radhika [Thu, 28 Aug 2014 20:05:28 +0000 (16:05 -0400)]
Merge branch 'master' into 3637-copy-selections
radhika [Thu, 28 Aug 2014 19:38:35 +0000 (15:38 -0400)]
3637: refactor code for better maintenance.
Peter Amstutz [Thu, 28 Aug 2014 19:25:35 +0000 (15:25 -0400)]
Fix arv-put tests refs #3709
radhika [Thu, 28 Aug 2014 19:20:03 +0000 (15:20 -0400)]
Merge branch 'master' into 3637-copy-selections
radhika [Thu, 28 Aug 2014 19:19:05 +0000 (15:19 -0400)]
3637: add copy selected items functionality to project selection dropdown.
Peter Amstutz [Thu, 28 Aug 2014 18:49:12 +0000 (14:49 -0400)]
Merge branch '3719-improve-subst-error-reporting' closes #3719
Peter Amstutz [Thu, 28 Aug 2014 18:48:49 +0000 (14:48 -0400)]
3719: Python style/wording fixes.
Peter Amstutz [Thu, 28 Aug 2014 18:42:03 +0000 (14:42 -0400)]
Merge branch '3709-arv-put-print-uuid' closes #3709
Peter Amstutz [Thu, 28 Aug 2014 17:58:24 +0000 (13:58 -0400)]
Fix nil dereference causing a fiddlesticks on the collections index page. no issue #
Peter Amstutz [Thu, 28 Aug 2014 17:35:12 +0000 (13:35 -0400)]
Merge branch 'master' into 3709-arv-put-print-uuid
Tom Clegg [Thu, 28 Aug 2014 17:33:28 +0000 (13:33 -0400)]
Complain and fail if exec() returns. No issue #
Tom Clegg [Thu, 28 Aug 2014 17:18:48 +0000 (13:18 -0400)]
Pass stdin to child process. closes #3751
Peter Amstutz [Thu, 28 Aug 2014 15:20:35 +0000 (11:20 -0400)]
3709: arv-put now prints collection uuid by default. Add --portable-data-hash
to arv-put to get the old behavior (print PDH). Crunch-job uses arv-put
--portable-data-hash to get the PDH to put in the log field. Crunch-job logs
both PDH and collection UUID.
Tom Clegg [Thu, 28 Aug 2014 15:06:38 +0000 (11:06 -0400)]
Run given command even if src tree already installed. No issue #
Peter Amstutz [Thu, 28 Aug 2014 14:06:37 +0000 (10:06 -0400)]
3719: Robust-put uses run-command logger.
Peter Amstutz [Thu, 28 Aug 2014 14:02:15 +0000 (10:02 -0400)]
3719: run-command uses its own logger instead of the default Python logger to
avoid cross talk with badly behaved modules.
radhika [Thu, 28 Aug 2014 14:02:14 +0000 (10:02 -0400)]
closes #3339
Merge branch '3339-truncate-project-descriptions'
radhika [Thu, 28 Aug 2014 14:01:38 +0000 (10:01 -0400)]
3339: fix typo in test
radhika [Thu, 28 Aug 2014 13:48:47 +0000 (09:48 -0400)]
Merge branch 'master' into 3339-truncate-project-descriptions
Peter Amstutz [Thu, 28 Aug 2014 13:30:25 +0000 (09:30 -0400)]
Remove assertion testing for obsolete output_is_persistent field. refs #3342
radhika [Thu, 28 Aug 2014 13:29:21 +0000 (09:29 -0400)]
Merge branch 'master' into 3339-truncate-project-descriptions
Peter Amstutz [Thu, 28 Aug 2014 13:25:52 +0000 (09:25 -0400)]
3719: Raise more specific SubstitutionError instead of generic exception on
user syntax errors. Don't print stack trace on SubstitutionError.
Peter Amstutz [Thu, 28 Aug 2014 12:53:12 +0000 (08:53 -0400)]
Set Gemfile version target for arvados-cli to correct version. refs #3342
radhika [Thu, 28 Aug 2014 12:05:49 +0000 (08:05 -0400)]
3339: some refactoring of the render textile impl. improve the test that verifies project description.
Tom Clegg [Wed, 27 Aug 2014 21:44:20 +0000 (17:44 -0400)]
Revert arvados gems to versions that actually exist. refs #3342
Peter Amstutz [Wed, 27 Aug 2014 21:04:24 +0000 (17:04 -0400)]
Merge branch '3342-pipeline-output-current-project' closes #3342
Peter Amstutz [Wed, 27 Aug 2014 21:03:58 +0000 (17:03 -0400)]
3342: Fix syntax error in pipeline_instance.rb. Restore code in crunch-job
that reads manifest text from arv-get pipe.
