Merge branch 'master' into 9998-unsigned_manifest

[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 ba41d7d97ea8085e1898daf075f327b8dd26d5cc..3bbcb8b091763cd565051c23a65ce13d1069f08f 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -110,6 +110,9 @@ def upload_docker(arvrunner, tool):
     if isinstance(tool, CommandLineTool):
         (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
         if docker_req:
+            if docker_req.get("dockerOutputDirectory"):
+                # TODO: can be supported by containers API, but not jobs API.
+                raise UnsupportedRequirement("Option 'dockerOutputDirectory' of DockerRequirement not supported.")
             arv_docker_get_image(arvrunner.api, docker_req, True, arvrunner.project_uuid)
     elif isinstance(tool, cwltool.workflow.Workflow):
         for s in tool.steps:
@@ -158,7 +161,7 @@ def arvados_jobs_image(arvrunner):
     return img
 
 class Runner(object):
-    def __init__(self, runner, tool, job_order, enable_reuse, output_name):
+    def __init__(self, runner, tool, job_order, enable_reuse, output_name, output_tags):
         self.arvrunner = runner
         self.tool = tool
         self.job_order = job_order
@@ -167,6 +170,7 @@ class Runner(object):
         self.uuid = None
         self.final_output = None
         self.output_name = output_name
+        self.output_tags = output_tags
 
     def update_pipeline_component(self, record):
         pass
@@ -191,7 +195,7 @@ class Runner(object):
         else:
             processStatus = "permanentFail"
 
-        outputs = None
+        outputs = {}
         try:
             try:
                 self.final_output = record["output"]
@@ -208,7 +212,7 @@ class Runner(object):
                 adjustFileObjs(outputs, keepify)
                 adjustDirObjs(outputs, keepify)
             except Exception as e:
-                logger.error("While getting final output object: %s", e)
+                logger.exception("While getting final output object: %s", e)
             self.arvrunner.output_callback(outputs, processStatus)
         finally:
             del self.arvrunner.processes[record["uuid"]]