Brett Smith [Mon, 13 Apr 2015 15:59:51 +0000 (11:59 -0400)]
5614: Workbench renders error flash separately from others.
Brett Smith [Wed, 8 Apr 2015 20:00:57 +0000 (16:00 -0400)]
5614: Use assert_includes more in Workbench tests for better diagnostics.
Brett Smith [Wed, 8 Apr 2015 19:42:53 +0000 (15:42 -0400)]
5614: Ruby SDK cp_r method creates streams as needed.
Brett Smith [Tue, 7 Apr 2015 19:50:31 +0000 (15:50 -0400)]
5614: Add Collection#each_file to Ruby SDK.
Brett Smith [Tue, 7 Apr 2015 19:29:40 +0000 (15:29 -0400)]
5614: Add Collection#exist? to Ruby SDK.
Peter Amstutz [Mon, 13 Apr 2015 17:10:09 +0000 (13:10 -0400)]
Merge branch '5692-pysdk-manifest-text-flush' closes #5692
Peter Amstutz [Mon, 13 Apr 2015 16:51:53 +0000 (12:51 -0400)]
5692: Don't call _get_manifest_text from test if we don't need to.
Radhika Chippada [Mon, 13 Apr 2015 16:02:12 +0000 (12:02 -0400)]
refs #5365
Merge branch '5365-not-link-unreadables'
Radhika Chippada [Mon, 13 Apr 2015 16:01:33 +0000 (12:01 -0400)]
5365: when the attrvalue is not a uuid, link_to_if_arvados_object
Peter Amstutz [Mon, 13 Apr 2015 15:23:09 +0000 (11:23 -0400)]
5692: Move implementation to internal _get_manifest_text(). Fix typos.
Peter Amstutz [Mon, 13 Apr 2015 14:18:16 +0000 (10:18 -0400)]
5692: Add flush flag to manifest_text() which calls commit_all(). Added
portable_manifest_text() which returns the stripped, normalized manifest text
free of side effects. Fixed tests.
Radhika Chippada [Sun, 12 Apr 2015 21:32:00 +0000 (17:32 -0400)]
closes #5365
Merge branch '5365-not-link-unreadables'
Radhika Chippada [Sun, 12 Apr 2015 21:29:28 +0000 (17:29 -0400)]
5365: add back data-toggle along with link disabled for Log tab.
Radhika Chippada [Sun, 12 Apr 2015 13:06:38 +0000 (09:06 -0400)]
5365: missed one updated signature update
Radhika Chippada [Sun, 12 Apr 2015 03:06:31 +0000 (23:06 -0400)]
5365: updated signature for link_to_arvados_object_if_readable
Peter Amstutz [Fri, 10 Apr 2015 20:24:22 +0000 (16:24 -0400)]
5692: Backed out commit_all() from Collection.manifest_text().
Collection.save() and Collection.save_new() now return unstripped manifest
text.
Peter Amstutz [Fri, 10 Apr 2015 19:27:05 +0000 (15:27 -0400)]
5692: Collection.manifest_text(strip=False) will flush open files and wait for
all blocks to be committed in order to return a manifest text with valid
authorization tokens. Fix tests affected by the change.
Radhika Chippada [Thu, 9 Apr 2015 15:54:59 +0000 (11:54 -0400)]
5365: do not link to docker_image_locator if not readable; also preload these.
Radhika Chippada [Thu, 9 Apr 2015 14:13:11 +0000 (10:13 -0400)]
Merge branch 'master' into 5365-not-link-unreadables
Radhika Chippada [Thu, 9 Apr 2015 14:08:36 +0000 (10:08 -0400)]
5365: add controller tests for preload_for_pdhs and collection_for_pdh methods
Radhika Chippada [Thu, 9 Apr 2015 13:37:46 +0000 (09:37 -0400)]
5365: preload editable component inputs
Radhika Chippada [Wed, 8 Apr 2015 23:48:13 +0000 (19:48 -0400)]
5365: add @distinct handling to workbench select queries and use this to preload portable_data_hashes as well.
Tom Clegg [Wed, 8 Apr 2015 18:40:42 +0000 (14:40 -0400)]
Merge branch '5416-git-config' refs #5416
Tom Clegg [Wed, 8 Apr 2015 16:41:31 +0000 (12:41 -0400)]
5416: Improve logging.
