arvados.git
10 years agoMerge branch '2189-log-in-as-user'
Tom Clegg [Mon, 10 Mar 2014 20:09:16 +0000 (16:09 -0400)]
Merge branch '2189-log-in-as-user'

closes #2189

10 years agoMerge branch '2076-check-config-at-boot'
Tom Clegg [Mon, 10 Mar 2014 20:09:04 +0000 (16:09 -0400)]
Merge branch '2076-check-config-at-boot'

closes #2076

10 years agoMerge branch 'master' into 2189-log-in-as-user
Tom Clegg [Mon, 10 Mar 2014 20:08:29 +0000 (16:08 -0400)]
Merge branch 'master' into 2189-log-in-as-user

10 years agoRename config[.defaults].yml to application[.default].yml
Tom Clegg [Mon, 10 Mar 2014 20:05:31 +0000 (16:05 -0400)]
Rename config[.defaults].yml to application[.default].yml

10 years agoMerge branch 'master' into 2076-check-config-at-boot
Tom Clegg [Mon, 10 Mar 2014 19:58:49 +0000 (15:58 -0400)]
Merge branch 'master' into 2076-check-config-at-boot

10 years agoFix incorrect API endpoints in api/schema/
Tom Clegg [Mon, 10 Mar 2014 17:21:55 +0000 (13:21 -0400)]
Fix incorrect API endpoints in api/schema/

10 years agoFix CollectionReader treating any collection with additional +hints as
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.

10 years agoMerge branch '1844-blob-signature'
Tom Clegg [Fri, 7 Mar 2014 20:02:14 +0000 (15:02 -0500)]
Merge branch '1844-blob-signature'

10 years agoMerge branch 'master' into 1844-blob-signature
Tom Clegg [Fri, 7 Mar 2014 20:02:00 +0000 (15:02 -0500)]
Merge branch 'master' into 1844-blob-signature

10 years agoCode review for 1844-blob-signature: documentation, slight refactoring (refs #1844)
Tim Pierce [Fri, 7 Mar 2014 19:35:49 +0000 (14:35 -0500)]
Code review for 1844-blob-signature: documentation, slight refactoring (refs #1844)

10 years agoFix check for crunch-job missing from path, and run it as arv-crunch-job.
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.

10 years agoFix crash when job script is nil.
Tom Clegg [Fri, 7 Mar 2014 18:31:59 +0000 (13:31 -0500)]
Fix crash when job script is nil.

10 years agoAdd arv-normalize to python SDK package.
Tom Clegg [Thu, 6 Mar 2014 22:54:07 +0000 (17:54 -0500)]
Add arv-normalize to python SDK package.

10 years agoAdd "rake config:check" task. refs #2076
Tom Clegg [Wed, 5 Mar 2014 19:46:09 +0000 (14:46 -0500)]
Add "rake config:check" task. refs #2076

10 years agoMerge branch '2107-radhika-user-guide-minor-updates'
radhika chippada [Wed, 5 Mar 2014 17:22:16 +0000 (12:22 -0500)]
Merge branch '2107-radhika-user-guide-minor-updates'

10 years agoFix Task#2268 by removing the extra space character
radhika chippada [Wed, 5 Mar 2014 17:20:17 +0000 (12:20 -0500)]
Fix Task#2268 by removing the extra space character

10 years agoRead configuration from config.defaults.yml and config.yml.
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

10 years agoAdd "Log in as user" button in Admin pane on users#show.
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

10 years agoFixed default inactive user page.
Peter Amstutz [Wed, 5 Mar 2014 02:57:40 +0000 (21:57 -0500)]
Fixed default inactive user page.

10 years agoAdd signing and verification code for blob permissions
Tom Clegg [Tue, 4 Mar 2014 22:12:25 +0000 (17:12 -0500)]
Add signing and verification code for blob permissions

10 years agoMerge branch 'master' into 2107-radhika-user-guide-minor-updates
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

10 years agoDocument baseurl and change to a useful default.
Tom Clegg [Tue, 4 Mar 2014 18:01:03 +0000 (13:01 -0500)]
Document baseurl and change to a useful default.

