diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/CellBaseExceptionMapper.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/exception/CellBaseExceptionMapper.java similarity index 90% rename from cellbase-server/src/main/java/org/opencb/cellbase/server/rest/CellBaseExceptionMapper.java rename to cellbase-server/src/main/java/org/opencb/cellbase/server/exception/CellBaseExceptionMapper.java index e354a64dbb..7c75c3284a 100644 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/CellBaseExceptionMapper.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/exception/CellBaseExceptionMapper.java @@ -14,15 +14,17 @@ * limitations under the License. */ -package org.opencb.cellbase.server.rest; +package org.opencb.cellbase.server.exception; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.MapperFeature; import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectWriter; +import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResponse; import org.opencb.cellbase.core.result.CellBaseDataResult; +import org.opencb.cellbase.server.rest.GenericRestWSServer; import org.opencb.commons.datastore.core.Event; import org.opencb.commons.datastore.core.ObjectMap; import org.opencb.commons.datastore.core.QueryOptions; @@ -43,7 +45,7 @@ * Created by imedina on 02/03/16. */ @Provider -public class CellBaseExceptionMapper implements ExceptionMapper { +public class CellBaseExceptionMapper implements ExceptionMapper { @Context private UriInfo uriInfo; @@ -64,7 +66,7 @@ public class CellBaseExceptionMapper implements ExceptionMapper { } @Override - public Response toResponse(Exception e) { + public Response toResponse(CellBaseException e) { // First we print the exception in Server logs logger.error("Catch error: " + e.getMessage(), e); @@ -88,7 +90,7 @@ public Response toResponse(Exception e) { jsonObjectWriter.writeValueAsString(queryOptions), ERROR); - return Response.ok(GenericRestWSServer.jsonObjectWriter.writeValueAsString(queryResponse), MediaType.APPLICATION_JSON_TYPE) + return Response.ok(GenericRestWSServer.getJsonObjectWriter().writeValueAsString(queryResponse), MediaType.APPLICATION_JSON_TYPE) .status(Response.Status.INTERNAL_SERVER_ERROR) .build(); } catch (JsonProcessingException e1) { diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/FileWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/FileWSServer.java index 533b1e4d22..08002e0970 100644 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/FileWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/FileWSServer.java @@ -48,7 +48,7 @@ public FileWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", value = ParamConstants.VERSION_DESCRIPTION, defaultValue = ParamConstants.DEFAULT_VERSION) String apiVersion, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { super(apiVersion, uriInfo, hsr); fileManager = cellBaseManagerFactory.getFileManager(); } diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java index e8a61d4f0a..1da7669371 100755 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java @@ -30,7 +30,6 @@ import org.opencb.cellbase.core.ParamConstants; import org.opencb.cellbase.core.api.key.ApiKeyJwtPayload; import org.opencb.cellbase.core.api.key.ApiKeyManager; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.config.CellBaseConfiguration; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResponse; @@ -60,7 +59,8 @@ import java.util.*; import java.util.concurrent.atomic.AtomicBoolean; -import static org.opencb.cellbase.core.ParamConstants.*; +import static org.opencb.cellbase.core.ParamConstants.API_KEY_PARAM; +import static org.opencb.cellbase.core.ParamConstants.DATA_RELEASE_PARAM; @Path("/{version}/{species}") @Produces("text/plain") @@ -101,21 +101,25 @@ public class GenericRestWSServer implements IWSServer { protected static ApiKeyManager apiKeyManager; public GenericRestWSServer(@PathParam("version") String version, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { this(version, DONT_CHECK_SPECIES, uriInfo, hsr); } public GenericRestWSServer(@PathParam("version") String version, @PathParam("species") String species, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { this.version = version; this.uriInfo = uriInfo; this.httpServletRequest = hsr; this.species = species; - init(); - initQuery(); + try { + init(); + initQuery(); + } catch (IOException e) { + throw new CellBaseException(e.getMessage()); + } } private void init() throws IOException, CellBaseException { @@ -467,4 +471,8 @@ private Response buildResponse(ResponseBuilder responseBuilder) { .header("Access-Control-Allow-Methods", "GET, POST, OPTIONS") .build(); } + + public static ObjectWriter getJsonObjectWriter() { + return jsonObjectWriter; + } } diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/MetaWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/MetaWSServer.java index 6f08a9fd27..a54adf3f41 100644 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/MetaWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/MetaWSServer.java @@ -20,7 +20,6 @@ import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.lang3.StringUtils; import