Fix typo.

[arvados.git] / sdk / cwl / arvados_cwl / arvworkflow.py

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index d0d2749064c90196719069adb65578f7af89f262..ab8ad035fd6c8d13d14b3d226135993e6c0792ce 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -6,7 +6,8 @@ import logging
 from cwltool.pack import pack
 from cwltool.load_tool import fetch_document
 from cwltool.process import shortname
-from cwltool.workflow import Workflow
+from cwltool.workflow import Workflow, WorkflowException
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
 
 import ruamel.yaml as yaml
 
@@ -58,28 +59,61 @@ class ArvadosWorkflow(Workflow):
         req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
         if req:
             document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
+
             workflowobj["requirements"] = self.requirements + workflowobj.get("requirements", [])
-            workflowobj["hints"] = self.requirements + workflowobj.get("hints", [])
+            workflowobj["hints"] = self.hints + workflowobj.get("hints", [])
             packed = pack(document_loader, workflowobj, uri, self.metadata)
+
+            upload_dependencies(self.arvrunner,
+                                kwargs.get("name", ""),
+                                document_loader,
+                                packed,
+                                uri,
+                                False)
+
+            upload_dependencies(self.arvrunner,
+                                os.path.basename(joborder.get("id", "#")),
+                                document_loader,
+                                joborder,
+                                joborder.get("id", "#"),
+                                False)
+
+            joborder_keepmount = copy.deepcopy(joborder)
+
+            def keepmount(obj):
+                if obj["location"].startswith("keep:"):
+                    obj["location"] = "/keep/" + obj["location"][5:]
+                elif obj["location"].startswith("_:"):
+                    pass
+                else:
+                    raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
+                if "listing" in obj:
+                    del obj["listing"]
+            adjustFileObjs(joborder_keepmount, keepmount)
+            adjustDirObjs(joborder_keepmount, keepmount)
+            adjustFileObjs(packed, keepmount)
+            adjustDirObjs(packed, keepmount)
+
             wf_runner = {
                 "class": "CommandLineTool",
                 "baseCommand": "cwltool",
                 "inputs": self.tool["inputs"],
                 "outputs": self.tool["outputs"],
                 "stdout": "cwl.output.json",
-                "requirements": [
+                "requirements": workflowobj["requirements"]+[
                     {"class": "InlineJavascriptRequirement"},
                     {
                     "class": "InitialWorkDirRequirement",
                     "listing": [{
-                            "entryname": "workflow.json",
-                            "entry": json.dumps(packed, sort_keys=True, indent=4)
+                            "entryname": "workflow.cwl",
+                            "entry": yaml.safe_dump(packed).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
                         }, {
-                            "entryname": "cwl.input.json",
-                            "entry": "$(JSON.stringify(inputs))"
+                            "entryname": "cwl.input.yml",
+                            "entry": yaml.safe_dump(joborder_keepmount).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
                         }]
                 }],
-                "arguments": ["--debug", "workflow.json", "cwl.input.json"]
+                "hints": workflowobj["hints"],
+                "arguments": ["--no-container", "--move-outputs", "workflow.cwl#main", "cwl.input.yml"]
             }
             kwargs["loader"] = self.doc_loader
             kwargs["avsc_names"] = self.doc_schema