Tom Clegg [Tue, 18 Sep 2018 19:40:26 +0000 (15:40 -0400)]
13994: Merge branch 'master' into 13994-proxy-remote
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 17 Sep 2018 18:34:05 +0000 (14:34 -0400)]
13994: Fix missing error message.
When the request failed too early to produce an HTTP status code, the
error returned to the client was:
"Could not write sufficient replicas: [0] ; [0] "
Now the error message is included. It gets truncated to 100 chars
later on, but it's something:
"Could not write sufficient replicas: [0] Put
http://localhost:52367/
831f95ffae4233b52059fbb8a0c62fbf: dial tcp [::1
]:52367: connect: conn; [0] Put
http://localhost:53807/
831f95ffae4233b52059fbb8a0c62fbf: dial tcp
[::1]:53807: connect: conn"
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 17 Sep 2018 18:33:59 +0000 (14:33 -0400)]
13994: Fix service discovery race.
Making keepclient.RefreshServiceDiscovery asynchronous didn't work
out: tests rely on it to ensure old services won't be used.
Instead, speed things up a bit by refreshing all known clients'
service lists concurrently instead of serially.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 17 Sep 2018 15:58:37 +0000 (11:58 -0400)]
Merge branch '14087-federated-collection-by-pdh' refs #14087
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 17 Sep 2018 15:58:22 +0000 (11:58 -0400)]
Merge branch '14203-crunch-run-mkdir' closes #14203
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 17 Sep 2018 15:54:35 +0000 (11:54 -0400)]
14087: Add Accept-Encoding to list of headers to delete when proxying
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 17 Sep 2018 14:34:43 +0000 (10:34 -0400)]
13994: Fix token handling in collection performance test.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 17 Sep 2018 14:07:35 +0000 (10:07 -0400)]
13994: Use entire token for blob signatures.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 14 Sep 2018 15:39:26 +0000 (11:39 -0400)]
14203: Tweak error messages.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 14 Sep 2018 15:27:11 +0000 (11:27 -0400)]
14087: Refactor federation search for collections by PDH
The shorter, non-PDH search case now comes first. Also adjusts the
logic that decides when to skip federation and makes it wrap the
federation endpoint routing.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Thu, 13 Sep 2018 20:46:02 +0000 (17:46 -0300)]
Merge branch '13773-will-fail-container-status'
Closes #13773
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Thu, 13 Sep 2018 20:05:48 +0000 (17:05 -0300)]
Merge branch 'master' into 13773-will-fail-container-status
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Thu, 13 Sep 2018 19:30:35 +0000 (16:30 -0300)]
13773: Update logging level checking for runtime status updates.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Thu, 13 Sep 2018 18:43:28 +0000 (14:43 -0400)]
13994: Fix import cycle.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Wed, 12 Sep 2018 20:58:00 +0000 (17:58 -0300)]
13773: Fix test
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 12 Sep 2018 20:14:41 +0000 (17:14 -0300)]
13773: Update test that confirms runtime_status is updated when a child fails
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Tue, 11 Sep 2018 16:55:05 +0000 (12:55 -0400)]
13994: Fix deadlock in keepstore tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 11 Sep 2018 16:54:41 +0000 (12:54 -0400)]
13994: Proxy to remote cluster if +R hint given.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 12 Sep 2018 19:37:33 +0000 (15:37 -0400)]
14203: Mkdir failing with os.ErrExist is not a fatal error
Don't fail CaptureOutput and cancel the container if a Mkdir returns
os.ErrExist because a directory already exists. Fixes bcbio failing
postprocess_variants step.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Wed, 12 Sep 2018 18:41:42 +0000 (15:41 -0300)]
13773: Removed superfluous documentation
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 12 Sep 2018 12:13:35 +0000 (09:13 -0300)]
13773: Add well known runtime_status' keys data type validation.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Tue, 11 Sep 2018 15:40:10 +0000 (11:40 -0400)]
Merge branch '13993-federated-collection' refs #13993
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 11 Sep 2018 13:52:27 +0000 (09:52 -0400)]
14087: Rate limit the number of parallel requests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 10 Sep 2018 21:03:19 +0000 (17:03 -0400)]
14087: Remove debug print. Comments.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 10 Sep 2018 20:49:18 +0000 (16:49 -0400)]
14087: Check for remote clusters before searching
Added some more comments about the implementation as well.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 10 Sep 2018 19:28:35 +0000 (15:28 -0400)]
14087: Fetch federated collection by PDH
Implement parallel query of remotes. First response is returned to
client, other responses in flight are cancelled. Adds tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 7 Sep 2018 22:14:26 +0000 (18:14 -0400)]
14087: Federated fetch by PDH WIP
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 11 Sep 2018 15:05:34 +0000 (11:05 -0400)]
13993: Add TestGetLocalCollection
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Tue, 11 Sep 2018 14:44:48 +0000 (11:44 -0300)]
13773: Enhance error/warning runtime status display on workbench.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 11 Sep 2018 14:42:37 +0000 (11:42 -0300)]
13773: Don't intercept logger.info() calls for runtime status.
