Peter Amstutz [Fri, 19 Sep 2014 19:26:30 +0000 (15:26 -0400)]
Merge branch 'master' into 3187-pipeline-instance-page
Conflicts:
apps/workbench/app/models/job.rb
apps/workbench/app/views/application/_content.html.erb
services/api/app/models/job.rb
Tom Clegg [Fri, 19 Sep 2014 18:01:17 +0000 (14:01 -0400)]
Fix Gemfile.lock to use a real gem, not a dev build. refs #3550
Tom Clegg [Fri, 19 Sep 2014 17:49:59 +0000 (13:49 -0400)]
Use new --run-pipeline-here instead of --run-here flag, which no longer does what crunch-dispatch wants. refs #3550
Tim Pierce [Fri, 19 Sep 2014 14:45:50 +0000 (10:45 -0400)]
Bug fix: migration requires CurrentApiClient
Migration 20140918141529_change_user_owner_uuid_not_null requires
system_user_uuid, which is defined in CurrentApiClient.
No issue # (bug fix)
Brett Smith [Thu, 18 Sep 2014 21:24:35 +0000 (17:24 -0400)]
3147: FUSE requires a built Python SDK.
Unlike our Ruby Gems, Python package versioning is sensitive to
commits that actually affect the package, rather than the entire
arvados repository. On the plus side, this makes it a little easier
to reliably name a package version that meets our requirements. This
commit does that. Refs #3147.
Phil Hodgson [Thu, 18 Sep 2014 21:17:31 +0000 (17:17 -0400)]
Merge branch '3661-copy-move-from-show' refs #3661
Phil Hodgson [Thu, 18 Sep 2014 21:07:03 +0000 (17:07 -0400)]
Merge branch 'master' into 3661-copy-move-from-show
Tom Clegg [Thu, 18 Sep 2014 20:45:15 +0000 (16:45 -0400)]
Merge branch '3901-cannot-find-commit' refs #3901
Brett Smith [Thu, 18 Sep 2014 20:37:18 +0000 (16:37 -0400)]
3147: Rebuild the Python SDK to satisfy FUSE version requirement.
When I wrote the FUSE driver's version dependency, I did my math
wrong, and it's newer than any version of the SDK. This commit will
cause a new SDK to be built with a new version number that satisfies
the dependency. Refs #3147.
Tom Clegg [Thu, 18 Sep 2014 20:34:03 +0000 (16:34 -0400)]
3901: Add missing error checks while copying git objects.
Phil Hodgson [Thu, 18 Sep 2014 20:32:53 +0000 (16:32 -0400)]
3661: visual bug fix: button should be a link
Brett Smith [Thu, 18 Sep 2014 19:56:28 +0000 (15:56 -0400)]
Merge branch '3147-py-collection-retries-wip2'
Closes #3147.
Brett Smith [Mon, 15 Sep 2014 22:13:40 +0000 (18:13 -0400)]
3147: crunch-job retries data uploads more for longer-running jobs.
Brett Smith [Tue, 16 Sep 2014 21:29:38 +0000 (17:29 -0400)]
3147: Add retry support to FUSE driver.
Brett Smith [Mon, 15 Sep 2014 14:58:11 +0000 (10:58 -0400)]
3147: FUSE driver requires a Python SDK with retry support.
I also took out some of the older log-handling code while I was at it,
since the stricter versioning makes it unnecessary.
Brett Smith [Mon, 15 Sep 2014 15:21:31 +0000 (11:21 -0400)]
3147: Add retry support to PySDK list_all utility.
Brett Smith [Mon, 15 Sep 2014 14:37:32 +0000 (10:37 -0400)]
3147: Add retry support to Python CLI tools.
Brett Smith [Tue, 16 Sep 2014 21:27:51 +0000 (17:27 -0400)]
3147: Add retry support to PySDK Collection objects.
This required updating the FUSE driver's SafeApi object to better
imitate a real API object, now that CollectionReader will pass it down
to the underlying KeepClient.
