X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/d63f3ade27bb506da049164789679f9fed171005..0ff7b94edaaaa07932ae757c0a2b7ba3fde026cb:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 570675bc4e..2e52b63ed6 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -25,6 +25,18 @@ cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
 
 def upload_dependencies(arvrunner, name, document_loader,
                         workflowobj, uri, loadref_run):
+    """Upload the dependencies of the workflowobj document to Keep.
+
+    Returns a pathmapper object mapping local paths to keep references.  Also
+    does an in-place update of references in "workflowobj".
+
+    Use scandeps to find $import, $include, $schemas, run, File and Directory
+    fields that represent external references.
+
+    If workflowobj has an "id" field, this will reload the document to ensure
+    it is scanning the raw document prior to preprocessing.
+    """
+
     loaded = set()
     def loadref(b, u):
         joined = urlparse.urljoin(b, u)
@@ -54,7 +66,7 @@ def upload_dependencies(arvrunner, name, document_loader,
 
     sc = scandeps(uri, scanobj,
                   loadref_fields,
-                  set(("$include", "$schemas")),
+                  set(("$include", "$schemas", "location")),
                   loadref)
 
     files = []
@@ -75,7 +87,8 @@ def upload_dependencies(arvrunner, name, document_loader,
                            name=name)
 
     def setloc(p):
-        p["location"] = mapper.mapper(p["location"]).target
+        if not p["location"].startswith("keep:"):
+            p["location"] = mapper.mapper(p["location"]).resolved
     adjustFileObjs(workflowobj, setloc)
     adjustDirObjs(workflowobj, setloc)