X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/925a1526383299a1ade38a18e616564ab8c38da4..04eca602e1bda34cfcfdd518d322050723de10d0:/sdk/cwl/arvados_cwl/arvworkflow.py diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py index 4db1f4f2f4..5aed871a12 100644 --- a/sdk/cwl/arvados_cwl/arvworkflow.py +++ b/sdk/cwl/arvados_cwl/arvworkflow.py @@ -1,3 +1,7 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + import os import json import copy @@ -9,23 +13,31 @@ from cwltool.pack import pack from cwltool.load_tool import fetch_document from cwltool.process import shortname from cwltool.workflow import Workflow, WorkflowException -from cwltool.pathmapper import adjustFileObjs, adjustDirObjs +from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class +from cwltool.builder import Builder import ruamel.yaml as yaml -from .runner import upload_dependencies, trim_listing, packed_workflow, upload_workflow_collection +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) + adjustDirObjs(job_order, trim_anonymous_location) main = [p for p in packed["$graph"] if p["id"] == "#main"][0] for inp in main["inputs"]: @@ -63,6 +75,37 @@ def dedup_reqs(reqs): 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.""" @@ -76,11 +119,13 @@ class ArvadosWorkflow(Workflow): kwargs["work_api"] = self.work_api req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer") if req: - with SourceLine(self.tool, None, WorkflowException): + with SourceLine(self.tool, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)): if "id" not in self.tool: 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", "#")), @@ -95,6 +140,39 @@ class ArvadosWorkflow(Workflow): 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, @@ -103,15 +181,25 @@ class ArvadosWorkflow(Workflow): 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): - with SourceLine(obj, None, WorkflowException): + remove_redundant_fields(obj) + with SourceLine(obj, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)): if "location" not in obj: raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj)) - with SourceLine(obj, "location", WorkflowException): + 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("_:"): @@ -119,8 +207,13 @@ class ArvadosWorkflow(Workflow): else: raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"]) - adjustFileObjs(joborder_keepmount, keepmount) - adjustDirObjs(joborder_keepmount, keepmount) + 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) @@ -133,7 +226,7 @@ class ArvadosWorkflow(Workflow): "inputs": self.tool["inputs"], "outputs": self.tool["outputs"], "stdout": "cwl.output.json", - "requirements": workflowobj["requirements"]+[ + "requirements": self.requirements+[ { "class": "InitialWorkDirRequirement", "listing": [{ @@ -147,11 +240,12 @@ class ArvadosWorkflow(Workflow): "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)