Merge branch 'develop' into TASK-6445

opencb · Oct 22, 2024 · 0022507 · 0022507
2 parents 909426a + 3b58fb7
commit 0022507
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Showing 7 changed files with 34 additions and 69 deletions.
diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml
@@ -10,12 +10,7 @@ jobs:
   build:
     uses: ./.github/workflows/build-java-app-workflow.yml
 
-  test:
-    uses: ./.github/workflows/test-analysis.yml
-    needs: build
-    secrets: inherit
-
   deploy-maven:
     uses: ./.github/workflows/deploy-maven-repository-workflow.yml
-    needs: test
+    needs: build
     secrets: inherit
diff --git a/.github/workflows/release-github-workflow.yml b/.github/workflows/release-github-workflow.yml
@@ -20,7 +20,7 @@ jobs:
         with:
           name: ${{ inputs.artifact }}
       - name: GitHub Release
-        uses: softprops/action-gh-release@v1
+        uses: softprops/action-gh-release@v2
         if: startsWith(github.ref, 'refs/tags/')
         with:
           name: ${{ github.ref_name }}

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
@@ -51,13 +51,10 @@ jobs:
           path: opencga-enterprise
           fetch-depth: "10"
       - id: get_opencga_branch
-        name: Get OpenCGA branch from 'pom.xml' property
+        name: Get OpenCGA branch
         run: |
-          pwd
-          ls -lrtha
-          ls -lrtha ./opencga-enterprise
           chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh
-          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh)
+          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh "${{ inputs.task }}")
           echo "opencga_branch=${opencga_branch}"
           echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT
       - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}'

diff --git a/.github/workflows/tmp-test-xetabase-branch.yml b/.github/workflows/tmp-test-xetabase-branch.yml
diff --git a/...ore-mongodb/src/test/java/org/opencb/commons/datastore/mongodb/MongoDBCollectionTest.java b/...ore-mongodb/src/test/java/org/opencb/commons/datastore/mongodb/MongoDBCollectionTest.java
@@ -441,15 +441,13 @@ public void testAggregate() {
 
         queryResult = mongoDBCollection.aggregate(dbObjectList, new QueryOptions(QueryOptions.LIMIT, 1).append(QueryOptions.SKIP, 0));
         assertEquals("There must be 1 results", 1, queryResult.getResults().size());
-        assertTrue(queryResult.getResults().contains(result.get(0)));
+        // As the order of result list change between executions, we must ensure the assertTrue doesn't depend on the order
+        assertTrue(result.contains(queryResult.getResults().get(0)));
 
         queryResult = mongoDBCollection.aggregate(dbObjectList, new QueryOptions(QueryOptions.LIMIT, 1).append(QueryOptions.SKIP, 1));
         assertEquals("There must be 1 results", 1, queryResult.getResults().size());
-
-        System.out.println("result = " + result);
-        System.out.println("queryResult.getResults() = " + queryResult.getResults());
-
-        assertTrue(queryResult.getResults().contains(result.get(1)));
+        // As the order of result list change between executions, we must ensure the assertTrue doesn't depend on the order
+        assertTrue(result.contains(queryResult.getResults().get(0)));
     }
 
     @Test

diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml
@@ -31,7 +31,6 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
@@ -65,8 +64,10 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-databind</artifactId>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.8.0</version>
+            <scope>compile</scope>
         </dependency>
     </dependencies>
 </project>
diff --git a/commons-lib/src/main/java/org/opencb/commons/utils/FileUtils.java b/commons-lib/src/main/java/org/opencb/commons/utils/FileUtils.java
@@ -18,6 +18,7 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.opencb.commons.exec.Command;
+import org.slf4j.LoggerFactory;
 
 import java.io.*;
 import java.nio.charset.Charset;
@@ -188,6 +189,27 @@ public static String[] getUserAndGroup(Path path, boolean numericId) throws IOEx
         return new String[]{split[2], split[3]};
     }
 
+
+    public static void copyFile(File src, File dest) throws IOException {
+        try {
+            org.apache.commons.io.FileUtils.copyFile(src, dest);
+        } catch (IOException e) {
+            try {
+                if (src.length() == dest.length()) {
+                    LoggerFactory.getLogger(FileUtils.class).warn(e.getMessage());
+                    return;
+                }
+                throw e;
+            } catch (Exception e1) {
+                throw e;
+            }
+        }
+    }
+
+    //-------------------------------------------------------------------------
+    // P R I V A T E     M E T H O D S
+    //-------------------------------------------------------------------------
+
     private static String getLsOutput(Path path, boolean numericId) throws IOException {
         FileUtils.checkPath(path);