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Merge branch 'release_24.0' into release_24.1
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nsoranzo committed Dec 10, 2024
2 parents b39c3b2 + ee5f807 commit e5f0a8c
Showing 7 changed files with 127 additions and 39 deletions.
18 changes: 10 additions & 8 deletions .github/workflows/pr-title-update.yml
Original file line number Diff line number Diff line change
@@ -2,26 +2,28 @@ name: Update PR title

on:
pull_request_target:
types: [opened, edited]
branches:
- "release_**"
types: [opened, edited, reopened]

jobs:
update-title:
if: github.event.action != 'edited' || github.event.changes.base.ref.from != ''
runs-on: ubuntu-latest
permissions:
pull-requests: write
steps:
- uses: actions/checkout@v4
- name: Update PR title
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
PR_NUMBER: ${{ github.event.pull_request.number }}
TARGET_BRANCH: "${{ github.base_ref }}"
PR_TITLE: "${{ github.event.pull_request.title }}"
REPO: "${{ github.repository }}"
run: |
VERSION=$(echo $TARGET_BRANCH | grep -oP '\d+\.\d+')
if [[ -n "$VERSION" && ! "$PR_TITLE" =~ ^\[$VERSION\] ]]; then
NEW_TITLE="[$VERSION] $PR_TITLE"
gh pr edit $PR_NUMBER --title "$NEW_TITLE"
VERSION=$(echo $TARGET_BRANCH | grep -oP '^release_\K\d+.\d+$' || true)
NEW_TITLE=$(echo "$PR_TITLE" | sed -E "s/\[[0-9]+\.[0-9]+\] //")
if [[ -n "$VERSION" ]]; then
NEW_TITLE="[$VERSION] $NEW_TITLE"
fi
if [[ "$NEW_TITLE" != "$PR_TITLE" ]]; then
gh pr edit $PR_NUMBER --repo "$REPO" --title "$NEW_TITLE"
fi
7 changes: 4 additions & 3 deletions lib/galaxy/managers/workflows.py
Original file line number Diff line number Diff line change
@@ -598,7 +598,7 @@ def read_workflow_from_path(self, app, user, path, allow_in_directory=None) -> m
import_options = ImportOptions()
import_options.deduplicate_subworkflows = True
as_dict = python_to_workflow(as_dict, galaxy_interface, workflow_directory=None, import_options=import_options)
raw_description = RawWorkflowDescription(as_dict, path)
raw_description = RawWorkflowDescription(as_dict)
created_workflow = self.build_workflow_from_raw_description(trans, raw_description, WorkflowCreateOptions())
return created_workflow.workflow

@@ -937,8 +937,9 @@ def to_format_2(wf_dict, **kwds):
return wf_dict

def _sync_stored_workflow(self, trans, stored_workflow):
workflow_path = stored_workflow.from_path
self.store_workflow_to_path(workflow_path, stored_workflow, stored_workflow.latest_workflow, trans=trans)
if trans.user_is_admin:
workflow_path = stored_workflow.from_path
self.store_workflow_to_path(workflow_path, stored_workflow, stored_workflow.latest_workflow, trans=trans)

def store_workflow_artifacts(self, directory, filename_base, workflow, **kwd):
modern_workflow_path = os.path.join(directory, f"{filename_base}.gxwf.yml")
19 changes: 13 additions & 6 deletions lib/galaxy/model/__init__.py
Original file line number Diff line number Diff line change
@@ -2630,7 +2630,7 @@ class PostJobAction(Base, RepresentById):
workflow_step_id: Mapped[Optional[int]] = mapped_column(ForeignKey("workflow_step.id"), index=True)
action_type: Mapped[str] = mapped_column(String(255))
output_name: Mapped[Optional[str]] = mapped_column(String(255))
action_arguments: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
_action_arguments: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
workflow_step: Mapped[Optional["WorkflowStep"]] = relationship(
back_populates="post_job_actions",
primaryjoin=(lambda: WorkflowStep.id == PostJobAction.workflow_step_id),
@@ -2643,6 +2643,18 @@ def __init__(self, action_type, workflow_step=None, output_name=None, action_arg
self.workflow_step = workflow_step
ensure_object_added_to_session(self, object_in_session=workflow_step)

@property
def action_arguments(self):
if self.action_type in ("HideDatasetAction", "DeleteIntermediatesAction") and self._action_arguments is True:
# Fix up broken workflows resulting from imports with gxformat2 <= 0.20.0
return {}
else:
return self._action_arguments

