def test_add_tool(self):
with TemporaryDirectory(prefix='test_add_tool_') as tmp_dir:
tool_name = 'test_1'
tool_version = 'fake.1'
add_content_main([
'-p', tmp_dir, 'tool', tool_name, tool_version, "--has_primary"
])
return
def test_add_tool_with_subtools(self):
with TemporaryDirectory(prefix='test_add_w_subtools_') as tmp_dir:
tool_name = 'test_2'
tool_version = 'fake.2'
subtools = ['subtool1', 'subtool2', 'subtool3']
add_content_main(['-p', tmp_dir, 'tool', tool_name, tool_version] +
subtools)
return
def test_add_tool_with_biotools_id(self):
with TemporaryDirectory(prefix='with_biotools_') as tmp_dir:
tool_name = 'test_biotools'
tool_version = 'fake.3'
biotools_id = 'malvirus'
subtools = ['subtool1', 'subtool2', 'subtool3']
options = ['--biotoolsID', biotools_id]
add_content_main(['-p', tmp_dir, 'tool', tool_name, tool_version] +
subtools + options)
return
def test_add_tool(self):
with TemporaryDirectory(prefix='test_add_tool_') as tmp_dir:
self.make_empty_tools_index(tmp_dir)
tool_name = 'test_1'
tool_version = 'fake.1'
add_content_main([
'--no-refresh-index', '-p', tmp_dir, 'tool', tool_name,
tool_version, "--has-primary"
])
return
def test_add_script(self):
with TemporaryDirectory() as tmp_dir:
group_name = 'test_group2'
project_name = 'fake_project_2'
script_name = 'new_script_2'
script_version = '2.nope'
add_content_main([
'-p', tmp_dir, 'script', group_name, project_name,
script_version, script_name
])
return
def test_add_common_script(self):
with TemporaryDirectory() as tmp_dir:
group_name = 'test_group1'
project_name = 'fake_project_1'
script_version = '1.nope'
file_name = "some_filename"
add_content_main([
'-p', tmp_dir, 'common_script', group_name, project_name,
script_version, file_name
])
return
def test_add_subtool(self):
with TemporaryDirectory(prefix='add_subtool_') as tmp_dir:
tool_name = 'test_4'
tool_version = 'fake.4'
subtool_name = 'new_subtool'
add_content_main(['-p', tmp_dir, 'tool', tool_name, tool_version])
add_content_main([
'-p', tmp_dir, 'subtool', tool_name, tool_version,
subtool_name, '-u'
])
return
def test_add_tool_with_subtools(self):
with TemporaryDirectory(prefix='test_add_w_subtools_') as tmp_dir:
self.make_empty_tools_index(tmp_dir)
tool_name = 'test_2'
tool_version = 'fake.2'
subtools = ['subtool1', 'subtool2', 'subtool3']
add_content_main([
'--no-refresh-index', '-p', tmp_dir, 'tool', tool_name,
tool_version
] + subtools)
return
def test_add_tool_with_subtools_with_init_url_main_only(self):
cwl_url = 'https://raw.githubusercontent.com/common-workflow-library/bio-cwl-tools/release/bandage/bandage-image.cwl'
tool_name = 'test_biotools'
tool_version = 'fake.3'
biotools_id = 'malvirus'
options = ['--biotoolsID', biotools_id, '--has-primary']
init_cwl = ['--init-cwl', cwl_url]
with TemporaryDirectory(prefix='add_with_url') as tmp_dir:
self.make_empty_tools_index(tmp_dir)
add_content_main([
'--no-refresh-index', '-p', tmp_dir, 'tool', tool_name,
tool_version
] + options + init_cwl)
def test_add_tool_instance_main(self):
tool_name = 'cat'
tool_version = '8.x'
tool_directory = get_main_tool_dir(tool_name,
base_dir=self.test_content_dir)
with TemporaryDirectory() as tmp_dir:
self.make_empty_tools_index(
tmp_dir, add_identifiers=['TL_d077f2.47', 'TL_d077f2_54.47'])
tool_temp_path = Path(tmp_dir) / tools_dir_name / tool_name
copytree(tool_directory, tool_temp_path)
add_content_main(
['-p', tmp_dir, 'tool-instance', tool_name, tool_version])
assert True # Just provides a place for a breakpoint to take a look.at tmp_dir
return
def test_add_subtool(self):
with TemporaryDirectory(prefix='add_subtool_') as tmp_dir:
self.make_empty_tools_index(tmp_dir)
tool_name = 'test_4'
tool_version = 'fake.4'
subtool_name = 'new_subtool'
add_content_main([
'--no-refresh-index', '-p', tmp_dir, 'tool', tool_name,
tool_version
])
add_content_main([
'-p', tmp_dir, 'subtool', tool_name, tool_version,
subtool_name, '-u'
])
return
def test_add_tool_with_wdl_url(self):
wdl_url = 'https://github.com/broadinstitute/warp/raw/develop/tasks/skylab/CreateCountMatrix.wdl'
tool_name = 'who_cares'
tool_version = 'fake.fake'
subtool_name = 'test_wdl_subtool'
with TemporaryDirectory(prefix='add_tool_with_wdl') as tmp_dir:
self.make_empty_tools_index(tmp_dir)
add_content_main([
'--no-refresh-index', '-p', tmp_dir, 'tool', tool_name,
tool_version
])
add_content_main([
'-p', tmp_dir, 'subtool', tool_name, tool_version,
subtool_name, '-u', '--init-wdl', wdl_url
])
assert True
return
def test_add_tool_instance(self):
tool_name = 'STAR'
tool_version = '2.5'
subtool_name = 'alignReads'
tool_directory = get_main_tool_dir(tool_name,
base_dir=self.test_content_dir)
with TemporaryDirectory() as tmp_dir:
self.make_empty_tools_index(
tmp_dir, add_identifiers=['TL_8ab263.82', 'TL_8ab263_a4.82'])
tool_temp_path = Path(tmp_dir) / tools_dir_name / tool_name
copytree(tool_directory, tool_temp_path)
add_content_main([
'-p', tmp_dir, 'tool-instance', tool_name, tool_version,
subtool_name
])
assert True # Just provides a place for a breakpoint to take a look.at tmp_dir
return
def test_add_tool_with_existing_cwl_url(self):
cwl_url = 'https://raw.githubusercontent.com/common-workflow-library/bio-cwl-tools/release/bandage/bandage-image.cwl'
biotools_id = 'bandage'
tool_name = 'bandage'
tool_version = 'fake.6'
subtool_name = 'image'
with TemporaryDirectory(prefix='add_tool_with_cwl_') as tmp_dir:
add_content_main([
'-p', tmp_dir, 'tool', tool_name, tool_version, '--biotoolsID',
biotools_id
])
add_content_main([
'-p', tmp_dir, 'subtool', tool_name, tool_version,
subtool_name, '-u', '--init_cwl', cwl_url
])
assert True
return