Merge branch 'release_21.09' into dev

.github/workflows/build_container_image.yaml

@@ -21,8 +21,10 @@ jobs:
       - name: Set branch name
         id: branch
         run: echo "::set-output name=name::$(BRANCH_NAME=${GITHUB_REF##*/}; echo ${BRANCH_NAME/release_/})"
-      - run: docker build . --build-arg GIT_COMMIT=$(git rev-parse HEAD) --build-arg BUILD_DATE=$(date -u +'%Y-%m-%dT%H:%M:%SZ') --build-arg IMAGE_TAG=${{ steps.branch.outputs.name }} --build-arg IMAGE_TAG=${{ steps.branch.outputs.name }} -t galaxy/galaxy-min:${{ steps.branch.outputs.name }} -f .k8s_ci.Dockerfile
-      - run: docker tag galaxy/galaxy-min:${{ steps.branch.outputs.name }} quay.io/galaxy-min/galaxy:${{ steps.branch.outputs.name }}
+      - name: Build container image
+        run: docker build . --build-arg GIT_COMMIT=$(git rev-parse HEAD) --build-arg BUILD_DATE=$(date -u +'%Y-%m-%dT%H:%M:%SZ') --build-arg IMAGE_TAG=${{ steps.branch.outputs.name }} -t galaxyproject/galaxy-min:${{ steps.branch.outputs.name }} -t quay.io/galaxyproject/galaxy-min:${{ steps.branch.outputs.name }} -f .k8s_ci.Dockerfile
+      - name: Create auto-expiring one for per-commit auto repository
+        run: echo "FROM galaxyproject/galaxy-min:${{ steps.branch.outputs.name }}" | docker build --label "quay.expires-after"="90d" -t "quay.io/galaxyproject/galaxy-k8s-auto:${{ steps.commit.outputs.sha_short }}" -
       - name: Login to quay.io
         uses: actions-hub/docker/login@master
         env:
@@ -32,4 +34,17 @@ jobs:
       - name: Push to quay.io with branch name
         uses: actions-hub/docker@master
         with:
-          args: push quay.io/galaxy-min/galaxy:${{ steps.branch.outputs.name }}
+          args: push quay.io/galaxyproject/galaxy-min:${{ steps.branch.outputs.name }}
+      - name: Push to quay.io with commit hash
+        uses: actions-hub/docker@master
+        with:
+          args: push quay.io/galaxyproject/galaxy-k8s-auto:${{ steps.commit.outputs.sha_short }}
+      - name: Login to DockerHub
+        uses: actions-hub/docker/login@master
+        env:
+          DOCKER_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+          DOCKER_PASSWORD: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - name: Push to DockerHub with branch name
+        uses: actions-hub/docker@master
+        with:
+          args: push galaxyproject/galaxy-min:${{ steps.branch.outputs.name }}

lib/galaxy/tools/repositories.py

@@ -12,14 +12,18 @@ from galaxy.util.dbkeys import GenomeBuilds
 class ValidationContext:
     """Minimal App object for tool validation."""
 
-    def __init__(self, app_name,
-                 security,
-                 model,
-                 tool_data_path,
-                 shed_tool_data_path,
-                 tool_data_tables=None,
-                 registry=None,
-                 hgweb_config_manager=None):
+    def __init__(
+        self,
+        app_name,
+        security,
+        model,
+        tool_data_path,
+        shed_tool_data_path,
+        tool_data_tables=None,
+        registry=None,
+        hgweb_config_manager=None,
+        biotools_metadata_source=None,
+    ):
         self.name = app_name
         self.security = security
         self.model = model
@@ -34,6 +38,7 @@ class ValidationContext:
         self.tool_shed_registry = Bunch(tool_sheds={})
         self.datatypes_registry = registry
         self.hgweb_config_manager = hgweb_config_manager
+        self.biotools_metadata_source = biotools_metadata_source
         self.config.len_file_path = os.path.join(self.temporary_path, 'chromlen.txt')
         # If the builds file path is set to None, tools/__init__.py will load the default.
         # Otherwise it will attempt to load a nonexistent file and log an error. This does
@@ -56,15 +61,19 @@ class ValidationContext:
             work_dir = tempfile.mkdtemp()
             cleanup = True
         tool_data_tables = ToolDataTableManager(work_dir)
-        with ValidationContext(app_name=app.name,
-                               security=app.security,
-                               model=app.model,
-                               tool_data_path=work_dir,
-                               shed_tool_data_path=work_dir,
-                               tool_data_tables=tool_data_tables,
-                               registry=app.datatypes_registry,
-                               hgweb_config_manager=getattr(app, 'hgweb_config_manager', None)
-                               ) as app:
-            yield app
-        if cleanup:
-            shutil.rmtree(work_dir, ignore_errors=True)
+        try:
+            with ValidationContext(
+                app_name=app.name,
+                security=app.security,
+                model=app.model,
+                tool_data_path=work_dir,
+                shed_tool_data_path=work_dir,
+                tool_data_tables=tool_data_tables,
+                registry=app.datatypes_registry,
+                hgweb_config_manager=getattr(app, 'hgweb_config_manager', None),
+                biotools_metadata_source=getattr(app, 'biotools_metadata_source', None),
+            ) as app:
+                yield app
+        finally:
+            if cleanup:
+                shutil.rmtree(work_dir, ignore_errors=True)

test/integration/test_shed_tool_tests.py

@@ -17,8 +17,8 @@ class ToolShedToolTestIntegrationTestCase(integration_util.IntegrationTestCase,
 
     @skip_if_toolshed_down
     def test_tool_test(self):
-        self.install_repository("devteam", "fastqc", "ff9530579d1f")
-        self._run_tool_test("toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71")
+        self.install_repository("devteam", "fastqc", "3d0c7bdf12f5")
+        self._run_tool_test("toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0")
 
 
 class ToolShedDatatypeTestIntegrationTestCase(integration_util.IntegrationTestCase, UsesShed):