@action_arguments.setter
def action_arguments(self, value: Dict[str, Any]):
self._action_arguments = value


class PostJobActionAssociation(Base, RepresentById):
__tablename__ = "post_job_action_association"
@@ -6900,11 +6912,6 @@ class HistoryDatasetCollectionAssociation(
primaryjoin=copied_from_history_dataset_collection_association_id == id,
remote_side=[id],
uselist=False,
back_populates="copied_to_history_dataset_collection_association",
)
copied_to_history_dataset_collection_association = relationship(
"HistoryDatasetCollectionAssociation",
back_populates="copied_from_history_dataset_collection_association",
)
implicit_input_collections: Mapped[List["ImplicitlyCreatedDatasetCollectionInput"]] = relationship(
primaryjoin=(
40 changes: 22 additions & 18 deletions lib/galaxy/model/store/__init__.py
Original file line number Diff line number Diff line change
@@ -999,14 +999,16 @@ def _import_collection_copied_associations(
# sense.
hdca_copied_from_sinks = object_import_tracker.hdca_copied_from_sinks
if copied_from_object_key in object_import_tracker.hdcas_by_key:
hdca.copied_from_history_dataset_collection_association = object_import_tracker.hdcas_by_key[
copied_from_object_key
]
source_hdca = object_import_tracker.hdcas_by_key[copied_from_object_key]
if source_hdca is not hdca:
# We may not have the copied source, in which case the first included HDCA in the chain
# acts as the source, so here we make sure we don't create a cycle.
hdca.copied_from_history_dataset_collection_association = source_hdca
else:
if copied_from_object_key in hdca_copied_from_sinks:
hdca.copied_from_history_dataset_collection_association = object_import_tracker.hdcas_by_key[
hdca_copied_from_sinks[copied_from_object_key]
]
source_hdca = object_import_tracker.hdcas_by_key[hdca_copied_from_sinks[copied_from_object_key]]
if source_hdca is not hdca:
hdca.copied_from_history_dataset_collection_association = source_hdca
else:
hdca_copied_from_sinks[copied_from_object_key] = dataset_collection_key

@@ -1072,7 +1074,7 @@ def attach_workflow_step(imported_object, attrs):
for step_attrs in invocation_attrs["steps"]:
imported_invocation_step = model.WorkflowInvocationStep()
imported_invocation_step.workflow_invocation = imported_invocation
ensure_object_added_to_session(imported_invocation, session=self.sa_session)
ensure_object_added_to_session(imported_invocation_step, session=self.sa_session)
attach_workflow_step(imported_invocation_step, step_attrs)
restore_times(imported_invocation_step, step_attrs)
imported_invocation_step.action = step_attrs["action"]
@@ -1926,12 +1928,14 @@ def __init__(
self.export_files = export_files
self.included_datasets: Dict[model.DatasetInstance, Tuple[model.DatasetInstance, bool]] = {}
self.dataset_implicit_conversions: Dict[model.DatasetInstance, model.ImplicitlyConvertedDatasetAssociation] = {}
self.included_collections: List[Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]] = []
self.included_collections: Dict[
Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation],
Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation],
] = {}
self.included_libraries: List[model.Library] = []
self.included_library_folders: List[model.LibraryFolder] = []
self.included_invocations: List[model.WorkflowInvocation] = []
self.collection_datasets: Set[int] = set()
self.collections_attrs: List[Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]] = []
self.dataset_id_to_path: Dict[int, Tuple[Optional[str], Optional[str]]] = {}

self.job_output_dataset_associations: Dict[int, Dict[str, model.DatasetInstance]] = {}
@@ -2298,8 +2302,7 @@ def export_collection(
def add_dataset_collection(
self, collection: Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]
) -> None:
self.collections_attrs.append(collection)
self.included_collections.append(collection)
self.included_collections[collection] = collection

def add_implicit_conversion_dataset(
self,
@@ -2362,7 +2365,7 @@ def to_json(attributes):

collections_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_COLLECTIONS)
with open(collections_attrs_filename, "w") as collections_attrs_out:
collections_attrs_out.write(to_json(self.collections_attrs))
collections_attrs_out.write(to_json(self.included_collections.values()))

conversions_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_CONVERSIONS)
with open(conversions_attrs_filename, "w") as conversions_attrs_out:
@@ -2383,12 +2386,12 @@ def to_json(attributes):
#

# Get all jobs associated with included HDAs.
jobs_dict: Dict[str, model.Job] = {}
jobs_dict: Dict[int, model.Job] = {}
implicit_collection_jobs_dict = {}

def record_job(job):
if not job:
# No viable job.
if not job or job.id in jobs_dict:
# No viable job or job already recorded.
return

jobs_dict[job.id] = job
@@ -2414,10 +2417,11 @@ def record_associated_jobs(obj):
)
job_hda = hda
while job_hda.copied_from_history_dataset_association: # should this check library datasets as well?
# record job (if one exists) even if dataset was copied
# copy could have been created manually through UI/API or using database operation tool,
# in which case we have a relevant job to export.
record_associated_jobs(job_hda)
job_hda = job_hda.copied_from_history_dataset_association
if not job_hda.creating_job_associations:
# No viable HDA found.
continue

record_associated_jobs(job_hda)

