Peter Amstutz [Tue, 29 Jul 2014 20:10:21 +0000 (16:10 -0400)]
Added "foreach" to run-command wrapper. Needs testing.
Peter Amstutz [Tue, 29 Jul 2014 19:32:16 +0000 (15:32 -0400)]
Don't split fastq, just organize into directories.
Peter Amstutz [Tue, 29 Jul 2014 18:59:56 +0000 (14:59 -0400)]
Full split-fastq wip
Tom Clegg [Tue, 29 Jul 2014 15:58:45 +0000 (11:58 -0400)]
Merge branch '3351-keep-timeout' closes #3351
Tom Clegg [Tue, 29 Jul 2014 14:35:26 +0000 (10:35 -0400)]
3351: Propagate caller-provided timeout from KeepClient to KeepWriterThread.
Also, use the timeout in the sign_for_old_server block (even though
this branch is unlikely to be used in real life now that the old Keep
server has been replaced).
Tom Clegg [Tue, 29 Jul 2014 14:00:03 +0000 (10:00 -0400)]
3235: Fix attribute keys. refs #3235
Tom Clegg [Tue, 29 Jul 2014 02:50:37 +0000 (22:50 -0400)]
Merge branch '3235-top-nav-site-search' refs #3235
Tom Clegg [Tue, 29 Jul 2014 01:18:40 +0000 (21:18 -0400)]
Do not show non-project groups in groups directory. no issue #
Tom Clegg [Tue, 29 Jul 2014 01:14:33 +0000 (21:14 -0400)]
Fix TypeError: Got an unexpected keyword argument "uuid". refs #3235
Tom Clegg [Tue, 29 Jul 2014 00:30:10 +0000 (20:30 -0400)]
3235: Fix hover highlighting on projects dropdowns.
Tom Clegg [Tue, 29 Jul 2014 00:12:42 +0000 (20:12 -0400)]
3235: Show selected project in project-filter dropdown title.
Tom Clegg [Mon, 28 Jul 2014 23:23:04 +0000 (19:23 -0400)]
Do not return non-project groups in groups#contents. refs #3235
Ward Vandewege [Mon, 28 Jul 2014 22:43:14 +0000 (00:43 +0200)]
Fix the auto_admin_user feature; it was broken by accident in
commit:
5f651773
refs #3219
Tom Clegg [Mon, 28 Jul 2014 21:52:51 +0000 (17:52 -0400)]
3235: Fix infinite scroll broken by merge.
Tom Clegg [Mon, 28 Jul 2014 21:20:38 +0000 (17:20 -0400)]
3235: Move filter-by-project to left side.
Tom Clegg [Mon, 28 Jul 2014 21:12:52 +0000 (17:12 -0400)]
3235: Merge branch 'master' into 3235-top-nav-site-search
Conflicts:
apps/workbench/app/views/layouts/application.html.erb
Tom Clegg [Mon, 28 Jul 2014 21:10:16 +0000 (17:10 -0400)]
Merge branch '3235-all-contents' refs #3235
Tom Clegg [Fri, 25 Jul 2014 17:49:27 +0000 (13:49 -0400)]
3235: Add test case.
Tom Clegg [Fri, 25 Jul 2014 02:10:30 +0000 (22:10 -0400)]
3235: Fix SQL query.
Tom Clegg [Thu, 24 Jul 2014 23:03:35 +0000 (19:03 -0400)]
3235: Split GroupsController#contents logic out to load_searchable_objects.
Tom Clegg [Mon, 28 Jul 2014 19:56:41 +0000 (15:56 -0400)]
3235: Remove errant action exemption.
Tom Clegg [Mon, 28 Jul 2014 19:45:23 +0000 (15:45 -0400)]
3235: Merge branch 'master' into 3235-top-nav-site-search
Conflicts:
apps/workbench/app/assets/javascripts/infinite_scroll.js
apps/workbench/app/views/application/_choose.html.erb
apps/workbench/app/views/layouts/application.html.erb
Peter Amstutz [Mon, 28 Jul 2014 13:13:59 +0000 (09:13 -0400)]
Set $CRUNCH_SRC correctly when running the Docker container. refs #3370
Tom Clegg [Sun, 27 Jul 2014 22:35:46 +0000 (18:35 -0400)]
3235: Bind Esc key to close modals.
Tom Clegg [Sun, 27 Jul 2014 22:28:18 +0000 (18:28 -0400)]
3235: Focus search box when chooser modal appears.
Tom Clegg [Sun, 27 Jul 2014 22:22:53 +0000 (18:22 -0400)]
3235: Show project filter by default (i.e., unless by_project=false).
