arvados.git
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 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>

6 years agoMerge branch '12614-node-states' refs #12614
Peter Amstutz [Wed, 13 Dec 2017 14:12:42 +0000 (09:12 -0500)]
Merge branch '12614-node-states' refs #12614

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

6 years agoTag arvados/jobs image with $cwl_runner_version instead of git hash refs #12811
Peter Amstutz [Tue, 12 Dec 2017 21:19:37 +0000 (16:19 -0500)]
Tag arvados/jobs image with $cwl_runner_version instead of git hash refs #12811

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

6 years ago12614: Can shutdown failed nodes.
Peter Amstutz [Tue, 12 Dec 2017 20:39:30 +0000 (15:39 -0500)]
12614: Can shutdown failed nodes.

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

6 years ago12614: Support daemon actor aware of 'fail' node state
Peter Amstutz [Tue, 12 Dec 2017 18:58:16 +0000 (13:58 -0500)]
12614: Support daemon actor aware of 'fail' node state

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

6 years ago12614: Make node manager aware of "fail" node state.
Peter Amstutz [Tue, 12 Dec 2017 18:35:21 +0000 (13:35 -0500)]
12614: Make node manager aware of "fail" node state.

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 [Tue, 12 Dec 2017 16:52:57 +0000 (17:52 +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 agoMerge branch '12803-unescaped-colon-filename'
Tom Clegg [Tue, 12 Dec 2017 16:51:44 +0000 (11:51 -0500)]
Merge branch '12803-unescaped-colon-filename'

fixes #12803

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

6 years agoMerge branch '12765-workbench-404-trashed' refs #12765
Peter Amstutz [Tue, 12 Dec 2017 16:29:48 +0000 (11:29 -0500)]
Merge branch '12765-workbench-404-trashed' refs #12765

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

6 years ago12803: Accept unescaped colons in filenames.
Tom Clegg [Tue, 12 Dec 2017 16:29:37 +0000 (11:29 -0500)]
12803: Accept unescaped colons in filenames.

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

6 years ago4019: Add index for efficient jsonb query on collection properties
Peter Amstutz [Tue, 12 Dec 2017 15:40:40 +0000 (10:40 -0500)]
4019: Add index for efficient jsonb query on collection properties

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

6 years ago4019: Add URI quoting option for keys. Update docs. Fix tests.
Peter Amstutz [Tue, 12 Dec 2017 15:32:15 +0000 (10:32 -0500)]
4019: Add URI quoting option for keys.  Update docs.  Fix tests.

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

6 years agoImplemented feature to get size of ArvadosFile or Subcollection
Fuad Muhic [Tue, 12 Dec 2017 15:01:08 +0000 (16:01 +0100)]
Implemented feature to get size of ArvadosFile or Subcollection

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

6 years ago4019: Update docs. Tweak syntax of 'exists' and add alternate form.
Peter Amstutz [Mon, 11 Dec 2017 22:50:00 +0000 (17:50 -0500)]
4019: Update docs.  Tweak syntax of 'exists' and add alternate form.

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

6 years agoMerge branch '12550-crunch1-exit-race'
Tom Clegg [Mon, 11 Dec 2017 22:00:40 +0000 (17:00 -0500)]
Merge branch '12550-crunch1-exit-race'

refs #12550

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

6 years agoMerge branch '12511-is-trashed-query' refs #12511
Peter Amstutz [Mon, 11 Dec 2017 21:34:37 +0000 (16:34 -0500)]
Merge branch '12511-is-trashed-query' refs #12511

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

6 years ago4019: Expand testing. Make behavior consistent for != and "not in"
Peter Amstutz [Mon, 11 Dec 2017 21:33:12 +0000 (16:33 -0500)]
4019: Expand testing.  Make behavior consistent for != and "not in"

Rename "?" to "exists" and add "not exists".

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

6 years agoMerge branch '12167-python-request-id'
Tom Clegg [Mon, 11 Dec 2017 21:16:13 +0000 (16:16 -0500)]
Merge branch '12167-python-request-id'

refs #12167

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

6 years ago12167: Allow --silent to be combined with -*-progress flags.
Tom Clegg [Mon, 11 Dec 2017 20:43:04 +0000 (15:43 -0500)]
12167: Allow --silent to be combined with -*-progress flags.

