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cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/IdWSServer.java
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| /* | ||
| * Copyright 2015-2020 OpenCB | ||
| * | ||
| * 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 org.opencb.cellbase.server.rest.feature; | ||
|
|
||
| import com.google.common.base.Splitter; | ||
| import io.swagger.annotations.Api; | ||
| import io.swagger.annotations.ApiOperation; | ||
| import io.swagger.annotations.ApiParam; | ||
| import org.bson.Document; | ||
| import org.opencb.biodata.models.core.Xref; | ||
| import org.opencb.cellbase.core.ParamConstants; | ||
| import org.opencb.cellbase.core.api.GeneDBAdaptor; | ||
| import org.opencb.cellbase.core.api.XRefDBAdaptor; | ||
| import org.opencb.cellbase.core.exception.CellbaseException; | ||
| import org.opencb.cellbase.core.result.CellBaseDataResult; | ||
| import org.opencb.cellbase.server.exception.SpeciesException; | ||
| import org.opencb.cellbase.server.exception.VersionException; | ||
| import org.opencb.cellbase.server.rest.GenericRestWSServer; | ||
| import org.opencb.commons.datastore.core.Query; | ||
|
|
||
| import javax.servlet.http.HttpServletRequest; | ||
| import javax.ws.rs.*; | ||
| import javax.ws.rs.core.Context; | ||
| import javax.ws.rs.core.MediaType; | ||
| import javax.ws.rs.core.Response; | ||
| import javax.ws.rs.core.UriInfo; | ||
| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
|
|
||
| /** | ||
| * @author imedina | ||
| */ | ||
| @Path("/{version}/{species}/feature/id") | ||
| @Produces(MediaType.APPLICATION_JSON) | ||
| @Api(value = "Xref", description = "External References RESTful Web Services API") | ||
| public class IdWSServer extends GenericRestWSServer { | ||
|
|
||
| public IdWSServer(@PathParam("version") | ||
| @ApiParam(name = "version", value = ParamConstants.VERSION_DESCRIPTION, | ||
| defaultValue = ParamConstants.DEFAULT_VERSION) String version, | ||
| @PathParam("species") | ||
| @ApiParam(name = "species", value = ParamConstants.SPECIES_DESCRIPTION) String species, | ||
| @Context UriInfo uriInfo, @Context HttpServletRequest hsr) throws VersionException, | ||
| SpeciesException, IOException, CellbaseException { | ||
| super(version, species, uriInfo, hsr); | ||
| } | ||
|
|
||
| @GET | ||
| @Path("/model") | ||
| @ApiOperation(httpMethod = "GET", value = ParamConstants.DATA_MODEL_DESCRIPTION, response = Map.class, | ||
| responseContainer = "QueryResponse") | ||
| public Response getModel() { | ||
| return createModelResponse(Xref.class); | ||
| } | ||
|
|
||
| @GET | ||
| @Path("/{id}/info") | ||
| @ApiOperation(httpMethod = "GET", value = "Retrieves the external reference(s) info for the ID(s)", | ||
| notes = "An independent database query will be issued for each id, meaning that results for each id will be" | ||
| + " returned in independent CellBaseDataResult objects within the QueryResponse object.", response = Xref.class, | ||
| responseContainer = "QueryResponse") | ||
| public Response getByFeatureIdInfo(@PathParam("id") | ||
| @ApiParam(name = "id", value = "Comma separated list of ids, e.g.: BRCA2. Exact " | ||
| + "text matches will be returned.", required = true) String id, | ||
| @QueryParam("exclude") | ||
| @ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude, | ||
| @QueryParam("include") | ||
| @ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include, | ||
| @QueryParam("sort") | ||
| @ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort) { | ||
| try { | ||
| parseIncludesAndExcludes(exclude, include, sort); | ||
| parseQueryParams(); | ||
| XRefDBAdaptor xRefDBAdaptor = dbAdaptorFactory.getXRefDBAdaptor(this.species, this.assembly); | ||
|
|
||
| List<String> list = Splitter.on(",").splitToList(id); | ||
| List<Query> queries = createQueries(id, XRefDBAdaptor.QueryParams.ID.key()); | ||
|
|
||
| List<CellBaseDataResult<Document>> dbNameList = xRefDBAdaptor.nativeGet(queries, queryOptions); | ||
| for (int i = 0; i < dbNameList.size(); i++) { | ||
| dbNameList.get(i).setId(list.get(i)); | ||
| for (Document document : dbNameList.get(i).getResults()) { | ||
| if (document.get("id").equals(list.get(i))) { | ||
| List<Document> objectList = new ArrayList<>(1); | ||
| objectList.add(document); | ||
| dbNameList.get(i).setResults(objectList); | ||
| break; | ||
| } | ||
| } | ||
| } | ||
| return createOkResponse(dbNameList); | ||
| } catch (Exception e) { | ||
| return createErrorResponse(e); | ||
| } | ||
| } | ||
|
|
||
| @GET | ||
| @Path("/{id}/xref") | ||
| @ApiOperation(httpMethod = "GET", value = "Retrieves all the external references related with given ID(s)", | ||
| response = Xref.class, responseContainer = "QueryResponse") | ||
| public Response getAllXrefsByFeatureId(@PathParam("id") | ||
| @ApiParam(name = "id", value = "Comma separated list of ids, e.g.: BRCA2." | ||
