* Build call for getEntitySetOverRepresentationAnalysis */ private com.squareup.okhttp.Call getEntitySetOverRepresentationAnalysisCall(String objectCategory, String objectCategory2, String objectSlim, List<String> subject, List<String> background, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'objectCategory' is set if (objectCategory == null) { throw new ApiException( "Missing the required parameter 'objectCategory' when calling getEntitySetOverRepresentationAnalysis(Async)"); } // verify the required parameter 'objectCategory2' is set if (objectCategory2 == null) { throw new ApiException( "Missing the required parameter 'objectCategory2' when calling getEntitySetOverRepresentationAnalysis(Async)"); } // create path and map variables String localVarPath = "/bioentityset/ora/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "object_category" + "\\}", apiClient.escapeString(objectCategory.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (objectSlim != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "object_slim", objectSlim)); if (objectCategory2 != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "object_category", objectCategory2)); if (subject != null) localVarQueryParams.addAll(apiClient.parameterToPairs("multi", "subject", subject)); if (background != null) localVarQueryParams.addAll(apiClient.parameterToPairs("multi", "background", background)); 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 Over-representation analysis * * @param objectCategory CATEGORY of entity at link OBJECT (target), e.g. phenotype, disease (required) * @param objectCategory2 E.g. phenotype, function (required) * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getEntitySetOverRepresentationAnalysis(String objectCategory, String objectCategory2, String objectSlim, List<String> subject, List<String> background) throws ApiException { getEntitySetOverRepresentationAnalysisWithHttpInfo(objectCategory, objectCategory2, objectSlim, subject, background); } /** * TODO Over-representation analysis * * @param objectCategory CATEGORY of entity at link OBJECT (target), e.g. phenotype, disease (required) * @param objectCategory2 E.g. phenotype, function (required) * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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> getEntitySetOverRepresentationAnalysisWithHttpInfo(String objectCategory, String objectCategory2, String objectSlim, List<String> subject, List<String> background) throws ApiException { com.squareup.okhttp.Call call = getEntitySetOverRepresentationAnalysisCall(objectCategory, objectCategory2, objectSlim, subject, background, null, null); return apiClient.execute(call); } /** * TODO Over-representation analysis (asynchronously) * * @param objectCategory CATEGORY of entity at link OBJECT (target), e.g. phenotype, disease (required) * @param objectCategory2 E.g. phenotype, function (required) * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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 getEntitySetOverRepresentationAnalysisAsync(String objectCategory, String objectCategory2, String objectSlim, List<String> subject, List<String> background, 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 = getEntitySetOverRepresentationAnalysisCall(objectCategory, objectCategory2, objectSlim, subject, background, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getEntitySetOverRepresentationAnalysis_0 */ private com.squareup.okhttp.Call getEntitySetOverRepresentationAnalysis_0Call(String objectCategory, String objectCategory2, String objectSlim, List<String> subject, List<String> background, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // verify the required parameter 'objectCategory' is set if (objectCategory == null) { throw new ApiException( "Missing the required parameter 'objectCategory' when calling getEntitySetOverRepresentationAnalysis_0(Async)"); } // verify the required parameter 'objectCategory2' is set if (objectCategory2 == null) { throw new ApiException( "Missing the required parameter 'objectCategory2' when calling getEntitySetOverRepresentationAnalysis_0(Async)"); } // create path and map variables String localVarPath = "/bioentityset/ora/{object_category}/".replaceAll("\\{format\\}", "json") .replaceAll("\\{" + "object_category" + "\\}", apiClient.escapeString(objectCategory.toString())); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (objectSlim != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "object_slim", objectSlim)); if (objectCategory2 != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "object_category", objectCategory2)); if (subject != null) localVarQueryParams.addAll(apiClient.parameterToPairs("multi", "subject", subject)); if (background != null) localVarQueryParams.addAll(apiClient.parameterToPairs("multi", "background", background)); 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 Over-representation analysis * * @param objectCategory CATEGORY of entity at link OBJECT (target), e.g. phenotype, disease (required) * @param objectCategory2 E.g. phenotype, function (required) * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getEntitySetOverRepresentationAnalysis_0(String objectCategory, String objectCategory2, String objectSlim, List<String> subject, List<String> background) throws ApiException { getEntitySetOverRepresentationAnalysis_0WithHttpInfo(objectCategory, objectCategory2, objectSlim, subject, background); } /** * TODO Over-representation analysis * * @param objectCategory CATEGORY of entity at link OBJECT (target), e.g. phenotype, disease (required) * @param objectCategory2 E.g. phenotype, function (required) * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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> getEntitySetOverRepresentationAnalysis_0WithHttpInfo(String objectCategory, String objectCategory2, String objectSlim, List<String> subject, List<String> background) throws ApiException { com.squareup.okhttp.Call call = getEntitySetOverRepresentationAnalysis_0Call(objectCategory, objectCategory2, objectSlim, subject, background, null, null); return apiClient.execute(call); } /** * TODO Over-representation analysis (asynchronously) * * @param objectCategory CATEGORY of entity at link OBJECT (target), e.g. phenotype, disease (required) * @param objectCategory2 E.g. phenotype, function (required) * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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 getEntitySetOverRepresentationAnalysis_0Async(String objectCategory, String objectCategory2, String objectSlim, List<String> subject, List<String> background, 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 = getEntitySetOverRepresentationAnalysis_0Call(objectCategory, objectCategory2, objectSlim, subject, background, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } /* Build call for getEntitySetSummary */ private com.squareup.okhttp.Call getEntitySetSummaryCall(String objectSlim, String objectCategory, List<String> subject, List<String> background, final ProgressResponseBody.ProgressListener progressListener, final ProgressRequestBody.ProgressRequestListener progressRequestListener) throws ApiException { Object localVarPostBody = null; // create path and map variables String localVarPath = "/bioentityset/descriptor/counts/".replaceAll("\\{format\\}", "json"); List<Pair> localVarQueryParams = new ArrayList<Pair>(); if (objectSlim != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "object_slim", objectSlim)); if (objectCategory != null) localVarQueryParams.addAll(apiClient.parameterToPairs("", "object_category", objectCategory)); if (subject != null) localVarQueryParams.addAll(apiClient.parameterToPairs("multi", "subject", subject)); if (background != null) localVarQueryParams.addAll(apiClient.parameterToPairs("multi", "background", background)); 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); } /** * Summary statistics for objects associated * * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param objectCategory E.g. phenotype, function (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (optional) * @throws ApiException If fail to call the API, e.g. server error or cannot deserialize the response body */ public void getEntitySetSummary(String objectSlim, String objectCategory, List<String> subject, List<String> background) throws ApiException { getEntitySetSummaryWithHttpInfo(objectSlim, objectCategory, subject, background); } /** * Summary statistics for objects associated * * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param objectCategory E.g. phenotype, function (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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> getEntitySetSummaryWithHttpInfo(String objectSlim, String objectCategory, List<String> subject, List<String> background) throws ApiException { com.squareup.okhttp.Call call = getEntitySetSummaryCall(objectSlim, objectCategory, subject, background, null, null); return apiClient.execute(call); } /** * Summary statistics for objects associated (asynchronously) * * @param objectSlim Slim or subset to which the descriptors are to be mapped, NOT IMPLEMENTED (optional) * @param objectCategory E.g. phenotype, function (optional) * @param subject Entity ids to be examined, e.g. NCBIGene:9342, NCBIGene:7227, NCBIGene:8131, NCBIGene:157570, NCBIGene:51164, NCBIGene:6689, NCBIGene:6387 (optional) * @param background Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests (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 getEntitySetSummaryAsync(String objectSlim, String objectCategory, List<String> subject, List<String> background, 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 = getEntitySetSummaryCall(objectSlim, objectCategory, subject, background, progressListener, progressRequestListener); apiClient.executeAsync(call, callback); return call; } }