arvados.git
9 years agoMerge branch 'master' into 3036-collection-uuids
Peter Amstutz [Mon, 25 Aug 2014 20:29:32 +0000 (16:29 -0400)]
Merge branch 'master' into 3036-collection-uuids

Conflicts:
sdk/python/arvados/commands/put.py
services/api/app/controllers/application_controller.rb
services/api/app/controllers/arvados/v1/collections_controller.rb
services/api/app/models/arvados_model.rb
services/api/test/fixtures/groups.yml
services/api/test/fixtures/links.yml

9 years ago3112: minor cleanup
radhika [Mon, 25 Aug 2014 20:25:58 +0000 (16:25 -0400)]
3112: minor cleanup

9 years agoMerge branch '3112-report-bug' into 3620-admin-only-gear-menu
radhika [Mon, 25 Aug 2014 18:37:38 +0000 (14:37 -0400)]
Merge branch '3112-report-bug' into 3620-admin-only-gear-menu

9 years agoMerge branch '3112-report-bug' into 3642-search-for-active-only
radhika [Mon, 25 Aug 2014 18:37:07 +0000 (14:37 -0400)]
Merge branch '3112-report-bug' into 3642-search-for-active-only

9 years agoMerge branch 'master' into 3112-report-bug
radhika [Mon, 25 Aug 2014 18:36:55 +0000 (14:36 -0400)]
Merge branch 'master' into 3112-report-bug

9 years ago3642: display search box in topnav only to active users
radhika [Mon, 25 Aug 2014 18:32:46 +0000 (14:32 -0400)]
3642: display search box in topnav only to active users

9 years agoMerge branch '3171-group-membership' refs #3171
Tom Clegg [Mon, 25 Aug 2014 18:16:11 +0000 (14:16 -0400)]
Merge branch '3171-group-membership' refs #3171

9 years ago3171: Merge branch 'master' into 3171-group-membership
Tom Clegg [Mon, 25 Aug 2014 18:15:57 +0000 (14:15 -0400)]
3171: Merge branch 'master' into 3171-group-membership

Conflicts:
services/api/test/fixtures/links.yml

9 years ago3171: Fix wording, update docs.
Tom Clegg [Mon, 25 Aug 2014 18:12:37 +0000 (14:12 -0400)]
3171: Fix wording, update docs.

9 years ago3620: display gear menu to admin users only. update the layout tests accordingly.
radhika [Mon, 25 Aug 2014 17:56:05 +0000 (13:56 -0400)]
3620: display gear menu to admin users only. update the layout tests accordingly.

9 years agoMerge branch '3448-keep-put-timestamps'
Tim Pierce [Mon, 25 Aug 2014 17:31:01 +0000 (13:31 -0400)]
Merge branch '3448-keep-put-timestamps'

Closes #3448.

9 years agoMerge branch 'master' into 3112-report-bug
radhika [Mon, 25 Aug 2014 17:29:39 +0000 (13:29 -0400)]
Merge branch 'master' into 3112-report-bug

9 years ago3112: minor update in application layout test
radhika [Mon, 25 Aug 2014 16:09:41 +0000 (12:09 -0400)]
3112: minor update in application layout test

9 years agoMerge branch 'master' into 3112-report-bug
radhika [Mon, 25 Aug 2014 16:04:20 +0000 (12:04 -0400)]
Merge branch 'master' into 3112-report-bug

9 years ago3112: Move profile testing out of application_layout_test.rb into it's own file for...
radhika [Mon, 25 Aug 2014 16:02:57 +0000 (12:02 -0400)]
3112: Move profile testing out of application_layout_test.rb into it's own file for better testability.

