Peter Amstutz [Fri, 31 Jul 2015 14:31:11 +0000 (10:31 -0400)]
Merge branch 'master' into 6676-document-sso
Peter Amstutz [Fri, 31 Jul 2015 14:28:23 +0000 (10:28 -0400)]
6676: Grammar fixes.
Brett Smith [Fri, 31 Jul 2015 14:26:42 +0000 (10:26 -0400)]
Fix type checks in arv-copy recursive collection copying.
This is necessary follow-up from
79564b0ac7d03327cc351bbd6df544ab1f776380. API objects are now
OrderedDicts instead of dicts, so `type(obj) == dict` is never true,
and calling this function on an API object is a noop.
No issue #. I found this after receiving a user report that arv-copy
did not copy dependent collections from a pipeline template.
Brett Smith [Fri, 31 Jul 2015 14:12:43 +0000 (10:12 -0400)]
arv-copy git check doesn't catch system exceptions.
No issue #.
Tom Clegg [Fri, 31 Jul 2015 05:02:23 +0000 (01:02 -0400)]
Whitespace
No issue #
Tom Clegg [Fri, 31 Jul 2015 05:02:11 +0000 (01:02 -0400)]
Merge branch 'git-commit-debug' of https://github.com/wtsi-hgi/arvados
No issue #
Joshua C. Randall [Fri, 31 Jul 2015 01:00:28 +0000 (02:00 +0100)]
Adds useful log warnings re: repo failures
Instruments the find_commit_range function such that it logs an
explanatory warning in any case when it fails to find any refs.
When no refs are found, find_commit_range returns an empty list
which typically causes its caller to throw an exception. Without
these added warnings, that exception is not at all helpful in
tracking down the underlying issue.
Brett Smith [Thu, 30 Jul 2015 21:43:55 +0000 (17:43 -0400)]
Fix stale "Install Ruby and Bundler" links.
Now that these instructions are an include, include them everywhere
they're referenced. No issue #.
Brett Smith [Thu, 30 Jul 2015 21:34:50 +0000 (17:34 -0400)]
RVM setup instructions tell you to install Bundler after activation.
On hosts that do not have any Ruby installed, the previous
instructions won't work, because the `gem` tool is only available
through RVM. RVM needs to be activated in the shell first.
No issue #.
Tom Clegg [Thu, 30 Jul 2015 19:37:03 +0000 (15:37 -0400)]
Merge branch '6592-retry-if-cleanupfail' closes #6592
Tom Clegg [Thu, 30 Jul 2015 19:16:43 +0000 (15:16 -0400)]
Merge branch '6663-bugfixes' refs #6663
Peter Amstutz [Thu, 30 Jul 2015 19:02:02 +0000 (15:02 -0400)]
6676: Reorganize instructions a bit more. Fix createdb instructions. Fix
rendering. Fix typo in Google+ authentication setup.
Tom Clegg [Thu, 30 Jul 2015 15:56:43 +0000 (11:56 -0400)]
Do not mess with PERLLIB in crunch-job tests; let run-tests.sh do that.
Replace this with mocking crunch-refresh-trigger, so crunchenv still
has a reason to live.
Tom Clegg [Thu, 30 Jul 2015 15:55:30 +0000 (11:55 -0400)]
6592: List runtime dependencies for Perl SDK.
Tom Clegg [Thu, 30 Jul 2015 14:04:02 +0000 (10:04 -0400)]
6663: Admins and repository owners can_manage, not just can_write
(even though that might not translate to any additional functions with
the current gitolite config).
Tom Clegg [Wed, 29 Jul 2015 21:35:40 +0000 (17:35 -0400)]
6663: Add explanatory comments and fix some unhelpful variable names.
Tom Clegg [Wed, 29 Jul 2015 19:12:58 +0000 (15:12 -0400)]
6592: Add crunch-job integration tests.
Tom Clegg [Wed, 29 Jul 2015 18:48:25 +0000 (14:48 -0400)]
6592: Exit RETRY_UNLOCKED if clean-work-dirs phase fails.
