Tom Clegg [Tue, 4 Aug 2015 17:38:39 +0000 (13:38 -0400)]
6663: Fix config/application.yml -> application.yml.
Tom Clegg [Tue, 4 Aug 2015 17:37:04 +0000 (13:37 -0400)]
6663: Finish editing sentence.
Tom Clegg [Tue, 4 Aug 2015 17:34:35 +0000 (13:34 -0400)]
6663: Add non-runit-dependent daemon startup script.
Tom Clegg [Tue, 4 Aug 2015 17:19:27 +0000 (13:19 -0400)]
6663: Remove unneeded nginx config, clarify where config should be added.
Tom Clegg [Tue, 4 Aug 2015 06:36:29 +0000 (02:36 -0400)]
6663: More explicit gitolite version advice, and link to home page.
Tom Clegg [Tue, 4 Aug 2015 05:58:06 +0000 (01:58 -0400)]
6663: Split "install runit" into debian and red hat variants.
Tom Clegg [Tue, 4 Aug 2015 05:49:38 +0000 (01:49 -0400)]
6663: Add "restart nginx" instructions.
Tom Clegg [Tue, 4 Aug 2015 05:41:45 +0000 (01:41 -0400)]
6663: Update nginx config to look more like API server's.
Tom Clegg [Tue, 4 Aug 2015 05:30:05 +0000 (01:30 -0400)]
6663: Formatting fixes.
Tom Clegg [Tue, 4 Aug 2015 05:22:15 +0000 (01:22 -0400)]
6663: Fix API config example for HTTPS, add corresponding SSH example.
Tom Clegg [Tue, 4 Aug 2015 05:21:59 +0000 (01:21 -0400)]
6663: gitolite, not arvados-git-sync.rb, creates empty repos.
Tom Clegg [Tue, 4 Aug 2015 05:08:28 +0000 (01:08 -0400)]
6663: Clarify "gitolite installed in X" vs. "hosted repos stored in X/repositories".
Tom Clegg [Tue, 4 Aug 2015 04:59:43 +0000 (00:59 -0400)]
6663: Clarify port 22 goes to sshd.
Tom Clegg [Tue, 4 Aug 2015 04:47:37 +0000 (00:47 -0400)]
6663: Clarify default vs. example git_repositories_dir.
Tom Clegg [Tue, 4 Aug 2015 04:46:00 +0000 (00:46 -0400)]
6663: Fix wrong bash prompt in example transcript.
Tom Clegg [Tue, 4 Aug 2015 04:45:27 +0000 (00:45 -0400)]
6663: Update default git_repositories_dir to match install guide.
Tom Clegg [Mon, 3 Aug 2015 19:50:28 +0000 (15:50 -0400)]
Merge branch 'master' into 6663-git-server
Conflicts:
doc/install/install-api-server.html.textile.liquid
Manoj [Mon, 3 Aug 2015 18:56:51 +0000 (14:56 -0400)]
closes #6414
Merge branch '6414-anonymous-public-projects-link'
Manoj [Mon, 3 Aug 2015 18:52:02 +0000 (14:52 -0400)]
6414: Added an assertion to test if objects are equal.
Brett Smith [Mon, 3 Aug 2015 18:04:21 +0000 (14:04 -0400)]
Merge branch '6591-6674-6676-nginx-docs-wip'
Closes #6591, #6674, #6676, #6739 (woo!).
Brett Smith [Mon, 3 Aug 2015 18:03:27 +0000 (14:03 -0400)]
6591: Add ssl_certificate lines to sample install nginx configs.
Brett Smith [Sat, 1 Aug 2015 19:07:04 +0000 (15:07 -0400)]
6676: Install docs recommend running SSO server behind Nginx.
This provides a straightforward way to get the server running as a
daemon, and matches our suggestions for other Web servers for
simplicity.
Brett Smith [Sat, 1 Aug 2015 19:05:23 +0000 (15:05 -0400)]
6591: Suggest proxy timeouts in install doc Nginx configs.
