Tom Clegg [Thu, 31 Jul 2014 15:30:01 +0000 (11:30 -0400)]
3261: Fix wrong test: wanted file size == 0, not string length == 0.
Tom Clegg [Thu, 31 Jul 2014 14:46:14 +0000 (10:46 -0400)]
3261: Propagate configured RAILS_ENV to Workbench build tasks.
Without this, the rake assets:precompile task defaults to development
mode and does nothing.
radhika [Thu, 31 Jul 2014 15:17:12 +0000 (11:17 -0400)]
3193: minor ui update
radhika [Thu, 31 Jul 2014 14:52:09 +0000 (10:52 -0400)]
3193: add contact admin blurb when the user has no virtual machines and repositories configured.
Tom Clegg [Thu, 31 Jul 2014 14:30:59 +0000 (10:30 -0400)]
3261: Add Keep blob_signing_key configuration.
Tom Clegg [Thu, 31 Jul 2014 14:11:46 +0000 (10:11 -0400)]
3261: Fix condition for showing SSH usage message.
Tom Clegg [Thu, 31 Jul 2014 14:10:54 +0000 (10:10 -0400)]
3261: Fix alternate SSO endpoint configuration.
radhika [Thu, 31 Jul 2014 14:02:54 +0000 (10:02 -0400)]
3193: use HISTIGNORE for current token display
radhika [Thu, 31 Jul 2014 13:46:46 +0000 (09:46 -0400)]
Merge branch 'master' into 3193-manage-account
radhika [Thu, 31 Jul 2014 13:45:07 +0000 (09:45 -0400)]
3193: use sshkey gem to validate the ssh key passed in.
radhika [Thu, 31 Jul 2014 09:21:30 +0000 (05:21 -0400)]
3193: add plus icon to add ssh key button
radhika [Wed, 30 Jul 2014 21:35:29 +0000 (17:35 -0400)]
refs #3016
Merge branch '3016-pipeline-template-search-string'
radhika [Wed, 30 Jul 2014 21:34:51 +0000 (17:34 -0400)]
Merge branch 'master' into 3016-pipeline-template-search-string
radhika [Wed, 30 Jul 2014 21:27:20 +0000 (17:27 -0400)]
Merge branch 'master' into 3193-manage-account
radhika [Wed, 30 Jul 2014 21:26:40 +0000 (17:26 -0400)]
3193: add horizontal scroll to ssh key
radhika [Wed, 30 Jul 2014 20:53:50 +0000 (16:53 -0400)]
3193: minor ui updates
radhika [Wed, 30 Jul 2014 20:33:32 +0000 (16:33 -0400)]
3193: minor ui updates
Tom Clegg [Wed, 30 Jul 2014 20:30:00 +0000 (16:30 -0400)]
Merge branch '3425-truncated-output' closes #3425
Tom Clegg [Wed, 30 Jul 2014 20:28:53 +0000 (16:28 -0400)]
3425: Smaller buffer.
Tom Clegg [Wed, 30 Jul 2014 20:19:36 +0000 (16:19 -0400)]
Merge branch '3349-install-docs' closes #3349
Tom Clegg [Wed, 30 Jul 2014 20:17:49 +0000 (16:17 -0400)]
3425: When reading from arv-get, repeat sysread until error or eof.
radhika [Wed, 30 Jul 2014 20:13:34 +0000 (16:13 -0400)]
Merge branch 'master' into 3193-manage-account
radhika [Wed, 30 Jul 2014 20:09:49 +0000 (16:09 -0400)]
closes #3065
Merge branch '2985-selection-button-move-copy'
radhika [Wed, 30 Jul 2014 20:04:42 +0000 (16:04 -0400)]
Merge branch '3193-manage-account' of git.curoverse.com:arvados into 3193-manage-account
Tom Clegg [Wed, 30 Jul 2014 20:03:19 +0000 (16:03 -0400)]
3349: More example/default config cleanup.
