Tom Clegg [Mon, 10 Mar 2014 20:09:16 +0000 (16:09 -0400)]
Merge branch '2189-log-in-as-user'
closes #2189
Tom Clegg [Mon, 10 Mar 2014 20:09:04 +0000 (16:09 -0400)]
Merge branch '2076-check-config-at-boot'
closes #2076
Tom Clegg [Mon, 10 Mar 2014 20:08:29 +0000 (16:08 -0400)]
Merge branch 'master' into 2189-log-in-as-user
Tom Clegg [Mon, 10 Mar 2014 20:05:31 +0000 (16:05 -0400)]
Rename config[.defaults].yml to application[.default].yml
Tom Clegg [Mon, 10 Mar 2014 19:58:49 +0000 (15:58 -0400)]
Merge branch 'master' into 2076-check-config-at-boot
Tom Clegg [Mon, 10 Mar 2014 17:21:55 +0000 (13:21 -0400)]
Fix incorrect API endpoints in api/schema/
Tom Clegg [Fri, 7 Mar 2014 21:49:47 +0000 (16:49 -0500)]
Fix CollectionReader treating any collection with additional +hints as
an empty manifest.
Now, accept hash+size+anyhints as a UUID, and if the argument looks
like neither a UUID nor a manifest, raise an exception instead of
proceeding with undefined results.
Tom Clegg [Fri, 7 Mar 2014 20:02:14 +0000 (15:02 -0500)]
Merge branch '1844-blob-signature'
Tom Clegg [Fri, 7 Mar 2014 20:02:00 +0000 (15:02 -0500)]
Merge branch 'master' into 1844-blob-signature
Tim Pierce [Fri, 7 Mar 2014 19:35:49 +0000 (14:35 -0500)]
Code review for 1844-blob-signature: documentation, slight refactoring (refs #1844)
Tom Clegg [Fri, 7 Mar 2014 18:37:03 +0000 (13:37 -0500)]
Fix check for crunch-job missing from path, and run it as arv-crunch-job.
Tom Clegg [Fri, 7 Mar 2014 18:31:59 +0000 (13:31 -0500)]
Fix crash when job script is nil.
Tom Clegg [Thu, 6 Mar 2014 22:54:07 +0000 (17:54 -0500)]
Add arv-normalize to python SDK package.
Tom Clegg [Wed, 5 Mar 2014 19:46:09 +0000 (14:46 -0500)]
Add "rake config:check" task. refs #2076
radhika chippada [Wed, 5 Mar 2014 17:22:16 +0000 (12:22 -0500)]
Merge branch '2107-radhika-user-guide-minor-updates'
radhika chippada [Wed, 5 Mar 2014 17:20:17 +0000 (12:20 -0500)]
Fix Task#2268 by removing the extra space character
Tom Clegg [Wed, 5 Mar 2014 09:35:45 +0000 (04:35 -0500)]
Read configuration from config.defaults.yml and config.yml.
Refuse to start if any configs are set to nil in config.default.yml
and not overridden in config/environments/*.rb or config.yml.
refs #2076
Tom Clegg [Wed, 5 Mar 2014 05:30:12 +0000 (00:30 -0500)]
Add "Log in as user" button in Admin pane on users#show.
refs #2189
Peter Amstutz [Wed, 5 Mar 2014 02:57:40 +0000 (21:57 -0500)]
Fixed default inactive user page.
Tom Clegg [Tue, 4 Mar 2014 22:12:25 +0000 (17:12 -0500)]
Add signing and verification code for blob permissions
radhika chippada [Tue, 4 Mar 2014 20:31:31 +0000 (15:31 -0500)]
Merge branch 'master' into 2107-radhika-user-guide-minor-updates
Conflicts:
doc/_config.yml
Tom Clegg [Tue, 4 Mar 2014 18:01:03 +0000 (13:01 -0500)]
Document baseurl and change to a useful default.
Tom Clegg [Tue, 4 Mar 2014 17:31:54 +0000 (12:31 -0500)]
Use require instead of rake_require. Fixes "Can't find
zenweb/tasks".
See
https://github.com/seattlerb/zenweb/commit/
4a28f3c8d766be7066658706d49b675d2a0f94ad
radhika chippada [Mon, 3 Mar 2014 20:17:42 +0000 (15:17 -0500)]
minor updates to user guide
Peter Amstutz [Mon, 3 Mar 2014 19:02:22 +0000 (14:02 -0500)]
Added section about installing libwarehouse-perl.