9 years agoDo not blow up in crunch-dispatch.rb: do not pass --jobs and --pipelines
Ward Vandewege [Mon, 25 Aug 2014 15:39:05 +0000 (11:39 -0400)]
Do not blow up in crunch-dispatch.rb: do not pass --jobs and --pipelines
arguments to Rails.

no issue #

9 years agoDo not blow up in crunch-dispatch: fix syntax error. Ouch.
Ward Vandewege [Mon, 25 Aug 2014 15:29:53 +0000 (11:29 -0400)]
Do not blow up in crunch-dispatch: fix syntax error. Ouch.

no issue #

9 years agoMerge branch 'master' into 3112-report-bug
radhika [Mon, 25 Aug 2014 15:13:51 +0000 (11:13 -0400)]
Merge branch 'master' into 3112-report-bug

9 years ago3448: update tests with "untouchable" volumes
Tim Pierce [Mon, 25 Aug 2014 14:40:28 +0000 (10:40 -0400)]
3448: update tests with "untouchable" volumes

Added a "Touchable" flag to MockVolume, so that we can test that
PutBlock does the right thing when Touch fails.  Previous code was using
volume.Bad as an attempt to test this, but that short-circuited the Put
request before it ever attempted to call Touch.

Added TODOs with more testing improvements we can make as time permits.

9 years ago3354: add integration tests verify textile descriptions for projects
radhika [Mon, 25 Aug 2014 14:40:27 +0000 (10:40 -0400)]
3354: add integration tests verify textile descriptions for projects

9 years agoMerge branch 'multiple-dispatch' no issue #
Tom Clegg [Mon, 25 Aug 2014 14:16:27 +0000 (10:16 -0400)]
Merge branch 'multiple-dispatch' no issue #

9 years agocrunch-dispatch can run --jobs, --pipelines, or both.
Tom Clegg [Mon, 25 Aug 2014 14:05:14 +0000 (10:05 -0400)]
crunch-dispatch can run --jobs, --pipelines, or both.

9 years ago3136: Fetch actual job objects for use in rendering pipeline jobs.
Peter Amstutz [Mon, 25 Aug 2014 13:23:34 +0000 (09:23 -0400)]
3136: Fetch actual job objects for use in rendering pipeline jobs.

9 years agoWith new apiserver, after upload, arv-put prints portable data hash instead of
Peter Amstutz [Mon, 25 Aug 2014 12:51:47 +0000 (08:51 -0400)]
With new apiserver, after upload, arv-put prints portable data hash instead of
collection uuid for compatibility with crunch.  refs #3504

9 years ago3149: Propagate filters from remote->dialog->infinite. Fix tests.
Tom Clegg [Mon, 25 Aug 2014 03:43:53 +0000 (23:43 -0400)]
3149: Propagate filters from remote->dialog->infinite. Fix tests.

9 years ago3149: Do not blow up on small devices/windows.
Tom Clegg [Mon, 25 Aug 2014 02:40:09 +0000 (22:40 -0400)]
3149: Do not blow up on small devices/windows.

9 years ago3149: Do not preload results in search dialog. Let infinite scroll do it.
Tom Clegg [Mon, 25 Aug 2014 02:23:43 +0000 (22:23 -0400)]
3149: Do not preload results in search dialog. Let infinite scroll do it.

9 years ago3149: Fix infinite scroll not updating after retry/refresh.
Tom Clegg [Mon, 25 Aug 2014 02:09:42 +0000 (22:09 -0400)]
3149: Fix infinite scroll not updating after retry/refresh.

9 years ago3149: Fix user-controlled filters overwriting page-controlled filters.
Tom Clegg [Mon, 25 Aug 2014 01:36:40 +0000 (21:36 -0400)]
3149: Fix user-controlled filters overwriting page-controlled filters.

9 years ago3149: Let Workbench server do all the filtering where infinite-scroll facilities...
Tom Clegg [Sun, 24 Aug 2014 23:58:54 +0000 (19:58 -0400)]
3149: Let Workbench server do all the filtering where infinite-scroll facilities exist.

9 years ago3149: Propagate search string to Workbench server using filters param.
Tom Clegg [Sun, 24 Aug 2014 22:46:29 +0000 (18:46 -0400)]
3149: Propagate search string to Workbench server using filters param.

9 years ago3149: Untabify.
Tom Clegg [Sun, 24 Aug 2014 21:22:50 +0000 (17:22 -0400)]
3149: Untabify.

9 years ago3149: Fix operator precedence in SQL statements built from record_filters.
Tom Clegg [Mon, 25 Aug 2014 01:50:22 +0000 (21:50 -0400)]
3149: Fix operator precedence in SQL statements built from record_filters.