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

6 years ago12167: Test arv-get and arv-put X-Request-Id logging.
Tom Clegg [Mon, 11 Dec 2017 19:32:01 +0000 (14:32 -0500)]
12167: Test arv-get and arv-put X-Request-Id logging.

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

6 years ago12511: readable_by filters on is_trashed directly
Peter Amstutz [Mon, 11 Dec 2017 16:54:52 +0000 (11:54 -0500)]
12511: readable_by filters on is_trashed directly

Fix performance problem in the negative join NOT EXISTS(...) used to filter out
trashed items for admin users.  The clause
(uuid = target_uuid OR owner_uuid = target_uuid) doesn't use the index
efficiently and results in a very expensive seq scan.

However, the "OR" in the negative clause is not necessary.  We only need
materialized_permission_view to know if "owner_uuid" is trashed (directly or
indirectly), not "uuid".  If the record type has an is_trashed flag (currently
only collections and groups) then it is more efficient to filter on that
directly.

This commit refactors the readable_by query to only check owner_uuid, and
additionally filter on "is_trashed" for collections and groups.

As an additional cleanup, because "readable_by" now explicitly knows to filter
on "is_trashed" this makes the default_scope in Collections redundant.  This
commit also removes default_scope & various uses of unscoped reduces complexity.

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

6 years ago12550: Fix race: read buffered data from stderr after child exits.
Tom Clegg [Mon, 11 Dec 2017 17:42:57 +0000 (12:42 -0500)]
12550: Fix race: read buffered data from stderr after child exits.

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

6 years agoRemoved debug logs.
Fuad Muhic [Mon, 11 Dec 2017 17:14:23 +0000 (18:14 +0100)]
Removed debug logs.

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 [Mon, 11 Dec 2017 16:36:50 +0000 (17:36 +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 agoMoved all classes from RefClass OOP model to R6 and made improvements
Fuad Muhic [Mon, 11 Dec 2017 16:34:20 +0000 (17:34 +0100)]
Moved all classes from RefClass OOP model to R6 and made improvements
to tree structure representing collection content.

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

6 years ago12721: Add missing _version.py, now part of source tree.
Tom Clegg [Mon, 11 Dec 2017 02:52:41 +0000 (21:52 -0500)]
12721: Add missing _version.py, now part of source tree.

refs #12721

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

6 years ago4019: Initial support for queries on jsonb subproperties.
Peter Amstutz [Sat, 9 Dec 2017 18:59:23 +0000 (13:59 -0500)]
4019: Initial support for queries on jsonb subproperties.

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

6 years agoMerge branch '12765-permission-graph-trash' refs #12765
Peter Amstutz [Sat, 9 Dec 2017 16:37:22 +0000 (11:37 -0500)]
Merge branch '12765-permission-graph-trash' refs #12765

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

6 years ago12765: Add explicit flag whether "trashed" propagates across an edge
Peter Amstutz [Fri, 8 Dec 2017 20:56:33 +0000 (15:56 -0500)]
12765: Add explicit flag whether "trashed" propagates across an edge

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

6 years ago12765: Add test case that "trashed" should not propagate over permission links.
Peter Amstutz [Fri, 8 Dec 2017 19:08:09 +0000 (14:08 -0500)]
12765: Add test case that "trashed" should not propagate over permission links.

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

6 years agoMerge branch '11908-properties-column-json'
Tom Clegg [Fri, 8 Dec 2017 18:49:34 +0000 (13:49 -0500)]
Merge branch '11908-properties-column-json'

refs #11908

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

6 years agoMerge branch '12721-build-package-version'
Tom Clegg [Fri, 8 Dec 2017 18:47:47 +0000 (13:47 -0500)]
Merge branch '12721-build-package-version'

refs #12721

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

6 years ago12167: Test X-Request-Id request headers in Keep get/put/head reqs.
Tom Clegg [Fri, 8 Dec 2017 18:01:54 +0000 (13:01 -0500)]
12167: Test X-Request-Id request headers in Keep get/put/head reqs.

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

6 years ago12167: Use one X-Request-Id per arv-put; display it if not --silent.
Tom Clegg [Fri, 8 Dec 2017 16:09:13 +0000 (11:09 -0500)]
12167: Use one X-Request-Id per arv-put; display it if not --silent.

