Merge branch '16039-fuse-forward-slash-sub'

[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 183e21cf95b01c046ea3acbbad2bc94f39fa41f5..2239e0f9df952b9ab75a7e9a96ab46953ab29f94 100644 (file)
--- 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
@@ -580,7 +578,8 @@ class Runner(Process):
     """Base class for runner processes, which submit an instance of
     arvados-cwl-runner and wait for the final result."""
 
-    def __init__(self, runner, tool, loadingContext, enable_reuse,
+    def __init__(self, runner, updated_tool,
+                 tool, loadingContext, enable_reuse,
                  output_name, output_tags, submit_runner_ram=0,
                  name=None, on_error=None, submit_runner_image=None,
                  intermediate_output_ttl=0, merged_map=None,
@@ -589,10 +588,9 @@ class Runner(Process):
                  collection_cache_is_default=True):
 
         loadingContext = loadingContext.copy()
-        loadingContext.metadata = loadingContext.metadata.copy()
-        loadingContext.metadata["cwlVersion"] = INTERNAL_VERSION
+        loadingContext.metadata = updated_tool.metadata.copy()
 
-        super(Runner, self).__init__(tool.tool, loadingContext)
+        super(Runner, self).__init__(updated_tool.tool, loadingContext)
 
         self.arvrunner = runner
         self.embedded_tool = tool