Tom Clegg [Tue, 11 Feb 2014 17:59:48 +0000 (09:59 -0800)]
Merge branch '2070-read-remote-arvados'
closes #2070
Tom Clegg [Tue, 11 Feb 2014 17:52:07 +0000 (09:52 -0800)]
Return log buffer "(not available)" instead of crashing if redis is down.
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!
Tom Clegg [Sun, 9 Feb 2014 23:29:00 +0000 (15:29 -0800)]
When retrieving a blob, if local Keep servers don't have it and the
locator has +K@xyzzy, try GET http://keep.xyzzy.arvadosapi.com/hash.
Tom Clegg [Sun, 9 Feb 2014 22:54:58 +0000 (14:54 -0800)]
Retrieve manifest_text from API server. If that fails, emit a warning
and fall back to reading directly from Keep.
This gives the API server an opportunity to provide additional
metadata, like hints about where the data blobs are stored.
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.