arvados.git
10 years agoAdd arv-tag to arvados-cli package
Tom Clegg [Fri, 10 Jan 2014 22:15:15 +0000 (14:15 -0800)]
Add arv-tag to arvados-cli package

10 years agoHide fetch_url column on repositories page. closes #1863
Tom Clegg [Fri, 10 Jan 2014 21:58:52 +0000 (13:58 -0800)]
Hide fetch_url column on repositories page. closes #1863

10 years agoRemove debug message
Tom Clegg [Fri, 10 Jan 2014 21:25:02 +0000 (13:25 -0800)]
Remove debug message

10 years agoFix crash when a discovered parameter is not supplied. closes #1866
Tom Clegg [Fri, 10 Jan 2014 21:11:36 +0000 (13:11 -0800)]
Fix crash when a discovered parameter is not supplied. closes #1866

10 years agoWorkbench explicitly requests 1000 results instead of getting the default
Peter Amstutz [Fri, 10 Jan 2014 20:35:29 +0000 (15:35 -0500)]
Workbench explicitly requests 1000 results instead of getting the default
result list from the API server (which is only 100 results)

10 years agoObject pages now show incoming/outgoing links.
Peter Amstutz [Fri, 10 Jan 2014 20:10:53 +0000 (15:10 -0500)]
Object pages now show incoming/outgoing links.

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Fri, 10 Jan 2014 17:21:25 +0000 (12:21 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

# 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 agoDocumentation tweaks based on Nadia's feedback.
Peter Amstutz [Fri, 10 Jan 2014 17:19:55 +0000 (12:19 -0500)]
Documentation tweaks based on Nadia's feedback.

10 years agoMerge branch '1530-arv-tag-commands'
Tim Pierce [Thu, 9 Jan 2014 23:16:56 +0000 (18:16 -0500)]
Merge branch '1530-arv-tag-commands'

10 years agoComplete `arv tag add' and `arv tag remove' support (fixes #1530)
Tim Pierce [Thu, 9 Jan 2014 23:14:21 +0000 (18:14 -0500)]
Complete `arv tag add' and `arv tag remove' support (fixes #1530)

10 years agoDefault redirect to workbench in production configuration to workbench.`hostname`
Peter Amstutz [Tue, 7 Jan 2014 19:03:34 +0000 (14:03 -0500)]
Default redirect to workbench in production configuration to workbench.`hostname`

10 years agoFix mime-type lookup.
Tom Clegg [Mon, 6 Jan 2014 23:04:50 +0000 (15:04 -0800)]
Fix mime-type lookup.

refs #1813

10 years agoAdded redirect to config file.
Peter Amstutz [Thu, 2 Jan 2014 18:21:34 +0000 (13:21 -0500)]
Added redirect to config file.

10 years agoMerge branch 'master' of git.curoverse.com:arvados
Ward Vandewege [Thu, 9 Jan 2014 22:17:30 +0000 (17:17 -0500)]
Merge branch 'master' of git.curoverse.com:arvados

10 years agoRemove hardcoded references to Arvados Workbench, replace with
Ward Vandewege [Thu, 9 Jan 2014 22:13:20 +0000 (17:13 -0500)]
Remove hardcoded references to Arvados Workbench, replace with
config.site_name. Also improve wording on the welcome page.

10 years agoAdd "Links" entry to Data menu. closes #1852
Tom Clegg [Thu, 9 Jan 2014 17:02:58 +0000 (09:02 -0800)]
Add "Links" entry to Data menu. closes #1852

10 years agoAdd "arv delete" example.
Tom Clegg [Thu, 9 Jan 2014 16:55:26 +0000 (08:55 -0800)]
Add "arv delete" example.

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Thu, 9 Jan 2014 17:09:45 +0000 (12:09 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoAdd "Links" entry to Data menu. closes #1852
Tom Clegg [Thu, 9 Jan 2014 17:02:58 +0000 (09:02 -0800)]
Add "Links" entry to Data menu. closes #1852

10 years agoTweaked user home template to make theming easier.
Peter Amstutz [Thu, 9 Jan 2014 17:02:04 +0000 (12:02 -0500)]
Tweaked user home template to make theming easier.

10 years agoAdd "arv delete" example.
Tom Clegg [Thu, 9 Jan 2014 16:55:26 +0000 (08:55 -0800)]
Add "arv delete" example.

