15028: Fixing 1.0 conformance 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 c35842616696f7dc00d047969ea74f27aad332df..20cff606007a3bf47fef2153107238cc96b75140 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -45,6 +45,7 @@ from ._version import __version__
 from cwltool.process import shortname, UnsupportedRequirement, use_custom_schema
 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, get_listing, visit_class
 from cwltool.command_line_tool import compute_checksums
+from cwltool.load_tool import load_tool
 
 logger = logging.getLogger('arvados.cwl-runner')
 metrics = logging.getLogger('arvados.cwl-runner.metrics')
@@ -187,6 +188,7 @@ 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 +444,16 @@ 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 +463,8 @@ 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
@@ -671,6 +673,11 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
                     "state": "RunningOnClient"}).execute(num_retries=self.num_retries)
             logger.info("Pipeline instance %s", self.pipeline["uuid"])
 
+        if not isinstance(tool, Runner):
+            loadingContext.do_update = True
+            tool = load_tool(tool.doc_loader.idx[tool.tool["id"]],
+                             loadingContext)
+
         if runtimeContext.cwl_runner_job is not None:
             self.uuid = runtimeContext.cwl_runner_job.get('uuid')