X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/803fbc7e350dfa6b70ac63c7bf5f9046a0625155..c7d692a3f09d8116cc52591f8852c4e0d6e4ab3c:/sdk/cwl/arvados_cwl/arvworkflow.py diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py index 72ef8fd4f4..c6bcd04776 100644 --- a/sdk/cwl/arvados_cwl/arvworkflow.py +++ b/sdk/cwl/arvados_cwl/arvworkflow.py @@ -2,6 +2,9 @@ # # SPDX-License-Identifier: Apache-2.0 +from past.builtins import basestring +from future.utils import viewitems + import os import json import copy @@ -12,17 +15,18 @@ 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.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') @@ -118,21 +122,46 @@ def get_overall_res_req(res_reqs): overall_res_req["class"] = "ResourceRequirement" 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): + 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): - check_cluster_target(self, self._init_job(joborder, runtimeContext), 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: @@ -145,7 +174,8 @@ class ArvadosWorkflow(Workflow): 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, @@ -161,11 +191,6 @@ class ArvadosWorkflow(Workflow): packed = pack(document_loader, workflowobj, uri, self.metadata) - builder = Builder(joborder, - requirements=workflowobj["requirements"], - hints=workflowobj["hints"], - resources={}) - def visit(item): for t in ("hints", "requirements"): if t not in item: @@ -186,6 +211,9 @@ class ArvadosWorkflow(Workflow): raise WorkflowException("Non-top-level ResourceRequirement in single container cannot have expressions") if not dyn: self.static_resource_req.append(req) + if req["class"] == "DockerRequirement": + if "http://arvados.org/cwl#dockerCollectionPDH" in req: + del req["http://arvados.org/cwl#dockerCollectionPDH"] visit_class(packed["$graph"], ("Workflow", "CommandLineTool"), visit) @@ -205,11 +233,6 @@ class ArvadosWorkflow(Workflow): if self.dynamic_resource_req: - builder = Builder(joborder, - requirements=self.requirements, - hints=self.hints, - resources={}) - # Evaluate dynamic resource requirements using current builder rs = copy.copy(self.static_resource_req) for dyn_rs in self.dynamic_resource_req: @@ -268,6 +291,10 @@ 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" + wf_runner = cmap({ "class": "CommandLineTool", "baseCommand": "cwltool", @@ -291,3 +318,13 @@ class ArvadosWorkflow(Workflow): "id": "#" }) return ArvadosCommandTool(self.arvrunner, wf_runner, self.loadingContext).job(joborder_resolved, output_callback, runtimeContext) + + def make_workflow_step(self, + toolpath_object, # type: Dict[Text, Any] + pos, # type: int + loadingContext, # type: LoadingContext + *argc, + **argv + ): + # (...) -> WorkflowStep + return ArvadosWorkflowStep(toolpath_object, pos, loadingContext, self.arvrunner, *argc, **argv)