Tom Clegg [Thu, 18 Dec 2014 15:14:59 +0000 (10:14 -0500)]
Merge branch '4515-search-empty-project' closes #4515
Tom Clegg [Wed, 17 Dec 2014 14:44:27 +0000 (09:44 -0500)]
Remove excess heading and divider. No issue #
Tom Clegg [Wed, 17 Dec 2014 14:41:49 +0000 (09:41 -0500)]
Restore scroll on projects menu. Do not offer "Add project" button in projects dropdown in chooser dialog. closes #4811
Tom Clegg [Tue, 16 Dec 2014 16:37:01 +0000 (11:37 -0500)]
Ignore .eggs/ (*.egg isn't enough: .eggs/README.txt gets installed too, as a human-readable .gitignore.)
No issue #
Tom Clegg [Tue, 16 Dec 2014 16:16:59 +0000 (11:16 -0500)]
4515: Add controller tests for search dialog.
Brett Smith [Mon, 15 Dec 2014 19:46:43 +0000 (14:46 -0500)]
4818: Node Manager unpairs Arvados node when cloud node shuts down.
Without this, Node Manager doesn't correctly pair the Arvados node
with a new cloud node that's booted later. Closes #4818.
Brett Smith [Mon, 15 Dec 2014 17:58:52 +0000 (12:58 -0500)]
Merge branch '4481-update-user-docs-TC'
Closes #4741, #4790.
Tom Clegg [Mon, 15 Dec 2014 17:18:33 +0000 (12:18 -0500)]
4481: Fix ambiguous "Keep id" -> "locator" in example scripts.
Brett Smith [Wed, 10 Dec 2014 21:40:13 +0000 (16:40 -0500)]
4481: Refresh Crunch script tutorial page.
* The script now normalizes the output path, for consistency with
other scripts, and it looks nicer.
* Modernize the job log output slightly, and adjust text to match.
Brett Smith [Mon, 8 Dec 2014 19:37:23 +0000 (14:37 -0500)]
4481: Update tutorial Crunch scripts to use newer PySDK methods.
Most focus is on the file Collection file methods added in #3603.
Brett Smith [Mon, 15 Dec 2014 17:57:25 +0000 (12:57 -0500)]
Merge branch '4792-arv-ls-normalize-wip'
Closes #4792, #4813.
Brett Smith [Fri, 12 Dec 2014 23:01:39 +0000 (18:01 -0500)]
4792: arv-ls normalizes the collection before listing.
I sort of ended up rewriting arv-ls to make it testable, but hey,
that's part of the support task. Normalization is the only functional
change I made.
Radhika Chippada [Fri, 12 Dec 2014 21:29:50 +0000 (16:29 -0500)]
closes #4414
Merge branch '4414-add-new-in-project-dropdown'
Radhika Chippada [Fri, 12 Dec 2014 21:20:44 +0000 (16:20 -0500)]
4414: use ensure_unique_name option to instruct api server to create unique name for new project.
Radhika Chippada [Fri, 12 Dec 2014 19:02:03 +0000 (14:02 -0500)]
4414: add "Add a new project" link to project dropdown.
Radhika Chippada [Fri, 12 Dec 2014 14:26:03 +0000 (09:26 -0500)]
closes #4476
closes #4804
Merge branch '4476-search-next-page-issue'
Radhika Chippada [Fri, 12 Dec 2014 14:22:14 +0000 (09:22 -0500)]
closes #4799
Merge branch '4799-move-selected-error'
Radhika Chippada [Fri, 12 Dec 2014 14:14:02 +0000 (09:14 -0500)]
refs #4754
Merge branch '4754-performance-benchmarks'
Radhika Chippada [Fri, 12 Dec 2014 14:13:31 +0000 (09:13 -0500)]
Merge branch 'master' into 4754-performance-benchmarks
Radhika Chippada [Thu, 11 Dec 2014 21:46:36 +0000 (16:46 -0500)]
4804: search dialog retains project_uuid param in next_page_href.