Tom Clegg [Sun, 27 Jul 2014 22:03:13 +0000 (18:03 -0400)]
3235: Fix "no filter / all projects" option.
Tom Clegg [Sun, 27 Jul 2014 21:58:17 +0000 (17:58 -0400)]
3235: Fix multiple-select.
Tom Clegg [Sun, 27 Jul 2014 21:48:28 +0000 (17:48 -0400)]
3235: Make filter-by-project play nice with infinite scroll.
Tom Clegg [Sun, 27 Jul 2014 19:34:31 +0000 (15:34 -0400)]
3235: Hide section header rows for empty sections. closes #3377
Tom Clegg [Sun, 27 Jul 2014 19:22:38 +0000 (15:22 -0400)]
3235: Fix infinite scroll in Search chooser.
Tom Clegg [Sun, 27 Jul 2014 19:19:49 +0000 (15:19 -0400)]
3235: Infinite scroll error handling: Show error message and "Retry" button
instead of immediately repeating the failed request ad infinitum.
Tom Clegg [Sat, 26 Jul 2014 21:23:42 +0000 (17:23 -0400)]
3235: Skip data-remote links in smoke test. They might not know format=html.
Tom Clegg [Sat, 26 Jul 2014 21:08:45 +0000 (17:08 -0400)]
3235: Show multiple object types in top-nav Search modal.
Tom Clegg [Sat, 26 Jul 2014 18:53:17 +0000 (14:53 -0400)]
3351: Fix CollectionReader usage in arv-ls.
Tom Clegg [Sat, 26 Jul 2014 18:51:19 +0000 (14:51 -0400)]
3351: Add comment about SSL timeouts.
Tom Clegg [Sat, 26 Jul 2014 18:49:02 +0000 (14:49 -0400)]
3351: Clean up some excess indentation.
Tom Clegg [Sat, 26 Jul 2014 18:48:13 +0000 (14:48 -0400)]
3351: Catch SSLError and show warning instead of stack trace.
Tom Clegg [Sat, 26 Jul 2014 18:17:43 +0000 (14:17 -0400)]
3351: Retry failed threads (servers) if replication is too low after one pass.
radhika [Sat, 26 Jul 2014 01:34:42 +0000 (21:34 -0400)]
refs #3138
Merge branch '3138-wiselinks'
radhika [Sat, 26 Jul 2014 01:33:50 +0000 (21:33 -0400)]
3138: test passing as is
radhika [Sat, 26 Jul 2014 01:24:04 +0000 (21:24 -0400)]
Merge branch 'master' into 3138-wiselinks
Conflicts:
apps/workbench/app/views/layouts/application.html.erb
Tom Clegg [Fri, 25 Jul 2014 22:42:18 +0000 (18:42 -0400)]
3351: Improve "already uploading" message (and send to stderr, not stdout).
Tom Clegg [Fri, 25 Jul 2014 22:36:38 +0000 (18:36 -0400)]
3351: Do not use resume cache at all if --no-resume flag is given.
radhika [Fri, 25 Jul 2014 21:56:51 +0000 (17:56 -0400)]
Merge branch 'master' into 3138-wiselinks
radhika [Fri, 25 Jul 2014 21:55:41 +0000 (17:55 -0400)]
3138: When wiselinks is initialized, selection.js does not work. Since we want to stop using selection.js in the near future, let's not initialize wiselinks object for now.
Tom Clegg [Fri, 25 Jul 2014 21:42:43 +0000 (17:42 -0400)]
3351: Set PUT request timeout to 60 seconds.
Tom Clegg [Fri, 25 Jul 2014 20:22:54 +0000 (16:22 -0400)]
Merge branch '3286-home-button' closes #3286
Tom Clegg [Fri, 25 Jul 2014 19:26:31 +0000 (15:26 -0400)]
3286: Split Home/Projects thing into Home button and Projects dropdown.
Tom Clegg [Fri, 25 Jul 2014 17:51:51 +0000 (13:51 -0400)]
Do not remove /dev/stdout on interrupt signal. No issue #
Tom Clegg [Fri, 25 Jul 2014 17:49:27 +0000 (13:49 -0400)]
3235: Add test case.
Brett Smith [Fri, 25 Jul 2014 12:04:33 +0000 (08:04 -0400)]
Merge branch 'staging'
Closes #3315. Thanks Guillermo!
Guillermo Carrasco [Wed, 9 Jul 2014 19:02:27 +0000 (15:02 -0400)]
Create temporary directory if it does not exist
Tom Clegg [Fri, 25 Jul 2014 02:10:30 +0000 (22:10 -0400)]
3235: Fix SQL query.
