def test_validate_subtool_metadata(self):
validate_subtool_metadata = metadata_validator_factory(SubtoolMetadata)
metadata_path = get_tool_metadata('STAR',
'2.5',
subtool_name='alignReads')
validate_subtool_metadata(metadata_path)
return
def test_handle_duplicate_subtool_identifier_2(self):
"""
Add two subtools and parent with one command.
:return:
"""
tool_name = 'samtools'
tool_version = '1.x'
subtool_name = 'dict' # both subtool identifiers start with 'bb'
subtool_name_2 = 'faidx'
with TemporaryDirectory() as temp_dir:
self.make_empty_tools_index(temp_dir)
add_tool(tool_name, tool_version, [subtool_name, subtool_name_2], root_repo_path=temp_dir, refresh_index=False)
subtool_1_metadata_path = get_tool_metadata(tool_name, tool_version, subtool_name, base_dir=temp_dir)
subtool_2_metadata_path = get_tool_metadata(tool_name, tool_version, subtool_name_2, base_dir=temp_dir)
subtool_1_metadata = SubtoolMetadata.load_from_file(subtool_1_metadata_path)
subtool_2_metadata = SubtoolMetadata.load_from_file(subtool_2_metadata_path)
self.assertNotEqual(subtool_1_metadata.identifier, subtool_2_metadata.identifier)
return
def test_validate_parent_tool_metadata_fail(self):
validate_parent_metadata = metadata_validator_factory(
ParentToolMetadata)
metadata_path = get_tool_metadata('cat',
'8.x',
parent=True,
base_dir=self.invalid_content_dir)
with self.assertRaises(AttributeError):
validate_parent_metadata(metadata_path)
return
def test_make_file(self):
p_metadata = ParentToolMetadata(name=TestMakeParentToolMetadata.test_dict['name'], softwareVersion=test_constants['test_software_version'])
with TemporaryDirectory(prefix='xD_test1', suffix='') as tmpdir:
parent_metadata_path = get_tool_metadata(TestMakeParentToolMetadata.test_dict['name'], test_constants['test_software_version']['versionName'], parent=True, base_dir=tmpdir)
if not parent_metadata_path.exists():
parent_metadata_path.parent.mkdir(parents=True)
p_metadata.mk_file(base_dir=tmpdir, replace_none=True)
with parent_metadata_path.open('r') as file:
test_file_dict = safe_load(file)
self.assertEqual(test_file_dict['name'], TestMakeParentToolMetadata.test_dict['name'])
def test_validate_subtool_metadata_fail(self):
validate_subtool_metadata = metadata_validator_factory(SubtoolMetadata)
# metadata_path = Path.cwd() / 'tests/test_files/test_content/invalid_content/cwl-tools/samtools/1.9/samtools_view/samtools-view-metadata.yaml' # Works for now. # subtool name not in parent featurelist.
metadata_path = get_tool_metadata('samtools',
'1.x',
subtool_name='view',
base_dir=self.invalid_content_dir)
assert metadata_path.exists()
with self.assertRaises(ValueError):
validate_subtool_metadata(metadata_path)
return
def test_handle_duplicate_subtool_identifier(self):
"""
Add subtools one at a time.
:return:
"""
tool_name = 'samtools'
tool_version = '1.x'
subtool_name = 'dict' # both subtool identifiers start with 'bb'
subtool_name_2 = 'faidx'
with TemporaryDirectory() as temp_dir:
self.make_empty_tools_index(temp_dir)
add_tool(tool_name, tool_version, subtool_name, root_repo_path=temp_dir, refresh_index=False)
add_subtool(tool_name, tool_version, subtool_name_2, root_repo_path=temp_dir, update_featureList=True)
subtool_1_metadata_path = get_tool_metadata(tool_name, tool_version, subtool_name, base_dir=temp_dir)
subtool_2_metadata_path = get_tool_metadata(tool_name, tool_version, subtool_name_2, base_dir=temp_dir)
with self.assertRaises(InIndexError):
subtool_1_metadata = SubtoolMetadata.load_from_file(subtool_1_metadata_path, _in_index=False, root_repo_path=temp_dir)
subtool_1_metadata = SubtoolMetadata.load_from_file(subtool_1_metadata_path, _in_index=True, root_repo_path=temp_dir)
subtool_2_metadata = SubtoolMetadata.load_from_file(subtool_2_metadata_path, _in_index=True,
root_repo_path=temp_dir)
self.assertNotEqual(subtool_1_metadata.identifier, subtool_2_metadata.identifier)
return
def test_add_parent_only(self):
with TemporaryDirectory(prefix='dont_see me_') as tmp_dir:
self.make_empty_tools_index(tmp_dir)
tool_name = 'test__1'
tool_version = '123'
add_tool(tool_name, tool_version, root_repo_path=tmp_dir, refresh_index=False) # Index is not refreshed because there is nothing in the content repo. Will throw FileNotFound error when trying to traverse directories.
# the tool added should be the only identifier in the index.
parent_metadata_path = get_tool_metadata(tool_name, tool_version, parent=True, base_dir=tmp_dir)
with self.assertRaises(InIndexError): # This should fail because trying to assign identifier that is already uses (by itself).
parent_metadata = ParentToolMetadata.load_from_file(parent_metadata_path, _in_index=False,
root_repo_path=tmp_dir)
assert True
parent_metadata = ParentToolMetadata.load_from_file(parent_metadata_path, root_repo_path=tmp_dir) # this should succeed with the _in_index flag.
assert True
return
def test_make_file(self):
parent_tool_name = 'parentName'
subtool_name = 'subtoolName'
tool_version = 'test_version'
with TemporaryDirectory(prefix='tool_instance_metadata') as tmpdir:
self.make_empty_tools_dir(tmpdir)
add_content([
'-p', tmpdir, 'tool', parent_tool_name, tool_version,
subtool_name
])
subtool_path = get_tool_metadata(parent_tool_name,
tool_version,
subtool_name,
base_dir=tmpdir)
subtool_metadata = SubtoolMetadata.load_from_file(subtool_path)
subtool_instance = subtool_metadata.mk_instance()
subtool_instance.mk_file(base_dir=tmpdir)
return
def test_make_file(self):
with TemporaryDirectory(prefix='xD_test1', suffix='') as tmpdir:
p_metadata = ParentToolMetadata(
name=TestMakeParentToolMetadata.test_dict['name'],
softwareVersion=test_constants['test_software_version'],
check_index=False,
root_repo_path=tmpdir)
self.make_empty_tools_index(tmpdir)
parent_metadata_path = get_tool_metadata(
TestMakeParentToolMetadata.test_dict['name'],
test_constants['test_software_version']['versionName'],
parent=True,
base_dir=tmpdir)
if not parent_metadata_path.exists():
parent_metadata_path.parent.mkdir(parents=True)
p_metadata.mk_file(
base_dir=tmpdir, replace_none=True, update_index=True
) # Don't try to update an index file. There isn't one.
with parent_metadata_path.open('r') as file:
test_file_dict = safe_load(file)
self.assertEqual(test_file_dict['name'],
TestMakeParentToolMetadata.test_dict['name'])
def test_validate_parent_tool_metadata(self):
validate_parent_metadata = metadata_validator_factory(
ParentToolMetadata)
metadata_path = get_tool_metadata('STAR', '2.5', parent=True)
validate_parent_metadata(metadata_path)