arvados.git
10 years agoRename owned_items to contents.
Tom Clegg [Tue, 29 Apr 2014 21:06:58 +0000 (17:06 -0400)]
Rename owned_items to contents.

10 years agoMerge branch '2640-folder-api' into 1970-folder-view
Tom Clegg [Tue, 29 Apr 2014 21:05:24 +0000 (17:05 -0400)]
Merge branch '2640-folder-api' into 1970-folder-view

10 years agoRename owned_items to contents, remove user method, update docs.
Tom Clegg [Tue, 29 Apr 2014 21:00:20 +0000 (17:00 -0400)]
Rename owned_items to contents, remove user method, update docs.

10 years agoMerge branch '2640-folder-api' into 1970-folder-view
Tom Clegg [Tue, 29 Apr 2014 04:38:22 +0000 (00:38 -0400)]
Merge branch '2640-folder-api' into 1970-folder-view

10 years agoSkip UserAgreement in owned_items. They are just collections again.
Tom Clegg [Tue, 29 Apr 2014 04:37:53 +0000 (00:37 -0400)]
Skip UserAgreement in owned_items. They are just collections again.

10 years agoAdd folders page, backed by groups.
Tom Clegg [Tue, 29 Apr 2014 04:37:01 +0000 (00:37 -0400)]
Add folders page, backed by groups.

10 years agoAdd sb-admin layout.
Tom Clegg [Tue, 29 Apr 2014 04:00:35 +0000 (00:00 -0400)]
Add sb-admin layout.

10 years agoShow folder contents with editable names.
Tom Clegg [Mon, 28 Apr 2014 23:30:35 +0000 (19:30 -0400)]
Show folder contents with editable names.

10 years agoapi: Support filters in API client auths index.
Brett Smith [Mon, 28 Apr 2014 17:01:18 +0000 (13:01 -0400)]
api: Support filters in API client auths index.

Per comments on Refs #1904.  filters is generally the preferred way to
do searching now.  I maintained existing limits on what can be
searched with this method.

10 years agoapi: Support scope searching in API token index.
Brett Smith [Wed, 23 Apr 2014 20:15:37 +0000 (16:15 -0400)]
api: Support scope searching in API token index.

10 years agoapi: Migrate VM auth scopes to new system.
Brett Smith [Mon, 28 Apr 2014 18:01:53 +0000 (14:01 -0400)]
api: Migrate VM auth scopes to new system.

VirtualMachinesController was the only one doing anything special with
API token scopes before we provided the more general-purpose system.
This commit removes its specialized code, and provides a database
migration to convert those specialized scopes to the general-purpose
schema.

10 years agoapi: Introduce path-based API token scopes.
Brett Smith [Tue, 22 Apr 2014 21:45:46 +0000 (17:45 -0400)]
api: Introduce path-based API token scopes.

Refs #1904, #2662 for background discussion.

10 years agoapi: Test VM login scopes.
Brett Smith [Tue, 22 Apr 2014 18:44:34 +0000 (14:44 -0400)]
api: Test VM login scopes.

The virtual machine controller is the only one doing anything
interesting with API token scopes right now.  I'm writing this test
for that functionality to make sure it stays effective through
refactoring.

10 years agoapi: Shorten name of authorized_keys index.
Brett Smith [Mon, 28 Apr 2014 15:03:22 +0000 (11:03 -0400)]
api: Shorten name of authorized_keys index.

I had trouble running the new TimestampsNotNull migration, because I
ran into the index name limit described in the migration comments.
Running this migration first worked around the problem for me, and I
hope it saves others from tripping over it too.

10 years agoRender group with folder view
Tom Clegg [Mon, 14 Apr 2014 15:44:23 +0000 (11:44 -0400)]
Render group with folder view

10 years agoFix patch_paging_vars args.
Tom Clegg [Tue, 29 Apr 2014 00:10:17 +0000 (20:10 -0400)]
Fix patch_paging_vars args.

