arvados.git
10 years agoMerge branch '2070-read-remote-arvados'
Tom Clegg [Tue, 11 Feb 2014 17:59:48 +0000 (09:59 -0800)]
Merge branch '2070-read-remote-arvados'

closes #2070

10 years agoReturn log buffer "(not available)" instead of crashing if redis is down.
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.

10 years agoFix up incorrect dependency on google-api-client
Ward Vandewege [Tue, 11 Feb 2014 16:38:50 +0000 (11:38 -0500)]
Fix up incorrect dependency on google-api-client

10 years agoFix comment - location of arvados configuration file has changed.
Ward Vandewege [Tue, 11 Feb 2014 15:00:07 +0000 (10:00 -0500)]
Fix comment - location of arvados configuration file has changed.

10 years agoAdded "vendor" to doc generation ignore list for deployment situations
Peter Amstutz [Tue, 11 Feb 2014 14:50:03 +0000 (09:50 -0500)]
Added "vendor" to doc generation ignore list for deployment situations

10 years agoRemoved mkpydoc.sh which is obsoleted by Rakefile task
Peter Amstutz [Tue, 11 Feb 2014 14:26:33 +0000 (09:26 -0500)]
Removed mkpydoc.sh which is obsoleted by Rakefile task

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Tue, 11 Feb 2014 14:23:55 +0000 (09:23 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoPython documentation step will now report a warning if epydoc isn't in PATH.
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.

10 years agoFix Gemfile(.lock) in sdk/cli
Ward Vandewege [Tue, 11 Feb 2014 02:39:36 +0000 (21:39 -0500)]
Fix Gemfile(.lock) in sdk/cli

10 years agoMerge branch '2008-show-log-buffer'
Tom Clegg [Mon, 10 Feb 2014 22:13:49 +0000 (14:13 -0800)]
Merge branch '2008-show-log-buffer'

closes #2008

10 years agoFix dashboard auto-refresh, and show last line of log_buffer (if any)
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.

10 years agoInclude log buffer in Job API response.
Tom Clegg [Mon, 10 Feb 2014 21:47:33 +0000 (13:47 -0800)]
Include log buffer in Job API response.

10 years agoMerge remote-tracking branch 'origin/master' into 1786-replace-jekyll-with-zenweb
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

10 years agoJekyll is dead, long live Zenweb!
Peter Amstutz [Mon, 10 Feb 2014 21:39:03 +0000 (16:39 -0500)]
Jekyll is dead, long live Zenweb!

10 years agoWhen retrieving a blob, if local Keep servers don't have it and the
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.

10 years agoRetrieve manifest_text from API server. If that fails, emit a warning
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.

10 years agoMerge branch 'master' into 1786-replace-jekyll-with-zenweb
Peter Amstutz [Fri, 7 Feb 2014 21:38:15 +0000 (16:38 -0500)]
Merge branch 'master' into 1786-replace-jekyll-with-zenweb

10 years agoMerge branch '1979-workbench-ui-TC'
Tom Clegg [Fri, 7 Feb 2014 20:01:00 +0000 (12:01 -0800)]
Merge branch '1979-workbench-ui-TC'

10 years agoFix top nav behavior when window is narrow.
Tom Clegg [Fri, 7 Feb 2014 20:00:36 +0000 (12:00 -0800)]
Fix top nav behavior when window is narrow.

10 years agoFill col-sm-3 space with left nav, and move it to the bottom when
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.

10 years agoFixed/refactored "smart-sizing" to adjust the content area to the size of the window...
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.

10 years agoClean up groups/index and add delete buttons.
Tom Clegg [Fri, 7 Feb 2014 14:23:05 +0000 (06:23 -0800)]
Clean up groups/index and add delete buttons.

10 years agoMerge branch '1979-workbench-ui-TC'
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

10 years agoAdd section headings to API examples.
Tom Clegg [Fri, 7 Feb 2014 01:48:33 +0000 (17:48 -0800)]
Add section headings to API examples.

10 years agoAdd space under tab row.
Tom Clegg [Fri, 7 Feb 2014 01:48:15 +0000 (17:48 -0800)]
Add space under tab row.

10 years agoFix up tab titles.
Tom Clegg [Fri, 7 Feb 2014 01:41:54 +0000 (17:41 -0800)]
Fix up tab titles.

10 years agoFix up collections#index search box with bootstrap3 styles.
Tom Clegg [Fri, 7 Feb 2014 01:27:59 +0000 (17:27 -0800)]
Fix up collections#index search box with bootstrap3 styles.

10 years agoFix up collections search box on dashboard.
Tom Clegg [Fri, 7 Feb 2014 01:24:33 +0000 (17:24 -0800)]
Fix up collections search box on dashboard.

10 years agoFix up pipeline_instances#index and #compare.
Tom Clegg [Fri, 7 Feb 2014 01:08:45 +0000 (17:08 -0800)]
Fix up pipeline_instances#index and #compare.

10 years agoRemove extra divider in notifications list.
Tom Clegg [Fri, 7 Feb 2014 00:41:36 +0000 (16:41 -0800)]
Remove extra divider in notifications list.