Also use "bash -o pipefail" so cleanup fails if mount or awk fails.
Tom Clegg [Wed, 29 Jul 2015 18:46:41 +0000 (14:46 -0400)]
6592: Do not overload $Job temporarily.
Fixes failure during croak/cleanup, which assumes Job is either undef
or a real Job.
Tom Clegg [Wed, 29 Jul 2015 18:44:50 +0000 (14:44 -0400)]
6592: 4534: Re-enable integration tests, now that run-tests.sh brings up an API server.
radhika [Wed, 29 Jul 2015 18:06:42 +0000 (14:06 -0400)]
closes #6657
Merge branch '6657-no-git-in-arv-copy'
radhika [Wed, 29 Jul 2015 18:05:35 +0000 (14:05 -0400)]
Merge branch 'master' into 6657-no-git-in-arv-copy
radhika [Wed, 29 Jul 2015 18:05:05 +0000 (14:05 -0400)]
closes #6602
Merge branch '6602-job-runtime-display'
radhika [Wed, 29 Jul 2015 17:47:43 +0000 (13:47 -0400)]
6602: enhance render_runtime method to display seconds when days, hours, and minutes are all zero even when round_to_min is true.
radhika [Wed, 29 Jul 2015 17:33:08 +0000 (13:33 -0400)]
6602: remove render_runtime_compact; instead use render_runtime with use_words = false and round_to_min.
Tom Clegg [Tue, 28 Jul 2015 22:11:59 +0000 (18:11 -0400)]
6663: Fix repository permissions.
Users with is_active==false (except anonymous_user) are not listed by
get_all_permissions.
A repository that is shared with a group is only shared with users who
have permissions on that group, not all users who have permissions on
*any* group.
{User --can_write--> group --can_read--> repo} is correctly listed as
{User --can_read--> repo}, not can_write.
Tests check that the permissions reported by get_all_permissions do
not exceed the API server's interpretation of the current permission
set.
Tom Clegg [Tue, 28 Jul 2015 21:58:25 +0000 (17:58 -0400)]
6663: Fix "duplicate public_key" test: OK if the key being updated has the same public_key.
Tom Clegg [Tue, 28 Jul 2015 21:52:30 +0000 (17:52 -0400)]
6663: Fix using default owner_uuid in repositories#create. refs #6652
radhika [Wed, 29 Jul 2015 12:06:34 +0000 (08:06 -0400)]
6657: refactor git check and reuse.
radhika [Tue, 28 Jul 2015 21:44:44 +0000 (17:44 -0400)]
Merge branch 'master' into 6657-no-git-in-arv-copy
Peter Amstutz [Tue, 28 Jul 2015 20:43:28 +0000 (16:43 -0400)]
Hotfix for test, transform "/dev/stdin" to "-" in arv-put refs #6681
Peter Amstutz [Tue, 28 Jul 2015 19:56:57 +0000 (15:56 -0400)]
Hotfix, inode cache find() returns list instead of single item now. refs #6643
radhika [Tue, 28 Jul 2015 19:36:17 +0000 (15:36 -0400)]
6657: copy_pipeline_template method also updated to check git existence.
radhika [Tue, 28 Jul 2015 19:28:44 +0000 (15:28 -0400)]
Merge branch 'master' into 6657-no-git-in-arv-copy
Peter Amstutz [Tue, 28 Jul 2015 19:21:24 +0000 (15:21 -0400)]
Merge branch '6681-arv-put-pipe' closes #6681
Peter Amstutz [Tue, 28 Jul 2015 19:09:08 +0000 (15:09 -0400)]
Merge branch '6643-fuse-del-crash' closes #6643
radhika [Tue, 28 Jul 2015 18:00:17 +0000 (14:00 -0400)]
6657: check git availability only when recursive copy is being used.
radhika [Tue, 28 Jul 2015 17:48:40 +0000 (13:48 -0400)]
Merge branch 'master' into 6657-no-git-in-arv-copy
Peter Amstutz [Tue, 28 Jul 2015 17:15:22 +0000 (13:15 -0400)]
Merge branch 'master' into 6676-document-sso
Conflicts:
doc/install/install-sso.html.textile.liquid
Brett Smith [Tue, 28 Jul 2015 16:29:37 +0000 (12:29 -0400)]
Fix duplicated id in SSO install documentation.