* On multi line log messages, use the first as a status and the rest as detail.
* Revert done.logtail() usage as it's no longer needed for failed childs
reporting.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Mon, 10 Sep 2018 21:04:37 +0000 (17:04 -0400)]
13993: Need to explicitly handle paths that don't end in /
Otherwise Go will generate a 301 Moved Permanently from collection to collections/
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 10 Sep 2018 20:20:32 +0000 (16:20 -0400)]
13993: Don't export internal types
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 10 Sep 2018 20:18:01 +0000 (16:18 -0400)]
13993: Consolidate SignedLocatorPattern with keepclient.SignedLocatorRe
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Mon, 10 Sep 2018 17:48:38 +0000 (14:48 -0300)]
13773: Updates documentation
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 7 Sep 2018 20:57:21 +0000 (17:57 -0300)]
13773: Intercept logging calls to update runtime_status on runner containers.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Fri, 7 Sep 2018 19:52:52 +0000 (15:52 -0400)]
13993: Support for federated collection requests by uuid
Do remote record retrevial using a salted token, update the block
signatures to "remote" signatures (changing +A to +R and adding the
remote cluster id), and return it to the original client.
Refactor routing and proxying of federated requeststo provide hooks to
support this and future types of requests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Fri, 7 Sep 2018 17:04:02 +0000 (14:04 -0300)]
13773: Update runtime_status_error() method to report warning & activity status
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Thu, 2 Aug 2018 20:09:52 +0000 (16:09 -0400)]
13146: Returns real json response
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 2 Aug 2018 19:35:17 +0000 (15:35 -0400)]
13146: Projects shared with me WIP
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Thu, 6 Sep 2018 14:51:40 +0000 (11:51 -0300)]
13773: Show 'Warning' label on jobs that have this runtime status and aren't failing.
* Show warning information panel on job detailed view
* Show tooltip with error/warning information on dashboard
* Fix test
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Ward Vandewege [Thu, 6 Sep 2018 14:46:10 +0000 (10:46 -0400)]
A new version of our libcloud fork is available.
refs #14150
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Tom Clegg [Thu, 6 Sep 2018 14:37:42 +0000 (10:37 -0400)]
Merge branch '11065-optional-audit-logging'
refs #11065
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 6 Sep 2018 14:29:25 +0000 (10:29 -0400)]
11065: Merge branch 'master' into 11065-optional-audit-logging
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 5 Sep 2018 21:37:57 +0000 (17:37 -0400)]
Add http_timeout to runtimeContext refs #13542
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 5 Sep 2018 20:22:31 +0000 (16:22 -0400)]
Merge branch '14082-round-off' refs #14082
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 5 Sep 2018 20:21:39 +0000 (16:21 -0400)]
Merge branch '13973-max-cr-priority' refs #13973
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 5 Sep 2018 19:44:46 +0000 (15:44 -0400)]
Fix gofmt in slurm.go refs #14110
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Wed, 5 Sep 2018 19:41:29 +0000 (16:41 -0300)]
13773: Containers & CRs show "Failing" when a child job failed.