Tim Pierce [Wed, 27 Aug 2014 20:59:11 +0000 (16:59 -0400)]
Merge branch '3414-keep-pull-handler'
Closes #3414.
Tim Pierce [Wed, 27 Aug 2014 20:56:17 +0000 (16:56 -0400)]
3414: fix log typo
%s -> %v
Peter Amstutz [Wed, 27 Aug 2014 19:02:20 +0000 (15:02 -0400)]
3342: Handle case in PipelineInstance#friendly_link_name where
pipeline_template_uuid doesn't return a PipelineTemplate. Removed unnecessary
code from crunch-job to calculate md5 hash of manifest_text (API server doesn't
require md5 hash to be provided with collection creation any more.)
radhika [Wed, 27 Aug 2014 18:24:33 +0000 (14:24 -0400)]
3339: update test to verify textile description in my projects panel in dashboard.
radhika [Wed, 27 Aug 2014 16:30:53 +0000 (12:30 -0400)]
3339: render truncated textile descriptions in dashboard
Tim Pierce [Wed, 27 Aug 2014 15:50:39 +0000 (11:50 -0400)]
3414: update comment for code review
Peter Amstutz [Wed, 27 Aug 2014 14:38:08 +0000 (10:38 -0400)]
3342: Update documentation. Add "output_name", remove "output_is_persistent".
Peter Amstutz [Wed, 27 Aug 2014 13:33:07 +0000 (09:33 -0400)]
3342: Tweak pipeline component status rendering. Support "output_name":false
to specify no output should be added to the current project.
Peter Amstutz [Wed, 27 Aug 2014 13:07:30 +0000 (09:07 -0400)]
3342: Fix links to log files to use portable_data_hash. Remove spurious puts.
Improve error logging.
Tim Pierce [Wed, 27 Aug 2014 01:18:51 +0000 (21:18 -0400)]
3414: rename replicator to pull_list
Renamed replicator.Replicator to pull_list.Manager.
Tim Pierce [Wed, 27 Aug 2014 00:50:01 +0000 (20:50 -0400)]
3414: update for code review
Added logging for pull lists. Unsuccessful pull lists are logged with
an error, successful ones are logged with the new pull list.
Renamed the Replicator interface with GetList and SetList.
Tom Clegg [Wed, 27 Aug 2014 00:26:02 +0000 (20:26 -0400)]
Merge branch '3354-render-textile' closes #3354
Tom Clegg [Wed, 27 Aug 2014 00:13:41 +0000 (20:13 -0400)]
3354: Merge branch 'master' into 3354-render-textile
Conflicts:
apps/workbench/app/assets/stylesheets/application.css.scss
apps/workbench/app/helpers/application_helper.rb
apps/workbench/app/models/group.rb
Tom Clegg [Tue, 26 Aug 2014 22:57:37 +0000 (18:57 -0400)]
Fix label for API endpoint. Re-order fields. refs #3112
Tom Clegg [Tue, 26 Aug 2014 22:51:53 +0000 (18:51 -0400)]
Ensure source_version is a string, even when it consists entirely of decimal digits. refs #3112
Tom Clegg [Tue, 26 Aug 2014 18:15:15 +0000 (14:15 -0400)]
Run the task setup script inside the container (if any), instead of
running setup on the host, using bind-mount for CRUNCH_SRC, and
assuming other directories have already been set up in the docker
image.
No issue #
Tom Clegg [Tue, 26 Aug 2014 23:51:26 +0000 (19:51 -0400)]
Merge branch '3627-selectable-projects' closes #3627
Peter Amstutz [Tue, 26 Aug 2014 21:12:35 +0000 (17:12 -0400)]
3342: Fixing outputs
Peter Amstutz [Tue, 26 Aug 2014 19:47:08 +0000 (15:47 -0400)]
3342: Removing remaining traces of output_is_persistent. Added code in
arv-run-pipeline-instance to create collections owned by appropriate project.
radhika [Tue, 26 Aug 2014 19:32:41 +0000 (15:32 -0400)]
refs #3620
Merge branch '3620-admin-only-gear-menu'
radhika [Tue, 26 Aug 2014 19:28:23 +0000 (15:28 -0400)]
3620: correct indentation when current user is available
Tim Pierce [Fri, 22 Aug 2014 15:12:53 +0000 (11:12 -0400)]
3414: adding PullHandler and Replicator
Added PullHandler and a "replicator" package to handle "PUT /pull" requests.