No issue #.
Brett Smith [Tue, 28 Jul 2015 16:28:58 +0000 (12:28 -0400)]
6691: Add reference to Ubuntu trusty in Ruby install instructions.
I confirmed that these packages are all installable on Ubuntu 14.04.
Refs #6691.
radhika [Tue, 28 Jul 2015 16:05:47 +0000 (12:05 -0400)]
Merge branch 'master' into 6657-no-git-in-arv-copy
radhika [Tue, 28 Jul 2015 16:05:12 +0000 (12:05 -0400)]
6657: check git is installed in arv-copy
Brett Smith [Mon, 27 Jul 2015 21:38:20 +0000 (17:38 -0400)]
6691: Add Ubuntu trusty packages to our install guide.
Closes #6691, #6694.
Peter Amstutz [Mon, 27 Jul 2015 20:57:28 +0000 (16:57 -0400)]
6676: Add note about git and curl. Describe how to run passenger standalone.
Peter Amstutz [Mon, 27 Jul 2015 20:21:20 +0000 (16:21 -0400)]
6676: Working through polishing SSO install documentation.
radhika [Mon, 27 Jul 2015 19:20:10 +0000 (15:20 -0400)]
Merge branch 'master' into 6602-job-runtime-display
radhika [Mon, 27 Jul 2015 19:19:21 +0000 (15:19 -0400)]
6602: update test assertion to match new format
radhika [Mon, 27 Jul 2015 18:31:02 +0000 (14:31 -0400)]
6602: display runtime using the formula (min_nodes * (finished_at - started_at))
Brett Smith [Mon, 27 Jul 2015 17:38:03 +0000 (13:38 -0400)]
6778: Remove git install from PostgreSQL install instructions.
Closes #6778.
Peter Amstutz [Mon, 27 Jul 2015 17:07:55 +0000 (13:07 -0400)]
Merge branch '6451-websockets-invalid-input' closes #6451
radhika [Mon, 27 Jul 2015 16:59:50 +0000 (12:59 -0400)]
Merge branch 'master' into 6602-job-runtime-display
Peter Amstutz [Mon, 27 Jul 2015 16:12:30 +0000 (12:12 -0400)]
Merge branch '5990-arv-run-default-runtime' closes #5990
Peter Amstutz [Mon, 27 Jul 2015 14:38:07 +0000 (10:38 -0400)]
Merge branch '6593-arv-get-stdout' closes #6593
Peter Amstutz [Mon, 27 Jul 2015 14:37:32 +0000 (10:37 -0400)]
6593: Typo fix in KeyboardInterrupt handling.
Peter Amstutz [Mon, 27 Jul 2015 14:25:57 +0000 (10:25 -0400)]
5990: Update arv-run subcommand cli doc.
Peter Amstutz [Mon, 27 Jul 2015 14:06:37 +0000 (10:06 -0400)]
6451: Refactor tests slightly to call subscribe_test() in two places.
Peter Amstutz [Mon, 27 Jul 2015 13:51:43 +0000 (09:51 -0400)]
6451: Validate that 500 error is returned to client. Tweak code comments.
Peter Amstutz [Mon, 27 Jul 2015 13:45:05 +0000 (09:45 -0400)]
6593: Change docstring references from /dev/stdout to just "stdout". Fix logic
to clean up open files on KeyboardInterrupt.
