radhika [Thu, 22 Oct 2015 17:03:18 +0000 (13:03 -0400)]
Merge branch 'master' into 7167-keep-rsync
Peter Amstutz [Thu, 22 Oct 2015 14:20:36 +0000 (10:20 -0400)]
7582: Better reporting in the log about user probe behavior.
Peter Amstutz [Thu, 22 Oct 2015 14:20:36 +0000 (10:20 -0400)]
7582: Better reporting in the log about user probe behavior.
Peter Amstutz [Thu, 22 Oct 2015 13:51:37 +0000 (09:51 -0400)]
7582: Runner uploads results. Feature complete.
Peter Amstutz [Thu, 22 Oct 2015 13:20:13 +0000 (09:20 -0400)]
7582: Uploader passes tests
Peter Amstutz [Wed, 21 Oct 2015 20:41:35 +0000 (16:41 -0400)]
7582: Uploader mostly done, writing tests
Brett Smith [Wed, 21 Oct 2015 19:37:53 +0000 (15:37 -0400)]
Fix multiple exception catching in arv-run.
The previous version catches IOError and binds the exception object to
the name OSError. No issue #.
Peter Amstutz [Wed, 21 Oct 2015 17:38:57 +0000 (13:38 -0400)]
7582: More tests, add vwd support
Peter Amstutz [Wed, 21 Oct 2015 17:04:07 +0000 (13:04 -0400)]
7582: Working on tests.
radhika [Wed, 21 Oct 2015 16:23:09 +0000 (12:23 -0400)]
7167: expand the src and dst help messages to list the config parameters that are to be included in the config files.
Bryan Cosca [Wed, 21 Oct 2015 15:36:25 +0000 (11:36 -0400)]
Merge branch '7015-update-user-guide'
closes #7015
Ward Vandewege [Wed, 21 Oct 2015 15:19:46 +0000 (11:19 -0400)]
SSO installation doc fix: to run rails console, you need to be in the
/var/www/arvados-sso/current directory.
closes #7623
Bryan Cosca [Wed, 21 Oct 2015 15:18:52 +0000 (11:18 -0400)]
7015: Removed whitespace
Peter Amstutz [Wed, 21 Oct 2015 13:03:27 +0000 (09:03 -0400)]
7582: Crunchrunner work in progress.
radhika [Wed, 21 Oct 2015 13:00:58 +0000 (09:00 -0400)]
Merge branch 'master' into 7492-keepproxy-upstream-errors
Tom Clegg [Tue, 20 Oct 2015 21:53:27 +0000 (17:53 -0400)]
6358: Fix probe order test logic.
This request order is OK with two threads: thread "0" just took a long
time to make its request.
expect 0 1 2 3 4 5 6 7
got 1 2 3 4 5 0 6 7
The inverse is not OK. This would mean 0 started before any of
1,2,3,4,5 finished.
expect 1 2 3 4 5 0 6 7
got 0 1 2 3 4 5 6 7
refs #6358
Tom Clegg [Tue, 20 Oct 2015 21:52:55 +0000 (17:52 -0400)]
6358: Fix race opportunity in ThreadLimiter.
refs #6358
Peter Amstutz [Tue, 20 Oct 2015 20:34:50 +0000 (16:34 -0400)]
7582: (1) Probe for non-root Docker user to use instead of assuming "crunch".
Tries the default user for the container, then 'crunch', then 'nobody', testing
for whether the actual user id is non-zero. This defends against mistakes but
not malice, but we intend to harden the security in the future so we don't want
anyone getting used to their jobs running as root in their Docker
containers.
(2) If arvados_sdk_version is not present, skip the "pipe to perl to install
the SDK" logic, but instead bootstrap with a small bash script that only
creates temporary directories and runs the crunch script.
radhika [Tue, 20 Oct 2015 17:41:29 +0000 (13:41 -0400)]
7546: update some of the failure tests to use keepclient.Retries = 0, so that the tests do not waste too much time
retrying a test that is designed for failures. This update brings down the keepclient_test runtime from 49s to 10s.
radhika [Tue, 20 Oct 2015 17:30:45 +0000 (13:30 -0400)]
Merge branch 'master' into 7546-put-retry
radhika [Tue, 20 Oct 2015 15:41:07 +0000 (11:41 -0400)]
Merge branch 'master' into 7492-keepproxy-upstream-errors
radhika [Tue, 20 Oct 2015 15:40:05 +0000 (11:40 -0400)]
7492: update keep-rsync test with bad blob signing key to expect Forbidden error instead of Block not found error.
radhika [Tue, 20 Oct 2015 15:21:34 +0000 (11:21 -0400)]
7546: also retry when status code is 0, which is the case when a closed connection was used.
