List of usage examples for com.mongodb BasicDBObject containsKey
@Deprecated
@Override
public boolean containsKey(final String key)
From source file:com.ikanow.infinit.e.api.knowledge.federated.SimpleFederatedQueryEngine.java
License:Open Source License
public BasicDBObject createDocFromJson(BasicDBList jsonList, String url, FederatedRequest request, SourceFederatedQueryConfigPojo endpointInfo) { BasicDBObject doc = null; // (don't create unless needed) BasicDBList ents = null;//from www.jav a 2 s. co m StringBuffer entVals = null; HashSet<String> entDedup = null; if (_testMode) { // In test mode, need to return the JSON even if no entities are specified doc = new BasicDBObject(); } if (null != endpointInfo.docConversionMap) { for (Map.Entry<String, String> docInfo : endpointInfo.docConversionMap.entrySet()) { for (Object jsonObj : jsonList) { BasicDBObject json = (BasicDBObject) jsonObj; try { String key = docInfo.getKey(); // (allow user to not prepend array: if they don't want to) if ((1 == json.size()) && json.containsKey((Object) "array")) { if (!key.startsWith("array:") && !key.startsWith(":array") && !key.startsWith("$:array") && !key.startsWith("::") && !key.startsWith("$::")) { if (key.startsWith(":")) { // jpath key = ":array" + key; } else if (key.startsWith("$:")) { // jpath key = "$:array" + key.substring(1); } else { key = "array:" + key; } } } //TESTED (by hand) if (key.startsWith(":")) { // jpath key = "$" + key; } // NOTE: *not* org.json.JSONArray JSONArray candidateEntities = null; if (key.startsWith("$")) { JSONArray candidateEntities_tmp = JsonPath.read(json.toString(), key.replace(':', '.')); if (null != candidateEntities_tmp) { candidateEntities = new JSONArray(); for (Object o : candidateEntities_tmp) { if (o instanceof String) { candidateEntities.add(o); } else if (o instanceof JSONArray) { candidateEntities.addAll((JSONArray) o); } } //TESTED (displayUrl vs entities, 3.2) } //DEBUG //System.out.println(candidateEntities); } //(TESTED (permutations above by hand)) else { String s = (String) MongoDbUtil.getProperty(json, key.replace(':', '.')); if (null != s) { candidateEntities = new JSONArray(); candidateEntities.add(s); } } //TESTED (3.1) if (null != candidateEntities) for (int i = 0; i < candidateEntities.size(); ++i) { Object o = candidateEntities.get(i); if (!(o instanceof String)) { continue; } String s = o.toString(); if (null == doc) { doc = new BasicDBObject(); //(various fields added below) } if (docInfo.getValue().equalsIgnoreCase(DocumentPojo.displayUrl_)) { doc.put(DocumentPojo.displayUrl_, s); } //TESTED (3.1, 4.*) else { // Entities! if (null == ents) { ents = new BasicDBList(); } String index = s.toLowerCase() + "/" + docInfo.getValue().toLowerCase(); if (null == entDedup) { entDedup = new HashSet<String>(); } else if (entDedup.contains(index)) { // Entity deduplication continue; } //TESTED (3.2) entDedup.add(index); if (null == entVals) { entVals = new StringBuffer(": "); } else { entVals.append(", "); } entVals.append(s); String dimension = null; if (null != endpointInfo.typeToDimensionMap) { try { dimension = EntityPojo.Dimension .valueOf( endpointInfo.typeToDimensionMap.get(docInfo.getValue())) .toString(); } catch (Exception e) { } } if (null == dimension) { dimension = EntityPojo.Dimension.What.toString(); } //TESTED (by hand) // (alternative to "made up" values would be to go looking in the existing docs/ents?) // (we'll try to avoid that for now...) BasicDBObject ent = new BasicDBObject(); ent.put(EntityPojo.disambiguated_name_, s); ent.put(EntityPojo.type_, docInfo.getValue()); ent.put(EntityPojo.dimension_, dimension); ent.put(EntityPojo.relevance_, 1.0); ent.put(EntityPojo.doccount_, 1L); // (ie relative to this query) ent.put(EntityPojo.averageFreq_, 1.0); ent.put(EntityPojo.datasetSignificance_, 10.0); // (ie relative to this query) ent.put(EntityPojo.significance_, 10.0); // (ie relative to this query) ent.put(EntityPojo.frequency_, 1.0); ent.put(EntityPojo.index_, index); ent.put(EntityPojo.queryCoverage_, 100.0); // (ie relative to this query) ent.put(EntityPojo.totalfrequency_, 1.0); // (ie relative to this query) ents.add(ent); } //TESTED (3.1, 4.