Brett Smith [Fri, 12 Sep 2014 13:28:47 +0000 (09:28 -0400)]
3147: Add retry support to PySDK StreamReader classes.
Brett Smith [Tue, 16 Sep 2014 21:24:31 +0000 (17:24 -0400)]
3147: Make PySDK KeepClient.get and put retry_methods.
Brett Smith [Fri, 12 Sep 2014 12:49:21 +0000 (08:49 -0400)]
3147: Add retry_method to the Python SDK.
This gives us a way to make retry support flexible and consistent
across SDK classes. Any class that has retryable operations should
take a num_retries argument at initialization. Then, the specific
methods that implement those operations should also take a num_retries
argument, which will fall back to the instance's setting by default.
This lets SDK users express their retry preferences wherever it's most
convenient for them.
Brett Smith [Thu, 11 Sep 2014 18:46:37 +0000 (14:46 -0400)]
3147: Fix variable name typo.
This variable was renamed in previous branch work, but this last user
of it wasn't caught until just now.
Brett Smith [Thu, 11 Sep 2014 18:22:12 +0000 (14:22 -0400)]
3147: PySDK StreamReader instantiates a KeepClient late.
Similarly with API client instantiation in KeepClient, this helps with
testing. Refs #3693.
Brett Smith [Fri, 12 Sep 2014 20:46:54 +0000 (16:46 -0400)]
3147: Move PySDK HTTP test infrastructure to testutil.
Making this available to other test collections.
Brett Smith [Wed, 10 Sep 2014 20:44:25 +0000 (16:44 -0400)]
3147: PySDK tests use mock>=1.0 and easier mock side_effect.
Phil Hodgson [Thu, 18 Sep 2014 19:13:41 +0000 (15:13 -0400)]
Merge branch 'master' into 3661-copy-move-from-show
Conflicts:
apps/workbench/app/assets/javascripts/selection.js.erb
apps/workbench/test/integration/collections_test.rb
Phil Hodgson [Thu, 18 Sep 2014 19:00:46 +0000 (15:00 -0400)]
Merge branch '3338-tab-counts' refs #3338
Phil Hodgson [Thu, 18 Sep 2014 18:32:04 +0000 (14:32 -0400)]
Merge branch 'master' into 3338-tab-counts
Peter Amstutz [Thu, 18 Sep 2014 17:47:52 +0000 (13:47 -0400)]
Merge branch '3605-queue-position-size' refs #3605
Peter Amstutz [Thu, 18 Sep 2014 17:38:05 +0000 (13:38 -0400)]
3605: Use #each_with_index instead of #each_index
Peter Amstutz [Thu, 18 Sep 2014 17:33:03 +0000 (13:33 -0400)]
Merge branch '3605-node-info-field' refs #3605
Conflicts:
services/api/db/structure.sql
Peter Amstutz [Thu, 18 Sep 2014 17:29:23 +0000 (13:29 -0400)]
3605: Do .to_i on total_cpu_cores, total_ram_mb, and total_scratch_mb in Node#ping.
Peter Amstutz [Thu, 18 Sep 2014 16:11:43 +0000 (12:11 -0400)]
3605: Add properties column to node. Put public-facing node information (cpu
cores, RAM, scratch space) into properties field. Info field is back to being
admin-only.
Tim Pierce [Thu, 18 Sep 2014 14:54:32 +0000 (10:54 -0400)]
Bug fix: Added missing owner_uuid to user fixture.
No issue #.
Tim Pierce [Thu, 18 Sep 2014 14:46:32 +0000 (10:46 -0400)]
Merge branch '3927-user-owner-uuid-not-null'
Closes #3927.
Tim Pierce [Thu, 18 Sep 2014 14:35:05 +0000 (10:35 -0400)]
3927: add NOT NULL constraint to User.owner_uuid
Added a migration setting all users with null owner_uuid to
system_user_uuid, and enforced a NOT NULL constraint on that column.
