Ward Vandewege [Tue, 11 Feb 2014 16:38:50 +0000 (11:38 -0500)]
Fix up incorrect dependency on google-api-client
Ward Vandewege [Tue, 11 Feb 2014 15:00:07 +0000 (10:00 -0500)]
Fix comment - location of arvados configuration file has changed.
Peter Amstutz [Tue, 11 Feb 2014 14:50:03 +0000 (09:50 -0500)]
Added "vendor" to doc generation ignore list for deployment situations
Peter Amstutz [Tue, 11 Feb 2014 14:26:33 +0000 (09:26 -0500)]
Removed mkpydoc.sh which is obsoleted by Rakefile task
Peter Amstutz [Tue, 11 Feb 2014 14:23:55 +0000 (09:23 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Tue, 11 Feb 2014 14:17:39 +0000 (09:17 -0500)]
Python documentation step will now report a warning if epydoc isn't in PATH.
Fixed liquid include errors.
Ward Vandewege [Tue, 11 Feb 2014 02:39:36 +0000 (21:39 -0500)]
Fix Gemfile(.lock) in sdk/cli
Tom Clegg [Mon, 10 Feb 2014 22:13:49 +0000 (14:13 -0800)]
Merge branch '2008-show-log-buffer'
closes #2008
Tom Clegg [Mon, 10 Feb 2014 22:12:29 +0000 (14:12 -0800)]
Fix dashboard auto-refresh, and show last line of log_buffer (if any)
for jobs whose logs have not yet been written to Keep.
Tom Clegg [Mon, 10 Feb 2014 21:47:33 +0000 (13:47 -0800)]
Include log buffer in Job API response.
Peter Amstutz [Mon, 10 Feb 2014 21:42:30 +0000 (16:42 -0500)]
Merge remote-tracking branch 'origin/master' into 1786-replace-jekyll-with-zenweb
Peter Amstutz [Mon, 10 Feb 2014 21:39:03 +0000 (16:39 -0500)]
Jekyll is dead, long live Zenweb!
Peter Amstutz [Fri, 7 Feb 2014 21:38:15 +0000 (16:38 -0500)]
Merge branch 'master' into 1786-replace-jekyll-with-zenweb
Tom Clegg [Fri, 7 Feb 2014 20:01:00 +0000 (12:01 -0800)]
Merge branch '1979-workbench-ui-TC'
Tom Clegg [Fri, 7 Feb 2014 20:00:36 +0000 (12:00 -0800)]
Fix top nav behavior when window is narrow.
Tom Clegg [Fri, 7 Feb 2014 19:58:34 +0000 (11:58 -0800)]
Fill col-sm-3 space with left nav, and move it to the bottom when
window is narrow.
Peter Amstutz [Fri, 7 Feb 2014 15:24:04 +0000 (10:24 -0500)]
Fixed/refactored "smart-sizing" to adjust the content area to the size of the window so that the content area scrolls but the page as a whole shouldn't scroll.
Tom Clegg [Fri, 7 Feb 2014 14:23:05 +0000 (06:23 -0800)]
Clean up groups/index and add delete buttons.
Tom Clegg [Fri, 7 Feb 2014 04:03:45 +0000 (20:03 -0800)]
Merge branch '1979-workbench-ui-TC'
refs #1979
refs #1976
closes #2005
closes #2006
refs #2008
Tom Clegg [Fri, 7 Feb 2014 01:48:33 +0000 (17:48 -0800)]
Add section headings to API examples.
Tom Clegg [Fri, 7 Feb 2014 01:48:15 +0000 (17:48 -0800)]
Add space under tab row.
Tom Clegg [Fri, 7 Feb 2014 01:41:54 +0000 (17:41 -0800)]
Fix up tab titles.
Tom Clegg [Fri, 7 Feb 2014 01:27:59 +0000 (17:27 -0800)]
Fix up collections#index search box with bootstrap3 styles.
Tom Clegg [Fri, 7 Feb 2014 01:24:33 +0000 (17:24 -0800)]
Fix up collections search box on dashboard.
Tom Clegg [Fri, 7 Feb 2014 01:08:45 +0000 (17:08 -0800)]
Fix up pipeline_instances#index and #compare.
Tom Clegg [Fri, 7 Feb 2014 00:41:36 +0000 (16:41 -0800)]
Remove extra divider in notifications list.
Tom Clegg [Fri, 7 Feb 2014 00:39:48 +0000 (16:39 -0800)]
Rearrange thread_with_api_token around_filters so current_user is
available even when using thread_with_optional_api_token.
