Merge branch 'release-3.2.x' into TASK-5964

.github/workflows/pull-request-approved.yml

@@ -1,19 +1,35 @@
 name: Pull request approve workflow
+run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}'
 
 on:
   pull_request_review:
-    types: [submitted]
+    types: [ submitted ]
 
 jobs:
-  build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
-    with:
-      maven_opts: -Phdp3.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip
+  calculate-xetabase-branch:
+    name: Calculate Xetabase branch
+    runs-on: ubuntu-22.04
+    outputs:
+      xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }}
+    steps:
+      - name: Clone project
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: '10'
+      - id: get_xetabase_branch
+        name: "Get current branch for Xetabase from target branch"
+        run: |
+          chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh
+          xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.base.ref }})
+          echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY}
+          echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT
 
   test:
-    name: "Run all tests before merging, ie. short, medium and long tests."
-    uses: ./.github/workflows/test-analysis.yml
-    needs: build
+    name: "Run all tests before merging"
+    needs: calculate-xetabase-branch
+    uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399
     with:
-      test_profile: runShortTests,runMediumTests,runLongTests
+      branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }}
+      task: ${{ github.event.pull_request.head.ref }}
     secrets: inherit
+

.github/workflows/scripts/get-xetabase-branch.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+
+# Function to calculate the corresponding branch of Xetabase project
+get_xetabase_branch() {
+  # Input parameter (branch name)
+  input_branch="$1"
+
+  # If the branch begins with 'TASK' and exists in the opencga-enterprise repository, I return it
+  if [[ $input_branch == TASK* ]]; then
+    if [ "$(git ls-remote https://github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then
+      echo "$GIT_BRANCH";
+      exit 0;
+    fi
+  fi
+
+  # Check if the branch name is "develop" in that case return the same branch name
+  if [[ "$input_branch" == "develop" ]]; then
+    echo "develop"
+    return 0
+  fi
+
+  # Check if the branch name starts with "release-" and follows the patterns "release-a.b.x" or "release-a.b.c.x"
+  if [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.([0-9]+)\.x$ ]]; then
+    # Extract the MAJOR part of the branch name
+    MAJOR=${BASH_REMATCH[1]}
+    # Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR
+    XETABASE_MAJOR=$((MAJOR - 1))
+    # Check if the XETABASE_MAJOR is negative
+    if (( XETABASE_MAJOR < 0 )); then
+      echo "Error: 'MAJOR' digit after subtraction results in a negative number."
+      return 1
+    fi
+    # Construct and echo the new branch name
+    echo "release-$XETABASE_MAJOR.${input_branch#release-$MAJOR.}"
+    return 0
+  fi
+
+  # If the branch name does not match any of the expected patterns
+  echo "Error: The branch name is not correct."
+  return 1
+}
+
+# Check if the script receives exactly one argument
+if [ "$#" -ne 1 ]; then
+  echo "Usage: $0 <branch-name>"
+  exit 1
+fi
+
+# Call the function with the input branch name
+get_xetabase_branch "$1"

opencga-app/app/misc/clients/javascript_client_generator.py

@@ -116,7 +116,7 @@ def get_method_definition(self, category, endpoint):
             f'"{self.get_endpoint_subcategory()}"' if self.subcategory else "null",
             self.get_endpoint_id2() if self.get_endpoint_id2() else "null",
             f'"{self.get_endpoint_action()}"' if self.get_endpoint_action() else "null",
-            "data" if self.has_body() else False,
+            "data" if self.has_body() else ("null" if self.get_endpoint_method(endpoint).lower() == "post" else False),
             query_string_params
         ] if s)
         return (f' {self.get_method_doc(endpoint)}'

opencga-client/src/main/javascript/ClinicalAnalysis.js

@@ -840,7 +840,7 @@ export default class ClinicalAnalysis extends OpenCGAParentClass {
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     clearInterpretation(clinicalAnalysis, interpretations, params) {
-        return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretations, "clear", params);
+        return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretations, "clear", null, params);
     }
 
     /** Delete interpretation
@@ -865,7 +865,7 @@ export default class ClinicalAnalysis extends OpenCGAParentClass {
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     revertInterpretation(clinicalAnalysis, interpretation, version, params) {
-        return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "revert", {version, ...params});
+        return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "revert", null, {version, ...params});
     }
 
     /** Update interpretation fields

opencga-client/src/main/javascript/File.js

@@ -266,7 +266,7 @@ export default class File extends OpenCGAParentClass {
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     upload(params) {
-        return this._post("files", null, null, null, "upload", params);
+        return this._post("files", null, null, null, "upload", null, params);
     }
 
     /** Return the acl defined for the file or folder. If member is provided, it will only return the acl for the member.

opencga-client/src/main/javascript/GA4GH.js

@@ -39,7 +39,7 @@ export default class GA4GH extends OpenCGAParentClass {
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     searchReads() {
-        return this._post("ga4gh", null, "reads", null, "search");
+        return this._post("ga4gh", null, "reads", null, "search", null);
     }
 
     /** Fetch alignment files using HTSget protocol
@@ -78,7 +78,7 @@ export default class GA4GH extends OpenCGAParentClass {
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     searchVariants() {
-        return this._post("ga4gh", null, "variants", null, "search");
+        return this._post("ga4gh", null, "variants", null, "search", null);
     }
 
 }

opencga-client/src/main/javascript/Job.js

@@ -213,7 +213,7 @@ export default class Job extends OpenCGAParentClass {
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     kill(job, params) {
-        return this._post("jobs", job, null, null, "kill", params);
+        return this._post("jobs", job, null, null, "kill", null, params);
     }
 
     /** Show the first lines of a log file (up to a limit)

opencga-client/src/main/javascript/Project.js

@@ -85,7 +85,7 @@ export default class Project extends OpenCGAParentClass {
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     incRelease(project) {
-        return this._post("projects", project, null, null, "incRelease");
+        return this._post("projects", project, null, null, "incRelease", null);
     }
 
     /** Fetch all the studies contained in the project

opencga-client/src/main/javascript/Study.js

@@ -281,7 +281,7 @@ export default class Study extends OpenCGAParentClass {
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     uploadTemplates(study, params) {
-        return this._post("studies", study, "templates", null, "upload", params);
+        return this._post("studies", study, "templates", null, "upload", null, params);
     }
 
     /** Delete template

opencga-client/src/main/javascript/User.js

@@ -39,7 +39,7 @@ export default class User extends OpenCGAParentClass {
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     anonymous(organization) {
-        return this._post("users", null, null, null, "anonymous", organization);
+        return this._post("users", null, null, null, "anonymous", null, organization);
     }
 
     /** Create a new user