12186: Filter nameroot from runner-submitted input object.

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

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 683f548c48cc835cd5ff7664cd0306cb0ea7f17e..39497098498792d1a4bb8595a77f6dcf9d1f6d47 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -18,7 +18,7 @@ from cwltool.draft2tool import CommandLineTool
 import cwltool.workflow
 from cwltool.process import get_feature, scandeps, UnsupportedRequirement, normalizeFilesDirs, shortname
 from cwltool.load_tool import fetch_document
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
 from cwltool.utils import aslist
 from cwltool.builder import substitute
 from cwltool.pack import pack
@@ -46,6 +46,22 @@ def trim_anonymous_location(obj):
     if obj.get("location", "").startswith("_:"):
         del obj["location"]
 
+def remove_redundant_fields(obj):
+    for field in ("path", "nameext", "nameroot", "dirname"):
+        if field in obj:
+            del obj[field]
+
+def find_defaults(d, op):
+    if isinstance(d, list):
+        for i in d:
+            find_defaults(i, op)
+    elif isinstance(d, dict):
+        if "default" in d:
+            op(d)
+        else:
+            for i in d.itervalues():
+                find_defaults(i, op)
+
 def upload_dependencies(arvrunner, name, document_loader,
                         workflowobj, uri, loadref_run, include_primary=True):
     """Upload the dependencies of the workflowobj document to Keep.
@@ -101,6 +117,23 @@ def upload_dependencies(arvrunner, name, document_loader,
         for s in workflowobj["$schemas"]:
             sc.append({"class": "File", "location": s})
 
+    def capture_default(obj):
+        remove = [False]
+        def add_default(f):
+            if "location" not in f and "path" in f:
+                f["location"] = f["path"]
+                del f["path"]
+            if "location" in f and not arvrunner.fs_access.exists(f["location"]):
+                # Remove from sc
+                sc[:] = [x for x in sc if x["location"] != f["location"]]
+                # Delete "default" from workflowobj
+                remove[0] = True
+        visit_class(obj["default"], ("File", "Directory"), add_default)
+        if remove[0]:
+            del obj["default"]
+
+    find_defaults(workflowobj, capture_default)
+
     mapper = ArvPathMapper(arvrunner, sc, "",
                            "keep:%s",
                            "keep:%s/%s",
@@ -133,6 +166,8 @@ def upload_docker(arvrunner, tool):
                 raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
                     "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
             arv_docker_get_image(arvrunner.api, docker_req, True, arvrunner.project_uuid)
+        else:
+            arv_docker_get_image(arvrunner.api, {"dockerPull": "arvados/jobs"}, True, arvrunner.project_uuid)
     elif isinstance(tool, cwltool.workflow.Workflow):
         for s in tool.steps:
             upload_docker(arvrunner, s.embedded_tool)