Phil Hodgson [Thu, 18 Sep 2014 00:42:23 +0000 (20:42 -0400)]
3338: move code that sets the share_links to its own before_filter
Tom Clegg [Thu, 18 Sep 2014 00:11:40 +0000 (20:11 -0400)]
Update Gemfiles to use latest arvados gem. refs #3550
Tom Clegg [Wed, 17 Sep 2014 22:01:03 +0000 (18:01 -0400)]
Merge branch '3550-local-pipeline' closes #3550
Tom Clegg [Wed, 17 Sep 2014 22:00:25 +0000 (18:00 -0400)]
3550: Merge branch 'master' into 3550-local-pipeline
Conflicts:
sdk/cli/bin/arv-run-pipeline-instance
Peter Amstutz [Wed, 17 Sep 2014 19:00:02 +0000 (15:00 -0400)]
3605: Test queue_size method and queue_position field. Adjust "GET queue"
tests for jobs controller to test that users don't see queue items for which
they do not have permissions.
radhika [Wed, 17 Sep 2014 18:56:02 +0000 (14:56 -0400)]
closes #2761
Merge branch '2761-diagnostic-suite'
radhika [Wed, 17 Sep 2014 18:55:17 +0000 (14:55 -0400)]
Merge branch 'master' into 2761-diagnostic-suite
mishaz [Wed, 17 Sep 2014 18:24:51 +0000 (18:24 +0000)]
Merge branch 'update-go-sdk-documentation'
Updating Go SDK Documentation,
no issue #
radhika [Wed, 17 Sep 2014 18:10:40 +0000 (14:10 -0400)]
no issue # - fix couple more places where description is failing on nil template name.
Tim Pierce [Wed, 17 Sep 2014 17:55:23 +0000 (13:55 -0400)]
3411: fix failing tests
The FuseSharedTest requires "pipeline_with_template.pipelineInstance" on
my machine, but not on Jenkins. Puzzling.
No issue # -- bug fix
Phil Hodgson [Wed, 17 Sep 2014 16:24:26 +0000 (12:24 -0400)]
3338: add a 'count-change' event that the tab panes listen for, and trigger it from destroy actions
Tim Pierce [Wed, 17 Sep 2014 15:46:38 +0000 (11:46 -0400)]
Merge branch '3411-expire-collections'
Refs #3411.
Tim Pierce [Wed, 17 Sep 2014 15:45:38 +0000 (11:45 -0400)]
3411: added new collection fixtures owned by active_user
radhika [Wed, 17 Sep 2014 15:38:37 +0000 (11:38 -0400)]
no issue # : fix nil issue in pipeline_templates page
Peter Amstutz [Wed, 17 Sep 2014 15:36:53 +0000 (11:36 -0400)]
3187: Fix tests and some debug spew.
Tom Clegg [Wed, 17 Sep 2014 15:13:14 +0000 (11:13 -0400)]
3550: Fix race conditions: avoid setting running/success/finished_at
attributes until output and log have been saved.
Tim Pierce [Wed, 17 Sep 2014 14:59:23 +0000 (10:59 -0400)]
Merge branch '3411-expire-collections'
Closes #3411.
Tom Clegg [Wed, 17 Sep 2014 14:57:41 +0000 (10:57 -0400)]
3550: Fix running local job repeatedly on subsequent loop iterations.
Phil Hodgson [Wed, 17 Sep 2014 14:51:06 +0000 (10:51 -0400)]
3661: proposed change of the selection javascript to use the new copies_to_projects? class method on Group
Tom Clegg [Wed, 17 Sep 2014 14:48:13 +0000 (10:48 -0400)]
3550: Add missing .andand
Tim Pierce [Wed, 17 Sep 2014 14:20:48 +0000 (10:20 -0400)]
3411: code review feedback
* Ensure each functional test issues only one request to the controller
* $application_config['default_trash_lifetime'] -> Rails.configuration.default_trash_lifetime
radhika [Wed, 17 Sep 2014 14:10:16 +0000 (10:10 -0400)]
2761: added some comments
radhika [Wed, 17 Sep 2014 14:04:49 +0000 (10:04 -0400)]
Merge branch 'master' into 2761-diagnostic-suite
Tom Clegg [Wed, 17 Sep 2014 13:49:43 +0000 (09:49 -0400)]
3550: Add missing .andand
Peter Amstutz [Wed, 17 Sep 2014 13:29:32 +0000 (09:29 -0400)]
3605: Add "queue_position" to jobs. Also add a route on jobs controller to get
the true size of the job queue.