org.opencb.cellbase.core.ParamConstants; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.common.GitRepositoryState; import org.opencb.cellbase.core.config.DownloadProperties; import org.opencb.cellbase.core.config.SpeciesConfiguration; @@ -50,7 +49,6 @@ import javax.ws.rs.core.Context; import javax.ws.rs.core.Response; import javax.ws.rs.core.UriInfo; -import java.io.IOException; import java.lang.reflect.Method; import java.lang.reflect.Parameter; import java.text.DateFormat; @@ -73,7 +71,7 @@ public MetaWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", value = ParamConstants.VERSION_DESCRIPTION, defaultValue = ParamConstants.DEFAULT_VERSION) String apiVersion, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { super(apiVersion, uriInfo, hsr); metaManager = cellBaseManagerFactory.getMetaManager(); } diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/OntologyWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/OntologyWSServer.java index c26df87caf..d4bb77a3e7 100644 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/OntologyWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/OntologyWSServer.java @@ -21,7 +21,6 @@ import org.apache.commons.lang3.StringUtils; import org.opencb.biodata.models.core.OntologyTerm; import org.opencb.cellbase.core.api.OntologyQuery; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.core.utils.SpeciesUtils; @@ -33,7 +32,6 @@ 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.Arrays; import java.util.List; import java.util.Map; @@ -55,7 +53,7 @@ public OntologyWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", int dataRelease, @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { super(apiVersion, species, uriInfo, hsr); List assemblies = uriInfo.getQueryParameters().get("assembly"); if (CollectionUtils.isNotEmpty(assemblies)) { diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/PublicationWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/PublicationWSServer.java index 4497c1e79d..238864c3be 100644 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/PublicationWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/PublicationWSServer.java @@ -20,7 +20,6 @@ import org.opencb.biodata.formats.pubmed.v233jaxb.PubmedArticle; import org.opencb.cellbase.core.ParamConstants; import org.opencb.cellbase.core.api.PublicationQuery; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.lib.managers.PublicationManager; @@ -30,7 +29,6 @@ import javax.ws.rs.core.Context; import javax.ws.rs.core.Response; import javax.ws.rs.core.UriInfo; -import java.io.IOException; import java.util.Map; import static org.opencb.cellbase.core.ParamConstants.*; @@ -55,7 +53,7 @@ public PublicationWSServer(@PathParam("apiVersion") @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { super(apiVersion, uriInfo, hsr); publicationManager = cellBaseManagerFactory.getPublicationManager(); } diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/SpeciesWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/SpeciesWSServer.java index 1d97e45a56..111d783318 100644 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/SpeciesWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/SpeciesWSServer.java @@ -19,7 +19,6 @@ import io.swagger.annotations.*; import org.opencb.biodata.models.core.Chromosome; import org.opencb.cellbase.core.api.GenomeQuery; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.lib.managers.GenomeManager; @@ -30,7 +29,6 @@ import javax.ws.rs.core.MediaType; import javax.ws.rs.core.Response; import javax.ws.rs.core.UriInfo; -import java.io.IOException; import static org.opencb.cellbase.core.ParamConstants.*; @@ -53,7 +51,8 @@ public SpeciesWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", v int dataRelease, @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, @Context UriInfo uriInfo, - @Context HttpServletRequest hsr) throws QueryException, IOException, CellBaseException { + @Context HttpServletRequest hsr) + throws CellBaseException { super(apiVersion, species, uriInfo, hsr); genomeManager = cellBaseManagerFactory.getGenomeManager(species, assembly); diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/ClinicalWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/ClinicalWSServer.java index b8ebddb599..300d3efddb 100644 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/ClinicalWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/ClinicalWSServer.java @@ -19,7 +19,6 @@ import io.swagger.annotations.*; import org.opencb.biodata.models.variant.Variant; import org.opencb.cellbase.core.api.ClinicalVariantQuery; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.core.utils.SpeciesUtils; @@ -32,7 +31,6 @@ import javax.ws.rs.core.MediaType; import javax.ws.rs.core.Response; import javax.ws.rs.core.UriInfo; -import java.io.IOException; import static org.opencb.cellbase.core.ParamConstants.