Tom Clegg [Fri, 30 Jan 2015 17:36:43 +0000 (12:36 -0500)]
5011: Add replication argument to CollectionWriter.
Tom Clegg [Fri, 30 Jan 2015 20:42:44 +0000 (15:42 -0500)]
Merge branch '5037-python-sdk-thread-safe' refs #5037
Tom Clegg [Fri, 30 Jan 2015 20:40:57 +0000 (15:40 -0500)]
5037: Mention where this cache is, instead of describing what a cache is.
Brett Smith [Fri, 30 Jan 2015 20:24:37 +0000 (15:24 -0500)]
5037: Remove unnecessary cache=False from arv-copy.
Brett Smith [Fri, 30 Jan 2015 20:09:34 +0000 (15:09 -0500)]
5037: Fix race condition in PySDK Websockets test.
This might just be bad luck, but for some reason when testing Tom's
changes I ran into a situation where this test failed because it
started processing the Websocket event about the new human before it
assigned self.h, so the assertion failed. Fix the race condition by
asserting against a thread-aware Queue.
Brett Smith [Fri, 30 Jan 2015 20:24:27 +0000 (15:24 -0500)]
5037: Add test for new PySDK API cache behavior.
Brett Smith [Fri, 30 Jan 2015 18:58:04 +0000 (13:58 -0500)]
Merge branch '4562-crunch-tools-docs-wip'
Closes #4562, #5015.
Brett Smith [Fri, 30 Jan 2015 16:23:11 +0000 (11:23 -0500)]
4562: Add Crunch tools overview to the documentation.
Tom Clegg [Fri, 30 Jan 2015 18:20:50 +0000 (13:20 -0500)]
5037: Remove connection pool. Now, api(cache=False) refers only to the discovery document cache.
Peter Amstutz [Fri, 30 Jan 2015 16:58:31 +0000 (11:58 -0500)]
4904: Fix documentation issues. Add comments to arv-web.py.
Peter Amstutz [Fri, 30 Jan 2015 16:10:39 +0000 (11:10 -0500)]
4904: Handle failure to delete non-existent cidfile. Fix docker_image in sample-static-page.
Peter Amstutz [Fri, 30 Jan 2015 16:03:27 +0000 (11:03 -0500)]
4904: Finally figured out a (hopefully) reliable way of sending SIGHUP to
service inside Docker container to get it to refresh.
Tom Clegg [Fri, 30 Jan 2015 07:26:05 +0000 (02:26 -0500)]
4472: Include output of failed tasks when generating job output manifest.
Peter Amstutz [Thu, 29 Jan 2015 22:13:25 +0000 (17:13 -0500)]
4904: Eliminate downtime switching collections.
* Now re-uses CollectionDirectory and loads new collection contents instead of
unmounting and remounting. Now sends sighup instead of restarting Docker if
the image is the same. Almost no downtime switching collections unless Docker
image changes as well.
* Refactor into functions instead executing directly as a module.
* Use arvados.arv-web logger
Radhika Chippada [Thu, 29 Jan 2015 18:13:16 +0000 (13:13 -0500)]
4523: full-text search is not supported for individual columns and only 'any' is supported.
Peter Amstutz [Thu, 29 Jan 2015 15:08:31 +0000 (10:08 -0500)]
Merge branch 'master' into 4904-arv-web
Radhika Chippada [Thu, 29 Jan 2015 02:59:30 +0000 (21:59 -0500)]
4523: full-text search migration script renamed
Radhika Chippada [Thu, 29 Jan 2015 02:56:18 +0000 (21:56 -0500)]
Merge branch 'master' into 4523-full-text-search
Radhika Chippada [Thu, 29 Jan 2015 02:56:01 +0000 (21:56 -0500)]
4523: prepare to merge master into branch
Radhika Chippada [Thu, 29 Jan 2015 01:45:16 +0000 (20:45 -0500)]
closes #3686
Merge branch '3686-sharing-repositories'
Radhika Chippada [Thu, 29 Jan 2015 01:43:03 +0000 (20:43 -0500)]
Merge branch 'master' into 3686-sharing-repositories
Radhika Chippada [Thu, 29 Jan 2015 01:41:32 +0000 (20:41 -0500)]
3686: correct one test assertion and refine some other assertions.