Peter Amstutz [Wed, 17 Sep 2014 13:11:36 +0000 (09:11 -0400)]
Merge branch '3605-node-info-field' refs #3605
Peter Amstutz [Wed, 17 Sep 2014 01:00:14 +0000 (21:00 -0400)]
Fix test
Tim Pierce [Wed, 17 Sep 2014 02:40:16 +0000 (22:40 -0400)]
Merge branch '3705-keep-blockworklist'
Closes #3705.
radhika [Wed, 17 Sep 2014 02:36:08 +0000 (22:36 -0400)]
Merge branch 'master' into 2761-diagnostic-suite
radhika [Wed, 17 Sep 2014 02:35:12 +0000 (22:35 -0400)]
2761: minor updates to diagnostics test config explanation.
Tim Pierce [Wed, 17 Sep 2014 02:34:20 +0000 (22:34 -0400)]
3705: use %v to format interface types
Peter Amstutz [Wed, 17 Sep 2014 02:30:21 +0000 (22:30 -0400)]
Fix arv-run-pipeline-instance to not crash when template is null. no issue #
Tim Pierce [Wed, 17 Sep 2014 02:09:34 +0000 (22:09 -0400)]
3705: drop unnecessary 'items' from BlockWorkList
Tim Pierce [Wed, 17 Sep 2014 01:56:55 +0000 (21:56 -0400)]
3705: use helper functions in tests
Phil Hodgson [Tue, 16 Sep 2014 23:09:32 +0000 (19:09 -0400)]
3338: move the user_is_manager and shared items to the already-overridden #find_object_by_uuid method so that these are available to all the same actions
Phil Hodgson [Tue, 16 Sep 2014 23:05:45 +0000 (19:05 -0400)]
3338: fix the integration test so that it checks the on-screen collection count
rather than trying to use the fixtures which doesn't work anyway
radhika [Tue, 16 Sep 2014 22:40:57 +0000 (18:40 -0400)]
Merge branch 'master' into 2761-diagnostic-suite
radhika [Tue, 16 Sep 2014 22:40:43 +0000 (18:40 -0400)]
2761: update config
Tim Pierce [Tue, 16 Sep 2014 21:54:40 +0000 (17:54 -0400)]
3705: drop unnecessary current_list pointer
radhika [Tue, 16 Sep 2014 21:27:33 +0000 (17:27 -0400)]
no issue # remove pipeline instance fixture to address failing test.
Merge branch '2875-pipeline-description'
radhika [Tue, 16 Sep 2014 21:26:13 +0000 (17:26 -0400)]
2875: remove pipeline instance fixture and use an existing one.
Tom Clegg [Tue, 16 Sep 2014 21:04:10 +0000 (17:04 -0400)]
Merge branch '3877-log-memory-leak' closes #3877
radhika [Tue, 16 Sep 2014 20:55:22 +0000 (16:55 -0400)]
2761: add diagnostics section to config
mishaz [Tue, 16 Sep 2014 20:52:40 +0000 (20:52 +0000)]
Combined all examples into one big, runable source file with syntax coloring.
Found and fixed some bugs in example code.
Added example of requesting manifest text.
Turned references to source directories into links.
syntax-colored import statemtns.
Tim Pierce [Tue, 16 Sep 2014 20:49:37 +0000 (16:49 -0400)]
3411: code review
Feedback from code review:
* Dropped unnecessary lambda from Collection.default_scope.
* Set owner_uuid of new collection test fixtures to user 'active',
removed unnecessary permission link test fixtures.
