arvados.git
10 years agoRe-order left nav and make labels consistent with arvados vocabulary.
Tom Clegg [Mon, 17 Feb 2014 19:15:34 +0000 (11:15 -0800)]
Re-order left nav and make labels consistent with arvados vocabulary.

10 years agoFix more namespace bugs.
Tom Clegg [Mon, 17 Feb 2014 17:27:21 +0000 (09:27 -0800)]
Fix more namespace bugs.

10 years agoFix missing : separator in PYTHONPATH.
Tom Clegg [Mon, 17 Feb 2014 16:57:53 +0000 (08:57 -0800)]
Fix missing : separator in PYTHONPATH.

10 years agoFix namespace bugs.
Tom Clegg [Mon, 17 Feb 2014 15:55:24 +0000 (07:55 -0800)]
Fix namespace bugs.

10 years agoAdd {repo}/arvados/sdk/python to Python search path during crunch job.
Tom Clegg [Mon, 17 Feb 2014 00:14:45 +0000 (16:14 -0800)]
Add {repo}/arvados/sdk/python to Python search path during crunch job.

10 years agoUpdate fixed header rows after new content arrives via ajax.
Tom Clegg [Sun, 16 Feb 2014 11:05:16 +0000 (03:05 -0800)]
Update fixed header rows after new content arrives via ajax.

10 years agoFix breadcrumb-hiding on user agreements page. closes #2191
Tom Clegg [Sun, 16 Feb 2014 10:39:22 +0000 (02:39 -0800)]
Fix breadcrumb-hiding on user agreements page. closes #2191

10 years agoFix fixed-header-row hack. closes #2194
Tom Clegg [Sun, 16 Feb 2014 10:36:32 +0000 (02:36 -0800)]
Fix fixed-header-row hack. closes #2194

10 years agoMerge branch '2179-demo-feedback'
Tom Clegg [Sun, 16 Feb 2014 02:55:57 +0000 (18:55 -0800)]
Merge branch '2179-demo-feedback'

refs #2179

10 years agoRender collection provenance graph top-down like other graphs.
Tom Clegg [Sun, 16 Feb 2014 02:50:18 +0000 (18:50 -0800)]
Render collection provenance graph top-down like other graphs.

closes #2184

10 years agoMerge branch 'master' into 2179-demo-feedback
Tom Clegg [Sun, 16 Feb 2014 02:08:26 +0000 (18:08 -0800)]
Merge branch 'master' into 2179-demo-feedback

10 years agoFix symbol key used in serialized attribute. closes #2186
Tom Clegg [Sun, 16 Feb 2014 02:04:47 +0000 (18:04 -0800)]
Fix symbol key used in serialized attribute. closes #2186

10 years agoFix crash if @notifications is nil.
Tom Clegg [Sun, 16 Feb 2014 01:43:14 +0000 (17:43 -0800)]
Fix crash if @notifications is nil.

10 years agoReturn only true or false for is_invited, never group uuid.
Tom Clegg [Sun, 16 Feb 2014 01:30:21 +0000 (17:30 -0800)]
Return only true or false for is_invited, never group uuid.

10 years agoHide top nav notifications and links to tokens/keys pages until user
Tom Clegg [Sun, 16 Feb 2014 01:29:38 +0000 (17:29 -0800)]
Hide top nav notifications and links to tokens/keys pages until user
is active.

closes #2188

10 years agoSay when re-using existing jobs, even without debug mode. closes #2183
Tom Clegg [Sat, 15 Feb 2014 23:43:34 +0000 (15:43 -0800)]
Say when re-using existing jobs, even without debug mode. closes #2183

10 years agoOutput a blank line between pipeline status updates. closes #2182
Tom Clegg [Sat, 15 Feb 2014 23:19:12 +0000 (15:19 -0800)]
Output a blank line between pipeline status updates. closes #2182

10 years agoMove HeaderRowFixer out to application.js and application.css.scss
Tom Clegg [Sat, 15 Feb 2014 23:13:38 +0000 (15:13 -0800)]
Move HeaderRowFixer out to application.js and application.css.scss

refs #2180

10 years agoPrevent table headings from scrolling out of view on collections index
Tom Clegg [Sat, 15 Feb 2014 23:08:12 +0000 (15:08 -0800)]
Prevent table headings from scrolling out of view on collections index
table.

closes #2180

10 years agoHide left nav panel if current_user is not active. refs #2078
Tom Clegg [Fri, 14 Feb 2014 19:49:07 +0000 (11:49 -0800)]
Hide left nav panel if current_user is not active. refs #2078

10 years agoProvide manifest_text in collections.get API response. refs #2070
Tom Clegg [Fri, 14 Feb 2014 19:26:44 +0000 (11:26 -0800)]
Provide manifest_text in collections.get API response. refs #2070

10 years agoFix crash in collections.provenance when a script_parameter is a Fixnum.
Tom Clegg [Fri, 14 Feb 2014 04:48:40 +0000 (20:48 -0800)]
Fix crash in collections.provenance when a script_parameter is a Fixnum.

