[ARVADOS] updated: 529a648458ceefc02d77abf470a2005a099d9907

[Git user]

Summary of changes:
 crunch_scripts/crunchrunner                    |  2 +-
 sdk/cli/bin/crunch-job                         | 14 +++++++++
 sdk/cwl/arvados_cwl/__init__.py                | 41 +++++++++++---------------
 sdk/go/crunchrunner/crunchrunner.go            | 24 ++++++++++-----
 tools/arvbox/bin/arvbox                        | 11 +------
 tools/arvbox/lib/arvbox/docker/crunch-setup.sh |  3 +-
 6 files changed, 51 insertions(+), 44 deletions(-)

       via  529a648458ceefc02d77abf470a2005a099d9907 (commit)
       via  204bba7b53a2f7eba36782facf6dc8903aee120a (commit)
       via  94f5be8c86ad975ee7aa9f3df87be23fbc154dec (commit)
       via  e9667fff4716e4990fec560f92c1e0f4a6cb686f (commit)
       via  dfc93aac9c256d6ebb868aeb6c2107821e9fd041 (commit)
       via  4727a3b6417bd254b3e8bca1bd19a77773493572 (commit)
      from  414ab8bf556c08065d8235a80822344ab5265aae (commit)

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commit 529a648458ceefc02d77abf470a2005a099d9907
Merge: 204bba7 94f5be8
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Mar 29 13:34:40 2016 -0400

    Merge branch '8815-crunchrunner-everywhere' into 8654-arv-jobs-cwl-runner
    
    Conflicts:
    	sdk/cwl/arvados_cwl/__init__.py

diff --cc sdk/cwl/arvados_cwl/__init__.py
index 42e0da2,e3fd1fc..5c7ec4d
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@@ -505,39 -393,9 +503,24 @@@ class ArvCwlRunner(object)
          self.uploaded[src] = pair
  
      def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
 +        self.debug = args.debug
 +
 +        if args.quiet:
 +            logger.setLevel(logging.WARN)
 +            logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
 +
-         try:
-             self.api.collections().get(uuid=crunchrunner_pdh).execute()
-         except arvados.errors.ApiError as e:
-             import httplib2
-             h = httplib2.Http(ca_certs=arvados.util.ca_certs_path())
-             resp, content = h.request(crunchrunner_download, "GET")
-             resp2, content2 = h.request(certs_download, "GET")
-             with arvados.collection.Collection() as col:
-                 with col.open("crunchrunner", "w") as f:
-                     f.write(content)
-                 with col.open("ca-certificates.crt", "w") as f:
-                     f.write(content2)
- 
-                 col.save_new("crunchrunner binary", ensure_unique_name=True)
- 
 +        useruuid = self.api.users().current().execute()["uuid"]
 +        self.project_uuid = args.project_uuid if args.project_uuid else useruuid
 +        self.pipeline = None
 +
 +        if args.submit:
 +            runnerjob = RunnerJob(self, tool, job_order, args.enable_reuse)
 +            if not args.wait:
 +                runnerjob.run()
 +                return
 +
          events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
  
 -        self.debug = args.debug
          self.fs_access = CollectionFsAccess(input_basedir)
  
          kwargs["fs_access"] = self.fs_access

commit 204bba7b53a2f7eba36782facf6dc8903aee120a
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Mar 29 13:30:17 2016 -0400

    8654: Make --submit --wait the default mode.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index eab5d4a..42e0da2 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -622,6 +622,7 @@ def versionstring():
 def main(args, stdout, stderr, api_client=None):
     args.insert(0, "--leave-outputs")
     parser = cwltool.main.arg_parser()
+
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--enable-reuse", action="store_true",
                         default=True, dest="enable_reuse",
@@ -629,11 +630,20 @@ def main(args, stdout, stderr, api_client=None):
     exgroup.add_argument("--disable-reuse", action="store_false",
                         default=True, dest="enable_reuse",
                         help="")
+
     parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs")
-    parser.add_argument("--submit", action="store_true", help="Submit job and print job uuid.",
-                        default=False)
-    parser.add_argument("--wait", action="store_true", help="Wait for completion after submitting cwl-runner job.",
-                        default=False)
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--submit", action="store_true", help="Submit runner job so workflow can run unattended.",
+                        default=True, dest="submit")
+    exgroup.add_argument("--local", action="store_false", help="Workflow runner runs on local host and submits jobs.",
+                        default=True, dest="submit")
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
+                        default=True, dest="wait")
+    exgroup.add_argument("--no-wait", action="store_false", help="Exit after submitting workflow runner job.",
+                        default=True, dest="wait")
 
     try:
         if api_client is None:

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