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 [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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
Tom Clegg [Fri, 26 Jan 2018 21:30:50 +0000 (16:30 -0500)]
12746: Don't stop hoststat until after capturing output.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Fri, 26 Jan 2018 20:44:13 +0000 (15:44 -0500)]
12746: Log host cgroup stats to hoststat.txt.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Fuad Muhic [Fri, 26 Jan 2018 15:09:31 +0000 (16:09 +0100)]
Updated unit test name to reflect changes made to getFileListing method
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Fri, 26 Jan 2018 15:04:32 +0000 (16:04 +0100)]
Updated test to reflect changes to getFileListing method
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Fri, 26 Jan 2018 15:00:59 +0000 (16:00 +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, 26 Jan 2018 14:59:47 +0000 (15:59 +0100)]
getFileListing now returns sorted list
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Peter Amstutz [Thu, 25 Jan 2018 19:27:38 +0000 (14:27 -0500)]
Fix missing files needed by arvados-tests.sh refs #12935
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fuad Muhic [Thu, 25 Jan 2018 14:15:04 +0000 (15:15 +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 [Thu, 25 Jan 2018 14:12:42 +0000 (15:12 +0100)]
ArvadosFile's connection method now returns curl connection instead of
textConnection when called with 'r' parameter
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Tom Clegg [Wed, 24 Jan 2018 15:49:21 +0000 (10:49 -0500)]
Merge branch '12891-log-on-cancel'
refs #12891
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Fuad Muhic [Wed, 24 Jan 2018 15:19:01 +0000 (16:19 +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 [Wed, 24 Jan 2018 15:17:36 +0000 (16:17 +0100)]
Added unit tests for HttpRequest class.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Tom Clegg [Tue, 23 Jan 2018 20:08:08 +0000 (15:08 -0500)]
12891: Don't wait for WaitContainer to receive loggingDone.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 23 Jan 2018 20:05:22 +0000 (15:05 -0500)]
12891: Fix some test races.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 23 Jan 2018 19:39:26 +0000 (14:39 -0500)]
12891: Simplify "arv-mount exits before container ends" detection.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 23 Jan 2018 17:40:14 +0000 (12:40 -0500)]
Merge branch '12990-fuse-shared' refs #12990
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 23 Jan 2018 16:33:58 +0000 (11:33 -0500)]
12990: Re-query project roots in order to get full record
Makes the query of all projects lighter.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fuad Muhic [Tue, 23 Jan 2018 16:29:08 +0000 (17:29 +0100)]
Removed plus sign hack from HttpRequests createFiltersQuery method
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Tue, 23 Jan 2018 16:16:50 +0000 (17:16 +0100)]
Fixed ArvadosFile/Subcollection move bug and improved http query
generation logic.
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Peter Amstutz [Tue, 23 Jan 2018 15:51:47 +0000 (10:51 -0500)]
12990: Add update lock to shared directory update.
Also limit fields returned using select.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fuad Muhic [Tue, 23 Jan 2018 11:38:18 +0000 (12:38 +0100)]
Added additional unit tests to Arvados class
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Tue, 23 Jan 2018 09:45:28 +0000 (10:45 +0100)]
Factored out HttpRequest and HttpParser classes from Arvados class to
RESTService class
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Lucas Di Pentima [Mon, 22 Jan 2018 21:00:25 +0000 (18:00 -0300)]
11454: Conditional login to remote API servers.
When adding new sites to the multi site search, if the remote
site allows federated logins from the local site, created a
salted token to be able to start a session.
If not, use the classic login method.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 22 Jan 2018 18:16:20 +0000 (15:16 -0300)]
11454: (WIP) Login to remote clusters using federated identity.
Expanded the multi site search's SessionDB to allow logins
using salted tokens.
Pending: Do the right thing on every combination of federation
settings.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Mon, 22 Jan 2018 15:57:18 +0000 (10:57 -0500)]
12891: Use docker "rm -f" instead of "stop" to cancel container.
"Stop" sends SIGTERM and then (after a timeout) SIGKILL to the main
process in the container. If the contained process catches SIGTERM,
the outcome depends on how much cleanup it manages to do in the
timeout period. We prefer a more predictable SIGKILL outcome.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 18 Jan 2018 21:41:39 +0000 (16:41 -0500)]
12891: Avoid flapping finalState after cancel.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 18 Jan 2018 21:41:14 +0000 (16:41 -0500)]
12891: Fix use of magic string.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
projects / arvados.git / log