Merge pull request #668 from opencb/TASK-4976-5.4.x

TASK-4976 Fix error handling when an exception raises in the CellBase Rest server constructors
opencb · Oct 2, 2023 · 8902508 · 8902508
2 parents 7965af5 + 6a578ea
commit 8902508
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Showing 22 changed files with 218 additions and 167 deletions.
diff --git a/...se-server/src/main/java/org/opencb/cellbase/server/exception/CellBaseServerException.java b/...se-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);
+    }
+}
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
@@ -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

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
@@ -28,7 +28,6 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.StopWatch;
 import org.opencb.cellbase.core.ParamConstants;
-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.models.DataRelease;
@@ -38,6 +37,7 @@
 import org.opencb.cellbase.lib.managers.CellBaseManagerFactory;
 import org.opencb.cellbase.lib.managers.DataReleaseManager;
 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;
@@ -96,21 +96,25 @@ public class GenericRestWSServer implements IWSServer {
     private static final String DONT_CHECK_SPECIES = "do not validate species";
 
     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 {

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
@@ -19,19 +19,19 @@
 import io.swagger.annotations.*;
 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;
 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.token.DataAccessTokenManager;
 import org.opencb.cellbase.core.token.DataAccessTokenSources;
 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.core.token.DataAccessTokenManager;
+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;
@@ -49,7 +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;
@@ -72,9 +71,13 @@ 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

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
@@ -21,19 +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;
@@ -56,17 +54,21 @@ public OntologyWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion",
                             @ApiParam(name = "token", value = DATA_ACCESS_TOKEN_DESCRIPTION) @DefaultValue("") @QueryParam("token")
                                     String token,
                             @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

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
@@ -20,17 +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 = "token", value = DATA_ACCESS_TOKEN_DESCRIPTION) @DefaultValue("") @QueryParam("token")
                                        String token,
                                @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

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
@@ -19,18 +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.*;
 
@@ -54,10 +52,13 @@ public SpeciesWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", v
                            @ApiParam(name = "token", value = DATA_ACCESS_TOKEN_DESCRIPTION) @DefaultValue("") @QueryParam("token")
                                    String token,
                            @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

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
@@ -19,11 +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.*;
 
@@ -56,13 +54,17 @@ public ClinicalWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion",
                             @ApiParam(name = "token", value = DATA_ACCESS_TOKEN_DESCRIPTION) @DefaultValue("") @QueryParam("token")
                                     String token,
                             @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

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
@@ -30,11 +30,13 @@
 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;
-import org.opencb.cellbase.lib.managers.*;
+import org.opencb.cellbase.lib.managers.GeneManager;
+import org.opencb.cellbase.lib.managers.ProteinManager;
+import org.opencb.cellbase.lib.managers.TranscriptManager;
+import org.opencb.cellbase.lib.managers.VariantManager;
+import org.opencb.cellbase.server.exception.CellBaseServerException;
 import org.opencb.cellbase.server.rest.GenericRestWSServer;
 
 import javax.servlet.http.HttpServletRequest;
@@ -43,7 +45,6 @@
 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.*;
 
@@ -71,21 +72,24 @@ public GeneWSServer(@PathParam("apiVersion") @ApiParam(name = "apiVersion", valu
                                 int dataRelease,
                         @ApiParam(name = "token", value = DATA_ACCESS_TOKEN_DESCRIPTION) @DefaultValue("") @QueryParam("token")
                                 String token,
-                        @Context UriInfo uriInfo, @Context HttpServletRequest hsr) throws QueryException, IOException,
-            CellBaseException {
+                        @Context UriInfo uriInfo, @Context HttpServletRequest hsr) 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();
+            }
 
-        geneManager = cellBaseManagerFactory.getGeneManager(species, assembly);
-        transcriptManager = cellBaseManagerFactory.getTranscriptManager(species, assembly);
-        variantManager = cellBaseManagerFactory.getVariantManager(species, assembly);
-        proteinManager = cellBaseManagerFactory.getProteinManager(species, assembly);
+            geneManager = cellBaseManagerFactory.getGeneManager(species, assembly);
+            transcriptManager = cellBaseManagerFactory.getTranscriptManager(species, assembly);
+            variantManager = cellBaseManagerFactory.getVariantManager(species, assembly);
+            proteinManager = cellBaseManagerFactory.getProteinManager(species, assembly);
+        } catch (Exception e) {
+            throw new CellBaseServerException(e.getMessage());
+        }
     }
 
     @GET