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
Peter Amstutz [Mon, 23 Mar 2015 18:10:12 +0000 (14:10 -0400)]
Merge branch '5524-crunch-temp-keep-errors' closes #5524
Peter Amstutz [Mon, 23 Mar 2015 18:08:58 +0000 (14:08 -0400)]
5524: Match magic string arvados.errors.Keep as likely part of an exception
backtrace and mark task as temporary failure.
Peter Amstutz [Mon, 23 Mar 2015 17:54:07 +0000 (13:54 -0400)]
5536: Keepproxy retry keep server discovery on error or empty list.
Peter Amstutz [Mon, 23 Mar 2015 17:47:17 +0000 (13:47 -0400)]
Merge branch '5425-set-docker-memory-limits' refs #5425
Radhika Chippada [Mon, 23 Mar 2015 16:24:15 +0000 (12:24 -0400)]
Merge branch 'master' into 3762-delete-list-worker
Radhika Chippada [Mon, 23 Mar 2015 16:11:42 +0000 (12:11 -0400)]
3762: create NewWorkQueue instances of pullq and trashq in handers_test and remove this logic from handlers.
it is expected that keepstore or the tests will create these objects and handlers should not have to.
Radhika Chippada [Mon, 23 Mar 2015 16:01:05 +0000 (12:01 -0400)]
3762: undo the api server discovery document update. trash worker can instead use permission_ttl in place of defaultTrashLifetime because these two will be the same.
Tom Clegg [Mon, 23 Mar 2015 14:54:18 +0000 (10:54 -0400)]
Merge branch '5198-remote-link-ctrl-click' refs #5198
Radhika Chippada [Mon, 23 Mar 2015 14:35:34 +0000 (10:35 -0400)]
Merge branch 'master' of git.curoverse.com:arvados into 3762-delete-list-worker
Peter Amstutz [Mon, 23 Mar 2015 13:05:18 +0000 (09:05 -0400)]
Merge branch '5318-git-sharing-note' closes #5318
Tom Clegg [Mon, 23 Mar 2015 05:52:50 +0000 (01:52 -0400)]
5198: Merge branch 'master' into 5198-remote-link-ctrl-click
Tom Clegg [Mon, 23 Mar 2015 05:46:47 +0000 (01:46 -0400)]
5198: Update comment.
Ward Vandewege [Mon, 23 Mar 2015 00:21:55 +0000 (20:21 -0400)]
Add a keepproxy docker image
refs #5529
Ward Vandewege [Sun, 22 Mar 2015 18:02:26 +0000 (14:02 -0400)]
Go SDK improvements:
- keepclient now respects the ARVADOS_API_HOST_INSECURE environment
variable
- arvadosclient and keepclient accept (1,yes,true) to enable the
insecure api host flag, case insensitive.
No issue #
Tom Clegg [Sat, 21 Mar 2015 20:37:00 +0000 (16:37 -0400)]
Merge branch '5276-job-graph-phantom-tooltip' closes #5276
Tom Clegg [Sat, 21 Mar 2015 20:19:09 +0000 (16:19 -0400)]
5276: Merge branch 'master' into 5276-job-graph-phantom-tooltip
Tom Clegg [Sat, 21 Mar 2015 20:19:03 +0000 (16:19 -0400)]
5276: Name log fixtures. Fix over-sensitive test.
Radhika Chippada [Sat, 21 Mar 2015 13:54:45 +0000 (09:54 -0400)]
refs #5375
Merge branch '5375-preview-collection-text-files'
Radhika Chippada [Sat, 21 Mar 2015 13:32:31 +0000 (09:32 -0400)]
5375: added javascript and rtf application types to white-listed application types after observing that these were disabled when testing in staging.
Radhika Chippada [Sat, 21 Mar 2015 10:44:03 +0000 (06:44 -0400)]
closes #5375
Merge branch '5375-preview-collection-text-files'
Radhika Chippada [Sat, 21 Mar 2015 10:42:04 +0000 (06:42 -0400)]
5375: small updates on comments
Radhika Chippada [Sat, 21 Mar 2015 03:14:43 +0000 (23:14 -0400)]
5375: and add the new test file
Radhika Chippada [Sat, 21 Mar 2015 03:11:34 +0000 (23:11 -0400)]
5375: move the mime type tests into a new collections_helper_test.
Radhika Chippada [Sat, 21 Mar 2015 03:01:04 +0000 (23:01 -0400)]
Merge branch 'master' into 5375-preview-collection-text-files
Radhika Chippada [Sat, 21 Mar 2015 02:59:42 +0000 (22:59 -0400)]
Merge branch 'master' into 3762-delete-list-worker
Radhika Chippada [Sat, 21 Mar 2015 02:58:05 +0000 (22:58 -0400)]
3762: Expose Discovery func in arvadosclient. Use Discovery to get defaultTrashLifetime in trash worker.
Brett Smith [Fri, 20 Mar 2015 21:16:43 +0000 (17:16 -0400)]
5319: Bound search in collection PDH fix migration.
Only search collections that exist when the migration begins. This
helps avoid an infinite loop where we yield a bad collection, it gets
fixed a new replacement is created, and then we find and yield the
replacement… Refs #5319.
Radhika Chippada [Fri, 20 Mar 2015 19:56:38 +0000 (15:56 -0400)]
Merge branch 'master' into 3762-delete-list-worker
Radhika Chippada [Fri, 20 Mar 2015 19:04:39 +0000 (15:04 -0400)]
5375: update the fixture pdh with the value got from keep put.
Radhika Chippada [Fri, 20 Mar 2015 18:30:35 +0000 (14:30 -0400)]
5375: improved mime_types initializer. enhance collections_helper to use mime_type sub_type instead of relying on suffix.
update config param name, value, and comment. add .seq, which is another supported extension of fasta to test.
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