bryan [Tue, 14 Jul 2015 20:48:06 +0000 (16:48 -0400)]
Note #15
bryan [Tue, 14 Jul 2015 20:35:58 +0000 (16:35 -0400)]
added note #13
bryan [Tue, 14 Jul 2015 19:07:31 +0000 (15:07 -0400)]
Fixed more syntax errors
bryan [Tue, 14 Jul 2015 19:00:54 +0000 (15:00 -0400)]
Fixed syntax
bryan [Tue, 14 Jul 2015 18:19:32 +0000 (14:19 -0400)]
Fixed more comments
bryan [Tue, 14 Jul 2015 18:01:19 +0000 (14:01 -0400)]
Fixed some changes but need to add copy git repos
bryan [Tue, 14 Jul 2015 17:53:49 +0000 (13:53 -0400)]
added png and need to switch to 6014 to grab the url
bryan [Tue, 14 Jul 2015 14:31:10 +0000 (10:31 -0400)]
added _arv_copy_expectations
bryan [Mon, 13 Jul 2015 17:02:58 +0000 (13:02 -0400)]
Ready for review
bryan [Mon, 13 Jul 2015 17:00:10 +0000 (13:00 -0400)]
changed formatting of cluster1 and cluster2
bryan [Mon, 13 Jul 2015 16:56:40 +0000 (12:56 -0400)]
changed arv-copy expectations and moved around words in the html file
bryan [Mon, 13 Jul 2015 16:47:12 +0000 (12:47 -0400)]
changed formatting and added words
bryan [Mon, 13 Jul 2015 15:41:12 +0000 (11:41 -0400)]
Added documentation for copying collections and pipeline templates and instances
bryan [Fri, 10 Jul 2015 19:43:48 +0000 (15:43 -0400)]
Change _config.yaml to point to arv-copy.html.textile.liquid
Brett Smith [Wed, 8 Jul 2015 21:19:53 +0000 (17:19 -0400)]
6358: Declare FUSE driver's dependency on llfuse >= 0.40.
The workaround added in
08284382 requires this version. Below that,
llfuse's Queue at least lives in a different place. We may be able to
support older versions with more nuance, but for now, just codify the
current reality.
Closes #6358. Refs #3198.
Nico Cesar [Wed, 8 Jul 2015 20:44:18 +0000 (16:44 -0400)]
qiuck fix to arvados-pam vulnerability
no issue #
Tom Clegg [Wed, 8 Jul 2015 18:56:30 +0000 (14:56 -0400)]
Merge branch '6377-dev-startup' refs #6377
Nico Cesar [Wed, 8 Jul 2015 18:09:07 +0000 (14:09 -0400)]
Merge branch '6384-libpam-arvados'
closes #6384
Ward Vandewege [Wed, 8 Jul 2015 17:58:41 +0000 (13:58 -0400)]
Whitespace fixes
refs #6384
Ward Vandewege [Wed, 8 Jul 2015 17:57:17 +0000 (13:57 -0400)]
Merge branch 'master' into 6384-libpam-arvados
Nico Cesar [Wed, 8 Jul 2015 17:53:31 +0000 (13:53 -0400)]
6384: reverting names
Ward Vandewege [Wed, 8 Jul 2015 16:47:07 +0000 (12:47 -0400)]
Rename file
refs #2256
Ward Vandewege [Wed, 8 Jul 2015 16:19:18 +0000 (12:19 -0400)]
Fix path for arvados_pam.py
refs #2256
Ward Vandewege [Wed, 8 Jul 2015 16:09:17 +0000 (12:09 -0400)]
Fix typo.
refs #2256
Nico Cesar [Wed, 8 Jul 2015 15:30:49 +0000 (11:30 -0400)]
added /etc/default/arvados_pam as a parameter
refs #6512
Tom Clegg [Wed, 8 Jul 2015 14:13:04 +0000 (10:13 -0400)]
Fix typo. No issue #
Tom Clegg [Wed, 8 Jul 2015 05:56:21 +0000 (01:56 -0400)]
6377: Update docs to use application.yml instead of omniauth.rb for SSO config.
Tom Clegg [Wed, 8 Jul 2015 05:12:58 +0000 (01:12 -0400)]
6377: Fix crash if no asset pipeline.
Tom Clegg [Tue, 7 Jul 2015 20:45:16 +0000 (16:45 -0400)]
6377: Update ruby to 2.1.6. Remove bundler version pin (not needed since
ca1d997).