*) } } catch (Exception e) { //(do nothing? null or the wrong type) //e.printStackTrace(); } } //end loop over various JSON objects retrieved } //(End loop over doc conversion elements) } //TESTED (3.*, 4.*) if ((null == ents) && !_testMode) { // don't return unless there are any entities return null; } else if (null != doc) { // Insert mandatory fields: // (Note the query format is a little bit different, the following fields are converted to arrays: // sourceKey, source, communityId, mediaType) doc.put(DocumentPojo._id_, new ObjectId()); doc.put(DocumentPojo.url_, url); doc.put(DocumentPojo.created_, new Date()); doc.put(DocumentPojo.modified_, new Date()); doc.put(DocumentPojo.publishedDate_, new Date()); doc.put(DocumentPojo.sourceKey_, endpointInfo.parentSource.getKey()); doc.put(DocumentPojo.source_, endpointInfo.parentSource.getTitle()); doc.put(DocumentPojo.communityId_, new ObjectId(request.communityIdStrs[0])); doc.put(DocumentPojo.mediaType_, endpointInfo.parentSource.getMediaType()); doc.put(DocumentPojo.metadata_, new BasicDBObject("json", jsonList.toArray())); if ((null != entVals) && (entVals.length() > 165)) { // (arbitrary length) entVals.setLength(165); entVals.append("..."); } doc.put(DocumentPojo.title_, new StringBuffer(endpointInfo.titlePrefix).append(": ") .append(request.requestParameter).append(entVals).toString()); doc.put(DocumentPojo.entities_, ents); Gson gson = new GsonBuilder().setPrettyPrinting().create(); JsonParser jp = new JsonParser(); JsonElement je = jp.parse(jsonList.toString()); doc.put(DocumentPojo.description_, gson.toJson(je)); // (prettified JSON) } //TESTED (3.*, 4.*) return doc; }
From source file:edu.slu.action.ObjectAction.java
/** * Public facing servlet to PATCH set values of an existing RERUM object. * @respond with state of new object in the body * @throws java.io.IOException// ww w . j a va 2 s. c o m * @throws javax.servlet.ServletException */ public void patchSetUpdate() throws IOException, ServletException, Exception { Boolean historyNextUpdatePassed = false; System.out.println("patch set update"); if (null != processRequestBody(request, true) && methodApproval(request, "set")) { BasicDBObject query = new BasicDBObject(); JSONObject received = JSONObject.fromObject(content); if (received.containsKey("@id")) { String updateHistoryNextID = received.getString("@id"); query.append("@id", updateHistoryNextID); BasicDBObject originalObject = (BasicDBObject) mongoDBService .findOneByExample(Constant.COLLECTION_ANNOTATION, query); //The originalObject DB object BasicDBObject updatedObject = (BasicDBObject) originalObject.copy(); //A copy of the original, this will be saved as a new object. Make all edits to this variable. boolean alreadyDeleted = checkIfDeleted(JSONObject.fromObject(originalObject)); boolean isReleased = checkIfReleased(JSONObject.fromObject(originalObject)); if (alreadyDeleted) { writeErrorResponse("The object you are trying to update is deleted.", HttpServletResponse.SC_FORBIDDEN); } else if (isReleased) { writeErrorResponse("The object you are trying to update is released. Fork to make changes.", HttpServletResponse.SC_FORBIDDEN); } else { if (null != originalObject) { Set<String> update_anno_keys = received.keySet(); int updateCount = 0; //If the object already in the database contains the key found from the object recieved from the user... for (String key : update_anno_keys) { if (originalObject.containsKey(key)) { //Keys matched. Ignore it, set only works for new keys. //@cubap @theHabes do we want to build that this happened into the response at all? } else { //this is a new key, this is a set. Allow null values. updatedObject.append(key, received.get(key)); updateCount += 1; } } if (updateCount > 0) { JSONObject newObject = JSONObject.fromObject(updatedObject);//The edited original object meant to be saved as a new object (versioning) newObject = configureRerumOptions(newObject, true); //__rerum for the new object being created because of the update action newObject.remove("@id"); //This is being saved as a new object, so remove this @id for the new one to be set. //Since we ignore changes to __rerum for existing objects, we do no configureRerumOptions(updatedObject); DBObject dbo = (DBObject) JSON.parse(newObject.toString()); String newNextID = mongoDBService.save(Constant.COLLECTION_ANNOTATION, dbo); String newNextAtID = Constant.RERUM_ID_PREFIX + newNextID; BasicDBObject dboWithObjectID = new BasicDBObject((BasicDBObject) dbo); dboWithObjectID.append("@id", newNextAtID); newObject.element("@id", newNextAtID); newObject.remove("_id"); mongoDBService.update(Constant.COLLECTION_ANNOTATION, dbo, dboWithObjectID); historyNextUpdatePassed = alterHistoryNext(updateHistoryNextID, newNextAtID); //update history.next or original object to include the newObject @id if (historyNextUpdatePassed) { System.out.println("object patch set updated: " + newNextAtID); JSONObject jo = new JSONObject(); JSONObject iiif_validation_response = checkIIIFCompliance(newNextAtID, "2.1"); jo.element("code", HttpServletResponse.SC_OK); jo.element("original_object_id", updateHistoryNextID); jo.element("new_obj_state", newObject); //FIXME: @webanno standards say this should be the response. jo.element("iiif_validation", iiif_validation_response); try { addWebAnnotationHeaders(newNextID, isContainerType(newObject), isLD(newObject)); addLocationHeader(newObject); response.addHeader("Content-Type", "application/json; charset=utf-8"); response.setContentType("UTF-8"); response.addHeader("Access-Control-Allow-Origin", "*"); response.setStatus(HttpServletResponse.SC_OK); out = response.getWriter(); out.write(mapper.writer().withDefaultPrettyPrinter().writeValueAsString(jo)); } catch (IOException ex) { Logger.getLogger(ObjectAction.class.getName()).log(Level.SEVERE, null, ex); } } else { //The error is already written to response.out, do nothing. } } else { // Nothing could be patched addLocationHeader(received); writeErrorResponse("Nothing could be PATCHed", HttpServletResponse.SC_NO_CONTENT); } } else { //This could means it was an external object, but those fail for PATCH updates. writeErrorResponse("Object " + received.getString("@id") + " not found in RERUM, could not update. PUT update to make this object a part of RERUM.", HttpServletResponse.SC_BAD_REQUEST); } } } else { writeErrorResponse("Object did not contain an @id, could not update.", HttpServletResponse.SC_BAD_REQUEST); } } }
From source file:edu.slu.action.ObjectAction.java
/** * Public facing servlet to PATCH unset values of an existing RERUM object. * @respond with state of new object in the body * @throws java.io.IOException/*from w w w. j a v a 2s . c o m*/ * @throws javax.servlet.ServletException */ public void patchUnsetUpdate() throws IOException, ServletException, Exception { Boolean historyNextUpdatePassed = false; System.out.println("Patch unset update"); if (null != processRequestBody(request, true) && methodApproval(request, "unset")) { BasicDBObject query = new BasicDBObject(); JSONObject received = JSONObject.fromObject(content); if (received.containsKey("@id")) { String updateHistoryNextID = received.getString("@id"); query.append("@id", updateHistoryNextID); BasicDBObject originalObject = (BasicDBObject) mongoDBService .findOneByExample(Constant.COLLECTION_ANNOTATION, query); //The originalObject DB object BasicDBObject updatedObject = (BasicDBObject) originalObject.copy(); //A copy of the original, this will be saved as a new object. Make all edits to this variable. boolean alreadyDeleted = checkIfDeleted(JSONObject.fromObject(originalObject)); boolean isReleased = checkIfReleased(JSONObject.fromObject(originalObject)); if (alreadyDeleted) { writeErrorResponse("The object you are trying to update is deleted.", HttpServletResponse.SC_FORBIDDEN); } else if (isReleased) { writeErrorResponse("The object you are trying to update is released. Fork to make changes.", HttpServletResponse.SC_FORBIDDEN); } else { if (null != originalObject) { Set<String> update_anno_keys = received.keySet(); int updateCount = 0; //If the object already in the database contains the key found from the object recieved from the user... for (String key : update_anno_keys) { if (originalObject.containsKey(key)) { if (key.equals("@id") || key.equals("__rerum") || key.equals("objectID") || key.equals("_id")) { // Ignore these in a PATCH. DO NOT update, DO NOT count as an attempt to update } else { if (null != received.get(key)) { //Found matching keys and value is not null. Ignore these. //@cubap @theHabes do we want to build that this happened into the response at all? } else { //Found matching keys and value is null, this is an unset updatedObject.remove(key); updateCount += 1; } } } else { //Original object does not contain this key, perhaps the user meant set. //@cubap @theHabes do we want to build that this happened into the response at all? } } if (updateCount > 0) { JSONObject newObject = JSONObject.fromObject(updatedObject);//The edited original object meant to be saved as a new object (versioning) newObject = configureRerumOptions(newObject, true); //__rerum for the new object being created because of the update action newObject.remove("@id"); //This is being saved as a new object, so remove this @id for the new one to be set. //Since we ignore changes to __rerum for existing objects, we do no configureRerumOptions(updatedObject); DBObject dbo = (DBObject) JSON.parse(newObject.toString()); String newNextID = mongoDBService.save(Constant.COLLECTION_ANNOTATION, dbo); String newNextAtID = Constant.RERUM_ID_PREFIX + newNextID; BasicDBObject dboWithObjectID = new BasicDBObject((BasicDBObject) dbo); dboWithObjectID.append("@id", newNextAtID); newObject.element("@id", newNextAtID); newObject.remove("_id"); mongoDBService.update(Constant.COLLECTION_ANNOTATION, dbo, dboWithObjectID); historyNextUpdatePassed = alterHistoryNext(updateHistoryNextID, newNextAtID); //update history.next or original object to include the newObject @id if (historyNextUpdatePassed) { System.out.println("Patch unset updated: " + newNextAtID); JSONObject jo = new JSONObject(); JSONObject iiif_validation_response = checkIIIFCompliance(newNextAtID, "2.1"); jo.element("code", HttpServletResponse.SC_OK); jo.element("original_object_id", updateHistoryNextID); jo.element("new_obj_state", newObject); //FIXME: @webanno standards say this should be the response. jo.element("iiif_validation", iiif_validation_response); try { addWebAnnotationHeaders(newNextID, isContainerType(newObject), isLD(newObject)); addLocationHeader(newObject); response.addHeader("Access-Control-Allow-Origin", "*"); response.setStatus(HttpServletResponse.SC_OK); response.addHeader("Content-Type", "application/json; charset=utf-8"); response.setContentType("UTF-8"); out = response.getWriter(); out.write(mapper.writer().withDefaultPrettyPrinter().writeValueAsString(jo)); } catch (IOException