X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/4d81515a381239b4b31ad7a41ed72c93dcadf08b..eb58fd945645f5a670c761f7046b10885941167e:/sdk/cwl/arvados_cwl/arvworkflow.py

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index fa543e3757..f514476b90 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -14,7 +14,6 @@ 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 +21,7 @@ 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')
@@ -119,27 +118,45 @@ 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(joborder, 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 joborder.items()}, 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)
+        runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
 
         req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
         if not req:
@@ -293,7 +310,8 @@ 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)