radhika [Wed, 30 Jul 2014 20:02:25 +0000 (16:02 -0400)]
2985: let error propagate during save
radhika [Wed, 30 Jul 2014 19:57:30 +0000 (15:57 -0400)]
2985: let errors propagate during save
Tom Clegg [Wed, 30 Jul 2014 19:56:46 +0000 (15:56 -0400)]
3349: Merge branch 'master' into 3349-install-docs
Peter Amstutz [Wed, 30 Jul 2014 19:54:47 +0000 (15:54 -0400)]
Combined contents of "Setting up SSH" into "Virtual Machines" panel. Added
"Command line" column to "virtual machines" table which user can cut and paste
the ssh command line.
radhika [Wed, 30 Jul 2014 19:43:51 +0000 (15:43 -0400)]
Merge branch 'master' into 2985-selection-button-move-copy
Tom Clegg [Wed, 30 Jul 2014 19:37:05 +0000 (15:37 -0400)]
3235: Fix empty collection migration: ensure anonymous_group exists in
the database before trying to create a permission link for it.
Tom Clegg [Wed, 30 Jul 2014 19:35:12 +0000 (15:35 -0400)]
3235: Enable "rename folder to project" migration.
radhika [Wed, 30 Jul 2014 19:29:35 +0000 (15:29 -0400)]
Merge branch 'master' into 3193-manage-account
Tom Clegg [Wed, 30 Jul 2014 19:20:40 +0000 (15:20 -0400)]
3235: Accept group_class="folder" as a project.
radhika [Wed, 30 Jul 2014 19:15:51 +0000 (15:15 -0400)]
3193: do not validate input submitted on client side
Tom Clegg [Wed, 30 Jul 2014 19:11:53 +0000 (15:11 -0400)]
3235: Show names of named collections instead of their uuids, but support searching by uuid.
Tom Clegg [Wed, 30 Jul 2014 19:01:33 +0000 (15:01 -0400)]
3235: Make collections show up in search results.
radhika [Wed, 30 Jul 2014 19:01:07 +0000 (15:01 -0400)]
Merge branch 'master' into 2985-selection-button-move-copy
Ward Vandewege [Wed, 30 Jul 2014 19:00:49 +0000 (21:00 +0200)]
Workbench: make the Setup User screen less confusing by labelling the
Repository Name and Shell Login field as such.
no issue #
radhika [Wed, 30 Jul 2014 18:59:18 +0000 (14:59 -0400)]
Merge branch 'master' into 3193-manage-account
radhika [Wed, 30 Jul 2014 18:16:51 +0000 (14:16 -0400)]
3016: prefill input search with value configured in the template
Peter Amstutz [Wed, 30 Jul 2014 18:10:20 +0000 (14:10 -0400)]
Fix $(node.cores)
Tim Pierce [Wed, 23 Jul 2014 17:40:48 +0000 (13:40 -0400)]
2769: implement DELETE.
The DeleteHandler method implements DELETE requests for Keep, checking
that the user is authorized to issue DELETE and then deleting the
requested block from local volumes.
* CanDelete checks that the user with the given token is authorized to
delete blocks from Keep.
* MockVolume and UnixVolume objects provide a Delete method for deleting
a block from that volume.
* TestDeleteHandler tests:
** Unauthenticated requests
** Requests from a non-admin user
** Requests from a non-admin user for a nonexistent block
** Requests from a non-admin user for an existing block
Tom Clegg [Wed, 30 Jul 2014 17:54:20 +0000 (13:54 -0400)]
3235: Update results as soon as search modal opens.
