Brett Smith [Tue, 24 Jun 2014 21:11:00 +0000 (17:11 -0400)]
Escape HTML entities in Workbench Job log viewer.
No issue #.
Brett Smith [Tue, 24 Jun 2014 19:02:39 +0000 (15:02 -0400)]
Fix bad interaction between llfuse and daemonization in arv-mount.
Following PEP 3143, daemon.DaemonContext drops all open file
descriptors by default. This causes arv-mount to fail, because
llfuse.init() opens /dev/fuse, and llfuse.main() uses that file
descriptor. We now daemonize before doing real work to prevent this
unintentional breakage.
This effectively reverts
83c873af. An alternative approach would've
been to call DaemonContext with a preserve_files argument. I decided
against that because I couldn't find a reliable way to determine
which file descriptors llfuse needs. If we really need the daemon to
report errors, and debugging with --foreground isn't sufficient, I
think we should implement proper logging to a file or syslog.
No issue #.
Tom Clegg [Mon, 23 Jun 2014 20:39:55 +0000 (16:39 -0400)]
Fix off-by-one-month in timestamp conversion. refs #2883
Brett Smith [Mon, 23 Jun 2014 17:20:46 +0000 (13:20 -0400)]
Merge branch '2891-workbench-errors-retain-login'
Closes #3032, #3074. Refs #2891.
Brett Smith [Mon, 23 Jun 2014 15:14:29 +0000 (11:14 -0400)]
2891: Rename and comment Workbench API token filters.
Brett Smith [Mon, 23 Jun 2014 14:43:02 +0000 (10:43 -0400)]
2891: Refactor Workbench API token filters.
Remove dead code and simplify the implementation, especially the
relationship between the "required" and "optional" filters, per
discussion with Peter.
Brett Smith [Fri, 20 Jun 2014 18:33:18 +0000 (14:33 -0400)]
2891: Workbench error page shows login status.
The tests here check that an error page shows the usual user
information for someone logged in, and renders okay for someone who
isn't.
Brett Smith [Fri, 20 Jun 2014 18:31:33 +0000 (14:31 -0400)]
2891: Workbench handles expired tokens more consistently.
Previously Workbench would behave differently depending on whether an
expired token was provided as a query parameter, or living in a
session. This makes it do the same thing in all cases. It also fixes
some small bugs around removing api_token from URL paths.
Brett Smith [Fri, 20 Jun 2014 15:19:20 +0000 (11:19 -0400)]
2891: Workbench integration tests cope when screenshots aren't supported.
Peter Amstutz [Mon, 23 Jun 2014 14:37:05 +0000 (10:37 -0400)]
Fix symlinks in sdk/cli/bin for arv-mount and arv-keepdocker. no issue #
Peter Amstutz [Mon, 23 Jun 2014 14:09:51 +0000 (10:09 -0400)]
Suppress "Resource or subcommand '' is not recognized." message when running
arv with no parameters. refs #2986
Tom Clegg [Mon, 23 Jun 2014 13:35:31 +0000 (09:35 -0400)]
Remove spurious puts. refs #2884
Tom Clegg [Mon, 23 Jun 2014 13:34:41 +0000 (09:34 -0400)]
Fix crash on unexpected case of a collection whose owner_uuid is not root.
closes #3047
Tom Clegg [Mon, 23 Jun 2014 13:30:30 +0000 (09:30 -0400)]
Handle UrlGenerationError as an application exception rather than a
404, even though it subclasses RoutingError. refs #3047
Peter Amstutz [Mon, 23 Jun 2014 13:11:38 +0000 (09:11 -0400)]
Merge branch '2986-arv-edit' closes #2986
Peter Amstutz [Fri, 20 Jun 2014 21:10:10 +0000 (17:10 -0400)]
2986: Handles collection ids in 'arv edit' (tells the user collections are not
editable.) Added error message when subcommand or resource is
unrecognized. Removed old reference to removed command line parameter
global_opts[:resources].
Peter Amstutz [Fri, 20 Jun 2014 20:34:58 +0000 (16:34 -0400)]
2986: Restored "arv pipeline run" subcommand. Arv edit will now ask you if you
want to retry if there is parse error. Fixed capitalization of Arvados.
