Peter Amstutz [Fri, 23 Feb 2018 19:31:40 +0000 (14:31 -0500)]
12315: Add abstract show_children query parameter
Can't use requesting_container_uuid filter directly because it breaks
query of jobs and pipelines. Add abstract show_children query
parameter. Default is to hide children processes.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Sat, 17 Feb 2018 04:18:17 +0000 (23:18 -0500)]
12315: Add "exclude child processes" checkbox to /all_processes.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 16 Feb 2018 19:09:30 +0000 (14:09 -0500)]
Merge branch '13098-assign-hostname'
refs #13098
refs #12199
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 16 Feb 2018 18:55:24 +0000 (13:55 -0500)]
13098: 12199: Fix hostname assigned but not saved.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 16 Feb 2018 17:48:34 +0000 (12:48 -0500)]
Merge branch '13063-update-azure-sdk'
refs #13063
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 16 Feb 2018 17:41:48 +0000 (12:41 -0500)]
13063: Use upstream azure-sdk-for-go.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 16 Feb 2018 16:41:01 +0000 (11:41 -0500)]
Merge branch '13090-eval-timeout' closes #13090
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 16 Feb 2018 15:53:49 +0000 (10:53 -0500)]
13090: Pass through --eval-timeout to container command line.
Also adds a check so that --ignore-docker-for-reuse can't be used with
containers, refs #12666
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 15 Feb 2018 20:31:33 +0000 (15:31 -0500)]
Add missing parameter to update call.
fixes #12199
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 15 Feb 2018 19:51:43 +0000 (14:51 -0500)]
Merge branch '11876-R-deps' refs #11876
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 15 Feb 2018 18:34:11 +0000 (13:34 -0500)]
11876: Pin R deps that are installed from gitub.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 15 Feb 2018 18:38:55 +0000 (13:38 -0500)]
Merge branch '13063-update-azure-sdk'
closes #13063
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Thu, 15 Feb 2018 16:53:26 +0000 (13:53 -0300)]
Merge branch '11454-remove-button-removal'
Refs #11454
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Thu, 15 Feb 2018 16:07:24 +0000 (11:07 -0500)]
R SDK documentation link fix refs #11876
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Thu, 15 Feb 2018 16:00:57 +0000 (13:00 -0300)]
11454: Code readability enhancement.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Thu, 15 Feb 2018 15:55:37 +0000 (10:55 -0500)]
13063: Don't use azure default delay-and-retry loop.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Thu, 15 Feb 2018 14:57:31 +0000 (11:57 -0300)]
11454: Don't show 'Remove' session button when listed on remoteHosts.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Wed, 14 Feb 2018 21:16:12 +0000 (16:16 -0500)]
13063: Update azure storage client library.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Wed, 14 Feb 2018 16:53:04 +0000 (13:53 -0300)]
Merge branch '12863-wb-cr-status'
Closes #12863
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 14 Feb 2018 16:08:05 +0000 (13:08 -0300)]
Merge branch '13023-wb-log-newlines'
Closes #13023
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Wed, 14 Feb 2018 15:33:49 +0000 (10:33 -0500)]
Merge branch '12199-dispatch-to-node-type'
refs #12199
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 14 Feb 2018 15:20:02 +0000 (10:20 -0500)]
Merge branch '13025-keepstore-metrics'
refs #13025
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 14 Feb 2018 15:10:24 +0000 (10:10 -0500)]
12199: Fix job_uuid missing from nodes#update response.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 13 Feb 2018 20:10:40 +0000 (15:10 -0500)]
12199: Ensure scratch space for tmp mounts when choosing node type.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Tue, 13 Feb 2018 19:45:59 +0000 (16:45 -0300)]
13023: Workaround firefox copy&paste bug on jobs & pipeline log viewers.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 13 Feb 2018 19:13:39 +0000 (16:13 -0300)]
13023: Fix integration test.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Tue, 13 Feb 2018 16:40:18 +0000 (11:40 -0500)]
12199: Move services/dispatchcloud to lib/dispatchcloud.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Tue, 13 Feb 2018 16:19:47 +0000 (13:19 -0300)]
13023: Fixes related tests.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 13 Feb 2018 16:01:30 +0000 (13:01 -0300)]
13023: Replaces div with pre tags on 'Recent logs' viewer.