Peter Amstutz [Mon, 27 Jul 2015 13:13:56 +0000 (09:13 -0400)]
Merge branch '6706-fuse-forget-crash' closes #6706
Peter Amstutz [Mon, 27 Jul 2015 13:13:20 +0000 (09:13 -0400)]
6706: Add docstrings to close()
Peter Amstutz [Mon, 27 Jul 2015 13:11:07 +0000 (09:11 -0400)]
6643: Support associating uuid with multiple inodes to fix double-remove bug.
Peter Amstutz [Fri, 24 Jul 2015 21:30:20 +0000 (17:30 -0400)]
6643: Add test case that reproduces the bug
radhika [Fri, 24 Jul 2015 19:17:23 +0000 (15:17 -0400)]
Merge branch 'master' into 6602-job-runtime-display
Peter Amstutz [Fri, 24 Jul 2015 18:38:47 +0000 (14:38 -0400)]
Merge branch '6705-fix-websockets-replay' closes #6705
Peter Amstutz [Fri, 24 Jul 2015 18:21:58 +0000 (14:21 -0400)]
6706: Add comments about what is going on with EventClient.close()
radhika [Fri, 24 Jul 2015 18:20:21 +0000 (14:20 -0400)]
6602: use min_nodes * (finished_at - started_at) to calculate the allocated node time for each job.
Peter Amstutz [Fri, 24 Jul 2015 18:08:18 +0000 (14:08 -0400)]
6706: Bonus websockets bugfix, close connection immediately instead of waiting
for server shutdown response that might never come, then block until websocket
thread is in terminate state.
Peter Amstutz [Fri, 24 Jul 2015 15:42:58 +0000 (11:42 -0400)]
6706: Fixup websocket tests of PollClient
radhika [Fri, 24 Jul 2015 16:07:32 +0000 (12:07 -0400)]
closes #6687
Merge branch '6687-install-guide-flow'
Peter Amstutz [Fri, 24 Jul 2015 15:31:29 +0000 (11:31 -0400)]
6706: Clear inode/inode cache dicts on destroy() instead of setting inodes to None.
Peter Amstutz [Fri, 24 Jul 2015 14:21:56 +0000 (10:21 -0400)]
6593: Use sys.stdout as special case instead of trying treat /dev/stdout as a regular file.
radhika [Fri, 24 Jul 2015 14:18:47 +0000 (10:18 -0400)]
6687: revisit build tools text and other minor updates
radhika [Fri, 24 Jul 2015 13:54:15 +0000 (09:54 -0400)]
6687: merge back nginx docs back into api server and workbench pages and remove the includes since they are not being shared.
radhika [Fri, 24 Jul 2015 13:46:16 +0000 (09:46 -0400)]
Merge branch 'master' into 6687-install-guide-flow
radhika [Fri, 24 Jul 2015 12:40:03 +0000 (08:40 -0400)]
refs #6279
Increased timeout to 2000ms; with the previous 1000ms value, the login to shell account was failing
sometimes as the token is being sent too early. With this value, it seems to work consistently.
radhika [Thu, 23 Jul 2015 23:43:47 +0000 (19:43 -0400)]
6687: install guide updates aimed at reducing jumping around during the process
Peter Amstutz [Thu, 23 Jul 2015 20:02:20 +0000 (16:02 -0400)]
6681: When input file is "-", get data directly from sys.stdin and use
CollectionWriter.write() instead of opening /dev/stdin and trying to write like
a normal file.
Peter Amstutz [Thu, 23 Jul 2015 19:07:57 +0000 (15:07 -0400)]
5990: If --docker-image not specified, don't provide
runtime_contraints.docker_image, use default server configuration. Update
documentation.
Peter Amstutz [Thu, 23 Jul 2015 16:17:40 +0000 (12:17 -0400)]
6451: Don't crash on ArgumentError. Add test to verify that it doesn't crash.
Peter Amstutz [Thu, 23 Jul 2015 15:22:32 +0000 (11:22 -0400)]
6705: Use EventMachine::next_tick (which always pushes task into work queue)
instead of EventMachine::schedule (which calls recursively). Also lower limit
of number of rows to fetch at a time.
