X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/2cf1740bfe7e5790752654ce1b7e0220bc194004..81693ee04f18e68558c9206705ef589cca2460b0:/sdk/cwl/arvados_cwl/arvworkflow.py

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index b26bee8247..8e6bff4f04 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
@@ -14,7 +17,6 @@ from cwltool.load_tool import fetch_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
@@ -22,7 +24,7 @@ import ruamel.yaml as yaml
 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, check_cluster_target
+from .arvtool import ArvadosCommandTool, set_cluster_target, make_builder
 from .perf import Perf
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -133,10 +135,14 @@ class ArvadosWorkflowStep(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."""
 
@@ -148,11 +154,12 @@ class ArvadosWorkflow(Workflow):
         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:
@@ -201,6 +208,9 @@ 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)