TASK-4913 - Unable to update cellbase-token

opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java

@@ -49,6 +49,7 @@
 import org.opencb.opencga.catalog.managers.StudyManager;
 import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.core.cellbase.CellBaseValidator;
+import org.opencb.opencga.core.common.ExceptionUtils;
 import org.opencb.opencga.core.common.UriUtils;
 import org.opencb.opencga.core.config.storage.CellBaseConfiguration;
 import org.opencb.opencga.core.config.storage.SampleIndexConfiguration;
@@ -564,7 +565,10 @@ public OpenCGAResult<Job> setCellbaseConfiguration(String project, CellBaseConfi
                                                        String annotationSaveId, String token)
             throws CatalogException, StorageEngineException {
         StopWatch stopwatch = StopWatch.createStarted();
-        return secureOperationByProject("configureCellbase", project, new ObjectMap(), token, engine -> {
+        return secureOperationByProject("configureCellbase", project, new ObjectMap()
+                .append("cellbaseConfiguration", cellbaseConfiguration)
+                .append("annotate", annotate)
+                .append("annotationSaveId", annotationSaveId), token, engine -> {
             OpenCGAResult<Job> result = new OpenCGAResult<>();
             result.setResultType(Job.class.getCanonicalName());
             result.setResults(new ArrayList<>());
@@ -1225,7 +1229,7 @@ private <R> R secureTool(String toolId, boolean isOperation, ObjectMap params, S
             throw e;
         } catch (Exception e) {
             exception = e;
-            throw new StorageEngineException("Error executing operation " + toolId, e);
+            throw new StorageEngineException("Error executing operation '" + toolId + "' : " + e.getMessage(), e);
         } finally {
             if (result instanceof DataResult) {
                 auditAttributes.append("dbTime", ((DataResult) result).getTime());
@@ -1237,6 +1241,8 @@ private <R> R secureTool(String toolId, boolean isOperation, ObjectMap params, S
             if (exception != null) {
                 auditAttributes.append("errorType", exception.getClass());
                 auditAttributes.append("errorMessage", exception.getMessage());
+                auditAttributes.append("errorMessageFull", ExceptionUtils.prettyExceptionMessage(exception, false, true));
+                auditAttributes.append("exceptionStackTrace", ExceptionUtils.prettyExceptionStackTrace(exception));
                 status = new AuditRecord.Status(AuditRecord.Status.Result.ERROR,
                         new Error(-1, exception.getClass().getName(), exception.getMessage()));
             } else {

opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java

@@ -1,20 +1,24 @@
 package org.opencb.opencga.core.cellbase;
 
+import io.jsonwebtoken.JwtException;
 import org.apache.commons.lang3.StringUtils;
+import org.opencb.biodata.models.variant.avro.VariantAnnotation;
 import org.opencb.cellbase.client.rest.CellBaseClient;
 import org.opencb.cellbase.core.config.SpeciesConfiguration;
 import org.opencb.cellbase.core.config.SpeciesProperties;
 import org.opencb.cellbase.core.models.DataRelease;
 import org.opencb.cellbase.core.result.CellBaseDataResponse;
 import org.opencb.cellbase.core.token.DataAccessTokenManager;
 import org.opencb.cellbase.core.token.DataAccessTokenSources;
+import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.opencga.core.common.VersionUtils;
 import org.opencb.opencga.core.config.storage.CellBaseConfiguration;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -46,6 +50,7 @@ private CellBaseClient newCellBaseClient(CellBaseConfiguration cellBaseConfigura
                 toCellBaseSpeciesName(species),
                 assembly,
                 cellBaseConfiguration.getDataRelease(),
+                cellBaseConfiguration.getToken(),
                 cellBaseConfiguration.toClientConfiguration());
     }
 
@@ -136,7 +141,7 @@ public void validate() throws IOException {
         validate(false);
     }
 
