Peter Amstutz [Wed, 1 Apr 2015 14:38:52 +0000 (10:38 -0400)]
4752: Update documentation related to docker
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
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.
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.
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
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.
Brett Smith [Fri, 20 Mar 2015 18:08:19 +0000 (14:08 -0400)]
Merge branch '5319-collection-pdh-fix-performance-2-wip'
Refs #5319.
Brett Smith [Wed, 18 Mar 2015 14:44:18 +0000 (10:44 -0400)]
5319: Improve collection PDH fix performance with LIKE searches.
PostgreSQL regexp searches use a lot of RAM, and these queries run out
of RAM on qr1hi. Prefer LIKE queries, which use less RAM and are more
portable. We have to do multiple searches, but that's life.
Radhika Chippada [Fri, 20 Mar 2015 15:30:59 +0000 (11:30 -0400)]
Merge branch 'master' into 5375-preview-collection-text-files
Radhika Chippada [Fri, 20 Mar 2015 15:27:34 +0000 (11:27 -0400)]
3762: Run trash worker. Add tests to test the trash worker.
Tom Clegg [Thu, 19 Mar 2015 22:23:19 +0000 (18:23 -0400)]
5276: Use using_wait_time 0 instead of evaluate_script.
Tom Clegg [Thu, 19 Mar 2015 22:12:21 +0000 (18:12 -0400)]
5276: Reveal and update the log graph as soon as the first data point
arrives, rather than waiting for the redraw timer.
Return an empty hover tooltip for the placeholder data point. (The
placeholder series is only added when the graph is empty and hideHover
is true, but it doesn't get deleted later when hideHover goes false.)
Render the graph in a show() callback to ensure the div is visible
when Morris creates its SVG element: otherwise the SVG can end up
being created with height=1px. This addresses bugs like "graph doesn't
show up sometimes" and "data point hover tooltips show up, but there's
no graph".
Tom Clegg [Thu, 19 Mar 2015 17:08:23 +0000 (13:08 -0400)]
5276: Improve job log graph tests.
* Run tests as a non-admin user. (This just needed an update in the
log simulator to insert the logs with the same owner_uuid as the
target job.)
* Test graph display/update behavior both with and without an existing
log entry in the database during initial page display.
Tom Clegg [Thu, 19 Mar 2015 16:24:49 +0000 (12:24 -0400)]
5276: Remove redundant test teardown.
Peter Amstutz [Thu, 19 Mar 2015 15:12:31 +0000 (11:12 -0400)]
Merge branch '5285-arpi-use-settings' closes #5285
Peter Amstutz [Thu, 19 Mar 2015 14:52:42 +0000 (10:52 -0400)]
5425: Set memory limit on container as a fraction of total system memory
allocated to task each when invoking Docker.
Tom Clegg [Thu, 19 Mar 2015 05:50:53 +0000 (01:50 -0400)]
5198: Remove href attributes from remote:true links to prevent ctrl-click et al. from doing the wrong thing.
Peter Amstutz [Wed, 18 Mar 2015 18:44:44 +0000 (14:44 -0400)]
5318: Add note on sharing page for repository object about lag time taking effect.
Peter Amstutz [Wed, 18 Mar 2015 18:36:23 +0000 (14:36 -0400)]
5285: Remove cruft made redundant by Ruby SDK
Peter Amstutz [Wed, 18 Mar 2015 17:52:58 +0000 (13:52 -0400)]
Merge branch '5500-crunch-temporary-failure' refs #5500
Peter Amstutz [Wed, 18 Mar 2015 17:48:11 +0000 (13:48 -0400)]
5500: Add TASK_TEMPFAIL constant. shell_or_die always exits non-zero on error.
Peter Amstutz [Wed, 18 Mar 2015 16:23:21 +0000 (12:23 -0400)]
5500: Add SLURM "Communication connection failure" to pattern of temporary node
failures. "pip install" failure returns temporary error status (111) so the
task can be retried.
Radhika Chippada [Wed, 18 Mar 2015 15:13:20 +0000 (11:13 -0400)]
5375: white space
Radhika Chippada [Wed, 18 Mar 2015 15:04:48 +0000 (11:04 -0400)]
5375: enhance the mime_types initializer to add a new type only when that type is not yet supported by the MIME types gem.
Radhika Chippada [Wed, 18 Mar 2015 14:04:29 +0000 (10:04 -0400)]
5375: after much hair pulling, found the syntax to replace MIME::Types.add(MIME::Type.from_array... since from_array is deprecated; now using MIME::Types.add(MIME::Type.new...
Ward Vandewege [Wed, 18 Mar 2015 13:50:44 +0000 (09:50 -0400)]
More tweaks for the manual install prerequisites doc page.
refs #5416
Radhika Chippada [Wed, 18 Mar 2015 13:45:21 +0000 (09:45 -0400)]
Merge branch 'master' into 5375-preview-collection-text-files
Radhika Chippada [Wed, 18 Mar 2015 13:44:32 +0000 (09:44 -0400)]
refs #5383
Merge branch '5383-api-db-current-time'
Radhika Chippada [Wed, 18 Mar 2015 13:41:23 +0000 (09:41 -0400)]
Merge branch 'master' into 5383-api-db-current-time
Radhika Chippada [Wed, 18 Mar 2015 13:38:26 +0000 (09:38 -0400)]
5383: Add back Time.parse(). Without it the value returned would be of the format 2015-03-18 13:37:11 UTC,
and with Time.parse it would be 2015-03-18 09:37:11 -0400, which is the same as Time.now.
Ward Vandewege [Wed, 18 Mar 2015 13:31:13 +0000 (09:31 -0400)]
Add git.uuid.local.domain to the manual install prerequisites page on
the overview of hostnames.
refs #5416
projects / arvados.git / log