def update_existing_tool_wrapper_status(tool_map_values,
base_dir=None,
update_dir=None):
base_dir = get_base_dir(base_dir=base_dir)
metadata_path = Path(base_dir) / tool_map_values['metadataPath']
subtool_metadata = SubtoolMetadata.load_from_file(metadata_path)
if tool_map_values['cwlStatus'] in unpublished_statuses and tool_map_values[
'cwlExists'] == True:
subtool_metadata.cwlStatus = 'Released'
if tool_map_values['wdlStatus'] in unpublished_statuses and tool_map_values[
'wdlExists'] == True:
subtool_metadata.wdlStatus = 'Released'
if tool_map_values[
'nextflowStatus'] in unpublished_statuses and tool_map_values[
'nextflowExists'] == True:
subtool_metadata.nextflowStatus = 'Released'
if tool_map_values[
'snakemakeStatus'] in unpublished_statuses and tool_map_values[
'snakemakeExists'] == True:
subtool_metadata.snakemakeStatus = 'Released'
if update_dir == None or base_dir == update_dir: # Need to overwrite the existing file.
subtool_metadata.mk_file()
else:
# updated_path = Path(update_dir) / tool_map_values['metadataPath']
subtool_metadata.root_repo_path = update_dir
subtool_metadata.mk_file()
return
def add_tool_instance(tool_name,
tool_version,
subtool_name,
init_job_file=True,
root_repo_path=Path.cwd()):
subtool_path = get_tool_metadata(tool_name,
tool_version,
subtool_name,
base_dir=root_repo_path)
subtool_metadata = SubtoolMetadata.load_from_file(
subtool_path, root_repo_path=root_repo_path, _in_index=True)
instance_meta = subtool_metadata.mk_instance()
instance_metadata_path = instance_meta.mk_file(base_dir=root_repo_path)
input_hash = instance_meta.identifier[-4:]
job_file_path = None
if init_job_file:
tool_sources = get_tool_sources(tool_name,
tool_version,
subtool_name,
base_dir=root_repo_path)
job_file_path = get_tool_instance_path(tool_name,
tool_version,
input_hash=input_hash,
subtool_name=subtool_name,
base_dir=root_repo_path)
tool_inputs_schema = InputsSchema(tool_sources['cwl'])
tool_inputs_schema.make_template_file(job_file_path)
return instance_metadata_path, job_file_path
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_make_subtool_metadata(self):
p_metadata = ParentToolMetadata(
name=TestMakeParentToolMetadata.test_dict['name'],
softwareVersion=test_constants['test_software_version'],
featureList=['subtool_name'])
st_metadata = SubtoolMetadata(
name=TestMakeSubtoolMetadata.test_dict['name'],
_parentMetadata=p_metadata)
self.assertTrue(
st_metadata.name == TestMakeSubtoolMetadata.test_dict['name'])
def make_subtool_map(tool_name, tool_version, subtool_name, base_dir=None):
subtool_cwl_path = get_cwl_tool(tool_name, tool_version, subtool_name=subtool_name, base_dir=base_dir)
subtool_rel_path = get_relative_path(subtool_cwl_path, base_path=base_dir)
subtool_metadata_path = get_tool_metadata(tool_name, tool_version, subtool_name=subtool_name, parent=False,
base_dir=base_dir)
subtool_metadata = SubtoolMetadata.load_from_file(subtool_metadata_path)
subdir_map = {}
subdir_map[subtool_metadata.identifier] = {'path': str(subtool_rel_path), 'name': subtool_metadata.name,
'metadataStatus': subtool_metadata.metadataStatus,
'cwlStatus': subtool_metadata.cwlStatus, 'type': 'subtool'}
return subdir_map
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_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 make_subtool_map(tool_name,
tool_version,
subtool_name,
base_dir=None,
specify_exists=False):
subtool_metadata_path = get_tool_metadata(tool_name,
tool_version,
subtool_name=subtool_name,
parent=False,
base_dir=base_dir)
subtool_metadata = SubtoolMetadata.load_from_file(subtool_metadata_path,
check_index=False)
subdir_map = {}
subtool_rel_path = get_relative_path(subtool_metadata_path,
base_path=base_dir)
if specify_exists:
files_exist = check_for_workflow_language_files(subtool_metadata_path)
subdir_map[subtool_metadata.identifier] = {
'metadataPath': str(subtool_rel_path),
'name': subtool_metadata.name,
'metadataStatus': subtool_metadata.metadataStatus,
'cwlStatus': subtool_metadata.cwlStatus,
'cwlExists': files_exist['cwl'],
'nextflowStatus': subtool_metadata.nextflowStatus,
'nextflowExists': files_exist['nextflow'],
'snakemakeStatus': subtool_metadata.snakemakeStatus,
'snakemakeExists': files_exist['snakemake'],
'wdlStatus': subtool_metadata.wdlStatus,
'wdlExists': files_exist['wdl'],
'type': 'subtool'
}
else:
subdir_map[subtool_metadata.identifier] = {
'metadataPath': str(subtool_rel_path),
'name': subtool_metadata.name,
'metadataStatus': subtool_metadata.metadataStatus,
'cwlStatus': subtool_metadata.cwlStatus,
'nextflowStatus': subtool_metadata.nextflowStatus,
'snakemakeStatus': subtool_metadata.snakemakeStatus,
'wdlStatus': subtool_metadata.wdlStatus,
'type': 'subtool'
}
return subdir_map