15028: Update cwltool/schema-salad deps, fix tests

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

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index 319e8a887114b88b55865ca673dbafb3e0b9a7dc..2875dbc22263314bd04c2699e93370d841c0c89c 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -87,7 +87,7 @@ class RuntimeStatusLoggingHandler(logging.Handler):
                     )
             finally:
                 self.updatingRuntimeStatus = False
-            
+
 
 class ArvCwlExecutor(object):
     """Execute a CWL tool or workflow, submit work (using either jobs or
@@ -187,6 +187,7 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
         self.loadingContext.fetcher_constructor = self.fetcher_constructor
         self.loadingContext.resolver = partial(collectionResolver, self.api, num_retries=self.num_retries)
         self.loadingContext.construct_tool_object = self.arv_make_tool
+        self.loadingContext.do_update = False
 
         # Add a custom logging handler to the root logger for runtime status reporting
         # if running inside a container
@@ -442,17 +443,16 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
                                               num_retries=self.num_retries)
 
         for k,v in generatemapper.items():
-            if k.startswith("_:"):
-                if v.type == "Directory":
+            if v.type == "Directory" and v.resolved.startswith("_:"):
                     continue
-                if v.type == "CreateFile":
-                    with final.open(v.target, "wb") as f:
-                        f.write(v.resolved.encode("utf-8"))
+            if v.type == "CreateFile" and (k.startswith("_:") or v.resolved.startswith("_:")):
+                with final.open(v.target, "wb") as f:
+                    f.write(v.resolved.encode("utf-8"))
                     continue
 
-            if not k.startswith("keep:"):
+            if not v.resolved.startswith("keep:"):
                 raise Exception("Output source is not in keep or a literal")
-            sp = k.split("/")
+            sp = v.resolved.split("/")
             srccollection = sp[0][5:]
             try:
                 reader = self.collection_cache.get(srccollection)
@@ -462,7 +462,8 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
                 logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
                 raise
             except IOError as e:
-                logger.warning("While preparing output collection: %s", e)
+                logger.error("While preparing output collection: %s", e)
+                raise
 
         def rewrite(fileobj):
             fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
@@ -475,7 +476,7 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
 
         with final.open("cwl.output.json", "w") as f:
             res = str(json.dumps(outputObj, sort_keys=True, indent=4, separators=(',',': '), ensure_ascii=False))
-            f.write(res)           
+            f.write(res)
 
         final.save_new(name=name, owner_uuid=self.project_uuid, storage_classes=storage_classes, ensure_unique_name=True)