arvados.git
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

10 years agoFix namespace bugs.
Tom Clegg [Mon, 17 Feb 2014 15:55:24 +0000 (07:55 -0800)]
Fix namespace bugs.

10 years agoAdded readfrom()
Peter Amstutz [Mon, 17 Feb 2014 03:21:31 +0000 (22:21 -0500)]
Added readfrom()

10 years agoUnit tests for arvados.locators_and_ranges
Peter Amstutz [Mon, 17 Feb 2014 03:14:04 +0000 (22:14 -0500)]
Unit tests for arvados.locators_and_ranges

10 years agoAdd {repo}/arvados/sdk/python to Python search path during crunch job.
Tom Clegg [Mon, 17 Feb 2014 00:14:45 +0000 (16:14 -0800)]
Add {repo}/arvados/sdk/python to Python search path during crunch job.

10 years agoMerge branch 'master' into 2060-edit-tags-in-workbench
Tom Clegg [Sun, 16 Feb 2014 11:05:35 +0000 (03:05 -0800)]
Merge branch 'master' into 2060-edit-tags-in-workbench

10 years agoUpdate fixed header rows after new content arrives via ajax.
Tom Clegg [Sun, 16 Feb 2014 11:05:16 +0000 (03:05 -0800)]
Update fixed header rows after new content arrives via ajax.

10 years agoLighten and add tooltips to "delete tag" buttons.
Tom Clegg [Sun, 16 Feb 2014 10:58:28 +0000 (02:58 -0800)]
Lighten and add tooltips to "delete tag" buttons.

10 years agoFix breadcrumb-hiding on user agreements page. closes #2191
Tom Clegg [Sun, 16 Feb 2014 10:39:22 +0000 (02:39 -0800)]
Fix breadcrumb-hiding on user agreements page. closes #2191

10 years agoMerge branch 'master' into 2060-edit-tags-in-workbench
Tom Clegg [Sun, 16 Feb 2014 10:36:57 +0000 (02:36 -0800)]
Merge branch 'master' into 2060-edit-tags-in-workbench

10 years agoFix fixed-header-row hack. closes #2194
Tom Clegg [Sun, 16 Feb 2014 10:36:32 +0000 (02:36 -0800)]
Fix fixed-header-row hack. closes #2194

10 years agoLight up "add tag" buttons on button hover, not cell hover.
Tom Clegg [Sun, 16 Feb 2014 10:23:07 +0000 (02:23 -0800)]
Light up "add tag" buttons on button hover, not cell hover.

10 years agoDo not show "delete tag" button unless current user owns tag.
Tom Clegg [Sun, 16 Feb 2014 10:23:02 +0000 (02:23 -0800)]
Do not show "delete tag" button unless current user owns tag.

10 years agoAdd and remove collection tags with ajax.
Tom Clegg [Sun, 16 Feb 2014 10:17:15 +0000 (02:17 -0800)]
Add and remove collection tags with ajax.

10 years agoFix up tag and "add tag" button display.
Tom Clegg [Sun, 16 Feb 2014 09:04:30 +0000 (01:04 -0800)]
Fix up tag and "add tag" button display.

10 years agoMerge branch 'master' into 2060-edit-tags-in-workbench
Tom Clegg [Sun, 16 Feb 2014 08:26:54 +0000 (00:26 -0800)]
Merge branch 'master' into 2060-edit-tags-in-workbench

Conflicts:
apps/workbench/app/assets/javascripts/application.js
apps/workbench/app/assets/stylesheets/application.css.scss

10 years agoMerge branch '2179-demo-feedback'
Tom Clegg [Sun, 16 Feb 2014 02:55:57 +0000 (18:55 -0800)]
Merge branch '2179-demo-feedback'

refs #2179

10 years agoRender collection provenance graph top-down like other graphs.
Tom Clegg [Sun, 16 Feb 2014 02:50:18 +0000 (18:50 -0800)]
Render collection provenance graph top-down like other graphs.

closes #2184

10 years agoMerge branch 'master' into 2179-demo-feedback
Tom Clegg [Sun, 16 Feb 2014 02:08:26 +0000 (18:08 -0800)]
Merge branch 'master' into 2179-demo-feedback

10 years agoFix symbol key used in serialized attribute. closes #2186
Tom Clegg [Sun, 16 Feb 2014 02:04:47 +0000 (18:04 -0800)]
Fix symbol key used in serialized attribute. closes #2186

10 years agoFix crash if @notifications is nil.
Tom Clegg [Sun, 16 Feb 2014 01:43:14 +0000 (17:43 -0800)]
Fix crash if @notifications is nil.

10 years agoReturn only true or false for is_invited, never group uuid.
Tom Clegg [Sun, 16 Feb 2014 01:30:21 +0000 (17:30 -0800)]
Return only true or false for is_invited, never group uuid.

