X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b1b7794d253c653a370200c2b33d477d3f7f231e..9b0654adfffaac018395de29f6e441b843d46e85:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index ba41d7d97e..2d13e6640b 100644
--- 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 +161,9 @@ 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, submit_runner_ram=0,
+                 name=None):
         self.arvrunner = runner
         self.tool = tool
         self.job_order = job_order
@@ -167,12 +172,23 @@ class Runner(object):
         self.uuid = None
         self.final_output = None
         self.output_name = output_name
+        self.output_tags = output_tags
+        self.name = name
+
+        if submit_runner_ram:
+            self.submit_runner_ram = submit_runner_ram
+        else:
+            self.submit_runner_ram = 1024
+
+        if self.submit_runner_ram <= 0:
+            raise Exception("Value of --submit-runner-ram must be greater than zero")
 
     def update_pipeline_component(self, record):
         pass
 
     def arvados_job_spec(self, *args, **kwargs):
-        self.name = os.path.basename(self.tool.tool["id"])
+        if self.name is None:
+            self.name = os.path.basename(self.tool.tool["id"])
         workflowmapper = upload_instance(self.arvrunner, self.name, self.tool, self.job_order)
         adjustDirObjs(self.job_order, trim_listing)
         return workflowmapper
@@ -191,7 +207,7 @@ class Runner(object):
         else:
             processStatus = "permanentFail"
 
-        outputs = None
+        outputs = {}
         try:
             try:
                 self.final_output = record["output"]
@@ -199,8 +215,10 @@ class Runner(object):
                                                            api_client=self.arvrunner.api,
                                                            keep_client=self.arvrunner.keep_client,
                                                            num_retries=self.arvrunner.num_retries)
-                with outc.open("cwl.output.json") as f:
-                    outputs = json.load(f)
+                if "cwl.output.json" in outc:
+                    with outc.open("cwl.output.json") as f:
+                        if f.size() > 0:
+                            outputs = json.load(f)
                 def keepify(fileobj):
                     path = fileobj["location"]
                     if not path.startswith("keep:"):
@@ -208,7 +226,8 @@ 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"]]
+            if record["uuid"] in self.arvrunner.processes:
+                del self.arvrunner.processes[record["uuid"]]