10 years agoConvert joins to subqueries to fix duplicates in owned_items
Tom Clegg [Mon, 28 Apr 2014 23:31:48 +0000 (19:31 -0400)]
Convert joins to subqueries to fix duplicates in owned_items

10 years agoExpose names for owned_items as list_response.name_for() in Workbench
Tom Clegg [Mon, 28 Apr 2014 19:53:31 +0000 (15:53 -0400)]
Expose names for owned_items as list_response.name_for() in Workbench

10 years agoUse name links instead of permission links to include objects in groups.
Tom Clegg [Mon, 28 Apr 2014 15:15:50 +0000 (11:15 -0400)]
Use name links instead of permission links to include objects in groups.

10 years agoworkbench: Add pipeline instance tag render test.
Brett Smith [Fri, 25 Apr 2014 21:33:32 +0000 (17:33 -0400)]
workbench: Add pipeline instance tag render test.

Sasha just tickled this, so we want to prevent future recurrences.

10 years agoFix crash when tags exist for items offered in selection widget.
Tom Clegg [Fri, 25 Apr 2014 21:10:12 +0000 (17:10 -0400)]
Fix crash when tags exist for items offered in selection widget.

10 years agoBugfix. Objects returned by owned_items are now sorted by uuid in order to get
Peter Amstutz [Fri, 25 Apr 2014 19:44:29 +0000 (15:44 -0400)]
Bugfix.  Objects returned by owned_items are now sorted by uuid in order to get
a stable sort order when paging with limit and offset.

10 years agoMerge branch '2505-update-docs'
Tom Clegg [Fri, 25 Apr 2014 16:56:02 +0000 (12:56 -0400)]
Merge branch '2505-update-docs'

refs #2505

Conflicts:
doc/api/methods/groups.html.textile.liquid
doc/api/methods/users.html.textile.liquid
doc/api/schema/Group.html.textile.liquid

10 years agoMerge branch '2640-folder-api'
Tom Clegg [Fri, 25 Apr 2014 14:07:36 +0000 (10:07 -0400)]
Merge branch '2640-folder-api'

refs #2640

Conflicts:
services/api/app/controllers/application_controller.rb
services/api/config/routes.rb

10 years agoRemove "Admin Guide" link from left nav.
Tom Clegg [Fri, 25 Apr 2014 13:53:12 +0000 (09:53 -0400)]
Remove "Admin Guide" link from left nav.

10 years agoFixing indentation. Closes #2688
Misha Zatsman [Thu, 24 Apr 2014 21:01:30 +0000 (21:01 +0000)]
Fixing indentation. Closes #2688

10 years agoMerge branch '2612-workbench-displays-user-storage'
Misha Zatsman [Thu, 24 Apr 2014 20:42:42 +0000 (20:42 +0000)]
Merge branch '2612-workbench-displays-user-storage'
closes #2612

10 years agoFixed indentation.
Misha Zatsman [Thu, 24 Apr 2014 20:33:39 +0000 (20:33 +0000)]
Fixed indentation.

10 years agoMerge branch 'master' of git.curoverse.com:arvados into 2612-workbench-displays-user...
Misha Zatsman [Thu, 24 Apr 2014 20:12:53 +0000 (20:12 +0000)]
Merge branch 'master' of git.curoverse.com:arvados into 2612-workbench-displays-user-storage

10 years agoAdded link to storage page, replaced tabs with spaces.
Misha Zatsman [Thu, 24 Apr 2014 20:11:49 +0000 (20:11 +0000)]
Added link to storage page, replaced tabs with spaces.

10 years agoFix & test edge cases (no script_parameters), fix pipeline instance fixture UUIDs
Tom Clegg [Thu, 24 Apr 2014 19:37:45 +0000 (15:37 -0400)]
Fix & test edge cases (no script_parameters), fix pipeline instance fixture UUIDs

10 years agoMerge branch '2409-remove-unused-controllers'
Tom Clegg [Thu, 24 Apr 2014 19:05:51 +0000 (15:05 -0400)]
Merge branch '2409-remove-unused-controllers'

closes #2409

10 years agoAdd detail about what script_version should look like.
Tom Clegg [Thu, 24 Apr 2014 16:40:39 +0000 (12:40 -0400)]
Add detail about what script_version should look like.

