arvados.git
6 years ago12876: Fix up error/usage messages.
Tom Clegg [Sun, 24 Dec 2017 19:44:36 +0000 (14:44 -0500)]
12876: Fix up error/usage messages.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12876: More compatibility with "arv get".
Tom Clegg [Sat, 23 Dec 2017 06:26:28 +0000 (01:26 -0500)]
12876: More compatibility with "arv get".

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12876: Util to accept subcommand after initial args.
Tom Clegg [Sat, 23 Dec 2017 06:14:11 +0000 (01:14 -0500)]
12876: Util to accept subcommand after initial args.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12876: arvados-client get [-format=yaml] uuid
Tom Clegg [Fri, 22 Dec 2017 14:45:58 +0000 (09:45 -0500)]
12876: arvados-client get [-format=yaml] uuid

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoDependency update.
Ward Vandewege [Thu, 28 Dec 2017 21:18:29 +0000 (16:18 -0500)]
Dependency update.

refs #11876

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years agoUpdate docs in README
Tom Morris [Mon, 18 Dec 2017 19:16:23 +0000 (14:16 -0500)]
Update docs in README

Arvados-DCO-1.1-Signed-off-by: Tom Morris <tfmorris@veritasgenetics.com>

6 years agoMerge branch '12755-python3-centos7'
Tom Clegg [Fri, 22 Dec 2017 19:32:24 +0000 (14:32 -0500)]
Merge branch '12755-python3-centos7'

fixes #12755

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12755: Resume packaging arvados-docker-cleaner for centos7.
Tom Clegg [Fri, 22 Dec 2017 19:31:36 +0000 (14:31 -0500)]
12755: Resume packaging arvados-docker-cleaner for centos7.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12479: Syntax error fixed.
Lucas Di Pentima [Fri, 22 Dec 2017 16:41:58 +0000 (13:41 -0300)]
12479: Syntax error fixed.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago12755: Revert ce0a973 for python33 packages.
Tom Clegg [Fri, 22 Dec 2017 16:16:48 +0000 (11:16 -0500)]
12755: Revert ce0a973 for python33 packages.

They started trying to claim directories like /opt/rh/python33 and
became uninstallable as a result.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoAdded methods listAllCollections and listAllProjects.
Fuad Muhic [Fri, 22 Dec 2017 15:43:45 +0000 (16:43 +0100)]
Added methods listAllCollections and listAllProjects.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agorefs #12850 Merge branch '12850-docker-tag-version'
Fernando Monserrat [Fri, 22 Dec 2017 15:18:01 +0000 (12:18 -0300)]
refs #12850 Merge branch '12850-docker-tag-version'
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago12479: Avoid saving tags with name and/or value being empty string.
Lucas Di Pentima [Fri, 22 Dec 2017 15:11:59 +0000 (12:11 -0300)]
12479: Avoid saving tags with name and/or value being empty string.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years agoAdded code to notify user when API is unable to locate webDAV server.
Fuad Muhic [Fri, 22 Dec 2017 13:01:05 +0000 (14:01 +0100)]
Added code to notify user when API is unable to locate webDAV server.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years ago12479: Add placeholder messages on selectize boxes. Filter keys/values
Lucas Di Pentima [Fri, 22 Dec 2017 12:53:16 +0000 (09:53 -0300)]
12479: Add placeholder messages on selectize boxes. Filter keys/values
when being empty strings (ie: when adding new tags).
Fixed bug that made the Save button behave incorrectly.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years agoSplit Collectin's add method to add and create methods.
Fuad Muhic [Fri, 22 Dec 2017 11:32:39 +0000 (12:32 +0100)]
Split Collectin's add method to add and create methods.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoCollections getFileContent method renamed to getFileListing.
Fuad Muhic [Fri, 22 Dec 2017 10:44:14 +0000 (11:44 +0100)]
Collections getFileContent method renamed to getFileListing.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoMethods listCollections and listProjects now work properly
Fuad Muhic [Fri, 22 Dec 2017 10:12:39 +0000 (11:12 +0100)]
Methods listCollections and listProjects now work properly
when called without parameters. Removed old comments.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoNote DCO requirement.
Tom Clegg [Thu, 21 Dec 2017 18:48:54 +0000 (13:48 -0500)]
Note DCO requirement.

