Peter Amstutz [Mon, 3 Nov 2014 20:07:10 +0000 (15:07 -0500)]
Merge remote-tracking branch 'origin/master' into 4031-fix-graph-connections
Conflicts:
services/api/test/fixtures/collections.yml
Peter Amstutz [Mon, 3 Nov 2014 20:06:09 +0000 (15:06 -0500)]
4031: Improve provenance graph tests for readability, use fixtures instead of
hardcoded hashes. Improve efficiency of matching collections in search_edges.
Remove spurious debug code.
Ward Vandewege [Mon, 3 Nov 2014 18:31:26 +0000 (13:31 -0500)]
The sso server docker image is not used by default at the moment, so
arvdock shouldn't try to start it unless explicitly requested (part 2).
refs #4383
Brett Smith [Mon, 3 Nov 2014 16:10:51 +0000 (11:10 -0500)]
4388: Ruby Keep::Manifest skips blank lines in manifests.
Closes #4388.
Ward Vandewege [Mon, 3 Nov 2014 15:33:54 +0000 (10:33 -0500)]
The sso server docker image is not used by default at the moment, so
arvdock shouldn't try to start it unless explicitly requested.
refs #4383
Ward Vandewege [Mon, 3 Nov 2014 04:39:40 +0000 (23:39 -0500)]
system_user and anonymous_user should be excluded from
auto_setup_new_user, always.
refs #4383
Ward Vandewege [Mon, 3 Nov 2014 02:03:34 +0000 (21:03 -0500)]
Enable auto_setup_new_users in the docker API server image.
refs #4383
Tim Pierce [Fri, 31 Oct 2014 20:45:56 +0000 (16:45 -0400)]
Merge branch '4040-fuse-tests'
Fixes #4040.
Tim Pierce [Fri, 31 Oct 2014 20:21:11 +0000 (16:21 -0400)]
4040: code review feedback
* Renamed
** collection_owned_by_fuse_1 -> collection_1_owned_by_fuse
** collection_owned_by_fuse_2 -> collection_2_owned_by_fuse
* Added fixtures pipeline_instance_owned_by_fuse and
pipeline_instance_in_fuse_project.
* Added name link for the empty collection, to exercise that links are
exposed in the filesystem in the expected way.
Ward Vandewege [Fri, 31 Oct 2014 20:13:52 +0000 (16:13 -0400)]
Fix broken link in docs. Duh.
refs #4186
Ward Vandewege [Fri, 31 Oct 2014 15:04:03 +0000 (11:04 -0400)]
Merge branch '4186-install-doc-improvements-2'
refs #4186
Ward Vandewege [Fri, 31 Oct 2014 15:03:30 +0000 (11:03 -0400)]
Clean up the installation overview pages a bit more.
refs #4186
Ward Vandewege [Fri, 31 Oct 2014 14:52:24 +0000 (10:52 -0400)]
Merge branch 'master' into 4186-install-doc-improvements-2
Ward Vandewege [Fri, 31 Oct 2014 14:47:45 +0000 (10:47 -0400)]
Add keepstore installation page.
refs #4186
Ward Vandewege [Fri, 31 Oct 2014 14:43:28 +0000 (10:43 -0400)]
Workbench: Change from yui to uglifier to compress javascript in
config/environments/production.rb.example
No issue #
Ward Vandewege [Fri, 31 Oct 2014 02:07:11 +0000 (22:07 -0400)]
Fix typo.
refs #4186
Ward Vandewege [Wed, 29 Oct 2014 16:27:45 +0000 (12:27 -0400)]
Keepproxy just needs an anonymous token.
refs #4186
Ward Vandewege [Wed, 29 Oct 2014 15:40:12 +0000 (11:40 -0400)]
Batch of improvements for the manual installation documentation:
* add prerequisites section
* add shell server section
* add keepproxy section
* many other updates throughout
refs #4186
Tom Clegg [Thu, 30 Oct 2014 21:13:31 +0000 (17:13 -0400)]
Merge branch '3824-crunch-container-setup' closes #3824
Tom Clegg [Thu, 30 Oct 2014 21:13:23 +0000 (17:13 -0400)]
3824: Merge branch 'master' into 3824-crunch-container-setup
Tom Clegg [Thu, 30 Oct 2014 21:05:25 +0000 (17:05 -0400)]
3824: Fix comment to state that tasks must not assume $TASK_KEEPMOUNT is /keep.
