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>
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>
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>
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>
Peter Amstutz [Wed, 31 Jan 2018 02:22:38 +0000 (21:22 -0500)]
Merge branch '12764-writable-file' refs #12764
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 31 Jan 2018 02:06:54 +0000 (21:06 -0500)]
12764: gofmt fix
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 31 Jan 2018 01:46:50 +0000 (20:46 -0500)]
12764: Handle empty directories. Fix test.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 31 Jan 2018 00:44:26 +0000 (19:44 -0500)]
12764: gofmt fix
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 30 Jan 2018 23:59:15 +0000 (18:59 -0500)]
12764: bump cwltool version for conformance fixes
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Tue, 30 Jan 2018 23:43:44 +0000 (20:43 -0300)]
11454: Cache the local session token's uuid after being requested from the API.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Tue, 30 Jan 2018 21:35:15 +0000 (16:35 -0500)]
Merge branch '13011-empty-block-error-411'
refs #13011
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 30 Jan 2018 21:04:34 +0000 (16:04 -0500)]
13011: Fix 411 error when writing empty block to Azure storage.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 30 Jan 2018 18:33:12 +0000 (13:33 -0500)]
12199: Keep SLURM's node properties up to date.
Change the semantics of ComputeNodeUpdateActor.sync_node so it gets
called every time a new Arvados node record appears, even if hostnames
match. The base actor's implementation now compares hostnames itself
before calling the cloud driver.
This allows the slurm update actor's sync_node method to sync SLURM
state periodically, even if hostnames don't go out of sync.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Tue, 30 Jan 2018 18:29:50 +0000 (15:29 -0300)]
Merge branch 'master' into 11454-wb-federated-search
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Tue, 30 Jan 2018 01:03:23 +0000 (20:03 -0500)]
12199: Assign slot and hostname when creating/reusing a node record.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Fuad Muhic [Tue, 30 Jan 2018 14:02:19 +0000 (15:02 +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 [Tue, 30 Jan 2018 14:00:40 +0000 (15:00 +0100)]
Added error checking code to Collection and Subcollection classes
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Peter Amstutz [Mon, 29 Jan 2018 20:58:46 +0000 (15:58 -0500)]
12764: Improve error handling around staging writable files
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 29 Jan 2018 20:02:48 +0000 (15:02 -0500)]
12764: Tweak docs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 12 Jan 2018 20:31:09 +0000 (15:31 -0500)]
12764: Support 'dockerOutputDirectory' for containers to get to 100% conformance.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 12 Jan 2018 19:12:01 +0000 (14:12 -0500)]
12764: Update documentation.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 12 Jan 2018 19:06:06 +0000 (14:06 -0500)]
12764: Support empty anonymous directories by creating a .keep placeholder.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 10 Jan 2018 22:43:49 +0000 (17:43 -0500)]
12764: Pass one cwl test
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 10 Jan 2018 21:58:29 +0000 (16:58 -0500)]
12764: Fixes
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 10 Jan 2018 20:44:50 +0000 (15:44 -0500)]
12764: arvados-cwl-runner support
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 7 Dec 2017 14:51:25 +0000 (09:51 -0500)]
12764: Writable file/directory support wip
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Mon, 29 Jan 2018 18:21:07 +0000 (15:21 -0300)]
Merge branch '12758-federated-id-group-sync'
Closes #12758
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Mon, 29 Jan 2018 18:10:27 +0000 (13:10 -0500)]
Merge branch '12746-crunch2-hoststat'
refs #12746
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 29 Jan 2018 16:48:43 +0000 (11:48 -0500)]
12199: Derate advertised node sizes by 5%.
This matches nodemanager's default behavior. It aims to account for
the difference between advertised and actual memory capacity, as well
as making some room for system processes on the host.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Thu, 25 Jan 2018 18:32:56 +0000 (15:32 -0300)]
12758: Query the API server for group memberships using a
'like' filter to retrieve all local and remote account links to groups.
Added a remote user to the fixture and updated test to confirm
remote users are able to be added & removed from local groups by
sync-groups.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Mon, 29 Jan 2018 15:22:26 +0000 (10:22 -0500)]
12199: Log timestamps in slow integration tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Fuad Muhic [Mon, 29 Jan 2018 11:35:11 +0000 (12:35 +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 [Mon, 29 Jan 2018 11:33:49 +0000 (12:33 +0100)]
Implemented custom print functions for all public classes
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Tom Clegg [Mon, 29 Jan 2018 04:04:22 +0000 (23:04 -0500)]
12199: Update integration tests.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 29 Jan 2018 03:32:08 +0000 (22:32 -0500)]
12199: Make mocks match real slurm output.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Sun, 28 Jan 2018 22:22:28 +0000 (17:22 -0500)]
12199: Update slurm features when nodes come up.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Sun, 28 Jan 2018 21:52:13 +0000 (16:52 -0500)]
12199: Rename instance type features: a1.xl => instancetype=a1.xl
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Sun, 28 Jan 2018 21:32:22 +0000 (16:32 -0500)]
12199: Use node type X to run jobs with constraint instancetype=X.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 26 Jan 2018 20:57:29 +0000 (15:57 -0500)]
Refactor arvbox Go setup and use govendor. refs #12935
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
projects / arvados.git / log