Brett Smith [Tue, 21 Oct 2014 18:13:37 +0000 (14:13 -0400)]
4139: Improve logging in Node Manager poll actors.
Brett Smith [Tue, 21 Oct 2014 15:19:05 +0000 (11:19 -0400)]
4139: Node Manager callback actor avoids redundant delivery calls.
This helps make it more responsive when it receives a shutdown
request.
radhika [Tue, 21 Oct 2014 17:48:35 +0000 (13:48 -0400)]
4227: some more test and fixture updates.
Tom Clegg [Tue, 21 Oct 2014 17:46:00 +0000 (13:46 -0400)]
4266: Tweak long-line handling.
Tom Clegg [Tue, 21 Oct 2014 17:29:05 +0000 (13:29 -0400)]
4266: Fix OOM when stderr has a lot of data with no newlines.
radhika [Tue, 21 Oct 2014 17:28:57 +0000 (13:28 -0400)]
4227: minor test upadtes
Tom Clegg [Tue, 21 Oct 2014 17:05:36 +0000 (13:05 -0400)]
4266: Clean up streambuf.split(newline) loop.
radhika [Tue, 21 Oct 2014 17:00:01 +0000 (13:00 -0400)]
Merge branch 'master' into 4227-date-display
radhika [Tue, 21 Oct 2014 16:56:33 +0000 (12:56 -0400)]
closes #4054
Merge branch '4054-sharing-email'
radhika [Tue, 21 Oct 2014 16:54:32 +0000 (12:54 -0400)]
4091: the test with 200 jobs and 10 pipelines is failing in jenkins env. reduce the number of pipelines to 2 to see if shorter runtime helps.
radhika [Tue, 21 Oct 2014 16:48:35 +0000 (12:48 -0400)]
Merge branch 'master' into 4054-sharing-email
radhika [Tue, 21 Oct 2014 16:47:37 +0000 (12:47 -0400)]
4227: AM / PM indicator fix
Ward Vandewege [Tue, 21 Oct 2014 14:11:43 +0000 (10:11 -0400)]
Arvados python SDK: do not blow up when HOME is not set.
No issue #
Tom Clegg [Mon, 20 Oct 2014 21:30:30 +0000 (17:30 -0400)]
4266: Fix log processing performance.
* Remove "max log table entries per job" limit (and its horrible
memory leak).
* When logs are coming fast, but under all throttle thresholds, group
them into fewer rows in the logs table.
* Optimize performance by making a short code path when any threshold
is exceeded. Now capable of ~200 MiB/s (of 100-character lines) on
lappy386.
* Bring stream buffer back up to a reasonable size, add a comment to
protect it from future style tweaks.
* Simplify time calculations by storing time-to-reopen-throttle
instead of time-throttle-last-opened.
* Log "# bytes skipped" to stderr (sysadmin logs) too, not just the
logs table.
Tim Pierce [Mon, 20 Oct 2014 20:24:07 +0000 (16:24 -0400)]
3699: bug fixes
* abort() should not crash the program because it's calling logging.info
wrong
* if the pipeline description is None, correctly substitute an empty
string in the destination pipeline.
* finish writing collection progress at 100%
Peter Amstutz [Mon, 20 Oct 2014 19:36:36 +0000 (15:36 -0400)]
Merge branch '3787-docker-docs' closes #3787
Peter Amstutz [Mon, 20 Oct 2014 19:35:48 +0000 (15:35 -0400)]
3787: docker group -> @docker@ group for consistency
Peter Amstutz [Mon, 20 Oct 2014 19:23:21 +0000 (15:23 -0400)]
3787: Add note about needing to be in docker group. A few other minor text tweaks.
Tim Pierce [Mon, 20 Oct 2014 18:45:08 +0000 (14:45 -0400)]
3699: bug fix
The re.sub 'repl' function takes a MatchObject as argument, not a
string. Oops.
Also we need to do manifest.splitlines(True) in order to be able to tell
whether the manifest ends with a newline in the first place.