Also, at the detailed view an error panel is displayed with the error message
and detail, if any.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Wed, 5 Sep 2018 18:56:46 +0000 (14:56 -0400)]
Merge branch 'wtsi/13809-root_url-protocol-port-configuration'
refs #13809
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 5 Sep 2018 18:53:17 +0000 (14:53 -0400)]
Merge branch 'wtsi/python-api-timeout' refs #13542
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 5 Sep 2018 18:47:19 +0000 (14:47 -0400)]
Merge branch 'wtsi/14110-c-d-s-limit-slurm-concurrency' refs #14110
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 5 Sep 2018 18:16:28 +0000 (14:16 -0400)]
13973: Use a straightforward maximum() query to compute max priority
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 5 Sep 2018 17:57:04 +0000 (13:57 -0400)]
14082: Round up numeric values in container request that must be integers
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 4 Sep 2018 19:45:45 +0000 (15:45 -0400)]
Merge branch '14152-s3-v4-signature'
refs #14152
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 4 Sep 2018 19:37:57 +0000 (15:37 -0400)]
Merge branch '14008-containers-index'
refs #14008
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 4 Sep 2018 15:25:51 +0000 (11:25 -0400)]
Add test case for filtering on is_trashed in groups#contents.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 4 Sep 2018 15:25:18 +0000 (11:25 -0400)]
Remove redundant test case.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 4 Sep 2018 19:03:58 +0000 (15:03 -0400)]
14008: Merge branch 'master' into 14008-containers-index
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 4 Sep 2018 18:00:04 +0000 (14:00 -0400)]
14152: Use V4 signer for S3 in regions that use V4 for EC2.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 4 Sep 2018 15:36:15 +0000 (11:36 -0400)]
Merge branch '14009-container-reuse-index'
refs #14009
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Thu, 23 Aug 2018 20:28:53 +0000 (17:28 -0300)]
13773: Updates tests checking that runtime_status_error() is called when needed
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Thu, 23 Aug 2018 15:04:56 +0000 (12:04 -0300)]
13773: Updates runner container's runtime_status on child failures.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 21 Aug 2018 15:10:58 +0000 (12:10 -0300)]
13773: Add runtime_status to be accesible via API
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 14 Aug 2018 15:36:39 +0000 (12:36 -0300)]
13773: Expand test to prove that non-error runtime_status doesn't avoid reuse.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 14 Aug 2018 14:25:10 +0000 (11:25 -0300)]
13773: Fix reuse query & add tests
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 6 Aug 2018 17:45:43 +0000 (14:45 -0300)]
13773: Add documentation.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Thu, 2 Aug 2018 18:51:01 +0000 (15:51 -0300)]
13773: Filter out running containers that will fail from reuse selection.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 31 Jul 2018 13:38:56 +0000 (10:38 -0300)]
13773: Adds runtime_status field to containers on API server
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Ward Vandewege [Tue, 4 Sep 2018 02:21:14 +0000 (22:21 -0400)]
14153: Merge branch '14153-support-ruby-2.3.7'
closes #14153
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Mon, 3 Sep 2018 19:53:27 +0000 (15:53 -0400)]
Change dependency from google-api-client to cure-google-api-client so
that we can use ruby 2.3.7
refs #14153
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Tue, 4 Sep 2018 02:15:56 +0000 (22:15 -0400)]
Make sure to bump the dependency on the arvados gems to the 1.2 series.
