radhika [Mon, 11 Aug 2014 22:00:22 +0000 (18:00 -0400)]
3296: minor updates to profile page display
radhika [Mon, 11 Aug 2014 21:47:54 +0000 (17:47 -0400)]
3296: split profile config into two parameters: one for fields and one for message.
radhika [Mon, 11 Aug 2014 20:36:18 +0000 (16:36 -0400)]
3296: check for prefs_changed instead of cycling through all changes.
radhika [Sun, 10 Aug 2014 18:25:30 +0000 (14:25 -0400)]
3296: profile redirection works perfectly now that session caching is removed.
radhika [Sun, 10 Aug 2014 18:10:52 +0000 (14:10 -0400)]
Merge branch '3296-user-profile' of git.curoverse.com:arvados into 3296-user-profile
radhika [Sun, 10 Aug 2014 11:19:45 +0000 (07:19 -0400)]
3296: after profile is filled in by user, bring the user back to profile page with message saying all set and provide button to take to the desired target. for improved ui experience.
Tom Clegg [Sat, 9 Aug 2014 20:12:17 +0000 (16:12 -0400)]
3296: Remove session cache of user record to prevent synchronization problems.
radhika [Sat, 9 Aug 2014 15:32:18 +0000 (11:32 -0400)]
3296: fix test
radhika [Sat, 9 Aug 2014 14:14:10 +0000 (10:14 -0400)]
3296: good tests do add value.
radhika [Sat, 9 Aug 2014 01:47:25 +0000 (21:47 -0400)]
3296: update tests
radhika [Sat, 9 Aug 2014 00:57:13 +0000 (20:57 -0400)]
3296: profile notification email setting is now on server
radhika [Sat, 9 Aug 2014 00:55:49 +0000 (20:55 -0400)]
3296: send email when profile is created by user. add tests to profile mailer.
radhika [Fri, 8 Aug 2014 22:02:12 +0000 (18:02 -0400)]
Merge branch 'master' into 3296-user-profile
radhika [Fri, 8 Aug 2014 22:01:11 +0000 (18:01 -0400)]
3296: use update method and remove unnecessary update_profile method
Tom Clegg [Fri, 8 Aug 2014 21:32:03 +0000 (17:32 -0400)]
Fix repositories.get_all_permissions, add tests. closes #3546
Tom Clegg [Fri, 8 Aug 2014 20:04:51 +0000 (16:04 -0400)]
Merge branch '2769-disable-delete-flag' closes #2769
Tom Clegg [Fri, 8 Aug 2014 19:58:53 +0000 (15:58 -0400)]
Fix excessive API calls in collection chooser. refs #3489
Tom Clegg [Fri, 8 Aug 2014 19:13:24 +0000 (15:13 -0400)]
2769: Add -never-delete command line flag.
Tom Clegg [Fri, 8 Aug 2014 17:51:42 +0000 (13:51 -0400)]
Add "wait_for_ajax" to avoid race condition. No issue #
radhika [Fri, 8 Aug 2014 17:58:48 +0000 (13:58 -0400)]
3296: add integration tests for topnav. also, enable profile as default test setting
Brett Smith [Fri, 8 Aug 2014 17:51:25 +0000 (13:51 -0400)]
Merge branch '3527-infer-docker-hash-wip'
Closes #3527, #3529.
Brett Smith [Fri, 8 Aug 2014 17:44:00 +0000 (13:44 -0400)]
3527: Support using a Docker image from any stream in a Collection.
This makes Docker image detection more consistent between crunch-job
and the API server, and is more user-friendly.
Brett Smith [Fri, 8 Aug 2014 14:46:51 +0000 (10:46 -0400)]
3527: Find Docker images natively inside Collections.
We previously relied on the docker_image_hash link to treat a
Collection as a Docker image. This was safer and simpler, but it
creates obstacles for project sharing. When we have a Collection
locator that we want to treat as a Docker image, we now check that it
has a single file with a single 64-hexdigit tar file in it, and use
that as the hash if so. This should still prevent clear mistakes
while removing some of the obstacles to sharing.
Tom Clegg [Fri, 8 Aug 2014 17:39:36 +0000 (13:39 -0400)]
Hide preview pane on narrow screens. closes #3496
Tom Clegg [Fri, 8 Aug 2014 17:14:59 +0000 (13:14 -0400)]
Update tests and user setup methods. refs #3525
Tom Clegg [Fri, 8 Aug 2014 15:44:50 +0000 (11:44 -0400)]
Merge branch '3499-home-project' closes #3499
Tom Clegg [Fri, 8 Aug 2014 15:31:32 +0000 (11:31 -0400)]
Merge branch '3525-manage-own-repo' refs #3525
Tom Clegg [Fri, 8 Aug 2014 15:27:08 +0000 (11:27 -0400)]
3499: Remove "not in any project" warning.
