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Use id entity attribute when setting exampleOfWork property #19396

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Use id entity attribute when setting exampleOfWork property #19396

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944450a
Uniform use of tmp_path in ro-crate tests
nsoranzo Jan 9, 2025
dad7c26
Use `id` entity attribute when setting `exampleOfWork` property
nsoranzo Jan 10, 2025
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60 changes: 22 additions & 38 deletions lib/galaxy/model/store/ro_crate_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,25 +123,27 @@ def _add_file(self, dataset: HistoryDatasetAssociation, properties: Dict[Any, An
def _add_files(self, crate: ROCrate):
for wfda in self.invocation.input_datasets:
if not self.file_entities.get(wfda.dataset.dataset.id):
dataset_formal_param = self._add_dataset_formal_parameter(wfda.dataset, crate)
crate.mainEntity.append_to("input", dataset_formal_param)
properties = {
"exampleOfWork": {"@id": f"#{wfda.dataset.dataset.uuid}"},
"exampleOfWork": {"@id": dataset_formal_param.id},
}
file_entity = self._add_file(wfda.dataset, properties, crate)
dataset_formal_param = self._add_dataset_formal_parameter(wfda.dataset, crate)
crate.mainEntity.append_to("input", dataset_formal_param)
self.create_action.append_to("object", file_entity)

for wfda in self.invocation.output_datasets:
if not self.file_entities.get(wfda.dataset.dataset.id):
dataset_formal_param = self._add_dataset_formal_parameter(wfda.dataset, crate)
crate.mainEntity.append_to("output", dataset_formal_param)
properties = {
"exampleOfWork": {"@id": f"#{wfda.dataset.dataset.uuid}"},
"exampleOfWork": {"@id": dataset_formal_param.id},
}
file_entity = self._add_file(wfda.dataset, properties, crate)
dataset_formal_param = self._add_dataset_formal_parameter(wfda.dataset, crate)
crate.mainEntity.append_to("output", dataset_formal_param)
self.create_action.append_to("result", file_entity)

def _add_collection(self, hdca: HistoryDatasetCollectionAssociation, crate: ROCrate) -> ContextEntity:
def _add_collection(
self, hdca: HistoryDatasetCollectionAssociation, crate: ROCrate, collection_formal_param: ContextEntity
) -> ContextEntity:
name = hdca.name
dataset_ids = []
for hda in hdca.dataset_instances:
Expand All @@ -158,7 +160,7 @@ def _add_collection(self, hdca: HistoryDatasetCollectionAssociation, crate: ROCr
"@type": "Collection",
"additionalType": self._get_collection_additional_type(hdca.collection.collection_type),
"hasPart": dataset_ids,
"exampleOfWork": {"@id": f"#{hdca.type_id}-param"},
"exampleOfWork": {"@id": collection_formal_param.id},
}
collection_entity = crate.add(
ContextEntity(
Expand All @@ -185,14 +187,14 @@ def _get_parameter_additional_type(self, parameter_type: Optional[str]) -> str:

def _add_collections(self, crate: ROCrate):
for wfdca in self.invocation.input_dataset_collections:
collection_entity = self._add_collection(wfdca.dataset_collection, crate)
collection_formal_param = self._add_collection_formal_parameter(wfdca.dataset_collection, crate)
collection_entity = self._add_collection(wfdca.dataset_collection, crate, collection_formal_param)
crate.mainEntity.append_to("input", collection_formal_param)
self.create_action.append_to("object", collection_entity)

for wfdca in self.invocation.output_dataset_collections:
collection_entity = self._add_collection(wfdca.dataset_collection, crate)
collection_formal_param = self._add_collection_formal_parameter(wfdca.dataset_collection, crate)
collection_entity = self._add_collection(wfdca.dataset_collection, crate, collection_formal_param)
crate.mainEntity.append_to("output", collection_formal_param)
self.create_action.append_to("result", collection_entity)

Expand Down Expand Up @@ -336,31 +338,14 @@ def _add_profiles(self, crate: ROCrate):
def _add_parameters(self, crate: ROCrate):
for step in self.invocation.steps:
if step.workflow_step.type == "parameter_input":
property_value = self._add_step_parameter_pv(step, crate)
formal_param = self._add_step_parameter_fp(step, crate)
crate.mainEntity.append_to("input", formal_param)
property_value = self._add_step_parameter(step, crate)
self.create_action.append_to("object", property_value)

def _add_step_parameter_pv(self, step: WorkflowInvocationStep, crate: ROCrate):
param_id = step.workflow_step.label
return crate.add(
ContextEntity(
crate,
f"{param_id}-pv",
properties={
"@type": "PropertyValue",
"name": f"{param_id}",
"value": step.output_value.value,
"exampleOfWork": {"@id": f"#{param_id}-param"},
},
)
)