Tom Clegg [Wed, 8 Apr 2015 16:03:44 +0000 (12:03 -0400)]
5416: Do not blow up tests when git global config is uninitialized.
Radhika Chippada [Wed, 8 Apr 2015 14:24:30 +0000 (10:24 -0400)]
5365: Additional test verifications for Log tab display.
Brett Smith [Wed, 8 Apr 2015 13:47:09 +0000 (09:47 -0400)]
Merge branch '5642-crunch-job-swap-limits-wip'
Closes #5642, #5664.
Brett Smith [Wed, 8 Apr 2015 13:46:51 +0000 (09:46 -0400)]
5642: crunch-job uses higher memory limit when running few tasks.
This gives a task all of the node's RAM when it's the only task
running this round, which is more in line with user expectations.
Brett Smith [Wed, 8 Apr 2015 13:46:23 +0000 (09:46 -0400)]
5642: Explicitly make all swap available under Docker in crunch-job.
Without this, Docker 1.2 through 1.5 send subprocesses SIGKILL if they
exceed the memory limit. Refer to #5642 for an example.
--memory-swap is pretty new (newer than 1.3.3), so we don't want to
require it. At the same time, we don't want to impose any memory
limits if we can't use it, because killing subprocesses that exceed a
--memory limit is too strict. This commit arranges to use both
--memory and --memory-swap only if the latter is available.
Radhika Chippada [Wed, 8 Apr 2015 13:43:23 +0000 (09:43 -0400)]
5365: trailing white space
Radhika Chippada [Wed, 8 Apr 2015 13:37:18 +0000 (09:37 -0400)]
Merge branch 'master' into 5365-not-link-unreadables
Radhika Chippada [Wed, 8 Apr 2015 13:35:55 +0000 (09:35 -0400)]
5365: preload output collection uuids and jobs to help improve performance when loading large pipelines.
Brett Smith [Tue, 7 Apr 2015 21:43:10 +0000 (17:43 -0400)]
Include arvados/collection in the Ruby SDK gem.
No issue #.
Radhika Chippada [Tue, 7 Apr 2015 18:05:43 +0000 (14:05 -0400)]
5365: preload jobs during pipeline display to improve performance.
Radhika Chippada [Tue, 7 Apr 2015 14:46:55 +0000 (10:46 -0400)]
Merge branch 'master' into 5365-not-link-unreadables
Radhika Chippada [Tue, 7 Apr 2015 14:46:16 +0000 (10:46 -0400)]
5365: refactor link to object if readable logic
Brett Smith [Tue, 7 Apr 2015 14:34:31 +0000 (10:34 -0400)]
Merge branch '5653-arv-copy-multiple-branches-wip'
Closes #5653, #5673.
Brett Smith [Mon, 6 Apr 2015 18:27:21 +0000 (14:27 -0400)]
5653: arv-copy copies multiple commits from the same repository+pipeline.
arv-copy previously used the repository name alone to determine which
job scripts it had already copied to the destination. If a pipeline
used unrelated commits from the same repository, it would skip copying
over all but the first. Track script versions throughout the copy
process and make sure all of them are copied to the destination
repository.
Brett Smith [Tue, 7 Apr 2015 13:57:19 +0000 (09:57 -0400)]
Merge branch '5352-crunch-dispatch-salloc-tempfail-wip'
Closes #5352, #5670.
Brett Smith [Sun, 5 Apr 2015 21:10:22 +0000 (17:10 -0400)]
5352: crunch-dispatch treats node allocation failure as temporary.
Imagine a scenario where multiple crunch-dispatch processes are
sitting idle, then suddenly a new job appears in the queue. They will
all race to dispatch the job. When this happens, we frequently see
that salloc fails for most of them, because they all requested the
same node(s) and only the winner will get them. crunch-dispatch has
no way to know the exit code "came from" salloc and not crunch-job,
and so marks the job failed.
This patch sets the SLURM_EXIT_IMMEDIATE environment variable to make
salloc use exit code 75 when the allocation fails. crunch-dispatch
already recognizes this exit code as a temporary failure, and will
leave the Arvados job record unchanged. Refer to salloc(1) and the
long comment in Dispatch#reap_children.
Radhika Chippada [Mon, 6 Apr 2015 23:49:10 +0000 (19:49 -0400)]
Merge branch 'master' into 5365-not-link-unreadables
Conflicts:
apps/workbench/test/integration/anonymous_access_test.rb
Radhika Chippada [Mon, 6 Apr 2015 23:43:56 +0000 (19:43 -0400)]
5365: job link in pipeline instance page
Radhika Chippada [Mon, 6 Apr 2015 20:58:05 +0000 (16:58 -0400)]
closes #5565
Merge branch '5565-breadcrumbs-in-anonyymous-view'
Radhika Chippada [Mon, 6 Apr 2015 20:54:22 +0000 (16:54 -0400)]
5565: show parent project hierarchy in breadcrumbs in anonymous view; not just current objects's parent.
Radhika Chippada [Mon, 6 Apr 2015 20:48:36 +0000 (16:48 -0400)]
Merge branch 'master' into 5565-breadcrumbs-in-anonyymous-view
Radhika Chippada [Mon, 6 Apr 2015 20:16:02 +0000 (16:16 -0400)]
closes #5492
Merge branch '5492-home-project-in-my-account'
Radhika Chippada [Mon, 6 Apr 2015 20:15:14 +0000 (16:15 -0400)]
Merge branch 'master' into 5492-home-project-in-my-account
Radhika Chippada [Mon, 6 Apr 2015 19:31:49 +0000 (15:31 -0400)]
Merge branch 'master' into 5565-breadcrumbs-in-anonyymous-view
Radhika Chippada [Mon, 6 Apr 2015 19:29:07 +0000 (15:29 -0400)]
5565: show trimmed down version of breadcrumbs in anonymous view.
Brett Smith [Mon, 6 Apr 2015 17:49:29 +0000 (13:49 -0400)]
Tighten up DNS check in arvdock.
I got arvdock stuck in an infinite loop because I had the right
nameserver line in /etc/resolv.conf, except it was commented out, so
arvdock kept checking for a name that it would never find. Use awk to
find and check the first functional nameserver line instead.
No issue #.
Radhika Chippada [Mon, 6 Apr 2015 16:43:54 +0000 (12:43 -0400)]
5492: add "Home project" link to my account menu.
Radhika Chippada [Mon, 6 Apr 2015 15:58:47 +0000 (11:58 -0400)]
Merge branch 'master' into 5365-not-link-unreadables
Radhika Chippada [Mon, 6 Apr 2015 15:58:26 +0000 (11:58 -0400)]
5365: white space
Brett Smith [Mon, 6 Apr 2015 15:38:08 +0000 (11:38 -0400)]
Add missing global declaration in arv-copy.
No issue #.
Radhika Chippada [Mon, 6 Apr 2015 15:04:11 +0000 (11:04 -0400)]
5365: couple more integration tests to access Log tab from within the Job page.
Radhika Chippada [Mon, 6 Apr 2015 14:15:39 +0000 (10:15 -0400)]
5365: additional test assertions for pipeline log tab display
Radhika Chippada [Mon, 6 Apr 2015 13:25:47 +0000 (09:25 -0400)]
Merge branch 'master' into 5365-not-link-unreadables
Brett Smith [Sun, 5 Apr 2015 21:39:33 +0000 (17:39 -0400)]
Fix debug log formatting in PySDK.
When multiple arguments are passed to a logger method, the first
argument is expected to be a printf-style format string, with the
remaining arguments expected to fill in the formatters.
No issue #.
Brett Smith [Sun, 5 Apr 2015 20:34:00 +0000 (16:34 -0400)]
5518: PySDK arvados.util must import arvados.
Closes #5518.
Radhika Chippada [Fri, 3 Apr 2015 21:29:08 +0000 (17:29 -0400)]
5365: add integration test to verify Log tab and other unreadable properties are disabled in anonymous view.
Radhika Chippada [Fri, 3 Apr 2015 15:58:51 +0000 (11:58 -0400)]
Merge branch 'master' into 5365-not-link-unreadables
Radhika Chippada [Fri, 3 Apr 2015 15:56:20 +0000 (11:56 -0400)]
5365: Do not link to job, log, output in pipeline instance if the user, mainly anonymous user, cannot read those objects.