Fix some typos.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoFix copyright header, and copyright header checker exit code.
Tom Clegg [Thu, 21 Dec 2017 18:25:18 +0000 (13:25 -0500)]
Fix copyright header, and copyright header checker exit code.

No issue #

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch '12844-webdav-move-into-self'
Tom Clegg [Thu, 21 Dec 2017 17:41:19 +0000 (12:41 -0500)]
Merge branch '12844-webdav-move-into-self'

fixes #12844

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch 'patch-2' of https://github.com/jrandall/arvados
Tom Clegg [Thu, 21 Dec 2017 16:53:26 +0000 (11:53 -0500)]
Merge branch 'patch-2' of https://github.com/jrandall/arvados

fixes #11621

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agofix bwa-mem.cwl docker repo
Joshua C. Randall [Thu, 21 Dec 2017 14:54:13 +0000 (14:54 +0000)]
fix bwa-mem.cwl docker repo

Change from missing `biodckr/bwa` repo to minimal bwa docker image `lh3lh3/bwa`
The new docker image has `bwa` set as entrypoint, so also change `baseCommand` from `[bwa, mem]` to `[mem]`
Fixes 11621

Arvados-DCO-1.1-Signed-off-by: Joshua C. Randall <jcrandall@alum.mit.edu>

6 years ago12844: Refuse to unreference a directory by moving it into itself.
Tom Clegg [Thu, 21 Dec 2017 15:21:04 +0000 (10:21 -0500)]
12844: Refuse to unreference a directory by moving it into itself.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago#12850 trim whitespaces for lint
Fernando Monserrat [Thu, 21 Dec 2017 15:14:35 +0000 (12:14 -0300)]
#12850 trim whitespaces for lint
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years agoMade updating groups and collections less verbose.
Fuad Muhic [Thu, 21 Dec 2017 14:39:10 +0000 (15:39 +0100)]
Made updating groups and collections less verbose.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoMerge branch '11876-r-sdk' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Thu, 21 Dec 2017 13:09:47 +0000 (14:09 +0100)]
Merge branch '11876-r-sdk' of git.curoverse.com:arvados into 11876-r-sdk

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoFixed some bugs and improved error handling.
Fuad Muhic [Thu, 21 Dec 2017 12:57:51 +0000 (13:57 +0100)]
Fixed some bugs and improved error handling.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoExpand the README a bit, fix some syntax errors, add instructions for
Ward Vandewege [Thu, 21 Dec 2017 02:50:15 +0000 (21:50 -0500)]
Expand the README a bit, fix some syntax errors, add instructions for
building/installing from source.

refs #11876

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years agoFix typo
Ward Vandewege [Thu, 21 Dec 2017 02:22:37 +0000 (21:22 -0500)]
Fix typo

refs #11876

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years agoMerge branch 'master' into 12479-wb-structured-vocabulary
Lucas Di Pentima [Wed, 20 Dec 2017 22:24:45 +0000 (19:24 -0300)]
Merge branch 'master' into 12479-wb-structured-vocabulary

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago#12850 add tag as input for docker tag
Fernando Monserrat [Wed, 20 Dec 2017 20:25:23 +0000 (17:25 -0300)]
#12850 add tag as input for docker tag
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago12479: When requesting the collection, only ask the api server for the
Lucas Di Pentima [Wed, 20 Dec 2017 19:13:14 +0000 (16:13 -0300)]
12479: When requesting the collection, only ask the api server for the
properties.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago12479: Save button changes state when having changes to save and after
Lucas Di Pentima [Wed, 20 Dec 2017 18:38:04 +0000 (15:38 -0300)]
12479: Save button changes state when having changes to save and after
saving. When no tags, show a proper message.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago12479: Replacing isDirty flag with dirty stream
Lucas Di Pentima [Wed, 20 Dec 2017 16:13:14 +0000 (13:13 -0300)]
12479: Replacing isDirty flag with dirty stream

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago12479: WIP making the save objject show the save state
Lucas Di Pentima [Wed, 20 Dec 2017 16:00:21 +0000 (13:00 -0300)]
12479: WIP making the save objject show the save state

