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This commit is contained in:
pauldg
2023-03-29 11:32:35 +02:00
parent e2882dc54c
commit 9105ba3ea5
3 changed files with 55 additions and 31 deletions
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lib/galaxy/model/store/ro_crate_utils.py
+46 -28
View File
@@ -3,7 +3,6 @@ import os
from typing import (
Any,
Dict,
Optional,
)
from rocrate.model.computationalworkflow import (
@@ -17,14 +16,9 @@ from rocrate.rocrate import ROCrate
from galaxy.model import (
HistoryDatasetAssociation,
HistoryDatasetCollectionAssociation,
JobParameter,
JobToInputDatasetAssociation,
JobToOutputDatasetAssociation,
Workflow,
WorkflowInvocation,
WorkflowInvocationStep,
WorkflowRequestInputStepParameter,
WorkflowStep,
)
logger = logging.getLogger(__name__)
@@ -249,9 +243,17 @@ class WorkflowRunCrateProfileBuilder:
self.roc_engine_run = roc_engine_run
def _add_attrs_files(self, crate: ROCrate):
targets = [ATTRS_FILENAME_HISTORY, ATTRS_FILENAME_DATASETS, ATTRS_FILENAME_JOBS, ATTRS_FILENAME_IMPLICIT_COLLECTION_JOBS,
ATTRS_FILENAME_COLLECTIONS, ATTRS_FILENAME_EXPORT, ATTRS_FILENAME_LIBRARIES, ATTRS_FILENAME_LIBRARY_FOLDERS,
ATTRS_FILENAME_INVOCATIONS]
targets = [
ATTRS_FILENAME_HISTORY,
ATTRS_FILENAME_DATASETS,
ATTRS_FILENAME_JOBS,
ATTRS_FILENAME_IMPLICIT_COLLECTION_JOBS,
ATTRS_FILENAME_COLLECTIONS,
ATTRS_FILENAME_EXPORT,
ATTRS_FILENAME_LIBRARIES,
ATTRS_FILENAME_LIBRARY_FOLDERS,
ATTRS_FILENAME_INVOCATIONS,
]
for attrs in targets:
attrs_path = os.path.join(self.model_store.export_directory, attrs)
description = " ".join(attrs.split("_")[:-1])
@@ -282,7 +284,7 @@ class WorkflowRunCrateProfileBuilder:
"version": GALAXY_EXPORT_VERSION,
"description": f"{description} provenance properties",
"encodingFormat": "json",
}
},
)
)
@@ -290,19 +292,35 @@ class WorkflowRunCrateProfileBuilder:
profiles = []
for p in "process", "workflow":
id_ = f"https://w3id.org/ro/wfrun/{p}/{PROFILES_VERSION}"
profiles.append(crate.add(ContextEntity(crate, id_, properties={
"@type": "CreativeWork",
"name": f"{p.title()} Run Crate",
"version": PROFILES_VERSION,
})))
profiles.append(
crate.add(
ContextEntity(
crate,
id_,
properties={
"@type": "CreativeWork",
"name": f"{p.title()} Run Crate",
"version": PROFILES_VERSION,
},
)
)
)
# FIXME: in the future, this could go out of sync with the wroc
# profile added by ro-crate-py to the metadata descriptor
wroc_profile_id = f"https://w3id.org/workflowhub/workflow-ro-crate/{WROC_PROFILE_VERSION}"
profiles.append(crate.add(ContextEntity(crate, wroc_profile_id, properties={
"@type": "CreativeWork",
"name": "Workflow RO-Crate",
"version": WROC_PROFILE_VERSION,
})))
profiles.append(
crate.add(
ContextEntity(
crate,
wroc_profile_id,
properties={
"@type": "CreativeWork",
"name": "Workflow RO-Crate",
"version": WROC_PROFILE_VERSION,
},
)
)
)
crate.root_dataset["conformsTo"] = profiles
def _add_parameters(self, crate: ROCrate):
@@ -314,7 +332,11 @@ class WorkflowRunCrateProfileBuilder:
self.create_action.append_to("object", property_value)
if step.workflow_step.type == "tool":
for tool_input in step.workflow_step.tool_inputs.keys():
if tool_input not in self.ignored_parameter_type and tool_input not in step.workflow_step.inputs_by_name.keys() and not tool_input.startswith("__"):
