Merge branch 'develop' into TASK-4988

.github/workflows/test-analysis.yml

@@ -1,4 +1,5 @@
 name: Build and test the project
+
 on:
   workflow_call:
     secrets:

cellbase-app/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.7.0-SNAPSHOT</version>
+        <version>5.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

cellbase-client/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.7.0-SNAPSHOT</version>
+        <version>5.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

cellbase-core/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.7.0-SNAPSHOT</version>
+        <version>5.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

cellbase-lib/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.7.0-SNAPSHOT</version>
+        <version>5.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

cellbase-lib/src/main/java/org/opencb/cellbase/lib/managers/MetaManager.java

@@ -69,7 +69,8 @@ public void checkQuota(String apiKey, ApiKeyJwtPayload payload) throws CellBaseE
             numQueries = quotaResult.first().getNumQueries();
         }
         if (numQueries >= payload.getQuota().getMaxNumQueries()) {
-            throw new CellBaseException("Exceeded the maximum number of queries");
+            throw new CellBaseException("Maximum query limit reached: Your current API key has a quota of "
+                    + payload.getQuota().getMaxNumQueries() + " queries");
         }
     }
 

cellbase-server/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.7.0-SNAPSHOT</version>
+        <version>5.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

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

@@ -0,0 +1,25 @@
+/*
+ * 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;
+
+public class CellBaseServerException extends WebApplicationException {
+    public CellBaseServerException(String msg) {
+        super(msg);
+    }
+}

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 QueryException, IOException, 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

@@ -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;
@@ -40,6 +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;
@@ -60,7 +60,8 @@
 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 +102,25 @@ 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 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 QueryException, IOException, CellBaseException {
+            throws CellBaseServerException {
 
         this.version = version;
         this.uriInfo = uriInfo;
         this.httpServletRequest = hsr;
         this.species = species;
 
-        init();
-        initQuery();
+        try {
+            init();
+            initQuery();
+        } catch (Exception e) {
+            throw new CellBaseServerException(e.getMessage());
+        }
     }
 
     private void init() throws IOException, CellBaseException {

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

@@ -20,19 +20,19 @@
 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.api.key.ApiKeyJwtPayload;
+import org.opencb.cellbase.core.api.key.ApiKeyManager;
 import org.opencb.cellbase.core.common.GitRepositoryState;
 import org.opencb.cellbase.core.config.DownloadProperties;
 import org.opencb.cellbase.core.config.SpeciesConfiguration;
 import org.opencb.cellbase.core.config.SpeciesProperties;
 import org.opencb.cellbase.core.exception.CellBaseException;
 import org.opencb.cellbase.core.models.DataRelease;
 import org.opencb.cellbase.core.result.CellBaseDataResult;
-import org.opencb.cellbase.core.api.key.ApiKeyManager;
-import org.opencb.cellbase.core.api.key.ApiKeyJwtPayload;
 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;
@@ -50,7 +50,6 @@
 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;
@@ -73,9 +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 QueryException, IOException, 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

@@ -21,19 +21,17 @@
 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;
 import org.opencb.cellbase.lib.managers.OntologyManager;
+import org.opencb.cellbase.server.exception.CellBaseServerException;
 
 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.Arrays;
 import java.util.List;
 import java.util.Map;
@@ -55,17 +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 QueryException, IOException, 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

@@ -20,17 +20,15 @@
 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;
+import org.opencb.cellbase.server.exception.CellBaseServerException;
 
 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.Map;
 
 import static org.opencb.cellbase.core.ParamConstants.*;
@@ -55,9 +53,13 @@ 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 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

@@ -19,18 +19,16 @@
 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;
+import org.opencb.cellbase.server.exception.CellBaseServerException;
 
 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 static org.opencb.cellbase.core.ParamConstants.*;
 
@@ -53,10 +51,13 @@ 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 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

@@ -19,11 +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.api.query.QueryException;
-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;
@@ -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.*;
 
@@ -53,13 +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 QueryException, IOException, 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