10 years agoFix admin user setup instructions, add some missing "bundle exec",
Tom Clegg [Thu, 24 Apr 2014 14:40:59 +0000 (10:40 -0400)]
Fix admin user setup instructions, add some missing "bundle exec",
remove unnecessary "Create an API token" section.

10 years agoCheck sanity when applying filters, and provide useful error messages.
Tom Clegg [Thu, 24 Apr 2014 01:02:07 +0000 (21:02 -0400)]
Check sanity when applying filters, and provide useful error messages.

10 years agoRemove excess controllers and routes. Add tests to detect accidental future additions.
Tom Clegg [Wed, 23 Apr 2014 23:28:20 +0000 (19:28 -0400)]
Remove excess controllers and routes. Add tests to detect accidental future additions.

10 years agoImprove examples, explanations, typography, tests
Tom Clegg [Wed, 23 Apr 2014 22:35:48 +0000 (18:35 -0400)]
Improve examples, explanations, typography, tests

10 years agoMerge branch 'master' into 2505-update-docs
Tom Clegg [Wed, 23 Apr 2014 21:31:14 +0000 (17:31 -0400)]
Merge branch 'master' into 2505-update-docs

Conflicts:
.gitignore

10 years agoAdded row to display totals.
Misha Zatsman [Wed, 23 Apr 2014 21:20:57 +0000 (21:20 +0000)]
Added row to display totals.

10 years agoMerge branch 'master' of git.curoverse.com:arvados into 2640-folder-api
Tom Clegg [Wed, 23 Apr 2014 21:06:51 +0000 (17:06 -0400)]
Merge branch 'master' of git.curoverse.com:arvados into 2640-folder-api

Conflicts:
services/api/db/schema.rb
services/api/test/test_helper.rb

10 years agoRename jresponse test helper to json_response.
Tom Clegg [Wed, 23 Apr 2014 21:00:39 +0000 (17:00 -0400)]
Rename jresponse test helper to json_response.

10 years agoMerge branch 'master' of git.curoverse.com:arvados into 2612-workbench-displays-user...
Misha Zatsman [Wed, 23 Apr 2014 20:54:45 +0000 (20:54 +0000)]
Merge branch 'master' of git.curoverse.com:arvados into 2612-workbench-displays-user-storage

10 years agoShortened date display, put long date view in mouseover text.
Misha Zatsman [Wed, 23 Apr 2014 20:54:01 +0000 (20:54 +0000)]
Shortened date display, put long date view in mouseover text.

10 years agoSupport filters=[["attr","=",nil]]
Tom Clegg [Wed, 23 Apr 2014 20:45:21 +0000 (16:45 -0400)]
Support filters=[["attr","=",nil]]

10 years agoAdd tests, rename include_indirect to _linked, improve wording in
Tom Clegg [Wed, 23 Apr 2014 20:39:03 +0000 (16:39 -0400)]
Add tests, rename include_indirect to _linked, improve wording in
docs, improve offset/limit validation

10 years agoAdd explanation comments to assertions.
Tom Clegg [Wed, 23 Apr 2014 20:36:41 +0000 (16:36 -0400)]
Add explanation comments to assertions.

10 years agoMade sizes human readable, added measurement date column.
Misha Zatsman [Wed, 23 Apr 2014 20:14:38 +0000 (20:14 +0000)]
Made sizes human readable, added measurement date column.

10 years agoStory 2352: Adding state and components_summary is completed.
radhika chippada [Wed, 23 Apr 2014 19:01:41 +0000 (15:01 -0400)]
Story 2352: Adding state and components_summary is completed.

10 years agoMerge branch 'master' into 2352-phased-pipeline-instance-state
radhika chippada [Wed, 23 Apr 2014 18:36:06 +0000 (14:36 -0400)]
Merge branch 'master' into 2352-phased-pipeline-instance-state

10 years agoAdded teardown to all tests which resets Thread.current[:user] and friends to
Peter Amstutz [Wed, 23 Apr 2014 17:36:16 +0000 (13:36 -0400)]
Added teardown to all tests which resets Thread.current[:user] and friends to
nil.  Fixed one faulty test that turned up as a result of this change.

