server: add CellBaseServerException to the endpoints, #TASK-4976

cellbase-core/src/main/java/org/opencb/cellbase/core/exception/CellBaseException.java

@@ -16,13 +16,10 @@
 
 package org.opencb.cellbase.core.exception;
 
-import javax.ws.rs.WebApplicationException;
-
-public class CellBaseException extends WebApplicationException {
+public class CellBaseException extends Exception {
 
     public CellBaseException(String msg) {
         super(msg);
     }
 
 }
-

cellbase-server/src/main/java/org/opencb/cellbase/server/exception/CellBaseServerException.java

@@ -0,0 +1,28 @@
+/*
+ * 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.exception;
+
+import javax.ws.rs.WebApplicationException;
+
+@SuppressWarnings("serial")
+public class CellBaseServerException extends WebApplicationException {
+
+    public CellBaseServerException(String msg) {
+        super(msg);
+    }
+
+}

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/AdminRestWebService.java

@@ -19,14 +19,12 @@
 import org.opencb.cellbase.core.result.CellBaseDataResponse;
 import org.opencb.cellbase.server.RestServer;
 
-
 import javax.servlet.ServletContext;
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.*;
 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.ArrayList;
 import java.util.List;
 
@@ -43,8 +41,7 @@ public class AdminRestWebService {
     private static RestServer server;
 
     public AdminRestWebService(@PathParam("apiVersion") String version, @Context UriInfo uriInfo,
-                               @Context HttpServletRequest httpServletRequest, @Context ServletContext context)
-        throws IOException {
+                               @Context HttpServletRequest httpServletRequest, @Context ServletContext context) {
 //        super(version, uriInfo, httpServletRequest, context);
         System.out.println("Build AdminWSServer");
     }

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/FileWSServer.java

@@ -23,9 +23,9 @@
 import org.opencb.cellbase.core.ParamConstants;
 import org.opencb.cellbase.core.api.FileQuery;
 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.FileManager;
+import org.opencb.cellbase.server.exception.CellBaseServerException;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.GET;
@@ -48,9 +48,13 @@ public FileWSServer(@PathParam("apiVersion")
                         @ApiParam(name = "apiVersion", value = ParamConstants.VERSION_DESCRIPTION,
                                 defaultValue = ParamConstants.DEFAULT_VERSION) String apiVersion,
                         @Context UriInfo uriInfo, @Context HttpServletRequest hsr)
-            throws CellBaseException {
+            throws CellBaseServerException {
         super(apiVersion, uriInfo, hsr);
-        fileManager = cellBaseManagerFactory.getFileManager();
+        try {
+            fileManager = cellBaseManagerFactory.getFileManager();
+        } catch (Exception e) {
+            throw new CellBaseServerException(e.getMessage());
+        }
     }
 
     @GET

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java

@@ -39,6 +39,7 @@
 import org.opencb.cellbase.lib.managers.DataReleaseManager;
 import org.opencb.cellbase.lib.managers.MetaManager;
 import org.opencb.cellbase.lib.monitor.Monitor;
+import org.opencb.cellbase.server.exception.CellBaseServerException;
 import org.opencb.commons.datastore.core.Event;
 import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.datastore.core.Query;
@@ -101,13 +102,13 @@ public class GenericRestWSServer implements IWSServer {
     protected static ApiKeyManager apiKeyManager;
 
     public GenericRestWSServer(@PathParam("version") String version, @Context UriInfo uriInfo, @Context HttpServletRequest hsr)
-            throws CellBaseException {
+            throws CellBaseServerException {
         this(version, DONT_CHECK_SPECIES, uriInfo, hsr);
     }
 
     public GenericRestWSServer(@PathParam("version") String version, @PathParam("species") String species, @Context UriInfo uriInfo,
                                @Context HttpServletRequest hsr)
-            throws CellBaseException {
+            throws CellBaseServerException {
 
         this.version = version;
         this.uriInfo = uriInfo;
@@ -117,8 +118,8 @@ public GenericRestWSServer(@PathParam("version") String version, @PathParam("spe
         try {
             init();
             initQuery();
-        } catch (IOException e) {
-            throw new CellBaseException(e.getMessage());
+        } catch (Exception e) {
+            throw new CellBaseServerException(e.getMessage());
         }
     }
 