*; @@ -53,7 +51,7 @@ public ClinicalWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", int dataRelease, @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { super(apiVersion, species, uriInfo, hsr); if (assembly == null) { assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName(); diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/PharmacogenomicsWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/PharmacogenomicsWSServer.java index 85e8875045..b0a38ae361 100644 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/PharmacogenomicsWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/PharmacogenomicsWSServer.java @@ -19,7 +19,6 @@ import io.swagger.annotations.*; import org.opencb.biodata.models.pharma.PharmaChemical; import org.opencb.cellbase.core.api.PharmaChemicalQuery; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.core.utils.SpeciesUtils; @@ -33,7 +32,6 @@ 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.Arrays; import java.util.List; @@ -58,7 +56,7 @@ public PharmacogenomicsWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVe @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { super(apiVersion, species, uriInfo, hsr); if (assembly == null) { assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName(); diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java index 96c84037d4..db2d0deacd 100755 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java @@ -30,7 +30,6 @@ import org.opencb.cellbase.core.api.TranscriptQuery; import org.opencb.cellbase.core.api.VariantQuery; import org.opencb.cellbase.core.api.query.LogicalList; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.core.utils.SpeciesUtils; @@ -43,7 +42,6 @@ import javax.ws.rs.core.MediaType; import javax.ws.rs.core.Response; import javax.ws.rs.core.UriInfo; -import java.io.IOException; import java.security.InvalidParameterException; import java.util.*; @@ -70,8 +68,8 @@ public GeneWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", valu @ApiParam(name = "dataRelease", value = DATA_RELEASE_DESCRIPTION) @DefaultValue("0") @QueryParam("dataRelease") int dataRelease, @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, - @Context UriInfo uriInfo, @Context HttpServletRequest hsr) throws QueryException, IOException, - CellBaseException { + @Context UriInfo uriInfo, @Context HttpServletRequest hsr) + throws CellBaseException { super(apiVersion, species, uriInfo, hsr); List assemblies = uriInfo.getQueryParameters().get("assembly"); if (CollectionUtils.isNotEmpty(assemblies)) { diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/IdWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/IdWSServer.java index 32c60cbe82..096398e61e 100755 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/IdWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/IdWSServer.java @@ -21,7 +21,6 @@ import org.opencb.biodata.models.core.Xref; import org.opencb.cellbase.core.api.GeneQuery; import org.opencb.cellbase.core.api.XrefQuery; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.core.utils.SpeciesUtils; @@ -35,7 +34,6 @@ 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.Arrays; import java.util.List; import java.util.Map; @@ -60,7 +58,8 @@ public IdWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", value @ApiParam(name = "dataRelease", value = DATA_RELEASE_DESCRIPTION) @DefaultValue("0") @QueryParam("dataRelease") int dataRelease, @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, - @Context UriInfo uriInfo, @Context HttpServletRequest hsr) throws QueryException, IOException, CellBaseException { + @Context UriInfo uriInfo, @Context HttpServletRequest hsr) + throws CellBaseException { super(apiVersion, species, uriInfo, hsr); if (assembly == null) { assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName(); diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/ProteinWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/ProteinWSServer.java index dab1a6d5f4..ab1ea9ac23 100755 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/ProteinWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/ProteinWSServer.java @@ -33,7 +33,6 @@ 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.Arrays; import java.util.List; import java.util.Map; @@ -56,7 +55,7 @@ public ProteinWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", v int dataRelease, @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { super(apiVersion, species, uriInfo, hsr); if (assembly == null) { assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName(); diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/TranscriptWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/TranscriptWSServer.java index e0ec1e4e85..a4fc6365a3 100755 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/TranscriptWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/TranscriptWSServer.java @@ -23,7 +23,6 @@ import org.opencb.cellbase.core.api.GeneQuery; import org.opencb.cellbase.core.api.ProteinQuery; import org.opencb.cellbase.core.api.TranscriptQuery; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.core.utils.SpeciesUtils; @@ -38,7 +37,6 @@ 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.*; import static org.opencb.cellbase.core.ParamConstants.