Merge pull request galaxyproject#18539 from nsoranzo/cwl_fixes

Random enhancements from CWL branch
bgruening · Jul 13, 2024 · 67fcb49 · 67fcb49
2 parents f1a4b56 + e8e1b4a
commit 67fcb49
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Showing 4 changed files with 14 additions and 9 deletions.
diff --git a/.github/workflows/cwl_conformance.yaml b/.github/workflows/cwl_conformance.yaml
@@ -4,10 +4,12 @@ on:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
   pull_request:
     paths-ignore:
       - 'client/**'
       - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
 env:
   GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
 concurrency:
@@ -59,7 +61,7 @@ jobs:
         uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
-          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
       - name: Run tests
         run: ./run_tests.sh --coverage --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}"
         working-directory: 'galaxy root'

diff --git a/lib/galaxy/structured_app.py b/lib/galaxy/structured_app.py
@@ -46,7 +46,10 @@
     from galaxy.managers.collections import DatasetCollectionManager
     from galaxy.managers.hdas import HDAManager
     from galaxy.managers.histories import HistoryManager
-    from galaxy.managers.workflows import WorkflowsManager
+    from galaxy.managers.workflows import (
+        WorkflowContentsManager,
+        WorkflowsManager,
+    )
     from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
     from galaxy.tools import ToolBox
     from galaxy.tools.cache import ToolCache
@@ -110,7 +113,7 @@ class MinimalManagerApp(MinimalApp):
     history_manager: "HistoryManager"
     hda_manager: "HDAManager"
     workflow_manager: "WorkflowsManager"
-    workflow_contents_manager: Any  # 'galaxy.managers.workflows.WorkflowContentsManager'
+    workflow_contents_manager: "WorkflowContentsManager"
     library_folder_manager: Any  # 'galaxy.managers.folders.FolderManager'
     library_manager: Any  # 'galaxy.managers.libraries.LibraryManager'
     role_manager: Any  # 'galaxy.managers.roles.RoleManager'

diff --git a/lib/galaxy/tool_util/cwl/parser.py b/lib/galaxy/tool_util/cwl/parser.py
@@ -903,7 +903,7 @@ def split_step_references(step_references, workflow_id=None, multiple=True):
     if multiple:
         return split_references
     else:
-        assert len(split_references) == 1
+        assert len(split_references) == 1, split_references
         return split_references[0]
 
 

diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py
@@ -2532,13 +2532,13 @@ def run_conformance_test(self, version: str, doc: str):
             raise Exception("Expected run to fail but it didn't.")
 
         expected_outputs = test["output"]
-        try:
-            for key, value in expected_outputs.items():
+        for key, value in expected_outputs.items():
+            try:
                 actual_output = run.get_output_as_object(key)
                 cwltest.compare.compare(value, actual_output)
-        except Exception:
-            self.dataset_populator._summarize_history(run.history_id)
-            raise
+            except Exception:
+                self.dataset_populator._summarize_history(run.history_id)
+                raise
 
 
 class LibraryPopulator: