Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Mixed enhancements from CWL branch #18539

Merged
merged 4 commits into from
Jul 13, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 3 additions & 1 deletion .github/workflows/cwl_conformance.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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'
Expand Down
7 changes: 5 additions & 2 deletions lib/galaxy/structured_app.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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'
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/tool_util/cwl/parser.py
Original file line number Diff line number Diff line change
Expand Up @@ -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]


Expand Down
10 changes: 5 additions & 5 deletions lib/galaxy_test/base/populators.py
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down
Loading