Disable Log tab and show tooltip in such a scenario.
Working in manual testing. Integration test updates are on the way.
Brett Smith [Fri, 3 Apr 2015 14:28:35 +0000 (10:28 -0400)]
Merge branch '5416-repo-dir-is-uuid'
Refs #5416.
Brett Smith [Thu, 2 Apr 2015 21:37:53 +0000 (17:37 -0400)]
4253: Gitolite migration makes a name symlink for arvados repository.
This is necessary for other supporting infrastructure around this
repository in Gitolite installs; e.g., the cron job that keeps them in
sync with upstream. Refs #4253.
Peter Amstutz [Thu, 2 Apr 2015 19:23:18 +0000 (15:23 -0400)]
Merge branch '4752-docker-websockets' closes #4752
Ward Vandewege [Thu, 2 Apr 2015 19:17:04 +0000 (15:17 -0400)]
Make arvdock abort with a nice error message if docker or curl can not
be found.
refs #4752
Peter Amstutz [Thu, 2 Apr 2015 16:02:43 +0000 (12:02 -0400)]
Merge branch '5626-git-server-hostname' closes #5626
Peter Amstutz [Thu, 2 Apr 2015 16:01:43 +0000 (12:01 -0400)]
5626: Expand test to check both positive and negative cases a bit per request.
Peter Amstutz [Thu, 2 Apr 2015 14:38:39 +0000 (10:38 -0400)]
5626: Add test for git_hostname configuration option.
Peter Amstutz [Thu, 2 Apr 2015 14:24:56 +0000 (10:24 -0400)]
4752: Websockets works. Fix compute node containers to restart correctly. Fix
git server hostname. Arvdock waits for API/workbench to be ready before telling
the user to go to workbench.
Peter Amstutz [Wed, 1 Apr 2015 20:14:19 +0000 (16:14 -0400)]
Merge branch '5626-git-server-hostname' into 4752-docker-websockets
Tom Clegg [Wed, 1 Apr 2015 20:12:35 +0000 (16:12 -0400)]
5416: Prefer repos stored locally by uuid, fall back to name. Update tests to suit 4523 fixtures.
Peter Amstutz [Wed, 1 Apr 2015 19:59:33 +0000 (15:59 -0400)]
5626: Add git_hostname configuration option.
Brett Smith [Wed, 1 Apr 2015 19:50:08 +0000 (15:50 -0400)]
5627: Python file-like objects use SEET_SET as the default whence.
This is a brown paper bag commit. All that time I spent grumbling
that we had the wrong default was completely incorrect. We had it
right earlier, and I blew it. See
<https://docs.python.org/2/library/stdtypes.html#file.seek>.
Closes #5627.
Peter Amstutz [Wed, 1 Apr 2015 16:08:35 +0000 (12:08 -0400)]
4752: Fix failing setup by polling for API server to come up.
Radhika Chippada [Wed, 1 Apr 2015 15:08:06 +0000 (11:08 -0400)]
closes #5420
Merge branch '5420-collection-checkbox-selections'
Peter Amstutz [Wed, 1 Apr 2015 14:38:52 +0000 (10:38 -0400)]
4752: Update documentation related to docker
Radhika Chippada [Wed, 1 Apr 2015 14:32:48 +0000 (10:32 -0400)]
5420: remove search box autocomplete off update so that this can be addressed in a separate issue.
Radhika Chippada [Wed, 1 Apr 2015 14:23:08 +0000 (10:23 -0400)]
Merge branch 'master' into 5420-collection-checkbox-selections
Brett Smith [Wed, 1 Apr 2015 14:13:39 +0000 (10:13 -0400)]
Merge branch '4253-gitolite-migration-wip'
Closes #4253, #5617.
Brett Smith [Tue, 31 Mar 2015 21:02:38 +0000 (17:02 -0400)]
4253: Add script to migrate existing Gitolite installations.