Tom Clegg [Thu, 24 Jul 2014 23:03:35 +0000 (19:03 -0400)]
3235: Split GroupsController#contents logic out to load_searchable_objects.
Brett Smith [Thu, 24 Jul 2014 20:18:35 +0000 (16:18 -0400)]
3321: Workbench copes when pipeline components have an odd form.
Closes #3321.
Ward Vandewege [Thu, 24 Jul 2014 16:58:43 +0000 (12:58 -0400)]
Add Keep install instructions (manual).
no issue #
Brett Smith [Thu, 24 Jul 2014 15:03:04 +0000 (11:03 -0400)]
Merge branch '3200-ajax-error-handling'
Closes #3200, #3207, #3251, #3276, #3322.
Brett Smith [Wed, 23 Jul 2014 20:50:18 +0000 (16:50 -0400)]
3200: Improve error handling in Workbench's API client.
* Fix the class used for error responses that can be parsed but don't
have a dedicated subclass.
* Ensure that exception.api_response[:errors] is always an array.
This improves the error reporting for #3207.
Brett Smith [Wed, 23 Jul 2014 20:29:12 +0000 (16:29 -0400)]
3200: X-Editable renders errors even without a message array.
The previous version was causing the X-Editable popup to spin
infinitely when the JSON errors were null. See #3207, #3251.
Brett Smith [Tue, 22 Jul 2014 22:04:58 +0000 (18:04 -0400)]
3200: Workbench copes better when a tab fails to load.
Brett Smith [Tue, 22 Jul 2014 20:12:59 +0000 (16:12 -0400)]
2044: Improve reporting when project sharing fails.
Our select modal knows how to render an errors key in the JSON
response. This commit adjusts the project controller to conform to
this convention. Refs #2044, #3200.
Tim Pierce [Tue, 22 Jul 2014 20:10:24 +0000 (16:10 -0400)]
Merge branch '2769-keep-delete-request'
Refs #2769
Tim Pierce [Tue, 22 Jul 2014 20:09:28 +0000 (16:09 -0400)]
2769: reorganize REST handlers
Reorganizing REST handlers into their own source file.
Refs #2769.
radhika [Tue, 22 Jul 2014 16:00:26 +0000 (12:00 -0400)]
Merge branch 'master' into 3138-wiselinks
radhika [Tue, 22 Jul 2014 15:59:28 +0000 (11:59 -0400)]
3138: add wiselinks data-push to project link.
Tom Clegg [Mon, 21 Jul 2014 22:27:03 +0000 (18:27 -0400)]
Fix extra row left behind after deleting a pipeline instance. closes #2929
Tom Clegg [Mon, 21 Jul 2014 21:56:35 +0000 (17:56 -0400)]
3138: Split body into a separate layout for wiselinks.
Brett Smith [Mon, 21 Jul 2014 20:57:07 +0000 (16:57 -0400)]
2044: Make project sharing tests more forgiving of Ajax timing.
Apparently waiting our default 5 seconds is not always sufficient to
get an Ajax response that requires a roundtrip to the API server.
Wait longer in these cases. Not the most elegant solution, but I
don't see a better option. Refs #2044.
Brett Smith [Mon, 21 Jul 2014 20:24:37 +0000 (16:24 -0400)]
2044: Workbench resource lists support Enumerable-style select.
Refs #2044. Enumerable-style select is used in places like the groups
index.
Tim Pierce [Mon, 21 Jul 2014 19:35:29 +0000 (15:35 -0400)]
Merge branch '3072-empty-collection-bugfix'
closes #3072.
radhika [Mon, 21 Jul 2014 19:06:50 +0000 (15:06 -0400)]
Merge branch 'master' into 3138-wiselinks
radhika [Mon, 21 Jul 2014 19:03:49 +0000 (15:03 -0400)]
closes #3140
Merge branch '3140-project-content-tabs'
radhika [Mon, 21 Jul 2014 19:03:33 +0000 (15:03 -0400)]
Merge branch 'master' into 3140-project-content-tabs
radhika [Mon, 21 Jul 2014 19:02:25 +0000 (15:02 -0400)]
Merge branch 'master' into 3140-project-content-tabs
Conflicts:
apps/workbench/app/controllers/projects_controller.rb
Tim Pierce [Mon, 21 Jul 2014 18:56:17 +0000 (14:56 -0400)]
3072: rendering "Empty Collection" in default_name
Collection.default_name now renders "Empty Collection" for collection
d41d8cd98f00b204e9800998ecf8427e.
Refs #3072.