Brett Smith [Tue, 20 Oct 2015 15:04:29 +0000 (11:04 -0400)]
Merge branch 'pr/28'
Closes #7324.
Brett Smith [Tue, 20 Oct 2015 15:03:55 +0000 (11:03 -0400)]
Clean redundant except: blocks in run_test_server.
Brett Smith [Tue, 20 Oct 2015 15:02:51 +0000 (11:02 -0400)]
7324: Tighten exception ignoring in run_test_server start_nginx.
We just want to make sure the FIFO's gone. Ignore the OSError that
says "can't remove it because it's already gone," and re-raise all
others.
radhika [Tue, 20 Oct 2015 15:02:19 +0000 (11:02 -0400)]
Merge branch 'master' into 7546-put-retry
radhika [Tue, 20 Oct 2015 14:59:41 +0000 (10:59 -0400)]
7492: better error reporting of upstream errors in keepproxy.
Tom Clegg [Mon, 19 Oct 2015 19:29:28 +0000 (15:29 -0400)]
Merge branch '6358-put-rendezvous' closes #6358
Tom Clegg [Mon, 19 Oct 2015 19:19:02 +0000 (15:19 -0400)]
5824: Leave "install keep-web" page out of install guide TOC for now.
Brett Smith [Mon, 19 Oct 2015 18:40:24 +0000 (14:40 -0400)]
7499: Update development link in Workbench "Getting Started" popup.
Also, de-hyphenate "open source."
Refs #7499.
radhika [Mon, 19 Oct 2015 18:13:25 +0000 (14:13 -0400)]
Merge branch 'master' into 7546-put-retry
radhika [Mon, 19 Oct 2015 18:12:00 +0000 (14:12 -0400)]
refs #7167
Merge branch '7167-keep-rsync'
radhika [Mon, 19 Oct 2015 18:11:41 +0000 (14:11 -0400)]
Merge branch 'master' into 7167-keep-rsync
Tom Clegg [Mon, 19 Oct 2015 17:22:53 +0000 (13:22 -0400)]
5824: Fixup nginx and workbench configs
radhika [Mon, 19 Oct 2015 03:21:58 +0000 (23:21 -0400)]
7546: enhance putReplicas method to retry.
Tom Clegg [Sat, 17 Oct 2015 04:39:25 +0000 (00:39 -0400)]
Merge branch '7173-jessie'
closes #7173
Tom Clegg [Fri, 2 Oct 2015 02:16:51 +0000 (22:16 -0400)]
5824: gofmt
Tom Clegg [Mon, 7 Sep 2015 07:43:59 +0000 (03:43 -0400)]
5824: Add -attachment-only-host feature.
Tom Clegg [Mon, 7 Sep 2015 06:39:10 +0000 (02:39 -0400)]
5824: Implement "trust all content" mode.
Tom Clegg [Sun, 30 Aug 2015 06:45:58 +0000 (02:45 -0400)]
5824: Add read-error and lots-of-blocks tests.
Tom Clegg [Fri, 28 Aug 2015 15:08:16 +0000 (11:08 -0400)]
5824: Fix up DNS docs.
Tom Clegg [Fri, 28 Aug 2015 06:30:45 +0000 (02:30 -0400)]
5824: Log X-Forwarded-For header value if provided.
Tom Clegg [Fri, 28 Aug 2015 05:45:35 +0000 (01:45 -0400)]
5824: Fail at startup if ARVADOS_API_HOST is not set.
Tom Clegg [Fri, 28 Aug 2015 05:28:43 +0000 (01:28 -0400)]
5824: Accept anonymous tokens on command line.
Tom Clegg [Fri, 28 Aug 2015 05:09:46 +0000 (01:09 -0400)]
5824: Handle various combinations of c= and t= more consistently. Use vhosts in integration tests.
Tom Clegg [Fri, 28 Aug 2015 02:34:21 +0000 (22:34 -0400)]
5824: Comment to explain "authorizer" test helpers.
Tom Clegg [Fri, 28 Aug 2015 02:33:44 +0000 (22:33 -0400)]
5824: Fix up support for PDH in vhostname.
Tom Clegg [Fri, 28 Aug 2015 02:31:19 +0000 (22:31 -0400)]
5824: Modernize install page, cf. other services.
Tom Clegg [Fri, 28 Aug 2015 02:17:54 +0000 (22:17 -0400)]
5824: Clarify difference between keepproxy and keepstore (bandwidth and convenience -- not security).
Tom Clegg [Fri, 28 Aug 2015 02:16:26 +0000 (22:16 -0400)]
5824: Update keepproxy usage.