Tom Clegg [Thu, 30 Oct 2014 20:33:23 +0000 (16:33 -0400)]
Fix google-api-client version deps. No issue #
Tom Clegg [Thu, 30 Oct 2014 20:30:56 +0000 (16:30 -0400)]
Merge branch '4359-project-paging' closes #4359
Tom Clegg [Thu, 30 Oct 2014 20:13:35 +0000 (16:13 -0400)]
Merge branch '4088-filterable-docs' refs #4088
Tom Clegg [Thu, 30 Oct 2014 18:48:05 +0000 (14:48 -0400)]
3824: Import GPG key needed for RVM installation.
Tom Clegg [Thu, 30 Oct 2014 18:27:58 +0000 (14:27 -0400)]
3824: Remove redundant "apt-get update", standardize on "apt-get update -qq" and "apt-get install -qqy".
Tom Clegg [Thu, 30 Oct 2014 18:04:14 +0000 (14:04 -0400)]
3824: Set mode on /etc/fuse.conf in compute image.
Brett Smith [Thu, 30 Oct 2014 17:45:10 +0000 (13:45 -0400)]
4307: Workbench: only pipeline components are not editable after start.
This fixes a regression from
d7fdbbab. Closes #4307.
Tom Clegg [Thu, 30 Oct 2014 17:43:34 +0000 (13:43 -0400)]
4088: Add usage docs to filterable.js
Tom Clegg [Thu, 30 Oct 2014 17:05:17 +0000 (13:05 -0400)]
3824: Bring back $! in error message, in case it's helpful.
Tom Clegg [Thu, 30 Oct 2014 17:02:56 +0000 (13:02 -0400)]
3824: Merge branch 'master' into 3824-crunch-container-setup
Tom Clegg [Thu, 30 Oct 2014 17:00:05 +0000 (13:00 -0400)]
3824: Use Data::Dumper instead of custom quoting to show srun/task exec args.
Tom Clegg [Wed, 29 Oct 2014 21:06:17 +0000 (17:06 -0400)]
4091: Use <=N instead of <N+1. Pass "uuid not in" filter to API instead of adding custom filter params.
Tim Pierce [Wed, 29 Oct 2014 20:23:08 +0000 (16:23 -0400)]
4040: clarify variable names
Per code review: give d1, d2, d3 more descriptive variable names.
radhika [Wed, 29 Oct 2014 19:23:45 +0000 (15:23 -0400)]
closes #4091
Merge branch '4091-test-infinite-scrolling'
radhika [Wed, 29 Oct 2014 19:23:07 +0000 (15:23 -0400)]
Merge branch 'master' into 4091-test-infinite-scrolling
radhika [Wed, 29 Oct 2014 19:21:45 +0000 (15:21 -0400)]
4091: set the limit size to 50 for "Jobs and pipelines" tab.
Tim Pierce [Wed, 29 Oct 2014 19:12:47 +0000 (15:12 -0400)]
4040: update FUSE driver tests with stable fixtures
Added test fixtures specifically for FUSE driver tests.
Brett Smith [Wed, 29 Oct 2014 18:58:59 +0000 (14:58 -0400)]
Fix Node Manager test bug introduced by last commit.
Bad Brett, only running specific tests. No issue #.
Brett Smith [Wed, 29 Oct 2014 18:22:16 +0000 (14:22 -0400)]
Fix race condition in Node Manager shutdown tests.
ComputeNodeMonitorActor considers a shutdown when it's initialized.