Tom Clegg [Wed, 28 Jan 2015 22:51:35 +0000 (17:51 -0500)]
Fix preview pane disappearing on narrow displays. closes #4918
Brett Smith [Wed, 28 Jan 2015 22:37:28 +0000 (17:37 -0500)]
Merge branch '5074-ruby-sdk-discovery-cache-wip'
Closes #5074, #5091.
Brett Smith [Tue, 27 Jan 2015 21:28:30 +0000 (16:28 -0500)]
5074: CLI SDK uses Google API client extensions from Ruby SDK.
Brett Smith [Tue, 27 Jan 2015 21:22:35 +0000 (16:22 -0500)]
5074: Improve discovery document caching in Ruby SDK.
* Report a warning if there's an error reading or parsing a cached
discovery document.
* Cache discovery documents to a tempfile and rename, to reduce the
chances that we'll write corrupted caches due to I/O errors.
* Make this extension a separate module that can be loaded by users
like the CLI SDK.
* Tighten exception handling throughout.
Radhika Chippada [Wed, 28 Jan 2015 21:48:37 +0000 (16:48 -0500)]
3686: add unit and controller tests for repository updates
Radhika Chippada [Wed, 28 Jan 2015 18:43:25 +0000 (13:43 -0500)]
3686: update the repository row to offer an exclusive Share link than make the repo name clickable.
Radhika Chippada [Wed, 28 Jan 2015 18:29:44 +0000 (13:29 -0500)]
3686: verify repositories testing uses hard coded repo info.
Radhika Chippada [Wed, 28 Jan 2015 16:11:04 +0000 (11:11 -0500)]
Merge branch 'master' into 3686-sharing-repositories
Radhika Chippada [Wed, 28 Jan 2015 16:07:12 +0000 (11:07 -0500)]
closes #4902
Merge branch '4902-use-fixture-to-rerun-pipelines'
Radhika Chippada [Wed, 28 Jan 2015 16:06:33 +0000 (11:06 -0500)]
Merge branch 'master' into 4902-use-fixture-to-rerun-pipelines
Radhika Chippada [Wed, 28 Jan 2015 15:48:10 +0000 (10:48 -0500)]
Merge branch 'master' into 3686-sharing-repositories
Radhika Chippada [Wed, 28 Jan 2015 00:42:11 +0000 (19:42 -0500)]
refs #4878
Merge branch '4878-rerun-job'
Radhika Chippada [Wed, 28 Jan 2015 00:40:53 +0000 (19:40 -0500)]
4878: add back the tab buttons partial.
Brett Smith [Tue, 27 Jan 2015 23:25:01 +0000 (18:25 -0500)]
Merge branch '4878-rerun-job-bcs-wip'
Closes #4878, #5067.
Brett Smith [Tue, 27 Jan 2015 23:09:20 +0000 (18:09 -0500)]
4878: Refactor Workbench "Re-run job" button for more code reuse.
* Avoid adding new routes: add the modal directly to the job show
page, and submit the new work with the existing job creation route.
* Fix id references; e.g., for labels.
Radhika Chippada [Tue, 27 Jan 2015 21:43:33 +0000 (16:43 -0500)]
4902: re-run pipeline instance tests use fixtures instead of creating a new pipeline to be re-run.
Radhika Chippada [Tue, 27 Jan 2015 20:59:03 +0000 (15:59 -0500)]
4878: update the popup display to not display radio button when only "use same" option is available.