9 years ago3149: Support "ilike" operator in record_filters.
Tom Clegg [Sun, 24 Aug 2014 23:48:28 +0000 (19:48 -0400)]
3149: Support "ilike" operator in record_filters.

9 years ago3149: Support "any" and array in filter "column" element.
Tom Clegg [Sun, 24 Aug 2014 22:48:48 +0000 (18:48 -0400)]
3149: Support "any" and array in filter "column" element.

9 years agoMerge branch 'master' into 3112-report-bug
radhika [Sun, 24 Aug 2014 22:55:51 +0000 (18:55 -0400)]
Merge branch 'master' into 3112-report-bug

Conflicts:
services/api/config/application.default.yml

9 years agocloses #3153
radhika [Sun, 24 Aug 2014 22:07:07 +0000 (18:07 -0400)]
closes #3153
Merge branch '3153-auto-setup-user'

9 years ago3153: update the newly added vm login link to not point to the "active" user
radhika [Sun, 24 Aug 2014 22:06:10 +0000 (18:06 -0400)]
3153: update the newly added vm login link to not point to the "active" user

9 years agocloses #3153
radhika [Sun, 24 Aug 2014 21:15:09 +0000 (17:15 -0400)]
closes #3153
Merge branch '3153-auto-setup-user'

9 years agoMerge branch 'master' into 3153-auto-setup-user
radhika [Sun, 24 Aug 2014 21:14:32 +0000 (17:14 -0400)]
Merge branch 'master' into 3153-auto-setup-user

9 years ago3627: Add hover highlight to Home project on dashboard.
Tom Clegg [Sun, 24 Aug 2014 20:24:11 +0000 (16:24 -0400)]
3627: Add hover highlight to Home project on dashboard.

9 years ago3627: Really make Home project selectable in project chooser.
Tom Clegg [Sun, 24 Aug 2014 20:19:27 +0000 (16:19 -0400)]
3627: Really make Home project selectable in project chooser.

9 years ago3627: More consistent icons/headings in projects dropdown and chooser.
Tom Clegg [Sun, 24 Aug 2014 20:11:00 +0000 (16:11 -0400)]
3627: More consistent icons/headings in projects dropdown and chooser.

9 years ago3627: Grey out unselectable projects in chooser.
Tom Clegg [Sun, 24 Aug 2014 20:10:21 +0000 (16:10 -0400)]
3627: Grey out unselectable projects in chooser.

9 years agoFix user agreements page when no signatures needed. Add tests. No issue #
Tom Clegg [Sun, 24 Aug 2014 20:05:15 +0000 (16:05 -0400)]
Fix user agreements page when no signatures needed. Add tests. No issue #

9 years ago3627: "My Projects" is now called "Home" and is always selectable in choosers.
Tom Clegg [Sun, 24 Aug 2014 18:57:25 +0000 (14:57 -0400)]
3627: "My Projects" is now called "Home" and is always selectable in choosers.

9 years agoFix disabled Continue button on user agreements page. No issue #
Tom Clegg [Sun, 24 Aug 2014 18:35:02 +0000 (14:35 -0400)]
Fix disabled Continue button on user agreements page. No issue #

9 years ago3354: ordinary Textile link markup was no longer working - fixed by checking to see...
Phil Hodgson [Sun, 24 Aug 2014 17:08:49 +0000 (13:08 -0400)]
3354: ordinary Textile link markup was no longer working - fixed by checking to see if the link was interpreted as an Arvados object.

9 years ago3354: Rename render_content_from_database helper to render_markup, as a more directly...
Phil Hodgson [Sun, 24 Aug 2014 17:07:34 +0000 (13:07 -0400)]
3354: Rename render_content_from_database helper to render_markup, as a more directly descriptive method name.

9 years ago3112: trailing white space
radhika [Sun, 24 Aug 2014 12:31:54 +0000 (08:31 -0400)]
3112: trailing white space

9 years ago3112: report issue success event handling working in 404 error page.
radhika [Sun, 24 Aug 2014 12:11:13 +0000 (08:11 -0400)]
3112: report issue success event handling working in 404 error page.

9 years ago3112: update report_issue.js to confine event handling to report issue. WIP: mostly...
radhika [Sun, 24 Aug 2014 04:12:44 +0000 (00:12 -0400)]
3112: update report_issue.js to confine event handling to report issue. WIP: mostly working, except from the 404 error page.