This is to workaround a Firefox bug:
https://bugzilla.mozilla.org/show_bug.cgi?id=
1174452
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 13 Feb 2018 13:56:44 +0000 (10:56 -0300)]
12863: Adds CR's state label on description cell.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 12 Feb 2018 22:41:13 +0000 (19:41 -0300)]
12863: Adds column showing process status on project pages.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Mon, 12 Feb 2018 22:28:22 +0000 (17:28 -0500)]
12199: Merge branch 'master' into 12199-dispatch-to-node-type
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Feb 2018 22:06:13 +0000 (17:06 -0500)]
12199: Improve race handling in busywait.
The previous implementation was "call f() until it's truthy, then
assert f()". The assertion fails if f() returns truthy but then
returns falsy on the next call.
The new implementation doesn't call f() again after it returns truthy
once.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Feb 2018 21:48:15 +0000 (16:48 -0500)]
12199: Fix errant uses of size.name that should be size.id.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Feb 2018 21:39:23 +0000 (16:39 -0500)]
12199: Update integration tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Feb 2018 19:53:50 +0000 (14:53 -0500)]
13025: Merge branch 'master' into 13025-keepstore-metrics
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Feb 2018 19:51:17 +0000 (14:51 -0500)]
13025: Revert returning WroteStatus()==200 if no header was written.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Mon, 12 Feb 2018 18:41:44 +0000 (15:41 -0300)]
Merge branch '11454-wb-federated-search'
Closes #11454
Refs #12959
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 12 Feb 2018 17:15:11 +0000 (14:15 -0300)]
11454: Avoid instantiating new SessionDB before autoRedirectToHomeCluster()
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 12 Feb 2018 16:40:11 +0000 (13:40 -0300)]
11454: A couple of fixes/enhancements:
* Only try to migrate non federated sessions on /sessions page.
* autoLoadRemoteHosts only loads missing remotes, without reactivating
disabled sessions.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Mon, 12 Feb 2018 16:30:43 +0000 (11:30 -0500)]
13025: Lint.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Mon, 12 Feb 2018 16:12:07 +0000 (13:12 -0300)]
11454: Removes workbench links on /sessions page.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Mon, 12 Feb 2018 02:27:32 +0000 (21:27 -0500)]
Merge branch '12840-cancelled-pipeline'
fixes #12840
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Feb 2018 02:24:48 +0000 (21:24 -0500)]
Merge branch '12991-docker-memory-limit'
fixes #12991
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 12 Feb 2018 02:23:40 +0000 (21:23 -0500)]
Merge branch '13022-tmp-cleanup'
fixes #13022
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 9 Feb 2018 19:20:32 +0000 (14:20 -0500)]
Merge branch '11876-r-sdk' documentation, refs #11876
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Feb 2018 19:10:43 +0000 (14:10 -0500)]
11876: Improve formatting
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Feb 2018 18:42:42 +0000 (13:42 -0500)]
11876: Update installation instructions
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Feb 2018 14:36:34 +0000 (09:36 -0500)]
11876: Update install instructions to r.arvados.org
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Feb 2018 14:11:18 +0000 (09:11 -0500)]
11876: Arvbox support for building R docs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 9 Feb 2018 14:14:51 +0000 (09:14 -0500)]
11876: Build R SDK reference pages for doc site
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Fri, 9 Feb 2018 02:26:57 +0000 (23:26 -0300)]
11454: Replaced javascript events with proper form values
on the search results form buttons.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Thu, 8 Feb 2018 22:11:44 +0000 (19:11 -0300)]
11454: Code cleanup. Removed local wb link on sessions page.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Thu, 8 Feb 2018 21:49:48 +0000 (18:49 -0300)]
11454: Replace link buttons with form buttons on search results,
so that embedded api tokens aren't shared accidentally.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Thu, 8 Feb 2018 20:22:02 +0000 (17:22 -0300)]
Merge branch '11454-fix-syntax-errors'
Refs #11454
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Thu, 8 Feb 2018 19:49:42 +0000 (16:49 -0300)]
11454: Syntax errors fixes.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Thu, 8 Feb 2018 19:04:37 +0000 (14:04 -0500)]
12840: Report pipeline state=Failed on job creation failure.