Radhika Chippada [Tue, 27 Jan 2015 20:55:53 +0000 (15:55 -0500)]
Merge branch 'master' into 4878-rerun-job
Radhika Chippada [Tue, 27 Jan 2015 18:43:18 +0000 (13:43 -0500)]
refs #4523
Merge branch '4523-search-index'
Radhika Chippada [Tue, 27 Jan 2015 18:30:42 +0000 (13:30 -0500)]
Merge branch 'master' into 3686-sharing-repositories
Radhika Chippada [Tue, 27 Jan 2015 18:20:38 +0000 (13:20 -0500)]
4523: a little bit simpler script
Radhika Chippada [Tue, 27 Jan 2015 17:38:42 +0000 (12:38 -0500)]
Merge branch 'master' into 4523-search-index
Brett Smith [Tue, 27 Jan 2015 17:00:41 +0000 (12:00 -0500)]
Merge branch '5087-fix-crunch-sigpipe-wip'
Closes #5087, #5089.
Brett Smith [Mon, 26 Jan 2015 19:02:56 +0000 (14:02 -0500)]
5087: crunch-job installer feeds tar incrementally.
When the input we give to tar is large enough (greater than 4-5MiB),
writing it all in one shot causes tar to die, and crunch-job to get
SIGPIPE. Prevent this by feeding the input to tar in a series of
smaller writes.
Radhika Chippada [Tue, 27 Jan 2015 14:23:37 +0000 (09:23 -0500)]
4878: show only the re-run popup option
Radhika Chippada [Mon, 26 Jan 2015 21:17:28 +0000 (16:17 -0500)]
Merge branch 'master' into 4878-rerun-job
Ward Vandewege [Mon, 26 Jan 2015 20:51:07 +0000 (15:51 -0500)]
Wording tweaks for doc.arvados.org.
No issue #
Phil Hodgson [Mon, 26 Jan 2015 16:47:08 +0000 (17:47 +0100)]
4232: remove "dependencies" entries from examples in the tutorials if the API is no longer going to be returning them
Ward Vandewege [Mon, 26 Jan 2015 16:05:12 +0000 (11:05 -0500)]
Merge branch '4340-arv-ws-fix-ssl-warning'
Closes #4340
Ward Vandewege [Mon, 26 Jan 2015 16:04:50 +0000 (11:04 -0500)]
Merge branch 'master' into 4340-arv-ws-fix-ssl-warning
Ward Vandewege [Mon, 26 Jan 2015 16:04:09 +0000 (11:04 -0500)]
A few tweaks based on review feedback.
refs #4340
Phil Hodgson [Mon, 26 Jan 2015 16:03:50 +0000 (17:03 +0100)]
4232: remove uselessness (commented out code and other wastes of spacetime)
Tim Pierce [Mon, 26 Jan 2015 15:52:49 +0000 (10:52 -0500)]
Merge branch '5010-trash-button-for-collections'
Fixes #5010.
Tim Pierce [Mon, 26 Jan 2015 15:24:40 +0000 (10:24 -0500)]
5010: fixed integration test
Fixed a failing integration test that checked for the presence of a
collection in the Home project after being deleted. Removed the
assertion that checked the Home project post-deletion.
Phil Hodgson [Mon, 26 Jan 2015 15:08:47 +0000 (16:08 +0100)]
Merge branch 'master' into 4232-slow-pipes-n-jobs
Radhika Chippada [Sun, 25 Jan 2015 03:23:06 +0000 (22:23 -0500)]
3686: improve manage account page test to click on the repository link.
Radhika Chippada [Sun, 25 Jan 2015 02:50:00 +0000 (21:50 -0500)]
3686: enhance manage account test to also verify a writable repository.
Radhika Chippada [Sat, 24 Jan 2015 18:36:33 +0000 (13:36 -0500)]
3686: repository.editable_attributes returns an empty array when the user is not an admin.
Radhika Chippada [Sat, 24 Jan 2015 18:07:42 +0000 (13:07 -0500)]
3686: when a repository is manageable by a user, make repository name a link in manage_account page. In addition, do not offer Attributes tab in repository page if the user is not an admin.