10 years agoNormalize collection hashes provided by clients as attribute values
Tom Clegg [Thu, 13 Feb 2014 20:49:21 +0000 (12:49 -0800)]
Normalize collection hashes provided by clients as attribute values
before storing in the database.

closes #2088
refs #1881

10 years agoFix crash when a script_parameter value is a Fixnum. fixes #2167
Tom Clegg [Thu, 13 Feb 2014 19:16:53 +0000 (11:16 -0800)]
Fix crash when a script_parameter value is a Fixnum. fixes #2167

10 years agoFixed {% include alert-stub %} that shouldn't have been there on a couple of pages.
Peter Amstutz [Thu, 13 Feb 2014 16:52:47 +0000 (16:52 +0000)]
Fixed {% include alert-stub %} that shouldn't have been there on a couple of pages.

10 years agoFix 404 at api_client_authorizations.create_system_auth and add tests.
Tom Clegg [Thu, 13 Feb 2014 16:01:57 +0000 (08:01 -0800)]
Fix 404 at api_client_authorizations.create_system_auth and add tests.

10 years agoMerge branch '2099-CORRECT-docker-stop-and-restart' (documentation update)
Tim Pierce [Thu, 13 Feb 2014 14:44:09 +0000 (09:44 -0500)]
Merge branch '2099-CORRECT-docker-stop-and-restart' (documentation update)

10 years agoUpdated Docker documentation to reference "arvdock". (refs #2099)
Tim Pierce [Thu, 13 Feb 2014 14:42:50 +0000 (09:42 -0500)]
Updated Docker documentation to reference "arvdock". (refs #2099)

10 years agoChange color of "running" job label to blue.
Tom Clegg [Wed, 12 Feb 2014 23:31:59 +0000 (15:31 -0800)]
Change color of "running" job label to blue.

10 years agoMerge branch '2096-demo-feedback'
Tom Clegg [Wed, 12 Feb 2014 22:03:24 +0000 (14:03 -0800)]
Merge branch '2096-demo-feedback'

10 years agoIn the pipeline instance comparison, do not blow up when a row component
Ward Vandewege [Wed, 12 Feb 2014 20:52:13 +0000 (15:52 -0500)]
In the pipeline instance comparison, do not blow up when a row component
is not defined (for example, when one or more of the pipeline instances
in the comparison has not yet been executed).

10 years agoMerge branch '2099-CORRECT-docker-stop-and-restart'
Tim Pierce [Wed, 12 Feb 2014 19:59:14 +0000 (14:59 -0500)]
Merge branch '2099-CORRECT-docker-stop-and-restart'

10 years agoMerge branch 'master' into 2096-demo-feedback
Tom Clegg [Wed, 12 Feb 2014 19:57:50 +0000 (11:57 -0800)]
Merge branch 'master' into 2096-demo-feedback

10 years agoShow owner name instead of uuid on pipeline_templates#index. Closes #2097
Tom Clegg [Wed, 12 Feb 2014 19:56:09 +0000 (11:56 -0800)]
Show owner name instead of uuid on pipeline_templates#index. Closes #2097

10 years agoHide "Create" button on pipeline_instances and pipeline_templates pages. Closes ...
Tom Clegg [Wed, 12 Feb 2014 19:52:46 +0000 (11:52 -0800)]
Hide "Create" button on pipeline_instances and pipeline_templates pages. Closes #2098

10 years agoLimit "compare" selection mechanism to 2 or 3 pipelines. Closes #2101
Tom Clegg [Wed, 12 Feb 2014 19:51:00 +0000 (11:51 -0800)]
Limit "compare" selection mechanism to 2 or 3 pipelines. Closes #2101

10 years agoAdd missing curly bracket in assets/stylesheets/application.css.scss
Ward Vandewege [Wed, 12 Feb 2014 19:49:03 +0000 (14:49 -0500)]
Add missing curly bracket in assets/stylesheets/application.css.scss

10 years agoRename clinicalfuture -> curoverse everywhere.
Ward Vandewege [Wed, 12 Feb 2014 19:41:39 +0000 (14:41 -0500)]
Rename clinicalfuture -> curoverse everywhere.