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years agoAdded a fix to project create and project update.
Fuad Muhic [Wed, 20 Dec 2017 10:25:47 +0000 (11:25 +0100)]
Added a fix to project create and project update.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Wed, 20 Dec 2017 09:25:34 +0000 (10:25 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoUsers are no longer able to delete root folder.
Fuad Muhic [Wed, 20 Dec 2017 09:24:27 +0000 (10:24 +0100)]
Users are no longer able to delete root folder.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years ago12479: Properties saving working. Remove tag button styling.
Lucas Di Pentima [Tue, 19 Dec 2017 22:04:10 +0000 (19:04 -0300)]
12479: Properties saving working. Remove tag button styling.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years agoMerge branch '12848-python-versions' 1.1.2
Tom Clegg [Tue, 19 Dec 2017 21:46:29 +0000 (16:46 -0500)]
Merge branch '12848-python-versions'

refs #12848

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12848: Fix python builder ignoring --build-version.
Tom Clegg [Tue, 19 Dec 2017 21:41:52 +0000 (16:41 -0500)]
12848: Fix python builder ignoring --build-version.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12479: Remove tag button working.
Lucas Di Pentima [Tue, 19 Dec 2017 18:45:30 +0000 (15:45 -0300)]
12479: Remove tag button working.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago12479: Refactoring to simplify the code.
Lucas Di Pentima [Tue, 19 Dec 2017 18:16:30 +0000 (15:16 -0300)]
12479: Refactoring to simplify the code.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years agoUpdated README file
Fuad Muhic [Tue, 19 Dec 2017 17:17:42 +0000 (18:17 +0100)]
Updated README file

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Tue, 19 Dec 2017 17:03:41 +0000 (18:03 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoAdded function to work with projects.
Fuad Muhic [Tue, 19 Dec 2017 17:02:45 +0000 (18:02 +0100)]
Added function to work with projects.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years ago12755: Stop building arvados-docker-cleaner for centos7.
Tom Clegg [Tue, 19 Dec 2017 16:19:00 +0000 (11:19 -0500)]
12755: Stop building arvados-docker-cleaner for centos7.

(until we make the package installable again)

refs #12755

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Tue, 19 Dec 2017 14:36:46 +0000 (15:36 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoAdded feature to move File-like object inside collection.
Fuad Muhic [Tue, 19 Dec 2017 14:34:44 +0000 (15:34 +0100)]
Added feature to move File-like object inside collection.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years ago12377: Update workbench test breaking since 484246ac0.
Tom Clegg [Tue, 19 Dec 2017 09:14:55 +0000 (04:14 -0500)]
12377: Update workbench test breaking since 484246ac0.

refs #12377

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch '12715-slow-propfind'
Tom Clegg [Tue, 19 Dec 2017 03:21:39 +0000 (22:21 -0500)]
Merge branch '12715-slow-propfind'

fixes #12715

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12479: Add Selectize via npm package
Lucas Di Pentima [Mon, 18 Dec 2017 22:12:04 +0000 (19:12 -0300)]
12479: Add Selectize via npm package

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years agoMerge branch '12822-keepproxy-token-scope'
Tom Clegg [Mon, 18 Dec 2017 22:04:36 +0000 (17:04 -0500)]
Merge branch '12822-keepproxy-token-scope'

refs #12822

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch '12377-workbench-composer-link' refs #12377
Peter Amstutz [Mon, 18 Dec 2017 20:36:10 +0000 (15:36 -0500)]
Merge branch '12377-workbench-composer-link' refs #12377

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago12479: Passing UUID & controller name data from data-mount-mithril element
Lucas Di Pentima [Mon, 18 Dec 2017 19:42:19 +0000 (16:42 -0300)]
12479: Passing UUID & controller name data from data-mount-mithril element
instead of parsing URL.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years agoMerge branch '12821-sbatch-script-race'
Tom Clegg [Mon, 18 Dec 2017 17:52:09 +0000 (12:52 -0500)]
Merge branch '12821-sbatch-script-race'

refs #12821

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoPrepare for packaging.
Ward Vandewege [Mon, 18 Dec 2017 16:06:09 +0000 (11:06 -0500)]
Prepare for packaging.