PUT /pull requests are routed to PullHandler, which authenticates the
request and validates the JSON in the request body. Valid requests are
sent to the replicator.
The Keepstore replicator runs a goroutine which repeatedly listens on
its input channel for a new pull list.
TestPullHandler tests each combination of: request from superuser;
request from ordinary user; properly formatted pull request; improperly
formatted pull request. It checks the state of the replicator when done
to make sure that it has the expected number of pull requests.
3414: add replicator.
radhika [Tue, 26 Aug 2014 18:47:46 +0000 (14:47 -0400)]
closes #3620
Merge branch '3620-admin-only-gear-menu'
radhika [Tue, 26 Aug 2014 18:45:43 +0000 (14:45 -0400)]
Merge branch 'master' into 3620-admin-only-gear-menu
radhika [Tue, 26 Aug 2014 18:45:03 +0000 (14:45 -0400)]
closes #3642
Merge branch '3642-search-for-active-only'
radhika [Tue, 26 Aug 2014 18:42:53 +0000 (14:42 -0400)]
3620: change menu item role from presentation to menuitem for clickable links. w3.org/TR/wai-aria/roles#role_definitions
Peter Amstutz [Tue, 26 Aug 2014 18:07:42 +0000 (14:07 -0400)]
3342: Migration to remove obsolete output_is_persistent column from jobs.
radhika [Tue, 26 Aug 2014 18:04:48 +0000 (14:04 -0400)]
Merge branch 'master' into 3642-search-for-active-only
radhika [Tue, 26 Aug 2014 18:00:05 +0000 (14:00 -0400)]
Merge branch 'master' into 3620-admin-only-gear-menu
radhika [Tue, 26 Aug 2014 17:57:50 +0000 (13:57 -0400)]
closes #3112
Merge branch '3112-report-bug'
radhika [Tue, 26 Aug 2014 17:57:19 +0000 (13:57 -0400)]
Merge branch 'master' into 3112-report-bug
radhika [Tue, 26 Aug 2014 17:56:30 +0000 (13:56 -0400)]
3112: 404 error page default message while reporting issue
Peter Amstutz [Tue, 26 Aug 2014 17:51:42 +0000 (13:51 -0400)]
Fixed missing import in robust_put. no issue #
radhika [Tue, 26 Aug 2014 17:20:43 +0000 (13:20 -0400)]
3112: login_tests works with javascript driver
radhika [Tue, 26 Aug 2014 17:10:23 +0000 (13:10 -0400)]
3112: still the login_tests fails when ran in the entire suite
radhika [Tue, 26 Aug 2014 16:30:26 +0000 (12:30 -0400)]
3112: removed rack_test driver and added selenium driver. still the test "trying to use expired token redirects to login page" fails when the entire suite is tested, but passes when this one test file is executed.
radhika [Tue, 26 Aug 2014 16:10:05 +0000 (12:10 -0400)]
3112: add scrollbar to the report issue popup
radhika [Tue, 26 Aug 2014 15:42:01 +0000 (11:42 -0400)]
Merge branch 'master' into 3112-report-bug
radhika [Tue, 26 Aug 2014 15:40:36 +0000 (11:40 -0400)]
3112: skip filters in actions controller, instead of application controller
Peter Amstutz [Tue, 26 Aug 2014 15:36:12 +0000 (11:36 -0400)]
Merge branch '3136-stale-pipeline-instance-display' closes #3136
radhika [Tue, 26 Aug 2014 15:32:59 +0000 (11:32 -0400)]
3112: no need to reload after sending report.
Brett Smith [Tue, 26 Aug 2014 15:32:10 +0000 (11:32 -0400)]
Merge branch '3147-pysdk-retries'
Closes #3147.
Brett Smith [Tue, 26 Aug 2014 00:58:37 +0000 (20:58 -0400)]
3147: Fix unwanted integer division in KeepClient logs.
Brett Smith [Fri, 22 Aug 2014 17:38:40 +0000 (13:38 -0400)]
3147: Add retry support to Python SDK's KeepClient.
Brett Smith [Fri, 22 Aug 2014 19:57:36 +0000 (15:57 -0400)]
3147: Remove old Keep signing support from Python SDK.
Per Tom.
Brett Smith [Tue, 26 Aug 2014 13:46:46 +0000 (09:46 -0400)]
3147: Add check_http_response_success to Python SDK.
Other parts of the SDK need to end loops based on the result of an
HTTP request. This function puts that logic in one place.
