fix: import profile task keeps running on failure (#4578)

fix: import profile task keeps running on failure improve logging output
molgenis · Dec 20, 2024 · eabb6e1 · eabb6e1
1 parent e68dcb8
commit eabb6e1
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Showing 4 changed files with 47 additions and 10 deletions.
diff --git a/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/io/ImportProfileTask.java b/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/io/ImportProfileTask.java
@@ -42,9 +42,15 @@ public void run() {
             commitTask.setDescription("Committing");
           });
     } catch (Exception e) {
-      commitTask.completeWithError("Commit failed: " + e.getMessage());
-      this.completeWithError(e.getMessage());
-      throw (e);
+      try {
+        commitTask.completeWithError("CommitTask failed: " + e.getMessage());
+      } catch (MolgenisException e2) {
+        try {
+          this.completeWithError("ImportProfileTask  failed: " + e2.getMessage());
+        } catch (Exception e3) {
+          throw (e3);
+        }
+      }
     }
     commitTask.complete();
     this.complete();
@@ -56,7 +62,12 @@ void load(Schema schema) {
     Profiles profiles = getProfiles(schema, schemaFromProfile);
 
     // create the schema using the selected profile tags within the big model
-    SchemaMetadata schemaMetadata = schemaFromProfile.create();
+    SchemaMetadata schemaMetadata = null;
+    try {
+      schemaMetadata = schemaFromProfile.create();
+    } catch (Exception e) {
+      throw new MolgenisException("Failed to create schema from profile: " + e.getMessage(), e);
+    }
 
     // special option: fixed schema import location for ontologies (not schema or data)
     Schema ontologySchema;

diff --git a/...olgenis-emx2-datamodels/src/test/java/org/molgenis/emx2/datamodels/TestProfileLoader.java b/...olgenis-emx2-datamodels/src/test/java/org/molgenis/emx2/datamodels/TestProfileLoader.java
@@ -4,11 +4,13 @@
 
 import org.junit.jupiter.api.*;
 import org.molgenis.emx2.Database;
+import org.molgenis.emx2.MolgenisException;
 import org.molgenis.emx2.Schema;
 import org.molgenis.emx2.datamodels.profiles.Profiles;
 import org.molgenis.emx2.datamodels.profiles.SchemaFromProfile;
 import org.molgenis.emx2.io.ImportProfileTask;
 import org.molgenis.emx2.sql.TestDatabaseFactory;
+import org.molgenis.emx2.tasks.TaskStatus;
 
 @TestMethodOrder(MethodOrderer.MethodName.class)
 @Tag("slow")
@@ -54,4 +56,13 @@ void testProfileLoader() {
     assertFalse(testIncludeProfileSchema.getTableNames().contains("Individuals"));
     assertTrue(testIncludeProfileSchema.getTableNames().contains("Distribution"));
   }
+
+  @Test
+  void testProfileLoaderWithError() {
+    database.dropSchemaIfExists(TEST_PROFILE);
+    Schema testProfileSchema = database.createSchema(TEST_PROFILE);
+    var task = new ImportProfileTask(testProfileSchema, "TestProfileWithError.yaml", true);
+    assertThrows(MolgenisException.class, task::run);
+    assertEquals(TaskStatus.ERROR, task.getStatus());
+  }
 }
diff --git a/backend/molgenis-emx2-datamodels/src/test/resources/TestProfileWithError.yaml b/backend/molgenis-emx2-datamodels/src/test/resources/TestProfileWithError.yaml
@@ -0,0 +1,8 @@
+---
+name: TestProfileError
+description: "Test profile with error"
+
+profileTags: DataCatalogue
+
+demoData: _demodata/application/imagetest
+
diff --git a/backend/molgenis-emx2-io/src/main/java/org/molgenis/emx2/io/ImportTableTask.java b/backend/molgenis-emx2-io/src/main/java/org/molgenis/emx2/io/ImportTableTask.java
@@ -38,7 +38,7 @@ public void run() {
     try {
       source.processTable(table.getName(), new ImportRowProcesssor(table, this));
     } catch (Exception e) {
-      this.setError("Import failed: " + e.getMessage());
+      this.setError("Import table (%s) failed: %s".formatted(table.getName(), e.getMessage()));
       throw e;
     }
 
@@ -176,12 +176,19 @@ public void process(Iterator<Row> iterator, TableStore source) {
           if (c.isFile()
               && source instanceof TableAndFileStore
               && row.getValueMap().get(c.getName()) != null) {
-            BinaryFileWrapper wrapper =
-                ((TableAndFileStore) source).getBinaryFileWrapper(row.getString(c.getName()));
-            if (row.containsName(c.getName() + "_filename")) {
-              wrapper.setFileName(row.getString(c.getName() + "_filename"));
+            try {
+              BinaryFileWrapper wrapper =
+                  ((TableAndFileStore) source).getBinaryFileWrapper(row.getString(c.getName()));
+              if (row.containsName(c.getName() + "_filename")) {
+                wrapper.setFileName(row.getString(c.getName() + "_filename"));
+              }
+              row.setBinary(c.getName(), wrapper);
+            } catch (Exception e) {
+              throw new MolgenisException(
+                  "Failed to read file attachment for column %s row %d"
+                      .formatted(c.getName(), index),
+                  e);
             }
-            row.setBinary(c.getName(), wrapper);
           }
         }
         batch.add(row);