X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/674ba49f7bce861326094231d4f4eb590abbb7ce..07dbd859d0b05d79680570c00c43a722102d7ea3:/sdk/cwl/arvados_cwl/arvworkflow.py diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py index 7ea5b58733..ddd3c00764 100644 --- a/sdk/cwl/arvados_cwl/arvworkflow.py +++ b/sdk/cwl/arvados_cwl/arvworkflow.py @@ -2,27 +2,32 @@ # # SPDX-License-Identifier: Apache-2.0 +from past.builtins import basestring +from future.utils import viewitems + import os import json import copy import logging from schema_salad.sourceline import SourceLine, cmap +import schema_salad.ref_resolver from cwltool.pack import pack -from cwltool.load_tool import fetch_document +from cwltool.load_tool import fetch_document, resolve_and_validate_document from cwltool.process import shortname from cwltool.workflow import Workflow, WorkflowException, WorkflowStep from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class -from cwltool.builder import Builder from cwltool.context import LoadingContext import ruamel.yaml as yaml from .runner import (upload_dependencies, packed_workflow, upload_workflow_collection, - trim_anonymous_location, remove_redundant_fields, discover_secondary_files) + trim_anonymous_location, remove_redundant_fields, discover_secondary_files, + make_builder) from .pathmapper import ArvPathMapper, trim_listing -from .arvtool import ArvadosCommandTool, check_cluster_target +from .arvtool import ArvadosCommandTool, set_cluster_target + from .perf import Perf logger = logging.getLogger('arvados.cwl-runner') @@ -119,27 +124,45 @@ def get_overall_res_req(res_reqs): return cmap(overall_res_req) class ArvadosWorkflowStep(WorkflowStep): + def __init__(self, + toolpath_object, # type: Dict[Text, Any] + pos, # type: int + loadingContext, # type: LoadingContext + arvrunner, + *argc, + **argv + ): # type: (...) -> None + + super(ArvadosWorkflowStep, self).__init__(toolpath_object, pos, loadingContext, *argc, **argv) + self.tool["class"] = "WorkflowStep" + self.arvrunner = arvrunner + def job(self, joborder, output_callback, runtimeContext): - builder = self._init_job({shortname(k): v for k,v in joborder.items()}, runtimeContext) - check_cluster_target(self, builder, runtimeContext) + runtimeContext = runtimeContext.copy() + runtimeContext.toplevel = True # Preserve behavior for #13365 + + builder = make_builder({shortname(k): v for k,v in viewitems(joborder)}, self.hints, self.requirements, runtimeContext) + runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext) return super(ArvadosWorkflowStep, self).job(joborder, output_callback, runtimeContext) + class ArvadosWorkflow(Workflow): """Wrap cwltool Workflow to override selected methods.""" def __init__(self, arvrunner, toolpath_object, loadingContext): - super(ArvadosWorkflow, self).__init__(toolpath_object, loadingContext) self.arvrunner = arvrunner self.wf_pdh = None self.dynamic_resource_req = [] self.static_resource_req = [] self.wf_reffiles = [] self.loadingContext = loadingContext + super(ArvadosWorkflow, self).__init__(toolpath_object, loadingContext) + self.cluster_target_req, _ = self.get_requirement("http://arvados.org/cwl#ClusterTarget") def job(self, joborder, output_callback, runtimeContext): - builder = self._init_job(joborder, runtimeContext) - check_cluster_target(self, builder, runtimeContext) + builder = make_builder(joborder, self.hints, self.requirements, runtimeContext) + runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext) req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer") if not req: @@ -150,25 +173,29 @@ class ArvadosWorkflow(Workflow): 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) + discover_secondary_files(self.arvrunner.fs_access, builder, + self.tool["inputs"], joborder) with Perf(metrics, "subworkflow upload_deps"): upload_dependencies(self.arvrunner, os.path.basename(joborder.get("id", "#")), - document_loader, + self.doc_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(self.loadingContext, self.tool["id"], loader=self.doc_loader) - packed = pack(document_loader, workflowobj, uri, self.metadata) + for p in packed["$graph"]: + if p["id"] == "#main": + p["requirements"] = dedup_reqs(self.requirements) + p["hints"] = dedup_reqs(self.hints) def visit(item): + if "requirements" in item: + item["requirements"] = [i for i in item["requirements"] if i["class"] != "DockerRequirement"] for t in ("hints", "requirements"): if t not in item: continue @@ -196,9 +223,9 @@ class ArvadosWorkflow(Workflow): upload_dependencies(self.arvrunner, runtimeContext.name, - document_loader, + self.doc_loader, packed, - uri, + self.tool["id"], False) # Discover files/directories referenced by the @@ -265,6 +292,20 @@ class ArvadosWorkflow(Workflow): adjustDirObjs(packed, keepmount) self.wf_pdh = upload_workflow_collection(self.arvrunner, shortname(self.tool["id"]), packed) + self.loadingContext = self.loadingContext.copy() + self.loadingContext.metadata = self.loadingContext.metadata.copy() + self.loadingContext.metadata["http://commonwl.org/cwltool#original_cwlVersion"] = "v1.0" + + if len(job_res_reqs) == 1: + # RAM request needs to be at least 128 MiB or the workflow + # runner itself won't run reliably. + if job_res_reqs[0].get("ramMin", 1024) < 128: + job_res_reqs[0]["ramMin"] = 128 + + arguments = ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl", "cwl.input.yml"] + if runtimeContext.debug: + arguments.insert(0, '--debug') + wf_runner = cmap({ "class": "CommandLineTool", "baseCommand": "cwltool", @@ -284,7 +325,7 @@ class ArvadosWorkflow(Workflow): }] }], "hints": self.hints, - "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"], + "arguments": arguments, "id": "#" }) return ArvadosCommandTool(self.arvrunner, wf_runner, self.loadingContext).job(joborder_resolved, output_callback, runtimeContext) @@ -293,7 +334,8 @@ class ArvadosWorkflow(Workflow): toolpath_object, # type: Dict[Text, Any] pos, # type: int loadingContext, # type: LoadingContext - parentworkflowProv=None # type: Optional[CreateProvProfile] + *argc, + **argv ): # (...) -> WorkflowStep - return ArvadosWorkflowStep(toolpath_object, pos, loadingContext, parentworkflowProv) + return ArvadosWorkflowStep(toolpath_object, pos, loadingContext, self.arvrunner, *argc, **argv)