Ward Vandewege [Fri, 23 Jan 2015 22:00:37 +0000 (17:00 -0500)]
arv-ws should prefer system's CA certificates (if available).
closes #4340
Ward Vandewege [Fri, 23 Jan 2015 21:55:30 +0000 (16:55 -0500)]
Merge branch '0000-workbench-user-profile-wording-changes'
No issue #
Ward Vandewege [Fri, 23 Jan 2015 19:21:17 +0000 (14:21 -0500)]
Merge branch 'master' into 0000-workbench-user-profile-wording-changes
Nancy Ouyang [Fri, 23 Jan 2015 19:15:35 +0000 (14:15 -0500)]
refs #4926 Merge branch '4926-getting-started'
Nancy Ouyang [Fri, 23 Jan 2015 19:11:37 +0000 (14:11 -0500)]
more typos
Nancy Ouyang [Fri, 23 Jan 2015 18:50:28 +0000 (13:50 -0500)]
minor typos
Tim Pierce [Fri, 23 Jan 2015 16:55:04 +0000 (11:55 -0500)]
5010: updated functional tests for new trash behavior
Renamed "project admin can remove items from the project" to "project
admin can remove collections from the project" and updated it to verify
that the target collection has actually been made inaccessible to API
queries.
Added "project admin can remove items from project other than
collections" test to verify that objects which don't support expires_at
continue to exhibit the old behavior.
Radhika Chippada [Fri, 23 Jan 2015 16:41:21 +0000 (11:41 -0500)]
4878: now the test works!
Radhika Chippada [Fri, 23 Jan 2015 16:25:55 +0000 (11:25 -0500)]
4878: add integration test for Re-run job with options.
Radhika Chippada [Fri, 23 Jan 2015 14:28:47 +0000 (09:28 -0500)]
Merge branch 'master' into 4878-rerun-job
Radhika Chippada [Fri, 23 Jan 2015 14:28:02 +0000 (09:28 -0500)]
4878: rerun job with options popup
Tim Pierce [Thu, 22 Jan 2015 22:08:20 +0000 (17:08 -0500)]
Merge branch '4889-crunch-deadlock'
Fixes #4889.
Tim Pierce [Thu, 22 Jan 2015 22:05:36 +0000 (17:05 -0500)]
4889: improve error message, unit test
Per review in #4889-17:
Updated the CopyPipeToChan error message to be more descriptive, for the
benefit of anyone reading log output.
Corrected the test to confirm that the error message is received even if
the child process does not close the stderr log (which matches the usage
patterns in production).
Ward Vandewege [Thu, 22 Jan 2015 21:37:40 +0000 (16:37 -0500)]
Merge branch 'master' into 0000-workbench-user-profile-wording-changes
Nancy Ouyang [Thu, 22 Jan 2015 20:52:08 +0000 (15:52 -0500)]
4926: typos & rewording
Tim Pierce [Thu, 22 Jan 2015 20:40:46 +0000 (15:40 -0500)]
4889: added CopyPipeToChan unit test
Added TestCopyPipeToChanLongLines test to confirm that when
CopyPipeToChan attempts to read a line too long for bufio.Scanner, that
it generates an error message on the output channel.
Radhika Chippada [Thu, 22 Jan 2015 18:40:08 +0000 (13:40 -0500)]
Merge branch 'master' into 4523-search-index
Radhika Chippada [Thu, 22 Jan 2015 18:37:37 +0000 (13:37 -0500)]
4523: add a new migration script that invokes search_index migration down and up methods when a search_index with description is found (due to an earlier migration of search_index with descriptions).
Radhika Chippada [Thu, 22 Jan 2015 17:06:53 +0000 (12:06 -0500)]
refs #4523
Merge branch '4523-search-index'
Radhika Chippada [Thu, 22 Jan 2015 16:36:00 +0000 (11:36 -0500)]
4523: do not include descriptions in search index and update tests accordingly.