10 years agoUse require instead of rake_require. Fixes "Can't find
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

10 years agominor updates to user guide
radhika chippada [Mon, 3 Mar 2014 20:17:42 +0000 (15:17 -0500)]
minor updates to user guide

10 years agoAdded section about installing libwarehouse-perl.
Peter Amstutz [Mon, 3 Mar 2014 19:02:22 +0000 (14:02 -0500)]
Added section about installing libwarehouse-perl.

10 years agoGemfile update using ruby 2.1.1
Peter Amstutz [Mon, 3 Mar 2014 19:02:05 +0000 (14:02 -0500)]
Gemfile update using ruby 2.1.1

10 years agoMerge pull request #1 from gitaway/patch-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

10 years agoCorrect 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!

10 years agoBe consistent in referring to the 'All users' group.
Ward Vandewege [Mon, 3 Mar 2014 16:33:54 +0000 (11:33 -0500)]
Be consistent in referring to the 'All users' group.

10 years agoFixed broken links in documentation that were using {{site.basedoc}} instead of ...
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.

10 years agoFix jobs.cancel and add integration test. closes #2258
Tom Clegg [Sat, 1 Mar 2014 00:29:34 +0000 (16:29 -0800)]
Fix jobs.cancel and add integration test. closes #2258

10 years agoFix usage message dependent on credentials. Remove unused argparse import.
Tom Clegg [Sat, 1 Mar 2014 00:15:38 +0000 (16:15 -0800)]
Fix usage message dependent on credentials. Remove unused argparse import.

10 years agoSet up virtualenv and install custom SDK only if SDK appears in
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 -> .).

10 years agoAdd build.sh step to Python SDK install recipe (part 2).
Tom Clegg [Fri, 28 Feb 2014 23:07:05 +0000 (15:07 -0800)]
Add build.sh step to Python SDK install recipe (part 2).

10 years agoAdd build.sh step to Python SDK install recipe.
Tom Clegg [Fri, 28 Feb 2014 23:04:15 +0000 (15:04 -0800)]
Add build.sh step to Python SDK install recipe.

10 years agoDo not try to extract git archive if none was provided by calling process.
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.

10 years agoFix text color of active+hover nav link
Tom Clegg [Fri, 28 Feb 2014 18:06:44 +0000 (10:06 -0800)]
Fix text color of active+hover nav link

10 years agoFix refresh feature on pipeline_instances/show.
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.

10 years agoRevert "Move left nav all the way to the top left corner."
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.

10 years agoMove left nav all the way to the top left corner.
Tom Clegg [Tue, 25 Feb 2014 22:40:27 +0000 (14:40 -0800)]
Move left nav all the way to the top left corner.

10 years agoDo not blow up on node create when the ec2 configuration values are not
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.

10 years agoMerge branch '2060-edit-tags-in-workbench'
Tom Clegg [Tue, 25 Feb 2014 18:48:08 +0000 (10:48 -0800)]
Merge branch '2060-edit-tags-in-workbench'

closes #2060
closes #1981

10 years agoTurn off CSS animation on loading graphic; make it red instead.
Tom Clegg [Tue, 25 Feb 2014 18:46:11 +0000 (10:46 -0800)]
Turn off CSS animation on loading graphic; make it red instead.

10 years agoFix spacing of tag labels.
Tom Clegg [Tue, 25 Feb 2014 18:44:46 +0000 (10:44 -0800)]
Fix spacing of tag labels.

10 years agoFix files=nil -> files=[] in API response for empty collection.
Tom Clegg [Tue, 25 Feb 2014 17:57:02 +0000 (09:57 -0800)]
Fix files=nil -> files=[] in API response for empty collection.

10 years agoMerge branch 'master' into 2060-edit-tags-in-workbench
Tom Clegg [Tue, 25 Feb 2014 17:22:43 +0000 (09:22 -0800)]
Merge branch 'master' into 2060-edit-tags-in-workbench

10 years agoMerge 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

10 years agoUpdate Python SDK docs to reflect new llfuse dependencies.
Tom Clegg [Mon, 24 Feb 2014 22:19:43 +0000 (14:19 -0800)]
Update Python SDK docs to reflect new llfuse dependencies.