-    public CellBaseConfiguration validate(boolean autoComplete) throws IOException {
+    private CellBaseConfiguration validate(boolean autoComplete) throws IOException {
         CellBaseConfiguration cellBaseConfiguration = getCellBaseConfiguration();
         String inputVersion = getVersion();
         CellBaseDataResponse<SpeciesProperties> species;
@@ -189,6 +194,41 @@ public CellBaseConfiguration validate(boolean autoComplete) throws IOException {
                 }
             }
         }
+        String token = getToken();
+        if (StringUtils.isEmpty(token)) {
+            cellBaseConfiguration.setToken(null);
+        } else {
+            // Check it's supported
+            if (!supportsToken(serverVersion)) {
+                throw new IllegalArgumentException("Token not supported for cellbase "
+                        + "url: '" + getURL() + "'"
+                        + ", version: '" + inputVersion + "'");
+            }
+
+            // Check it's an actual token
+            DataAccessTokenManager tokenManager = new DataAccessTokenManager();
+            try {
+                tokenManager.decode(token);
+            } catch (JwtException e) {
+                throw new IllegalArgumentException("Malformed token for cellbase "
+                        + "url: '" + getURL() + "'"
+                        + ", version: '" + inputVersion
+                        + "', species: '" + getSpecies()
+                        + "', assembly: '" + getAssembly() + "'");
+            }
+
+            // Check it's a valid token
+            CellBaseDataResponse<VariantAnnotation> response = cellBaseClient.getVariantClient()
+                    .getAnnotationByVariantIds(Collections.singletonList("1:1:N:C"), new QueryOptions(), true);
+            if (response.firstResult() == null) {
+                throw new IllegalArgumentException("Invalid token for cellbase "
+                        + "url: '" + getURL() + "'"
+                        + ", version: '" + inputVersion
+                        + "', species: '" + getSpecies()
+                        + "', assembly: '" + getAssembly() + "'");
+            }
+        }
+
         return cellBaseConfiguration;
     }
 
@@ -231,6 +271,11 @@ public static boolean supportsDataReleaseActiveByDefaultIn(String serverVersion)
         return VersionUtils.isMinVersion("5.5.0", serverVersion, true);
     }
 
+    public static boolean supportsToken(String serverVersion) {
+        // Tokens support starts at version 5.4.0
+        return VersionUtils.isMinVersion("5.4.0", serverVersion);
+    }
+
     public String getVersionFromServerMajor() throws IOException {
         return major(getVersionFromServer());
     }

opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java

@@ -1,6 +1,8 @@
 package org.opencb.opencga.core.cellbase;
 
+import org.apache.commons.lang3.StringUtils;
 import org.junit.Assert;
+import org.junit.Assume;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
@@ -70,4 +72,45 @@ public void testNoActiveReleases() throws IOException {
         thrown.expectMessage("No active data releases found on cellbase");
         CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.1", null, null), "mmusculus", "GRCm38", true);
     }
+
+    @Test
+    public void testToken() throws IOException {
+        String token = System.getenv("CELLBASE_HGMD_TOKEN");
+        Assume.assumeTrue(StringUtils.isNotEmpty(token));
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.4", null, token), "hsapiens", "grch38", true);
+        Assert.assertNotNull(validated.getToken());
+    }
+
+    @Test
+    public void testTokenNotSupported() throws IOException {
+        String token = System.getenv("CELLBASE_HGMD_TOKEN");
+        Assume.assumeTrue(StringUtils.isNotEmpty(token));
+        thrown.expectMessage("Token not supported");
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.1", null, token), "hsapiens", "grch38", true);
+        Assert.assertNotNull(validated.getToken());
+    }
+
+    @Test
+    public void testTokenEmpty() throws IOException {
+        String token = "";
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.1", null, token), "hsapiens", "grch38", true);
+        Assert.assertNull(validated.getToken());
+    }
+
+    @Test
+    public void testMalformedToken() throws IOException {
+        thrown.expectMessage("Malformed token for cellbase");
+        String token = "MALFORMED_TOKEN";
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.4", null, token), "hsapiens", "grch38", true);
+        Assert.assertNotNull(validated.getToken());
+    }
+
+    @Test
+    public void testUnsignedToken() throws IOException {
+        thrown.expectMessage("Invalid token for cellbase");
+        String token = "eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImhnbWQiOjkyMjMzNzIwMzY4NTQ3NzU4MDd9LCJ2ZXJzaW9uIjoiMS4wIiwic3ViIjoiWkVUVEEiLCJpYXQiOjE2OTMyMTY5MDd9.invalidsignature";
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.4", null, token), "hsapiens", "grch38", true);
+        Assert.assertNotNull(validated.getToken());
+    }
+
 }