10 years agoRearrange thread_with_api_token around_filters so current_user is
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.

10 years agoHighlight "Dashboard" instead "Users" in left nav when on
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.

10 years agoClean up collections index and show->files tables.
Tom Clegg [Fri, 7 Feb 2014 00:00:47 +0000 (16:00 -0800)]
Clean up collections index and show->files tables.

10 years agoUse .badge-alert to highlight notification badges.
Tom Clegg [Thu, 6 Feb 2014 23:42:23 +0000 (15:42 -0800)]
Use .badge-alert to highlight notification badges.

10 years agoRemove extra breadcrumb separator in "no breadcrumbs" mode.
Tom Clegg [Thu, 6 Feb 2014 23:31:59 +0000 (15:31 -0800)]
Remove extra breadcrumb separator in "no breadcrumbs" mode.

10 years agoExpand graph border to tab pane width.
Tom Clegg [Thu, 6 Feb 2014 23:25:43 +0000 (15:25 -0800)]
Expand graph border to tab pane width.

10 years agoFix progress bars on pipeline_instances#show
Tom Clegg [Thu, 6 Feb 2014 23:25:17 +0000 (15:25 -0800)]
Fix progress bars on pipeline_instances#show

10 years agoFix up job/pipeline progress bars on dashboard.
Tom Clegg [Thu, 6 Feb 2014 23:19:38 +0000 (15:19 -0800)]
Fix up job/pipeline progress bars on dashboard.

10 years agoAdd progress bars to pipeline instances table 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

10 years agoMerge branch '1979-workbench-ui-PA'
Peter Amstutz [Thu, 6 Feb 2014 21:14:36 +0000 (16:14 -0500)]
Merge branch '1979-workbench-ui-PA'

10 years agobadges.css.scss doesn't actually require bootstrap
Peter Amstutz [Thu, 6 Feb 2014 20:58:43 +0000 (15:58 -0500)]
badges.css.scss doesn't actually require bootstrap

10 years agoLock to a version of the arvados-cli gem that's been pushed to the world.
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.

10 years agoAdded css to put back badge styles that went away in bootstrap 3
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

10 years agoMissing from previous commit
Peter Amstutz [Thu, 6 Feb 2014 20:05:15 +0000 (15:05 -0500)]
Missing from previous commit

10 years agoHarmonized all sections to use the new content template and layout
Peter Amstutz [Thu, 6 Feb 2014 20:04:19 +0000 (15:04 -0500)]
Harmonized all sections to use the new content template and layout

10 years agoFixed up some glyphicons
Peter Amstutz [Thu, 6 Feb 2014 15:37:03 +0000 (10:37 -0500)]
Fixed up some glyphicons

10 years agoEditable fields works again
Peter Amstutz [Thu, 6 Feb 2014 15:27:34 +0000 (10:27 -0500)]
Editable fields works again

10 years agoUpdating bootstrap-editable to bootstrap3-x-editable
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.

10 years ago* Left nav correctly highlights current section
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

10 years agoFixed search box for chrome
Peter Amstutz [Thu, 6 Feb 2014 01:19:08 +0000 (20:19 -0500)]
Fixed search box for chrome

10 years agoMake the config_uuid field match what we expect in our tests.
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.

10 years agoMenubar and left nav redesign in progress.
Peter Amstutz [Wed, 5 Feb 2014 22:37:36 +0000 (17:37 -0500)]
Menubar and left nav redesign in progress.

10 years agoCall super in pipeline_instances#show to make preview/js/json
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

10 years agoFix handling of pipeline components with no job/output yet.
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

10 years agoReworked top menu. Started upgrading to bootstrap 3.
Peter Amstutz [Wed, 5 Feb 2014 16:54:18 +0000 (11:54 -0500)]
Reworked top menu.  Started upgrading to bootstrap 3.

10 years agoSkip repeated find() calls for the same object during a single page
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.

10 years agoFix script_parameters comparison on pipeline_instances.compare.
Tom Clegg [Tue, 4 Feb 2014 21:10:04 +0000 (13:10 -0800)]
Fix script_parameters comparison on pipeline_instances.compare.

refs #1978

10 years agoAdded stroke-linecap: round to make lines look nicer.
Peter Amstutz [Tue, 4 Feb 2014 20:57:00 +0000 (15:57 -0500)]
Added stroke-linecap: round to make lines look nicer.

10 years agoMerge branch '1977-provenance-report' of git.clinicalfuture.com:arvados into 1977...
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.

10 years ago* Added used_by query for collections
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

10 years agoMerge branch '1979-workbench-ui'
Tom Clegg [Tue, 4 Feb 2014 16:50:25 +0000 (08:50 -0800)]
Merge branch '1979-workbench-ui'

10 years agoRemove old views/collections/show template.
Tom Clegg [Tue, 4 Feb 2014 16:49:53 +0000 (08:49 -0800)]
Remove old views/collections/show template.

refs #1979

10 years agoFix (and add test for) 404 at repositories.get_all_permissions.
Tom Clegg [Tue, 4 Feb 2014 15:58:25 +0000 (07:58 -0800)]
Fix (and add test for) 404 at repositories.get_all_permissions.