Brett Smith [Tue, 26 Aug 2014 13:46:17 +0000 (09:46 -0400)]
3147: Add RetryLoop to the Python SDK.
This provides a general-purpose mechanism for us to retry all kinds of
operations.
Brett Smith [Thu, 21 Aug 2014 15:13:23 +0000 (11:13 -0400)]
3147: Move fake Python HTTP response generation to arvados_testutil.
Other tests can use this functionality.
Peter Amstutz [Tue, 26 Aug 2014 15:25:01 +0000 (11:25 -0400)]
3136: Use map to correctly get the list of uuids. Check that there is a job
record before trying to use it.
Tom Clegg [Tue, 26 Aug 2014 15:24:32 +0000 (11:24 -0400)]
Fix test. refs #3149
radhika [Tue, 26 Aug 2014 15:17:24 +0000 (11:17 -0400)]
Merge branch 'master' into 3112-report-bug
Tom Clegg [Tue, 26 Aug 2014 15:14:07 +0000 (11:14 -0400)]
Fix migration and api templates that rely on changes that did not end up happening. refs #3036
Tom Clegg [Tue, 26 Aug 2014 15:00:53 +0000 (11:00 -0400)]
Merge branch '3149-server-side-search' closes #3149
Tom Clegg [Tue, 26 Aug 2014 15:00:16 +0000 (11:00 -0400)]
3149: Merge branch 'master' into 3149-server-side-search
Tom Clegg [Tue, 26 Aug 2014 13:49:37 +0000 (09:49 -0400)]
Set up arvados env vars when running arv-normalize. No issue #
Peter Amstutz [Tue, 26 Aug 2014 14:45:17 +0000 (10:45 -0400)]
Merge branch '3036-collection-uuids' closes #3036
Peter Amstutz [Tue, 26 Aug 2014 14:43:41 +0000 (10:43 -0400)]
Merge branch 'master' into 3036-collection-uuids
Conflicts:
services/api/test/fixtures/groups.yml
Peter Amstutz [Tue, 26 Aug 2014 12:48:08 +0000 (08:48 -0400)]
3036: Fix merge conflicts. One python sdk test still fails.
Tom Clegg [Tue, 26 Aug 2014 05:41:53 +0000 (01:41 -0400)]
Move styles out of tab partial. No issue #
Tom Clegg [Tue, 26 Aug 2014 05:29:04 +0000 (01:29 -0400)]
Propagate query params to tab panes. No issue #
Tom Clegg [Tue, 26 Aug 2014 04:20:13 +0000 (00:20 -0400)]
Remove uuid-guessing code from "combine selected files". refs #3504
Tom Clegg [Tue, 26 Aug 2014 03:51:25 +0000 (23:51 -0400)]
Do not blow up in install stage when TASK_WORK is not set. No issue #
Tom Clegg [Tue, 26 Aug 2014 03:26:38 +0000 (23:26 -0400)]
Do not blow up when tmp directory already exists. No issue #
radhika [Tue, 26 Aug 2014 03:16:58 +0000 (23:16 -0400)]
Merge branch '3112-report-bug' into 3642-search-for-active-only
radhika [Tue, 26 Aug 2014 03:16:22 +0000 (23:16 -0400)]
Merge branch '3112-report-bug' into 3620-admin-only-gear-menu
radhika [Tue, 26 Aug 2014 03:12:55 +0000 (23:12 -0400)]
3112: alert left justification
radhika [Tue, 26 Aug 2014 03:09:37 +0000 (23:09 -0400)]
Merge branch 'master' into 3112-report-bug
Tom Clegg [Tue, 26 Aug 2014 02:29:11 +0000 (22:29 -0400)]
3149: Clarify comments. Stick with a-b-c data keys where possible;
when not possible, explain why not.
Tom Clegg [Tue, 26 Aug 2014 01:50:41 +0000 (21:50 -0400)]
Merge branch '3149-filter-any' refs #3149
Tom Clegg [Tue, 26 Aug 2014 01:48:47 +0000 (21:48 -0400)]
3149: Explain what "any" does as a filter attribute.
Tom Clegg [Tue, 26 Aug 2014 01:33:57 +0000 (21:33 -0400)]
Fix test fixtures breaking Workbench tests. refs #3171
radhika [Tue, 26 Aug 2014 01:26:43 +0000 (21:26 -0400)]
Merge branch 'master' into 3112-report-bug
Tom Clegg [Tue, 26 Aug 2014 00:59:37 +0000 (20:59 -0400)]
Do not blow up when stdout!=subprocess.PIPE. no issue #
projects / arvados.git / log