def _add_step_parameter_fp(self, step: WorkflowInvocationStep, crate: ROCrate):
def _add_step_parameter(self, step: WorkflowInvocationStep, crate: ROCrate) -> ContextEntity:
param_id = step.workflow_step.label
assert step.workflow_step.tool_inputs
param_type = step.workflow_step.tool_inputs["parameter_type"]
return crate.add(
formal_param = crate.add(
ContextEntity(
crate,
f"{param_id}-param",
Expand All @@ -373,19 +358,16 @@ def _add_step_parameter_fp(self, step: WorkflowInvocationStep, crate: ROCrate):
},
)
)

def _add_step_tool_pv(self, step: WorkflowInvocationStep, tool_input: str, crate: ROCrate):
param_id = tool_input
assert step.workflow_step.tool_inputs
crate.mainEntity.append_to("input", formal_param)
return crate.add(
ContextEntity(
crate,
f"{param_id}-pv",
properties={
"@type": "PropertyValue",
"name": f"{step.workflow_step.label}",
"value": step.workflow_step.tool_inputs[tool_input],
"exampleOfWork": {"@id": f"#{param_id}-param"},
"name": f"{param_id}",
"value": step.output_value.value,
"exampleOfWork": {"@id": formal_param.id},
},
)
)
Expand Down Expand Up @@ -419,7 +401,9 @@ def _add_dataset_formal_parameter(self, hda: HistoryDatasetAssociation, crate: R
)
)

def _add_collection_formal_parameter(self, hdca: HistoryDatasetCollectionAssociation, crate: ROCrate):
def _add_collection_formal_parameter(
self, hdca: HistoryDatasetCollectionAssociation, crate: ROCrate
) -> ContextEntity:
return crate.add(
ContextEntity(
crate,
Expand Down
59 changes: 24 additions & 35 deletions test/unit/data/model/test_model_store.py
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Original file line number Diff line number Diff line change
Expand Up @@ -383,7 +383,7 @@ def test_import_library_require_permissions():
assert error_caught


def test_import_export_library():
def test_import_export_library(tmp_path):
"""Test basics of library, library folder, and library dataset import/export."""
app = _mock_app()
sa_session = app.model.context
Expand Down Expand Up @@ -412,12 +412,11 @@ def test_import_export_library():
assert len(root_folder.datasets) == 1
assert len(root_folder.folders) == 1

temp_directory = mkdtemp()
with store.DirectoryModelExportStore(temp_directory, app=app) as export_store:
with store.DirectoryModelExportStore(tmp_path, app=app) as export_store:
export_store.export_library(library)

import_model_store = store.get_import_model_store_for_directory(
temp_directory, app=app, user=u, import_options=store.ImportOptions(allow_library_creation=True)
tmp_path, app=app, user=u, import_options=store.ImportOptions(allow_library_creation=True)
)
import_model_store.perform_import()

Expand Down Expand Up @@ -593,7 +592,7 @@ def validate_invocation_collection_crate_directory(crate_directory):
assert dataset in root["hasPart"]


def test_export_history_with_missing_hid():
def test_export_history_with_missing_hid(tmp_path):
# The dataset's hid was used to compose the file name during the export but it
# can be missing sometimes. We now use the dataset's encoded id instead.
app = _mock_app()
Expand All @@ -603,46 +602,41 @@ def test_export_history_with_missing_hid():
d1.hid = None
app.commit()

temp_directory = mkdtemp()
with store.DirectoryModelExportStore(temp_directory, app=app, export_files="copy") as export_store:
with store.DirectoryModelExportStore(tmp_path, app=app, export_files="copy") as export_store:
export_store.export_history(history)


def test_export_history_to_ro_crate(tmp_path):
app = _mock_app()
u, history, d1, d2, j = _setup_simple_cat_job(app)

crate_directory = tmp_path / "crate"
with store.ROCrateModelExportStore(crate_directory, app=app) as export_store:
with store.ROCrateModelExportStore(tmp_path, app=app) as export_store:
export_store.export_history(history)
validate_history_crate_directory(crate_directory)
validate_history_crate_directory(tmp_path)


def test_export_invocation_to_ro_crate(tmp_path):
app = _mock_app()
workflow_invocation = _setup_invocation(app)
crate_directory = tmp_path / "crate"
with store.ROCrateModelExportStore(crate_directory, app=app) as export_store:
with store.ROCrateModelExportStore(tmp_path, app=app) as export_store:
export_store.export_workflow_invocation(workflow_invocation)
validate_invocation_crate_directory(crate_directory)
validate_invocation_crate_directory(tmp_path)


def test_export_simple_invocation_to_ro_crate(tmp_path):
app = _mock_app()
workflow_invocation = _setup_simple_invocation(app)
crate_directory = tmp_path / "crate"
with store.ROCrateModelExportStore(crate_directory, app=app) as export_store:
with store.ROCrateModelExportStore(tmp_path, app=app) as export_store:
export_store.export_workflow_invocation(workflow_invocation)
validate_invocation_crate_directory(crate_directory)
validate_invocation_crate_directory(tmp_path)