10 years agoFix up legend colors and labels on pipeline_instances > compare > graph.
Tom Clegg [Wed, 12 Feb 2014 19:40:21 +0000 (11:40 -0800)]
Fix up legend colors and labels on pipeline_instances > compare > graph.

10 years agoFix terminology agreement between left nav and elsewhere in docs/pages.
Tom Clegg [Wed, 12 Feb 2014 19:37:57 +0000 (11:37 -0800)]
Fix terminology agreement between left nav and elsewhere in docs/pages.

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Wed, 12 Feb 2014 19:36:58 +0000 (14:36 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoMake sure to abort nicely when run with a version of ruby older than 1.9.3
Ward Vandewege [Wed, 12 Feb 2014 19:36:24 +0000 (14:36 -0500)]
Make sure to abort nicely when run with a version of ruby older than 1.9.3

10 years agoFix pipeline_instances#show by renaming partial.
Tom Clegg [Wed, 12 Feb 2014 19:36:47 +0000 (11:36 -0800)]
Fix pipeline_instances#show by renaming partial.

10 years agoMerge branch '2061-update-docs'
Peter Amstutz [Wed, 12 Feb 2014 19:36:04 +0000 (14:36 -0500)]
Merge branch '2061-update-docs'

10 years agoRename to "arvdock" per code review.
Tim Pierce [Wed, 12 Feb 2014 19:35:06 +0000 (14:35 -0500)]
Rename to "arvdock" per code review.

10 years agoFinished updating tutorials for latest sprint
Peter Amstutz [Wed, 12 Feb 2014 19:33:07 +0000 (14:33 -0500)]
Finished updating tutorials for latest sprint

10 years agoCorrect comments to account for new verbs.
Tim Pierce [Wed, 12 Feb 2014 19:27:43 +0000 (14:27 -0500)]
Correct comments to account for new verbs.

10 years agoRenamed run.sh -> arvctl, added per-service "stop" and "restart" commands (fixes...
Tim Pierce [Wed, 12 Feb 2014 19:15:17 +0000 (14:15 -0500)]
Renamed run.sh -> arvctl, added per-service "stop" and "restart" commands (fixes #2099)

10 years agoFix regular expression for collection UUIDs to it can also handle with UUIDs like
Ward Vandewege [Wed, 12 Feb 2014 17:42:25 +0000 (12:42 -0500)]
Fix regular expression for collection UUIDs to it can also handle with UUIDs like

  8764db1235674a08afabcdef709f6c49+2986

10 years agoHack to fix job log links (because crunch still produces identifiers with +K@qr1hi)
Peter Amstutz [Wed, 12 Feb 2014 14:30:17 +0000 (09:30 -0500)]
Hack to fix job log links (because crunch still produces identifiers with +K@qr1hi)

10 years agoThe list-inactive-users.rb script has been moved to the puppet tree for
Ward Vandewege [Wed, 12 Feb 2014 14:22:19 +0000 (09:22 -0500)]
The list-inactive-users.rb script has been moved to the puppet tree for
now.

10 years agoFix git_dir path in CommitAncestor model. Fixes #2089
Tom Clegg [Wed, 12 Feb 2014 14:20:03 +0000 (06:20 -0800)]
Fix git_dir path in CommitAncestor model. Fixes #2089

10 years agoFill in missing example locators for crunch wrappers.
Tom Clegg [Wed, 12 Feb 2014 05:11:45 +0000 (21:11 -0800)]
Fill in missing example locators for crunch wrappers.

10 years agoAllow passing hashes as resource attributes. This lets crunch-job keep
Tom Clegg [Wed, 12 Feb 2014 05:07:52 +0000 (21:07 -0800)]
Allow passing hashes as resource attributes. This lets crunch-job keep
jobs.tasks_summary up to date.

10 years agoShow first 200 items on index page, not 1000.
Tom Clegg [Wed, 12 Feb 2014 01:07:39 +0000 (17:07 -0800)]
Show first 200 items on index page, not 1000.

10 years agoApply usual parameter encoding logic to method[request] parameter too.
Tom Clegg [Wed, 12 Feb 2014 00:56:55 +0000 (16:56 -0800)]
Apply usual parameter encoding logic to method[request] parameter too.