Peter Amstutz [Mon, 3 Mar 2014 19:02:05 +0000 (14:02 -0500)]
Gemfile update using ruby 2.1.1
tetron [Mon, 3 Mar 2014 16:51:57 +0000 (11:51 -0500)]
Merge pull request #1 from gitaway/patch-1
Correct parameterized input collection reference
Phil Hodgson [Mon, 3 Mar 2014 16:40:15 +0000 (11:40 -0500)]
Correct parameterized input collection reference
Attempting to follow the tutorial I was blocked because the UUID for the alternate input supplied as a command line parameter was incomplete. This can be easily overlooked because in fact the final filtered output is a zero-length file in either case: it's just that currently it is zero-length only because its input is empty!
Ward Vandewege [Mon, 3 Mar 2014 16:33:54 +0000 (11:33 -0500)]
Be consistent in referring to the 'All users' group.
Peter Amstutz [Sat, 1 Mar 2014 02:36:00 +0000 (21:36 -0500)]
Fixed broken links in documentation that were using {{site.basedoc}} instead of {{site.baseurl}}.
Fixed some other links so that documentation can be browsed from file:///
Made some updates to API server setup guide.
Tom Clegg [Sat, 1 Mar 2014 00:29:34 +0000 (16:29 -0800)]
Fix jobs.cancel and add integration test. closes #2258
Tom Clegg [Sat, 1 Mar 2014 00:15:38 +0000 (16:15 -0800)]
Fix usage message dependent on credentials. Remove unused argparse import.
Tom Clegg [Fri, 28 Feb 2014 23:28:55 +0000 (15:28 -0800)]
Set up virtualenv and install custom SDK only if SDK appears in
arvados/sdk/python -- ignore sdk/python.
This means scripts that are run straight from the arvados tree will
use whatever SDK is installed on the compute node, rather than
installing the SDK and dependencies into a virtualenv.
If you want your scripts to be in [a fork of] the arvados tree rather
than bringing in arvados as a submodule, *and* you want to pin jobs to
a specific SDK version, add a symbolic link in your source tree
(/arvados -> .).
Tom Clegg [Fri, 28 Feb 2014 23:07:05 +0000 (15:07 -0800)]
Add build.sh step to Python SDK install recipe (part 2).
Tom Clegg [Fri, 28 Feb 2014 23:04:15 +0000 (15:04 -0800)]
Add build.sh step to Python SDK install recipe.
Tom Clegg [Fri, 28 Feb 2014 22:58:28 +0000 (14:58 -0800)]
Do not try to extract git archive if none was provided by calling process.
Tom Clegg [Fri, 28 Feb 2014 18:06:44 +0000 (10:06 -0800)]
Fix text color of active+hover nav link
Tom Clegg [Thu, 27 Feb 2014 23:24:58 +0000 (15:24 -0800)]
Fix refresh feature on pipeline_instances/show.
Note symbolic link to ../application/show.html.erb seems to be
necessary for "render template: 'pipeline_instances/show'" to work;
rails doesn't fall back to application/show automatically here.
Tom Clegg [Thu, 27 Feb 2014 22:43:35 +0000 (14:43 -0800)]
Revert "Move left nav all the way to the top left corner."
This reverts commit
d7a07294a8d4a546852a33417972924f658e4024.
Tom Clegg [Tue, 25 Feb 2014 22:40:27 +0000 (14:40 -0800)]
Move left nav all the way to the top left corner.
Ward Vandewege [Tue, 25 Feb 2014 20:36:25 +0000 (15:36 -0500)]
Do not blow up on node create when the ec2 configuration values are not
set.
All this ec2-specific stuff needs to be ripped out, but for now this
will have to do.
Tom Clegg [Tue, 25 Feb 2014 18:48:08 +0000 (10:48 -0800)]
Merge branch '2060-edit-tags-in-workbench'
closes #2060
closes #1981
Tom Clegg [Tue, 25 Feb 2014 18:46:11 +0000 (10:46 -0800)]
Turn off CSS animation on loading graphic; make it red instead.
Tom Clegg [Tue, 25 Feb 2014 18:44:46 +0000 (10:44 -0800)]
Fix spacing of tag labels.
Tom Clegg [Tue, 25 Feb 2014 17:57:02 +0000 (09:57 -0800)]
Fix files=nil -> files=[] in API response for empty collection.