refs #14032
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Mon, 3 Sep 2018 18:37:44 +0000 (14:37 -0400)]
Documentation fix: make the use of $uuid_prefix consistent.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Peter Amstutz [Sat, 25 Aug 2018 14:53:32 +0000 (10:53 -0400)]
Revert ruamel.yaml build to 0.14.12 refs #14075
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Sat, 25 Aug 2018 13:19:15 +0000 (09:19 -0400)]
Fix test for changed expectation refs #13973
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Sat, 25 Aug 2018 00:37:41 +0000 (20:37 -0400)]
'trollop' gem renamed to 'optimist' fix build no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 24 Aug 2018 21:27:35 +0000 (17:27 -0400)]
Build ruamel.yaml 0.15.26 for a-c-r
This is last version before a serious regression was introduced in
parsing flow mapping
https://bitbucket.org/ruamel/yaml/issues/227/regression-parsing-flow-mapping
This affects 0.15.27 to 0.15.51
0.15.52 haven't been tested because they have a different
compatibility problem:
https://github.com/common-workflow-language/schema_salad/pull/195
refs #14075
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Fri, 24 Aug 2018 19:45:08 +0000 (15:45 -0400)]
Merge branch '13456-controller-timeout'
refs #13456
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 23 Aug 2018 18:32:03 +0000 (14:32 -0400)]
13456: Use HTTPRequestTimeout in test suite.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 24 Aug 2018 19:33:56 +0000 (15:33 -0400)]
Merge branch '13973-child-priority' refs #13973
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 24 Aug 2018 19:33:05 +0000 (15:33 -0400)]
Merge branch '14075-uploadfiles' refs #14075
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 24 Aug 2018 19:28:16 +0000 (15:28 -0400)]
Merge branch 'master' into 14075-uploadfiles
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 24 Aug 2018 17:51:56 +0000 (13:51 -0400)]
14075: Tweak ruamel.yaml verision range in setup.py
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 24 Aug 2018 16:12:47 +0000 (12:12 -0400)]
14075: Fix cwl unit tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Joshua C. Randall [Mon, 20 Aug 2018 16:31:29 +0000 (17:31 +0100)]
fix slow queries in uploadfiles
change uploadfiles to include pdh in name of collection rather then using ensure_unique_names=True
also don't bother listing existing empty collections
Arvados-DCO-1.1-Signed-off-by: Joshua C. Randall <jcrandall@alum.mit.edu>
Tom Clegg [Fri, 24 Aug 2018 16:06:56 +0000 (12:06 -0400)]
Merge branch '13959-timeouts-and-logging'
fixes #13959
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 24 Aug 2018 16:06:18 +0000 (12:06 -0400)]
13959: Merge branch 'master' into 13959-timeouts-and-logging
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 24 Aug 2018 16:01:50 +0000 (12:01 -0400)]
14008: Merge branch 'master' into 14008-containers-index
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 24 Aug 2018 15:57:07 +0000 (11:57 -0400)]
14008: Add container queue index.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 24 Aug 2018 15:36:10 +0000 (11:36 -0400)]
14009: Index containers table for reuse searches.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 24 Aug 2018 14:13:44 +0000 (10:13 -0400)]
13973: Tweak test for inheriting CR priority
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Ward Vandewege [Fri, 24 Aug 2018 05:50:41 +0000 (01:50 -0400)]
We need to build ws 0.4.2 for ubuntu1404 and ubuntu1604
refs #13823
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Fri, 24 Aug 2018 05:49:40 +0000 (01:49 -0400)]
Switch to use ha.pool.sks-keyservers.net everywhere, which is more reliable
than pool.sks-keyservers.net
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Thu, 23 Aug 2018 21:39:56 +0000 (17:39 -0400)]
Improvement for run-tests.sh: support multiple occurrences of the
--only argument - syntax fix.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Thu, 23 Aug 2018 21:27:18 +0000 (17:27 -0400)]
Bugfix for run-tests.sh: run sdk/R install if docs are being built,
they rely on it.
Improvement for run-tests.sh: support multiple occurrences of the
--only argument.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Joshua C. Randall [Thu, 23 Aug 2018 19:49:44 +0000 (19:49 +0000)]
limit concurrent slurm commands
use a semaphore channel to limit concurrent sbatch/scancel/scontrol commands to 3.
squeue is already limited to one at a time.
fixes 14110
Arvados-DCO-1.1-Signed-off-by: Joshua C. Randall <jcrandall@alum.mit.edu>
Ward Vandewege [Thu, 23 Aug 2018 16:16:08 +0000 (12:16 -0400)]
Fix for run-tests.sh: do not run sdk/R install if the --skip sdk/R option is
set.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Thu, 23 Aug 2018 13:01:27 +0000 (09:01 -0400)]
Merge branch '13823-bionic'
refs #13823
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Wed, 22 Aug 2018 12:40:41 +0000 (08:40 -0400)]
Add support for package testing to our ubuntu 18.04 packages.
refs #13823
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Wed, 22 Aug 2018 12:38:34 +0000 (08:38 -0400)]
Remove spurious error output in package testing script.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Wed, 22 Aug 2018 12:38:34 +0000 (08:38 -0400)]
Remove spurious error output in package testing script.
No issue #
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
projects / arvados.git / log