10 years agoBug fixes (API requires request to be delivered in request_body)
Tim Pierce [Wed, 8 Jan 2014 22:12:46 +0000 (17:12 -0500)]
Bug fixes (API requires request to be delivered in request_body)

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Wed, 8 Jan 2014 21:33:20 +0000 (16:33 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoAdded theme support to workbench.
Peter Amstutz [Wed, 8 Jan 2014 21:21:02 +0000 (16:21 -0500)]
Added theme support to workbench.

10 years agoBug fixes.
Tim Pierce [Wed, 8 Jan 2014 18:45:38 +0000 (13:45 -0500)]
Bug fixes.

10 years agoFix up collection links on workbench home page.
Tom Clegg [Wed, 8 Jan 2014 18:14:53 +0000 (10:14 -0800)]
Fix up collection links on workbench home page.

10 years agoFix up "age" column contents on workbench home page.
Tom Clegg [Wed, 8 Jan 2014 18:09:34 +0000 (10:09 -0800)]
Fix up "age" column contents on workbench home page.

10 years agoFix check for whether adding response[:_profile] is safe. refs #1815
Tom Clegg [Wed, 8 Jan 2014 18:05:33 +0000 (10:05 -0800)]
Fix check for whether adding response[:_profile] is safe. refs #1815

10 years agoMerge branch '1788-support-and-feedback'
Peter Amstutz [Wed, 8 Jan 2014 13:39:01 +0000 (08:39 -0500)]
Merge branch '1788-support-and-feedback'

10 years agoMerge branch '1792-workbench-performance'
Tom Clegg [Wed, 8 Jan 2014 09:26:25 +0000 (01:26 -0800)]
Merge branch '1792-workbench-performance'

10 years agoObey profiling_enabled config. refs #1815
Tom Clegg [Wed, 8 Jan 2014 09:26:09 +0000 (01:26 -0800)]
Obey profiling_enabled config. refs #1815

10 years agoUse operating system's bundled CA certificates if available.
Tom Clegg [Wed, 8 Jan 2014 09:16:50 +0000 (01:16 -0800)]
Use operating system's bundled CA certificates if available.

refs #1782

10 years agoShow some params in profiling output. refs #1815
Tom Clegg [Wed, 8 Jan 2014 04:47:00 +0000 (20:47 -0800)]
Show some params in profiling output. refs #1815

10 years agoShow profile data in log if config.profiling_enabled. refs #1815
Tom Clegg [Wed, 8 Jan 2014 04:22:04 +0000 (20:22 -0800)]
Show profile data in log if config.profiling_enabled. refs #1815

10 years agoAdded 'add' and 'remove' functionality.
Tim Pierce [Tue, 7 Jan 2014 22:48:09 +0000 (17:48 -0500)]
Added 'add' and 'remove' functionality.

10 years agoMissing period.
Peter Amstutz [Tue, 7 Jan 2014 22:16:16 +0000 (17:16 -0500)]
Missing period.

10 years agoAdded more links
Peter Amstutz [Tue, 7 Jan 2014 22:10:28 +0000 (17:10 -0500)]
Added more links

10 years agoAdded mailing lists, irc
Peter Amstutz [Tue, 7 Jan 2014 21:57:14 +0000 (16:57 -0500)]
Added mailing lists, irc

10 years agoProvide response[_profile][request_time] if requested by client. refs #1815
Tom Clegg [Tue, 7 Jan 2014 21:07:33 +0000 (13:07 -0800)]
Provide response[_profile][request_time] if requested by client. refs #1815

10 years agoAsk API server for profile information. refs #1815
Tom Clegg [Tue, 7 Jan 2014 21:04:16 +0000 (13:04 -0800)]
Ask API server for profile information. refs #1815

10 years agoCheck HTTP status before using API responses.
Tom Clegg [Tue, 7 Jan 2014 20:56:11 +0000 (12:56 -0800)]
Check HTTP status before using API responses.

10 years agoAdded config.arvados_docsite, updated links, all tested and working.
Peter Amstutz [Tue, 7 Jan 2014 20:08:05 +0000 (15:08 -0500)]
Added config.arvados_docsite, updated links, all tested and working.