10 years agoSecurity bug fix to act_as_system_user to restore correct user if an
Peter Amstutz [Wed, 23 Apr 2014 17:00:03 +0000 (13:00 -0400)]
Security bug fix to act_as_system_user to restore correct user if an
exception is raised.  Also adds tests for act_as_system_user.

Also a minor style cleanup of "== []" to ".empty?" and some additional
checks to test "refuse to activate a user before signing UA".

10 years agoMerge branch 'master' of git.curoverse.com:arvados into 2612-workbench-displays-user...
Misha Zatsman [Wed, 23 Apr 2014 16:11:45 +0000 (16:11 +0000)]
Merge branch 'master' of git.curoverse.com:arvados into 2612-workbench-displays-user-storage

10 years agoWorking users/storage page!
Misha Zatsman [Wed, 23 Apr 2014 01:14:31 +0000 (01:14 +0000)]
Working users/storage page!

10 years agoHave a new view showing users at /users/storage. No storage info yet, but it's a...
Misha Zatsman [Tue, 22 Apr 2014 23:00:00 +0000 (23:00 +0000)]
Have a new view showing users at /users/storage. No storage info yet, but it's a start.

10 years agoImprove wording of the welcome e-mail a bit.
Ward Vandewege [Tue, 22 Apr 2014 21:00:16 +0000 (17:00 -0400)]
Improve wording of the welcome e-mail a bit.

10 years agoUser.full_name should not contain just a space when first_name and
Ward Vandewege [Tue, 22 Apr 2014 20:55:34 +0000 (16:55 -0400)]
User.full_name should not contain just a space when first_name and
last_name are not set.

Add a test for that, too.

10 years agoProperties should not have symbol keys. Our API runs on JSON, which does
Ward Vandewege [Tue, 22 Apr 2014 20:06:00 +0000 (16:06 -0400)]
Properties should not have symbol keys. Our API runs on JSON, which does
not have symbol keys. We want to be consistent in our use of keys, so we
don't use symbol keys within the API server for object properties.

This fixes pre-authenticating users. Again.

10 years agoFix test that was expecting a (now) incorrect number of links.
Ward Vandewege [Tue, 22 Apr 2014 19:18:14 +0000 (15:18 -0400)]
Fix test that was expecting a (now) incorrect number of links.

10 years agoSet default value for
Ward Vandewege [Tue, 22 Apr 2014 19:16:01 +0000 (15:16 -0400)]
Set default value for

  I18n.enforce_available_locales

in config/environments/test.rb.example

10 years agoMerge branch 'master' into 2352-phased-pipeline-instance-state
radhika chippada [Tue, 22 Apr 2014 18:24:55 +0000 (14:24 -0400)]
Merge branch 'master' into 2352-phased-pipeline-instance-state

10 years agoUse the renamed components_look_ready? method during migration.
radhika chippada [Tue, 22 Apr 2014 18:00:20 +0000 (14:00 -0400)]
Use the renamed components_look_ready? method during migration.

10 years agoRename is_ready method to components_look_ready? and add additional tests for state...
radhika chippada [Tue, 22 Apr 2014 17:48:36 +0000 (13:48 -0400)]
Rename is_ready method to components_look_ready? and add additional tests for state change.

10 years agoCreate a can_login link for a new user object, even if there are already
Ward Vandewege [Tue, 22 Apr 2014 17:37:59 +0000 (13:37 -0400)]
Create a can_login link for a new user object, even if there are already
stray can_login link objects for another user object with the same
e-mail address in the database. Add a test for that scenario, too.

10 years agoAdd two missing sudo.
Tom Clegg [Tue, 22 Apr 2014 16:09:00 +0000 (12:09 -0400)]
Add two missing sudo.

10 years agoSet state during save
radhika chippada [Tue, 22 Apr 2014 04:59:53 +0000 (00:59 -0400)]
Set state during save

10 years agoBuild response objects based on item type rather than list type.
Tom Clegg [Tue, 22 Apr 2014 04:52:42 +0000 (00:52 -0400)]
Build response objects based on item type rather than list type.