*; @@ -64,7 +62,7 @@ public TranscriptWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion" @QueryParam("dataRelease") int dataRelease, @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { super(apiVersion, species, uriInfo, hsr); if (assembly == null) { assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName(); diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/ChromosomeWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/ChromosomeWSServer.java index 9ed642a6ea..6620e272ed 100644 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/ChromosomeWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/ChromosomeWSServer.java @@ -21,7 +21,6 @@ import org.apache.commons.lang3.StringUtils; import org.opencb.biodata.models.core.Chromosome; import org.opencb.cellbase.core.api.GenomeQuery; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.core.utils.SpeciesUtils; @@ -34,7 +33,6 @@ 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.List; import static org.opencb.cellbase.core.ParamConstants.*; @@ -58,7 +56,7 @@ public ChromosomeWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion" @QueryParam("dataRelease") int dataRelease, @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { super(apiVersion, species, uriInfo, hsr); List assemblies = uriInfo.getQueryParameters().get("assembly"); if (CollectionUtils.isNotEmpty(assemblies)) { diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/RegionWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/RegionWSServer.java index 5d12fb65fc..5530a47618 100755 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/RegionWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/RegionWSServer.java @@ -22,7 +22,6 @@ import org.opencb.biodata.models.variant.Variant; import org.opencb.biodata.models.variant.avro.Repeat; import org.opencb.cellbase.core.api.*; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.core.utils.SpeciesUtils; @@ -35,7 +34,6 @@ 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.Collections; import java.util.List; @@ -65,7 +63,8 @@ public RegionWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", va int dataRelease, @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, @Context UriInfo uriInfo, - @Context HttpServletRequest hsr) throws QueryException, IOException, CellBaseException { + @Context HttpServletRequest hsr) + throws CellBaseException { super(apiVersion, species, uriInfo, hsr); if (assembly == null) { assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName(); diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/VariantWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/VariantWSServer.java index 6a8034298b..c2997a7486 100755 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/VariantWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/VariantWSServer.java @@ -21,7 +21,6 @@ import org.opencb.biodata.models.variant.Variant; import org.opencb.biodata.models.variant.avro.VariantAnnotation; import org.opencb.cellbase.core.api.VariantQuery; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.core.utils.SpeciesUtils; @@ -34,7 +33,6 @@ 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.Arrays; import java.util.List; import java.util.Map; @@ -57,7 +55,7 @@ public VariantWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", v int dataRelease, @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { super(apiVersion, species, uriInfo, hsr); if (assembly == null) { assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName(); diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/network/PathwayWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/network/PathwayWSServer.java index b9bc698acf..cb290b8724 100755 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/network/PathwayWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/network/PathwayWSServer.java @@ -16,7 +16,6 @@ package org.opencb.cellbase.server.rest.network; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.server.rest.GenericRestWSServer; @@ -28,14 +27,14 @@ import javax.ws.rs.core.Context; import javax.ws.rs.core.Response; import javax.ws.rs.core.UriInfo; -import java.io.IOException; @Path("/{version}/{species}/network/pathway") @Produces("text/plain") public class PathwayWSServer extends GenericRestWSServer { public PathwayWSServer(@PathParam("version") String version, @PathParam("species") String species, @Context UriInfo uriInfo, - @Context HttpServletRequest hsr) throws QueryException, IOException, CellBaseException { + @Context HttpServletRequest hsr) + throws CellBaseException { super(version, species, uriInfo, hsr); } diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/network/PathwayWSServerMongo.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/network/PathwayWSServerMongo.java index d5b68f6dea..89184997e0 100644 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/network/PathwayWSServerMongo.