refs #12837

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Mon, 18 Dec 2017 15:39:41 +0000 (16:39 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoMade Subcollection and ArvadosFile more flexible.
Fuad Muhic [Mon, 18 Dec 2017 15:37:44 +0000 (16:37 +0100)]
Made Subcollection and ArvadosFile more flexible.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years ago12479: Assign default vocabulary on model instantiation
Lucas Di Pentima [Mon, 18 Dec 2017 13:57:34 +0000 (10:57 -0300)]
12479: Assign default vocabulary on model instantiation

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago12479: Get remote vocabulary definition, use a fallback is it doesn't exist.
Lucas Di Pentima [Mon, 18 Dec 2017 13:06:03 +0000 (10:06 -0300)]
12479: Get remote vocabulary definition, use a fallback is it doesn't exist.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago12479: New tag editor for structured vocabulary. There are pending
Lucas Di Pentima [Mon, 18 Dec 2017 11:10:21 +0000 (08:10 -0300)]
12479: New tag editor for structured vocabulary. There are pending
issues to be solved.

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

6 years ago12821: Fix race in concurrent calls to submit().
Tom Clegg [Sat, 16 Dec 2017 00:13:24 +0000 (19:13 -0500)]
12821: Fix race in concurrent calls to submit().

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch '12721-build-test-version'
Tom Clegg [Fri, 15 Dec 2017 20:21:26 +0000 (15:21 -0500)]
Merge branch '12721-build-test-version'

refs #12721

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12721: Add run-build-test-packages-one-target.sh --build-version arg
Tom Clegg [Fri, 15 Dec 2017 17:51:07 +0000 (12:51 -0500)]
12721: Add run-build-test-packages-one-target.sh --build-version arg

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12715: Rename flag !reading => alwaysReadEOF.
Tom Clegg [Fri, 15 Dec 2017 15:14:13 +0000 (10:14 -0500)]
12715: Rename flag !reading => alwaysReadEOF.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoAdd composer_url to arvbox workbench config refs #12377
Peter Amstutz [Fri, 15 Dec 2017 14:25:32 +0000 (09:25 -0500)]
Add composer_url to arvbox workbench config refs #12377

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Fri, 15 Dec 2017 12:01:48 +0000 (13:01 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoAdded feature to delete file from a collection.
Fuad Muhic [Fri, 15 Dec 2017 12:00:41 +0000 (13:00 +0100)]
Added feature to delete file from a collection.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years ago12715: Fix slow PROPFIND by avoiding content probing.
Tom Clegg [Fri, 15 Dec 2017 03:25:38 +0000 (22:25 -0500)]
12715: Fix slow PROPFIND by avoiding content probing.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12822: Allow reading from keepproxy with collection sharing tokens.
Tom Clegg [Fri, 15 Dec 2017 03:13:17 +0000 (22:13 -0500)]
12822: Allow reading from keepproxy with collection sharing tokens.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago12377: Add link to composer on workbench
Peter Amstutz [Thu, 14 Dec 2017 23:05:23 +0000 (18:05 -0500)]
12377: Add link to composer on workbench

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years agoMerge branch '8311-mount-git'
Tom Clegg [Thu, 14 Dec 2017 21:52:50 +0000 (16:52 -0500)]
Merge branch '8311-mount-git'

closes #8311

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Fix gitUrl discovery doc for config git_repo_https_base: true.
Tom Clegg [Thu, 14 Dec 2017 21:22:08 +0000 (16:22 -0500)]
8311: Fix gitUrl discovery doc for config git_repo_https_base: true.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Ensure git tree is readable even with umask 077.
Tom Clegg [Thu, 14 Dec 2017 21:14:00 +0000 (16:14 -0500)]
8311: Ensure git tree is readable even with umask 077.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Remove support for writable git_tree mount.
Tom Clegg [Thu, 14 Dec 2017 21:01:19 +0000 (16:01 -0500)]
8311: Remove support for writable git_tree mount.

Feature is of dubious value, and expected behavior isn't clear --
e.g., should all files be world-writable?

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Ensure git tree tmpdir is readable by container.
Tom Clegg [Thu, 14 Dec 2017 20:56:18 +0000 (15:56 -0500)]
8311: Ensure git tree tmpdir is readable by container.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Pass in container token to extractTree
Peter Amstutz [Thu, 14 Dec 2017 20:22:24 +0000 (15:22 -0500)]
8311: Pass in container token to extractTree

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago8311: Ensure gitUrl is always a string in the discovery doc.
Tom Clegg [Thu, 14 Dec 2017 20:22:18 +0000 (15:22 -0500)]
8311: Ensure gitUrl is always a string in the discovery doc.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Fix API tests broken in 4343e1f.
Tom Clegg [Thu, 14 Dec 2017 18:17:12 +0000 (13:17 -0500)]
8311: Fix API tests broken in 4343e1f.

