server: the exception mapper handles the CellBaseException, #TASK-4976

opencb · Sep 12, 2023 · ad3ae74 · ad3ae74
1 parent 41d9e96
commit ad3ae74
Show file tree

Hide file tree

Showing 22 changed files with 48 additions and 68 deletions.
diff --git a/.../server/rest/CellBaseExceptionMapper.java → ...er/exception/CellBaseExceptionMapper.java b/.../server/rest/CellBaseExceptionMapper.java → ...er/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<Exception> {
+public class CellBaseExceptionMapper implements ExceptionMapper<CellBaseException> {
 
     @Context
     private UriInfo uriInfo;
@@ -64,7 +66,7 @@ public class CellBaseExceptionMapper implements ExceptionMapper<Exception> {
     }
 
     @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
@@ -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
@@ -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
@@ -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
@@ -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<String> 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
@@ -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
@@ -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
@@ -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/...rver/src/main/java/org/opencb/cellbase/server/rest/clinical/PharmacogenomicsWSServer.java b/...rver/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
@@ -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<String> 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
@@ -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
@@ -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/...base-server/src/main/java/org/opencb/cellbase/server/rest/feature/TranscriptWSServer.java b/...base-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/...base-server/src/main/java/org/opencb/cellbase/server/rest/genomic/ChromosomeWSServer.java b/...base-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<String> assemblies = uriInfo.getQueryParameters().get("assembly");
         if (CollectionUtils.isNotEmpty(assemblies)) {