Peter Amstutz [Fri, 20 Jun 2014 20:12:44 +0000 (16:12 -0400)]
2986: Report parsing errors and print out contents instead of just blowing up.
Peter Amstutz [Fri, 20 Jun 2014 19:57:44 +0000 (15:57 -0400)]
2986: Writes tempfile with appropriate extension so editor can apply proper editing mode.
Peter Amstutz [Fri, 20 Jun 2014 15:16:54 +0000 (11:16 -0400)]
2986: Can now specify which fields you want to edit, because fields like 'uuid'
and 'modified_at' are not updatable.
Peter Amstutz [Fri, 20 Jun 2014 15:05:32 +0000 (11:05 -0400)]
Fix pipeline instance creation workbench tests. refs #2884
Brett Smith [Fri, 20 Jun 2014 14:40:02 +0000 (10:40 -0400)]
3031: Improve "Docker image not found" error message.
Rails automatically adds the column name to rendered error message, so
the old version was coming out as "Docker image locator Docker image
not found." This version reads better. Refs #3031.
Brett Smith [Thu, 19 Jun 2014 20:39:34 +0000 (16:39 -0400)]
Make Job runtime constraints documentation up-to-date.
Refs #2879, #2880.
Peter Amstutz [Thu, 19 Jun 2014 20:36:01 +0000 (16:36 -0400)]
Merge branch '2884-improved-picker' closes #2884
Peter Amstutz [Thu, 19 Jun 2014 20:32:13 +0000 (16:32 -0400)]
Merge remote-tracking branch 'origin/master' into 2884-improved-picker
Peter Amstutz [Thu, 19 Jun 2014 20:27:26 +0000 (16:27 -0400)]
2884: Added fail callback preview loading fails. Added comments explaining a
couple of things. Removed spurious puts.
Peter Amstutz [Thu, 19 Jun 2014 19:35:01 +0000 (15:35 -0400)]
2986: Implemented "arv edit" command. Refactored 'arv' to be easier to follow.
Changed control flow of command line processing so that trollop gets a chance
to see command line before subcommands. Improved help text for subcommands.
Peter Amstutz [Thu, 19 Jun 2014 19:29:48 +0000 (15:29 -0400)]
2986: Make arv-run-pipeline-instance be nicer to the user when run without
command line parameters.
Brett Smith [Thu, 19 Jun 2014 19:14:57 +0000 (15:14 -0400)]
Refactor show_file_links.html.erb to reduce duplication.
No issue #, just something I did while working on the previous commit.
Brett Smith [Thu, 19 Jun 2014 19:14:07 +0000 (15:14 -0400)]
2937: Make sure Collection share links end with /.
This is necessary to prevent wget from saving a plain HTML file with
the name of the reader token. With a file there, it's not possible to
make a directory tree for recursive downloads.
Closes #2937.
Brett Smith [Thu, 19 Jun 2014 17:26:03 +0000 (13:26 -0400)]
Merge branch '2879-docker-image-job-reuse'
Closes #2879, #2924, #3030.
Brett Smith [Thu, 19 Jun 2014 14:49:56 +0000 (10:49 -0400)]
2879: Docker filters on Jobs accept an array of search terms.
Brett Smith [Thu, 19 Jun 2014 17:24:47 +0000 (13:24 -0400)]
2879: Job Docker filters respect reader tokens.
Brett Smith [Tue, 17 Jun 2014 17:52:52 +0000 (13:52 -0400)]
2879: Document new Job API filters.
Brett Smith [Tue, 17 Jun 2014 17:51:18 +0000 (13:51 -0400)]
2879: Support tag search in "in docker" Job filters.
The search uses the same `reponame:tagname` format used by
`docker tag`.
Brett Smith [Tue, 17 Jun 2014 16:23:32 +0000 (12:23 -0400)]
2879: Use Job-specific filters in #index too.
This brings #index consistency with the #create method, and enables
clients to do the same kind of sophisticated searching.
Brett Smith [Thu, 19 Jun 2014 17:24:27 +0000 (13:24 -0400)]
2879: API server can find_or_create Jobs based on Docker image.
Brett Smith [Mon, 16 Jun 2014 20:49:15 +0000 (16:49 -0400)]
2879: API server can find_or_create Jobs based on filters.
This will make it easier to support new criteria for find_or_create.