Amends fbd62569bca926fc12917eb60eada82a6d8a83b0

Fixes:

encountered object 'Arvados::ResourceProxy=HASH(0x31fb2f8)', but neither allow_blessed nor convert_blessed settings are enabled at arvados/sdk/perl/lib/Arvados/Request.pm line 42.

10 years agoReplace weird "loading" animation with a nice plain glyphicon.
Tom Clegg [Tue, 11 Feb 2014 23:58:57 +0000 (15:58 -0800)]
Replace weird "loading" animation with a nice plain glyphicon.

10 years agoMerge branch 'master' of git.curoverse.com:arvados
Ward Vandewege [Tue, 11 Feb 2014 22:43:21 +0000 (17:43 -0500)]
Merge branch 'master' of git.curoverse.com:arvados

10 years agoHandle the situation where config.workbench_address is unset more
Ward Vandewege [Tue, 11 Feb 2014 22:42:44 +0000 (17:42 -0500)]
Handle the situation where config.workbench_address is unset more
gracefully: do not try to redirect and blow up, instead send a
json-encoded error message.

10 years agoLook in method[request][properties][$ref] for resource object
Tom Clegg [Tue, 11 Feb 2014 22:28:32 +0000 (14:28 -0800)]
Look in method[request][properties][$ref] for resource object
argument.

Fixes #2084

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Tim Pierce [Tue, 11 Feb 2014 22:14:25 +0000 (17:14 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoUpdate docserver build process for zenweb (refs #1786)
Tim Pierce [Tue, 11 Feb 2014 22:10:01 +0000 (17:10 -0500)]
Update docserver build process for zenweb (refs #1786)

10 years agoCan now click through to group pages on groups table
Peter Amstutz [Tue, 11 Feb 2014 21:24:05 +0000 (16:24 -0500)]
Can now click through to group pages on groups table

10 years agoFixed bug with incoming links not showing in metadata tab. Resolves #2080
Peter Amstutz [Tue, 11 Feb 2014 21:10:52 +0000 (16:10 -0500)]
Fixed bug with incoming links not showing in metadata tab.  Resolves #2080

10 years agoUpdating documentation
Peter Amstutz [Tue, 11 Feb 2014 20:59:00 +0000 (15:59 -0500)]
Updating documentation

10 years agoDismiss "paste your SSH key here" notification when key successfully saved.
Tom Clegg [Tue, 11 Feb 2014 20:02:00 +0000 (12:02 -0800)]
Dismiss "paste your SSH key here" notification when key successfully saved.

fixes #2079

10 years agoMerge branch '2072-workbench-docker'
Tim Pierce [Tue, 11 Feb 2014 19:40:59 +0000 (14:40 -0500)]
Merge branch '2072-workbench-docker'

10 years agoAdded missing workbench configuration directives to Docker (fixes #2072)
Tim Pierce [Tue, 11 Feb 2014 19:37:16 +0000 (14:37 -0500)]
Added missing workbench configuration directives to Docker (fixes #2072)

10 years agoMerge remote-tracking branch 'origin/master' into 2061-update-docs
Peter Amstutz [Tue, 11 Feb 2014 19:29:14 +0000 (14:29 -0500)]
Merge remote-tracking branch 'origin/master' into 2061-update-docs

10 years agoFixed bug with notification triggering on wrong condition. Also removed old "notific...
Peter Amstutz [Tue, 11 Feb 2014 19:08:25 +0000 (14:08 -0500)]
Fixed bug with notification triggering on wrong condition.  Also removed old "notifications" partial.

10 years agoMerge remote-tracking branch 'origin/master' into 2061-update-docs
Peter Amstutz [Tue, 11 Feb 2014 19:00:57 +0000 (14:00 -0500)]
Merge remote-tracking branch 'origin/master' into 2061-update-docs

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 agoUpdated theme to bootstrap 3 to match workbench. Started updating ssh keys tutorial.
Peter Amstutz [Tue, 11 Feb 2014 17:14:58 +0000 (12:14 -0500)]
Updated theme to bootstrap 3 to match workbench.  Started updating ssh keys tutorial.

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 agoStarted updating docs page to bootstrap 3.0
Peter Amstutz [Tue, 11 Feb 2014 14:48:11 +0000 (09:48 -0500)]
Started updating docs page to bootstrap 3.0

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 agoUpdate api/production.rb.in with changes from services/api.
Tim Pierce [Mon, 10 Feb 2014 22:28:39 +0000 (17:28 -0500)]
Update api/production.rb.in with changes from services/api.

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.