X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/0b187b107128a57c1f0c00057d39979ab53d4137..d3a82af33386c99c0fd3d6471df7e6696560089c:/sdk/cwl/arvados_cwl/arvworkflow.py diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py index fb14ab4a78..4db1f4f2f4 100644 --- a/sdk/cwl/arvados_cwl/arvworkflow.py +++ b/sdk/cwl/arvados_cwl/arvworkflow.py @@ -1,19 +1,31 @@ import os import json import copy +import logging + +from schema_salad.sourceline import SourceLine, cmap 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 + +import ruamel.yaml as yaml + +from .runner import upload_dependencies, trim_listing, packed_workflow, upload_workflow_collection +from .arvtool import ArvadosCommandTool +from .perf import Perf -from .runner import upload_docker, upload_dependencies +logger = logging.getLogger('arvados.cwl-runner') +metrics = logging.getLogger('arvados.cwl-runner.metrics') -def make_workflow(arvRunner, tool, job_order, project_uuid, update_uuid): - upload_docker(arvRunner, tool) +def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None, + submit_runner_ram=0, name=None): - document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"]) + packed = packed_workflow(arvRunner, tool) - packed = pack(document_loader, workflowobj, uri, tool.metadata) + adjustDirObjs(job_order, trim_listing) main = [p for p in packed["$graph"] if p["id"] == "#main"][0] for inp in main["inputs"]: @@ -21,19 +33,125 @@ def make_workflow(arvRunner, tool, job_order, project_uuid, update_uuid): if sn in job_order: inp["default"] = job_order[sn] - name = os.path.basename(tool.tool["id"]) - upload_dependencies(arvRunner, name, document_loader, - packed, uri, "keep:", False) + if not name: + name = tool.tool.get("label", os.path.basename(tool.tool["id"])) + + upload_dependencies(arvRunner, name, tool.doc_loader, + packed, tool.tool["id"], False) + + # TODO nowhere for submit_runner_ram to go. body = { "workflow": { - "owner_uuid": project_uuid, - "name": tool.tool.get("label", name), + "name": name, "description": tool.tool.get("doc", ""), - "workflow":json.dumps(packed, sort_keys=True, indent=4, separators=(',',': ')) + "definition":yaml.round_trip_dump(packed) }} + if project_uuid: + body["workflow"]["owner_uuid"] = project_uuid - if update_uuid: - return arvRunner.api.workflows().update(uuid=update_uuid, body=body).execute(num_retries=arvRunner.num_retries)["uuid"] + if uuid: + call = arvRunner.api.workflows().update(uuid=uuid, body=body) else: - return arvRunner.api.workflows().create(body=body).execute(num_retries=arvRunner.num_retries)["uuid"] + call = arvRunner.api.workflows().create(body=body) + return call.execute(num_retries=arvRunner.num_retries)["uuid"] + +def dedup_reqs(reqs): + dedup = {} + for r in reversed(reqs): + if r["class"] not in dedup and not r["class"].startswith("http://arvados.org/cwl#"): + dedup[r["class"]] = r + return [dedup[r] for r in sorted(dedup.keys())] + +class ArvadosWorkflow(Workflow): + """Wrap cwltool Workflow to override selected methods.""" + + def __init__(self, arvrunner, toolpath_object, **kwargs): + super(ArvadosWorkflow, self).__init__(toolpath_object, **kwargs) + self.arvrunner = arvrunner + self.work_api = kwargs["work_api"] + self.wf_pdh = None + + def job(self, joborder, output_callback, **kwargs): + kwargs["work_api"] = self.work_api + req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer") + if req: + with SourceLine(self.tool, None, WorkflowException): + 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"]) + + with Perf(metrics, "subworkflow upload_deps"): + upload_dependencies(self.arvrunner, + os.path.basename(joborder.get("id", "#")), + document_loader, + joborder, + joborder.get("id", "#"), + False) + + if self.wf_pdh is None: + workflowobj["requirements"] = dedup_reqs(self.requirements) + workflowobj["hints"] = dedup_reqs(self.hints) + + packed = pack(document_loader, workflowobj, uri, self.metadata) + + upload_dependencies(self.arvrunner, + kwargs.get("name", ""), + document_loader, + packed, + uri, + False) + + with Perf(metrics, "subworkflow adjust"): + joborder_keepmount = copy.deepcopy(joborder) + + def keepmount(obj): + with SourceLine(obj, None, WorkflowException): + if "location" not in obj: + raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj)) + with SourceLine(obj, "location", WorkflowException): + if obj["location"].startswith("keep:"): + obj["location"] = "/keep/" + obj["location"][5:] + if "listing" in obj: + del obj["listing"] + elif obj["location"].startswith("_:"): + del obj["location"] + else: + raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"]) + + adjustFileObjs(joborder_keepmount, keepmount) + adjustDirObjs(joborder_keepmount, keepmount) + + if self.wf_pdh is None: + adjustFileObjs(packed, keepmount) + adjustDirObjs(packed, keepmount) + self.wf_pdh = upload_workflow_collection(self.arvrunner, shortname(self.tool["id"]), packed) + + wf_runner = cmap({ + "class": "CommandLineTool", + "baseCommand": "cwltool", + "inputs": self.tool["inputs"], + "outputs": self.tool["outputs"], + "stdout": "cwl.output.json", + "requirements": workflowobj["requirements"]+[ + { + "class": "InitialWorkDirRequirement", + "listing": [{ + "entryname": "workflow.cwl", + "entry": { + "class": "File", + "location": "keep:%s/workflow.cwl" % self.wf_pdh + } + }, { + "entryname": "cwl.input.yml", + "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"] + }) + kwargs["loader"] = self.doc_loader + kwargs["avsc_names"] = self.doc_schema + return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder, output_callback, **kwargs) + else: + return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)