This makes notifications show up on users#home when accessed via root
url.
Tom Clegg [Fri, 7 Feb 2014 00:12:14 +0000 (16:12 -0800)]
Highlight "Dashboard" instead "Users" in left nav when on
dashboard. Also bring back "System" nav links.
Tom Clegg [Fri, 7 Feb 2014 00:00:47 +0000 (16:00 -0800)]
Clean up collections index and show->files tables.
Tom Clegg [Thu, 6 Feb 2014 23:42:23 +0000 (15:42 -0800)]
Use .badge-alert to highlight notification badges.
Tom Clegg [Thu, 6 Feb 2014 23:31:59 +0000 (15:31 -0800)]
Remove extra breadcrumb separator in "no breadcrumbs" mode.
Tom Clegg [Thu, 6 Feb 2014 23:25:43 +0000 (15:25 -0800)]
Expand graph border to tab pane width.
Tom Clegg [Thu, 6 Feb 2014 23:25:17 +0000 (15:25 -0800)]
Fix progress bars on pipeline_instances#show
Tom Clegg [Thu, 6 Feb 2014 23:19:38 +0000 (15:19 -0800)]
Fix up job/pipeline progress bars on dashboard.
Tom Clegg [Thu, 6 Feb 2014 19:33:16 +0000 (11:33 -0800)]
Add progress bars to pipeline instances table on dashboard.
refs #2006
Conflicts:
apps/workbench/app/assets/stylesheets/application.css.scss
Peter Amstutz [Thu, 6 Feb 2014 21:14:36 +0000 (16:14 -0500)]
Merge branch '1979-workbench-ui-PA'
Peter Amstutz [Thu, 6 Feb 2014 20:58:43 +0000 (15:58 -0500)]
badges.css.scss doesn't actually require bootstrap
Ward Vandewege [Thu, 6 Feb 2014 20:46:23 +0000 (15:46 -0500)]
Lock to a version of the arvados-cli gem that's been pushed to the world.
Peter Amstutz [Thu, 6 Feb 2014 20:19:06 +0000 (15:19 -0500)]
Added css to put back badge styles that went away in bootstrap 3
Peter Amstutz [Thu, 6 Feb 2014 20:05:15 +0000 (15:05 -0500)]
Missing from previous commit
Peter Amstutz [Thu, 6 Feb 2014 20:04:19 +0000 (15:04 -0500)]
Harmonized all sections to use the new content template and layout
Peter Amstutz [Thu, 6 Feb 2014 15:37:03 +0000 (10:37 -0500)]
Fixed up some glyphicons
Peter Amstutz [Thu, 6 Feb 2014 15:27:34 +0000 (10:27 -0500)]
Editable fields works again
Peter Amstutz [Thu, 6 Feb 2014 14:39:19 +0000 (09:39 -0500)]
Updating bootstrap-editable to bootstrap3-x-editable
Almost works, just need to figure one thing out.
Peter Amstutz [Thu, 6 Feb 2014 04:04:40 +0000 (23:04 -0500)]
* Left nav correctly highlights current section
* Refactored pipeline instances and job pages to use tabs
* Uses javascript to adjust height of tab pane so that scrollbars show up in the right place
* Fixed some glyphicons broken by bootstrap 3
Peter Amstutz [Thu, 6 Feb 2014 01:19:08 +0000 (20:19 -0500)]
Fixed search box for chrome
Ward Vandewege [Thu, 6 Feb 2014 00:45:48 +0000 (19:45 -0500)]
Make the config_uuid field match what we expect in our tests.
Peter Amstutz [Wed, 5 Feb 2014 22:37:36 +0000 (17:37 -0500)]
Menubar and left nav redesign in progress.
Tom Clegg [Wed, 5 Feb 2014 20:30:03 +0000 (12:30 -0800)]
Call super in pipeline_instances#show to make preview/js/json
rendering work.
refs #1977
Tom Clegg [Wed, 5 Feb 2014 20:29:13 +0000 (12:29 -0800)]
Fix handling of pipeline components with no job/output yet.
refs #1977
Peter Amstutz [Wed, 5 Feb 2014 16:54:18 +0000 (11:54 -0500)]
Reworked top menu. Started upgrading to bootstrap 3.
Tom Clegg [Tue, 4 Feb 2014 21:18:08 +0000 (13:18 -0800)]
Skip repeated find() calls for the same object during a single page
request.