10 years agoMerge branch '1685-api-server-redirect-to-workbench'
Peter Amstutz [Tue, 7 Jan 2014 19:04:23 +0000 (14:04 -0500)]
Merge branch '1685-api-server-redirect-to-workbench'

10 years agoDefault redirect to workbench in production configuration to workbench.`hostname`
Peter Amstutz [Tue, 7 Jan 2014 19:03:34 +0000 (14:03 -0500)]
Default redirect to workbench in production configuration to workbench.`hostname`

10 years agoAdding `tag' command: initial commit.
Tim Pierce [Mon, 6 Jan 2014 23:17:23 +0000 (18:17 -0500)]
Adding `tag' command: initial commit.

10 years agoFix mime-type lookup.
Tom Clegg [Mon, 6 Jan 2014 23:04:50 +0000 (15:04 -0800)]
Fix mime-type lookup.

refs #1813

10 years agoUse docker build -q to fix Docker build failures.
Tim Pierce [Mon, 6 Jan 2014 23:02:39 +0000 (18:02 -0500)]
Use docker build -q to fix Docker build failures.
(see https://github.com/dotcloud/docker/issues/3172)

Also fix deprecated `docker tag' statements in mkimage-debootstrap.sh.

10 years agoIf there is only one user agreement, show it inline with an OBJECT tag
Tom Clegg [Mon, 6 Jan 2014 23:00:35 +0000 (15:00 -0800)]
If there is only one user agreement, show it inline with an OBJECT tag
instead of making the user open it in a separate window.

closes #1797
closes #1813

10 years agoRead data from local file if an absolute filename is given for an
Tom Clegg [Mon, 6 Jan 2014 21:32:15 +0000 (13:32 -0800)]
Read data from local file if an absolute filename is given for an
object or array parameter.

10 years agoRemove extra line breaks in textile paragraphs.
Tom Clegg [Mon, 6 Jan 2014 20:27:44 +0000 (12:27 -0800)]
Remove extra line breaks in textile paragraphs.

10 years agoReword tag convention. refs #1508
Tom Clegg [Mon, 6 Jan 2014 20:08:38 +0000 (12:08 -0800)]
Reword tag convention. refs #1508

10 years agoAccept comma-separated list of locators in Keep.get()
Tom Clegg [Mon, 6 Jan 2014 20:04:18 +0000 (12:04 -0800)]
Accept comma-separated list of locators in Keep.get()

10 years agoDocument a convention for using Links to define tags on Collections.
Tim Pierce [Fri, 3 Jan 2014 20:32:37 +0000 (15:32 -0500)]
Document a convention for using Links to define tags on Collections.

10 years agoDocumentation for `Log'.
Tim Pierce [Fri, 3 Jan 2014 00:02:35 +0000 (19:02 -0500)]
Documentation for `Log'.

10 years agoRemove json.dumps() from example and tutorial code.
Tom Clegg [Fri, 3 Jan 2014 00:29:28 +0000 (16:29 -0800)]
Remove json.dumps() from example and tutorial code.

(Not necessary since 4c69fbec263b5eeea23d11ee93fb002d028e2b6f)

closes #1819

10 years agoSerialize objects/arrays in query params with json.dumps() instead of str().
Tom Clegg [Thu, 2 Jan 2014 23:50:46 +0000 (15:50 -0800)]
Serialize objects/arrays in query params with json.dumps() instead of str().

closes #1818

10 years agoMerge branch '1694-user-agreement'
Tom Clegg [Thu, 2 Jan 2014 22:00:42 +0000 (14:00 -0800)]
Merge branch '1694-user-agreement'

10 years agoMerge branch '1748-workbench-view-files'
Tom Clegg [Thu, 2 Jan 2014 20:52:13 +0000 (12:52 -0800)]
Merge branch '1748-workbench-view-files'

closes #1748

10 years agoFix error message: print the exit status, not the string "$?".
Tom Clegg [Tue, 31 Dec 2013 18:48:28 +0000 (10:48 -0800)]
Fix error message: print the exit status, not the string "$?".

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados into 1685-api-server-redirect...
Peter Amstutz [Thu, 2 Jan 2014 18:22:35 +0000 (13:22 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados into 1685-api-server-redirect-to-workbench

10 years agoAdded redirect to config file.
Peter Amstutz [Thu, 2 Jan 2014 18:21:34 +0000 (13:21 -0500)]
Added redirect to config file.