There's no failed job in this case, because there's no job, but
a-r-p-i does set components_summary.failed > 0.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Thu, 8 Feb 2018 16:59:10 +0000 (13:59 -0300)]
Merge branch '11454-wb-federated-search'
Refs #11454
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Fuad Muhic [Thu, 8 Feb 2018 11:45:34 +0000 (12:45 +0100)]
Added documentation for print classes
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Wed, 7 Feb 2018 16:42:56 +0000 (17:42 +0100)]
Added documentation to each public class of SDK.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Wed, 7 Feb 2018 11:19:25 +0000 (12:19 +0100)]
Replaced README with README.Rmd
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Tom Clegg [Tue, 6 Feb 2018 22:52:18 +0000 (17:52 -0500)]
13025: Add request time metrics at /metrics and /metrics.json.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 6 Feb 2018 18:15:17 +0000 (13:15 -0500)]
Merge branch '11876-r-sdk' refs #11876
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fuad Muhic [Tue, 6 Feb 2018 15:06:39 +0000 (16:06 +0100)]
Fix 5 failing tests
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Tue, 6 Feb 2018 09:46:30 +0000 (10:46 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Tom Clegg [Mon, 5 Feb 2018 22:00:27 +0000 (17:00 -0500)]
12991: Propagate memory and CPU limits to docker container.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Mon, 5 Feb 2018 21:27:07 +0000 (18:27 -0300)]
11454: Remotes listed on remoteHosts show "enable/disable" action button
instead of "Log in/Log out".
When a listed remote rejects the salted token, the session shows as
disabled.
When a user entered (ie: not listed) remote rejects the salted token,
classic login is attempted.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 5 Feb 2018 19:33:40 +0000 (16:33 -0300)]
11454: When adding a uuid prefix on the add session box, append
'.arvadosapi.com' before trying to get the API server url.
When a salted token is rejected, save the the session as logged out.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Mon, 5 Feb 2018 16:34:55 +0000 (11:34 -0500)]
13022: Don't abandon cleanup tasks on SIGTERM.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 5 Feb 2018 14:52:18 +0000 (09:52 -0500)]
12199: Make operator precedence more obvious.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 2 Feb 2018 21:46:32 +0000 (16:46 -0500)]
12199: Track slurm node features, avoid redundant updates.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Sat, 3 Feb 2018 04:11:46 +0000 (23:11 -0500)]
11876: Add sdk/R to run-tests.sh
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Fri, 2 Feb 2018 22:29:37 +0000 (19:29 -0300)]
11454: On /search & /sessions page, check if the current user is
from a remote cluster, and if that's the case, redirect to the
proper home cluster workbench's page.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Thu, 1 Feb 2018 15:32:53 +0000 (10:32 -0500)]
12840: Differentiate "Cancelled" from "Failed" pipeline instances.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Fri, 2 Feb 2018 20:49:00 +0000 (17:49 -0300)]
11454: Add the salted token on search result links from federated
remote hosts to get auto-logged in when clicking through.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 2 Feb 2018 19:23:58 +0000 (16:23 -0300)]
Merge branch '12268-libcloud-2-3-0'
Refs #12268
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 2 Feb 2018 18:01:53 +0000 (15:01 -0300)]
12268: Update the libcloud dependency to our forked version 2.2.2.dev4
that's really 2.3.0 release candidate from the libcloud project, to
be able to do some stress testing.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 2 Feb 2018 14:53:48 +0000 (11:53 -0300)]
11454: Removed unnecessary call on migrateNonFederatedSessions()
Added auto loading of remote hosts listed on home cluster's api discovery doc. (WIP)
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Fuad Muhic [Fri, 2 Feb 2018 14:45:41 +0000 (15:45 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Fri, 2 Feb 2018 14:41:44 +0000 (15:41 +0100)]
Arvados class now accepts additional parameter which specifies max
number of failed connection retries
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Tom Clegg [Thu, 1 Feb 2018 16:51:40 +0000 (11:51 -0500)]
Merge branch '12902-queued-to-cancelled'
refs #12902
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Thu, 1 Feb 2018 16:40:17 +0000 (13:40 -0300)]
11454: Show a link to the remote workbench on the sessions page.