Radhika Chippada [Thu, 11 Dec 2014 19:38:21 +0000 (14:38 -0500)]
4476: include filters in search next_page_href url.
Radhika Chippada [Thu, 11 Dec 2014 17:26:30 +0000 (12:26 -0500)]
4799: do not offer "move selected" option when current user cannot write to the project.
Brett Smith [Thu, 11 Dec 2014 15:54:28 +0000 (10:54 -0500)]
4027: Document arvados_sdk_version's virtualenv requirement.
Refs #4027.
Radhika Chippada [Thu, 11 Dec 2014 14:16:26 +0000 (09:16 -0500)]
4754: add command to be used to run diagnostics testing as a comment.
Radhika Chippada [Wed, 10 Dec 2014 22:41:32 +0000 (17:41 -0500)]
4754: update assertion to look for a data-object-uuid
Radhika Chippada [Wed, 10 Dec 2014 22:18:19 +0000 (17:18 -0500)]
4754: support RAILS_ENV=performance
Radhika Chippada [Wed, 10 Dec 2014 19:18:24 +0000 (14:18 -0500)]
Merge branch 'master' into 4754-performance-benchmarks
Tim Pierce [Wed, 10 Dec 2014 16:26:10 +0000 (11:26 -0500)]
Merge branch '4499-one-task-per-input-file-normalize'
Fixes #4499.
Ward Vandewege [Wed, 10 Dec 2014 14:49:09 +0000 (09:49 -0500)]
Download bwa and samtools from a self-hosted mirror, sf.net downloads
are way too unreliable.
No issue #
Brett Smith [Wed, 10 Dec 2014 13:04:08 +0000 (08:04 -0500)]
Merge branch '4293-node-manager-timed-bootstrap-wip'
Closes #4293, #4732. Refs #4380.
Brett Smith [Fri, 5 Dec 2014 22:27:37 +0000 (17:27 -0500)]
4293: Node Manager shuts down nodes that fail to boot.
This helps Node Manager detect and correct when a node fails to
bootstrap.
Brett Smith [Fri, 5 Dec 2014 22:45:13 +0000 (17:45 -0500)]
4380: Node Manager SLURM dispatcher proceeds from more states.
Per discussion with Ward. Our main concern is that Node Manager
shouldn't shut down nodes that are doing work. We feel comfortable
broadening the definition of "not doing work" to this set of states.
Tom Clegg [Wed, 10 Dec 2014 07:15:13 +0000 (02:15 -0500)]
Merge branch '3781-browser-upload' closes #3781
Tom Clegg [Wed, 10 Dec 2014 05:54:23 +0000 (00:54 -0500)]
3781: Fix test that assumes only one empty collection is readable.
Wait longer for browser timeout in upload-fail test.
Tom Clegg [Wed, 10 Dec 2014 05:00:51 +0000 (00:00 -0500)]
3781: Merge branch 'master' into 3781-browser-upload
Radhika Chippada [Wed, 10 Dec 2014 01:31:02 +0000 (20:31 -0500)]
4754: move search test into browsing_test.rb instead of having its own file.
Radhika Chippada [Tue, 9 Dec 2014 21:57:06 +0000 (16:57 -0500)]
4754: search_test assertions
Tom Clegg [Tue, 9 Dec 2014 21:44:50 +0000 (16:44 -0500)]
3781: Add singletest function.
Tom Clegg [Tue, 9 Dec 2014 21:44:00 +0000 (16:44 -0500)]
3781: Add test cases: empty files, renaming, and error reporting.
Radhika Chippada [Tue, 9 Dec 2014 21:18:50 +0000 (16:18 -0500)]
4754: add rails-perftest and ruby-prof gems to enable performance benchmarking and add search_test.rb
Tim Pierce [Mon, 8 Dec 2014 18:53:02 +0000 (13:53 -0500)]
4499: Normalize manifest in one_task_per_input_file
* arvados.job_setup.one_task_per_input_file now calls cr.normalize()
before creating tasks.