10 years agoOffer to show html files in browser, too. refs #1748
Tom Clegg [Thu, 2 Jan 2014 17:59:46 +0000 (09:59 -0800)]
Offer to show html files in browser, too. refs #1748

10 years agoLink to show/download files from collections. refs #1748
Tom Clegg [Thu, 2 Jan 2014 17:41:06 +0000 (09:41 -0800)]
Link to show/download files from collections. refs #1748

10 years agoAdded `gen_api_schema_docs.py' used to generate schema documentation pages.
Tim Pierce [Tue, 31 Dec 2013 21:54:17 +0000 (16:54 -0500)]
Added `gen_api_schema_docs.py' used to generate schema documentation pages.

10 years agoFix error message: print the exit status, not the string "$?".
Tom Clegg [Tue, 31 Dec 2013 18:48:28 +0000 (10:48 -0800)]
Fix error message: print the exit status, not the string "$?".

10 years agoAdded gen_api_method_docs.py used to generate API documentation files.
Tim Pierce [Tue, 31 Dec 2013 18:23:24 +0000 (13:23 -0500)]
Added gen_api_method_docs.py used to generate API documentation files.

10 years agoUse items_available in API response instead of retrieving all items.
Tom Clegg [Tue, 31 Dec 2013 18:01:48 +0000 (10:01 -0800)]
Use items_available in API response instead of retrieving all items.

10 years agoAdd "items_available" (integer) to generic list response.
Tom Clegg [Tue, 31 Dec 2013 17:44:57 +0000 (09:44 -0800)]
Add "items_available" (integer) to generic list response.

10 years agoDo not check for user agreement signature before showing user agreement.
Tom Clegg [Tue, 31 Dec 2013 17:41:13 +0000 (09:41 -0800)]
Do not check for user agreement signature before showing user agreement.

refs #1699

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Peter Amstutz [Tue, 31 Dec 2013 17:09:16 +0000 (12:09 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoBetter CSS fix for menu bar obscuring the target when following intra-document links.
Peter Amstutz [Tue, 31 Dec 2013 17:08:31 +0000 (12:08 -0500)]
Better CSS fix for menu bar obscuring the target when following intra-document links.

10 years agoFix unexpected nil in @required_user_agreements. refs #1699
Tom Clegg [Tue, 31 Dec 2013 15:20:13 +0000 (07:20 -0800)]
Fix unexpected nil in @required_user_agreements. refs #1699

10 years agoMerge branch '1692-redesign-dashboard'
Peter Amstutz [Tue, 31 Dec 2013 15:09:47 +0000 (10:09 -0500)]
Merge branch '1692-redesign-dashboard'

10 years ago* Updated ssh-access documentation for workbench dashboard changes
Peter Amstutz [Tue, 31 Dec 2013 15:08:09 +0000 (10:08 -0500)]
* Updated ssh-access documentation for workbench dashboard changes
* Fixed problem where links within the document were cut off by top menu bar

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Tim Pierce [Tue, 31 Dec 2013 06:28:10 +0000 (01:28 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoFix makefile brittleness.
Tim Pierce [Tue, 31 Dec 2013 06:26:24 +0000 (01:26 -0500)]
Fix makefile brittleness.

* `clean' should remove any empty */generated directories (so
  base/generated will be marked as a target to rebuild)

* Dockerfiles should use && instead of ; whenever possible so
  `docker build' will properly fail if a critical step cannot
  be completed.

10 years agoDo not set is_active flag for new users. They do that themselves now,
Tom Clegg [Tue, 31 Dec 2013 02:05:17 +0000 (18:05 -0800)]
Do not set is_active flag for new users. They do that themselves now,
after accepting user agreements.

refs #1699

10 years agoMerge branch '1675-preactivation'
Tom Clegg [Tue, 31 Dec 2013 02:02:33 +0000 (18:02 -0800)]
Merge branch '1675-preactivation'

closes #1722
closes #1785

10 years agoRequest activation if is_active==false but no user agreements seem to
Tom Clegg [Tue, 31 Dec 2013 01:58:29 +0000 (17:58 -0800)]
Request activation if is_active==false but no user agreements seem to
be required.

refs #1699

10 years agoSupport pre-activation by creating a new user record and OpenID
Tom Clegg [Tue, 31 Dec 2013 01:50:53 +0000 (17:50 -0800)]
Support pre-activation by creating a new user record and OpenID
permission link.

refs #1785
refs #1722

10 years agoAllow authentication from multiple OpenIDs using permission links with
Tom Clegg [Tue, 31 Dec 2013 01:48:08 +0000 (17:48 -0800)]
Allow authentication from multiple OpenIDs using permission links with
matching email and OpenID prefix.

refs #1722

10 years agoMerge branch '1694-user-agreement'
Tom Clegg [Mon, 30 Dec 2013 23:17:17 +0000 (15:17 -0800)]
Merge branch '1694-user-agreement'

10 years agoFix makefile syntax for `realclean' target.
Tim Pierce [Mon, 30 Dec 2013 23:15:53 +0000 (18:15 -0500)]
Fix makefile syntax for `realclean' target.

