diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml
index 196fc122b..3029b0fdb 100644
--- 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/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh
index be89ffbf2..6e62a8ff6 100644
--- a/.github/workflows/scripts/get-xetabase-branch.sh
+++ b/.github/workflows/scripts/get-xetabase-branch.sh
@@ -22,6 +22,7 @@ get_xetabase_branch() {
# Check if the branch name starts with "release-" and follows the patterns "release-a.x.x" or "release-a.b.x"
if [[ "$input_branch" =~ ^release-([0-9]+)\.x\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]]; then
+
# Extract the MAJOR part of the branch name
MAJOR=${BASH_REMATCH[1]}
# Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR
diff --git a/.github/workflows/tmp-test-xetabase-branch.yml b/.github/workflows/tmp-test-xetabase-branch.yml
deleted file mode 100644
index c10d99ec5..000000000
--- a/.github/workflows/tmp-test-xetabase-branch.yml
+++ /dev/null
@@ -1,48 +0,0 @@
-name: TMP test-xetabase-branch
-run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}'
-
-on:
- push:
- branches:
- - TASK-*
-
-
-jobs:
- calculate-xetabase-branch:
- name: Calculate Xetabase branch
- runs-on: ubuntu-22.04
- outputs:
- xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }}
- steps:
- - name: Clone java-common-libs
- uses: actions/checkout@v4
- with:
- fetch-depth: '10'
- ## This is important to avoid the error in the next step: "fatal: repository 'https://github.com/zetta-genomics/opencga-enterprise.git/' not found"
- persist-credentials: false
- - id: get_xetabase_branch
- name: "Get current branch for Xetabase from target branch"
- run: |
- if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/opencb/opencga.git "TASK-6879" )" ] ; then
- echo "OPENCGA TASK-6879 branch";
- fi
-
- if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then
- echo "Here it is TASK-6807 branch";
- fi
- chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh
- echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" | tee -a ${GITHUB_STEP_SUMMARY}
- xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6879" )
- echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY}
- echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT
- env:
- ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
-
- test:
- name: "Run all tests before merging"
- needs: calculate-xetabase-branch
- uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop
- with:
- branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }}
- task: TASK-6879
- secrets: inherit
\ No newline at end of file
diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml
index 9147f9b33..84a6c880b 100644
--- a/commons-lib/pom.xml
+++ b/commons-lib/pom.xml
@@ -67,6 +67,13 @@
com.fasterxml.jackson.core
jackson-databind
+ test
+
+
+ commons-io
+ commons-io
+ 2.8.0
+ compile
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
index 93fba0f0d..1ae5ba87d 100644
--- 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);