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.
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.
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.
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.
radhika [Fri, 22 Aug 2014 14:30:59 +0000 (10:30 -0400)]
Merge branch 'master' into 3153-auto-setup-user
radhika [Fri, 22 Aug 2014 14:30:10 +0000 (10:30 -0400)]
Merge branch 'master' into 3112-report-bug
radhika [Fri, 22 Aug 2014 14:29:35 +0000 (10:29 -0400)]
3112: limit ajax event handling only to the report form
Peter Amstutz [Fri, 22 Aug 2014 13:58:19 +0000 (09:58 -0400)]
Merge branch '3504-clients-compatible-with-3036' refs #3504
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
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.
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
Peter Amstutz [Thu, 21 Aug 2014 21:10:45 +0000 (17:10 -0400)]
3504: Support copy and moving collections on new 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
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.
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.
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.
Tom Clegg [Fri, 22 Aug 2014 00:12:48 +0000 (20:12 -0400)]
3171: Outdent giant "if ... else return self" construct.
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.
radhika [Thu, 21 Aug 2014 22:54:52 +0000 (18:54 -0400)]
3153: trailing white space
radhika [Thu, 21 Aug 2014 22:25:16 +0000 (18:25 -0400)]
3153: return nil if no unique username can be derived from an email address. no setup will happen in that case.
Peter Amstutz [Thu, 21 Aug 2014 21:11:19 +0000 (17:11 -0400)]
3036: Most workbench tests pass.
Peter Amstutz [Thu, 21 Aug 2014 21:10:45 +0000 (17:10 -0400)]
3504: Support copy and moving collections on new apiserver
radhika [Thu, 21 Aug 2014 20:50:29 +0000 (16:50 -0400)]
3112: change submit button text
Tim Pierce [Thu, 21 Aug 2014 20:43:46 +0000 (16:43 -0400)]
3448: add error checking
Code review comments in https://arvados.org/issues/3448#note-9
* volume.Touch() must fail if the file cannot be locked
* if volume.Touch() fails, continue looking for other volumes that can
fulfill the request.
Refs #3448.
Tim Pierce [Thu, 21 Aug 2014 20:33:50 +0000 (16:33 -0400)]
3448: unit tests for deleting new blocks
Added cases to TestDeleteHandler to test that blocks newer than
-permission_ttl will not be removed from the volume even if
volume.Delete() returned true.
Refs #3448.
radhika [Thu, 21 Aug 2014 20:22:51 +0000 (16:22 -0400)]
Merge branch 'master' into 3112-report-bug
Tim Pierce [Thu, 21 Aug 2014 19:55:47 +0000 (15:55 -0400)]
3448: code review comments.
Extend GetBlock() to optionally update the file modification time, so
PUT operations can update the timestamp of an existing block.
UnixVolume.Delete() returns nil if the file is too new to delete (the
reasoning here is that this is the correct thing for the server to do,
even if the result technically does not fulfill the user's request, so
the server should return success).
Refs #3448.
radhika [Thu, 21 Aug 2014 19:43:50 +0000 (15:43 -0400)]
3153: use loop with counter than while(true) to derive unique username
Peter Amstutz [Thu, 21 Aug 2014 19:08:38 +0000 (15:08 -0400)]
3504: Remove link to links index page on tags. Add comment to
CollectionsController#choose. Adjust column width in collections file table.
Peter Amstutz [Thu, 21 Aug 2014 19:08:38 +0000 (15:08 -0400)]
3504: Remove link to links index page on tags. Add comment to
CollectionsController#choose. Adjust column width in collections file table.
radhika [Thu, 21 Aug 2014 18:52:00 +0000 (14:52 -0400)]
3153: update tests to check for existing repo name
Peter Amstutz [Thu, 21 Aug 2014 18:49:28 +0000 (14:49 -0400)]
3504: Don't set owner_uuid redundantly.
Peter Amstutz [Thu, 21 Aug 2014 18:44:30 +0000 (14:44 -0400)]
3036: Use preload_objects to fetch owner_uuids in the controller instead of in the view.
Peter Amstutz [Thu, 21 Aug 2014 18:44:30 +0000 (14:44 -0400)]
3036: Use preload_objects to fetch owner_uuids in the controller instead of in the view.
Tim Pierce [Thu, 21 Aug 2014 18:25:29 +0000 (14:25 -0400)]
3448: minor bugfixes
Refs #3448.
Tom Clegg [Thu, 21 Aug 2014 18:10:01 +0000 (14:10 -0400)]
3171: Add tests for desired behavior. Start using FactoryGirl.
radhika [Thu, 21 Aug 2014 17:56:28 +0000 (13:56 -0400)]
3153: username regexp is updated
Tim Pierce [Thu, 21 Aug 2014 17:50:18 +0000 (13:50 -0400)]
3448: check block timestamp before DELETE
volume.Delete locks the target file and checks the timestamp before
proceeding. If the file is newer than permission_ttl specifies, return a
PermissionError. This way, a block that has been marked for recycling by
Data Manager but subsequently was re-added by a user will not be
prematurely deleted.
