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
logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
+max_res_pars = ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax")
+sum_res_pars = ("outdirMin", "outdirMax")
+
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)
dedup[r["class"]] = r
return [dedup[r] for r in sorted(dedup.keys())]
+def get_overall_res_req(res_reqs):
+ """Take the overall of a list of ResourceRequirement,
+ i.e., the max of coresMin, coresMax, ramMin, ramMax, tmpdirMin, tmpdirMax
+ and the sum of outdirMin, outdirMax."""
+
+ all_res_req = {}
+ exception_msgs = []
+ for a in max_res_pars + sum_res_pars:
+ all_res_req[a] = []
+ for res_req in res_reqs:
+ if a in res_req:
+ if isinstance(res_req[a], int): # integer check
+ all_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:
+ overall_res_req = {}
+ for a in all_res_req:
+ if all_res_req[a]:
+ if a in max_res_pars:
+ overall_res_req[a] = max(all_res_req[a])
+ elif a in sum_res_pars:
+ overall_res_req[a] = sum(all_res_req[a])
+ if overall_res_req:
+ overall_res_req["class"] = "ResourceRequirement"
+ return cmap(overall_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 = workflowobj["requirements"]
+ builder.hints = workflowobj["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 max_res_pars + sum_res_pars:
+ 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)
+ overall_res_req = {"requirements": get_overall_res_req(res_reqs["requirements"]),
+ "hints": get_overall_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 overall_res_req[t]:
+ new_spec[t].append(overall_res_req[t])
+
upload_dependencies(self.arvrunner,
kwargs.get("name", ""),
document_loader,