ex) { Logger.getLogger(ObjectAction.class.getName()).log(Level.SEVERE, null, ex); } } else { //The error is already written to response.out, do nothing. } } else { // Nothing could be patched addLocationHeader(received); writeErrorResponse("Nothing could be PATCHed", HttpServletResponse.SC_NO_CONTENT); } } else { //This could means it was an external object, but those fail for PATCH updates. writeErrorResponse("Object " + received.getString("@id") + " not found in RERUM, could not update. PUT update to make this object a part of RERUM.", HttpServletResponse.SC_BAD_REQUEST); } } } else { writeErrorResponse("Object did not contain an @id, could not update.", HttpServletResponse.SC_BAD_REQUEST); } } }
From source file:edu.slu.action.ObjectAction.java
/** * Update a given annotation. Cannot set or unset keys. * @respond with state of new object in the body *//*w ww. j a v a2 s . c o m*/ public void patchUpdateObject() throws ServletException, Exception { Boolean historyNextUpdatePassed = false; System.out.println("trying to patch"); if (null != processRequestBody(request, true) && methodApproval(request, "patch")) { BasicDBObject query = new BasicDBObject(); JSONObject received = JSONObject.fromObject(content); if (received.containsKey("@id")) { String updateHistoryNextID = received.getString("@id"); query.append("@id", updateHistoryNextID); BasicDBObject originalObject = (BasicDBObject) mongoDBService .findOneByExample(Constant.COLLECTION_ANNOTATION, query); //The originalObject DB object boolean alreadyDeleted = checkIfDeleted(JSONObject.fromObject(originalObject)); boolean isReleased = checkIfReleased(JSONObject.fromObject(originalObject)); if (alreadyDeleted) { writeErrorResponse("The object you are trying to update is deleted.", HttpServletResponse.SC_FORBIDDEN); } else if (isReleased) { writeErrorResponse("The object you are trying to update is released. Fork to make changes.", HttpServletResponse.SC_FORBIDDEN); } else { if (null != originalObject) { BasicDBObject updatedObject = (BasicDBObject) originalObject.copy(); //A copy of the original, this will be saved as a new object. Make all edits to this variable. Set<String> update_anno_keys = received.keySet(); boolean triedToSet = false; int updateCount = 0; //If the object already in the database contains the key found from the object recieved from the user, update it barring a few special keys //Users cannot update the __rerum property, so we ignore any update action to that particular field. for (String key : update_anno_keys) { if (originalObject.containsKey(key)) { //Skip keys we want to ignore and keys that match but have matching values if (!(key.equals("@id") || key.equals("__rerum") || key.equals("objectID") || key.equals("_id")) && received.get(key) != originalObject.get(key)) { updatedObject.remove(key); updatedObject.append(key, received.get(key)); updateCount += 1; } } else { triedToSet = true; // break; } } if (triedToSet) { System.out.println("Patch meh 1"); //@cubap @theHabes We continued with what we could patch. Do we tell the user at all? //writeErrorResponse("A key you are trying to update does not exist on the object. You can set with the patch_set or put_update action.", HttpServletResponse.SC_BAD_REQUEST); } else if (updateCount == 0) { System.out.println("Patch meh 2"); addLocationHeader(received); writeErrorResponse("Nothing could be PATCHed", HttpServletResponse.SC_NO_CONTENT); } else { JSONObject newObject = JSONObject.fromObject(updatedObject);//The edited original object meant to be saved as a new object (versioning) newObject = configureRerumOptions(newObject, true); //__rerum for the new object being created because of the update action newObject.remove("@id"); //This is being saved as a new object, so remove this @id for the