* Added unit test in test_sdk.py to confirm that the expected number of
tasks are created when called on a normalized manifest.
Brett Smith [Tue, 9 Dec 2014 15:21:28 +0000 (10:21 -0500)]
4027: Update arvados-cli in API server bundle.
Refs #4027.
Brett Smith [Tue, 9 Dec 2014 15:14:30 +0000 (10:14 -0500)]
Merge branch '4027-crunch-sdk-install-wip'
Closes #4027, #4667.
Brett Smith [Mon, 8 Dec 2014 15:45:23 +0000 (10:45 -0500)]
4027: crunch-job logs its own version information.
By request in code review, to help detect situations where
crunch-dispatch and crunch-job are out of sync.
Brett Smith [Mon, 24 Nov 2014 21:55:38 +0000 (16:55 -0500)]
4027: Crunch installs jobs' requested arvados_sdk_version.
* crunch-dispatch fetches the requested SDK version into its internal
git repository, just like it does for the Crunch script. Refactored
crunch-dispatch to make that code reusable.
* crunch-job's main script archives the sdk subdirectory as of that
commit, sending it along to compute nodes in the same .tar as the
Crunch script, under .arvados.sdk.
* crunch-job's __DATA__ dispatch section looks for the SDK under
.arvados.sdk, and installs it as much as possible.
Since I was messing with it so much already, I changed the semantics
of crunch-job's __DATA__ section: it is now either in installation
mode or run mode, based on whether there's anything in @ARGV. I
confirmed that this is consistent with current calls to the section.
Brett Smith [Mon, 8 Dec 2014 23:15:39 +0000 (18:15 -0500)]
4027: arvados/jobs includes virtualenv.
This lets you use the arvados/jobs image with the arvados_sdk_version
feature of Crunch.
Brett Smith [Mon, 24 Nov 2014 20:53:44 +0000 (15:53 -0500)]
4027: Bugfix update-gitolite.rb in Docker.
* Load a YAML library.
* Support ARVADOS_API_HOST_INSECURE, and set it in normal Docker use.
Brett Smith [Mon, 24 Nov 2014 20:53:00 +0000 (15:53 -0500)]
4027: Revamp SSH use in our Docker images.
* Don't install or run SSH in most of our Docker images. `docker
exec` is now preferred to inspect running images.
* Do run SSH on the API server, always, for Gitolite.
There is a feature regression here: the user's SSH key is not
automatically installed on the shell account. This needs to be fixed
another way. In the meantime, it's not difficult to run
`docker exec -ti --user=self shell /bin/bash`, and you can clone the
repository from the host system.
Tom Clegg [Tue, 9 Dec 2014 08:37:48 +0000 (03:37 -0500)]
3781: Fix trigger() usage: second argument is an array of handler args.
Tom Clegg [Tue, 9 Dec 2014 08:02:15 +0000 (03:02 -0500)]
3781: Fix progress% (100, not NaN) and manifest format (>=1 data locator) for zero-byte files.
Tim Pierce [Mon, 8 Dec 2014 22:02:33 +0000 (17:02 -0500)]
Merge branch '4269-no-collection-uuid-in-script-params'
Refs #4269.
Tim Pierce [Mon, 8 Dec 2014 21:44:17 +0000 (16:44 -0500)]
4269: clean up uuid regex matching
Code review feedback:
* Improved name for validation "no_collection_uuids" to
"ensure_no_collection_uuids_in_script_params"
* Added ArvadosModel.uuid_regex (along the lines of uuid_like_pattern)
and substituted it for hardcoded uuid regexes throughout the code.
Radhika Chippada [Mon, 8 Dec 2014 21:34:05 +0000 (16:34 -0500)]
closes #4477
closes #4719
Merge branch '4477-no-job-log'
Tom Clegg [Mon, 8 Dec 2014 20:26:52 +0000 (15:26 -0500)]
3781: Go to "Done!" state when the last upload completes despite a late call to stop().