Tom Clegg [Wed, 30 Jul 2014 17:48:52 +0000 (13:48 -0400)]
3235: Merge branch 'master' into 3235-top-nav-site-search
Peter Amstutz [Wed, 30 Jul 2014 17:37:50 +0000 (13:37 -0400)]
str or unicode
Peter Amstutz [Wed, 30 Jul 2014 17:36:08 +0000 (13:36 -0400)]
extra / after dir
Peter Amstutz [Wed, 30 Jul 2014 17:32:07 +0000 (13:32 -0400)]
Better error from glob
Peter Amstutz [Wed, 30 Jul 2014 17:25:51 +0000 (13:25 -0400)]
Pretty print
Peter Amstutz [Wed, 30 Jul 2014 17:23:15 +0000 (13:23 -0400)]
Rearranged exception handling a little more
Peter Amstutz [Wed, 30 Jul 2014 17:20:52 +0000 (13:20 -0400)]
More logging
Peter Amstutz [Wed, 30 Jul 2014 17:15:51 +0000 (13:15 -0400)]
Print traceback on exception
radhika [Wed, 30 Jul 2014 16:04:11 +0000 (12:04 -0400)]
3016: Update per Tom's review feedback.
Peter Amstutz [Wed, 30 Jul 2014 15:40:29 +0000 (11:40 -0400)]
Set first task to success
radhika [Wed, 30 Jul 2014 15:36:55 +0000 (11:36 -0400)]
Merge branch 'master' into 3016-pipeline-template-search-string
Peter Amstutz [Wed, 30 Jul 2014 15:36:05 +0000 (11:36 -0400)]
import copy
Peter Amstutz [Wed, 30 Jul 2014 15:34:38 +0000 (11:34 -0400)]
.st_mode
Peter Amstutz [Wed, 30 Jul 2014 15:32:41 +0000 (11:32 -0400)]
import stat
Peter Amstutz [Wed, 30 Jul 2014 15:30:47 +0000 (11:30 -0400)]
Fix syntax error
Peter Amstutz [Wed, 30 Jul 2014 14:58:08 +0000 (10:58 -0400)]
Refactored and generalized list expansion, can use "foreach" to repeat portions
of the command line.
Peter Amstutz [Wed, 30 Jul 2014 14:54:41 +0000 (10:54 -0400)]
Simpler split-fastq, doesn't try to upload the collection, assume crunch-job
will create the collection for us.
Tom Clegg [Wed, 30 Jul 2014 14:35:09 +0000 (10:35 -0400)]
Report validation error messages in server log. refs #3415
radhika [Wed, 30 Jul 2014 14:32:43 +0000 (10:32 -0400)]
3193: update the ssh popup to not require name.
radhika [Wed, 30 Jul 2014 14:03:04 +0000 (10:03 -0400)]
Merge branch 'master' into 3193-manage-account
Tom Clegg [Tue, 29 Jul 2014 23:28:07 +0000 (19:28 -0400)]
3235: Fix missed filter update after paste event.
Tom Clegg [Tue, 29 Jul 2014 23:19:02 +0000 (19:19 -0400)]
3235: Don't blow up when calling 404 from ActionsController.
Before:
At .../app/views/application/404.html.erb:17
#<ActionController::UrlGenerationError: No route matches {:action=>"index", :controller=>"actions"}>
After:
Use the class_name deduced from the uuid to determine the most
likely controller, instead of assuming the current controller is the
right one.
Tom Clegg [Tue, 29 Jul 2014 23:13:42 +0000 (19:13 -0400)]
3235: Do not bring up search dialog until enter/click in top nav
widget. Add special case "feeling lucky" behavior when the search
string is an Arvados UUID.
Ward Vandewege [Tue, 29 Jul 2014 21:54:43 +0000 (23:54 +0200)]
Documentation fix: add a link to the Keep installation page in the left
nav bar under "Manual installation".
no issue #
Ward Vandewege [Tue, 29 Jul 2014 21:48:38 +0000 (23:48 +0200)]
Whitespace fix in docker install documentation.
