Merge branch '12479-wb-structured-vocabulary'

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

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index b79c453cfbeb115eae736f5fbd621453950d1a05..d15acf767fc90cc3e594be1fca0e67ae96f034ec 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -113,6 +113,7 @@ class ArvCwlRunner(object):
                                                 fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
                                                 num_retries=self.num_retries,
                                                 overrides=kwargs.get("override_tools"))
+        kwargs["resolver"] = partial(collectionResolver, self.api, num_retries=self.num_retries)
         if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
             return ArvadosCommandTool(self, toolpath_object, **kwargs)
         elif "class" in toolpath_object and toolpath_object["class"] == "Workflow":
@@ -236,7 +237,7 @@ class ArvCwlRunner(object):
                 self.check_features(v)
         elif isinstance(obj, list):
             for i,v in enumerate(obj):
-                with SourceLine(obj, i, UnsupportedRequirement):
+                with SourceLine(obj, i, UnsupportedRequirement, logger.isEnabledFor(logging.DEBUG)):
                     self.check_features(v)
 
     def make_output_collection(self, name, tagsString, outputObj):
@@ -280,7 +281,7 @@ class ArvCwlRunner(object):
 
         def rewrite(fileobj):
             fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
-            for k in ("basename", "listing", "contents"):
+            for k in ("basename", "listing", "contents", "nameext", "nameroot", "dirname"):
                 if k in fileobj:
                     del fileobj[k]
 
@@ -424,14 +425,8 @@ class ArvCwlRunner(object):
         if kwargs.get("submit"):
             # Submit a runner job to run the workflow for us.
             if self.work_api == "containers":
-                if tool.tool["class"] == "CommandLineTool":
+                if tool.tool["class"] == "CommandLineTool" and kwargs.get("wait"):
                     kwargs["runnerjob"] = tool.tool["id"]
-                    upload_dependencies(self,
-                                        kwargs["name"],
-                                        tool.doc_loader,
-                                        tool.tool,
-                                        tool.tool["id"],
-                                        False)
                     runnerjob = tool.job(job_order,
                                          self.output_callback,
                                          **kwargs).next()
@@ -688,7 +683,8 @@ def add_arv_hints():
         "http://arvados.org/cwl#PartitionRequirement",
         "http://arvados.org/cwl#APIRequirement",
         "http://commonwl.org/cwltool#LoadListingRequirement",
-        "http://arvados.org/cwl#IntermediateOutput"
+        "http://arvados.org/cwl#IntermediateOutput",
+        "http://arvados.org/cwl#ReuseRequirement"
     ])
 
 def main(args, stdout, stderr, api_client=None, keep_client=None):
@@ -754,7 +750,7 @@ def main(args, stdout, stderr, api_client=None, keep_client=None):
     arvargs.conformance_test = None
     arvargs.use_container = True
     arvargs.relax_path_checks = True
-    arvargs.validate = None
+    arvargs.print_supported_versions = False
 
     make_fs_access = partial(CollectionFsAccess,
                            collection_cache=runner.collection_cache)