7 changes: 3 additions & 4 deletions lib/galaxy/tools/__init__.py
Original file line number Diff line number Diff line change
@@ -3786,14 +3786,13 @@ def produce_outputs(self, trans, out_data, output_collections, incoming, history
final_sorted_identifiers = [
element.element_identifier for element in elements1 if element.element_identifier in old_elements2_dict
]
# Raise Exception if it is empty
if len(final_sorted_identifiers) == 0:
# Create empty collections:
output_collections.create_collection(
next(iter(self.outputs.values())), "output1", elements={}, propagate_hda_tags=False
self.outputs["output1"], "output1", elements={}, propagate_hda_tags=False
)
output_collections.create_collection(
next(iter(self.outputs.values())), "output2", elements={}, propagate_hda_tags=False
self.outputs["output2"], "output2", elements={}, propagate_hda_tags=False
)
return

@@ -3811,7 +3810,7 @@ def output_with_selected_identifiers(old_elements_dict, output_label):
self._add_datasets_to_history(history, new_elements.values())
# Create collections:
output_collections.create_collection(
next(iter(self.outputs.values())), output_label, elements=new_elements, propagate_hda_tags=False
self.outputs[output_label], output_label, elements=new_elements, propagate_hda_tags=False
)

# Create outputs:
31 changes: 31 additions & 0 deletions lib/galaxy/tools/harmonize_two_collections_list.xml
Original file line number Diff line number Diff line change
@@ -171,6 +171,37 @@
<output_collection name="output1" type="list" count="0"/>
<output_collection name="output2" type="list" count="0"/>
</test>
<!-- test that collection types get propagated to outputs correctly -->
<test>
<param name="input1">
<collection type="list">
<element name="element_1" value="simple_line.txt" />
</collection>
</param>
<param name="input2">
<collection type="list:paired">
<element name="element_1">
<collection type="paired">
<element name="forward" value="1.fastqsanger" ftype="fastqsanger" />
<element name="reverse" value="1.fastqsanger" ftype="fastqsanger" />
</collection>
</element>
</collection>
</param>
<output_collection name="output1" type="list" count="1">
<element name="element_1">
<assert_contents>
<has_text_matching expression="^This is a line of text.\n$" />
</assert_contents>
</element>
</output_collection>
<output_collection name="output2" type="list:paired" count="1">
<element name="element_1">
<element name="forward" file="1.fastqsanger" ftype="fastqsanger" />
<element name="reverse" file="1.fastqsanger" ftype="fastqsanger" />
</element>
</output_collection>
</test>
</tests>
<help><![CDATA[
44 changes: 44 additions & 0 deletions test/integration/test_workflow_tasks.py
Original file line number Diff line number Diff line change
@@ -17,6 +17,7 @@
from galaxy_test.base import api_asserts
from galaxy_test.base.api import UsesCeleryTasks
from galaxy_test.base.populators import (
DatasetCollectionPopulator,
DatasetPopulator,
RunJobsSummary,
WorkflowPopulator,
@@ -27,6 +28,7 @@

class TestWorkflowTasksIntegration(PosixFileSourceSetup, IntegrationTestCase, UsesCeleryTasks, RunsWorkflowFixtures):
dataset_populator: DatasetPopulator
dataset_collection_populator: DatasetCollectionPopulator
framework_tool_and_types = True

@classmethod
@@ -37,6 +39,7 @@ def handle_galaxy_config_kwds(cls, config):
def setUp(self):
super().setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
self._write_file_fixtures()

@@ -124,6 +127,47 @@ def test_export_import_invocation_with_step_parameter(self):
invocation_details = self._export_and_import_workflow_invocation(summary, use_uris)
self._rerun_imported_workflow(summary, invocation_details)

def test_export_import_invocation_with_copied_hdca_and_database_operation_tool(self):
with self.dataset_populator.test_history() as history_id:
self.dataset_collection_populator.create_list_in_history(history_id=history_id, wait=True).json()
new_history = self.dataset_populator.copy_history(history_id=history_id).json()
copied_collection = self.dataset_populator.get_history_collection_details(new_history["id"])
workflow_id = self.workflow_populator.upload_yaml_workflow(
"""class: GalaxyWorkflow
inputs:
input:
type: collection
collection_type: list
steps:
extract_dataset:
tool_id: __EXTRACT_DATASET__
in:
input:
source: input
"""
)
inputs = {"input": {"src": "hdca", "id": copied_collection["id"]}}
workflow_request = {"history": f"hist_id={new_history['id']}", "inputs_by": "name", "inputs": inputs}
invocation = self.workflow_populator.invoke_workflow_raw(
workflow_id, workflow_request, assert_ok=True
).json()
invocation_id = invocation["id"]
self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id)
jobs = self.workflow_populator.get_invocation_jobs(invocation_id)
summary = RunJobsSummary(
history_id=history_id,
workflow_id=workflow_id,
invocation_id=invocation["id"],
inputs=inputs,
jobs=jobs,
invocation=invocation,
workflow_request=workflow_request,
)
imported_invocation_details = self._export_and_import_workflow_invocation(summary)
original_contents = self.dataset_populator.get_history_contents(new_history["id"])
contents = self.dataset_populator.get_history_contents(imported_invocation_details["history_id"])
assert len(contents) == len(original_contents) == 5

def _export_and_import_workflow_invocation(
self, summary: RunJobsSummary, use_uris: bool = True, model_store_format="tgz"
) -> Dict[str, Any]:

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