if (
tool_input not in self.ignored_parameter_type
and tool_input not in step.workflow_step.inputs_by_name.keys()
and not tool_input.startswith("__")
):
property_value = self._add_step_tool_pv(step, tool_input, crate)
formal_param = self._add_step_tool_fp(step, tool_input, crate)
crate.mainEntity.append_to("input", formal_param)
@@ -337,7 +359,7 @@ class WorkflowRunCrateProfileBuilder:
def _add_step_parameter_fp(self, step: WorkflowInvocationStep, crate: ROCrate):
param_id = step.workflow_step.label
param_type = step.workflow_step.tool_inputs['parameter_type']
param_type = step.workflow_step.tool_inputs["parameter_type"]
return ContextEntity(
crate,
f"{param_id}-param",
@@ -388,9 +410,7 @@ class WorkflowRunCrateProfileBuilder:
properties={
"@type": "FormalParameter",
"additionalType": "File", # TODO: always a dataset/File?
"description": hda.annotations[0].annotation
if hda.annotations
else hda.info or "",
"description": hda.annotations[0].annotation if hda.annotations else hda.info or "",
"name": hda.name,
},
)
@@ -404,9 +424,7 @@ class WorkflowRunCrateProfileBuilder:
properties={
"@type": "FormalParameter",
"additionalType": "File", # TODO: always a dataset/File?
"description": hdca.annotations[0].annotation
if hdca.annotations
else "",
"description": hdca.annotations[0].annotation if hdca.annotations else "",
"name": hdca.name,
},
)
lib/galaxy_test/api/test_workflows.py
+4 -1
View File
@@ -2826,7 +2826,10 @@ input collection 2:
collections = [_ for _ in crate.contextual_entities if "Collection" in _.type]
assert len(collections) == 3
collection = collections[0]
assert collection["additionalType"] == "https://training.galaxyproject.org/training-material/faqs/galaxy/collections_build_list.html"
assert (
collection["additionalType"]
== "https://training.galaxyproject.org/training-material/faqs/galaxy/collections_build_list.html"
)
assert collection.type == "Collection"
assert len(collection["hasPart"]) == 2
assert collection in wf_objects
test/unit/data/model/test_model_store.py
+5 -2
View File
@@ -21,6 +21,7 @@ from sqlalchemy.orm.scoping import scoped_session
from galaxy import model
from galaxy.model import store
from galaxy.model.metadata import MetadataTempFile
from galaxy.model.orm.now import now
from galaxy.model.unittest_utils import GalaxyDataTestApp
from galaxy.model.unittest_utils.store_fixtures import (
deferred_hda_model_store_dict,
@@ -36,7 +37,6 @@ from ..test_galaxy_mapping import (
_invocation_for_workflow,
_workflow_from_steps,
)
from galaxy.model.orm.now import now
TESTCASE_DIRECTORY = pathlib.Path(__file__).parent
TEST_PATH_1 = TESTCASE_DIRECTORY / "1.txt"
@@ -466,7 +466,10 @@ def validate_invocation_collection_crate_directory(crate_directory):
assert len(collections) == 3
collection = collections[0]
assert collection.type == "Collection"
assert collection["additionalType"] == "https://training.galaxyproject.org/training-material/faqs/galaxy/collections_build_list.html"
assert (
collection["additionalType"]
== "https://training.galaxyproject.org/training-material/faqs/galaxy/collections_build_list.html"
)
assert len(collection["hasPart"]) == 2
for dataset in collection["hasPart"]:
assert dataset in root["hasPart"]