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
-from .runner import upload_dependencies, packed_workflow, upload_workflow_collection, trim_anonymous_location, remove_redundant_fields
-from .pathmapper import trim_listing
+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
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."""
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", "#")),
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,
False)
with Perf(metrics, "subworkflow adjust"):
+ joborder_resolved = copy.deepcopy(joborder)
joborder_keepmount = copy.deepcopy(joborder)
+ reffiles = []
+ visit_class(joborder_keepmount, ("File", "Directory"), lambda x: reffiles.append(x))
+
+ mapper = ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
+ "/keep/%s",
+ "/keep/%s/%s",
+ **kwargs)
+
def keepmount(obj):
remove_redundant_fields(obj)
with SourceLine(obj, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
with SourceLine(obj, "location", WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if obj["location"].startswith("keep:"):
- obj["location"] = "/keep/" + obj["location"][5:]
+ obj["location"] = mapper.mapper(obj["location"]).target
if "listing" in obj:
del obj["listing"]
elif obj["location"].startswith("_:"):
visit_class(joborder_keepmount, ("File", "Directory"), keepmount)
+ def resolved(obj):
+ if obj["location"].startswith("keep:"):
+ obj["location"] = mapper.mapper(obj["location"]).resolved
+
+ visit_class(joborder_resolved, ("File", "Directory"), resolved)
+
if self.wf_pdh is None:
adjustFileObjs(packed, keepmount)
adjustDirObjs(packed, keepmount)
"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
- return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder, output_callback, **kwargs)
+ return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder_resolved, output_callback, **kwargs)
else:
return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)
projects / arvados.git / blobdiff