8460: Merge branch 'master' into 8460-websocket-go

[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 6b5cd71b167a1346e18f1bbecdb1a9e55651e326..dea47567a767b34dd0252781a1d1031b9990deec 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -57,7 +57,7 @@ def upload_dependencies(arvrunner, name, document_loader,
 
     loaded = set()
     def loadref(b, u):
-        joined = urlparse.urljoin(b, u)
+        joined = document_loader.fetcher.urljoin(b, u)
         defrg, _ = urlparse.urldefrag(joined)
         if defrg not in loaded:
             loaded.add(defrg)
@@ -85,7 +85,7 @@ def upload_dependencies(arvrunner, name, document_loader,
     sc = scandeps(uri, scanobj,
                   loadref_fields,
                   set(("$include", "$schemas", "location")),
-                  loadref)
+                  loadref, urljoin=document_loader.fetcher.urljoin)
 
     normalizeFilesDirs(sc)
 
@@ -161,7 +161,9 @@ def arvados_jobs_image(arvrunner):
     return img
 
 class Runner(object):
-    def __init__(self, runner, tool, job_order, enable_reuse, output_name, output_tags):
+    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
@@ -171,12 +173,28 @@ class Runner(object):
         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 = self.tool.tool.get("label") or os.path.basename(self.tool.tool["id"])
+
+        # Need to filter this out, gets added by cwltool when providing
+        # parameters on the command line.
+        if "job_order" in self.job_order:
+            del self.job_order["job_order"]
+
         workflowmapper = upload_instance(self.arvrunner, self.name, self.tool, self.job_order)
         adjustDirObjs(self.job_order, trim_listing)
         return workflowmapper
@@ -203,8 +221,10 @@ 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:"):