In particular, this will be the basis for searching based on Docker
image.
Peter Amstutz [Thu, 19 Jun 2014 15:21:16 +0000 (11:21 -0400)]
2986: Cleaned up arv cli help to be more helpful and consistent. refs #1667.
Peter Amstutz [Thu, 19 Jun 2014 14:05:53 +0000 (10:05 -0400)]
Merge branch 'origin-2883-job-log-viewer' closes #2883 refs #3027
peter [Thu, 19 Jun 2014 13:40:21 +0000 (13:40 +0000)]
2883: Fixed select all/select none messing with the "show task" radio buttons.
peter [Thu, 19 Jun 2014 13:16:30 +0000 (13:16 +0000)]
2883: Changed "task-output" category to "task-print" and "output" to
"diagnostic" in the UI text based on AWZ feedback.
peter [Thu, 19 Jun 2014 12:56:34 +0000 (12:56 +0000)]
2883: Fixed variable being used before it was declared, and fixed assignment of
ids to rows.
Peter Amstutz [Wed, 18 Jun 2014 21:08:11 +0000 (17:08 -0400)]
Merge branch '2883-job-log-viewer' of git.curoverse.com:arvados into origin-2883-job-log-viewer
Conflicts:
apps/workbench/app/views/jobs/_show_log.html.erb
Peter Amstutz [Wed, 18 Jun 2014 20:56:43 +0000 (16:56 -0400)]
Add error handling when log collection is not found. refs #3027.
Peter Amstutz [Wed, 18 Jun 2014 14:41:43 +0000 (14:41 +0000)]
2883: Use smart scrolling so keep the sorting and filtering selections on the
page when scrolling the output.
Peter Amstutz [Wed, 18 Jun 2014 14:05:00 +0000 (10:05 -0400)]
Merge branch 'master' into origin-2883-job-log-viewer
Peter Amstutz [Wed, 18 Jun 2014 14:04:12 +0000 (10:04 -0400)]
Fixed smart scrolling as intended for svg divs. refs #2919
Peter Amstutz [Wed, 18 Jun 2014 13:26:55 +0000 (09:26 -0400)]
2884: Adjusted column size on components page to work better when used in
chooser preview pane. Removed spurious console.log statement.
Peter Amstutz [Wed, 18 Jun 2014 13:03:13 +0000 (09:03 -0400)]
2884: Added spinner to indicate infinite scroll is loading.
Peter Amstutz [Wed, 18 Jun 2014 02:22:33 +0000 (22:22 -0400)]
2884: Fixed horizontal scroll in folder selection dialog
Peter Amstutz [Wed, 18 Jun 2014 02:06:42 +0000 (22:06 -0400)]
2884: Selecting folders works for run pipeline dialog. Increased page size
from 20 items to 40 items.
radhika [Tue, 17 Jun 2014 23:31:55 +0000 (19:31 -0400)]
closes #2896
Merge branch '2896-websocket-cli'
radhika [Tue, 17 Jun 2014 23:30:54 +0000 (19:30 -0400)]
Merge branch 'master' into 2896-websocket-cli
Peter Amstutz [Tue, 17 Jun 2014 21:04:42 +0000 (17:04 -0400)]
2884: Can now choose a specific folder to browse in the file selector modal.
Brett Smith [Tue, 17 Jun 2014 20:06:43 +0000 (16:06 -0400)]
crunch-job passes ARVADOS envvars to Docker.
No issue #.
Tim Pierce [Tue, 17 Jun 2014 19:42:45 +0000 (15:42 -0400)]
Merge branch '2936-job-progress-bar'
Closes #2936.
Tim Pierce [Tue, 17 Jun 2014 19:03:07 +0000 (15:03 -0400)]
2936: fix job progress bars
Add edge case settings for when a crunch job could not be started, or
when no tasks were ever created.
Calculate percent_total_tasks as a float, to ensure that it will be
nonzero even if there are more than 100 tasks altogether. Calculate
percentages of individual task progress with .ceil to ensure that there
will be at least 1% shown for each nonzero task status.