Tom Clegg [Tue, 4 Feb 2014 21:10:04 +0000 (13:10 -0800)]
Fix script_parameters comparison on pipeline_instances.compare.
refs #1978
Peter Amstutz [Tue, 4 Feb 2014 20:57:00 +0000 (15:57 -0500)]
Added stroke-linecap: round to make lines look nicer.
Peter Amstutz [Tue, 4 Feb 2014 20:50:12 +0000 (15:50 -0500)]
Merge branch '1977-provenance-report' of git.clinicalfuture.com:arvados into 1977-provenance-report
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
Peter Amstutz [Tue, 4 Feb 2014 20:48:46 +0000 (15:48 -0500)]
* Added used_by query for collections
* Fixed svg div javascript/layouts after Tom's changes
* Added hover css effect for graph lines
* Added graph to pipeline instance comparison page
Tom Clegg [Tue, 4 Feb 2014 16:50:25 +0000 (08:50 -0800)]
Merge branch '1979-workbench-ui'
Tom Clegg [Tue, 4 Feb 2014 16:49:53 +0000 (08:49 -0800)]
Remove old views/collections/show template.
refs #1979
Tom Clegg [Tue, 4 Feb 2014 15:58:25 +0000 (07:58 -0800)]
Fix (and add test for) 404 at repositories.get_all_permissions.
Peter Amstutz [Tue, 4 Feb 2014 15:25:40 +0000 (10:25 -0500)]
Merge branch '1977-provenance-report' of git.clinicalfuture.com:arvados into 1977-provenance-report
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
Peter Amstutz [Tue, 4 Feb 2014 15:25:23 +0000 (10:25 -0500)]
Can now use 'contains' to query individual columns in where() queries, not just any: contains.
Tom Clegg [Tue, 4 Feb 2014 10:54:23 +0000 (02:54 -0800)]
Move show-object content into tabs.
refs #1979
Tom Clegg [Tue, 4 Feb 2014 10:31:51 +0000 (02:31 -0800)]
Use object type or friendly_link_name as browser title.
refs #1979
Tom Clegg [Tue, 4 Feb 2014 10:25:45 +0000 (02:25 -0800)]
Move all index content into Recent and Help tabs.
refs #1979
Tom Clegg [Tue, 4 Feb 2014 09:14:03 +0000 (01:14 -0800)]
Merge branch 'master' into 1979-workbench-ui
Tom Clegg [Tue, 4 Feb 2014 09:13:19 +0000 (01:13 -0800)]
Hide loading indicator after refreshing dashboard tables.
refs #1976
Tom Clegg [Tue, 4 Feb 2014 09:11:22 +0000 (01:11 -0800)]
Merge top nav menus into brand dropdown, move breadcrumbs into top
nav, and lighten up the top nav.
refs #1979
Tom Clegg [Tue, 4 Feb 2014 07:52:28 +0000 (23:52 -0800)]
Merge branch '1977-provenance-report'
Tom Clegg [Tue, 4 Feb 2014 07:50:54 +0000 (23:50 -0800)]
Move can_read permission logic into ArvadosModel.readable_by scope,
and use that in collections.provenance instead of plain where().
refs #1977
refs #2037
Tom Clegg [Tue, 4 Feb 2014 01:49:20 +0000 (17:49 -0800)]
Add tests for permissions enforcement in collections.provenance.
refs #2037
refs #1977
Tom Clegg [Tue, 4 Feb 2014 00:24:06 +0000 (16:24 -0800)]
Ensure permissions can be propagated via group owner_uuid attribute.
Closes #1945
Closes #2022
Tom Clegg [Mon, 3 Feb 2014 22:52:10 +0000 (14:52 -0800)]
Hide this/other/both legend if only one pipeline_instance is shown.
Tom Clegg [Mon, 3 Feb 2014 22:56:30 +0000 (14:56 -0800)]
Merge branch '1976-pipeline-progress'
Conflicts:
apps/workbench/app/views/pipeline_instances/show.html.erb
Tom Clegg [Mon, 3 Feb 2014 22:44:19 +0000 (14:44 -0800)]
Merge branch 'master' into 1977-provenance-report
Conflicts:
apps/workbench/app/controllers/pipeline_instances_controller.rb
apps/workbench/app/views/jobs/show.html.erb
Tim Pierce [Mon, 3 Feb 2014 20:32:59 +0000 (15:32 -0500)]
Fix build.sh bugs.
