import ruamel.yaml as yaml
-from .runner import upload_dependencies, packed_workflow, upload_workflow_collection, trim_anonymous_location, remove_redundant_fields
+from .runner import (upload_dependencies, packed_workflow, upload_workflow_collection,
+ trim_anonymous_location, remove_redundant_fields, discover_secondary_files)
from .pathmapper import ArvPathMapper, trim_listing
from .arvtool import ArvadosCommandTool
from .perf import Perf
metrics = logging.getLogger('arvados.cwl-runner.metrics')
def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
- submit_runner_ram=0, name=None):
+ submit_runner_ram=0, name=None, merged_map=None):
- packed = packed_workflow(arvRunner, tool)
+ packed = packed_workflow(arvRunner, tool, merged_map)
adjustDirObjs(job_order, trim_listing)
adjustFileObjs(job_order, trim_anonymous_location)
raise WorkflowException("%s object must have 'id'" % (self.tool["class"]))
document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
+ discover_secondary_files(self.tool["inputs"], joborder)
+
with Perf(metrics, "subworkflow upload_deps"):
upload_dependencies(self.arvrunner,
os.path.basename(joborder.get("id", "#")),
"inputs": self.tool["inputs"],
"outputs": self.tool["outputs"],
"stdout": "cwl.output.json",
- "requirements": workflowobj["requirements"]+[
+ "requirements": self.requirements+[
{
"class": "InitialWorkDirRequirement",
"listing": [{
"entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
- "hints": workflowobj["hints"],
- "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"]
+ "hints": self.hints,
+ "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
+ "id": "#"
})
kwargs["loader"] = self.doc_loader
kwargs["avsc_names"] = self.doc_schema