9 years ago3660: Show add/run buttons if project is writable.
Tom Clegg [Sun, 24 Aug 2014 01:14:23 +0000 (21:14 -0400)]
3660: Show add/run buttons if project is writable.

Hide move/delete buttons if move is impossible.

9 years ago3171: Add administrator UI for toggling user<->role permissions.
Tom Clegg [Sun, 24 Aug 2014 00:00:59 +0000 (20:00 -0400)]
3171: Add administrator UI for toggling user<->role permissions.

9 years agoMerge branch 'master' into 3153-auto-setup-user
radhika [Sat, 23 Aug 2014 22:22:19 +0000 (18:22 -0400)]
Merge branch 'master' into 3153-auto-setup-user

9 years ago3153: minor test updates: rename the variable "active_recipients" as "new_user_recipi...
radhika [Sat, 23 Aug 2014 19:32:02 +0000 (15:32 -0400)]
3153: minor test updates: rename the variable "active_recipients" as "new_user_recipients" to ensure test readability.

9 years ago3153: update tests to look for new user created message also when an inactive user...
radhika [Sat, 23 Aug 2014 19:17:15 +0000 (15:17 -0400)]
3153: update tests to look for new user created message also when an inactive user is being created.

9 years ago3153: when new_users_are_active config param is set, even blacklisted users will...
radhika [Sat, 23 Aug 2014 17:19:39 +0000 (13:19 -0400)]
3153: when new_users_are_active config param is set, even blacklisted users will be "active", and hence the email notification would say the user is setup when auto_setup_new_users is set.

9 years agoMerge branch '3153-auto-setup-tests' into 3153-auto-setup-user
radhika [Sat, 23 Aug 2014 15:07:57 +0000 (11:07 -0400)]
Merge branch '3153-auto-setup-tests' into 3153-auto-setup-user

9 years ago3153: change variable name in test from valid_username to ok_to_auto_setup
radhika [Sat, 23 Aug 2014 15:00:29 +0000 (11:00 -0400)]
3153: change variable name in test from valid_username to ok_to_auto_setup

9 years ago3153: directly invoke setup method during auto-setup
radhika [Sat, 23 Aug 2014 14:50:43 +0000 (10:50 -0400)]
3153: directly invoke setup method during auto-setup

9 years ago3153: Add integration tests.
Tom Clegg [Sat, 23 Aug 2014 02:46:53 +0000 (22:46 -0400)]
3153: Add integration tests.

9 years agoAccomodate otherwise valid user-supplied portable data hashes with no size
Peter Amstutz [Fri, 22 Aug 2014 20:51:10 +0000 (16:51 -0400)]
Accomodate otherwise valid user-supplied portable data hashes with no size
hint, as provided by crunch.

9 years agoMerge branch 'master' into 3112-report-bug
radhika [Fri, 22 Aug 2014 20:22:32 +0000 (16:22 -0400)]
Merge branch 'master' into 3112-report-bug

9 years agoMerge branch 'master' into 3036-collection-uuids
Peter Amstutz [Fri, 22 Aug 2014 20:14:03 +0000 (16:14 -0400)]
Merge branch 'master' into 3036-collection-uuids

9 years agoReject empty fields in job creation filters. no issue #
Peter Amstutz [Fri, 22 Aug 2014 20:10:42 +0000 (16:10 -0400)]
Reject empty fields in job creation filters. no issue #

9 years agoMerge branch 'master' into 3112-report-bug
radhika [Fri, 22 Aug 2014 20:09:32 +0000 (16:09 -0400)]
Merge branch 'master' into 3112-report-bug

9 years agocloses #3183
radhika [Fri, 22 Aug 2014 20:08:46 +0000 (16:08 -0400)]
closes #3183
Merge branch '3188-remove-selected-button'

9 years agoMerge branch 'master' into 3188-remove-selected-button
radhika [Fri, 22 Aug 2014 20:05:43 +0000 (16:05 -0400)]
Merge branch 'master' into 3188-remove-selected-button

9 years ago3153: fix the while loop logic.
radhika [Fri, 22 Aug 2014 20:02:19 +0000 (16:02 -0400)]
3153: fix the while loop logic.