* Removed permit_unsigned_manifests from unit tests
* Added tests for :show and :update to expired and unexpired
collections.
* Added rake config:check test to make sure default_trash_lifetime is at
least 24 hours.
Ward Vandewege [Tue, 16 Sep 2014 20:36:03 +0000 (16:36 -0400)]
Make sure to run apt-get update before trying to install
openjdk-7-jre-headless into the java-bwa-samtools arvados docker image.
no issue #
Phil Hodgson [Tue, 16 Sep 2014 20:23:08 +0000 (16:23 -0400)]
3661: add centralized method for defining whether an object can be copied to a project
Phil Hodgson [Tue, 16 Sep 2014 20:22:14 +0000 (16:22 -0400)]
3661: removed useless method to wrong project
(fix from last commit)
Peter Amstutz [Tue, 16 Sep 2014 20:05:18 +0000 (16:05 -0400)]
Merge branch '3878-arv-mount-block-cache' closes #3878
Peter Amstutz [Tue, 16 Sep 2014 20:04:37 +0000 (16:04 -0400)]
3878: Remove raise debugging exception.
mishaz [Tue, 16 Sep 2014 20:01:56 +0000 (20:01 +0000)]
Moved file.
Tom Clegg [Tue, 16 Sep 2014 20:00:11 +0000 (16:00 -0400)]
3550: Fix crash when --template loaded from local JSON file has no uuid.
Tom Clegg [Tue, 16 Sep 2014 19:59:04 +0000 (15:59 -0400)]
3550: Remove extraneous "to" in usage message.
Tim Pierce [Tue, 16 Sep 2014 04:57:44 +0000 (00:57 -0400)]
3411: set default collection expiration policy
* Added default_scope to Collections restricting them to collections that
have not yet expired
* Added a default_trash_lifetime setting in application.default.yml,
exposed in the discovery doc setting 'defaultTrashLifetime' (default:
2 weeks)
* Added test fixtures to exercise fetching expired collections and
collections that expire in the future.
Peter Amstutz [Tue, 16 Sep 2014 18:49:38 +0000 (14:49 -0400)]
3878: Fix block cache sharing across threads so arv-mount uses a bounded amount
of memory to store block. Also fixes bug in cache management code and cleans
some exception handler error reporting.
radhika [Tue, 16 Sep 2014 17:01:26 +0000 (13:01 -0400)]
Merge branch 'master' into 2761-diagnostic-suite
radhika [Tue, 16 Sep 2014 15:28:53 +0000 (11:28 -0400)]
closes #2875
Merge branch '2875-pipeline-description'
radhika [Tue, 16 Sep 2014 15:27:30 +0000 (11:27 -0400)]
2875: minor text update
radhika [Tue, 16 Sep 2014 15:22:02 +0000 (11:22 -0400)]
2875: collection description is now textile and also the display is updated.
radhika [Tue, 16 Sep 2014 14:54:53 +0000 (10:54 -0400)]
2875: remove junk migration lines
Tom Clegg [Tue, 16 Sep 2014 14:51:27 +0000 (10:51 -0400)]
3877: Fix memory leak after "log truncated" decision. Clean up code.
Tim Pierce [Tue, 16 Sep 2014 06:15:13 +0000 (02:15 -0400)]
3705: update for code review
* Changed the type of the NextItem channel from *list.Element to
interface{} (i.e. a list.Element.Value)
* Better comments
* Cleaner testing framework
* TestBlockWorkListReaderBlocks to exercise the case where readers block
when the list is exhausted, and resume when new data is supplied.
Tim Pierce [Mon, 15 Sep 2014 22:19:40 +0000 (18:19 -0400)]
3705: describe BlockWorkList flow more explicitly
Updated file comments to describe the overall data flow for a
BlockWorkList manager and worker more explicitly.
Tom Clegg [Mon, 15 Sep 2014 16:20:15 +0000 (12:20 -0400)]
3550: Update docs to match new flag name. Add note about job re-use.
projects / arvados.git / log