Tom Clegg [Tue, 25 Feb 2014 17:22:43 +0000 (09:22 -0800)]
Merge branch 'master' into 2060-edit-tags-in-workbench
Tom Clegg [Tue, 25 Feb 2014 17:21:54 +0000 (09:21 -0800)]
Merge branch 'master' into 2060-edit-tags-in-workbench
Tom Clegg [Mon, 24 Feb 2014 22:19:43 +0000 (14:19 -0800)]
Update Python SDK docs to reflect new llfuse dependencies.
Tom Clegg [Mon, 24 Feb 2014 22:10:09 +0000 (14:10 -0800)]
Document pkg-config dependency for llfuse.
Tom Clegg [Mon, 24 Feb 2014 21:49:13 +0000 (13:49 -0800)]
Consume all arguments after arv-mount --exec, and fork subprocess
without a shell to avoid double shell expansion.
Tom Clegg [Mon, 24 Feb 2014 21:25:33 +0000 (13:25 -0800)]
Use fusermount -z to force detach and avoid hanging on exit.
Tim Pierce [Mon, 24 Feb 2014 21:27:21 +0000 (16:27 -0500)]
Update Docker-based services to ruby-2.1.0.
Tom Clegg [Mon, 24 Feb 2014 20:14:04 +0000 (12:14 -0800)]
Use rvm-exec to eliminate extra bash process provided by "rvm do". closes #2095
Tom Clegg [Mon, 24 Feb 2014 20:12:28 +0000 (12:12 -0800)]
Update Python SDK install step, add virtualenv dependency
Tom Clegg [Mon, 24 Feb 2014 19:32:41 +0000 (11:32 -0800)]
Use %N instead of %n format and parse node ranges ourselves if slurm <2.3
Tim Pierce [Mon, 24 Feb 2014 19:24:43 +0000 (14:24 -0500)]
Update arvdock instructions.
Tom Clegg [Fri, 21 Feb 2014 19:50:14 +0000 (14:50 -0500)]
Remove -h flag from arv examples in docs, now that it means --help.
Peter Amstutz [Fri, 21 Feb 2014 18:23:58 +0000 (13:23 -0500)]
Merge branch 'master' of git.clinicalfuture.com:arvados
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
Peter Amstutz [Fri, 21 Feb 2014 18:23:19 +0000 (13:23 -0500)]
Merge branch '1965-fuse-support-directories'
Conflicts:
sdk/python/arvados/keep.py
Peter Amstutz [Fri, 21 Feb 2014 16:34:44 +0000 (11:34 -0500)]
Hash now uses get_task_param_mount() to read from fuse mount instead of CollectionReader.
Peter Amstutz [Fri, 21 Feb 2014 16:23:46 +0000 (11:23 -0500)]
Added alternate option to one_task_per_input_file to encode specification of input files as collection/stream/file instead of raw manifest text.
Peter Amstutz [Fri, 21 Feb 2014 16:02:34 +0000 (11:02 -0500)]
Added StreamFileReader.as_manifest() back and added test for it.
Refactored manifest text generation a bit.
Tom Clegg [Fri, 21 Feb 2014 15:14:13 +0000 (10:14 -0500)]
Merge branch 'master' into 2199-crunch-virtualenv
Peter Amstutz [Thu, 20 Feb 2014 19:33:09 +0000 (19:33 +0000)]
get_job_param_mount() and get_task_param_mount() tested and working.
Peter Amstutz [Thu, 20 Feb 2014 19:25:12 +0000 (19:25 +0000)]
Added symlink arv-mount, arv-normalize, arv-ls to cli/bin
Peter Amstutz [Thu, 20 Feb 2014 19:25:12 +0000 (14:25 -0500)]
Added get_job_param_mount() and get_task_param_mount()
Peter Amstutz [Thu, 20 Feb 2014 19:18:01 +0000 (14:18 -0500)]
Changed JOB_WORK to TASK_WORK in mounting keep directory.
Peter Amstutz [Thu, 20 Feb 2014 18:39:50 +0000 (13:39 -0500)]
Added arv-mount
Peter Amstutz [Thu, 20 Feb 2014 15:27:33 +0000 (15:27 +0000)]
--exec works
Peter Amstutz [Thu, 20 Feb 2014 15:17:43 +0000 (10:17 -0500)]
Added --exec, needs testing.
Peter Amstutz [Thu, 20 Feb 2014 03:15:44 +0000 (03:15 +0000)]
Fixed caching so that reads by other threads for a block which is already
being downloaded will block all threads until the block is downloaded.