@@ -183,16 +184,15 @@ private void initQuery() throws CellBaseException {
 
         // Set default API key, if necessary
         String apiKey = uriParams.getOrDefault(API_KEY_PARAM, null);
-        logger.info("Before checking, API key {}", apiKey);
         if (StringUtils.isEmpty(apiKey)) {
             apiKey = defaultApiKey;
             uriParams.put(API_KEY_PARAM, apiKey);
         }
-        logger.info("After checking, API key {}", uriParams.get(API_KEY_PARAM));
 
+        // Check limit
         checkLimit();
 
-        // check version. species is validated later
+        // Check version (species is validated later)
         checkVersion();
 
         // Set default data release if necessary

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/MetaWSServer.java

@@ -32,6 +32,7 @@
 import org.opencb.cellbase.core.utils.SpeciesUtils;
 import org.opencb.cellbase.lib.managers.DataReleaseManager;
 import org.opencb.cellbase.lib.managers.MetaManager;
+import org.opencb.cellbase.server.exception.CellBaseServerException;
 import org.opencb.cellbase.server.rest.clinical.ClinicalWSServer;
 import org.opencb.cellbase.server.rest.feature.GeneWSServer;
 import org.opencb.cellbase.server.rest.feature.IdWSServer;
@@ -71,9 +72,13 @@ public MetaWSServer(@PathParam("apiVersion")
                         @ApiParam(name = "apiVersion", value = ParamConstants.VERSION_DESCRIPTION,
                                 defaultValue = ParamConstants.DEFAULT_VERSION) String apiVersion,
                         @Context UriInfo uriInfo, @Context HttpServletRequest hsr)
-            throws CellBaseException {
+            throws CellBaseServerException {
         super(apiVersion, uriInfo, hsr);
-        metaManager = cellBaseManagerFactory.getMetaManager();
+        try {
+            metaManager = cellBaseManagerFactory.getMetaManager();
+        } catch (Exception e) {
+            throw new CellBaseServerException(e.getMessage());
+        }
     }
 
     @GET

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/OntologyWSServer.java

@@ -21,10 +21,10 @@
 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.exception.CellBaseException;
 import org.opencb.cellbase.core.result.CellBaseDataResult;
 import org.opencb.cellbase.core.utils.SpeciesUtils;
 import org.opencb.cellbase.lib.managers.OntologyManager;
+import org.opencb.cellbase.server.exception.CellBaseServerException;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.*;
@@ -53,17 +53,21 @@ 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 CellBaseException {
+            throws CellBaseServerException {
         super(apiVersion, species, uriInfo, hsr);
-        List<String> assemblies = uriInfo.getQueryParameters().get("assembly");
-        if (CollectionUtils.isNotEmpty(assemblies)) {
-            assembly = assemblies.get(0);
-        }
-        if (StringUtils.isEmpty(assembly)) {
-            assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName();
-        }
+        try {
+            List<String> assemblies = uriInfo.getQueryParameters().get("assembly");
+            if (CollectionUtils.isNotEmpty(assemblies)) {
+                assembly = assemblies.get(0);
+            }
+            if (StringUtils.isEmpty(assembly)) {
+                assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName();
+            }
 
-        ontologyManager = cellBaseManagerFactory.getOntologyManager(species, assembly);
+            ontologyManager = cellBaseManagerFactory.getOntologyManager(species, assembly);
+        } catch (Exception e) {
+            throw new CellBaseServerException(e.getMessage());
+        }
     }
 
     @GET

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/PublicationWSServer.java

@@ -20,9 +20,9 @@
 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.exception.CellBaseException;
 import org.opencb.cellbase.core.result.CellBaseDataResult;
 import org.opencb.cellbase.lib.managers.PublicationManager;
+import org.opencb.cellbase.server.exception.CellBaseServerException;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.*;
@@ -46,16 +46,20 @@ public class PublicationWSServer extends GenericRestWSServer {
     private static final String PONG = "pong";
 
     public PublicationWSServer(@PathParam("apiVersion")
-                        @ApiParam(name = "apiVersion", value = ParamConstants.VERSION_DESCRIPTION,
-                                defaultValue = ParamConstants.DEFAULT_VERSION) String apiVersion,
+                               @ApiParam(name = "apiVersion", value = ParamConstants.VERSION_DESCRIPTION,
+                                       defaultValue = ParamConstants.DEFAULT_VERSION) String apiVersion,
                                @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 CellBaseException {
+            throws CellBaseServerException {
         super(apiVersion, uriInfo, hsr);
-        publicationManager = cellBaseManagerFactory.getPublicationManager();
+        try {
+            publicationManager = cellBaseManagerFactory.getPublicationManager();
+        } catch (Exception e) {
+            throw new CellBaseServerException(e.getMessage());
+        }
     }
 