Tim Pierce [Mon, 20 Oct 2014 18:13:37 +0000 (14:13 -0400)]
3699: collection copying bug fixes
From code review #3699-35:
* Updated help text
* Find collection UUIDs and hashes throughout script_parameters even if
buried in command arguments
* Use logger consistently in preference to "print >>sys.stderr"
* isinstance(obj, basestr)
* Fix ensure_unique_name handling
* copy_collection now correctly handles manifests without a trailing
newline
Peter Amstutz [Mon, 20 Oct 2014 18:12:41 +0000 (14:12 -0400)]
3787: Update title, grammar, add "Share Docker images", add job-pipeline-ref.html based on review feedback.
radhika [Mon, 20 Oct 2014 17:49:08 +0000 (13:49 -0400)]
Merge branch 'master' into 4026-project-move-admin
Conflicts:
apps/workbench/test/integration/projects_test.rb
radhika [Mon, 20 Oct 2014 17:34:10 +0000 (13:34 -0400)]
Merge branch 'master' into 4054-sharing-email
Tom Clegg [Mon, 20 Oct 2014 16:34:58 +0000 (12:34 -0400)]
3826: Merge branch 'master' into 3826-crunchstat-netstats
Tom Clegg [Mon, 20 Oct 2014 16:18:48 +0000 (12:18 -0400)]
3826: Fix confusing reuse of variable name.
Tom Clegg [Mon, 20 Oct 2014 16:18:13 +0000 (12:18 -0400)]
3826: Use strconv instead of scanner + sscanf.
Tom Clegg [Mon, 20 Oct 2014 16:10:12 +0000 (12:10 -0400)]
3826: Use global logChan. Use ioutil.ReadFile.
Tom Clegg [Mon, 20 Oct 2014 15:57:27 +0000 (11:57 -0400)]
3826: Clean up slice initialization.
Peter Amstutz [Mon, 20 Oct 2014 15:39:13 +0000 (11:39 -0400)]
4058: Tests for portable data hash redirection and multiple matches page.
radhika [Mon, 20 Oct 2014 15:25:19 +0000 (11:25 -0400)]
closes #4062
Merge branch '4062-infinite-scroll-repeat-TC'
Tom Clegg [Mon, 20 Oct 2014 14:47:32 +0000 (10:47 -0400)]
4062: Do not clobber next_page_url filters with local filters.
Peter Amstutz [Mon, 20 Oct 2014 14:45:10 +0000 (10:45 -0400)]
4058: If a portable data hash correpsonds to a single collection, automatically
redirect to the collection page. If not, show a special "menu" page listing
the matching collections.
Tom Clegg [Mon, 20 Oct 2014 14:24:10 +0000 (10:24 -0400)]
4062: Merge branch 'master' into 4062-infinite-scroll-repeat-TC
radhika [Mon, 20 Oct 2014 13:22:35 +0000 (09:22 -0400)]
4026: admin user can move a project under another user's home project.
radhika [Sat, 18 Oct 2014 00:37:34 +0000 (20:37 -0400)]
4054: minor test update
radhika [Sat, 18 Oct 2014 00:09:29 +0000 (20:09 -0400)]
Merge branch 'master' into 4054-sharing-email
radhika [Fri, 17 Oct 2014 22:40:28 +0000 (18:40 -0400)]
4054: show email address in sharing tab and update test to verify.
Peter Amstutz [Fri, 17 Oct 2014 20:54:31 +0000 (16:54 -0400)]
Merge branch '3698-invalid-output-of' closes #3698
Ward Vandewege [Fri, 17 Oct 2014 19:47:11 +0000 (15:47 -0400)]
Make sure to use httpclient 2.5.0 or higher for Workbench. Older
versions force the use of SSLv3, which is no longer advisable now that
Poodle is a thing.
No issue #
Peter Amstutz [Fri, 17 Oct 2014 19:36:49 +0000 (15:36 -0400)]
3698: Fix: components keys are symbols, not strings. Tweaked error message to
tell you what the invalid output_of actually is.
Peter Amstutz [Fri, 17 Oct 2014 19:17:01 +0000 (15:17 -0400)]
3698: Add check that output_of refers to an actual component.