Tom Clegg [Fri, 8 Aug 2014 14:26:33 +0000 (10:26 -0400)]
3499: Do not show Home in breadcrumbs when viewing dashboard page.
Tom Clegg [Fri, 8 Aug 2014 13:41:17 +0000 (09:41 -0400)]
3499: Do not show "Sharing" tab on Home project.
Tom Clegg [Fri, 8 Aug 2014 13:38:31 +0000 (09:38 -0400)]
3499: Show "Home" in "My projects" panel on dashboard.
Tom Clegg [Fri, 8 Aug 2014 13:31:11 +0000 (09:31 -0400)]
3499: Do not show "Move" and "Delete" buttons on Home project.
Tom Clegg [Fri, 8 Aug 2014 00:00:30 +0000 (20:00 -0400)]
3499: Merge branch 'master' into 3499-home-project
Tom Clegg [Thu, 7 Aug 2014 23:56:38 +0000 (19:56 -0400)]
3499: Update arv-put usage message to reflect new behavior.
Tom Clegg [Thu, 7 Aug 2014 23:47:53 +0000 (19:47 -0400)]
3499: Reconcile Python tests to new arv-put "home project" behavior.
Tom Clegg [Thu, 7 Aug 2014 23:46:36 +0000 (19:46 -0400)]
3499: Fix Python SDK tests to accept signed blob locators.
Tom Clegg [Thu, 7 Aug 2014 23:45:12 +0000 (19:45 -0400)]
3499: Improve Python SDK's ability to read apiserver's config files.
Use a hardcoded secret in the default "test" configuration, rather
than generating a random string with erb. Otherwise, the Python test
suite can't figure out what blob signing key the test server actually
ends up using.
Tom Clegg [Thu, 7 Aug 2014 20:46:20 +0000 (16:46 -0400)]
Merge branch '3036-mutable-collections' refs #3504
Tom Clegg [Thu, 7 Aug 2014 20:32:59 +0000 (16:32 -0400)]
3036: Merge branch 'master' into 3036-mutable-collections
Tom Clegg [Thu, 7 Aug 2014 20:32:25 +0000 (16:32 -0400)]
3036: Remove unnecessary code path.
Tom Clegg [Thu, 7 Aug 2014 19:59:27 +0000 (15:59 -0400)]
3525: Users can manage permissions on their own repositories
Tom Clegg [Thu, 7 Aug 2014 14:58:31 +0000 (10:58 -0400)]
3499: arv-put collections in home project if no --project-uuid specified.
Brett Smith [Thu, 7 Aug 2014 14:44:53 +0000 (10:44 -0400)]
3438: Show input title when choosing Collections for pipeline instances.
Closes #3438.
Brett Smith [Thu, 7 Aug 2014 13:54:07 +0000 (09:54 -0400)]
3482: crunch-job logs locator of job output sans permission hints.
This makes crunch-job log a locator that's consistent with the output
locator that it sets for the job in the database. Closes #3482.
radhika [Thu, 7 Aug 2014 13:17:42 +0000 (09:17 -0400)]
3296: improve config parameter explanation
Brett Smith [Thu, 7 Aug 2014 13:10:31 +0000 (09:10 -0400)]
Re-disable preview pane in project sharing popup.
This was the original behavior, but was lost in a later merge.
No issue #.
Brett Smith [Thu, 7 Aug 2014 12:44:21 +0000 (08:44 -0400)]
3436: Don't show Projects pulldown on project sharing popups.
Closes #3436.
radhika [Thu, 7 Aug 2014 03:52:10 +0000 (23:52 -0400)]
3296: profile config edge cases
radhika [Thu, 7 Aug 2014 01:23:40 +0000 (21:23 -0400)]
3296: add profile also in the notification email
radhika [Thu, 7 Aug 2014 01:11:30 +0000 (21:11 -0400)]
Merge branch 'master' into 3296-user-profile
radhika [Thu, 7 Aug 2014 01:09:53 +0000 (21:09 -0400)]
3296: add "message" to profile config
Tom Clegg [Wed, 6 Aug 2014 23:19:50 +0000 (19:19 -0400)]
3499: Merge branch 'master' into 3499-home-project
Tom Clegg [Wed, 6 Aug 2014 23:16:03 +0000 (19:16 -0400)]
3499: Show Home at root of projects tree. closes #3517
Tom Clegg [Wed, 6 Aug 2014 23:07:30 +0000 (19:07 -0400)]
3499: Show home project at /projects/{user_uuid}. closes #3515
Tom Clegg [Wed, 6 Aug 2014 22:41:43 +0000 (18:41 -0400)]
3499: Update breadcrumbs. closes #3513
Tom Clegg [Wed, 6 Aug 2014 22:36:06 +0000 (18:36 -0400)]
3499: groups/{user_uuid}/contents returns home project contents. closes #3514
Brett Smith [Wed, 6 Aug 2014 22:16:10 +0000 (18:16 -0400)]
3388: Workbench only lists user groups when sharing a project with groups.