9 years agoImprove error checking a bit on find_commit_range for bad revisions and missing
Peter Amstutz [Fri, 22 Aug 2014 19:54:12 +0000 (15:54 -0400)]
Improve error checking a bit on find_commit_range for bad revisions and missing
repositories.  no issue #

9 years ago3112: reload current location when error report modal is closing. otherwise, the...
radhika [Fri, 22 Aug 2014 19:51:08 +0000 (15:51 -0400)]
3112: reload current location when error report modal is closing. otherwise, the modal does not show up if the help menu dropdown option is used right after sending an error report from within the 404 page.

9 years ago3112: modal is shown by js
radhika [Fri, 22 Aug 2014 19:31:32 +0000 (15:31 -0400)]
3112: modal is shown by js

9 years agoDisplay first file in collection if name field is nil or empty. refs #3504
Peter Amstutz [Fri, 22 Aug 2014 17:56:59 +0000 (13:56 -0400)]
Display first file in collection if name field is nil or empty. refs #3504

9 years agoChange 'expire_time' column to 'expires_at' for consistency with other date
Peter Amstutz [Fri, 22 Aug 2014 17:59:06 +0000 (13:59 -0400)]
Change 'expire_time' column to 'expires_at' for consistency with other date
columns.

9 years agoDisplay first file in collection if name field is nil or empty. refs #3504
Peter Amstutz [Fri, 22 Aug 2014 17:56:59 +0000 (13:56 -0400)]
Display first file in collection if name field is nil or empty. refs #3504

9 years ago3448: unit tests, bug fixes
Tim Pierce [Fri, 22 Aug 2014 17:52:33 +0000 (13:52 -0400)]
3448: unit tests, bug fixes

UnixVolume.Delete tests the return status of lockfile (oops, left out of
previous commit)

New unit/integration tests:

* TestPutTouch (volume_unix_test.go): issues a volume.Put for a block
  that already exists, and confirms that the mtime of the existing block
  is updated.

* TestPutBlockTouchFails (keepstore_test.go): issues PutBlock for a
  block that already exists but cannot be modified, confirms that the
  mtime on the old block is unchanged and that a new copy has been
  stored.

Added a volume.Mtime() method to return the block mtime, to assist in
testing.

9 years ago3112: ajax event handling on form not working. reverting back to document for now.
radhika [Fri, 22 Aug 2014 17:49:21 +0000 (13:49 -0400)]
3112: ajax event handling on form not working. reverting back to document for now.

9 years agoMerge branch 'master' into 3036-collection-uuids
Peter Amstutz [Fri, 22 Aug 2014 17:25:46 +0000 (13:25 -0400)]
Merge branch 'master' into 3036-collection-uuids

9 years ago3171: Do not use select param for database lookup during create/destroy actions.
Tom Clegg [Fri, 22 Aug 2014 15:58:41 +0000 (11:58 -0400)]
3171: Do not use select param for database lookup during create/destroy actions.

9 years ago3171: Skip find_object_by_uuid during :create action.
Tom Clegg [Fri, 22 Aug 2014 15:58:27 +0000 (11:58 -0400)]
3171: Skip find_object_by_uuid during :create action.

9 years ago3171: Add fixtures to make Workbench tests pass under new permission rules.
Tom Clegg [Fri, 22 Aug 2014 15:56:20 +0000 (11:56 -0400)]
3171: Add fixtures to make Workbench tests pass under new permission rules.

9 years ago3036: Move manifest_text validation into Collection model. Change
Peter Amstutz [Fri, 22 Aug 2014 15:22:23 +0000 (11:22 -0400)]
3036: Move manifest_text validation into Collection model.  Change
uuids_for_docker_image to find_all_for_docker_image which returns Collection
objects instead of uuids.  Remove unused stripped_portable_data_hash helper.
Improved error messages.  Tests pass.

9 years ago3153: when exsiting repository name or vm login link is used as username, assert...
radhika [Fri, 22 Aug 2014 15:14:32 +0000 (11:14 -0400)]
3153: when exsiting repository name or vm login link is used as username, assert the generated unique username starts with the given username and ends with a number.