Tim Pierce [Fri, 17 Oct 2014 19:15:29 +0000 (15:15 -0400)]
3699: allow script_version to be a branch
Fix copy_git_repo to behave properly when the source script_version
refers to a branch on the source repository:
* clone the source repo with git clone --bare (ensuring that local
branch refs are created for all remote branch refs)
* name the destination branch for "repository_script_version" to prevent
merge conflicts, if we copy different branches on the source
repository to the same destination repository
Peter Amstutz [Fri, 17 Oct 2014 17:58:50 +0000 (13:58 -0400)]
4083: Searched for everything using strptime and added import _strptime where it was missing. closes #4083
Tom Clegg [Fri, 17 Oct 2014 15:45:33 +0000 (11:45 -0400)]
Merge branch '4229-close-files' closes #4229
Tim Pierce [Fri, 17 Oct 2014 15:40:36 +0000 (11:40 -0400)]
3699: bugfix: some leftover recursive/force options
recursive -> args.recursive
force -> args.force
dst_git_repo -> args.dst_git_repo
Tim Pierce [Thu, 16 Oct 2014 18:46:24 +0000 (14:46 -0400)]
3699: report on collection copying progress
Nancy Ouyang [Fri, 17 Oct 2014 13:52:17 +0000 (09:52 -0400)]
added by_id subdirectory notes and arvados#collection
No issue #.
Brett Smith [Fri, 17 Oct 2014 14:22:01 +0000 (10:22 -0400)]
4239: Update Python SDK for google-api-python-client 1.3.
This package renames the module from apiclient to googleapiclient. It
provides a shim apiclient module for compatibility, but it only
exports the appropriate names, not real submodules. Using it requires
changing imports like
import apiclient.errors
to
from apiclient import errors
This approach works (has been tested) with both versions 1.2 and 1.3.
Closes #4239.
Brett Smith [Fri, 17 Oct 2014 12:36:54 +0000 (08:36 -0400)]
4189: Diagnostics suite doesn't try to clear Rails cache.
Refs #4189.
radhika [Fri, 17 Oct 2014 03:28:29 +0000 (23:28 -0400)]
Merge branch 'master' into 4062-infinite-scroll-repeat-issue
Conflicts:
services/api/test/fixtures/collections.yml
services/api/test/fixtures/jobs.yml
radhika [Fri, 17 Oct 2014 03:19:57 +0000 (23:19 -0400)]
4062: Do not include offset in the next_page_href when objects of multiple kinds are being fetched; instead, we will rely on created_at filter alone.
Updated the tests and fixtures to expect all 200+ objects in the pipelines and jobs tab.
The test however is still not working as the created_at filter based fetch is not working.
Brett Smith [Thu, 16 Oct 2014 21:23:57 +0000 (17:23 -0400)]
Merge branch '4189-workbench-project-admin-attr-editing-wip'
Closes #4189, #4202.
Brett Smith [Wed, 15 Oct 2014 18:04:12 +0000 (14:04 -0400)]
4189: Workbench lets users with write permission rename objects in projects.
The key part of this commit are the changes to ApplicationHelper.
There's also some refactoring to more consistently answer questions
about whether or not an attribute is editable.
There are also some tests in here that I wrote while I was tracking
down the problem. They seem like a useful addition.
Brett Smith [Wed, 15 Oct 2014 17:29:48 +0000 (13:29 -0400)]
4189: Workbench tests clear more state during teardown.
I'm working on some new tests that pick up on stale state without
these changes.
Brett Smith [Thu, 16 Oct 2014 21:00:39 +0000 (17:00 -0400)]
4189: Document the API server's writable_by field.
Tom Clegg [Thu, 16 Oct 2014 20:17:51 +0000 (16:17 -0400)]
4189: Add writable_by to User API response, so writable_by is available for every owner_uuid.
Tom Clegg [Thu, 16 Oct 2014 20:11:13 +0000 (16:11 -0400)]
4189: Admit in writable_by that an object is writable when its owner_uuid is writable.
Tom Clegg [Thu, 16 Oct 2014 20:09:16 +0000 (16:09 -0400)]
4189: Look up owner's writable_by when API did not provide writable_by for the object in question.
radhika [Thu, 16 Oct 2014 20:41:21 +0000 (16:41 -0400)]
4062: test updates
Tom Clegg [Thu, 16 Oct 2014 20:39:18 +0000 (16:39 -0400)]
3826: Reverse fields in "stat not found" warning.