Blocking on the subscription we send ensures that message is fully
processed before the tests continue. This is important because
several of them change the shutdown state immediately after, and that
might be seen by the internal shutdown consideration without this.
No issue #, but see
<https://ci.curoverse.com/job/arvados-api-server/1027/console>.
Tim Pierce [Wed, 29 Oct 2014 16:53:19 +0000 (12:53 -0400)]
Fix the goldang consarned FUSE tests again.
No issue #, dammit
Tim Pierce [Wed, 29 Oct 2014 16:07:07 +0000 (12:07 -0400)]
Merge branch '4088-collection-show-files-filter'
Refs #4088.
Tim Pierce [Wed, 29 Oct 2014 15:40:52 +0000 (11:40 -0400)]
4088: filter only on files
Only apply the regex filter to files; continue to process subdirectories
as normal in order to keep the appropriate filename hierarchy.
Tim Pierce [Wed, 29 Oct 2014 15:19:32 +0000 (11:19 -0400)]
4088: fix alignment for right-floating input field
Ward Vandewege [Wed, 29 Oct 2014 02:18:37 +0000 (22:18 -0400)]
Improve config/application.yml.example for the API server and workbench:
* API server: define prefix_uuid in development mode
* workbench: add a production section
No issue #
Tim Pierce [Tue, 28 Oct 2014 21:26:58 +0000 (17:26 -0400)]
4088: code review feedback
* Filter files by regex before .take(10000)
* Added "regular expression" placeholder in the filter input box
* Issue a Rails "alert" div if the regex could not be parsed
* Test that we're actually viewing a collection when no matches are
found (and not a fiddlesticks page or something)
Peter Amstutz [Tue, 28 Oct 2014 20:05:42 +0000 (16:05 -0400)]
4031: Test for collection provenance/used_by
Peter Amstutz [Tue, 28 Oct 2014 18:18:10 +0000 (14:18 -0400)]
4031: Find for collection dependencies even in the middle of script parameter
fields. Server side collections with same PDH into a single entry with a
special name. Fix node descriptions, hyperlinks. More options to eliminate
certain node types for certain graphs to make them easier to read. Handle both
PDH and UUID when identifying collections.
Brett Smith [Tue, 28 Oct 2014 17:32:05 +0000 (13:32 -0400)]
Fix off-by-one error in Node Manager server calculations.
This bug prevented Node Manager from starting nodes for a job that
requested a number of nodes equal to the daemon's max_nodes setting.
No issue #.
radhika [Tue, 28 Oct 2014 17:16:43 +0000 (13:16 -0400)]
4091: update jobs fixture to set same created_at timestamp for some of the jobs.
radhika [Tue, 28 Oct 2014 16:18:17 +0000 (12:18 -0400)]
4091: enhance code to handle the case where there are more than one item in the next page matching the previous page's last object's created_at time.
Also, handle the case where the entire next page has the same created_at time as the previous page's last item; to keep things simple, stop scrolling in this case.
Tim Pierce [Tue, 28 Oct 2014 15:14:47 +0000 (11:14 -0400)]
4088: filter collection file view by regex
Added a "Filter" field for supplying a regular expression to filter
filenames. Updated integration tests.
Tom Clegg [Tue, 28 Oct 2014 14:59:40 +0000 (10:59 -0400)]
3824: Remove redundant addition of arvados package repo and key.
Tom Clegg [Tue, 28 Oct 2014 14:35:13 +0000 (10:35 -0400)]
3824: Add sources.list file missing from commit:
0f9aaf1
Tom Clegg [Tue, 28 Oct 2014 05:06:02 +0000 (01:06 -0400)]
3824: Fix up logging messages.
