from arvados.errors import ApiError
import arvados_cwl.util
-from .arvcontainer import RunnerContainer
+from .arvcontainer import RunnerContainer, cleanup_name_for_collection
from .runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, make_builder
from .arvtool import ArvadosCommandTool, validate_cluster_target, ArvadosExpressionTool
from .arvworkflow import ArvadosWorkflow, upload_workflow
loadingContext = self.loadingContext.copy()
loadingContext.do_validate = False
+ loadingContext.disable_js_validation = True
if submitting:
loadingContext.do_update = False
# Document may have been auto-updated. Reload the original
# Upload direct dependencies of workflow steps, get back mapping of files to keep references.
# Also uploads docker images.
+ logger.info("Uploading workflow dependencies")
merged_map = upload_workflow_deps(self, tool, runtimeContext)
# Recreate process object (ArvadosWorkflow or
if not self.output_name:
self.output_name = "Output from workflow %s" % runtimeContext.name
+ self.output_name = cleanup_name_for_collection(self.output_name)
+
if self.work_api == "containers":
if self.ignore_docker_for_reuse:
raise Exception("--ignore-docker-for-reuse not supported with containers API.")