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

6 years ago12167: Use one X-Request-Id per arv-get process; display it if -v.
Tom Clegg [Fri, 8 Dec 2017 15:16:08 +0000 (10:16 -0500)]
12167: Use one X-Request-Id per arv-get process; display it if -v.

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

6 years ago12167: Send caller-provided or random X-Request-Id in Keep requests.
Tom Clegg [Fri, 8 Dec 2017 15:13:27 +0000 (10:13 -0500)]
12167: Send caller-provided or random X-Request-Id in Keep requests.

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

6 years ago12167: Send caller-provided or random X-Request-Id in API requests.
Tom Clegg [Fri, 8 Dec 2017 15:11:21 +0000 (10:11 -0500)]
12167: Send caller-provided or random X-Request-Id in API requests.

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

6 years agoWrite composer.yml instead of arvados-configuration.yml refs #12353
Peter Amstutz [Fri, 8 Dec 2017 17:48:18 +0000 (12:48 -0500)]
Write composer.yml instead of arvados-configuration.yml refs #12353

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

6 years ago12765: Fix untrash button on 404 page.
Peter Amstutz [Fri, 8 Dec 2017 17:40:39 +0000 (12:40 -0500)]
12765: Fix untrash button on 404 page.

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

6 years ago12765: Add test for untrash on 404 page
Peter Amstutz [Fri, 8 Dec 2017 14:52:10 +0000 (09:52 -0500)]
12765: Add test for untrash on 404 page

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, 8 Dec 2017 16:22:53 +0000 (17:22 +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 ability to read file from a collection and made minor fixes to
Fuad Muhic [Fri, 8 Dec 2017 16:20:12 +0000 (17:20 +0100)]
Added ability to read file from a collection and made minor fixes to
collection content tree.

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

6 years agoMerge branch '11453-federated-tokens'
Tom Clegg [Fri, 8 Dec 2017 14:34:09 +0000 (09:34 -0500)]
Merge branch '11453-federated-tokens'

refs #11453

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

6 years ago11453: Restore update of email/prefs/name on subsequent remote auth.
Tom Clegg [Thu, 7 Dec 2017 21:59:59 +0000 (16:59 -0500)]
11453: Restore update of email/prefs/name on subsequent remote auth.

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

6 years ago11453: Test username is not updated once assigned.
Tom Clegg [Thu, 7 Dec 2017 21:48:16 +0000 (16:48 -0500)]
11453: Test username is not updated once assigned.

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

6 years ago11453: Assign username when creating mirror of remote user.
Tom Clegg [Thu, 7 Dec 2017 20:47:09 +0000 (15:47 -0500)]
11453: Assign username when creating mirror of remote user.

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

6 years ago11453: "sso_insecure" config applies to remote Arvados auth, too.
Tom Clegg [Thu, 7 Dec 2017 20:33:22 +0000 (15:33 -0500)]
11453: "sso_insecure" config applies to remote Arvados auth, too.

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

6 years agoUpdated README and did some minor fixes to Arvados.R and Collection.R
Fuad Muhic [Thu, 7 Dec 2017 17:18:33 +0000 (18:18 +0100)]
Updated README and did some minor fixes to Arvados.R and Collection.R

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

6 years ago11453: Merge branch 'master' into 11453-federated-tokens
Tom Clegg [Thu, 7 Dec 2017 16:42:07 +0000 (11:42 -0500)]
11453: Merge branch 'master' into 11453-federated-tokens

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

6 years agoAdded ability to extract Subcollection from collection content tree.
Fuad Muhic [Thu, 7 Dec 2017 15:38:57 +0000 (16:38 +0100)]
Added ability to extract Subcollection from collection content tree.

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

6 years ago11908: Add comment about dropping/recreating FT index.
Tom Clegg [Tue, 11 Jul 2017 15:14:01 +0000 (11:14 -0400)]
11908: Add comment about dropping/recreating FT index.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>

6 years ago11908: Fix crash if index being deleted is already deleted.
Tom Clegg [Tue, 11 Jul 2017 14:25:16 +0000 (10:25 -0400)]
11908: Fix crash if index being deleted is already deleted.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>

6 years ago11908: Migrate collections.properties to jsonb.
Tom Clegg [Thu, 6 Jul 2017 20:21:55 +0000 (16:21 -0400)]
11908: Migrate collections.properties to jsonb.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>

6 years ago11807: Migrate data from YAML to JSON.
Tom Clegg [Wed, 5 Jul 2017 02:14:23 +0000 (22:14 -0400)]
11807: Migrate data from YAML to JSON.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curoverse.com>

6 years ago11453: Add IP: alt names to self-signed cert so python accepts it.
Tom Clegg [Thu, 7 Dec 2017 15:12:33 +0000 (10:12 -0500)]
11453: Add IP: alt names to self-signed cert so python accepts it.