These settings match what we use in production. The defaults are more
aggressive and can cause 503 responses for larger requests.
Brett Smith [Sat, 1 Aug 2015 19:03:15 +0000 (15:03 -0400)]
6591: Improve install docs around $external_client variable.
Our Nginx configuration uses this variable to automatically set
X-External-Client: 1 in API request headers when clients don't have
direct access to Keep stores.
* Document the variable definition, and how to customize it, in the
suggested API server configuration.
* Remove the variable from the Workbench configuration. Workbench
does not currently read this header, so it isn't necessary.
Brett Smith [Sat, 1 Aug 2015 18:59:42 +0000 (14:59 -0400)]
6674: Install docs use Phusion's install instructions exclusively.
Don't suggest installing nginx packages from a distribution or
backports collection, because that conflicts with the instructions
provided by Phusion.
Tom Clegg [Mon, 3 Aug 2015 16:19:06 +0000 (12:19 -0400)]
6663: Use a more obviously fake token.
Brett Smith [Mon, 3 Aug 2015 16:08:52 +0000 (12:08 -0400)]
Merge branch '6221-write-trash-list'
Closes #6221, #6673.
Tom Clegg [Mon, 3 Aug 2015 03:10:55 +0000 (23:10 -0400)]
Merge branch '6598-crunch-progress-stats' closes #6598
Brett Smith [Mon, 3 Aug 2015 00:10:17 +0000 (20:10 -0400)]
Merge branch '6847-docker-dns-wip'
Closes #6847, #6853.
Brett Smith [Sun, 2 Aug 2015 14:07:16 +0000 (10:07 -0400)]
6847: Handle Docker DNS in Docker daemon configuration.
crunch-job currently uses the host's public IP address as a DNS
resolver for containers. This requires all compute nodes to run DNS,
which isn't strictly necessary. Remove this code, and document how to
set nameservers in the Docker daemon configuration.
Brett Smith [Sat, 1 Aug 2015 20:24:54 +0000 (16:24 -0400)]
Merge branch '6590-api-config-docs'
I am breaking our own rules here, since this merge includes a
non-trivial commit from me that hasn't been reviewed. I'm going ahead
with it because I understand the driving motivation of branch reviews
is to make sure two sets of eyes see changes that could impact future
work, and I think that's been accomplished here. My changes only
touch what Peter had already changed.
Plus, with Peter out for a week, the benefits of merging outweigh the
value of holding back. Users get the benefit of improved
documentation immediately; we'll look better at sprint review; and
documentation mistakes are comparatively easy to fix after the fact.
Closes #6590, #6721.
Brett Smith [Sat, 1 Aug 2015 20:02:15 +0000 (16:02 -0400)]
6590: Aesthetic improvements to the API install guide.
This implements the flow and grammar fixes requested in
<https://arvados.org/issues/6590#note-7>. It also separates the
documentation for git_repositories_dir and git_internal_dir, and adds
a note that git_internal_dir should not be a subdirectory of
git_repositories_dir.
Tom Clegg [Fri, 31 Jul 2015 17:10:03 +0000 (13:10 -0400)]
6598: Fix misreported "running tasks" stat.
Peter Amstutz [Fri, 31 Jul 2015 14:31:46 +0000 (10:31 -0400)]
Merge branch '6676-document-sso' refs #6676
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 13:37:58 +0000 (09:37 -0400)]
6663: Document git setup.
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 19:10:07 +0000 (15:10 -0400)]
6590: Rename database.yml.sample to database.yml.example so be consistent
between application.yml.example and database.yml.example
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.
Manoj [Thu, 30 Jul 2015 18:51:18 +0000 (14:51 -0400)]
6414: When viewing a public project, the text "Public Projects" now
links to the main public projects page. Added a test to verify link
is there.
Peter Amstutz [Thu, 30 Jul 2015 17:23:27 +0000 (13:23 -0400)]
6590: Reorganize application.default.yml. Improve documentation for essential
API server configuration. Remove obsolete hardcoded api tokens setting.
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.
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