PutBlock now updates the timestamp on the target block if it already
exists on disk, to prevent DELETE from recycling old blocks that have
just been refreshed.
To update block timestamps, the blob server uses the new volume.Touch
method. MockVolume and UnixVolume have been updated appropriately.
Refs #3448.
Ward Vandewege [Thu, 21 Aug 2014 17:23:08 +0000 (13:23 -0400)]
Be smarter about cleanup in crunch-job after a job finishes. This should
resolve the problem of the many leftover stale mount points.
no issue #
radhika [Thu, 21 Aug 2014 17:21:16 +0000 (13:21 -0400)]
Merge branch 'master' into 3153-auto-setup-user
radhika [Thu, 21 Aug 2014 17:19:25 +0000 (13:19 -0400)]
3153: update regexp, email message
Peter Amstutz [Thu, 21 Aug 2014 16:13:30 +0000 (12:13 -0400)]
Merge remote-tracking branch 'refs/remotes/origin/3504-clients-compatible-with-3036' into 3036-collection-uuids
Conflicts:
sdk/python/arvados/commands/put.py
sdk/python/tests/test_arv_put.py
Peter Amstutz [Thu, 21 Aug 2014 16:13:11 +0000 (12:13 -0400)]
3504: Set owner_uuid when creating collection (will set owner_uuid of name link
on old apiserver, and set owner of collection object directly on new
apiserver.)
Peter Amstutz [Thu, 21 Aug 2014 15:39:09 +0000 (11:39 -0400)]
3504: Set the capybara driver explicitly so tests pass again.
Peter Amstutz [Thu, 21 Aug 2014 15:04:17 +0000 (11:04 -0400)]
Merge remote-tracking branch 'origin/master' into 3504-clients-compatible-with-3036
Peter Amstutz [Thu, 21 Aug 2014 15:03:58 +0000 (11:03 -0400)]
3504: Fixed preload_links_for_objects to use @objects.to_a. Fix collections
page to restore link names. Remove obsolete tests for "persist" button. Tweak
pipeline instance tests.
radhika [Thu, 21 Aug 2014 02:08:18 +0000 (22:08 -0400)]
Merge branch 'master' into 3153-auto-setup-user
radhika [Thu, 21 Aug 2014 02:06:28 +0000 (22:06 -0400)]
3112: move ajax event handling into a separate js file
radhika [Wed, 20 Aug 2014 22:38:02 +0000 (18:38 -0400)]
3112: use jquery syntax for find buttons
radhika [Wed, 20 Aug 2014 21:37:17 +0000 (17:37 -0400)]
3112: and it would help if that said partial is committed :)
radhika [Wed, 20 Aug 2014 21:26:31 +0000 (17:26 -0400)]
Merge branch 'master' into 3112-report-bug
radhika [Wed, 20 Aug 2014 21:23:52 +0000 (17:23 -0400)]
3112: use partial to report error
Peter Amstutz [Wed, 20 Aug 2014 21:10:37 +0000 (17:10 -0400)]
3504: Use preload_links_for_objects in projects_controller. Use
self[:portable_data_hash] in collection.rb to avoid recursive definition of
.uuid and .portable_data_hash. Revert change to show_attributes. Removed
column from collections show_recent. Reverted python tests to correspond to
behavior of pre-3036 API server so test pass.
Brett Smith [Wed, 20 Aug 2014 20:42:11 +0000 (16:42 -0400)]
Fix run_test_server Keep blob filename handling.
No issue #.
Peter Amstutz [Wed, 20 Aug 2014 20:33:27 +0000 (16:33 -0400)]
3504: CollectionReader accepts arvados object collection uuids. 'arv-put' sets
owner_uuid when collection is created. Fixed indentation.
Peter Amstutz [Wed, 20 Aug 2014 02:10:10 +0000 (22:10 -0400)]
3036: Fix arv-put to write name/owner of collections object directly when
'name' field is present on the returned object. Python SDK tests pass.
Peter Amstutz [Wed, 20 Aug 2014 20:15:05 +0000 (16:15 -0400)]
3036: Commented out failing FUSE tests. Fixed uuids on fixtures to use zzzzz
prefix. Made events.py less noisy.
Brett Smith [Wed, 20 Aug 2014 20:08:38 +0000 (16:08 -0400)]
2800: run_test_server only uses tests/tmp for real Python tests.
tests/tmp is not available for Go tests.
This fixes a bug introduced in
da01d7e1.