Tom Clegg [Wed, 1 Jul 2015 02:47:50 +0000 (22:47 -0400)]
6377: Avoid "incompatible encoding" errors by using blank template0 instead of site-specific template1.
Tom Clegg [Tue, 30 Jun 2015 15:20:38 +0000 (11:20 -0400)]
6377: Fix reversed condition in "site application.yml is optional" fix.
Tom Clegg [Tue, 30 Jun 2015 15:19:04 +0000 (11:19 -0400)]
6377: Use fork of themes_for_rails with fixed gemspec.
Allows installing with current bundler versions, which treat the invalid
gemspec as an error.
Tom Clegg [Tue, 30 Jun 2015 15:07:24 +0000 (11:07 -0400)]
6377: Support loading omniauth config from application.yml.
Brett Smith [Tue, 7 Jul 2015 21:02:06 +0000 (17:02 -0400)]
Merge branch '5989-api-all-repos-permissions-wip'
Closes #5989, #6479.
Brett Smith [Sun, 5 Jul 2015 11:39:09 +0000 (07:39 -0400)]
5989: API repo perms method always returns all repos.
Previously the method would not return repositories that were not
accessible to any authorized key. This change helps deployment tools
like update-gitolite do repository setup correctly with a single API
call.
Tom Clegg [Fri, 26 Jun 2015 15:19:54 +0000 (11:19 -0400)]
6377: Missing application.yml is not an error.
Ward Vandewege [Mon, 6 Jul 2015 12:28:36 +0000 (08:28 -0400)]
Add arvados_pam.py and shellinabox pam configuration file.
Refs #2256
Nico Cesar [Thu, 2 Jul 2015 14:35:03 +0000 (10:35 -0400)]
5989: bug_1 added puppet repository patch
this is duplicated code from:
puppet/modules/arvados-git-server/templates/usr-local-arvados-update-gitolite.rb.erb
I just copy the code that was there
Nico Cesar [Wed, 1 Jul 2015 20:23:33 +0000 (16:23 -0400)]
5989: create directory structure for temp files
refs #5989 bug_1
Tom Clegg [Tue, 7 Jul 2015 15:42:12 +0000 (11:42 -0400)]
Merge branch '5677-plpgsql-warning' closes #5677
Tom Clegg [Fri, 26 Jun 2015 06:54:31 +0000 (02:54 -0400)]
5677: Edit structure.sql after db:structure:dump: avoid warnings when loading, and editwars when committing.
Manoj [Tue, 7 Jul 2015 13:08:21 +0000 (09:08 -0400)]
closes #6466
Merge branch '6466-disable-public-projects'
Manoj [Tue, 7 Jul 2015 13:07:33 +0000 (09:07 -0400)]
Merge branch 'master' into 6466-disable-public-projects
Brett Smith [Mon, 6 Jul 2015 21:37:21 +0000 (17:37 -0400)]
Merge branch '6438-multiplatform-install-guide-wip'
Closes #6438, #6455. Refs #6388.
Brett Smith [Mon, 6 Jul 2015 21:29:03 +0000 (17:29 -0400)]
6455: Include more steps in Crunch install docs.
* Document the necessary API server configuration change for
crunch-dispatch.
* Document Docker installation.
* Note compute node crunch users need to be in the fuse group.
Brett Smith [Mon, 6 Jul 2015 21:27:08 +0000 (17:27 -0400)]
6438: Modernize Rails server installation guides.
Document the package-based installation procedure, and associated
Nginx configuration.
Brett Smith [Mon, 6 Jul 2015 21:26:10 +0000 (17:26 -0400)]
6388: Add CentOS 6.6 instructions to install docs.
Manoj [Mon, 6 Jul 2015 18:00:24 +0000 (14:00 -0400)]
6466 - Update body html for enable public page and added tests to project controller test.
radhika [Mon, 6 Jul 2015 16:08:29 +0000 (12:08 -0400)]
closes #6013
Merge branch '6013-cleanup-setup-impl'
radhika [Fri, 3 Jul 2015 21:03:32 +0000 (17:03 -0400)]
6013: revert back the deactivate user button leading text in workbench user admin page.
radhika [Fri, 3 Jul 2015 20:56:53 +0000 (16:56 -0400)]
6013: update user notification email upon setup.
radhika [Fri, 3 Jul 2015 19:44:26 +0000 (15:44 -0400)]
6013: remove "repository" from user setup popup in workbench
Manoj [Fri, 3 Jul 2015 16:06:22 +0000 (12:06 -0400)]
6466:Added config parameter to disable public projects page and added a test to projects controller.
