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 18:03:57 +0000 (14:03 -0400)]
5493: minor refactoring
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
Radhika Chippada [Tue, 31 Mar 2015 19:28:42 +0000 (15:28 -0400)]
5493: one more stale update
Radhika Chippada [Tue, 31 Mar 2015 19:21:21 +0000 (15:21 -0400)]
5493: test uncovered an issue with getting_started_shown handling; fixed it.
Radhika Chippada [Tue, 31 Mar 2015 18:51:19 +0000 (14:51 -0400)]
Merge branch 'master' into 5493-getting-started-modal
Peter Amstutz [Tue, 31 Mar 2015 15:18:58 +0000 (11:18 -0400)]
Merge branch '5539-better-docker' closes #5539
Radhika Chippada [Tue, 31 Mar 2015 13:56:46 +0000 (09:56 -0400)]
Merge branch 'master' into 5493-getting-started-modal
Radhika Chippada [Tue, 31 Mar 2015 13:55:59 +0000 (09:55 -0400)]
5493: improve test to verify Next button disables when last page is accessed
Radhika Chippada [Tue, 31 Mar 2015 01:51:38 +0000 (21:51 -0400)]
5493: getting_started modal is served from layout html
Tom Clegg [Mon, 30 Mar 2015 19:56:34 +0000 (15:56 -0400)]
Merge branch '5416-arv-git-httpd' refs #5416
Radhika Chippada [Mon, 30 Mar 2015 19:42:48 +0000 (15:42 -0400)]
5493: do not show "Public pipelines and datasets" link in help menu if config parameter is not set.
Radhika Chippada [Mon, 30 Mar 2015 19:15:40 +0000 (15:15 -0400)]
5493: update tests to use updated fixture active_no_prefs_profile_no_getting_started_shown
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.
Radhika Chippada [Sun, 29 Mar 2015 13:26:27 +0000 (09:26 -0400)]
5493: add pager-count where text such as "1 of 10" is shown.
Radhika Chippada [Fri, 27 Mar 2015 23:45:53 +0000 (19:45 -0400)]
Merge branch 'master' into 5493-getting-started-modal
Radhika Chippada [Fri, 27 Mar 2015 23:44:25 +0000 (19:44 -0400)]
5493: remove the helper method update_getting_started_shown_user_pref, and instead perform prefs update in the view itself.
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 20:52:03 +0000 (16:52 -0400)]
5493: add test for the getting_started help menu item.
Radhika Chippada [Fri, 27 Mar 2015 17:51:47 +0000 (13:51 -0400)]
5493: update user_profile test to expect getting_started modal for users with no previous profile configuration;
also, add one more user scenario where prefs exists with getting_started_shown but no profile.
Radhika Chippada [Fri, 27 Mar 2015 13:54:25 +0000 (09:54 -0400)]
Merge branch 'master' into 5420-collection-checkbox-selections
Radhika Chippada [Fri, 27 Mar 2015 13:52:49 +0000 (09:52 -0400)]
5493: (thanks to tom) modal paging is awesome.
Radhika Chippada [Fri, 27 Mar 2015 01:25:36 +0000 (21:25 -0400)]
5493: fix a bug in user profile handling where any pre-existing prefs are being lost.
Radhika Chippada [Thu, 26 Mar 2015 18:55:37 +0000 (14:55 -0400)]
5493: wiring for 'getting started' popup
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'
Radhika Chippada [Wed, 25 Mar 2015 19:47:17 +0000 (15:47 -0400)]
Merge branch 'master' into 5556-collection-show-timeout
Radhika Chippada [Wed, 25 Mar 2015 18:59:09 +0000 (14:59 -0400)]
refs #5247
closes #5248
Merge branch '5247-anonymous-doc'
Radhika Chippada [Wed, 25 Mar 2015 18:58:27 +0000 (14:58 -0400)]
5247: couple more caption updates.
Radhika Chippada [Wed, 25 Mar 2015 18:26:45 +0000 (14:26 -0400)]
Merge branch 'master' into 5556-collection-show-timeout
Radhika Chippada [Wed, 25 Mar 2015 18:19:01 +0000 (14:19 -0400)]
5247: some caption updates.
Tom Clegg [Wed, 25 Mar 2015 17:48:39 +0000 (13:48 -0400)]
5416: Fix overly sensitive error message regexp.
Radhika Chippada [Wed, 25 Mar 2015 17:37:18 +0000 (13:37 -0400)]
Merge branch 'master' into 5247-anonymous-doc
Radhika Chippada [Wed, 25 Mar 2015 17:26:34 +0000 (13:26 -0400)]
closes #5534
Merge branch '5534-limit-log-lines'
Radhika Chippada [Wed, 25 Mar 2015 17:25:46 +0000 (13:25 -0400)]
Merge branch 'master' into 5534-limit-log-lines
Radhika Chippada [Wed, 25 Mar 2015 17:24:50 +0000 (13:24 -0400)]
closes #3762
Merge branch '3762-delete-list-worker'
Radhika Chippada [Wed, 25 Mar 2015 17:23:33 +0000 (13:23 -0400)]
Merge branch 'master' into 3762-delete-list-worker
Radhika Chippada [Wed, 25 Mar 2015 17:15:54 +0000 (13:15 -0400)]
Merge branch 'master' into 5420-collection-checkbox-selections
Radhika Chippada [Wed, 25 Mar 2015 17:15:11 +0000 (13:15 -0400)]
5420: address checkbox selection caching issue with Safari and Chrome.