9 years ago3153: when deriving unique name, look for all can_login links, not just the vm_uuid...
radhika [Fri, 22 Aug 2014 15:09:31 +0000 (11:09 -0400)]
3153: when deriving unique name, look for all can_login links, not just the vm_uuid configured. update tests to assert the generated username ends with a number when using a preconfigured username for this link.

9 years agoMerge branch 'master' into 3153-auto-setup-user
radhika [Fri, 22 Aug 2014 14:30:59 +0000 (10:30 -0400)]
Merge branch 'master' into 3153-auto-setup-user

9 years agoMerge branch 'master' into 3112-report-bug
radhika [Fri, 22 Aug 2014 14:30:10 +0000 (10:30 -0400)]
Merge branch 'master' into 3112-report-bug

9 years ago3112: limit ajax event handling only to the report form
radhika [Fri, 22 Aug 2014 14:29:35 +0000 (10:29 -0400)]
3112: limit ajax event handling only to the report form

9 years agoMerge branch '3504-clients-compatible-with-3036' refs #3504
Peter Amstutz [Fri, 22 Aug 2014 13:58:19 +0000 (09:58 -0400)]
Merge branch '3504-clients-compatible-with-3036' refs #3504

9 years agoMerge remote-tracking branch 'remotes/origin/3504-clients-compatible-with-3036' into...
Peter Amstutz [Fri, 22 Aug 2014 13:07:40 +0000 (09:07 -0400)]
Merge remote-tracking branch 'remotes/origin/3504-clients-compatible-with-3036' into 3036-collection-uuids

Conflicts:
apps/workbench/app/views/projects/_show_contents_rows.html.erb

9 years ago3036: Always select "id" column unless distinct = true. Include uuid =
Peter Amstutz [Fri, 22 Aug 2014 12:48:01 +0000 (08:48 -0400)]
3036: Always select "id" column unless distinct = true.  Include uuid =
portable_data_hash when requesting collection by uuid.  Changed test fixture
"owned_by_aproject_with_no_name" to be a "human" instead of a "specimen"
because the human table has a "name" column required by projects_test.

9 years ago3504: Don't create stand-in "name" links for post #3036 apiserver
Peter Amstutz [Fri, 22 Aug 2014 12:42:45 +0000 (08:42 -0400)]
3504: Don't create stand-in "name" links for post #3036 apiserver

9 years ago3504: Support copy and moving collections on new apiserver
Peter Amstutz [Thu, 21 Aug 2014 21:10:45 +0000 (17:10 -0400)]
3504: Support copy and moving collections on new apiserver

9 years ago3504: Don't create stand-in "name" links for post #3036 apiserver
Peter Amstutz [Fri, 22 Aug 2014 12:42:45 +0000 (08:42 -0400)]
3504: Don't create stand-in "name" links for post #3036 apiserver

9 years ago3504: Back out tags on project rows. Revisit in a later story.
Peter Amstutz [Fri, 22 Aug 2014 12:35:01 +0000 (08:35 -0400)]
3504: Back out tags on project rows.  Revisit in a later story.

9 years ago3171: Update tests to conform to new permission behavior.
Tom Clegg [Fri, 22 Aug 2014 03:14:25 +0000 (23:14 -0400)]
3171: Update tests to conform to new permission behavior.

Obey "select" parameter during #show too, not just #index.

9 years ago3171: Do not follow permission graph through a User, unless permission on the User...
Tom Clegg [Fri, 22 Aug 2014 00:16:47 +0000 (20:16 -0400)]
3171: Do not follow permission graph through a User, unless permission on the User is can_manage. Restore usual permission model to user lookups. Add tests.

9 years ago3171: Outdent giant "if ... else return self" construct.
Tom Clegg [Fri, 22 Aug 2014 00:12:48 +0000 (20:12 -0400)]
3171: Outdent giant "if ... else return self" construct.

9 years ago3448: add error checking in volume.Touch()
Tim Pierce [Thu, 21 Aug 2014 23:00:18 +0000 (19:00 -0400)]
3448: add error checking in volume.Touch()

Add error checking that was erroneously left out of previous commit.

Refs #3448.

9 years ago3153: trailing white space
radhika [Thu, 21 Aug 2014 22:54:52 +0000 (18:54 -0400)]
3153: trailing white space