On page load, detect those non-federated active sessions and try to
migrate them to federated logins just in case they're stale sessions.
If the federated login doesn't succeed, keep the session's previous state.
Removed workbench remote_hosts config.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Thu, 1 Feb 2018 16:35:30 +0000 (11:35 -0500)]
Merge branch '12764-secure-tmp-parent' refs #12764
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 1 Feb 2018 16:32:33 +0000 (11:32 -0500)]
12764: Set mode on copied single files. Fix tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 1 Feb 2018 15:59:53 +0000 (10:59 -0500)]
12764: Explicitly set desired permissions on copied files/dirs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 31 Jan 2018 21:59:50 +0000 (16:59 -0500)]
12764: Remove CleanupTempDir. Better name for parent temp.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 31 Jan 2018 21:22:31 +0000 (16:22 -0500)]
12764: crunch-run temporary directories have common parent
Some directories created by crunch-run need to be world
readable/writable. Apply path-based security using parent directory
with mode 0700. Enables crunch-run to bind into the container while
avoiding making the directory trivially accessible to anyone on the
host.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Wed, 31 Jan 2018 19:37:15 +0000 (16:37 -0300)]
11454: Do federated logins by requesting the current user object
instead of the classic login flow.
When the user is inactive on the remote cluster, label the session
properly and exclude it from SessionDB.loadActive()'s results.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Wed, 31 Jan 2018 19:34:26 +0000 (14:34 -0500)]
Writable staged files/dirs need to be 0777 to match outdir mode. refs #12764
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 31 Jan 2018 16:26:53 +0000 (11:26 -0500)]
Fix sdk/cwl unit test refs #12934
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 31 Jan 2018 15:51:44 +0000 (10:51 -0500)]
Merge branch '12934-cwl-dir-output' refs #12934
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 31 Jan 2018 15:17:21 +0000 (10:17 -0500)]
12902: Offer Cancel button for "on hold" containers.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 31 Jan 2018 15:09:11 +0000 (10:09 -0500)]
12902: Say "created at" instead of "started at" for a queued ctr.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 31 Jan 2018 14:48:03 +0000 (09:48 -0500)]
12902: Fix crash on null container_request name.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 31 Jan 2018 03:41:01 +0000 (22:41 -0500)]
12902: Label CRs "Cancelled" if finalized with incomplete container.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 30 Jan 2018 22:56:13 +0000 (17:56 -0500)]
12902: Update state=Final when cancelling a container request.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 23 Jan 2018 15:40:21 +0000 (10:40 -0500)]
12902: Leave child CR "cancelled" (not "on hold") when parent exits.
Changing a container's priority to 0 effects "cancel" only after it
has started. Before that, it just gets held in the queue with priority
0. The child CRs of a terminated container are presumed abandoned, so
it makes more sense to finalize them.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 31 Jan 2018 14:23:57 +0000 (09:23 -0500)]
12934: Tweak output of directories to pass conformance tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fuad Muhic [Wed, 31 Jan 2018 13:36:57 +0000 (14:36 +0100)]
Reworkder HttpRequest class to use RETRY functionality
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Wed, 31 Jan 2018 09:28:51 +0000 (10:28 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
projects / arvados.git / log