Tom Clegg [Sun, 16 Aug 2015 04:16:27 +0000 (00:16 -0400)]
5824: Fix up error checking and early-close behavior inCollectionFileReader.
Tom Clegg [Wed, 29 Jul 2015 07:33:19 +0000 (03:33 -0400)]
5824: Add Content-Length header.
Tom Clegg [Wed, 29 Jul 2015 05:56:55 +0000 (01:56 -0400)]
5824: Use vhosts in curl integration tests. Add large file test.
Tom Clegg [Thu, 23 Jul 2015 05:20:28 +0000 (01:20 -0400)]
5824: Support vhost-based collection lookups.
Tom Clegg [Fri, 16 Oct 2015 23:40:22 +0000 (19:40 -0400)]
6358: Test partial ordering with multiple writer threads.
Tom Clegg [Fri, 16 Oct 2015 22:26:14 +0000 (18:26 -0400)]
6358: Fix rendezvous probe order on Put.
Bug #1 was that KeepClient.put() was starting threads in the order
given by roots_map.iteritems(), instead of the order they were
supplied by weighted_service_roots(). This is fixed by using the same
logic get() was using.
Bug #2 was that ThreadLimiter didn't unblock threads in the same order
they were created by put(). This is fixed by adding a "set_sequence"
method to ThreadLimiter to indicate the order in which threads should
be unblocked.
The new test case confirms that put(copies=1) always makes requests in
the correct order.
Bryan Cosca [Fri, 16 Oct 2015 21:07:59 +0000 (17:07 -0400)]
7015: Finished going through user guide
Peter Amstutz [Fri, 16 Oct 2015 15:42:01 +0000 (11:42 -0400)]
Merge branch '6321-slurm-oserror' closes #6321
Peter Amstutz [Fri, 16 Oct 2015 15:40:36 +0000 (11:40 -0400)]
6321: Add note about rationale for retrying on OSError.
Peter Amstutz [Fri, 16 Oct 2015 15:16:49 +0000 (11:16 -0400)]
6321: Add test that OSError is caught from slurm subprocess invocations.
radhika [Fri, 16 Oct 2015 14:23:12 +0000 (10:23 -0400)]
7167: Remove StartKeepWithParams and StopKeepWithParams and make StartKeep and StopKeep with parameters the only exposed funcs.
The update was small enough, about 10 usages in the entire code, and hence did not make sense to postpone it for a "better" time.
Colin Nolan [Fri, 16 Oct 2015 13:15:09 +0000 (14:15 +0100)]
7324: Implemented deletion of previous nginx access log fifo before creation,
as discussed with @jrandall to address issue raised by @brettcs
(see: https://github.com/curoverse/arvados/pull/28#discussion_r39689972).
radhika [Fri, 16 Oct 2015 02:55:03 +0000 (22:55 -0400)]
7167: Break all the code from keep-rsync main method into a separate func so that arg parsing can also be tested.
Rather than using default flag parsing, use FlagSet so that flags can be set multiple times from multiple tests.
Bryan Cosca [Thu, 15 Oct 2015 21:10:19 +0000 (17:10 -0400)]
7015: Checked up to Concurrent Crunch tasks
Tom Clegg [Thu, 25 Jun 2015 03:33:08 +0000 (23:33 -0400)]
5824: add (*KeepClient)CollectionFileReader()
Tom Clegg [Thu, 23 Jul 2015 05:09:02 +0000 (01:09 -0400)]
5824: Add doc.go
Tom Clegg [Tue, 23 Jun 2015 23:12:58 +0000 (19:12 -0400)]
5824: Add install doc
Tom Clegg [Wed, 17 Jun 2015 06:47:49 +0000 (02:47 -0400)]
5824: Assign MIME type by file extension. closes #6327
Tom Clegg [Thu, 23 Jul 2015 04:02:11 +0000 (00:02 -0400)]
5824: Add keepdl.
Tom Clegg [Thu, 15 Oct 2015 20:27:58 +0000 (16:27 -0400)]
Merge branch '7159-keepexercise' refs #7159
Tom Clegg [Thu, 15 Oct 2015 20:25:14 +0000 (16:25 -0400)]
7159: Add keep-exercise
Tom Clegg [Thu, 15 Oct 2015 19:47:11 +0000 (15:47 -0400)]
Merge branch 'wtsi-hgi-feature/arv-view'
refs #7204
Tom Clegg [Thu, 15 Oct 2015 19:42:37 +0000 (15:42 -0400)]
7204: Tweak usage message, add a .shellescape, fix error-reporting error
radhika [Thu, 15 Oct 2015 16:35:32 +0000 (12:35 -0400)]
closes #7167
Merge branch '7167-keep-rsync'
radhika [Thu, 15 Oct 2015 16:35:15 +0000 (12:35 -0400)]
Merge branch 'master' into 7167-keep-rsync
radhika [Thu, 15 Oct 2015 16:32:07 +0000 (12:32 -0400)]
Merge branch 'master' into 7167-keep-rsync
Conflicts:
sdk/go/keepclient/keepclient.go
Tom Clegg [Thu, 15 Oct 2015 16:22:57 +0000 (12:22 -0400)]
7173: Update bundle.
