storage: Do not fail vairant-walker if no output is produced. #TASK-6722

opencb · Nov 27, 2024 · f87686e · f87686e
1 parent ccf7438
commit f87686e
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Showing 2 changed files with 26 additions and 6 deletions.
diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/VariantWalkerTool.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/VariantWalkerTool.java
@@ -87,11 +87,13 @@ protected void run() throws Exception {
         });
         step("move-files", () -> {
             // Move files to final directory
-            IOManager ioManager = catalogManager.getIoManagerFactory().get(uris.get(0));
-            for (URI uri : uris) {
-                String fileName = UriUtils.fileName(uri);
-                logger.info("Moving file -- " + fileName);
-                ioManager.move(uri, getOutDir().resolve(fileName).toUri());
+            if (!uris.isEmpty()) {
+                IOManager ioManager = catalogManager.getIoManagerFactory().get(uris.get(0));
+                for (URI uri : uris) {
+                    String fileName = UriUtils.fileName(uri);
+                    logger.info("Moving file -- " + fileName);
+                    ioManager.move(uri, getOutDir().resolve(fileName).toUri());
+                }
             }
         });
     }

diff --git a/...e/src/main/java/org/opencb/opencga/storage/hadoop/variant/HadoopVariantStorageEngine.java b/...e/src/main/java/org/opencb/opencga/storage/hadoop/variant/HadoopVariantStorageEngine.java
@@ -44,6 +44,7 @@
 import org.opencb.opencga.storage.core.exceptions.StorageEngineException;
 import org.opencb.opencga.storage.core.exceptions.StoragePipelineException;
 import org.opencb.opencga.storage.core.exceptions.VariantSearchException;
+import org.opencb.opencga.storage.core.io.managers.IOConnector;
 import org.opencb.opencga.storage.core.io.managers.IOConnectorProvider;
 import org.opencb.opencga.storage.core.metadata.VariantMetadataFactory;
 import org.opencb.opencga.storage.core.metadata.VariantStorageMetadataManager;
@@ -342,7 +343,24 @@ public List<URI> walkData(URI outputFile, VariantWriterFactory.VariantOutputForm
                         .append(StreamVariantDriver.INPUT_FORMAT_PARAM, format.toString())
                         .append(StreamVariantDriver.OUTPUT_PARAM, outputFile)
         ), "Walk data");
-        return Arrays.asList(outputFile, UriUtils.createUriSafe(outputFile.toString() + StreamVariantDriver.STDERR_TXT_GZ));
+        List<URI> uris = new ArrayList<>();
+        URI stderrFile = UriUtils.createUriSafe(outputFile.toString() + StreamVariantDriver.STDERR_TXT_GZ);
+        try {
+            IOConnector ioConnector = ioConnectorProvider.get(outputFile);
+            if (ioConnector.exists(outputFile)) {
+                uris.add(outputFile);
+            } else {
+                logger.warn("Output file not found: {}", outputFile);
+            }
+            if (ioConnector.exists(stderrFile)) {
+                uris.add(stderrFile);
+            } else {
+                logger.warn("Stderr file not found: {}", stderrFile);
+            }
+        } catch (IOException e) {
+            throw new StorageEngineException("Error checking output file", e);
+        }
+        return uris;
     }
 
     @Override