new one to be set. //Since we ignore changes to __rerum for existing objects, we do no configureRerumOptions(updatedObject); DBObject dbo = (DBObject) JSON.parse(newObject.toString()); String newNextID = mongoDBService.save(Constant.COLLECTION_ANNOTATION, dbo); String newNextAtID = Constant.RERUM_ID_PREFIX + newNextID; BasicDBObject dboWithObjectID = new BasicDBObject((BasicDBObject) dbo); dboWithObjectID.append("@id", newNextAtID); newObject.element("@id", newNextAtID); newObject.remove("_id"); mongoDBService.update(Constant.COLLECTION_ANNOTATION, dbo, dboWithObjectID); historyNextUpdatePassed = alterHistoryNext(updateHistoryNextID, newNextAtID); //update history.next or original object to include the newObject @id if (historyNextUpdatePassed) { System.out.println("Patch updated object: " + newNextAtID); JSONObject jo = new JSONObject(); JSONObject iiif_validation_response = checkIIIFCompliance(newNextAtID, "2.1"); jo.element("code", HttpServletResponse.SC_OK); jo.element("original_object_id", updateHistoryNextID); jo.element("new_obj_state", newObject); //FIXME: @webanno standards say this should be the response. jo.element("iiif_validation", iiif_validation_response); try { addWebAnnotationHeaders(newNextID, isContainerType(newObject), isLD(newObject)); addLocationHeader(newObject); response.addHeader("Access-Control-Allow-Origin", "*"); response.setStatus(HttpServletResponse.SC_OK); response.addHeader("Content-Type", "application/json; charset=utf-8"); response.setContentType("UTF-8"); out = response.getWriter(); out.write(mapper.writer().withDefaultPrettyPrinter().writeValueAsString(jo)); } catch (IOException ex) { Logger.getLogger(ObjectAction.class.getName()).log(Level.SEVERE, null, ex); } } else { //The error is already written to response.out, do nothing. } } } else { writeErrorResponse( "Object " + received.getString("@id") + " not found in RERUM, could not patch update.", HttpServletResponse.SC_BAD_REQUEST); } } } else { writeErrorResponse("Object did not contain an @id, could not patch update.", HttpServletResponse.SC_BAD_REQUEST); } } }
From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java
License:Apache License
private List<QueryResult> prepareClinvarQueryResultList(List<QueryResult> clinicalQueryResultList) { List<QueryResult> queryResultList = new ArrayList<>(); for (QueryResult clinicalQueryResult : clinicalQueryResultList) { QueryResult queryResult = new QueryResult(); queryResult.setId(clinicalQueryResult.getId()); queryResult.setDbTime(clinicalQueryResult.getDbTime()); BasicDBList basicDBList = new BasicDBList(); int numResults = 0; for (BasicDBObject clinicalRecord : (List<BasicDBObject>) clinicalQueryResult.getResult()) { if (clinicalRecord.containsKey("clinvarList")) { basicDBList.add(clinicalRecord); numResults += 1;/*from www . j a v a 2 s. co m*/ } } queryResult.setResult(basicDBList); queryResult.setNumResults(numResults); queryResultList.add(queryResult); } return queryResultList; }
From source file:org.opencb.cellbase.mongodb.db.variation.VariantAnnotationMongoDBAdaptor.java
License:Apache License
public List<QueryResult> getAnnotationByVariantList(List<GenomicVariant> variantList, QueryOptions queryOptions) {/* w ww.j a va 2 s. c om*/ // TODO: validation of queryoption 'include' values List<String> includeList = queryOptions.getAsStringList("include"); if (includeList.isEmpty()) { includeList = Arrays.asList("variation", "clinical", "consequenceType", "conservation", "drugInteraction"); } List<QueryResult> annotations = null; List<QueryResult> variationQueryResultList = null; if (includeList.contains("variation")) { variationQueryResultList = variationDBAdaptor.getAllByVariantList(variantList, queryOptions); annotations = variationQueryResultList; } List<QueryResult> clinicalQueryResultList = null; if (includeList.contains("clinical")) { clinicalQueryResultList = clinicalDBAdaptor.getAllByGenomicVariantList(variantList, queryOptions); if (annotations == null) { annotations = clinicalQueryResultList; } } // List<QueryResult> variationConsequenceTypeList = null; // if (includeList.contains("consequenceType")) { // variationConsequenceTypeList = getAllConsequenceTypesByVariantList(variantList, queryOptions); // if (annotations == null) { // annotations = variationConsequenceTypeList; // } // } List<QueryResult> conservedRegionQueryResultList = null; if (includeList.contains("conservation")) { conservedRegionQueryResultList = conservedRegionDBAdaptor .getAllScoresByRegionList(variantListToRegionList(variantList), queryOptions); if (annotations == null) { annotations = conservedRegionQueryResultList; } } for (int i = 0; i < variantList.size(); i++) { // TODO: start & end are both being set to variantList.get(i).getPosition(), modify this for indels VariantAnnotation variantAnnotation = new VariantAnnotation(variantList.get(i).getChromosome(), variantList.get(i).getPosition(), variantList.get(i).getPosition(), variantList.get(i).getReference(), variantList.get(i).getAlternative()); if (clinicalQueryResultList != null) { QueryResult clinicalQueryResult = clinicalQueryResultList.get(i); if (clinicalQueryResult.getResult() != null && clinicalQueryResult.getResult().size() > 0) { variantAnnotation.setClinical((Map<String, Object>) clinicalQueryResult.getResult().get(0)); } } // if (variationConsequenceTypeList != null) { if (includeList.contains("consequenceType")) { variantAnnotation.setConsequenceTypes( (List<ConsequenceType>) getAllConsequenceTypesByVariant(variantList.get(i), new QueryOptions()).getResult()); } if (includeList.contains("drugInteraction")) { Map<String, List<Object>> geneDrugInteractionMap = new HashMap<>(1); geneDrugInteractionMap.put("dgidb", getGeneDrugInteractions(variantList.get(i))); variantAnnotation.setGeneDrugInteraction(geneDrugInteractionMap); } if (conservedRegionQueryResultList != null) { variantAnnotation .setConservationScores((List<Score>) conservedRegionQueryResultList.get(i).getResult()); } List<BasicDBObject> variationDBList = null; if (variationQueryResultList != null) { variationDBList = (List<BasicDBObject>) variationQueryResultList.get(i).getResult(); } if (variationDBList != null && variationDBList.size() > 0) { String id = variationDBList.get(0).get("id").toString(); variantAnnotation.setId(id); BasicDBList freqsDBList = (BasicDBList) variationDBList.get(0).get("populationFrequencies"); if (freqsDBList != null) { BasicDBObject freqDBObject; for (int j = 0; j < freqsDBList.size(); j++) { freqDBObject = ((BasicDBObject) freqsDBList.get(j)); if (freqDBObject != null) { if (freqDBObject.containsKey("study")) { variantAnnotation.addPopulationFrequency(new PopulationFrequency( freqDBObject.get("study").toString(), freqDBObject.get("pop").toString(), freqDBObject.get("superPop").toString(), freqDBObject.get("refAllele").toString(), freqDBObject.get("altAllele").toString(), Float.valueOf(freqDBObject.get("refAlleleFreq").toString()), Float.valueOf(freqDBObject.get("altAlleleFreq").toString()))); } else { variantAnnotation.addPopulationFrequency(new PopulationFrequency("1000G_PHASE_3", freqDBObject.get("pop").toString(), freqDBObject.get("superPop").toString(), freqDBObject.get("refAllele").toString(), freqDBObject.get("altAllele").toString(), Float.valueOf(freqDBObject.get("refAlleleFreq").toString()), Float.valueOf(freqDBObject.get("altAlleleFreq").toString()))); } } } } } List<VariantAnnotation> value = Collections.singletonList(variantAnnotation); annotations.get(i).setResult(value); } return annotations; // return clinicalQueryResultList; }