10 years agoAdd unit test for User#owned_items.
Tom Clegg [Tue, 22 Apr 2014 04:51:56 +0000 (00:51 -0400)]
Add unit test for User#owned_items.

10 years ago2352: Add state to pipeline_instance. Db migration and unit testing.
radhika chippada [Tue, 22 Apr 2014 04:20:56 +0000 (00:20 -0400)]
2352: Add state to pipeline_instance. Db migration and unit testing.

10 years agoAdd docs for owned_items.
Tom Clegg [Tue, 22 Apr 2014 03:55:06 +0000 (23:55 -0400)]
Add docs for owned_items.

10 years agoRename include_managed to include_indirect.
Tom Clegg [Tue, 22 Apr 2014 03:50:22 +0000 (23:50 -0400)]
Rename include_managed to include_indirect.

10 years agoSupport limit and offset params in owned_items.
Tom Clegg [Tue, 22 Apr 2014 03:39:20 +0000 (23:39 -0400)]
Support limit and offset params in owned_items.

10 years agoAdd owned_items action for groups and users.
Tom Clegg [Mon, 21 Apr 2014 21:50:49 +0000 (17:50 -0400)]
Add owned_items action for groups and users.

10 years agoFill in "I'm in a folder" fixtures
Tom Clegg [Mon, 21 Apr 2014 19:46:19 +0000 (15:46 -0400)]
Fill in "I'm in a folder" fixtures

10 years agoImprove permission link examples.
Tom Clegg [Mon, 21 Apr 2014 19:43:34 +0000 (15:43 -0400)]
Improve permission link examples.

10 years agoAdd some test fixtures that are owned by folders.
Tom Clegg [Mon, 21 Apr 2014 17:46:30 +0000 (13:46 -0400)]
Add some test fixtures that are owned by folders.

10 years agoSet :null=>false explicitly on timestamp columns.
Tom Clegg [Mon, 21 Apr 2014 16:15:56 +0000 (12:15 -0400)]
Set :null=>false explicitly on timestamp columns.

New versions of Rails do this automatically, but dev instances keep
having edit wars because some of them have never been told to add the
not-null constraint.

10 years agoRemove _kind columns from schema.
Tom Clegg [Mon, 21 Apr 2014 15:32:35 +0000 (11:32 -0400)]
Remove _kind columns from schema.

(Seemingly reintroduced by accident in
cc5023d40182e503e8ba109fc86e09efd6337836)

10 years agoExpose generate_uuid class method, e.g., for making test fixtures.
Tom Clegg [Mon, 21 Apr 2014 15:16:33 +0000 (11:16 -0400)]
Expose generate_uuid class method, e.g., for making test fixtures.

10 years agoAdd group_class attribute.
Tom Clegg [Mon, 21 Apr 2014 15:00:10 +0000 (11:00 -0400)]
Add group_class attribute.

10 years agoFix failing test in 8d6efcbfb559e377a8f21873b736390035bc44ed.
Tom Clegg [Sun, 20 Apr 2014 03:14:24 +0000 (23:14 -0400)]
Fix failing test in 8d6efcbfb559e377a8f21873b736390035bc44ed.

10 years agoPermit a job to update its output and log attributes even if those
Tom Clegg [Sun, 20 Apr 2014 02:50:54 +0000 (22:50 -0400)]
Permit a job to update its output and log attributes even if those
collections have not yet been registered with apiserver.

10 years agoHide refresh button on "show pipeline instance" page.
Tom Clegg [Sat, 19 Apr 2014 17:57:47 +0000 (13:57 -0400)]
Hide refresh button on "show pipeline instance" page.

10 years agoAdd dependency info to Workbench install page. Fix "is_trusted" recipe.
Tom Clegg [Sat, 19 Apr 2014 03:46:21 +0000 (23:46 -0400)]
Add dependency info to Workbench install page. Fix "is_trusted" recipe.

10 years agoRemove updated_at from API responses.
Tom Clegg [Sat, 19 Apr 2014 02:36:05 +0000 (22:36 -0400)]
Remove updated_at from API responses.

10 years agoDescribe logins and get_all_logins methods.
Tom Clegg [Sat, 19 Apr 2014 02:29:00 +0000 (22:29 -0400)]
Describe logins and get_all_logins methods.