Peter Amstutz [Mon, 27 Oct 2014 21:04:43 +0000 (17:04 -0400)]
4031: Refresh provenance helper graph generation to fix bugs and make better
use of available human readable names such as collections and components. Added tests.
radhika [Mon, 27 Oct 2014 20:38:38 +0000 (16:38 -0400)]
4091: retain filters in project contents collections and similar tabs.
radhika [Mon, 27 Oct 2014 20:24:07 +0000 (16:24 -0400)]
Merge branch 'master' into 4091-test-infinite-scrolling
radhika [Mon, 27 Oct 2014 20:23:21 +0000 (16:23 -0400)]
4091: change project contents order from uuid to created_at.
Tim Pierce [Mon, 27 Oct 2014 20:13:12 +0000 (16:13 -0400)]
Merge branch '4015-collection-chooser-portable-data-hash'
Fixes #4015.
Tim Pierce [Mon, 27 Oct 2014 19:49:00 +0000 (15:49 -0400)]
4015: update FUSE mount tests (again)
Tim Pierce [Mon, 27 Oct 2014 18:06:12 +0000 (14:06 -0400)]
4015: simplify integration tests
Responding to code review in #4015-8:
We can (and should) test that the collection portable_data_hash is
recorded in individual tests without adding explicit new tests or
fixtures.
Updated test 'Create and run a pipeline' and the helper
create_and_run_pipeline_in_aproject to check that the collection
portable_data_hash, uuid and name have been recorded correctly in the
Advanced tab.
radhika [Mon, 27 Oct 2014 17:46:33 +0000 (13:46 -0400)]
Merge branch 'master' into 4091-test-infinite-scrolling
Tom Clegg [Mon, 27 Oct 2014 17:35:34 +0000 (13:35 -0400)]
Merge branch '4297-dispatch-load' refs #4297
Tom Clegg [Mon, 27 Oct 2014 16:54:16 +0000 (12:54 -0400)]
4297: Merge branch 'master' into 4297-dispatch-load
Tom Clegg [Mon, 27 Oct 2014 16:53:28 +0000 (12:53 -0400)]
4297: Rename @have_tags -> @job_tags, @have_commits -> @fetched_commits. Add comments.
Tom Clegg [Mon, 27 Oct 2014 16:52:52 +0000 (12:52 -0400)]
4297: Use save! instead of save to ensure failures get logged.
Tom Clegg [Thu, 23 Oct 2014 20:39:07 +0000 (16:39 -0400)]
3824: Use keep volumes big enough to store the arvados/jobs docker image. Do not clobber settings.conf if not starting apiserver.
Tom Clegg [Thu, 23 Oct 2014 20:38:04 +0000 (16:38 -0400)]
3824: Do not say "There are jobs in the queue ahead of this one" if queue_position is unknown.
Tom Clegg [Thu, 23 Oct 2014 20:35:05 +0000 (16:35 -0400)]
3824: Add dnsmasq to compute images, to make docker-in-docker work. refs #3333
Tom Clegg [Thu, 23 Oct 2014 17:19:31 +0000 (13:19 -0400)]
3824: Use a docker volume for TASK_WORK, clean up env var and tmp dir handling, improve logging.
radhika [Mon, 27 Oct 2014 15:38:01 +0000 (11:38 -0400)]
closes #4285
Merge branch '4285-view-download-collection-subdir-files'
radhika [Mon, 27 Oct 2014 15:28:19 +0000 (11:28 -0400)]
4285: use regexp to prepent ./ to file path
radhika [Sat, 25 Oct 2014 14:01:40 +0000 (10:01 -0400)]
4285: prepend './' to file path being retrieved when it is in a subdir in a collection.
radhika [Fri, 24 Oct 2014 19:01:55 +0000 (15:01 -0400)]
Merge branch 'master' into 4091-test-infinite-scrolling
radhika [Fri, 24 Oct 2014 19:00:09 +0000 (15:00 -0400)]
4091: add offset to next page url
Tim Pierce [Fri, 24 Oct 2014 17:58:15 +0000 (13:58 -0400)]
Merge branch '3699-arv-copy'
Refs #3699.