Peter Amstutz [Thu, 23 Jul 2015 15:21:04 +0000 (11:21 -0400)]
6705: PollClient checks if there are more items and sends another query
immediately instead of waiting. Better error reporting from events.py on
failure to connect to websockets.
Brett Smith [Thu, 23 Jul 2015 14:11:48 +0000 (10:11 -0400)]
6750: API install guide doesn't tell users to copy omniauth.rb.example.
This completes the work started in
2ecf7efbab5ceb082739dcffd98c18bb4b14447e. omniauth.rb.example doesn't
exist anymore, so users can't copy it. The application.yml
configuration method is preferred. Closes #6750.
Brett Smith [Wed, 22 Jul 2015 21:00:14 +0000 (17:00 -0400)]
Add standard Python .gitignore for CWL SDK.
No issue #.
Peter Amstutz [Wed, 22 Jul 2015 14:34:52 +0000 (10:34 -0400)]
Merge branch '6264-cwl-runner' closes #6264
radhika [Wed, 22 Jul 2015 13:59:27 +0000 (09:59 -0400)]
closes #6473
Merge branch '6473-fetch-events-starting-at'
radhika [Wed, 22 Jul 2015 13:57:29 +0000 (09:57 -0400)]
6473: update message for start_time input argument.
radhika [Wed, 22 Jul 2015 13:55:08 +0000 (09:55 -0400)]
Merge branch 'master' into 6473-fetch-events-starting-at
radhika [Wed, 22 Jul 2015 12:41:33 +0000 (08:41 -0400)]
refs #6465
Merge branch '6465-optimize-workbench-integration-tests'
radhika [Wed, 22 Jul 2015 12:34:04 +0000 (08:34 -0400)]
6465: Noticed a slight dip in code coverage in two areas and added tests to cover those situations. Details:
1. Removal of integration "Test dashboard button all {jobs}" resulted in no test at all to visit /jobs page.
Added a controller test for this.
2. Not visiting the hash match page when only one collection matches (the controller test just verified the redirection),
resulted in the unforeseen side effect of not testing preview allowed status for a file name extention that is not listed
in application_mimetypes_with_view_icon (tar file in this case). Added this to test.
Tom Clegg [Tue, 21 Jul 2015 21:37:02 +0000 (17:37 -0400)]
Merge branch '6438-multiplatform-install-guide-TC' refs #6499
Manoj [Tue, 21 Jul 2015 20:17:57 +0000 (16:17 -0400)]
refs #6465
Merge branch '6465-optimize-workbench-integration-tests'
Manoj [Tue, 21 Jul 2015 20:11:30 +0000 (16:11 -0400)]
6465: Changed "test dashboard button all #{target}" to use assert_includes
instead of css_select. css_select is throwing a wierd message.
radhika [Tue, 21 Jul 2015 19:08:11 +0000 (15:08 -0400)]
6473: last_log_id null error
Peter Amstutz [Tue, 21 Jul 2015 17:57:04 +0000 (13:57 -0400)]
6264: Typo fix.
Peter Amstutz [Tue, 21 Jul 2015 17:56:20 +0000 (13:56 -0400)]
6264: Code cleanup: rename "i" in _match() to "filename" and "t" and "r" in
arvExecutor to "tool" and "runnable".
radhika [Tue, 21 Jul 2015 17:32:17 +0000 (13:32 -0400)]
Merge branch 'master' into 6473-fetch-events-starting-at
radhika [Tue, 21 Jul 2015 17:31:44 +0000 (13:31 -0400)]
6473: fix issue with last_log_id argument.
Manoj [Tue, 21 Jul 2015 17:18:15 +0000 (13:18 -0400)]
refs #6465
Merge branch '6465-optimize-workbench-integration-tests'
Manoj [Tue, 21 Jul 2015 15:34:30 +0000 (11:34 -0400)]
closes #6652
Merge branch '6652-test-system-menu'
projects / arvados.git / log