no issue #
Peter Amstutz [Tue, 29 Jul 2014 20:53:06 +0000 (16:53 -0400)]
Change collection create request
Peter Amstutz [Tue, 29 Jul 2014 20:48:13 +0000 (16:48 -0400)]
Debug manifest format to see why api server is rejecting it
Peter Amstutz [Tue, 29 Jul 2014 20:43:16 +0000 (16:43 -0400)]
debug print manifest_text
Peter Amstutz [Tue, 29 Jul 2014 20:41:01 +0000 (16:41 -0400)]
Left debugging in by accident
Peter Amstutz [Tue, 29 Jul 2014 20:39:45 +0000 (16:39 -0400)]
Same bug, different place
Peter Amstutz [Tue, 29 Jul 2014 20:38:16 +0000 (16:38 -0400)]
Input is "reads" not "input"
Peter Amstutz [Tue, 29 Jul 2014 20:37:03 +0000 (16:37 -0400)]
typo fix get_job_param() -> getjobparam()
Ward Vandewege [Tue, 29 Jul 2014 20:34:14 +0000 (22:34 +0200)]
Merge branch '3219-further-docker-improvements'
refs #3219
Ward Vandewege [Tue, 29 Jul 2014 20:32:56 +0000 (22:32 +0200)]
Merge branch 'master' into 3219-further-docker-improvements
Peter Amstutz [Tue, 29 Jul 2014 20:32:50 +0000 (16:32 -0400)]
foreach just refers to other parameter to use as iterator variable.
Peter Amstutz [Tue, 29 Jul 2014 20:10:21 +0000 (16:10 -0400)]
Added "foreach" to run-command wrapper. Needs testing.
radhika [Tue, 29 Jul 2014 20:07:45 +0000 (16:07 -0400)]
3193: improve virtual machines section to add a sample.
Peter Amstutz [Tue, 29 Jul 2014 19:32:16 +0000 (15:32 -0400)]
Don't split fastq, just organize into directories.
radhika [Tue, 29 Jul 2014 19:31:44 +0000 (15:31 -0400)]
3193: split ssh section into two sections
radhika [Tue, 29 Jul 2014 19:15:01 +0000 (15:15 -0400)]
3193: show only a portion of the ssh key so that the page does not have to scroll too far down when there are multiple ssh keys configured.
Peter Amstutz [Tue, 29 Jul 2014 18:59:56 +0000 (14:59 -0400)]
Full split-fastq wip
Tom Clegg [Tue, 29 Jul 2014 18:44:10 +0000 (14:44 -0400)]
3235: Merge branch 'master' into 3235-top-nav-site-search
radhika [Tue, 29 Jul 2014 18:09:58 +0000 (14:09 -0400)]
3193: minor text updates in the UI panels.
radhika [Tue, 29 Jul 2014 17:44:13 +0000 (13:44 -0400)]
3193: add head_uuid is a arvados#repository filter when looking for recpositories.
radhika [Tue, 29 Jul 2014 17:29:56 +0000 (13:29 -0400)]
Merge branch 'master' into 3193-manage-account
radhika [Tue, 29 Jul 2014 17:25:45 +0000 (13:25 -0400)]
3016: schema doc updated with new search_for attribute details.
Tom Clegg [Tue, 29 Jul 2014 15:58:45 +0000 (11:58 -0400)]
Merge branch '3351-keep-timeout' closes #3351
radhika [Tue, 29 Jul 2014 15:03:37 +0000 (11:03 -0400)]
2985: forgot to use ruby's cool syntax
radhika [Tue, 29 Jul 2014 14:38:33 +0000 (10:38 -0400)]
2985: pass move items only when available
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).
radhika [Tue, 29 Jul 2014 14:28:06 +0000 (10:28 -0400)]
Merge branch 'master' into 2985-selection-button-move-copy
Conflicts:
apps/workbench/config/routes.rb
radhika [Tue, 29 Jul 2014 14:14:18 +0000 (10:14 -0400)]
Merge branch 'master' into 3193-manage-account
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 02:49:07 +0000 (22:49 -0400)]
3235: Replace link with search widget in top nav.
Tom Clegg [Tue, 29 Jul 2014 01:18:40 +0000 (21:18 -0400)]
Do not show non-project groups in groups directory. no issue #