Peter Amstutz [Thu, 16 Oct 2014 19:35:00 +0000 (15:35 -0400)]
Merge branch '3609-arv-ws' refs #3609
Peter Amstutz [Thu, 16 Oct 2014 19:34:25 +0000 (15:34 -0400)]
3609: Fix PollClient for case when there are no filters (get everything).
Peter Amstutz [Thu, 16 Oct 2014 19:24:51 +0000 (15:24 -0400)]
3609: Testing fixups.
Peter Amstutz [Thu, 16 Oct 2014 18:59:18 +0000 (14:59 -0400)]
3609: Back out setting api_version, api_host, and api_insecure on api client
and instead document that caller to arvados.events.subscribe() should pass in a
freshly created api client. Add event variable to indicate when subscription
is a success instead of sleeping. Removed unused "import time". Fixed "web
sockets" -> "websockets".
Tom Clegg [Thu, 16 Oct 2014 18:20:10 +0000 (14:20 -0400)]
4229: Add missing Close() calls
Tom Clegg [Thu, 16 Oct 2014 18:19:51 +0000 (14:19 -0400)]
4229: Get rid of sleep() in test
radhika [Thu, 16 Oct 2014 18:09:10 +0000 (14:09 -0400)]
4062: update python testing to handle the multiple fixture object creation, similar to workbench test_helper update.
Peter Amstutz [Thu, 16 Oct 2014 17:20:12 +0000 (13:20 -0400)]
3609: import signal; add_mutually_exclusive_group doesn't take any arguments.
Brett Smith [Thu, 16 Oct 2014 16:47:09 +0000 (12:47 -0400)]
Python SDK is not compatible with apiclient 1.3.
Figuring out why this is needs more investigation. It's something I'd
like to do, but it seems urgent to push this fix so builds can pass
again. No issue #, but see
<https://ci.curoverse.com/job/arvados-api-server/980/>.
radhika [Thu, 16 Oct 2014 16:45:09 +0000 (12:45 -0400)]
Merge branch 'master' into 4062-infinite-scroll-repeat-issue
radhika [Thu, 16 Oct 2014 16:41:20 +0000 (12:41 -0400)]
4062: test update
Peter Amstutz [Thu, 16 Oct 2014 16:23:41 +0000 (12:23 -0400)]
3609: Add additional api_ fields to api client object so that subscribe() can
create a new api client. Change test to use event variable instead of
sleeping. Fix "Web sockets" -> "Websockets". Make some command line options
mutually exclusive.
Tom Clegg [Thu, 16 Oct 2014 15:51:56 +0000 (11:51 -0400)]
Merge branch '4219-verify-with-hints' closes #4219
Tom Clegg [Thu, 16 Oct 2014 15:34:16 +0000 (11:34 -0400)]
4219: Add test for missing size hint. Dry up "known signature hint" consts.
Tim Pierce [Thu, 16 Oct 2014 15:31:59 +0000 (11:31 -0400)]
Merge branch 'master' into 3699-arv-copy
Tom Clegg [Thu, 16 Oct 2014 15:05:45 +0000 (11:05 -0400)]
3826: Roll up Open() attempts into a slice and a loop.
radhika [Thu, 16 Oct 2014 14:57:38 +0000 (10:57 -0400)]
Merge branch 'master' into 4062-infinite-scroll-repeat-issue
radhika [Thu, 16 Oct 2014 14:54:55 +0000 (10:54 -0400)]
4062: trailing white space
Tom Clegg [Thu, 16 Oct 2014 14:52:05 +0000 (10:52 -0400)]
3826: Fix up formatting cf. gofmt
Tom Clegg [Thu, 16 Oct 2014 14:48:27 +0000 (10:48 -0400)]
3826: Just modify lastSample maps in place, instead of returning the supplied pointer.
radhika [Thu, 16 Oct 2014 14:45:24 +0000 (10:45 -0400)]
4062: fix greedy infinite scrolling in tabs displaying more than one kind (Jobs and pipelines tab and Other objects tab).
Not only did scrolling never stopped, it never reloaded the next page and reloaded the same first page again and again.
Added test fixtures with many objects to test scrolling.