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

6 years ago12721: Install bundles in builder images.
Tom Clegg [Thu, 7 Dec 2017 07:39:49 +0000 (02:39 -0500)]
12721: Install bundles in builder images.

Avoids downloading/building the entire bundle every time a Rails
package is built.

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

6 years ago12721: Omit cache dirs for platform A in package for platform B.
Tom Clegg [Thu, 7 Dec 2017 07:37:23 +0000 (02:37 -0500)]
12721: Omit cache dirs for platform A in package for platform B.

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

6 years ago12721: Fix dev-version build.
Tom Clegg [Wed, 6 Dec 2017 23:16:26 +0000 (18:16 -0500)]
12721: Fix dev-version build.

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

6 years ago12721: Don't rebuild libcloud if package already exists.
Tom Clegg [Wed, 6 Dec 2017 23:11:34 +0000 (18:11 -0500)]
12721: Don't rebuild libcloud if package already exists.

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

6 years ago12721: Fix ignored iteration numbers in build.list.
Tom Clegg [Wed, 6 Dec 2017 22:57:21 +0000 (17:57 -0500)]
12721: Fix ignored iteration numbers in build.list.

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

6 years ago12721: Merge branch 'master' into 12721-build-package-version
Tom Clegg [Wed, 6 Dec 2017 22:33:10 +0000 (17:33 -0500)]
12721: Merge branch 'master' into 12721-build-package-version

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

6 years ago11453: Tests for invalid / future-proof / reanimated tokens.
Tom Clegg [Wed, 6 Dec 2017 16:39:57 +0000 (11:39 -0500)]
11453: Tests for invalid / future-proof / reanimated tokens.

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

6 years ago11453: Test group membership with regular groups.
Tom Clegg [Wed, 6 Dec 2017 16:22:27 +0000 (11:22 -0500)]
11453: Test group membership with regular groups.

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

6 years ago11453: Fix & test remote token caching.
Tom Clegg [Wed, 6 Dec 2017 16:22:13 +0000 (11:22 -0500)]
11453: Fix & test remote token caching.

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

6 years agoCreated in-memory representation of collection file structure.
Fuad Muhic [Wed, 6 Dec 2017 16:03:40 +0000 (17:03 +0100)]
Created in-memory representation of collection file structure.

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

6 years ago12721: Handle --build-version 1.2.3-4-5 (v="1.2.3-4", iter="5")
Tom Clegg [Wed, 6 Dec 2017 14:25:50 +0000 (09:25 -0500)]
12721: Handle --build-version 1.2.3-4-5 (v="1.2.3-4", iter="5")

...using the debian version string rules (the last hyphen is the
version-iteration separator).

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

6 years ago12721: Fix python package iteration and rails fpm invocation.
Tom Clegg [Wed, 6 Dec 2017 07:40:17 +0000 (02:40 -0500)]
12721: Fix python package iteration and rails fpm invocation.

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 [Wed, 6 Dec 2017 09:22:38 +0000 (10:22 +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 agoCredentials fix.
Fuad Muhic [Wed, 6 Dec 2017 09:21:13 +0000 (10:21 +0100)]
Credentials fix.

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

6 years agoUpdate documentation to the new name of the sync-groups tool.
Ward Vandewege [Tue, 5 Dec 2017 21:26:12 +0000 (16:26 -0500)]
Update documentation to the new name of the sync-groups tool.

refs #12018

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

6 years agoSmall build script fixes.
Ward Vandewege [Tue, 5 Dec 2017 21:14:27 +0000 (16:14 -0500)]
Small build script fixes.