Refs #2936
radhika [Tue, 17 Jun 2014 17:58:48 +0000 (13:58 -0400)]
Merge branch 'master' into 2896-websocket-cli
radhika [Tue, 17 Jun 2014 17:58:12 +0000 (13:58 -0400)]
2896: add logging to events.py
Tim Pierce [Tue, 17 Jun 2014 17:16:55 +0000 (13:16 -0400)]
Merge branch '2934-limit-crunch-logs-bugfix'
Refs #2934.
Tim Pierce [Tue, 17 Jun 2014 17:15:28 +0000 (13:15 -0400)]
2934: add crunch-dispatch default settings
Add default values to application.default.yml for:
* crunch_limit_log_events_per_job
* crunch_limit_log_event_bytes_per_job
* crunch_log_bytes_per_event
* crunch_log_seconds_between_events
Refs #2934.
radhika [Tue, 17 Jun 2014 15:45:06 +0000 (11:45 -0400)]
Merge branch 'master' into 2896-websocket-cli
radhika [Tue, 17 Jun 2014 15:43:38 +0000 (11:43 -0400)]
2896: incorporate review comments: add logging, enhance creating filter object.
Peter Amstutz [Tue, 17 Jun 2014 15:37:08 +0000 (11:37 -0400)]
2884: AJAX load a preview panel in collection and pipeline template picker.
Peter Amstutz [Tue, 17 Jun 2014 14:21:41 +0000 (14:21 +0000)]
Fixed bug in Keep proxy when talking to Keep server that doesn't report
Content-Length correctly. no issue #
Tim Pierce [Tue, 17 Jun 2014 13:57:00 +0000 (09:57 -0400)]
2936: improve progress bar for failed jobs
Ensure that:
* All job progress bars reflect at least one task. If a job has no
tasks at all (done, failed, finished, or todo) that should be
considered a failed job, so render a progress bar as though one task
ran and failed.
* A failed job (j[:success] == false) always shows at least one failed
task. If a job is marked as failed but has no failed tasks, then
pretend there was one failed task so at least some red will appear in
the progress bar.
Fixes #2936.
Peter Amstutz [Tue, 17 Jun 2014 13:43:48 +0000 (09:43 -0400)]
Ajax load of tab panels now includes any query parameters the page was
originally loaded with. Also fixed related problem where the 'compare' route
of pipeline_instances controller wasn't aware of tab partials. closes #3013
Peter Amstutz [Tue, 17 Jun 2014 13:11:20 +0000 (13:11 +0000)]
2883: Improved pagination control a bit, added search.
Peter Amstutz [Tue, 17 Jun 2014 02:22:43 +0000 (02:22 +0000)]
2883: Added pagination for large logs.
Peter Amstutz [Mon, 16 Jun 2014 20:59:16 +0000 (20:59 +0000)]
2883: Added big red "show failed tasks" button.
Peter Amstutz [Mon, 16 Jun 2014 20:31:38 +0000 (20:31 +0000)]
2883: Distinguish between complete/incomplete and success/failure.
radhika [Mon, 16 Jun 2014 19:58:40 +0000 (15:58 -0400)]
2896: Add test file. Currently, the test only checks that arv-ws command is available and the options.
Peter Amstutz [Mon, 16 Jun 2014 19:54:07 +0000 (19:54 +0000)]
2883: Added node slots as its own column.
Brett Smith [Mon, 16 Jun 2014 19:27:26 +0000 (15:27 -0400)]
Merge branch '2879-job-api-docker-images'
Closes #2923, #3010.
radhika [Mon, 16 Jun 2014 19:18:31 +0000 (15:18 -0400)]
Merge branch 'master' into 2896-websocket-cli
Brett Smith [Thu, 12 Jun 2014 19:52:21 +0000 (15:52 -0400)]
2879: crunch-job uses Job Docker information provided by API server.
Brett Smith [Wed, 11 Jun 2014 21:43:27 +0000 (17:43 -0400)]
2879: API server maps Job Docker image constraints to Collections.
Doing this translation in the API server helps ensure that one piece
of software makes one consistent decision about which Docker image
should be used to run the Job.
Brett Smith [Mon, 16 Jun 2014 14:27:38 +0000 (10:27 -0400)]
2879: Let ArvadosModel.readable_by callers specify table name.
This makes it possible to use readable_by in queries with arbitrary
joins.
