9767: set name of the container_request based on the workflow name.

[arvados.git] / crunch_scripts / cwl-runner

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 4b6ff44a2c6ff69d7d87d674642c3189dda530be..fe4e8009aca1af0b04fb483983a09fd59de25390 100755 (executable)
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -18,8 +18,9 @@ import logging
 import os
 import json
 import argparse
+import re
 from arvados.api import OrderedJsonModel
-from cwltool.process import adjustFileObjs
+from cwltool.process import adjustFileObjs, adjustDirObjs
 from cwltool.load_tool import load_tool
 
 # Print package versions
@@ -30,25 +31,28 @@ api = arvados.api("v1")
 try:
     job_order_object = arvados.current_job()['script_parameters']
 
+    pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
+
     def keeppath(v):
-        if arvados.util.keep_locator_pattern.match(v):
-            return "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
+        if pdh_path.match(v):
+            return "keep:%s" % v
         else:
             return v
 
     def keeppathObj(v):
         v["location"] = keeppath(v["location"])
 
-    job_order_object["cwl:tool"] = keeppath(job_order_object["cwl:tool"])
+    job_order_object["cwl:tool"] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object["cwl:tool"])
 
     for k,v in job_order_object.items():
         if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
             job_order_object[k] = {
                 "class": "File",
-                "path": keeppath(v)
+                "location": "keep:%s" % v
             }
 
     adjustFileObjs(job_order_object, keeppathObj)
+    adjustDirObjs(job_order_object, keeppathObj)
 
     runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))