def test_export_collection_invocation_to_ro_crate(tmp_path):
app = _mock_app()
workflow_invocation = _setup_collection_invocation(app)
crate_directory = tmp_path / "crate"
with store.ROCrateModelExportStore(crate_directory, app=app) as export_store:
with store.ROCrateModelExportStore(tmp_path, app=app) as export_store:
export_store.export_workflow_invocation(workflow_invocation)
validate_invocation_collection_crate_directory(crate_directory)
validate_invocation_collection_crate_directory(tmp_path)


def test_export_invocation_to_ro_crate_archive(tmp_path):
Expand Down Expand Up @@ -727,7 +721,7 @@ def test_import_export_edit_datasets():
assert d1.dataset.object_store_id == "foo1", d1.dataset.object_store_id


def test_import_export_edit_collection():
def test_import_export_edit_collection(tmp_path):
"""Test modifying existing collections with imports."""
app = _mock_app()
sa_session = app.model.context
Expand All @@ -743,13 +737,12 @@ def test_import_export_edit_collection():
import_history = model.History(name="Test History for Import", user=u)
app.add_and_commit(import_history)

temp_directory = mkdtemp()
with store.DirectoryModelExportStore(temp_directory, app=app, for_edit=True) as export_store:
with store.DirectoryModelExportStore(tmp_path, app=app, for_edit=True) as export_store:
export_store.add_dataset_collection(hc1)

# Fabric editing metadata for collection...
collections_metadata_path = os.path.join(temp_directory, store.ATTRS_FILENAME_COLLECTIONS)
datasets_metadata_path = os.path.join(temp_directory, store.ATTRS_FILENAME_DATASETS)
collections_metadata_path = os.path.join(tmp_path, store.ATTRS_FILENAME_COLLECTIONS)
datasets_metadata_path = os.path.join(tmp_path, store.ATTRS_FILENAME_DATASETS)
with open(collections_metadata_path) as f:
hdcas_metadata = json.load(f)

Expand Down Expand Up @@ -798,14 +791,14 @@ def test_import_export_edit_collection():
with open(collections_metadata_path, "w") as collections_f:
json.dump(hdcas_metadata, collections_f)

_perform_import_from_directory(temp_directory, app, u, import_history, store.ImportOptions(allow_edit=True))
_perform_import_from_directory(tmp_path, app, u, import_history, store.ImportOptions(allow_edit=True))

sa_session.refresh(c1)
assert c1.populated_state == model.DatasetCollection.populated_states.OK, c1.populated_state
assert len(c1.elements) == 2


def test_import_export_composite_datasets():
def test_import_export_composite_datasets(tmp_path):
app = _mock_app()
sa_session = app.model.context

Expand All @@ -819,13 +812,12 @@ def test_import_export_composite_datasets():
app.write_primary_file(d1, "cool primary file")
app.write_composite_file(d1, "cool composite file", "child_file")

temp_directory = mkdtemp()
with store.DirectoryModelExportStore(temp_directory, app=app, export_files="copy") as export_store:
with store.DirectoryModelExportStore(tmp_path, app=app, export_files="copy") as export_store:
export_store.add_dataset(d1)

import_history = model.History(name="Test History for Import", user=u)
app.add_and_commit(import_history)
_perform_import_from_directory(temp_directory, app, u, import_history)
_perform_import_from_directory(tmp_path, app, u, import_history)
assert len(import_history.datasets) == 1
import_dataset = import_history.datasets[0]
_assert_extra_files_has_parent_directory_with_single_file_containing(
Expand All @@ -848,7 +840,7 @@ def _assert_extra_files_has_parent_directory_with_single_file_containing(
assert contents == expected_contents


def test_edit_metadata_files():
def test_edit_metadata_files(tmp_path):
app = _mock_app(store_by="uuid")
sa_session = app.model.context

Expand All @@ -864,15 +856,12 @@ def test_edit_metadata_files():
assert d1.metadata.bam_index
assert isinstance(d1.metadata.bam_index, model.MetadataFile)

temp_directory = mkdtemp()
with store.DirectoryModelExportStore(
temp_directory, app=app, for_edit=True, strip_metadata_files=False
) as export_store:
with store.DirectoryModelExportStore(tmp_path, app=app, for_edit=True, strip_metadata_files=False) as export_store:
export_store.add_dataset(d1)

import_history = model.History(name="Test History for Import", user=u)
app.add_and_commit(import_history)
_perform_import_from_directory(temp_directory, app, u, import_history, store.ImportOptions(allow_edit=True))
_perform_import_from_directory(tmp_path, app, u, import_history, store.ImportOptions(allow_edit=True))


def test_sessionless_import_edit_datasets():
Expand Down
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