Added tests to use vertical scrollbar. The test itself is not able to test infinite scrolling by reloading the next page.
This may be because in integration testing new content is displayed only due to a click action.
Peter Amstutz [Thu, 16 Oct 2014 14:43:34 +0000 (10:43 -0400)]
Merge branch 'master' into 3609-arv-ws
Peter Amstutz [Thu, 16 Oct 2014 14:41:17 +0000 (10:41 -0400)]
Missing file
Peter Amstutz [Thu, 16 Oct 2014 14:40:25 +0000 (10:40 -0400)]
3787: Extra note that once inside the container the user can do anything.
Tom Clegg [Thu, 16 Oct 2014 14:36:34 +0000 (10:36 -0400)]
3826: Change FindStat to OpenStatFile to eliminate redundant Stat()
calls and races. Log every time we change our mind about where to read
a given statistic.
Peter Amstutz [Thu, 16 Oct 2014 14:35:54 +0000 (10:35 -0400)]
3787: Completed first draft explaining how to pull, configure, commit and upload a custom docker image.
Tom Clegg [Thu, 16 Oct 2014 13:48:16 +0000 (09:48 -0400)]
3826: Use correct variable Sscanf. CPU stats work again.
Peter Amstutz [Thu, 16 Oct 2014 13:30:48 +0000 (09:30 -0400)]
3609: Prefetch pipeline components to find out which jobs to subscribe to.
Tom Clegg [Thu, 16 Oct 2014 05:29:09 +0000 (01:29 -0400)]
4219: Use a precompiled global regexp for signature verification.
Tom Clegg [Wed, 15 Oct 2014 22:27:35 +0000 (18:27 -0400)]
4219: Accept signatures even if other hints are present in URL.
mishaz [Wed, 15 Oct 2014 21:18:25 +0000 (21:18 +0000)]
Merge branch '4197-remove-enforce-permissions-check-from-index-handler'
Closes #4197
Peter Amstutz [Wed, 15 Oct 2014 21:12:59 +0000 (17:12 -0400)]
3609: PollClient waits on event object instead of time.sleep, fix filters. Also fix --poll-interval and --no-poll
Peter Amstutz [Wed, 15 Oct 2014 21:09:52 +0000 (17:09 -0400)]
3609: Roll back schema change, not appropriate for this branch
mishaz [Tue, 14 Oct 2014 22:11:40 +0000 (22:11 +0000)]
Modified IndexHandler to match TrashHandler and PullHandler
* No longer checks for the enforce-permissions flag.
* Still checks for DataManager auth token.
* The HTTP error returned when we don't find the DataManager auth token is now Unauthorized instead of Forbidden.
Modified tests to check for new behavior.
Tom Clegg [Wed, 15 Oct 2014 20:59:07 +0000 (16:59 -0400)]
Resolve race condition: wait for response before checking mock expectations. refs #3782
Peter Amstutz [Wed, 15 Oct 2014 20:22:26 +0000 (16:22 -0400)]
3609: Add test case for PollClient. arvados.event.subscribe() starts a new
polling thread by default so as to provide the same behavior as websockets.
Add documentation strings to ws.py command line parameters.
Peter Amstutz [Wed, 15 Oct 2014 20:20:04 +0000 (16:20 -0400)]
3609: Fix schema so 'order' parameter of 'list' is an array instead of a string.
Brett Smith [Wed, 15 Oct 2014 13:22:40 +0000 (09:22 -0400)]
4196: arv-keepdocker uses Docker 1.0 pull syntax.
`docker pull -t` was the old way of pulling an image with a specific
tag. Docker 1.0 introduced `docker pull repo:tag`, and Docker 1.2
removes support for `-t` completely. We're well-standardized on 1.1+
at this point, and considering an upgrade to 1.2+, so now's the time
to switch.
Closes #4196.
Brett Smith [Tue, 14 Oct 2014 20:30:21 +0000 (16:30 -0400)]
4126: API server uses fixed a-r-p-i (again).
Refs #4126.
Brett Smith [Tue, 14 Oct 2014 20:15:16 +0000 (16:15 -0400)]
4126: a-r-p-i dereferences parameter values when creating jobs.
Refs #4126. This is required to run jobs.