def test_create_wf_include(test_data_dir, tmpdir, helpers):
wf_path = test_data_dir / 'test_galaxy_wf.ga'
extra_file1 = test_data_dir / 'test_file_galaxy.txt'
extra_file2 = test_data_dir / 'test_file_galaxy2.txt'
files_list = [extra_file1, extra_file2]
wf_crate = roc_api.make_workflow_rocrate(wf_path,
wf_type='Galaxy',
include_files=files_list)
assert isinstance(wf_crate, ROCrate)
out_path = tmpdir / 'ro_crate_out'
out_path.mkdir()
wf_crate.write_crate(out_path)
json_entities = helpers.read_json_entities(out_path)
helpers.check_wf_crate(json_entities, wf_path.name)
wf_out_path = out_path / wf_path.name
file1 = out_path / extra_file1.name
file2 = out_path / extra_file2.name
assert wf_out_path.exists()
with open(wf_path) as f1, open(wf_out_path) as f2:
assert f1.read() == f2.read()
assert file1.exists()
with open(extra_file1) as f1, open(file1) as f2:
assert f1.read() == f2.read()
assert file2.exists()
with open(extra_file2) as f1, open(file2) as f2:
assert f1.read() == f2.read()
def test_galaxy_wf_crate(test_data_dir, tmpdir, helpers):
wf_id = 'test_galaxy_wf.ga'
wf_path = test_data_dir / wf_id
wf_crate = roc_api.make_workflow_rocrate(wf_path, wf_type='Galaxy')
assert isinstance(wf_crate, ROCrate)
wf = wf_crate.dereference(wf_id)
assert wf._default_type == "ComputationalWorkflow"
assert wf_crate.mainEntity is wf
lang = wf_crate.dereference("#galaxy")
assert hasattr(lang, "name")
assert lang.version == GALAXY_DEFAULT_VERSION
assert wf["programmingLanguage"] is lang
assert wf["subjectOf"] is not None
assert helpers.WORKFLOW_TYPES.issubset(wf["subjectOf"].type)
out_path = tmpdir / 'ro_crate_out'
out_path.mkdir()
wf_crate.write_crate(out_path)
json_entities = helpers.read_json_entities(out_path)
helpers.check_wf_crate(json_entities, wf_id)
wf_entity = json_entities[wf_id]
assert "subjectOf" in wf_entity
abstract_wf_id = wf_entity["subjectOf"]["@id"]
abstract_wf_entity = json_entities[abstract_wf_id]
assert helpers.WORKFLOW_TYPES.issubset(abstract_wf_entity["@type"])
wf_out_path = out_path / wf_id
assert wf_out_path.exists()
with open(wf_path) as f1, open(wf_out_path) as f2:
assert f1.read() == f2.read()
abstract_wf_out_path = out_path / abstract_wf_id
assert abstract_wf_out_path.exists()
def test_create_wf_include(self):
wf_path = self.test_data_dir / 'test_galaxy_wf.ga'
extra_file1 = self.test_data_dir / 'test_file_galaxy.txt'
extra_file2 = self.test_data_dir / 'test_file_galaxy2.txt'
files_list = [extra_file1, extra_file2]
wc_crate = roc_api.make_workflow_rocrate(wf_path,
wf_type='Galaxy',
include_files=files_list)
self.assertIsInstance(wc_crate, ROCrate)
def test_cwl_wf_crate(test_data_dir, tmpdir, helpers):
wf_path = test_data_dir / 'sample_cwl_wf.cwl'
wf_crate = roc_api.make_workflow_rocrate(wf_path, wf_type='CWL')
assert isinstance(wf_crate, ROCrate)
out_path = tmpdir / 'ro_crate_out'
out_path.mkdir()
wf_crate.write_crate(out_path)
json_entities = helpers.read_json_entities(out_path)
helpers.check_wf_crate(json_entities, wf_path.name)
wf_out_path = out_path / wf_path.name
assert wf_out_path.exists()
with open(wf_path) as f1, open(wf_out_path) as f2:
assert f1.read() == f2.read()
def test_create_wf_include(test_data_dir, tmpdir, helpers):
wf_id = 'test_galaxy_wf.ga'
wf_path = test_data_dir / wf_id
extra_file1 = test_data_dir / 'test_file_galaxy.txt'
extra_file2 = test_data_dir / 'test_file_galaxy2.txt'
files_list = [extra_file1, extra_file2]
wf_crate = roc_api.make_workflow_rocrate(wf_path,
wf_type='Galaxy',
include_files=files_list)
assert isinstance(wf_crate, ROCrate)
wf = wf_crate.dereference(wf_id)
assert wf_crate.mainEntity is wf
lang = wf_crate.dereference("#galaxy")
assert hasattr(lang, "name")