Brett Smith [Thu, 12 Jun 2014 14:10:24 +0000 (10:10 -0400)]
2879: Fix SLURM node separator when installing Docker images.
Brett Smith [Fri, 13 Jun 2014 17:40:45 +0000 (13:40 -0400)]
2879: Store Docker image repo+tag together in one tag.
It doesn't make sense to query the tag independently of the
repository, and this change will make the common case of querying both
together easier.
radhika [Mon, 16 Jun 2014 19:17:20 +0000 (15:17 -0400)]
2896: add arv-ws cli tool to arv.
Peter Amstutz [Mon, 16 Jun 2014 19:11:08 +0000 (19:11 +0000)]
2883: Added overview, node column and sort by node, style tweaks.
Tim Pierce [Mon, 16 Jun 2014 17:27:54 +0000 (13:27 -0400)]
Merge branch '2934-limit-crunch-logs'
Closes #2934
Tim Pierce [Mon, 16 Jun 2014 17:19:32 +0000 (13:19 -0400)]
2934: document stderr messages for commit tests
Some unit tests for the Commit models issue alarming but expected git
error messages on stderr. Added comments documenting these in
commits_controller_test.rb.
Refs #2934.
Peter Amstutz [Mon, 16 Jun 2014 15:46:06 +0000 (15:46 +0000)]
2883: Fix pattern for discovering success/failure of tasks.
Peter Amstutz [Mon, 16 Jun 2014 15:43:20 +0000 (15:43 +0000)]
2883: Fixes secondary key sort bug. Adds filtering on successful/failed tasks.
Tim Pierce [Mon, 16 Jun 2014 14:56:44 +0000 (10:56 -0400)]
2934: add crunch_dispatch_test repository
Move files for crunch_dispatch_test to their own test fixture
repository.
Refs #2934.
Peter Amstutz [Mon, 16 Jun 2014 14:19:04 +0000 (14:19 +0000)]
Merge remote-tracking branch 'origin/origin-2883-job-log-viewer' into 2883-job-log-viewer
Peter Amstutz [Mon, 16 Jun 2014 13:56:38 +0000 (09:56 -0400)]
some refactoring and added detection of task success or failure
Peter Amstutz [Mon, 16 Jun 2014 13:56:38 +0000 (09:56 -0400)]
2883: Added radio buttons to filter tasks by success/failure.
Tim Pierce [Fri, 13 Jun 2014 21:24:42 +0000 (17:24 -0400)]
Merge branch 'master' into 2934-limit-crunch-logs
Refs #2934
Tom Clegg [Fri, 13 Jun 2014 20:06:48 +0000 (16:06 -0400)]
Fix infinite scroll in chooser. refs #2872
Tim Pierce [Fri, 13 Jun 2014 19:08:48 +0000 (15:08 -0400)]
2934: add "bar" repository to test fixture
Add the "bar" repository to test/fixtures/repositories.yml so
CrunchDispatchTest may create a job using a commit from that
repository. (Change lost in a bad rebase.)
Refs #2934
Tim Pierce [Fri, 13 Jun 2014 18:03:04 +0000 (14:03 -0400)]
2934: count events and bytes in-memory
To avoid thrashing the database, crunch-dispatch.rb counts log events
and bytes in RAM instead of reading the database each time.
Refs #2934.
Peter Amstutz [Fri, 13 Jun 2014 17:31:04 +0000 (13:31 -0400)]
Fix fuse driver tests broken by changes to test fixtures. no issue #
Tom Clegg [Fri, 13 Jun 2014 15:12:10 +0000 (11:12 -0400)]
2872: Merge branch '2872-folder-nav' closes #2872
Tom Clegg [Fri, 13 Jun 2014 14:44:42 +0000 (10:44 -0400)]
2872: Add data binding for project names in dropdown.
Tim Pierce [Fri, 13 Jun 2014 14:44:21 +0000 (10:44 -0400)]
2934: add launch_crunch_dispatch to integration test
Added functionality for launching crunch-dispatch in
crunch_dispatch_test.rb while integration tests are running.
Refs #2934.
Tim Pierce [Fri, 13 Jun 2014 14:39:00 +0000 (10:39 -0400)]
Merge branch '2934-limit-crunch-logs' of git.curoverse.com:arvados into 2934-limit-crunch-logs
Fixing broken rebase