Nico Cesar [Thu, 2 Jul 2015 14:37:38 +0000 (10:37 -0400)]
Merge branch '5989-bug_1' merge with puppet repo "copy and paste" to sync up duplicated code.
refs #5989
Nico Cesar [Thu, 2 Jul 2015 14:35:03 +0000 (10:35 -0400)]
5989: bug_1 added puppet repository patch
this is duplicated code from:
puppet/modules/arvados-git-server/templates/usr-local-arvados-update-gitolite.rb.erb
I just copy the code that was there
Peter Amstutz [Thu, 2 Jul 2015 14:25:20 +0000 (10:25 -0400)]
Merge branch '6264-run-command-task-env' refs #6264
Peter Amstutz [Thu, 2 Jul 2015 13:47:52 +0000 (09:47 -0400)]
6264: Add task.env to documentation.
Peter Amstutz [Wed, 1 Jul 2015 21:43:28 +0000 (17:43 -0400)]
6264: Support setting environment variables.
Nico Cesar [Wed, 1 Jul 2015 20:23:33 +0000 (16:23 -0400)]
5989: create directory structure for temp files
refs #5989 bug_1
Brett Smith [Wed, 1 Jul 2015 12:25:15 +0000 (08:25 -0400)]
Invoke crunch-job with `/usr/bin/env perl`.
No issue #.
Nico Cesar [Mon, 29 Jun 2015 15:00:01 +0000 (11:00 -0400)]
Dockerfile had an error. fixed
no issue #
Nico Cesar [Mon, 29 Jun 2015 14:53:18 +0000 (10:53 -0400)]
we need to manually install python-pyasn1=0.1.7 python-pyasn1-modules=0.0.5 because apt-get wont resolve correctly.
apt-get install are less quiet now too.
no issue #
Tom Clegg [Fri, 26 Jun 2015 22:28:57 +0000 (18:28 -0400)]
6440: Display AJAX errors as text, not HTML. closes #6440
Brett Smith [Fri, 26 Jun 2015 19:52:46 +0000 (15:52 -0400)]
Fix bad CollectionReader reference in arv-put.
No issue #.
Brett Smith [Fri, 26 Jun 2015 15:42:10 +0000 (11:42 -0400)]
Merge branch '6432-pysdk-more-ca-certs-wip'
Closes #6432, #6434.
Brett Smith [Thu, 25 Jun 2015 23:36:52 +0000 (19:36 -0400)]
6432: Python SDK can find and use CA certs on Red Hat.
radhika [Fri, 26 Jun 2015 14:36:08 +0000 (10:36 -0400)]
closes #6234
Merge branch '6234-user-edit-self'
radhika [Fri, 26 Jun 2015 14:34:33 +0000 (10:34 -0400)]
Merge branch 'master' into 6234-user-edit-self
Peter Amstutz [Thu, 25 Jun 2015 17:55:07 +0000 (13:55 -0400)]
Update arvados_fuse version dependency on arvados-python-client. refs #3198
Peter Amstutz [Thu, 25 Jun 2015 17:52:18 +0000 (13:52 -0400)]
Merge branch '3198-writable-fuse' closes #3198
Peter Amstutz [Thu, 25 Jun 2015 14:30:28 +0000 (10:30 -0400)]
3198: Rename --enable-write to --read-write. Tweak docs.
radhika [Wed, 24 Jun 2015 14:24:14 +0000 (10:24 -0400)]
refs #6218
Merge branch '6218-add-performance-profiling-to-python-sdk'
radhika [Wed, 24 Jun 2015 14:22:46 +0000 (10:22 -0400)]
6218: update the exception handling.
radhika [Wed, 24 Jun 2015 13:58:39 +0000 (09:58 -0400)]
6218: correct exception handling.
Brett Smith [Tue, 23 Jun 2015 14:21:46 +0000 (10:21 -0400)]
6320: Update Workbench test for active user VM setup.
Now that the test fixtures give the active user access to testvm2,
this test needs to be updated to account for it, just like the API
server tests were. Refs #6320.
Brett Smith [Tue, 23 Jun 2015 14:13:46 +0000 (10:13 -0400)]
Remove unused modules from PySDK setup.py.
No issue #.
radhika [Tue, 23 Jun 2015 13:25:08 +0000 (09:25 -0400)]
6218: update the symlink and comment
Brett Smith [Mon, 22 Jun 2015 20:55:07 +0000 (16:55 -0400)]
Merge branch '4410-slurm-fails-are-tempfails-wip'
Closes #4410, #6283.
