import ruamel.yaml as yaml
import arvados_cwl.arvdocker
-from .pathmapper import ArvPathMapper, trim_listing
+from .pathmapper import ArvPathMapper, trim_listing, collection_pdh_pattern, collection_uuid_pattern
from ._version import __version__
from . import done
from . context import ArvRuntimeContext
if isinstance(primary, (Mapping, Sequence)):
set_secondary(fsaccess, builder, inputschema, None, primary, discovered)
-collection_uuid_pattern = re.compile(r'^keep:([a-z0-9]{5}-4zz18-[a-z0-9]{15})(/.*)?$')
-collection_pdh_pattern = re.compile(r'^keep:([0-9a-f]{32}\+\d+)(/.*)?')
-
def upload_dependencies(arvrunner, name, document_loader,
workflowobj, uri, loadref_run,
include_primary=True, discovered_secondaryfiles=None):
builder_job_order,
discovered)
- visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
+ copied, _ = document_loader.resolve_all(copy.deepcopy(cmap(workflowobj)), base_url=uri, checklinks=False)
+ visit_class(copied, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
for d in list(discovered):
# Only interested in discovered secondaryFiles which are local