10129: Ensure that directory literals get preserved when trimming keep directory...

[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 ab3940998bd669c3f5bc389866b19effb9a708d3..3bb0a34197594774f81049ff5ccdf606dc2dfcde 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -6,12 +6,12 @@ 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
 
-from .runner import upload_docker, upload_dependencies
+from .runner import upload_docker, upload_dependencies, del_listing
 from .arvtool import ArvadosCommandTool
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -23,6 +23,8 @@ def upload_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
 
     packed = pack(document_loader, workflowobj, uri, tool.metadata)
 
+    adjustDirObjs(job_order, del_listing)
+
     main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
     for inp in main["inputs"]:
         sn = shortname(inp["id"])
@@ -83,10 +85,13 @@ class ArvadosWorkflow(Workflow):
             def keepmount(obj):
                 if obj["location"].startswith("keep:"):
                     obj["location"] = "/keep/" + obj["location"][5:]
+                    if "listing" in obj:
+                        del obj["listing"]
+                elif obj["location"].startswith("_:"):
+                    del obj["location"]
                 else:
-                    raise Exception("Uh oh %s" % obj["location"])
-                if "listing" in obj:
-                    del obj["listing"]
+                    raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
+
             adjustFileObjs(joborder_keepmount, keepmount)
             adjustDirObjs(joborder_keepmount, keepmount)
             adjustFileObjs(packed, keepmount)
@@ -106,12 +111,12 @@ class ArvadosWorkflow(Workflow):
                             "entryname": "workflow.cwl",
                             "entry": yaml.safe_dump(packed).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
                         }, {
-                            "entryname": "cwl.input.json",
+                            "entryname": "cwl.input.yml",
                             "entry": yaml.safe_dump(joborder_keepmount).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
                         }]
                 }],
                 "hints": workflowobj["hints"],
-                "arguments": ["--no-container", "--move-outputs", "workflow.cwl#main", "cwl.input.json"]
+                "arguments": ["--no-container", "--move-outputs", "workflow.cwl#main", "cwl.input.yml"]
             }
             kwargs["loader"] = self.doc_loader
             kwargs["avsc_names"] = self.doc_schema