Tom Clegg [Mon, 3 Feb 2014 19:04:06 +0000 (11:04 -0800)]
Fix breadcrumbs crash if link has no tail_kind or head_kind.
Peter Amstutz [Mon, 3 Feb 2014 19:04:56 +0000 (14:04 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Mon, 3 Feb 2014 19:04:26 +0000 (14:04 -0500)]
Tweaked text a little to make tail/subject head/object correspondence a little clearer.
Tom Clegg [Mon, 3 Feb 2014 16:21:05 +0000 (08:21 -0800)]
Ensure util.mkdir_dash_p() fails if its target is a non-directory, and
succeeds if the target directory exists after an mkdir() race with
another process.
Tom Clegg [Mon, 3 Feb 2014 16:01:19 +0000 (08:01 -0800)]
Show "loading" indicator in nav bar while waiting for AJAX requests.
refs #1976
closes #2040
Tom Clegg [Mon, 3 Feb 2014 08:45:11 +0000 (00:45 -0800)]
Refresh dashboard with AJAX every 60 seconds.
refs #1976
closes #2004
Tom Clegg [Mon, 3 Feb 2014 08:21:52 +0000 (00:21 -0800)]
Use AJAX/remote requests when deleting objects. Add delete button to
pipeline_instances index.
refs #1976
Tom Clegg [Mon, 3 Feb 2014 08:07:24 +0000 (00:07 -0800)]
Improve progress view on pipeline_instances.show page and add AJAX
auto-refresh.
refs #1976
refs #2004
Tom Clegg [Mon, 3 Feb 2014 01:49:24 +0000 (17:49 -0800)]
Add arv-mount.
Tom Clegg [Mon, 3 Feb 2014 01:27:26 +0000 (17:27 -0800)]
Add StreamFileReader.seek() method.
Tom Clegg [Mon, 3 Feb 2014 01:26:59 +0000 (17:26 -0800)]
Fix scoping for error classes.
Tom Clegg [Sun, 2 Feb 2014 00:06:33 +0000 (16:06 -0800)]
Fix crash when component has missing attributes (e.g., no job was run).
refs #1978
Tom Clegg [Sun, 2 Feb 2014 00:05:55 +0000 (16:05 -0800)]
Add basic select-and-compare interface to pipeline_instances#index.
refs #1978
Tom Clegg [Sat, 1 Feb 2014 23:34:44 +0000 (15:34 -0800)]
Merge branch 'master' into 1978-compare-pipelines
Conflicts:
apps/workbench/app/controllers/pipeline_instances_controller.rb
apps/workbench/app/views/pipeline_instances/compare.html.erb
Tom Clegg [Sat, 1 Feb 2014 23:17:10 +0000 (15:17 -0800)]
Remove extra breadcrumbs bar.
Tom Clegg [Sat, 1 Feb 2014 23:16:52 +0000 (15:16 -0800)]
Allow controller to override page name for breadcrumbs.
Tom Clegg [Fri, 31 Jan 2014 21:59:33 +0000 (13:59 -0800)]
Add breadcrumbs bar to #index and #show pages.
Tom Clegg [Fri, 31 Jan 2014 21:32:39 +0000 (13:32 -0800)]
Use generic index page for /users
Tom Clegg [Wed, 29 Jan 2014 02:15:43 +0000 (18:15 -0800)]
Show condensed data about pipeline instances side by side on "compare"
page.
refs #1978
Tom Clegg [Tue, 28 Jan 2014 15:57:47 +0000 (07:57 -0800)]
Add pipeline_instances/compare page
Tom Clegg [Fri, 31 Jan 2014 20:50:35 +0000 (12:50 -0800)]
Fix "show all pipeline templates" link target on dashboard page.
Peter Amstutz [Sat, 1 Feb 2014 20:19:57 +0000 (15:19 -0500)]
Fixed bug in vertical scrolling by setting padding to size of graph or max size instead of dynamic size based on screen position.
Tim Pierce [Fri, 31 Jan 2014 22:59:04 +0000 (17:59 -0500)]
Fix some arv unit tests.
Peter Amstutz [Fri, 31 Jan 2014 21:59:31 +0000 (16:59 -0500)]
Tweak to account for width of scrolbar
Peter Amstutz [Fri, 31 Jan 2014 21:43:36 +0000 (16:43 -0500)]
Working on javascript magic to resize svg div so scrolling works nicely. Seems to work pretty well except when the svg div is the last thing on the page.