Tim Pierce [Fri, 24 Oct 2014 17:57:23 +0000 (13:57 -0400)]
3699: fix namespace clash: rename module to arv_copy
Prevents confusion with the Python 'copy' module.
No issue # (bug fix)
Tim Pierce [Fri, 24 Oct 2014 17:20:48 +0000 (13:20 -0400)]
Merge branch '3699-arv-copy'
Closes #3699.
radhika [Fri, 24 Oct 2014 14:19:19 +0000 (10:19 -0400)]
Merge branch 'master' into 4091-test-infinite-scrolling
radhika [Fri, 24 Oct 2014 14:17:56 +0000 (10:17 -0400)]
4091: adjust the test fixture to use less data to match the limit size of 100 for the Jobs and pipelines tab in project.
Peter Amstutz [Fri, 24 Oct 2014 14:13:56 +0000 (10:13 -0400)]
Increase the timeout on "lots of events" websocket test. refs #4295
Peter Amstutz [Fri, 24 Oct 2014 13:03:07 +0000 (09:03 -0400)]
Merge branch '4295-efficient-websockets' closes #4295
Peter Amstutz [Fri, 24 Oct 2014 13:02:40 +0000 (09:02 -0400)]
4295: Use EventMachine::schedule when there is potentially more events to send instead of pushing an event to the channel (which wakes up all listeners).
Peter Amstutz [Fri, 24 Oct 2014 12:47:45 +0000 (08:47 -0400)]
4295: Fix typo in comment
radhika [Fri, 24 Oct 2014 10:10:50 +0000 (06:10 -0400)]
Merge branch 'master' into 4091-test-infinite-scrolling
Tim Pierce [Thu, 23 Oct 2014 22:35:19 +0000 (18:35 -0400)]
Merge branch 'master' into 4015-collection-chooser-portable-data-hash
Tim Pierce [Thu, 23 Oct 2014 22:34:03 +0000 (18:34 -0400)]
4015: fix pipeline instance tests
radhika [Thu, 23 Oct 2014 22:01:02 +0000 (18:01 -0400)]
closes #4195
Merge branch '4195-pipeline-tutorial'
radhika [Thu, 23 Oct 2014 22:00:12 +0000 (18:00 -0400)]
Merge branch 'master' into 4195-pipeline-tutorial
radhika [Thu, 23 Oct 2014 21:59:04 +0000 (17:59 -0400)]
4195: update workbench dashboard pic
Ward Vandewege [Thu, 23 Oct 2014 21:32:00 +0000 (17:32 -0400)]
Merge branch '4186-install-doc-improvements'
refs #4186
Ward Vandewege [Thu, 23 Oct 2014 21:31:38 +0000 (17:31 -0400)]
Merge branch 'master' into 4186-install-doc-improvements
radhika [Thu, 23 Oct 2014 21:24:29 +0000 (17:24 -0400)]
Merge branch 'master' into 4195-pipeline-tutorial
radhika [Thu, 23 Oct 2014 21:23:00 +0000 (17:23 -0400)]
closes #4228
Merge branch '4228-collection-subdir-files'
radhika [Thu, 23 Oct 2014 21:03:44 +0000 (17:03 -0400)]
Merge branch 'master' into 4195-pipeline-tutorial
Tim Pierce [Thu, 23 Oct 2014 21:00:54 +0000 (17:00 -0400)]
4015: test recording collection hashes for pipeline inputs
Tim Pierce [Wed, 22 Oct 2014 16:44:53 +0000 (12:44 -0400)]
4015: use portable_data_hash to populate chooser
Ward Vandewege [Thu, 23 Oct 2014 20:58:53 +0000 (16:58 -0400)]
Add install dependencies for the SSO server.
refs #4186
radhika [Thu, 23 Oct 2014 20:52:06 +0000 (16:52 -0400)]
Merge branch 'master' into 4228-collection-subdir-files
Conflicts:
apps/workbench/test/integration/collections_test.rb
projects / arvados.git / log