Tom Clegg [Mon, 21 Jul 2014 18:52:35 +0000 (14:52 -0400)]
Merge branch '3182-workbench-test-race'
closes #3182
Tom Clegg [Mon, 21 Jul 2014 18:50:10 +0000 (14:50 -0400)]
3182: Fix races by using find() instead of {sleep; page.has_text?}.
Tom Clegg [Mon, 21 Jul 2014 18:30:05 +0000 (14:30 -0400)]
3235: Fix errant merge.
Tom Clegg [Mon, 21 Jul 2014 18:28:17 +0000 (14:28 -0400)]
3235: Merge branch 'master' into 3235-top-nav-site-search
Conflicts:
apps/workbench/app/views/application/_choose.html.erb
Tom Clegg [Mon, 21 Jul 2014 18:17:34 +0000 (14:17 -0400)]
3235: Fix project dropdown, use it when choosing collections.
Tom Clegg [Mon, 21 Jul 2014 18:15:13 +0000 (14:15 -0400)]
Remove extra spinner. closes #3301
Tom Clegg [Mon, 21 Jul 2014 17:37:53 +0000 (13:37 -0400)]
3170: Use find().all() instead of page.all() to accommodate ajax content. refs #3170, #2044
Tom Clegg [Mon, 21 Jul 2014 17:24:28 +0000 (13:24 -0400)]
3170: Fix stale use of tab_pane_valid_state. refs #3170
Tom Clegg [Mon, 21 Jul 2014 17:20:51 +0000 (13:20 -0400)]
3235: Hide projects dropdown unless caller asked for it.
Tom Clegg [Mon, 21 Jul 2014 17:02:17 +0000 (13:02 -0400)]
Merge branch '3170-refresh-tab-pane'
closes #3170
Tom Clegg [Mon, 21 Jul 2014 17:00:42 +0000 (13:00 -0400)]
3170: Merge branch 'master' into 3170-refresh-tab-pane
Tom Clegg [Mon, 21 Jul 2014 17:00:34 +0000 (13:00 -0400)]
3170: Add comments.
Brett Smith [Mon, 21 Jul 2014 16:42:03 +0000 (12:42 -0400)]
Merge branch '2044-workbench-project-sharing'
Closes #2044, #2749, #3238.
Brett Smith [Tue, 15 Jul 2014 20:16:38 +0000 (16:16 -0400)]
2044: Add Workbench interface to manage project sharing.
This empowers administrators to add, modify, and remove permission
links on projects.
Brett Smith [Mon, 21 Jul 2014 16:18:24 +0000 (12:18 -0400)]
2044: Workbench route to share a project with others.
This route is intended to support AJAX requests from the interface to
share a project with one or more users/groups.
Brett Smith [Thu, 17 Jul 2014 15:39:24 +0000 (11:39 -0400)]
2044: Workbench can query the API /permissions method.
Brett Smith [Tue, 15 Jul 2014 19:35:12 +0000 (15:35 -0400)]
2044: Add more helpers to get FA icons for objects.
Brett Smith [Thu, 3 Jul 2014 18:10:31 +0000 (14:10 -0400)]
2044: Workbench supports API select parameter.
This can help ensure symmetry between admin and non-admin requests for
the user index.
Brett Smith [Fri, 18 Jul 2014 20:13:11 +0000 (16:13 -0400)]
2044: API server lets group managers see group permission links.
This implementation hooks into find_object_by_uuid because that was
the simplest thing that could work and unblock larger development on
this story. Longer-term, we would like to solve this problem more
generally. See the comments added to the links controller test for
more explanation about that.
Brett Smith [Mon, 14 Jul 2014 21:07:39 +0000 (17:07 -0400)]
2044: All users can give all other users folder permissions.
This supports a Workbench sharing button, the same way that the
changes to users#index does.
radhika [Mon, 21 Jul 2014 16:34:20 +0000 (12:34 -0400)]
3138: Wrap breadcrumps and page-wrapper in a body-wrapper div. Update this target for wiselinks for each request.
radhika [Mon, 21 Jul 2014 16:03:05 +0000 (12:03 -0400)]
Merge branch 'master' into 3138-wiselinks
radhika [Mon, 21 Jul 2014 16:01:49 +0000 (12:01 -0400)]
3138: update page-wrapper for each refresh.
Brett Smith [Mon, 21 Jul 2014 15:33:30 +0000 (11:33 -0400)]
3303: Add logfile support to arv-mount.
The primary thrust of this commit is to teach arv-mount to log to a
file. This can help make it easier to track down exceptions that
happen while the process is daemonized.
To support better logging information, it also sends exception
tracebacks directly to the log. This required reorganizing the code
to daemonize earlier.
Refs #3303.
projects / arvados.git / log