No issue #.
Tom Clegg [Wed, 20 Aug 2014 20:05:11 +0000 (16:05 -0400)]
Update "standard objects" page to reflect change from keep_disks to
keep_services, and add some sanity checks. No issue #
radhika [Wed, 20 Aug 2014 19:54:12 +0000 (15:54 -0400)]
Merge branch 'master' into 3112-report-bug
Tom Clegg [Wed, 20 Aug 2014 19:51:41 +0000 (15:51 -0400)]
Add libpcre3-dev dependency. Sort package names in apt-get install command.
No issue #
radhika [Wed, 20 Aug 2014 19:33:18 +0000 (15:33 -0400)]
Merge branch 'master' into 3153-auto-setup-user
radhika [Wed, 20 Aug 2014 19:29:29 +0000 (15:29 -0400)]
3153: update the new user email to include a phrase saying the user is setup when config is on.
Brett Smith [Wed, 20 Aug 2014 19:12:20 +0000 (15:12 -0400)]
2800: Delay API client creation in Python CollectionReader.
This more closely matches prior behavior, and is necessary to make the
Keep tests pass. See included comments for detailed rationale.
Refs #2800.
Tom Clegg [Wed, 20 Aug 2014 19:04:33 +0000 (15:04 -0400)]
Treat success=true exitcode!=0 as success when collating output,
just like we did when we decided the task completed. No issue #
radhika [Wed, 20 Aug 2014 18:36:25 +0000 (14:36 -0400)]
3153: tests with duplicate username
Brett Smith [Wed, 20 Aug 2014 18:18:24 +0000 (14:18 -0400)]
Merge branch '2800-pysdk-no-global-keep-client-wip'
Closes #2800, #3639.
Brett Smith [Wed, 20 Aug 2014 13:24:22 +0000 (09:24 -0400)]
2800: Use local KeepClients in Python SDK tests.
This improves test isolation, and demonstrates the preferred way to
use the API.
Brett Smith [Wed, 20 Aug 2014 13:46:49 +0000 (09:46 -0400)]
2800: Introduce TestCaseWithServers to Python SDK.
This is a subclass of unittest.TestCase. It looks for specific class
variables to launch supporting Arvados servers for subclass test
cases, taking care to adjust the environment and local Arvados
configuration to match. Put another away, this refactors a number of
similar setUpClass/tearDownClass methods throughout the SDK tests.
Brett Smith [Tue, 19 Aug 2014 20:41:33 +0000 (16:41 -0400)]
2800: Make run_test_server put Keep tempfiles in tests/tmp/.
Brett Smith [Tue, 19 Aug 2014 20:37:42 +0000 (16:37 -0400)]
2800: Use dedicated logger in Python SDK api module.
Brett Smith [Wed, 20 Aug 2014 13:46:33 +0000 (09:46 -0400)]
2800: Migrate from Keep to KeepClient in the Python SDK.
Brett Smith [Tue, 19 Aug 2014 14:17:57 +0000 (10:17 -0400)]
2800: Remove global state from KeepClient.
This commit makes it possible to build and use a KeepClient that isn't
influenced by changes in outside state. Changing the KeepClient based
on global state has been pushed up to the simple Keep class.
This commit changes the tests as little as possible to demonstrate
backward compatibility. Refactoring the tests to build KeepClients
directly will come in the future.
Brett Smith [Tue, 19 Aug 2014 14:01:36 +0000 (10:01 -0400)]
2800: Improve spec conformance of Python SDK KeepLocator.
* Require size to immediately follow digest.
* Accept all valid hints.
Brett Smith [Tue, 19 Aug 2014 13:59:53 +0000 (09:59 -0400)]
2800: Introduce config.flag_is_true() to Python SDK.
radhika [Wed, 20 Aug 2014 15:43:34 +0000 (11:43 -0400)]
Merge branch 'master' into 3153-auto-setup-user
radhika [Wed, 20 Aug 2014 15:40:49 +0000 (11:40 -0400)]
Merge branch 'master' into 3112-report-bug
radhika [Wed, 20 Aug 2014 15:39:58 +0000 (11:39 -0400)]
3112: update config param names for report notification
Brett Smith [Wed, 20 Aug 2014 15:18:54 +0000 (11:18 -0400)]
Merge branch '3499-home-project-docs-wip'
Closes #3516. Refs #3499.
Brett Smith [Fri, 15 Aug 2014 20:08:52 +0000 (16:08 -0400)]
3499: Update Keep tutorial for recent UI changes.
Brett Smith [Fri, 15 Aug 2014 19:38:04 +0000 (15:38 -0400)]
3499: Update pipeline tutorial for recent UI changes.
Brett Smith [Fri, 15 Aug 2014 15:44:46 +0000 (11:44 -0400)]
3499: Improve style consistency throughout docs.