Tom Clegg [Mon, 8 Dec 2014 18:59:45 +0000 (13:59 -0500)]
3781: Fix use of committed flag. That is now called state==="Done".
Tom Clegg [Mon, 8 Dec 2014 18:58:25 +0000 (13:58 -0500)]
3781: Fix exaggerated claims of being finished.
Tom Clegg [Mon, 8 Dec 2014 18:49:27 +0000 (13:49 -0500)]
3781: Merge branch 'master' into 3781-browser-upload
Tom Clegg [Sun, 7 Dec 2014 23:09:00 +0000 (18:09 -0500)]
Reset listener=nil before running main() from test cases, so
waitForListener() does not get confused by listener!=nil left over
from previous tests. Fixes intermittent test failures.
refs #3828
Tom Clegg [Sun, 7 Dec 2014 08:06:04 +0000 (03:06 -0500)]
4533: Wait up to 10s for "lock tables". refs #4533
Tom Clegg [Sat, 6 Dec 2014 02:13:31 +0000 (21:13 -0500)]
3781: Update tests.
Tom Clegg [Sat, 6 Dec 2014 01:46:05 +0000 (20:46 -0500)]
3781: Merge branch 'master' into 3781-browser-upload
Tom Clegg [Sat, 6 Dec 2014 01:36:23 +0000 (20:36 -0500)]
3781: Add ng-cloak style.
Tom Clegg [Sat, 6 Dec 2014 01:02:28 +0000 (20:02 -0500)]
3781: Add Uploaded state, fix handling of Pause during appendToCollection.
Tom Clegg [Fri, 5 Dec 2014 23:00:40 +0000 (18:00 -0500)]
3781: Do not portray "stopped" state as an error if it was reached by clicking Pause.
Tom Clegg [Fri, 5 Dec 2014 22:45:05 +0000 (17:45 -0500)]
3781: Tweak link text. Remove redundant title attributes.
Tom Clegg [Fri, 5 Dec 2014 18:25:12 +0000 (13:25 -0500)]
Merge branch '4156-no-gemfile-lock-for-gem' refs #4156
Tom Clegg [Fri, 5 Dec 2014 18:24:49 +0000 (13:24 -0500)]
4533: Lock all tables, not just the ones with fixtures. refs #4533
Tom Clegg [Fri, 5 Dec 2014 18:07:48 +0000 (13:07 -0500)]
3781: Fix more {==,!=} -> {===,!==}.
Peter Amstutz [Fri, 5 Dec 2014 15:44:07 +0000 (10:44 -0500)]
Merge branch '4314-trigger-job-update' closes #4314
Radhika Chippada [Fri, 5 Dec 2014 15:15:44 +0000 (10:15 -0500)]
closes #4559
Merge branch '4559-long-component-names'
Radhika Chippada [Fri, 5 Dec 2014 15:14:42 +0000 (10:14 -0500)]
4559: missing quote
Radhika Chippada [Fri, 5 Dec 2014 15:10:01 +0000 (10:10 -0500)]
Merge branch 'master' into 4559-long-component-names
Radhika Chippada [Fri, 5 Dec 2014 14:58:04 +0000 (09:58 -0500)]
closes #4638
Merge branch '4638-ssh-notification'
Radhika Chippada [Fri, 5 Dec 2014 14:57:39 +0000 (09:57 -0500)]
Merge branch 'master' into 4638-ssh-notification
Radhika Chippada [Fri, 5 Dec 2014 14:57:12 +0000 (09:57 -0500)]
4638: update test to reflect link text change.
Radhika Chippada [Fri, 5 Dec 2014 14:34:32 +0000 (09:34 -0500)]
closes #4638
Merge branch '4638-ssh-notification'
Radhika Chippada [Fri, 5 Dec 2014 14:33:33 +0000 (09:33 -0500)]
4638: update link text
Radhika Chippada [Fri, 5 Dec 2014 14:22:53 +0000 (09:22 -0500)]
Merge branch 'master' into 4638-ssh-notification
Tom Clegg [Fri, 5 Dec 2014 06:49:26 +0000 (01:49 -0500)]
4465: Link to arvados.org revision history instead of github.com code view.