10 years agoFix up job create/cancel descriptions.
Tom Clegg [Sat, 19 Apr 2014 02:24:51 +0000 (22:24 -0400)]
Fix up job create/cancel descriptions.

10 years agoClean up API schema and method pages.
Tom Clegg [Sat, 19 Apr 2014 02:18:32 +0000 (22:18 -0400)]
Clean up API schema and method pages.

Fill in missing object descriptions.
Remove redundant updated_at attributes.
Move methods sections from schema pages to method pages.
Remove some unnecessary empty sections.
Remove obsolete Commit and CommitAncestor.

10 years agoRemove spurious "destroy" methods from API docs.
Tom Clegg [Sat, 19 Apr 2014 01:23:08 +0000 (21:23 -0400)]
Remove spurious "destroy" methods from API docs.

10 years agoRemove spurious "show" methods from API docs.
Tom Clegg [Sat, 19 Apr 2014 01:21:24 +0000 (21:21 -0400)]
Remove spurious "show" methods from API docs.

10 years agoUse "filters" instead of "where" in examples and docs. Remove
Tom Clegg [Sat, 19 Apr 2014 01:16:36 +0000 (21:16 -0400)]
Use "filters" instead of "where" in examples and docs. Remove
references to unsupported "q" and "pageToken" parameters.

10 years agoAccept minimum_script_version, excluded_script_versions, and
Tom Clegg [Sat, 19 Apr 2014 01:00:31 +0000 (21:00 -0400)]
Accept minimum_script_version, excluded_script_versions, and
find_or_create flag as parameters to create, instead of treating them
as if they were attributes of the Job resource.

Accept find_or_create as a positive flag, rather than no_reuse as a
negative flag.

Behave as requested by the find_or_create flag even if
nondeterministic=true in the submitted job: i.e., a client can use the
find_or_create feature when submitting a job which itself will never
be reused. (It's up to the client to decide whether this is ever
useful.)

For now, both old and new flag names/locations are accepted and
supplied by API server and arv-run-pipeline-instance respectively.

10 years agoExtricate flags controlling jobs.create behavior from the Job resource itself.
Tom Clegg [Fri, 18 Apr 2014 23:36:59 +0000 (19:36 -0400)]
Extricate flags controlling jobs.create behavior from the Job resource itself.

10 years agoFix here-doc usage.
Tom Clegg [Fri, 18 Apr 2014 22:27:46 +0000 (18:27 -0400)]
Fix here-doc usage.

10 years agoClean up .gitignore files
Tom Clegg [Fri, 18 Apr 2014 22:27:22 +0000 (18:27 -0400)]
Clean up .gitignore files

10 years agoReorganize Keep code in preparation for dividing into modules.
Tim Pierce [Fri, 18 Apr 2014 20:00:59 +0000 (16:00 -0400)]
Reorganize Keep code in preparation for dividing into modules.

Refs #2620

10 years agoAdd Postgres setup instructions. Fix missing "bundle exec".
Tom Clegg [Fri, 18 Apr 2014 17:44:11 +0000 (13:44 -0400)]
Add Postgres setup instructions. Fix missing "bundle exec".

10 years agoFix missing --format=uuid, fix obsolete version=repo:commit example.
Tom Clegg [Fri, 18 Apr 2014 17:08:18 +0000 (13:08 -0400)]
Fix missing --format=uuid, fix obsolete version=repo:commit example.

10 years agoFix up MD5 and Git capitalization/typeface and some Git vocabulary
Tom Clegg [Fri, 18 Apr 2014 16:57:16 +0000 (12:57 -0400)]
Fix up MD5 and Git capitalization/typeface and some Git vocabulary

10 years agoFix up SSH capitalization/typeface
Tom Clegg [Fri, 18 Apr 2014 16:34:47 +0000 (12:34 -0400)]
Fix up SSH capitalization/typeface

10 years agoAdd missing </span> tag.
Tom Clegg [Fri, 18 Apr 2014 16:05:49 +0000 (12:05 -0400)]
Add missing </span> tag.