10 years agoDocument pkg-config dependency for llfuse.
Tom Clegg [Mon, 24 Feb 2014 22:10:09 +0000 (14:10 -0800)]
Document pkg-config dependency for llfuse.

10 years agoConsume all arguments after arv-mount --exec, and fork subprocess
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.

10 years agoUse fusermount -z to force detach and avoid hanging on exit.
Tom Clegg [Mon, 24 Feb 2014 21:25:33 +0000 (13:25 -0800)]
Use fusermount -z to force detach and avoid hanging on exit.

10 years agoUpdate Docker-based services to ruby-2.1.0.
Tim Pierce [Mon, 24 Feb 2014 21:27:21 +0000 (16:27 -0500)]
Update Docker-based services to ruby-2.1.0.

10 years agoUse rvm-exec to eliminate extra bash process provided by "rvm do". closes #2095
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

10 years agoUpdate Python SDK install step, add virtualenv dependency
Tom Clegg [Mon, 24 Feb 2014 20:12:28 +0000 (12:12 -0800)]
Update Python SDK install step, add virtualenv dependency

10 years agoUse %N instead of %n format and parse node ranges ourselves if slurm <2.3
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

10 years agoUpdate arvdock instructions.
Tim Pierce [Mon, 24 Feb 2014 19:24:43 +0000 (14:24 -0500)]
Update arvdock instructions.

10 years agoRemove -h flag from arv examples in docs, now that it means --help.
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.

10 years agoMerge branch 'master' of git.clinicalfuture.com:arvados
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.

10 years agoMerge branch '1965-fuse-support-directories'
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

10 years agoHash now uses get_task_param_mount() to read from fuse mount instead of CollectionReader.
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.

10 years agoAdded alternate option to one_task_per_input_file to encode specification of input...
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.

10 years agoAdded StreamFileReader.as_manifest() back and added test for it.
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.

10 years agoMerge branch 'master' into 2199-crunch-virtualenv
Tom Clegg [Fri, 21 Feb 2014 15:14:13 +0000 (10:14 -0500)]
Merge branch 'master' into 2199-crunch-virtualenv

10 years agoget_job_param_mount() and get_task_param_mount() tested and working.
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.

10 years agoAdded symlink arv-mount, arv-normalize, arv-ls to cli/bin
Peter Amstutz [Thu, 20 Feb 2014 19:25:12 +0000 (19:25 +0000)]
Added symlink arv-mount, arv-normalize, arv-ls to cli/bin

10 years agoAdded get_job_param_mount() and get_task_param_mount()
Peter Amstutz [Thu, 20 Feb 2014 19:25:12 +0000 (14:25 -0500)]
Added get_job_param_mount() and get_task_param_mount()

10 years agoChanged JOB_WORK to TASK_WORK in mounting keep directory.
Peter Amstutz [Thu, 20 Feb 2014 19:18:01 +0000 (14:18 -0500)]
Changed JOB_WORK to TASK_WORK in mounting keep directory.

10 years agoAdded arv-mount
Peter Amstutz [Thu, 20 Feb 2014 18:39:50 +0000 (13:39 -0500)]
Added arv-mount

10 years ago--exec works
Peter Amstutz [Thu, 20 Feb 2014 15:27:33 +0000 (15:27 +0000)]
--exec works

10 years agoAdded --exec, needs testing.
Peter Amstutz [Thu, 20 Feb 2014 15:17:43 +0000 (10:17 -0500)]
Added --exec, needs testing.

10 years agoFixed caching so that reads by other threads for a block which is already
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.

10 years agocaching wip
Peter Amstutz [Wed, 19 Feb 2014 22:10:26 +0000 (22:10 +0000)]
caching wip

10 years agoAdded test for magic directories.
Peter Amstutz [Wed, 19 Feb 2014 20:29:30 +0000 (15:29 -0500)]
Added test for magic directories.

10 years agoAdded basic unit test for fuse mount.
Peter Amstutz [Wed, 19 Feb 2014 20:24:43 +0000 (15:24 -0500)]
Added basic unit test for fuse mount.

