X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/98911cfe4792b20798858cefb353c451460e1a80..6c78b28f9f54664babc57a4b4372c502065ed5d1:/sdk/cwl/arvados_cwl/crunch_script.py

diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py
index bf940eca4b..c886550d41 100644
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -10,6 +10,9 @@
 # tool.  When the workflow completes, record the output object in an output
 # collection for this runner job.
 
+from past.builtins import basestring
+from future.utils import viewitems
+
 import arvados
 import arvados_cwl
 import arvados.collection
@@ -27,6 +30,7 @@ from cwltool.process import shortname
 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, normalizeFilesDirs
 from cwltool.load_tool import load_tool
 from cwltool.errors import WorkflowException
+from arvados_cwl.context import ArvRuntimeContext
 
 from .fsaccess import CollectionFetcher, CollectionFsAccess
 
@@ -60,7 +64,7 @@ def run():
             if "location" in v:
                 v["location"] = keeppath(v["location"])
 
-        for k,v in job_order_object.items():
+        for k,v in viewitems(job_order_object):
             if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
                 job_order_object[k] = {
                     "class": "File",
@@ -97,25 +101,28 @@ def run():
             debug = job_order_object["arv:debug"]
             del job_order_object["arv:debug"]
 
-        runner = arvados_cwl.ArvCwlRunner(api_client=arvados.safeapi.ThreadSafeApiCache(
+        arvargs = argparse.Namespace()
+        arvargs.work_api = "jobs"
+        arvargs.output_name = output_name
+        arvargs.output_tags = output_tags
+        arvargs.thread_count = 1
+        arvargs.collection_cache_size = None
+
+        runner = arvados_cwl.ArvCwlExecutor(api_client=arvados.safeapi.ThreadSafeApiCache(
             api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}),
-                                          output_name=output_name, output_tags=output_tags)
+                                          arvargs=arvargs)
 
         make_fs_access = functools.partial(CollectionFsAccess,
                                  collection_cache=runner.collection_cache)
 
-        t = load_tool(toolpath, runner.arv_make_tool,
-                      fetcher_constructor=functools.partial(CollectionFetcher,
-                                                  api_client=runner.api,
-                                                  fs_access=make_fs_access(""),
-                                                  num_retries=runner.num_retries))
+        t = load_tool(toolpath, runner.loadingContext)
 
         if debug:
             logger.setLevel(logging.DEBUG)
             logging.getLogger('arvados').setLevel(logging.DEBUG)
             logging.getLogger("cwltool").setLevel(logging.DEBUG)
 
-        args = argparse.Namespace()
+        args = ArvRuntimeContext(vars(arvargs))
         args.project_uuid = arvados.current_job()["owner_uuid"]
         args.enable_reuse = enable_reuse
         args.on_error = on_error
@@ -132,8 +139,9 @@ def run():
         args.priority = arvados_cwl.DEFAULT_PRIORITY
         args.do_validate = True
         args.disable_js_validation = False
+        args.tmp_outdir_prefix = "tmp"
 
-        runner.arv_executor(t, job_order_object, **vars(args))
+        runner.arv_executor(t, job_order_object, args, logger=logger)
     except Exception as e:
         if isinstance(e, WorkflowException):
             logging.info("Workflow error %s", e)