No issue #

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

6 years agoMerge branch '12018-rename-sync-groups'
Ward Vandewege [Tue, 5 Dec 2017 20:49:33 +0000 (15:49 -0500)]
Merge branch '12018-rename-sync-groups'

refs #12018

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

6 years agoDo not hardcode the name of the executable in the sync-groups code.
Ward Vandewege [Tue, 5 Dec 2017 20:40:49 +0000 (15:40 -0500)]
Do not hardcode the name of the executable in the sync-groups code.

refs #12018

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

6 years ago11453: Mollify python by giving 127.0.0.1 as the first cert CN.
Tom Clegg [Tue, 5 Dec 2017 20:38:23 +0000 (15:38 -0500)]
11453: Mollify python by giving 127.0.0.1 as the first cert CN.

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

6 years agoRename the group sync tool to follow our standard naming scheme.
Ward Vandewege [Tue, 5 Dec 2017 20:24:30 +0000 (15:24 -0500)]
Rename the group sync tool to follow our standard naming scheme.

refs #12018

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

6 years ago12721: --version => --build-version. Make iteration mandatory.
Tom Clegg [Tue, 5 Dec 2017 20:08:56 +0000 (15:08 -0500)]
12721: --version => --build-version. Make iteration mandatory.

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

6 years ago12721: Support package iterations via --version 1.2.3-5
Tom Clegg [Tue, 5 Dec 2017 19:31:48 +0000 (14:31 -0500)]
12721: Support package iterations via --version 1.2.3-5

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

6 years agoMerge branch '12752-discover-keep-web-service' refs #12752
Peter Amstutz [Tue, 5 Dec 2017 19:25:24 +0000 (14:25 -0500)]
Merge branch '12752-discover-keep-web-service' refs #12752

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

6 years ago12752: Add keep_web_service_url config to arvbox.
Peter Amstutz [Tue, 5 Dec 2017 18:07:15 +0000 (13:07 -0500)]
12752: Add keep_web_service_url config to arvbox.

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

6 years ago12752: Publish keepWebServiceUrl in discovery doc.
Peter Amstutz [Tue, 5 Dec 2017 17:55:01 +0000 (12:55 -0500)]
12752: Publish keepWebServiceUrl in discovery doc.

Adds keep_web_service_url to API config.

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 [Tue, 5 Dec 2017 16:14:32 +0000 (17:14 +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 ago12721: Fix python pkg iteration overridde.
Tom Clegg [Tue, 5 Dec 2017 15:57:21 +0000 (10:57 -0500)]
12721: Fix python pkg iteration overridde.

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

6 years ago12721: Fix centos7 python-daemon build.
Tom Clegg [Tue, 5 Dec 2017 14:23:41 +0000 (09:23 -0500)]
12721: Fix centos7 python-daemon build.

Package on pypi is called "python-daemon", not "daemon".

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

6 years ago12721: Package build scripts accept --version argument.
Tom Clegg [Mon, 4 Dec 2017 22:42:10 +0000 (17:42 -0500)]
12721: Package build scripts accept --version argument.

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

6 years agoRefactored most of the code.
Fuad Muhic [Tue, 5 Dec 2017 14:35:27 +0000 (15:35 +0100)]
Refactored most of the code.

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

6 years agoMerge branch '12683-keepstore-buffers'
Tom Clegg [Mon, 4 Dec 2017 22:52:40 +0000 (17:52 -0500)]
Merge branch '12683-keepstore-buffers'

refs #12683

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

6 years ago12683: Add #max-buffers anchor.
Tom Clegg [Mon, 4 Dec 2017 22:51:35 +0000 (17:51 -0500)]
12683: Add #max-buffers anchor.

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

6 years agoPackage arv-sync-groups.
Ward Vandewege [Mon, 4 Dec 2017 21:39:48 +0000 (16:39 -0500)]
Package arv-sync-groups.

No issue #

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

6 years ago12683: Adjust max-buffers recommendation.
Tom Clegg [Mon, 4 Dec 2017 21:39:05 +0000 (16:39 -0500)]
12683: Adjust max-buffers recommendation.

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

6 years agoMerge branch '12573-crunch2-slurm-priority' closes #12573
Peter Amstutz [Mon, 4 Dec 2017 21:32:04 +0000 (16:32 -0500)]
Merge branch '12573-crunch2-slurm-priority' closes #12573

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

6 years agoMerge branch '12662-current-user-test'
Lucas Di Pentima [Mon, 4 Dec 2017 21:28:35 +0000 (18:28 -0300)]
Merge branch '12662-current-user-test'
Closes #12662

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