Brett Smith [Wed, 25 Mar 2015 15:51:08 +0000 (11:51 -0400)]
Merge branch '4253-user-usernames-wip'
Refs #4253. Closes #5512.
Peter Amstutz [Wed, 25 Mar 2015 15:48:06 +0000 (11:48 -0400)]
Added a comment to volume Delete() about race condition.
Brett Smith [Wed, 18 Mar 2015 20:00:01 +0000 (16:00 -0400)]
4253: Use new username to set up repository and VM logins.
The usernames added in 4253 have stricter limits than past usernames
generated to set up a repository and VM login. Use the new generated
username to avoid a weird disconnect between that and these related
objects. Do a little cleanup in the tests, including removing some
test parameters that now seem redundant under the new rules.
Brett Smith [Wed, 18 Mar 2015 19:59:51 +0000 (15:59 -0400)]
4253: Clean up some user setup methods.
As much as possible, use more methods provided by Rails, rather than
reimplementing them ourselves.
Brett Smith [Tue, 17 Mar 2015 22:10:14 +0000 (18:10 -0400)]
4253: Add a username attribute to users.
* Add the column, and propagate it based on available VM logins or
e-mail address, if possible.
* Add format validation and tests.
* Set new usernames based on e-mail address, with tests.
Radhika Chippada [Wed, 25 Mar 2015 15:02:25 +0000 (11:02 -0400)]
5556: add test to invoke collection#show with and without include_accept_encoding_header_in_api_requests config parameter.
Radhika Chippada [Wed, 25 Mar 2015 14:16:27 +0000 (10:16 -0400)]
5556: Added select() to @logs in CollectionsController#show to avoid trasporting the unneeded log properties.
Also, added Accept-Encoding request header in workbench request to api server.
Ward Vandewege [Tue, 24 Mar 2015 20:53:05 +0000 (16:53 -0400)]
Documentation: installation pages improvements. Be clear about the
purpose of each installation method, and its limitations.
No issue #
Tom Clegg [Tue, 24 Mar 2015 20:22:46 +0000 (16:22 -0400)]
5416: Merge remote-tracking branch 'origin/5416-arv-git-httpd' into 5416-arv-git-httpd
Tom Clegg [Tue, 24 Mar 2015 20:20:06 +0000 (16:20 -0400)]
5416: gofmt formatting changes.
Tom Clegg [Tue, 24 Mar 2015 20:19:50 +0000 (16:19 -0400)]
5416: Add BasicAuth compatibility shim for go1.3.
Radhika Chippada [Tue, 24 Mar 2015 18:28:46 +0000 (14:28 -0400)]
5247: white space
Radhika Chippada [Tue, 24 Mar 2015 18:27:04 +0000 (14:27 -0400)]
5247: anonymous access documentation
Peter Amstutz [Tue, 24 Mar 2015 14:32:58 +0000 (10:32 -0400)]
5539: Require that the user update resolv.conf, and use FQDN (api.dev.arvados,
workbench.dev.arvados) to refer to services more consistently.
Radhika Chippada [Tue, 24 Mar 2015 13:49:38 +0000 (09:49 -0400)]
5534: When a pipeline has long running jobs with hundreds of thousands of log lines, the log line display is timing out
fetching all those lines. Limiting the number of log lines retrieved helped resolve this issue. Using limit size of 2000.
I was able to see log when I limited to 10000 log lines as well, but it took much longer wait time and I felt a quicker
response might provide a better user experience and hence using 2000 log lines as the limit. Thus the most recent 2000
log lines are fetched, followed by newer log lines from event log if the job is still running.
Peter Amstutz [Tue, 24 Mar 2015 13:30:01 +0000 (09:30 -0400)]
Merge branch 'master' into 5539-better-docker
Peter Amstutz [Tue, 24 Mar 2015 13:29:38 +0000 (09:29 -0400)]
Merge branch '5536-retry-discover-servers' closes #5536
Peter Amstutz [Tue, 24 Mar 2015 02:36:01 +0000 (22:36 -0400)]
5539: Retry keepproxy if it quits (this happens when restarting the container,
the api server isn't ready yet, so need to keep trying).
Peter Amstutz [Mon, 23 Mar 2015 21:12:55 +0000 (17:12 -0400)]
5539: Arvados-in-Docker improvements
* arvdock start now restarts existing containers instead of deleting them. Use arvdock reset to delete the containers.
* Uses docker data container for keep.
* Prints a note about adding the nameserver to /etc/resolv.conf
Ward Vandewege [Mon, 23 Mar 2015 20:06:20 +0000 (16:06 -0400)]
Merge branch '5529-add-keepproxy-docker-image'
refs #5529
Ward Vandewege [Mon, 23 Mar 2015 20:06:10 +0000 (16:06 -0400)]
Merge branch 'master' into 5529-add-keepproxy-docker-image
projects / arvados.git / log