Peter Amstutz [Thu, 22 Jan 2015 13:55:14 +0000 (08:55 -0500)]
Merge branch 'master' into 4904-arv-web
Peter Amstutz [Thu, 22 Jan 2015 13:55:01 +0000 (08:55 -0500)]
Revert "4838: Add --set-executable-bit option to make all files from mounted collections be executable."
This reverts commit
b97ac7f96234cbbb491bdbaade840ab50802f357.
Radhika Chippada [Thu, 22 Jan 2015 13:45:38 +0000 (08:45 -0500)]
4523: a few more test cases
Radhika Chippada [Thu, 22 Jan 2015 05:32:42 +0000 (00:32 -0500)]
Merge branch 'master' into 4523-full-text-search
Radhika Chippada [Thu, 22 Jan 2015 05:31:11 +0000 (00:31 -0500)]
4523: add full text search index to collections, groups, jobs, pipeline_instances and pipeline_templates.
Tim Pierce [Wed, 21 Jan 2015 20:50:56 +0000 (15:50 -0500)]
5010: remove_items sets the expired_at date if available
On objects which support expired_at, remove_items will set that date
rather than moving them out of the current project.
Tim Pierce [Wed, 21 Jan 2015 20:18:16 +0000 (15:18 -0500)]
4889: close the child stderr pipe before returning
Updated CopyPipeToChan to close the child's stderr pipe before
returning, so that even if it returns for some reason other than
EOF (e.g. line too long) the child will not deadlock on writing stderr
output.
Tom Clegg [Wed, 21 Jan 2015 20:03:34 +0000 (15:03 -0500)]
Merge branch '3021-api-performance' refs #3021
Brett Smith [Wed, 21 Jan 2015 19:11:00 +0000 (14:11 -0500)]
4967: Fix API server Gemfile.
I'm kind of at a loss to explain what happened here. Refs #4967.
Brett Smith [Wed, 21 Jan 2015 18:40:11 +0000 (13:40 -0500)]
4967: API server bundle uses bugfixed crunch-job.
Refs #4967, #4970.
Brett Smith [Wed, 21 Jan 2015 18:38:28 +0000 (13:38 -0500)]
Merge branch '4967-crunch-mount-cleanup-wip'
Closes #4967, #4970, #5039.
Brett Smith [Wed, 21 Jan 2015 16:38:18 +0000 (11:38 -0500)]
4967: crunch-job unmounts old Keep mounts more robustly.
The previous version looked for mounts under $JOB_WORK before
unmounting anything. We long ago started mounting under $TASK_WORK,
so unmounting hasn't been working for a while. This version unmounts
every FUSE mount with "keep" in the path, so it will be much more
flexible.
I also changed the cleanup to use bash -e, so the logs are more likely
to indicate if there was trouble during the cleanup step.
Nancy Ouyang [Wed, 21 Jan 2015 05:10:05 +0000 (00:10 -0500)]
4926: Added 'getting started' section with three image galleries.
Peter Amstutz [Wed, 21 Jan 2015 15:51:51 +0000 (10:51 -0500)]
Merge branch '5016-ctrl-c-arv-ws' closes #5016
Radhika Chippada [Wed, 21 Jan 2015 04:15:31 +0000 (23:15 -0500)]
4523: use file_names column instead of manifest_text column for full text search of collections.
Radhika Chippada [Tue, 20 Jan 2015 20:05:43 +0000 (15:05 -0500)]
Merge branch 'master' into 4523-full-text-search
Brett Smith [Tue, 20 Jan 2015 19:52:29 +0000 (14:52 -0500)]
5029: API server uses bugfixed crunch-job.
Refs #5029.
Brett Smith [Tue, 20 Jan 2015 19:42:48 +0000 (14:42 -0500)]
5029: Fix crunch-job logging when SDK requested+virtualenv unavailable.
* Properly concatenate the message.
* Query and log installed SDK packages in this scenario, since we
might fall back to what's available in the Docker image.
Closes #5029.
Radhika Chippada [Tue, 20 Jan 2015 18:37:04 +0000 (13:37 -0500)]
refs #4926
Merge branch '4926-browser-based-upload'