Also, remove spurious helper inclusions, and fix 'locally modified'
detection (it was broken because "" is truthy).
refs #4465
Tom Clegg [Thu, 4 Dec 2014 22:58:51 +0000 (17:58 -0500)]
3781: One less Regexp.
Tom Clegg [Thu, 4 Dec 2014 22:43:49 +0000 (17:43 -0500)]
3781: Use regexp instead of split: avoid making big arrays when working on big manifests.
Tim Pierce [Thu, 4 Dec 2014 22:12:57 +0000 (17:12 -0500)]
4269: added job validation forbidding collection uuids
Added Job validation no_collection_uuids, searching recursively through
script_parameters for any field matching a collection uuid pattern.
Radhika Chippada [Thu, 4 Dec 2014 21:38:52 +0000 (16:38 -0500)]
4719: change "There are currently no job in the queue" to "your" queue.
Radhika Chippada [Thu, 4 Dec 2014 21:28:50 +0000 (16:28 -0500)]
4477: don't crash on no job log
Tom Clegg [Thu, 4 Dec 2014 21:24:55 +0000 (16:24 -0500)]
3781: Fix push-to-bottom-when-Done so it works on the last item, too.
Radhika Chippada [Thu, 4 Dec 2014 21:05:27 +0000 (16:05 -0500)]
closes #4525
closes #4694
Merge branch '4525-remove-stale-clippy-code'
Tom Clegg [Thu, 4 Dec 2014 21:00:03 +0000 (16:00 -0500)]
3781: Fix up dropdown: match appearance of other buttons, tweak wording,
remove min-width style (which was added for clippy, but has been
affecting all dropdowns).
Radhika Chippada [Thu, 4 Dec 2014 20:58:00 +0000 (15:58 -0500)]
4525: when dataclass is Class, return attrvalue similar to the Array case.
Radhika Chippada [Thu, 4 Dec 2014 20:23:11 +0000 (15:23 -0500)]
4525: delete assets/stylesheets/selection.css
Tom Clegg [Thu, 4 Dec 2014 20:04:44 +0000 (15:04 -0500)]
3781: Use $.each for simple loops.
Tom Clegg [Thu, 4 Dec 2014 19:59:57 +0000 (14:59 -0500)]
3781: Deobfuscate.
Tom Clegg [Thu, 4 Dec 2014 19:34:23 +0000 (14:34 -0500)]
3781: Use ===, !== instead of ==, !=
Tom Clegg [Thu, 4 Dec 2014 19:03:13 +0000 (14:03 -0500)]
3781: Fix error message, and add actual error detection.
Radhika Chippada [Thu, 4 Dec 2014 18:48:10 +0000 (13:48 -0500)]
4525: link_to to be used when dataclass is a String or Fixnum
Tom Clegg [Thu, 4 Dec 2014 18:39:04 +0000 (13:39 -0500)]
3781: Fix up comments.
Tom Clegg [Thu, 4 Dec 2014 18:34:59 +0000 (13:34 -0500)]
3781: Disable start button when there is nothing to do.
Tom Clegg [Thu, 4 Dec 2014 18:16:27 +0000 (13:16 -0500)]
3781: Report as KiB instead of K.
Radhika Chippada [Thu, 4 Dec 2014 18:32:00 +0000 (13:32 -0500)]
4525: keep link_to in application_helper, which will be used when attr value is a String or Fixnum etc
radhika [Thu, 4 Dec 2014 18:12:23 +0000 (13:12 -0500)]
4525: remove add_form_selection_sources (one more time) and all references.
Tom Clegg [Thu, 4 Dec 2014 18:03:20 +0000 (13:03 -0500)]
3781: Merge branch 'master' into 3781-browser-upload
Conflicts:
apps/workbench/app/assets/javascripts/application.js
apps/workbench/app/views/projects/show.html.erb