Peter Amstutz [Wed, 19 Feb 2014 22:10:26 +0000 (22:10 +0000)]
caching wip
Peter Amstutz [Wed, 19 Feb 2014 20:29:30 +0000 (15:29 -0500)]
Added test for magic directories.
Peter Amstutz [Wed, 19 Feb 2014 20:24:43 +0000 (15:24 -0500)]
Added basic unit test for fuse mount.
Peter Amstutz [Wed, 19 Feb 2014 20:00:40 +0000 (20:00 +0000)]
changed fusepy to llfuse
Peter Amstutz [Wed, 19 Feb 2014 19:59:09 +0000 (19:59 +0000)]
installing llfuse from pip instead of debian
Peter Amstutz [Wed, 19 Feb 2014 14:46:22 +0000 (09:46 -0500)]
Added comments and some refactoring.
Ward Vandewege [Wed, 19 Feb 2014 02:45:31 +0000 (21:45 -0500)]
Improve headings in Python SDK installation section.
Ward Vandewege [Wed, 19 Feb 2014 02:42:58 +0000 (21:42 -0500)]
Update Python SDK documentation to reflect availability of PyPI package,
as well as the updated build-from-source instructions.
Ward Vandewege [Wed, 19 Feb 2014 02:33:37 +0000 (21:33 -0500)]
Improve python sdk package building to allow for easy distribution via
pypi.
Ward Vandewege [Tue, 18 Feb 2014 22:40:02 +0000 (17:40 -0500)]
Update url field in python sdk setup.py file.
peter [Tue, 18 Feb 2014 22:36:01 +0000 (22:36 +0000)]
Robustness improvements
peter [Tue, 18 Feb 2014 21:07:37 +0000 (21:07 +0000)]
Fuse driver works for mounting collections and reading files. Tested with jlake collection, spot checked m5dsum values of several files which matched the md5sum catalog in the jlake collection.
Peter Amstutz [Tue, 18 Feb 2014 15:59:40 +0000 (10:59 -0500)]
Working on fuse mount
Peter Amstutz [Tue, 18 Feb 2014 03:05:43 +0000 (22:05 -0500)]
Directory browsing works, working on error handling for file reading.
Peter Amstutz [Mon, 17 Feb 2014 22:11:39 +0000 (17:11 -0500)]
Work in progress arv-mount based on llfuse and supporting directories listings.
Peter Amstutz [Mon, 17 Feb 2014 20:29:28 +0000 (15:29 -0500)]
Fixed file page to sort by stream name, then by file name
Peter Amstutz [Mon, 17 Feb 2014 20:13:48 +0000 (15:13 -0500)]
Do a partial normalization of file list before sending to client.
Peter Amstutz [Mon, 17 Feb 2014 19:34:41 +0000 (14:34 -0500)]
Put some code into collection model to do normalization but I don't think that is the right place for it.
Tom Clegg [Mon, 17 Feb 2014 19:15:34 +0000 (11:15 -0800)]
Re-order left nav and make labels consistent with arvados vocabulary.
Peter Amstutz [Mon, 17 Feb 2014 19:06:00 +0000 (14:06 -0500)]
Added arv keep normalized
Peter Amstutz [Mon, 17 Feb 2014 19:05:48 +0000 (14:05 -0500)]
Added arv-normalize
Peter Amstutz [Mon, 17 Feb 2014 18:50:32 +0000 (18:50 +0000)]
added -s option
Peter Amstutz [Mon, 17 Feb 2014 18:41:51 +0000 (18:41 +0000)]
implemented arv-ls to replace whls
Peter Amstutz [Mon, 17 Feb 2014 18:22:48 +0000 (13:22 -0500)]
Working on arv-ls
Tom Clegg [Mon, 17 Feb 2014 17:30:35 +0000 (09:30 -0800)]
Merge branch 'master' into 2199-crunch-virtualenv
Tom Clegg [Mon, 17 Feb 2014 17:27:21 +0000 (09:27 -0800)]
Fix more namespace bugs.
Tom Clegg [Mon, 17 Feb 2014 17:26:52 +0000 (09:26 -0800)]
Install Python SDK from repository (if present) into virtualenv for
crunch job.
Tom Clegg [Mon, 17 Feb 2014 16:57:53 +0000 (08:57 -0800)]
Fix missing : separator in PYTHONPATH.
Peter Amstutz [Mon, 17 Feb 2014 16:52:21 +0000 (11:52 -0500)]
Tests pass