[ARVADOS] updated: e4a51416586f73593ac68bf0d2a74c53a4875f7e
Git user
git at public.curoverse.com
Tue Nov 22 14:07:52 EST 2016
Summary of changes:
.../app/controllers/projects_controller.rb | 4 +-
.../app/views/projects/_show_dashboard.html.erb | 16 ++-
.../app/views/projects/_show_processes.html.erb | 5 +
apps/workbench/app/views/projects/show.html.erb | 16 ++-
.../test/controllers/disabled_api_test.rb | 4 +
.../test/integration/application_layout_test.rb | 2 +-
.../test/integration/pipeline_instances_test.rb | 2 +-
apps/workbench/test/integration/projects_test.rb | 2 +-
apps/workbench/test/integration/work_units_test.rb | 2 +-
apps/workbench/test/performance/browsing_test.rb | 2 +-
doc/_includes/_crunch1only_begin.liquid | 2 +
doc/_includes/_crunch1only_end.liquid | 1 +
doc/_includes/_notebox_begin_warning.liquid | 2 +
doc/_includes/_pipeline_deprecation_notice.liquid | 2 +-
doc/install/install-keep-web.html.textile.liquid | 2 +-
doc/install/install-keepproxy.html.textile.liquid | 2 +-
doc/user/cwl/cwl-runner.html.textile.liquid | 8 +-
doc/user/topics/arv-run.html.textile.liquid | 4 +
...nning-pipeline-command-line.html.textile.liquid | 4 +
...tutorial-pipeline-workbench.html.textile.liquid | 4 +
sdk/cli/bin/crunch-job | 6 +-
sdk/cwl/arvados_cwl/__init__.py | 47 +++++---
sdk/cwl/arvados_cwl/arvcontainer.py | 11 +-
sdk/cwl/arvados_cwl/arvdocker.py | 5 +-
sdk/cwl/arvados_cwl/arvjob.py | 25 ++--
sdk/cwl/arvados_cwl/arvworkflow.py | 12 +-
sdk/cwl/tests/test_submit.py | 90 ++++++++++-----
sdk/go/httpserver/id_generator.go | 31 +++++
sdk/python/arvados/arvfile.py | 2 +-
services/keepstore/azure_blob_volume.go | 2 +-
services/keepstore/azure_blob_volume_test.go | 2 +-
services/keepstore/bufferpool.go | 3 +-
services/keepstore/config.go | 22 +++-
services/keepstore/config_test.go | 2 +-
services/keepstore/count.go | 44 +++++++
services/keepstore/handler_test.go | 2 +-
services/keepstore/handlers.go | 55 ++++++---
services/keepstore/keepstore.go | 8 +-
services/keepstore/logging_router.go | 60 ++++++++--
services/keepstore/pull_worker.go | 3 +-
services/keepstore/s3_volume.go | 127 +++++++++++++++++++--
services/keepstore/s3_volume_test.go | 32 +++++-
services/keepstore/trash_worker.go | 2 +-
services/keepstore/usage.go | 4 +
services/keepstore/volume.go | 45 ++++++--
services/keepstore/volume_unix.go | 10 +-
tools/arvbox/lib/arvbox/docker/common.sh | 4 +
47 files changed, 598 insertions(+), 144 deletions(-)
create mode 100644 apps/workbench/app/views/projects/_show_processes.html.erb
create mode 100644 doc/_includes/_crunch1only_begin.liquid
create mode 100644 doc/_includes/_crunch1only_end.liquid
create mode 100644 doc/_includes/_notebox_begin_warning.liquid
create mode 100644 sdk/go/httpserver/id_generator.go
create mode 100644 services/keepstore/count.go
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commit e4a51416586f73593ac68bf0d2a74c53a4875f7e
Author: radhika <radhika at curoverse.com>
Date: Tue Nov 22 14:06:59 2016 -0500
10293: invoke output_callback in a try/except block
diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index b127f68..c349839 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -115,9 +115,9 @@ class ArvadosContainer(object):
body=container_request
).execute(num_retries=self.arvrunner.num_retries)
- self.arvrunner.processes[response["uuid"]] = response["uuid"]
+ self.arvrunner.processes[response["uuid"]] = self
- logger.info("Container request %s (%s) state is %s with container %s %s", self.name, response["uuid"], response["state"])
+ logger.info("Container request %s (%s) state is %s", self.name, response["uuid"], response["state"])
if response["state"] == "Final":
self.done(response)
@@ -146,9 +146,14 @@ class ArvadosContainer(object):
processStatus = "permanentFail"
outputs = {}
+
if container["output"]:
outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
- self.output_callback(outputs, processStatus)
+ try:
+ self.output_callback(outputs, processStatus)
+ except Exception as e:
+ logger.error("Got error %s" % str(e))
+ self.output_callback({}, "permanentFail")
finally:
del self.arvrunner.processes[record["uuid"]]
commit 81ccd9264d0742ba1bf0b9dfbc31ff4f15929f3e
Merge: 9f53e08 6f461f4
Author: radhika <radhika at curoverse.com>
Date: Tue Nov 22 13:38:27 2016 -0500
Merge branch 'master' into 10293-cwl-cr-output
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