from functools import partial
import logging
import json
-import re
import subprocess
from StringIO import StringIO
logger = logging.getLogger('arvados.cwl-runner')
-cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r".*")
-
def trim_listing(obj):
"""Remove 'listing' field from Directory objects that are keep references.
def upload_docker(arvrunner, tool):
- """Visitor which uploads Docker images referenced in CommandLineTool objects."""
+ """Uploads Docker images used in CommandLineTool objects."""
+
if isinstance(tool, CommandLineTool):
(docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
if docker_req:
raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
"Option 'dockerOutputDirectory' of DockerRequirement not supported.")
arv_docker_get_image(arvrunner.api, docker_req, True, arvrunner.project_uuid)
+ elif isinstance(tool, cwltool.workflow.Workflow):
+ for s in tool.steps:
+ upload_docker(arvrunner, s.embedded_tool)
def packed_workflow(arvrunner, tool):
"""Create a packed workflow.
def upload_workflow_deps(arvrunner, tool):
# Ensure that Docker images needed by this workflow are available
- tool.visit(partial(upload_docker, arvrunner))
+
+ upload_docker(arvrunner, tool)
document_loader = tool.doc_loader