This ensures that projects aren't included in the listing, which is
not useful and confusing. Closes #3388.
radhika [Wed, 6 Aug 2014 21:50:10 +0000 (17:50 -0400)]
3296: some cleanup
radhika [Wed, 6 Aug 2014 21:34:13 +0000 (17:34 -0400)]
3296: remove skip_profile and add params[:partial] handling
Brett Smith [Wed, 6 Aug 2014 21:28:12 +0000 (17:28 -0400)]
3427: Restore arv-put's resume functionality.
The refactoring in
0d1a48e accidentally introduced a bug where arv-put
wipes its resume cache clean before building the uploader. Because
the refactor always arranges `resume_cache = None` when the user
doesn't want to resume, we can fix the bug by just skipping the wipe.
Closes #3427.
radhika [Wed, 6 Aug 2014 19:33:46 +0000 (15:33 -0400)]
3296: profile path routing
Tom Clegg [Wed, 6 Aug 2014 15:49:50 +0000 (11:49 -0400)]
Merge branch '3463-make-sharing-dialog-with-users-more-useful' closes #3463
Tom Clegg [Wed, 6 Aug 2014 15:37:50 +0000 (11:37 -0400)]
Merge branch '3444-no-folders' closes #3444
Tom Clegg [Wed, 6 Aug 2014 15:37:20 +0000 (11:37 -0400)]
3444: Update documentation referring to obsolete group_class=folder
Peter Amstutz [Wed, 6 Aug 2014 14:52:15 +0000 (10:52 -0400)]
Merge branch '3372-update-pipeline-template-schema-docs' refs #3372
Peter Amstutz [Wed, 6 Aug 2014 14:48:52 +0000 (10:48 -0400)]
Add documentation to PipelineTemplate schema for title, description, link_name of pipeline template script_parameters.
Tom Clegg [Wed, 6 Aug 2014 14:40:26 +0000 (10:40 -0400)]
3444: Remove support for obsolete group_class=folder
radhika [Wed, 6 Aug 2014 00:03:01 +0000 (20:03 -0400)]
3296: check profile if request method is get.
radhika [Tue, 5 Aug 2014 20:44:31 +0000 (16:44 -0400)]
Merge branch 'master' into 3296-user-profile
Brett Smith [Tue, 5 Aug 2014 20:42:00 +0000 (16:42 -0400)]
Merge branch '3415-py-sdk-api-errors-wip'
Refs #3415. Closes #3478.
Brett Smith [Tue, 5 Aug 2014 19:18:14 +0000 (15:18 -0400)]
3415: API exceptions from Python SDK include more error information.
The apiclient module doesn't give us a lot of opportunities to
customize error handling. Request objects can have response
callbacks, but they only get access to the response headers, not body,
which we need to pass along JSON errors. After that, apiclient.http
imports apiclient.errors.HttpError directly, and raises that directly
whenever there's a permanent error in an HTTP response.
arvados.api already makes a few monkeypatches to apiclient, and this
commit adds one more: it customizes HttpError's __new__ method to
return a new customized subclass instead. This is pretty evil,
because it will mess with any other instantiations of HttpError in
client programs. Its only mitigating grace is that the new subclass
is fully API-compatible with the original.
radhika [Tue, 5 Aug 2014 18:59:17 +0000 (14:59 -0400)]
3296: When invoking sudo operations, skip profile check. Profile check is problematic when an admin user does "login as" a different user who has no profile set because after login as that user, the profile page is displayed and needs to be filled. To address this, send an additional "skip_profile" parameter when doing a "login as" or any other sudo operations.
radhika [Tue, 5 Aug 2014 18:32:18 +0000 (14:32 -0400)]
3296: save button placement
radhika [Tue, 5 Aug 2014 18:20:45 +0000 (14:20 -0400)]
3296: display read-only email, first name, last name, and identity url in the profile page.
radhika [Tue, 5 Aug 2014 17:25:40 +0000 (13:25 -0400)]
3296: send notification email when the user first creates profile, provided an address is configured
Brett Smith [Tue, 5 Aug 2014 17:23:31 +0000 (13:23 -0400)]
3415: Python SDK can pass extra arguments to the client constructor.