10 years agoMerge branch '1977-provenance-report' of git.clinicalfuture.com:arvados into 1977...
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.

10 years agoCan now use 'contains' to query individual columns in where() queries, not just any...
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.

10 years agoMove show-object content into tabs.
Tom Clegg [Tue, 4 Feb 2014 10:54:23 +0000 (02:54 -0800)]
Move show-object content into tabs.

refs #1979

10 years agoUse object type or friendly_link_name as browser title.
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

10 years agoMove all index content into Recent and Help tabs.
Tom Clegg [Tue, 4 Feb 2014 10:25:45 +0000 (02:25 -0800)]
Move all index content into Recent and Help tabs.

refs #1979

10 years agoMerge branch 'master' into 1979-workbench-ui
Tom Clegg [Tue, 4 Feb 2014 09:14:03 +0000 (01:14 -0800)]
Merge branch 'master' into 1979-workbench-ui

10 years agoHide loading indicator after refreshing dashboard tables.
Tom Clegg [Tue, 4 Feb 2014 09:13:19 +0000 (01:13 -0800)]
Hide loading indicator after refreshing dashboard tables.

refs #1976

10 years agoMerge top nav menus into brand dropdown, move breadcrumbs into top
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

10 years agoMerge branch '1977-provenance-report'
Tom Clegg [Tue, 4 Feb 2014 07:52:28 +0000 (23:52 -0800)]
Merge branch '1977-provenance-report'

10 years agoMove can_read permission logic into ArvadosModel.readable_by scope,
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

10 years agoAdd tests for permissions enforcement in collections.provenance.
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

10 years agoEnsure permissions can be propagated via group owner_uuid attribute.
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

10 years agoHide this/other/both legend if only one pipeline_instance is shown.
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.

10 years agoMerge branch '1976-pipeline-progress'
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

10 years agoMerge branch 'master' into 1977-provenance-report
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

10 years agoFix build.sh bugs.
Tim Pierce [Mon, 3 Feb 2014 20:32:59 +0000 (15:32 -0500)]
Fix build.sh bugs.

10 years agoFix breadcrumbs crash if link has no tail_kind or head_kind.
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.

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Mon, 3 Feb 2014 19:04:56 +0000 (14:04 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoTweaked text a little to make tail/subject head/object correspondence a little clearer.
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.

10 years agoEnsure util.mkdir_dash_p() fails if its target is a non-directory, and
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.

10 years agoShow "loading" indicator in nav bar while waiting for AJAX requests.
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

10 years agoRefresh dashboard with AJAX every 60 seconds.
Tom Clegg [Mon, 3 Feb 2014 08:45:11 +0000 (00:45 -0800)]
Refresh dashboard with AJAX every 60 seconds.

refs #1976
closes #2004

10 years agoUse AJAX/remote requests when deleting objects. Add delete button to
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

10 years agoImprove progress view on pipeline_instances.show page and add AJAX
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

10 years agoAdd arv-mount.
Tom Clegg [Mon, 3 Feb 2014 01:49:24 +0000 (17:49 -0800)]
Add arv-mount.

10 years agoAdd StreamFileReader.seek() method.
Tom Clegg [Mon, 3 Feb 2014 01:27:26 +0000 (17:27 -0800)]
Add StreamFileReader.seek() method.

10 years agoFix scoping for error classes.
Tom Clegg [Mon, 3 Feb 2014 01:26:59 +0000 (17:26 -0800)]
Fix scoping for error classes.

10 years agoFix crash when component has missing attributes (e.g., no job was run).
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

10 years agoAdd basic select-and-compare interface to pipeline_instances#index.
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

10 years agoMerge branch 'master' into 1978-compare-pipelines
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

10 years agoRemove extra breadcrumbs bar.
Tom Clegg [Sat, 1 Feb 2014 23:17:10 +0000 (15:17 -0800)]
Remove extra breadcrumbs bar.

10 years agoAllow controller to override page name for breadcrumbs.
Tom Clegg [Sat, 1 Feb 2014 23:16:52 +0000 (15:16 -0800)]
Allow controller to override page name for breadcrumbs.

10 years agoAdd breadcrumbs bar to #index and #show pages.
Tom Clegg [Fri, 31 Jan 2014 21:59:33 +0000 (13:59 -0800)]
Add breadcrumbs bar to #index and #show pages.

10 years agoUse generic index page for /users
Tom Clegg [Fri, 31 Jan 2014 21:32:39 +0000 (13:32 -0800)]
Use generic index page for /users

10 years agoShow condensed data about pipeline instances side by side on "compare"
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

10 years agoAdd pipeline_instances/compare page
Tom Clegg [Tue, 28 Jan 2014 15:57:47 +0000 (07:57 -0800)]
Add pipeline_instances/compare page

10 years agoFix "show all pipeline templates" link target on dashboard page.
Tom Clegg [Fri, 31 Jan 2014 20:50:35 +0000 (12:50 -0800)]
Fix "show all pipeline templates" link target on dashboard page.