Peter Amstutz [Wed, 1 Apr 2015 13:51:51 +0000 (09:51 -0400)]
4752: Use passenger standalone for API server instead of passenger apache module and set ARVADOS_WEBSOCKETS=1
Brett Smith [Wed, 1 Apr 2015 13:45:07 +0000 (09:45 -0400)]
Merge branch '4253-user-repos-wip'
Refs #4253. Closes #5605.
Brett Smith [Mon, 30 Mar 2015 20:06:38 +0000 (16:06 -0400)]
4253: Add Workbench interface to create repositories.
Commit includes contributions from Tom Clegg.
Brett Smith [Mon, 30 Mar 2015 18:28:40 +0000 (14:28 -0400)]
4253: Let Workbench Manage Account partials render their whole pane.
I'm about to add another "Add" button to the Repositories pane, so I'd
rather do it this way than try to maintain a generic loop inside
_manage_account.html.erb.
Brett Smith [Mon, 30 Mar 2015 15:06:51 +0000 (11:06 -0400)]
4253: Sync up Docker with our production Gitolite setup.
This updates our API server Docker image to store repositories by
UUID, with name aliases available. .gitolite.rc enables the aliasing,
and update-gitolite.rb generates the necessary configuration. This
makes it possible to test the recent repository changes in Docker.
Brett Smith [Tue, 31 Mar 2015 13:23:56 +0000 (09:23 -0400)]
4253: Users can manage their own repositories.
This commit allows users to create their own repositories, as long as
the repository name starts with their own username.
To support this change, we've modified our Gitolite setup to store
repositories primarily by UUID, with a name alias for easier
checkout. fetch_url and push_url become generated attributes
accordingly. This makes it easier to rename the repository later and
allow checkouts to continue to work.
Commit includes contributions from Tom Clegg.
Peter Amstutz [Wed, 1 Apr 2015 13:09:26 +0000 (09:09 -0400)]
Merge branch '5612-munge-docker-cleanup' closes #5612
Peter Amstutz [Tue, 31 Mar 2015 21:13:06 +0000 (17:13 -0400)]
5612: Wrap munge with startup script that cleans up /var/run/munge of stale
sockets and pidfiles. Can now run jobs after stopping and restarting
containers.
Radhika Chippada [Tue, 31 Mar 2015 19:55:54 +0000 (15:55 -0400)]
Merge branch 'master' into 5420-collection-checkbox-selections
Peter Amstutz [Tue, 31 Mar 2015 15:18:58 +0000 (11:18 -0400)]
Merge branch '5539-better-docker' closes #5539
Tom Clegg [Mon, 30 Mar 2015 19:56:34 +0000 (15:56 -0400)]
Merge branch '5416-arv-git-httpd' refs #5416
Tom Clegg [Mon, 30 Mar 2015 17:00:59 +0000 (13:00 -0400)]
5416: Merge branch 'master' into 5416-arv-git-httpd
Tom Clegg [Mon, 30 Mar 2015 16:56:53 +0000 (12:56 -0400)]
5416: Add permission-denied tests.
Tom Clegg [Mon, 30 Mar 2015 16:56:00 +0000 (12:56 -0400)]
5416: Improve variable names & filenames. Report original error if git fails with nothing on stderr.
Brett Smith [Fri, 27 Mar 2015 21:16:09 +0000 (17:16 -0400)]
Merge branch '5502-node-manager-gce-ssd-wip'
Refs #5502.
Radhika Chippada [Fri, 27 Mar 2015 13:54:25 +0000 (09:54 -0400)]
Merge branch 'master' into 5420-collection-checkbox-selections
Brett Smith [Thu, 26 Mar 2015 17:31:01 +0000 (13:31 -0400)]
5502: Node Manager attaches a local SSD to GCE compute nodes.
This is the best option to provide temporary working space for compute
work on GCE.
Brett Smith [Thu, 26 Mar 2015 16:29:38 +0000 (12:29 -0400)]
5502: Adjust id and name of Node Manager cloud object mocks.
Some GCE objects like disk types have predictable names, so it's
helpful to be able to mock objects with the same name. Use the
name_id argument is the literal name, and generate an id from it.
Radhika Chippada [Wed, 25 Mar 2015 23:00:55 +0000 (19:00 -0400)]
closes #5556
Merge branch '5556-collection-show-timeout'
projects / arvados.git / log