Tom Clegg [Mon, 22 Jun 2015 20:55:06 +0000 (16:55 -0400)]
6218: Refactor profiler as a decorator
Brett Smith [Mon, 15 Jun 2015 17:54:36 +0000 (13:54 -0400)]
4410: Crunch retries jobs when all SLURM nodes fail.
See the ticket for detailed background discussion and implementation
rationale, especially notes 13 and 14.
This required a couple of ancillary changes:
* crunch-job now makes a distinction between "task failed because a
node failed," and "task failed for other temporary reason." It uses
this additional information to decide when it should retry tasks
itself, and when it needs to give up and kick the problem up to
crunch-dispatch.
* crunch-job now handles creating log collections itself from
manifests generated by arv-put. This enables it to append to logs
generated during previous attempts to run the job.
Brett Smith [Mon, 15 Jun 2015 21:04:25 +0000 (17:04 -0400)]
4410: crunch-dispatch logs crunch-job exit later.
This makes it easier to log the exit code, and makes the logs look
nicer because the exit log doesn't interrupt crunch-job's stderr.
radhika [Mon, 22 Jun 2015 15:31:40 +0000 (11:31 -0400)]
6218: fix typo in sample test
radhika [Fri, 19 Jun 2015 21:01:32 +0000 (17:01 -0400)]
6218: add performance profiling and a sample test in python sdk.
Peter Amstutz [Thu, 18 Jun 2015 20:55:22 +0000 (16:55 -0400)]
3198: Fix test
Peter Amstutz [Thu, 18 Jun 2015 20:32:21 +0000 (16:32 -0400)]
3198: concurrency test and associated fixes
Peter Amstutz [Wed, 17 Jun 2015 21:06:57 +0000 (17:06 -0400)]
WIP
Brett Smith [Thu, 18 Jun 2015 15:35:40 +0000 (11:35 -0400)]
Merge branch '6320-api-logins-include-groups-wip'
Refs #6320. Closes #6325.
Brett Smith [Tue, 16 Jun 2015 13:40:58 +0000 (09:40 -0400)]
6320: API virtual machines login method include groups information.
This is necessary for the virtual machine user setup script to see the
groups information added in #6254.
This required updating a few tests that assumed the active user had no
access to testvm2.
Brett Smith [Tue, 16 Jun 2015 13:18:32 +0000 (09:18 -0400)]
6320: Add tests for API virtual machines login method.
radhika [Thu, 18 Jun 2015 14:49:23 +0000 (10:49 -0400)]
closes #6156
Merge branch '6156-hostnames-in-nodes'
radhika [Thu, 18 Jun 2015 14:47:54 +0000 (10:47 -0400)]
6156: convert the ping-should-fail test when hostname config is malformed into a controller test.
radhika [Thu, 18 Jun 2015 14:22:55 +0000 (10:22 -0400)]
Merge branch 'master' into 6156-hostnames-in-nodes
radhika [Thu, 18 Jun 2015 02:06:46 +0000 (22:06 -0400)]
refs #6277
Merge branch '6277-manifest-validation-api'
radhika [Thu, 18 Jun 2015 02:04:10 +0000 (22:04 -0400)]
6277: since locators are added to multilevel_collection_1 fixture, the collection retrieved after an update will have
a signed manifest; hence, the test needs to compare the old manifest with the new one after stripping signatures.
radhika [Wed, 17 Jun 2015 23:26:41 +0000 (19:26 -0400)]
refs #6277
Merge branch '6277-manifest-validation-api'
radhika [Wed, 17 Jun 2015 23:06:00 +0000 (19:06 -0400)]
6277: rename the before_validation filter check_manifest_validity as log_invalid_manifest_format until we are ready to actually validate manifest formats.
radhika [Wed, 17 Jun 2015 22:54:36 +0000 (18:54 -0400)]
Merge branch 'master' into 6277-manifest-validation-api
radhika [Wed, 17 Jun 2015 22:34:17 +0000 (18:34 -0400)]
6156: use only sprintf formatting for node slot_number config.
radhika [Wed, 17 Jun 2015 21:36:58 +0000 (17:36 -0400)]
Merge branch 'master' into 6156-hostnames-in-nodes
radhika [Wed, 17 Jun 2015 21:33:46 +0000 (17:33 -0400)]
6234: admin user can see other users' home projects; also add link to users' home projects in /users page rows.
projects / arvados.git / log