X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b521d2c5254e439e23cd750f86d55eadffb3e4b9..4e5838bd9e1a7baa5b3e53e97e308140e4b6105f:/sdk/cwl/arvados_cwl/arvworkflow.py

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 56c6f39e9d..51e7cd8b9e 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -17,7 +17,7 @@ from cwltool.pack import pack
 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.utils import adjustFileObjs, adjustDirObjs, visit_class, normalizeFilesDirs
 from cwltool.context import LoadingContext
 
 import ruamel.yaml as yaml
@@ -37,11 +37,12 @@ metrics = logging.getLogger('arvados.cwl-runner.metrics')
 max_res_pars = ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax")
 sum_res_pars = ("outdirMin", "outdirMax")
 
-def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
+def upload_workflow(arvRunner, tool, job_order, project_uuid,
+                    runtimeContext, uuid=None,
                     submit_runner_ram=0, name=None, merged_map=None,
                     submit_runner_image=None):
 
-    packed = packed_workflow(arvRunner, tool, merged_map)
+    packed = packed_workflow(arvRunner, tool, merged_map, runtimeContext)
 
     adjustDirObjs(job_order, trim_listing)
     adjustFileObjs(job_order, trim_anonymous_location)
@@ -57,7 +58,8 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
         name = tool.tool.get("label", os.path.basename(tool.tool["id"]))
 
     upload_dependencies(arvRunner, name, tool.doc_loader,
-                        packed, tool.tool["id"], False)
+                        packed, tool.tool["id"], False,
+                        runtimeContext)
 
     wf_runner_resources = None
 
@@ -72,7 +74,9 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
         wf_runner_resources = {"class": "http://arvados.org/cwl#WorkflowRunnerResources"}
         hints.append(wf_runner_resources)
 
-    wf_runner_resources["acrContainerImage"] = arvados_jobs_image(arvRunner, submit_runner_image or "arvados/jobs:"+__version__)
+    wf_runner_resources["acrContainerImage"] = arvados_jobs_image(arvRunner,
+                                                                  submit_runner_image or "arvados/jobs:"+__version__,
+                                                                  runtimeContext)
 
     if submit_runner_ram:
         wf_runner_resources["ramMin"] = submit_runner_ram
@@ -186,6 +190,7 @@ class ArvadosWorkflow(Workflow):
 
         discover_secondary_files(self.arvrunner.fs_access, builder,
                                  self.tool["inputs"], joborder)
+        normalizeFilesDirs(joborder)
 
         with Perf(metrics, "subworkflow upload_deps"):
             upload_dependencies(self.arvrunner,
@@ -193,7 +198,8 @@ class ArvadosWorkflow(Workflow):
                                 self.doc_loader,
                                 joborder,
                                 joborder.get("id", "#"),
-                                False)
+                                False,
+                                runtimeContext)
 
             if self.wf_pdh is None:
                 packed = pack(self.loadingContext, self.tool["id"], loader=self.doc_loader)
@@ -236,7 +242,8 @@ class ArvadosWorkflow(Workflow):
                                     self.doc_loader,
                                     packed,
                                     self.tool["id"],
-                                    False)
+                                    False,
+                                    runtimeContext)
 
                 # Discover files/directories referenced by the
                 # workflow (mainly "default" values)
@@ -300,7 +307,7 @@ class ArvadosWorkflow(Workflow):
             if self.wf_pdh is None:
                 adjustFileObjs(packed, keepmount)
                 adjustDirObjs(packed, keepmount)
-                self.wf_pdh = upload_workflow_collection(self.arvrunner, shortname(self.tool["id"]), packed)
+                self.wf_pdh = upload_workflow_collection(self.arvrunner, shortname(self.tool["id"]), packed, runtimeContext)
 
         self.loadingContext = self.loadingContext.copy()
         self.loadingContext.metadata = self.loadingContext.metadata.copy()