def main(argsl=None):
if not argsl:
argsl = sys.argv[1:]
parser = get_parser()
args = parser.parse_args(argsl)
logger.debug("command:{}".format(args.command))
if args.command == 'tool':
logger.debug("subtool names:{}".format(args.subtool_names))
add_tool(args.tool_name,
args.version_name,
subtool_names=args.subtool_names,
biotools_id=args.biotoolsID,
has_primary=args.has_primary,
init_cwl=args.init_cwl,
init_wdl=args.init_wdl,
init_sm=args.init_sm,
init_nf=args.init_nf,
root_repo_path=args.root_path,
refresh_index=args.refresh_index,
no_clobber=args.no_clobber)
elif args.command == 'subtool':
add_subtool(args.tool_name,
args.version_name,
args.subtool_name,
update_featureList=args.update_featureList,
init_cwl=args.init_cwl,
init_wdl=args.init_wdl,
init_sm=args.init_sm,
init_nf=args.init_nf,
root_repo_path=args.root_path,
no_clobber=args.no_clobber)
elif args.command == 'tool-instance':
add_tool_instance(args.tool_name,
args.version_name,
args.subtool_name,
root_repo_path=args.root_path)
elif args.command == 'common-script':
add_common_script_metadata(args.group_name,
args.project_name,
args.script_version,
args.filename,
root_repo_path=args.root_path)
elif args.command == 'script':
add_script(args.group_name,
args.project_name,
args.script_version,
args.script_name,
parentMetadata=args.parent_metadata,
init_cwl=args.init_cwl,
root_repo_path=args.root_path)
elif args.command == 'script-instance':
raise NotImplementedError
elif args.command == 'workflow':
print(add_workflow.__name__)
add_workflow(args.group_name, args.workflow_name,
args.workflow_version)
else:
parser.print_help()
return
def test_add_with_main(self):
with TemporaryDirectory() as tmp_dir:
self.make_empty_tools_index(tmp_dir)
tool_name = 'test___2'
tool_version = '123'
add_tool(tool_name, tool_version, has_primary=True, root_repo_path=tmp_dir, refresh_index=False)
return
def test_add_with_subtools(self):
with TemporaryDirectory() as tmp_dir:
self.make_empty_tools_index(tmp_dir)
tool_name = 'test___3'
tool_version = '123'
add_tool(tool_name, tool_version, subtool_names=['first', 'second'], has_primary=True, root_repo_path=tmp_dir, refresh_index=False)
assert True
return
def test_add_parent_then_subtool(self):
with TemporaryDirectory() as tmp_dir:
self.make_empty_tools_index(tmp_dir)
tool_name = 'test_tool'
tool_version = '0.1'
add_tool(tool_name, tool_version, root_repo_path=tmp_dir, refresh_index=False)
add_subtool(tool_name, tool_version, 'subtool1', root_repo_path=tmp_dir, update_featureList=True)
assert True
return
def test_add_with_main(self):
with TemporaryDirectory() as tmp_dir:
tool_name = 'test___2'
tool_version = '123'
add_tool(tool_name,
tool_version,
has_primary=True,
root_repo_path=tmp_dir)
return
def test_make_file(self):
with TemporaryDirectory(prefix="xD_test") as tmpdir:
self.make_empty_tools_index(tmpdir)
add_tool('test1',
'1.0',
'subtool1',
root_repo_path=tmpdir,
refresh_index=False)
assert True
return
def test_add_with_subtools(self):
with TemporaryDirectory() as tmp_dir:
tool_name = 'test___3'
tool_version = '123'
add_tool(tool_name,
tool_version,
subtool_names=['first', 'second'],
has_primary=True,
root_repo_path=tmp_dir)
return
def test_add_parent_then_subtool(self):
with TemporaryDirectory() as tmp_dir:
tool_name = 'test_tool'
tool_version = '0.1'
add_tool(tool_name, tool_version, root_repo_path=tmp_dir)
add_subtool(tool_name,
tool_version,
'subtool1',
root_repo_path=tmp_dir,
update_featureList=True)
assert True
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_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 main(argsl=None):
if not argsl:
argsl = sys.argv[1:]
parser = get_parser()
args = parser.parse_args(argsl)
if args.command == 'tool':
add_tool(args.tool_name,
args.version_name,
subtool_names=args.subtool_names,
biotools_id=args.biotoolsID,
has_primary=args.has_primary,
init_cwl=args.init_cwl,
root_repo_path=args.root_path)
elif args.command == 'subtool':
add_subtool(args.tool_name,
args.version_name,
args.subtool_name,
update_featureList=args.update_featureList,
init_cwl=args.init_cwl,
root_repo_path=args.root_path)
elif args.command == 'common_script':
add_common_script_metadata(args.group_name,
args.project_name,
args.script_version,
args.filename,
root_repo_path=args.root_path)
elif args.command == 'script':
add_script(args.group_name,
args.project_name,
args.script_version,
args.script_name,
parentMetadata=args.parent_metadata,
init_cwl=args.init_cwl,
root_repo_path=args.root_path)
elif args.command == 'workflow':
add_workflow(args.group_name, args.workflow_name,
args.workflow_version)
else:
parser.print_help()
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_multiple(self):
with TemporaryDirectory() as tmp_dir:
self.make_empty_tools_index(tmp_dir)
add_tool('fake_1', '123', root_repo_path=tmp_dir, refresh_index=False) # parent only. Don't try to assemble index. Paths it would need to access aren't there yet.
add_tool('fake_2', '123', has_primary=True, root_repo_path=tmp_dir) # # parent with main tool
add_tool('fake_3', '123', subtool_names=['first', 'second'], has_primary=True,
root_repo_path=tmp_dir)
assert True
return
def test_add_multiple(self):
with TemporaryDirectory() as tmp_dir:
add_tool('fake_1', '123', root_repo_path=tmp_dir) # parent only.
add_tool('fake_2', '123', has_primary=True,
root_repo_path=tmp_dir) # # parent with main tool
add_tool('fake_3',
'123',
subtool_names=['first', 'second'],
has_primary=True,
root_repo_path=tmp_dir)
assert True
return
def test_add_parent_only(self):
with TemporaryDirectory(prefix='dont_see me_') as tmp_dir:
tool_name = 'test__1'
tool_version = '123'
add_tool(tool_name, tool_version, root_repo_path=tmp_dir)
return
def test_make_file(self):
with TemporaryDirectory(prefix="xD_test") as tmpdir:
add_tool('test1', '1.0', 'subtool1', root_repo_path=tmpdir)
assert True
return