13111: Merge branch 'master' into 13111-webdav-projects

[arvados.git] / 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 8073620be15f7e653bd382c21aad325f791aac2c..aaeffea24b22ef0a3dc4a2de3b35e78f4d5d8e46 100644 (file)
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -1,3 +1,7 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
 # Crunch script integration for running arvados-cwl-runner (importing
 # arvados_cwl module) inside a crunch job.
 #
@@ -19,11 +23,12 @@ import re
 import functools
 
 from arvados.api import OrderedJsonModel
-from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, normalizeFilesDirs
+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 .fsaccess import CollectionFetcher
+from .fsaccess import CollectionFetcher, CollectionFsAccess
 
 logger = logging.getLogger('arvados.cwl-runner')
 
@@ -52,7 +57,8 @@ def run():
                 return v
 
         def keeppathObj(v):
-            v["location"] = keeppath(v["location"])
+            if "location" in v:
+                v["location"] = keeppath(v["location"])
 
         for k,v in job_order_object.items():
             if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
@@ -69,6 +75,8 @@ def run():
         output_tags = None
         enable_reuse = True
         on_error = "continue"
+        debug = False
+
         if "arv:output_name" in job_order_object:
             output_name = job_order_object["arv:output_name"]
             del job_order_object["arv:output_name"]
@@ -85,25 +93,45 @@ def run():
             on_error = job_order_object["arv:on_error"]
             del job_order_object["arv:on_error"]
 
+        if "arv:debug" in job_order_object:
+            debug = job_order_object["arv:debug"]
+            del job_order_object["arv:debug"]
+
         runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
                                           output_name=output_name, output_tags=output_tags)
 
+        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=api,
-                                                            keep_client=arvados.keep.KeepClient(api_client=api, num_retries=4)))
+                                                  api_client=runner.api,
+                                                  fs_access=make_fs_access(""),
+                                                  num_retries=runner.num_retries))
+
+        if debug:
+            logger.setLevel(logging.DEBUG)
+            logging.getLogger('arvados').setLevel(logging.DEBUG)
+            logging.getLogger("cwltool").setLevel(logging.DEBUG)
 
         args = argparse.Namespace()
         args.project_uuid = arvados.current_job()["owner_uuid"]
         args.enable_reuse = enable_reuse
         args.on_error = on_error
         args.submit = False
-        args.debug = False
+        args.debug = debug
         args.quiet = False
         args.ignore_docker_for_reuse = False
         args.basedir = os.getcwd()
         args.name = None
         args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
+        args.make_fs_access = make_fs_access
+        args.trash_intermediate = False
+        args.intermediate_output_ttl = 0
+        args.priority = arvados_cwl.DEFAULT_PRIORITY
+        args.do_validate = True
+        args.disable_js_validation = False
+
         runner.arv_executor(t, job_order_object, **vars(args))
     except Exception as e:
         if isinstance(e, WorkflowException):