#
# SPDX-License-Identifier: Apache-2.0
+from past.builtins import basestring
+from future.utils import viewitems
+
import os
import json
import copy
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)
from .pathmapper import ArvPathMapper, trim_listing
-from .arvtool import ArvadosCommandTool, set_cluster_target
+from .arvtool import ArvadosCommandTool, set_cluster_target, make_builder
from .perf import Perf
logger = logging.getLogger('arvados.cwl-runner')
runtimeContext = runtimeContext.copy()
runtimeContext.toplevel = True # Preserve behavior for #13365
- builder = self._init_job({shortname(k): v for k,v in joborder.items()}, runtimeContext)
+ 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)
def job(self, joborder, output_callback, runtimeContext):
- builder = self._init_job(joborder, 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")
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)
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",