from cwltool.process import shortname
from cwltool.workflow import Workflow, WorkflowException
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
+from cwltool.builder import Builder
import ruamel.yaml as yaml
dedup[r["class"]] = r
return [dedup[r] for r in sorted(dedup.keys())]
+def get_max_res_req(res_reqs):
+ """Take the max of a list of ResourceRequirement."""
+
+ total_res_req = {}
+ exception_msgs = []
+ for a in ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax"):
+ total_res_req[a] = []
+ for res_req in res_reqs:
+ if a in res_req:
+ if isinstance(res_req[a], int): # integer check
+ total_res_req[a].append(res_req[a])
+ else:
+ msg = SourceLine(res_req).makeError(
+ "Non-top-level ResourceRequirement in single container cannot have expressions")
+ exception_msgs.append(msg)
+ if exception_msgs:
+ raise WorkflowException("\n".join(exception_msgs))
+ else:
+ max_res_req = {}
+ for a in total_res_req:
+ if total_res_req[a]:
+ max_res_req[a] = max(total_res_req[a])
+ if max_res_req:
+ max_res_req["class"] = "ResourceRequirement"
+ return cmap(max_res_req)
+
class ArvadosWorkflow(Workflow):
"""Wrap cwltool Workflow to override selected methods."""
packed = pack(document_loader, workflowobj, uri, self.metadata)
+ builder = Builder()
+ builder.job = joborder
+ builder.requirements = self.requirements
+ builder.hints = self.hints
+ builder.resources = {}
+
+ res_reqs = {"requirements": [], "hints": []}
+ for t in ("requirements", "hints"):
+ for item in packed["$graph"]:
+ if t in item:
+ if item["id"] == "#main": # evaluate potential expressions in the top-level requirements/hints
+ for req in item[t]:
+ if req["class"] == "ResourceRequirement":
+ eval_req = {"class": "ResourceRequirement"}
+ for a in ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax"):
+ if a in req:
+ eval_req[a] = builder.do_eval(req[a])
+ res_reqs[t].append(eval_req)
+ else:
+ for req in item[t]:
+ if req["class"] == "ResourceRequirement":
+ res_reqs[t].append(req)
+ max_res_req = {"requirements": get_max_res_req(res_reqs["requirements"]),
+ "hints": get_max_res_req(res_reqs["hints"])}
+
+ new_spec = {"requirements": self.requirements, "hints": self.hints}
+ for t in ("requirements", "hints"):
+ for req in new_spec[t]:
+ if req["class"] == "ResourceRequirement":
+ new_spec[t].remove(req)
+ if max_res_req[t]:
+ new_spec[t].append(max_res_req[t])
+
upload_dependencies(self.arvrunner,
kwargs.get("name", ""),
document_loader,
"inputs": self.tool["inputs"],
"outputs": self.tool["outputs"],
"stdout": "cwl.output.json",
- "requirements": self.requirements+[
+ "requirements": new_spec["requirements"]+[
{
"class": "InitialWorkDirRequirement",
"listing": [{
"entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
- "hints": self.hints,
+ "hints": new_spec["hints"],
"arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
"id": "#"
})