Use TestDataResolver in tool framework tests (6706e87a) · Commits · NDIP / Galaxy

lib/galaxy/tool_util/client/staging.py

+3 −0

Original line number	Diff line number	Diff line
		@@ -11,6 +11,7 @@ import os
		from typing import (
		Any,
		BinaryIO,
		Callable,
		Dict,
		List,
		Optional,
		@@ -85,6 +86,7 @@ class StagingInterface(metaclass=abc.ABCMeta):
		use_path_paste: bool = LOAD_TOOLS_FROM_PATH,
		to_posix_lines: bool = True,
		job_dir: str = ".",
		resolve_data: Optional[Callable[[str], Optional[str]]] = None,
		) -> Tuple[Dict[str, Any], List[Dict[str, Any]]]:
		def upload_func_fetch(upload_target: UploadTarget) -> Dict[str, Any]:
		def _attach_file(upload_payload: Dict[str, Any], uri: str, index: int = 0) -> Dict[str, Union[str, bool]]:
		@@ -271,6 +273,7 @@ class StagingInterface(metaclass=abc.ABCMeta):
		upload,
		create_collection_func,
		tool_or_workflow,
		resolve_data=resolve_data,
		)

		# extension point for planemo to override logging

lib/galaxy/tool_util/cwl/util.py

+9 −5

Original line number	Diff line number	Diff line
		@@ -100,11 +100,14 @@ def _handle_pseudo_location(properties, pseudo_location):
		properties["location"] = properties["basename"]


		def abs_path_or_uri(path_or_uri: str, relative_to: str) -> str:
		def abs_path_or_uri(path_or_uri: str, relative_to: str, resolve_data: Optional[Callable[[str], Optional[str]]]) -> str:
		"""Return the absolute path if this isn't a URI, otherwise keep the URI the same."""
		if "://" in path_or_uri:
		return path_or_uri
		abs_path_ = os.path.abspath(os.path.join(relative_to, path_or_uri))
		if resolve_data and not os.path.exists(abs_path_):
		if resolved_data := resolve_data(path_or_uri):
		abs_path_ = resolved_data
		_ensure_file_exists(abs_path_)
		return abs_path_

		@@ -136,6 +139,7 @@ def galactic_job_json(
		upload_func: Callable[["UploadTarget"], Dict[str, Any]],
		collection_create_func: Callable[[List[Dict[str, Any]], str], Dict[str, Any]],
		tool_or_workflow: Literal["tool", "workflow"] = "workflow",
		resolve_data: Optional[Callable[[str], Optional[str]]] = None,
		) -> Tuple[Dict[str, Any], List[Dict[str, Any]]]:
		"""Adapt a CWL job object to the Galaxy API.

		@@ -159,7 +163,7 @@ def galactic_job_json(
		return {"src": "hda", "id": dataset_id}

		def upload_file(file_path: str, secondary_files: Optional[str], **kwargs) -> Dict[str, str]:
		file_path = abs_path_or_uri(file_path, test_data_directory)
		file_path = abs_path_or_uri(file_path, test_data_directory, resolve_data=resolve_data)
		target = FileUploadTarget(file_path, secondary_files, **kwargs)
		upload_response = upload_func(target)
		return response_to_hda(target, upload_response)
		@@ -170,17 +174,17 @@ def galactic_job_json(
		return response_to_hda(target, upload_response)

		def upload_tar(file_path: str, file_type: str = "directory", name: str = "uploaded tar file") -> Dict[str, str]:
		file_path = abs_path_or_uri(file_path, test_data_directory)
		file_path = abs_path_or_uri(file_path, test_data_directory, resolve_data=resolve_data)
		target = DirectoryUploadTarget(file_path, file_type=file_type, name=name)
		upload_response = upload_func(target)
		return response_to_hda(target, upload_response)

		def upload_file_with_composite_data(file_path: Optional[str], composite_data, **kwargs) -> Dict[str, str]:
		if file_path is not None:
		file_path = abs_path_or_uri(file_path, test_data_directory)
		file_path = abs_path_or_uri(file_path, test_data_directory, resolve_data=resolve_data)
		composite_data_resolved = []
		for cd in composite_data:
		composite_data_resolved.append(abs_path_or_uri(cd, test_data_directory))
		composite_data_resolved.append(abs_path_or_uri(cd, test_data_directory, resolve_data=resolve_data))
		target = FileUploadTarget(file_path, composite_data=composite_data_resolved, **kwargs)
		upload_response = upload_func(target)
		return response_to_hda(target, upload_response)

lib/galaxy/tool_util/verify/interactor.py

+12 −1

Original line number	Diff line number	Diff line
		@@ -44,6 +44,7 @@ from galaxy.tool_util.parser.interface import (
		ToolSourceTestOutputs,
		XmlTestCollectionDefDict,
		)
		from galaxy.tool_util.verify.test_data import TestDataResolver
		from galaxy.util import requests
		from galaxy.util.bunch import Bunch
		from galaxy.util.hash_util import (
		@@ -145,6 +146,7 @@ def stage_data_in_history(
		force_path_paste=False,
		maxseconds=DEFAULT_TOOL_TEST_WAIT,
		tool_version=None,
		test_data_resolver: Optional[TestDataResolver] = None,
		):
		assert tool_id

		@@ -155,7 +157,14 @@ def stage_data_in_history(
		test_data=test_data, tool_id=tool_id, force_path_paste=force_path_paste, tool_version=tool_version
		)
		job[test_data["fname"]] = test_dict
		staging_interface.stage("tool", history_id=history, job=job, use_path_paste=force_path_paste)
		resolve_data = test_data_resolver.get_filename if test_data_resolver else None
		staging_interface.stage(
		"tool",
		history_id=history,
		job=job,
		use_path_paste=force_path_paste,
		resolve_data=resolve_data,
		)
		galaxy_interactor.uploads = job
		return

		@@ -1312,6 +1321,7 @@ def verify_tool(
		skip_with_reference_data: bool = False,
		skip_on_dynamic_param_errors: bool = False,
		_tool_test_dicts: Optional[List[ToolTestDescriptionDict]] = None, # extension point only for tests
		test_data_resolver: Optional[TestDataResolver] = None,
		):
		if resource_parameters is None:
		resource_parameters = {}
		@@ -1382,6 +1392,7 @@ def verify_tool(
		force_path_paste=force_path_paste,
		maxseconds=maxseconds,
		tool_version=tool_version,
		test_data_resolver=test_data_resolver,
		)
		except Exception as e:
		input_staging_exception = e

lib/galaxy_test/base/populators.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -3434,6 +3434,7 @@ def stage_inputs(
		job=job,
		use_path_paste=use_path_paste,
		to_posix_lines=to_posix_lines,
		resolve_data=galaxy_interactor._find_in_test_data_directories,
		**kwds,
		)

lib/galaxy_test/driver/driver_util.py

+2 −0

Original line number	Diff line number	Diff line
		@@ -34,6 +34,7 @@ from galaxy.tool_util.verify.interactor import (
		GalaxyInteractorApi,
		verify_tool,
		)
		from galaxy.tool_util.verify.test_data import TestDataResolver
		from galaxy.util import (
		asbool,
		download_to_file,
		@@ -965,6 +966,7 @@ class GalaxyTestDriver(TestDriver):
		test_index=index,
		galaxy_interactor=galaxy_interactor,
		resource_parameters=resource_parameters,
		test_data_resolver=TestDataResolver(),
		**kwd,
		)

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