10081: Dump as yaml instead of json. Add test for extracted subworkflow.

[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..6883c10e31420e39f49ff40b9a969c71f1937fe9 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -7,6 +7,7 @@ from cwltool.pack import pack
 from cwltool.load_tool import fetch_document
 from cwltool.process import shortname
 from cwltool.workflow import Workflow
+from cwltool.pathmapper import adjustDirObjs
 
 import ruamel.yaml as yaml
 
@@ -59,27 +60,34 @@ class ArvadosWorkflow(Workflow):
         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)
+
+            def prune_directories(obj):
+                if obj["location"].startswith("keep:"):
+                    del obj["listing"]
+            adjustDirObjs(joborder, prune_directories)
+
             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)
+                            "entry": yaml.safe_dump(packed).replace('$(', '\$(').replace('${', '\${')
                         }, {
                             "entryname": "cwl.input.json",
                             "entry": "$(JSON.stringify(inputs))"
                         }]
                 }],
-                "arguments": ["--debug", "workflow.json", "cwl.input.json"]
+                "hints": workflowobj["hints"],
+                "arguments": ["--no-container", "--move-outputs", "workflow.json", "cwl.input.json"]
             }
             kwargs["loader"] = self.doc_loader
             kwargs["avsc_names"] = self.doc_schema