| + "Exact text matches will be searched.", required = true) String ids, | ||
| @DefaultValue("") | ||
| @QueryParam("dbname") | ||
| @ApiParam(name = "dbname", value = "Comma separated list of source DB names" | ||
| + " to include in the search, e.g.: ensembl_gene,vega_gene,havana_gene." | ||
| + " Available db names are shown by this web service: " | ||
| + " https://bioinfo.hpc.cam.ac.uk/cellbase/webservices/#!/Xref/" | ||
| + "getDBNames", required = false) String dbname) { | ||
| try { | ||
| parseQueryParams(); | ||
| XRefDBAdaptor xRefDBAdaptor = dbAdaptorFactory.getXRefDBAdaptor(this.species, this.assembly); | ||
|
|
||
| Query query = new Query(); | ||
| query.put(XRefDBAdaptor.QueryParams.ID.key(), ids); | ||
| if (dbname != null && !dbname.isEmpty()) { | ||
| query.put(XRefDBAdaptor.QueryParams.DBNAME.key(), dbname); | ||
| } | ||
| CellBaseDataResult queryResult = xRefDBAdaptor.nativeGet(query, queryOptions); | ||
| queryResult.setId(ids); | ||
| return createOkResponse(queryResult); | ||
| } catch (Exception e) { | ||
| return createErrorResponse(e); | ||
| } | ||
| } | ||
|
|
||
| @GET | ||
| @Path("/{id}/startsWith") | ||
| @ApiOperation(httpMethod = "GET", value = "Get the gene HGNC symbols of genes for which there is an Xref id that " | ||
| + "matches the beginning of the given string", response = Map.class, responseContainer = "QueryResponse") | ||
| public Response getByLikeQuery(@PathParam("id") | ||
| @ApiParam(name = "id", value = "One single string to be matched at the beginning of" | ||
| + " the Xref id", required = true) String id) { | ||
| try { | ||
| parseQueryParams(); | ||
| XRefDBAdaptor x = dbAdaptorFactory.getXRefDBAdaptor(this.species, this.assembly); | ||
| CellBaseDataResult queryResult = x.startsWith(id, queryOptions); | ||
| queryResult.setId(id); | ||
| return createOkResponse(queryResult); | ||
| } catch (Exception e) { | ||
| return createErrorResponse(e); | ||
| } | ||
| } | ||
|
|
||
| @GET | ||
| @Path("/{id}/contains") | ||
| @ApiOperation(httpMethod = "GET", value = "Get gene HGNC symbols for which there is an Xref id containing the given " | ||
| + "string", response = Map.class, responseContainer = "QueryResponse") | ||
| public Response getByContainsQuery(@PathParam("id") | ||
| @ApiParam(name = "id", value = "Comma separated list of strings to " | ||
| + "be contained within the xref id, e.g.: BRCA2", required = true) String id) { | ||
| try { | ||
| parseQueryParams(); | ||
| XRefDBAdaptor xRefDBAdaptor = dbAdaptorFactory.getXRefDBAdaptor(this.species, this.assembly); | ||
| CellBaseDataResult xrefs = xRefDBAdaptor.contains(id, queryOptions); | ||
| xrefs.setId(id); | ||
| return createOkResponse(xrefs); | ||
| } catch (Exception e) { | ||
| return createErrorResponse(e); | ||
| } | ||
| } | ||
|
|
||
| @GET | ||
| @Path("/{id}/gene") | ||
| @ApiOperation(httpMethod = "GET", value = "Get the gene(s) for the given ID(s)", notes = "An independent" | ||
| + " database query will be issued for each id, meaning that results for each id will be" | ||
| + " returned in independent CellBaseDataResult objects within the QueryResponse object.", | ||
| responseContainer = "QueryResponse") | ||
| public Response getGeneByEnsemblId(@PathParam("id") | ||
| @ApiParam(name = "id", value = "Comma separated list of ids to look" | ||
| + " for within gene xrefs, e.g.: BRCA2", required = true) String id) { | ||
| try { | ||
| parseQueryParams(); | ||
| GeneDBAdaptor geneDBAdaptor = dbAdaptorFactory.getGeneDBAdaptor(this.species, this.assembly); | ||
|
|
||
| String[] ids = id.split(","); | ||
| List<Query> queries = new ArrayList<>(ids.length); | ||
| for (String s : ids) { | ||
| queries.add(new Query(GeneDBAdaptor.QueryParams.XREFS.key(), s)); | ||
| } | ||
| List<CellBaseDataResult> queryResults = geneDBAdaptor.nativeGet(queries, queryOptions); | ||
| for (int i = 0; i < ids.length; i++) { | ||
| queryResults.get(i).setId(ids[i]); | ||
| } | ||
| return createOkResponse(queryResults); | ||
| } catch (Exception e) { | ||
| return createErrorResponse(e); | ||
| } | ||
| } | ||
|
|
||
| @GET | ||
| @Path("/dbnames") | ||
| @ApiOperation(httpMethod = "GET", value = "Get list of distinct source DB names from which xref ids were collected ", | ||
| response = String.class, responseContainer = "QueryResponse") | ||
| public Response getDBNames() { | ||
| try { | ||
| parseQueryParams(); | ||
| XRefDBAdaptor xRefDBAdaptor = dbAdaptorFactory.getXRefDBAdaptor(this.species, this.assembly); | ||
| CellBaseDataResult xrefs = xRefDBAdaptor.distinct(query, "transcripts.xrefs.dbName"); | ||
| return createOkResponse(xrefs); | ||
| } catch (Exception e) { | ||
| return createErrorResponse(e); | ||
| } | ||
| } | ||
|
|
||
| @GET | ||
| @Path("/help") | ||
| public Response help() { | ||
| return createOkResponse("Usage:"); | ||
| } | ||
|
|
||
| } |
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