     @GET

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/SpeciesWSServer.java

@@ -19,9 +19,9 @@
 import io.swagger.annotations.*;
 import org.opencb.biodata.models.core.Chromosome;
 import org.opencb.cellbase.core.api.GenomeQuery;
-import org.opencb.cellbase.core.exception.CellBaseException;
 import org.opencb.cellbase.core.result.CellBaseDataResult;
 import org.opencb.cellbase.lib.managers.GenomeManager;
+import org.opencb.cellbase.server.exception.CellBaseServerException;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.*;
@@ -52,10 +52,13 @@ public SpeciesWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", v
                            @ApiParam(name = "apiKey", value = API_KEY_DESCRIPTION) @DefaultValue("") @QueryParam("apiKey") String apiKey,
                            @Context UriInfo uriInfo,
                            @Context HttpServletRequest hsr)
-            throws CellBaseException {
+            throws CellBaseServerException {
         super(apiVersion, species, uriInfo, hsr);
-
-        genomeManager = cellBaseManagerFactory.getGenomeManager(species, assembly);
+        try {
+            genomeManager = cellBaseManagerFactory.getGenomeManager(species, assembly);
+        } catch (Exception e) {
+            throw new CellBaseServerException(e.getMessage());
+        }
     }
 
     @GET

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/ClinicalWSServer.java

@@ -19,10 +19,10 @@
 import io.swagger.annotations.*;
 import org.opencb.biodata.models.variant.Variant;
 import org.opencb.cellbase.core.api.ClinicalVariantQuery;
-import org.opencb.cellbase.core.exception.CellBaseException;
 import org.opencb.cellbase.core.result.CellBaseDataResult;
 import org.opencb.cellbase.core.utils.SpeciesUtils;
 import org.opencb.cellbase.lib.managers.ClinicalManager;
+import org.opencb.cellbase.server.exception.CellBaseServerException;
 import org.opencb.cellbase.server.rest.GenericRestWSServer;
 
 import javax.servlet.http.HttpServletRequest;
@@ -51,13 +51,17 @@ 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 CellBaseException {
+            throws CellBaseServerException {
         super(apiVersion, species, uriInfo, hsr);
-        if (assembly == null) {
-            assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName();
-        }
+        try {
+            if (assembly == null) {
+                assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName();
+            }
 
-        clinicalManager = cellBaseManagerFactory.getClinicalManager(species, assembly);
+            clinicalManager = cellBaseManagerFactory.getClinicalManager(species, assembly);
+        } catch (Exception e) {
+            throw new CellBaseServerException(e.getMessage());
+        }
     }
 
     @GET

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/clinical/PharmacogenomicsWSServer.java

@@ -19,11 +19,11 @@
 import io.swagger.annotations.*;
 import org.opencb.biodata.models.pharma.PharmaChemical;
 import org.opencb.cellbase.core.api.PharmaChemicalQuery;
-import org.opencb.cellbase.core.exception.CellBaseException;
 import org.opencb.cellbase.core.result.CellBaseDataResult;
 import org.opencb.cellbase.core.utils.SpeciesUtils;
 import org.opencb.cellbase.lib.managers.ClinicalManager;
 import org.opencb.cellbase.lib.managers.PharmacogenomicsManager;
+import org.opencb.cellbase.server.exception.CellBaseServerException;
 import org.opencb.cellbase.server.rest.GenericRestWSServer;
 
 import javax.servlet.http.HttpServletRequest;
@@ -56,14 +56,18 @@ 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 CellBaseException {
+            throws CellBaseServerException {
         super(apiVersion, species, uriInfo, hsr);
-        if (assembly == null) {
-            assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName();
-        }
+        try {
+            if (assembly == null) {
+                assembly = SpeciesUtils.getDefaultAssembly(cellBaseConfiguration, species).getName();
+            }
 
-        clinicalManager = cellBaseManagerFactory.getClinicalManager(species, assembly);
-        pharmacogenomicsManager = cellBaseManagerFactory.getPharmacogenomicsManager(species, assembly);
+            clinicalManager = cellBaseManagerFactory.getClinicalManager(species, assembly);
+            pharmacogenomicsManager = cellBaseManagerFactory.getPharmacogenomicsManager(species, assembly);
+        } catch (Exception e) {
+            throw new CellBaseServerException(e.getMessage());
+        }
     }
 
     @GET