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 d7858cf5e0039fe12fd413bff9812a0342a99cd8..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)
 
@@ -162,7 +162,8 @@ def arvados_jobs_image(arvrunner):
 
 class Runner(object):
     def __init__(self, runner, tool, job_order, enable_reuse,
-                 output_name, output_tags, submit_runner_ram=0):
+                 output_name, output_tags, submit_runner_ram=0,
+                 name=None):
         self.arvrunner = runner
         self.tool = tool
         self.job_order = job_order
@@ -172,6 +173,8 @@ 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:
@@ -184,7 +187,14 @@ class Runner(object):
         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