10 years agoHide top nav notifications and links to tokens/keys pages until user
Tom Clegg [Sun, 16 Feb 2014 01:29:38 +0000 (17:29 -0800)]
Hide top nav notifications and links to tokens/keys pages until user
is active.

closes #2188

10 years agoSay when re-using existing jobs, even without debug mode. closes #2183
Tom Clegg [Sat, 15 Feb 2014 23:43:34 +0000 (15:43 -0800)]
Say when re-using existing jobs, even without debug mode. closes #2183

10 years agoOutput a blank line between pipeline status updates. closes #2182
Tom Clegg [Sat, 15 Feb 2014 23:19:12 +0000 (15:19 -0800)]
Output a blank line between pipeline status updates. closes #2182

10 years agoMove HeaderRowFixer out to application.js and application.css.scss
Tom Clegg [Sat, 15 Feb 2014 23:13:38 +0000 (15:13 -0800)]
Move HeaderRowFixer out to application.js and application.css.scss

refs #2180

10 years agoPrevent table headings from scrolling out of view on collections index
Tom Clegg [Sat, 15 Feb 2014 23:08:12 +0000 (15:08 -0800)]
Prevent table headings from scrolling out of view on collections index
table.

closes #2180

10 years agoFixing things up
Peter Amstutz [Sat, 15 Feb 2014 00:56:36 +0000 (19:56 -0500)]
Fixing things up

10 years agoWork in progress
Peter Amstutz [Fri, 14 Feb 2014 22:11:55 +0000 (17:11 -0500)]
Work in progress

10 years agoHide left nav panel if current_user is not active. refs #2078
Tom Clegg [Fri, 14 Feb 2014 19:49:07 +0000 (11:49 -0800)]
Hide left nav panel if current_user is not active. refs #2078

10 years agoCollections are now automatically normalized on both read and write. Tests updated.
Peter Amstutz [Fri, 14 Feb 2014 19:41:22 +0000 (14:41 -0500)]
Collections are now automatically normalized on both read and write.  Tests updated.

10 years agoProvide manifest_text in collections.get API response. refs #2070
Tom Clegg [Fri, 14 Feb 2014 19:26:44 +0000 (11:26 -0800)]
Provide manifest_text in collections.get API response. refs #2070

10 years agoNormalize method seems to work pretty well now.
Peter Amstutz [Fri, 14 Feb 2014 16:43:06 +0000 (11:43 -0500)]
Normalize method seems to work pretty well now.

10 years agoFix crash in collections.provenance when a script_parameter is a Fixnum.
Tom Clegg [Fri, 14 Feb 2014 04:48:40 +0000 (20:48 -0800)]
Fix crash in collections.provenance when a script_parameter is a Fixnum.

10 years agoworking on normalization
Peter Amstutz [Thu, 13 Feb 2014 23:05:51 +0000 (23:05 +0000)]
working on normalization

10 years agoNormalize collection hashes provided by clients as attribute values
Tom Clegg [Thu, 13 Feb 2014 20:49:21 +0000 (12:49 -0800)]
Normalize collection hashes provided by clients as attribute values
before storing in the database.

closes #2088
refs #1881

10 years agoFix crash when a script_parameter value is a Fixnum. fixes #2167
Tom Clegg [Thu, 13 Feb 2014 19:16:53 +0000 (11:16 -0800)]
Fix crash when a script_parameter value is a Fixnum. fixes #2167

10 years agoFixed {% include alert-stub %} that shouldn't have been there on a couple of pages.
Peter Amstutz [Thu, 13 Feb 2014 16:52:47 +0000 (16:52 +0000)]
Fixed {% include alert-stub %} that shouldn't have been there on a couple of pages.

10 years agoFix 404 at api_client_authorizations.create_system_auth and add tests.
Tom Clegg [Thu, 13 Feb 2014 16:01:57 +0000 (08:01 -0800)]
Fix 404 at api_client_authorizations.create_system_auth and add tests.

10 years agoMerge branch '2099-CORRECT-docker-stop-and-restart' (documentation update)
Tim Pierce [Thu, 13 Feb 2014 14:44:09 +0000 (09:44 -0500)]
Merge branch '2099-CORRECT-docker-stop-and-restart' (documentation update)

10 years agoUpdated Docker documentation to reference "arvdock". (refs #2099)
Tim Pierce [Thu, 13 Feb 2014 14:42:50 +0000 (09:42 -0500)]
Updated Docker documentation to reference "arvdock". (refs #2099)

10 years agoChange color of "running" job label to blue.
Tom Clegg [Wed, 12 Feb 2014 23:31:59 +0000 (15:31 -0800)]
Change color of "running" job label to blue.

10 years agoMerge branch '2096-demo-feedback'
Tom Clegg [Wed, 12 Feb 2014 22:03:24 +0000 (14:03 -0800)]
Merge branch '2096-demo-feedback'

10 years agoIn the pipeline instance comparison, do not blow up when a row component
Ward Vandewege [Wed, 12 Feb 2014 20:52:13 +0000 (15:52 -0500)]
In the pipeline instance comparison, do not blow up when a row component
is not defined (for example, when one or more of the pipeline instances
in the comparison has not yet been executed).

10 years agoMerge branch '2099-CORRECT-docker-stop-and-restart'
Tim Pierce [Wed, 12 Feb 2014 19:59:14 +0000 (14:59 -0500)]
Merge branch '2099-CORRECT-docker-stop-and-restart'

10 years agoMerge branch 'master' into 2096-demo-feedback
Tom Clegg [Wed, 12 Feb 2014 19:57:50 +0000 (11:57 -0800)]
Merge branch 'master' into 2096-demo-feedback