10 years agoDivert processing when user agreements are needed, instead of just
Tom Clegg [Mon, 30 Dec 2013 22:33:29 +0000 (14:33 -0800)]
Divert processing when user agreements are needed, instead of just
omitting page content from layout.

closes #1699

10 years agoSupport user agreement viewing and signing in Workbench.
Tom Clegg [Mon, 30 Dec 2013 14:09:49 +0000 (06:09 -0800)]
Support user agreement viewing and signing in Workbench.

refs #1699

10 years agoStore correct collection uuid in signature/click link.
Tom Clegg [Mon, 30 Dec 2013 21:44:32 +0000 (13:44 -0800)]
Store correct collection uuid in signature/click link.

closes #1706

10 years agoDo not self-activate, or show user agreements to, an uninvited user:
Tom Clegg [Fri, 27 Dec 2013 21:56:34 +0000 (13:56 -0800)]
Do not self-activate, or show user agreements to, an uninvited user:
i.e., one who is neither invited by default according to site policy,
nor a member of the "All users" group.

refs #1706

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
Tim Pierce [Mon, 30 Dec 2013 22:20:52 +0000 (17:20 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados

10 years agoAdd `make realclean' target for removing cached Docker images from a build.
Tim Pierce [Mon, 30 Dec 2013 22:20:13 +0000 (17:20 -0500)]
Add `make realclean' target for removing cached Docker images from a build.

10 years agoReplaces shelling out to 'curl' with httpclient library.
Peter Amstutz [Mon, 30 Dec 2013 22:03:03 +0000 (17:03 -0500)]
Replaces shelling out to 'curl' with httpclient library.

10 years agoAccount status is now part of the "notifications" area
Peter Amstutz [Mon, 30 Dec 2013 20:08:42 +0000 (15:08 -0500)]
Account status is now part of the "notifications" area

10 years agoAdded system status box
Peter Amstutz [Mon, 30 Dec 2013 17:19:22 +0000 (12:19 -0500)]
Added system status box

10 years agoNew two-column dashboard layout suggested by Adam
Peter Amstutz [Mon, 30 Dec 2013 16:54:28 +0000 (11:54 -0500)]
New two-column dashboard layout suggested by Adam

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados into 1692-redesign-dashboard
Peter Amstutz [Mon, 30 Dec 2013 14:05:05 +0000 (09:05 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados into 1692-redesign-dashboard

10 years agoUpdated Gemfile to include all dependencies of 'arv' command line tool so bundler
Peter Amstutz [Sun, 29 Dec 2013 01:51:12 +0000 (20:51 -0500)]
Updated Gemfile to include all dependencies of 'arv' command line tool so bundler
can auto-install them.

10 years agoAdded pip requirements.txt to automatically install python dependencies for Arvados...
Peter Amstutz [Sun, 29 Dec 2013 01:32:29 +0000 (20:32 -0500)]
Added pip requirements.txt to automatically install python dependencies for Arvados Python SDK.

10 years agoFixed more broken links, normalized styles. (refs #1608)
Tim Pierce [Fri, 27 Dec 2013 23:00:16 +0000 (18:00 -0500)]
Fixed more broken links, normalized styles. (refs #1608)

10 years agoDisplays contents of manifest instead of manifest locator.
Peter Amstutz [Fri, 27 Dec 2013 22:07:42 +0000 (17:07 -0500)]
Displays contents of manifest instead of manifest locator.

10 years agoNormalize API documentation names, fix links, etc. (refs #1608)
Tim Pierce [Fri, 27 Dec 2013 21:40:59 +0000 (16:40 -0500)]
Normalize API documentation names, fix links, etc. (refs #1608)

10 years agoDashboard now consists of recent collections, jobs, and pipeline instances.
Peter Amstutz [Fri, 27 Dec 2013 21:26:40 +0000 (16:26 -0500)]
Dashboard now consists of recent collections, jobs, and pipeline instances.