* Capitalize Dashboard.
* Article use: "access Workbench," "access the Dashboard."
* Bold references to Workbench UI elements.
* Make example Arvados environment variables more realistic.
radhika [Wed, 20 Aug 2014 14:51:09 +0000 (10:51 -0400)]
Merge branch 'master' into 3112-report-bug
radhika [Wed, 20 Aug 2014 14:31:50 +0000 (10:31 -0400)]
Merge branch 'master' into 3112-report-bug. Also, break search testing into a separate project.
Conflicts:
apps/workbench/app/controllers/application_controller.rb
apps/workbench/config/application.default.yml
apps/workbench/test/integration/application_layout_test.rb
Tom Clegg [Wed, 20 Aug 2014 14:10:33 +0000 (10:10 -0400)]
Merge branch '3610-pipeline-log-refresh' closes #3610
Phil Hodgson [Wed, 20 Aug 2014 13:04:54 +0000 (09:04 -0400)]
Merge branch 'master' into 3354-render-textile
Conflicts (resolved):
apps/workbench/app/controllers/application_controller.rb
Peter Amstutz [Wed, 20 Aug 2014 02:10:10 +0000 (22:10 -0400)]
3036: Fix arv-put to write name/owner of collections object directly when
'name' field is present on the returned object. Python SDK tests pass.
Peter Amstutz [Wed, 20 Aug 2014 02:09:02 +0000 (22:09 -0400)]
3036: Fix #updating collection objects. Fixed database seed for empty_collection.
Tom Clegg [Wed, 20 Aug 2014 00:57:46 +0000 (20:57 -0400)]
3610: Move live log display into its own tab, avoid clobbering with tab reload.
* PipelineInstances#show gets a Log tab dedicated to the live log
window, rather than hiding it below the components table.
* Jobs#show uses its Log tab to show a live log window (instead of a
teaser) when the log is not yet finished/written to disk.
* In both cases, the live log window's tab pane intercepts and ignores
the arv:tab:reload event. (Previously, in addition to appending log
entries to the live window, websocket events would trigger a
"refresh all tabs" event, which would blow away the whole log viewer
anyway.)
* Behave sensibly when multiple lines of stderr arrive in a single
websocket update event.
* Stop displaying "update {pipeline-uuid}" messages that have no
additional content.
* Stop scrolling to bottom every time an ajax:complete fires
somewhere. (Previously, seeing anything above the last page of logs
was somewhere between annoying and impossible.)
* Make the log window taller.
radhika [Tue, 19 Aug 2014 21:30:26 +0000 (17:30 -0400)]
Merge branch 'master' into 3153-auto-setup-user
radhika [Tue, 19 Aug 2014 21:29:46 +0000 (17:29 -0400)]
3153: auto-setup user during creation.
Peter Amstutz [Tue, 19 Aug 2014 17:19:52 +0000 (13:19 -0400)]
3036: Fix merge mistakes in collection_controller.
Peter Amstutz [Tue, 19 Aug 2014 15:37:24 +0000 (11:37 -0400)]
3036: Fixed migration to migrate modified_by_client_uuid and
modified_by_user_uuid (because modified_by isn't a column, whoops). Also fills
in in useless updated_at column because it has a NOT NULL constraint.
Peter Amstutz [Tue, 19 Aug 2014 15:36:15 +0000 (11:36 -0400)]
Merge branch 'master' into 3036-collection-uuids
Conflicts:
services/api/app/controllers/arvados/v1/collections_controller.rb
services/api/app/models/collection.rb
Peter Amstutz [Tue, 19 Aug 2014 15:07:00 +0000 (11:07 -0400)]
3036: Updated migration to set modified_at instead of updated_at, added modified_by.
Peter Amstutz [Tue, 19 Aug 2014 15:05:33 +0000 (11:05 -0400)]
Merge branch 'master' into 3504-clients-compatible-with-3036
Peter Amstutz [Tue, 19 Aug 2014 13:40:07 +0000 (09:40 -0400)]
3504: Fix collection chooser. Fix generic link render to use uuid if nothing
else is available. Fix tags for objects other than collections.
Peter Amstutz [Tue, 19 Aug 2014 03:13:19 +0000 (23:13 -0400)]
3504: Fix collection page rendering to work with collections as regular uuids.
Render tags onn project page. Improve helper function for rendering links to
Arvados objects.
Tom Clegg [Mon, 18 Aug 2014 22:58:06 +0000 (18:58 -0400)]
Merge branch '3114-copy-to-project' closes #3114
Tom Clegg [Mon, 18 Aug 2014 22:19:29 +0000 (18:19 -0400)]
3114: Follow return_to param, if given, when redirecting users#show to projects#show.
Don't redirect non-html requests.