10 years agochanged fusepy to llfuse
Peter Amstutz [Wed, 19 Feb 2014 20:00:40 +0000 (20:00 +0000)]
changed fusepy to llfuse

10 years agoinstalling llfuse from pip instead of debian
Peter Amstutz [Wed, 19 Feb 2014 19:59:09 +0000 (19:59 +0000)]
installing llfuse from pip instead of debian

10 years agoAdded comments and some refactoring.
Peter Amstutz [Wed, 19 Feb 2014 14:46:22 +0000 (09:46 -0500)]
Added comments and some refactoring.

10 years agoImprove headings in Python SDK installation section.
Ward Vandewege [Wed, 19 Feb 2014 02:45:31 +0000 (21:45 -0500)]
Improve headings in Python SDK installation section.

10 years agoUpdate Python SDK documentation to reflect availability of PyPI package,
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.

10 years agoImprove python sdk package building to allow for easy distribution via
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.

10 years agoUpdate url field in python sdk setup.py file.
Ward Vandewege [Tue, 18 Feb 2014 22:40:02 +0000 (17:40 -0500)]
Update url field in python sdk setup.py file.

10 years agoRobustness improvements
peter [Tue, 18 Feb 2014 22:36:01 +0000 (22:36 +0000)]
Robustness improvements

10 years agoFuse driver works for mounting collections and reading files. Tested with jlake...
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.

10 years agoWorking on fuse mount
Peter Amstutz [Tue, 18 Feb 2014 15:59:40 +0000 (10:59 -0500)]
Working on fuse mount

10 years agoDirectory browsing works, working on error handling for file reading.
Peter Amstutz [Tue, 18 Feb 2014 03:05:43 +0000 (22:05 -0500)]
Directory browsing works, working on error handling for file reading.

10 years agoWork in progress arv-mount based on llfuse and supporting directories listings.
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.

10 years agoFixed file page to sort by stream name, then by file name
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

10 years agoDo a partial normalization of file list before sending to client.
Peter Amstutz [Mon, 17 Feb 2014 20:13:48 +0000 (15:13 -0500)]
Do a partial normalization of file list before sending to client.

10 years agoPut some code into collection model to do normalization but I don't think that is...
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.

10 years agoRe-order left nav and make labels consistent with arvados vocabulary.
Tom Clegg [Mon, 17 Feb 2014 19:15:34 +0000 (11:15 -0800)]
Re-order left nav and make labels consistent with arvados vocabulary.

10 years agoAdded arv keep normalized
Peter Amstutz [Mon, 17 Feb 2014 19:06:00 +0000 (14:06 -0500)]
Added arv keep normalized

10 years agoAdded arv-normalize
Peter Amstutz [Mon, 17 Feb 2014 19:05:48 +0000 (14:05 -0500)]
Added arv-normalize

10 years agoadded -s option
Peter Amstutz [Mon, 17 Feb 2014 18:50:32 +0000 (18:50 +0000)]
added -s option

10 years agoimplemented arv-ls to replace whls
Peter Amstutz [Mon, 17 Feb 2014 18:41:51 +0000 (18:41 +0000)]
implemented arv-ls to replace whls

10 years agoWorking on arv-ls
Peter Amstutz [Mon, 17 Feb 2014 18:22:48 +0000 (13:22 -0500)]
Working on arv-ls

10 years agoMerge branch 'master' into 2199-crunch-virtualenv
Tom Clegg [Mon, 17 Feb 2014 17:30:35 +0000 (09:30 -0800)]
Merge branch 'master' into 2199-crunch-virtualenv

10 years agoFix more namespace bugs.
Tom Clegg [Mon, 17 Feb 2014 17:27:21 +0000 (09:27 -0800)]
Fix more namespace bugs.

10 years agoInstall Python SDK from repository (if present) into virtualenv for
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.

10 years agoFix missing : separator in PYTHONPATH.
Tom Clegg [Mon, 17 Feb 2014 16:57:53 +0000 (08:57 -0800)]
Fix missing : separator in PYTHONPATH.

10 years agoTests pass
Peter Amstutz [Mon, 17 Feb 2014 16:52:21 +0000 (11:52 -0500)]
Tests pass