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/network/PathwayWSServerMongo.java @@ -16,7 +16,6 @@ package org.opencb.cellbase.server.rest.network; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.server.rest.GenericRestWSServer; @@ -28,14 +27,14 @@ import javax.ws.rs.core.Context; import javax.ws.rs.core.Response; import javax.ws.rs.core.UriInfo; -import java.io.IOException; @Path("/{version}/{species}/network/reactome-pathway") @Produces("text/plain") public class PathwayWSServerMongo extends GenericRestWSServer { public PathwayWSServerMongo(@PathParam("version") String version, @PathParam("species") String species, @Context UriInfo uriInfo, - @Context HttpServletRequest hsr) throws QueryException, IOException, CellBaseException { + @Context HttpServletRequest hsr) + throws CellBaseException { super(version, species, uriInfo, hsr); } diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/network/ProteinProteinInteractionWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/network/ProteinProteinInteractionWSServer.java index 167d4c16f6..f5e566a130 100644 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/network/ProteinProteinInteractionWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/network/ProteinProteinInteractionWSServer.java @@ -17,7 +17,6 @@ package org.opencb.cellbase.server.rest.network; import org.opencb.biodata.models.protein.Interaction; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.server.rest.GenericRestWSServer; @@ -30,7 +29,6 @@ import javax.ws.rs.core.MediaType; import javax.ws.rs.core.Response; import javax.ws.rs.core.UriInfo; -import java.io.IOException; /** * Created with IntelliJ IDEA. @@ -45,7 +43,7 @@ public class ProteinProteinInteractionWSServer extends GenericRestWSServer { public ProteinProteinInteractionWSServer(@PathParam("version") String version, @PathParam("species") String species, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { super(version, species, uriInfo, hsr); } diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/regulatory/RegulatoryWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/regulatory/RegulatoryWSServer.java index 41dbfdeb4f..f435c13ee2 100755 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/regulatory/RegulatoryWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/regulatory/RegulatoryWSServer.java @@ -19,7 +19,6 @@ import io.swagger.annotations.*; import org.opencb.biodata.models.core.RegulatoryFeature; import org.opencb.cellbase.core.api.RegulationQuery; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.core.utils.SpeciesUtils; @@ -31,7 +30,6 @@ import javax.ws.rs.core.Context; import javax.ws.rs.core.Response; import javax.ws.rs.core.UriInfo; -import java.io.IOException; import static org.opencb.cellbase.core.ParamConstants.*; @@ -51,7 +49,8 @@ public RegulatoryWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion" @QueryParam("dataRelease") int dataRelease, @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, @Context UriInfo uriInfo, - @Context HttpServletRequest hsr) throws QueryException, IOException, CellBaseException { + @Context HttpServletRequest hsr) + throws CellBaseException { super(apiVersion, species, uriInfo, hsr); if (assembly == null) { assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName(); diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/regulatory/TfWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/regulatory/TfWSServer.java index 46df7fc28b..4d802bec56 100755 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/regulatory/TfWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/regulatory/TfWSServer.java @@ -22,7 +22,6 @@ import org.opencb.cellbase.core.api.GeneQuery; import org.opencb.cellbase.core.api.RegulationQuery; import org.opencb.cellbase.core.api.query.LogicalList; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.cellbase.lib.managers.GeneManager; @@ -35,7 +34,6 @@ 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.Arrays; import java.util.List; @@ -60,7 +58,7 @@ public TfWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", value int dataRelease, @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey, @Context UriInfo uriInfo, @Context HttpServletRequest hsr) - throws QueryException, IOException, CellBaseException { + throws CellBaseException { super(apiVersion, species, assembly, dataRelease, apiKey, uriInfo, hsr); regulatoryManager = cellBaseManagerFactory.getRegulatoryManager(species, assembly); diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/utils/UtilsWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/utils/UtilsWSServer.java index 35e489fc0f..4706002082 100755 --- a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/utils/UtilsWSServer.java +++ b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/utils/UtilsWSServer.java @@ -16,7 +16,6 @@ package org.opencb.cellbase.server.rest.utils; -import org.opencb.cellbase.core.api.query.QueryException; import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.server.rest.GenericRestWSServer; @@ -26,14 +25,14 @@ import javax.ws.rs.Produces; import javax.ws.rs.core.Context; import javax.ws.rs.core.UriInfo; -import java.io.IOException; @Path("/{version}/utils") @Produces("text/plain") public class UtilsWSServer extends GenericRestWSServer { public UtilsWSServer(@PathParam("version") String version, @PathParam("species") String species, @Context UriInfo uriInfo, - @Context HttpServletRequest hsr) throws QueryException, IOException, CellBaseException { + @Context HttpServletRequest hsr) + throws CellBaseException { super(version, species, uriInfo, hsr); }