core: Fix validation test #TASK-4913

opencb · Aug 31, 2023 · 483d556 · 483d556
1 parent 8abd155
commit 483d556
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Showing 3 changed files with 18 additions and 3 deletions.
diff --git a/...ysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java b/...ysis/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<>());
@@ -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 {

diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java
@@ -174,7 +174,8 @@ private CellBaseConfiguration validate(boolean autoComplete) throws IOException
                 }
             }
         }
-        if (StringUtils.isEmpty(getToken())) {
+        String token = getToken();
+        if (StringUtils.isEmpty(token)) {
             cellBaseConfiguration.setToken(null);
         } else {
             // Check it's supported
@@ -187,7 +188,7 @@ private CellBaseConfiguration validate(boolean autoComplete) throws IOException
             // Check it's an actual token
             DataAccessTokenManager tokenManager = new DataAccessTokenManager();
             try {
-                tokenManager.decode(getToken());
+                tokenManager.decode(token);
             } catch (JwtException e) {
                 throw new IllegalArgumentException("Malformed token for cellbase "
                         + "url: '" + getURL() + "'"

diff --git a/opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java b/opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java
@@ -85,10 +85,18 @@ public void testToken() throws IOException {
     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");