assert lang.version == GALAXY_DEFAULT_VERSION
assert wf["programmingLanguage"] is lang
assert wf["subjectOf"] is not None
assert helpers.WORKFLOW_TYPES.issubset(wf["subjectOf"].type)
assert wf_crate.dereference(extra_file1.name) is not None
assert wf_crate.dereference(extra_file2.name) is not None
out_path = tmpdir / 'ro_crate_out'
out_path.mkdir()
wf_crate.write_crate(out_path)
json_entities = helpers.read_json_entities(out_path)
helpers.check_wf_crate(json_entities, wf_id)
wf_out_path = out_path / wf_id
file1 = out_path / extra_file1.name
file2 = out_path / extra_file2.name
assert wf_out_path.exists()
with open(wf_path) as f1, open(wf_out_path) as f2:
assert f1.read() == f2.read()
assert file1.exists()
with open(extra_file1) as f1, open(file1) as f2:
assert f1.read() == f2.read()
assert file2.exists()
with open(extra_file2) as f1, open(file2) as f2:
assert f1.read() == f2.read()
def test_galaxy_wf_crate(test_data_dir, tmpdir, helpers):
wf_path = test_data_dir / 'test_galaxy_wf.ga'
wf_crate = roc_api.make_workflow_rocrate(wf_path, wf_type='Galaxy')
assert isinstance(wf_crate, ROCrate)
out_path = tmpdir / 'ro_crate_out'
out_path.mkdir()
wf_crate.write_crate(out_path)
json_entities = helpers.read_json_entities(out_path)
helpers.check_wf_crate(json_entities, wf_path.name)
wf_entity = json_entities[wf_path.name]
assert "subjectOf" in wf_entity
abstract_wf_id = wf_entity["subjectOf"]["@id"]
abstract_wf_entity = json_entities[abstract_wf_id]
assert helpers.WORKFLOW_TYPES.issubset(abstract_wf_entity["@type"])
wf_out_path = out_path / wf_path.name
assert wf_out_path.exists()
with open(wf_path) as f1, open(wf_out_path) as f2:
assert f1.read() == f2.read()
abstract_wf_out_path = out_path / abstract_wf_id
assert abstract_wf_out_path.exists()
def test_cwl_wf_crate(test_data_dir, tmpdir, helpers):
wf_id = 'sample_cwl_wf.cwl'
wf_path = test_data_dir / wf_id
wf_crate = roc_api.make_workflow_rocrate(wf_path, wf_type='CWL')
assert isinstance(wf_crate, ROCrate)
wf = wf_crate.dereference(wf_id)
assert wf_crate.mainEntity is wf
lang = wf_crate.dereference("#cwl")
assert hasattr(lang, "name")
assert lang.version == CWL_DEFAULT_VERSION
assert wf["programmingLanguage"] is lang
assert wf["subjectOf"] is None
out_path = tmpdir / 'ro_crate_out'
out_path.mkdir()
wf_crate.write_crate(out_path)
json_entities = helpers.read_json_entities(out_path)
helpers.check_wf_crate(json_entities, wf_id)
wf_out_path = out_path / wf_id
assert wf_out_path.exists()
with open(wf_path) as f1, open(wf_out_path) as f2:
assert f1.read() == f2.read()
from rocrate.model.workflow import Workflow
from rocrate.model.file import File
from rocrate.model import entity
from rocrate.model import contextentity
import rocrate.rocrate as roc
with open('/data/docker/RO-crates/arguments.json') as f:
data = json.load(f)
wf_path = data['location']
files_list = []
Workflow.TYPES = ["File", "SoftwareSourceCode"]
wf_crate = rocrate_api.make_workflow_rocrate(workflow_path=wf_path,
wf_type="CWL",
include_files=files_list)
wf_crate.isBasedOn = data['software_url']
wf_crate.name = data['software_name']
wf_crate.description = data['software_description']
wf_crate.creator = data['creator']
print(data['image'])
wf_crate.image = data['image']
main_entity = entity.Entity(
wf_crate,
data['software_url'],
properties={
"@id":
data['software_url'],
def test_galaxy_wf_crate(self):
wf_path = self.test_data_dir / 'test_galaxy_wf.ga'
wc_crate = roc_api.make_workflow_rocrate(wf_path, wf_type='Galaxy')
self.assertIsInstance(wc_crate, ROCrate)
def test_cwl_wf_crate(self):
wf_path = self.test_data_dir / 'sample_cwl_wf.cwl'
wc_crate = roc_api.make_workflow_rocrate(wf_path, wf_type='CWL')
self.assertIsInstance(wc_crate, ROCrate)
