def make_group_workflow_map(group_name, base_dir=None):
group_workflow_map = {}
workflow_group_dir = get_workflow_group_dir(group_name, base_dir)
for project_dir in workflow_group_dir.iterdir():
workflow_project_map = make_project_workflow_map(
group_name, project_dir.name, base_dir)
no_clobber_update(group_workflow_map, workflow_project_map)
return group_workflow_map
def combine_yaml_files_into_dict(file_path, *file_paths):
# make a 'master map' that contains all file
combined_dict = {}
with file_path.open('r') as f:
no_clobber_update(combined_dict, safe_load(f))
for file in file_paths:
with file.open('r') as f:
no_clobber_update(combined_dict, safe_load(f))
return combined_dict
def make_project_workflow_map(group_name, project_name, base_dir=None):
workflow_project_map = {}
workflow_project_dir = get_workflow_project_dir(group_name, project_name,
base_dir)
for version_dir in workflow_project_dir.iterdir():
version_map = make_workflow_map(group_name, project_name,
version_dir.name, base_dir)
no_clobber_update(workflow_project_map, version_map)
return workflow_project_map
def make_group_script_map(group_name, base_dir=None):
group_script_map = {}
script_group_dir = get_script_group_dir(group_name, base_dir=base_dir)
for project_dir in script_group_dir.iterdir():
script_project_map = make_project_script_map(group_name,
project_dir.name,
base_dir=base_dir)
no_clobber_update(group_script_map, script_project_map)
return group_script_map
def make_scripts_map_dict(base_dir=None):
scripts_dir = get_root_scripts_dir(base_dir=base_dir)
scripts_map = {}
for group_dir in scripts_dir.iterdir():
group_script_map = make_group_script_map(group_dir.name,
base_dir=base_dir)
no_clobber_update(scripts_map, group_script_map)
return scripts_map
def make_project_script_map(group_name, project_name, base_dir=None):
script_project_map = {}
script_project_dir = get_script_project_dir(group_name,
project_name,
base_dir=base_dir)
for version_dir in script_project_dir.iterdir():
version_map = make_script_version_map(group_name,
project_name,
version_dir.name,
base_dir=base_dir)
no_clobber_update(script_project_map, version_map)
return script_project_map
def make_main_tool_map(tool_name, base_dir=None):
"""
Make a yaml file that specifies paths and attributes of tools in a single tool directory. If outfile is provided, dump contents to outfile.
"""
main_tool_map = {}
tool_dir = get_main_tool_dir(tool_name, base_dir=base_dir)
for version_dir in tool_dir.iterdir():
no_clobber_update(
main_tool_map,
make_tool_version_dir_map(tool_name,
version_dir.name,
base_dir=base_dir))
return main_tool_map
def make_tools_map_dict(base_dir=None, specify_exists=False):
tools_dir = get_root_tools_dir(base_dir=base_dir)
tools_map = {}
for tool_dir in tools_dir.iterdir():
if tool_dir.name == '.DS_Store':
continue
assert tool_dir.is_dir()
for version_dir in tool_dir.iterdir():
if version_dir.name == '.DS_Store':
continue
assert version_dir.is_dir()
tool_map = make_tool_version_dir_map(tool_dir.name,
version_dir.name,
base_dir=base_dir,
specify_exists=specify_exists)
no_clobber_update(tools_map, tool_map)
return tools_map
def make_script_version_map(group_name,
project_name,
version_name,
base_dir=None):
script_version_map = {}
script_version_dir = get_script_version_dir(group_name,
project_name,
version_name,
base_dir=base_dir)
for script_dir in script_version_dir.iterdir():
if script_dir.name == 'common':
continue
script_map = make_script_map(group_name,
project_name,
version_name,
script_dir.name,
base_dir=base_dir)
no_clobber_update(script_version_map, script_map)
return script_version_map
def make_tool_version_dir_map(tool_name,
tool_version,
base_dir=None,
specify_exists=False):
tool_version_map = {}
tool_version_dir = get_tool_version_dir(tool_name,
tool_version,
base_dir=base_dir)
parent_metadata_path = get_tool_metadata(tool_name,
tool_version,
parent=True,
base_dir=base_dir)
parent_metadata = ParentToolMetadata.load_from_file(parent_metadata_path,
check_index=False)
parent_rel_path = get_relative_path(parent_metadata_path,
base_path=base_dir)
tool_version_map[parent_metadata.identifier] = {
'metadataPath': str(parent_rel_path),
'metadataStatus': parent_metadata.metadataStatus,
'name': parent_metadata.name,
'versionName': parent_metadata.softwareVersion.versionName,
'type': 'parent'
}
for subtool_dir in tool_version_dir.iterdir():
if subtool_dir.name in ['.DS_Store', 'common']:
continue
assert subtool_dir.is_dir(
), subtool_dir.name + " is not a directory. You likely have an extra file."
tool_name_length = len(
tool_name
) # Use to get directory name string after 'tool_name'. In case there are underscores in tool_name.
subtool_name = subtool_dir.name[tool_name_length + 1:]
if subtool_name == '':
subtool_name = None
subdir_map = make_subtool_map(tool_name,
tool_version,
subtool_name,
base_dir=base_dir,
specify_exists=specify_exists)
no_clobber_update(tool_version_map, subdir_map)
return tool_version_map
def make_workflow_maps_dict(base_dir=None):
workflows_dir = get_workflows_root_dir(base_dir=base_dir)
master_workflow_map = {}
for group_dir in workflows_dir.iterdir():
if group_dir.name == '.DS_Store':
continue
assert group_dir.is_dir()
for project_dir in group_dir.iterdir():
if project_dir.name == '.DS_Store':
continue
assert project_dir.is_dir()
for version_dir in project_dir.iterdir():
if version_dir.name == '.DS_Store':
continue
assert version_dir.is_dir()
workflow_dict = make_workflow_map(group_dir.name,
project_dir.name,
version_dir.name,
base_dir=base_dir)
no_clobber_update(master_workflow_map, workflow_dict)
return master_workflow_map
def test_no_clobber_update_fail(self):
with self.assertRaises(ValueError):
no_clobber_update(test_dict_1, test_dict_2)
return
def test_no_clobber_update(self):
updated_dict = no_clobber_update(test_dict_1, test_dict_2)
self.assertEqual(updated_dict, test_dict_1.update(test_dict_2))
return
