X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/6c78b28f9f54664babc57a4b4372c502065ed5d1..02a9d43ab7340d2cf6ce6c13d42e579729595071:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 183e21cf95..19a6dd98b3 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -44,7 +44,7 @@ from .util import collectionUUID
 import ruamel.yaml as yaml
 
 import arvados_cwl.arvdocker
-from .pathmapper import ArvPathMapper, trim_listing
+from .pathmapper import ArvPathMapper, trim_listing, collection_pdh_pattern, collection_uuid_pattern
 from ._version import __version__
 from . import done
 from . context import ArvRuntimeContext
@@ -174,7 +174,7 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             if pattern is None:
                 continue
             sfpath = substitute(primary["location"], pattern)
-            required = builder.do_eval(sf["required"], context=primary)
+            required = builder.do_eval(sf.get("required"), context=primary)
 
             if fsaccess.exists(sfpath):
                 primary["secondaryFiles"].append({"location": sfpath, "class": "File"})
@@ -194,9 +194,6 @@ def discover_secondary_files(fsaccess, builder, inputs, job_order, discovered=No
         if isinstance(primary, (Mapping, Sequence)):
             set_secondary(fsaccess, builder, inputschema, None, primary, discovered)
 
-collection_uuid_pattern = re.compile(r'^keep:([a-z0-9]{5}-4zz18-[a-z0-9]{15})(/.*)?$')
-collection_pdh_pattern = re.compile(r'^keep:([0-9a-f]{32}\+\d+)(/.*)?')
-
 def upload_dependencies(arvrunner, name, document_loader,
                         workflowobj, uri, loadref_run,
                         include_primary=True, discovered_secondaryfiles=None):
@@ -337,7 +334,8 @@ def upload_dependencies(arvrunner, name, document_loader,
                                  builder_job_order,
                                  discovered)
 
-    visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
+    copied, _ = document_loader.resolve_all(copy.deepcopy(cmap(workflowobj)), base_url=uri, checklinks=False)
+    visit_class(copied, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
 
     for d in list(discovered):
         # Only interested in discovered secondaryFiles which are local