This gives API authors more flexibility, and lets us write tests using
apiclient's built-in mock functionality. This is needed to test
#3415.
radhika [Tue, 5 Aug 2014 14:47:38 +0000 (10:47 -0400)]
3296: tests passing and addressed trailing white spaces
Brett Smith [Tue, 5 Aug 2014 14:15:54 +0000 (10:15 -0400)]
3321: Add test for rendering unusual pipeline templates.
I wrote this along with the rest of the code for refs #3321, but
failed to commit it.
radhika [Tue, 5 Aug 2014 14:10:14 +0000 (10:10 -0400)]
Merge branch 'master' into 3296-user-profile
radhika [Tue, 5 Aug 2014 14:07:38 +0000 (10:07 -0400)]
3296: add comments to applicaiton.defaults.yml describing the user_profile_form_fields configuration parameter.
Peter Amstutz [Tue, 5 Aug 2014 12:44:04 +0000 (08:44 -0400)]
Fixed link to installing python sdk page. refs #3232
radhika [Tue, 5 Aug 2014 01:49:23 +0000 (21:49 -0400)]
3296: redirect to the page that resulted in manage profile page
radhika [Tue, 5 Aug 2014 01:37:04 +0000 (21:37 -0400)]
Merge branch 'master' into 3296-user-profile
radhika [Tue, 5 Aug 2014 01:36:22 +0000 (21:36 -0400)]
3296: manage profile page added
Peter Amstutz [Mon, 4 Aug 2014 21:02:48 +0000 (17:02 -0400)]
Merge branch '3232-user-guide-updates' closes #3232
Peter Amstutz [Mon, 4 Aug 2014 20:58:50 +0000 (16:58 -0400)]
Added explicit instructions on sample data to use for tutorial pipeline.
Tim Pierce [Mon, 4 Aug 2014 20:21:31 +0000 (16:21 -0400)]
Merge branch '2769-keep-delete-request'
Refs #2769.
Peter Amstutz [Mon, 4 Aug 2014 17:43:18 +0000 (13:43 -0400)]
Fix bug in StreamFileReader incorrectly updating self._filepos resulting in
incomplete file reads. closes #3466
Peter Amstutz [Mon, 4 Aug 2014 15:28:28 +0000 (11:28 -0400)]
Fixed "Tutorial align using bwa mem and SortSam" template. Tweaked
instructions for creating and editing template. Fixed docker image in template
provided on "writing a crunch script".
Ward Vandewege [Sun, 3 Aug 2014 21:54:10 +0000 (23:54 +0200)]
Merge branch '3363-docker-add-option-to-use-auth.curoverse.com'
refs #3363
Ward Vandewege [Sun, 3 Aug 2014 21:52:07 +0000 (23:52 +0200)]
Provide a bit more detail about build.sh in the documentation.
refs #3363
Ward Vandewege [Sun, 3 Aug 2014 21:51:11 +0000 (23:51 +0200)]
Only the deepclean Make action should remove the skydns-image and skydock-image files.
refs #3363
Ward Vandewege [Sun, 3 Aug 2014 21:33:11 +0000 (23:33 +0200)]
Update Docker install documentation:
* suggest use of build.sh to generate config.yml
* reflect now default use of Curoverse SSO server
refs #3363
Ward Vandewege [Sun, 3 Aug 2014 21:23:14 +0000 (23:23 +0200)]
* Default to using the auth.curoverse.com SSO server. Add instructions
in config.yml.example for using a local SSO server.
* Do not prepopulate the config.yml file generated by build.sh with
random values for _PW and _SECRET variables, let config.rb deal with
that at build time.
* Make config.rb a bit more robust in choosing those values for _PW and
_SECRET by not depending on any particular key order in the config Hash.
refs #3363
Ward Vandewege [Sun, 3 Aug 2014 20:30:48 +0000 (22:30 +0200)]
Be less presumptuous about the GNU/Linux distribution we are being run
on, and do not try to install ruby >= 1.9.3 automatically.
refs #3363
Ward Vandewege [Sun, 3 Aug 2014 20:27:09 +0000 (22:27 +0200)]
Merge branch '3261-keep-docker-config'
refs #3261
Ward Vandewege [Sun, 3 Aug 2014 20:17:15 +0000 (22:17 +0200)]
Merge branch 'master' into 3261-keep-docker-config
Ward Vandewege [Sun, 3 Aug 2014 20:16:59 +0000 (22:16 +0200)]
3261: simplify Makefile
Ward Vandewege [Sun, 3 Aug 2014 09:32:08 +0000 (11:32 +0200)]
Add user e-mail address to the list of users an object can be shared with
refs #3463
Ward Vandewege [Sat, 2 Aug 2014 18:36:12 +0000 (20:36 +0200)]
Do not blow up on the 'Manage account' page if the db contains an ssh
key record that contains an invalid ssh key.
no issue #