Recent firefox requires recent selenium-webdriver.
Tom Clegg [Thu, 15 Oct 2015 16:21:07 +0000 (12:21 -0400)]
Merge branch '7173-jessie' refs #7173
Tom Clegg [Mon, 31 Aug 2015 19:00:13 +0000 (15:00 -0400)]
7173: Add jessie to supported distro list.
radhika [Thu, 15 Oct 2015 16:18:20 +0000 (12:18 -0400)]
7167: update the progress message to say "est. time remaining" instead of "ETA" which is not accurate in this case.
radhika [Thu, 15 Oct 2015 15:56:36 +0000 (11:56 -0400)]
7167: rename the newly added StopKeepServers as StopKeepWithParams; it now sounds similar to StartKeepWithParams and is self explanatory.
radhika [Thu, 15 Oct 2015 15:08:10 +0000 (11:08 -0400)]
Merge branch '7167-keep-rsync' of git.curoverse.com:arvados into 7167-keep-rsync
Tom Clegg [Thu, 15 Oct 2015 15:02:30 +0000 (11:02 -0400)]
7167: Always pass --num-keep-servers to python wrapper. Update comments.
Tom Clegg [Thu, 15 Oct 2015 14:50:13 +0000 (10:50 -0400)]
7167: Rename conf flags to -src and -dst to match arv-copy. Always add .conf for short form.
Tom Clegg [Thu, 15 Oct 2015 14:48:33 +0000 (10:48 -0400)]
7167: Fix up progress/ETA logging.
Peter Amstutz [Thu, 15 Oct 2015 14:32:26 +0000 (10:32 -0400)]
Merge branch '7491-go-keepclient-retry' closes #7491
Peter Amstutz [Thu, 15 Oct 2015 14:16:27 +0000 (10:16 -0400)]
7491: Remove unnecessary writable service roots from GET tests.
Tom Clegg [Thu, 15 Oct 2015 13:18:43 +0000 (09:18 -0400)]
Merge branch 'master' into wtsi-hgi-feature/arv-view
Conflicts:
sdk/cli/bin/arv
radhika [Thu, 15 Oct 2015 03:01:13 +0000 (23:01 -0400)]
Merge branch 'master' into 7167-keep-rsync
radhika [Thu, 15 Oct 2015 03:00:05 +0000 (23:00 -0400)]
7167: log progress during keep-rsync and several test improvements.
Bryan Cosca [Wed, 14 Oct 2015 21:09:07 +0000 (17:09 -0400)]
7015: Checked up to Working with data sets
Brett Smith [Wed, 14 Oct 2015 20:59:40 +0000 (16:59 -0400)]
API server needs an arvados-cli with crunch-job --docker-bin.
crunch-dispatch was extended to use `crunch-job --docker-bin` in
#6838. This commit simply updates the Gemfile to ensure this
dependency is satisfied. No issue #.
radhika [Wed, 14 Oct 2015 19:15:15 +0000 (15:15 -0400)]
Merge branch 'master' into 7167-keep-rsync
Bryan Cosca [Wed, 14 Oct 2015 19:01:00 +0000 (15:01 -0400)]
7015: Tested up to Accessing an Arvados VM with Webshell
Tom Clegg [Wed, 14 Oct 2015 18:51:34 +0000 (14:51 -0400)]
Merge branch '7167-propagate-error' refs #7167
Tom Clegg [Wed, 14 Oct 2015 18:51:01 +0000 (14:51 -0400)]
Merge branch '7159-clean-index' refs #7159 refs #7168
radhika [Wed, 14 Oct 2015 17:43:54 +0000 (13:43 -0400)]
7167: loadConfig setupKeepclient do only one set at a time.
Peter Amstutz [Wed, 14 Oct 2015 14:49:49 +0000 (10:49 -0400)]
6321: Add OSError to slurm shutdown actor retry conditions, to catch and retry
subprocess errors from the operating system, which is preferrable to crashing
the shutdown actor.
radhika [Wed, 14 Oct 2015 02:27:41 +0000 (22:27 -0400)]
7167: when the config file does not contain '/', use $HOME/.config/arvados/<filename>.