* Restore arvados repo dropped from tarball.

* Fix git repo fixtures being removed in API test teardown.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Tidy up integration test services.
Tom Clegg [Thu, 14 Dec 2017 17:14:48 +0000 (12:14 -0500)]
8311: Tidy up integration test services.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Update docs to describe current implementation.
Tom Clegg [Thu, 14 Dec 2017 16:37:10 +0000 (11:37 -0500)]
8311: Update docs to describe current implementation.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Reject invalid/unsupported git mounts. Default to path="/".
Tom Clegg [Thu, 14 Dec 2017 16:26:02 +0000 (11:26 -0500)]
8311: Reject invalid/unsupported git mounts. Default to path="/".

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Thu, 14 Dec 2017 16:26:32 +0000 (17:26 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoAdded feature to create new file in a particular collection.
Fuad Muhic [Thu, 14 Dec 2017 16:22:01 +0000 (17:22 +0100)]
Added feature to create new file in a particular collection.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years ago8311: Try some git_tree mounts in TestSetupMounts.
Tom Clegg [Wed, 13 Dec 2017 22:13:42 +0000 (17:13 -0500)]
8311: Try some git_tree mounts in TestSetupMounts.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Add git_tree mount type.
Tom Clegg [Tue, 12 Dec 2017 23:56:07 +0000 (18:56 -0500)]
8311: Add git_tree mount type.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Add auth handler tests.
Tom Clegg [Thu, 14 Dec 2017 15:29:10 +0000 (10:29 -0500)]
8311: Add auth handler tests.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Access git repos by UUID.
Tom Clegg [Tue, 12 Dec 2017 23:58:15 +0000 (18:58 -0500)]
8311: Access git repos by UUID.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Fix "read" or "write" mistakenly appended to response data.
Tom Clegg [Thu, 14 Dec 2017 15:26:08 +0000 (10:26 -0500)]
8311: Fix "read" or "write" mistakenly appended to response data.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years ago8311: Remove debug printf.
Tom Clegg [Thu, 14 Dec 2017 15:25:14 +0000 (10:25 -0500)]
8311: Remove debug printf.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

6 years agoFix Access-Control-Allow-Headers CORS header tests refs #12060
Peter Amstutz [Thu, 14 Dec 2017 14:41:03 +0000 (09:41 -0500)]
Fix Access-Control-Allow-Headers CORS header tests refs #12060

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years agoAdd Content-Type to Access-Control-Allow-Headers CORS headers refs #12060
Peter Amstutz [Wed, 13 Dec 2017 21:17:43 +0000 (16:17 -0500)]
Add Content-Type to Access-Control-Allow-Headers CORS headers refs #12060

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years agoMerge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk
Fuad Muhic [Wed, 13 Dec 2017 17:08:49 +0000 (18:08 +0100)]
Merge branch 'master' of git.curoverse.com:arvados into 11876-r-sdk

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoRefactored collection tree into separate file.
Fuad Muhic [Wed, 13 Dec 2017 17:07:54 +0000 (18:07 +0100)]
Refactored collection tree into separate file.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years agoMerge branch '4019-query-properties' closes #4019
Peter Amstutz [Wed, 13 Dec 2017 16:12:56 +0000 (11:12 -0500)]
Merge branch '4019-query-properties' closes #4019

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years ago4019: More tests for error cases
Peter Amstutz [Wed, 13 Dec 2017 15:01:38 +0000 (10:01 -0500)]
4019: More tests for error cases

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

6 years agoAdded ability to write to a collection file.
Fuad Muhic [Wed, 13 Dec 2017 14:59:36 +0000 (15:59 +0100)]
Added ability to write to a collection file.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

6 years ago4019: Improve error checking, add tests for some error cases
Peter Amstutz [Wed, 13 Dec 2017 14:50:53 +0000 (09:50 -0500)]
4019: Improve error checking, add tests for some error cases

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>