arvados.git
5 years agoMerge branch 'master' into 14873-api-rails5-upgrade
Lucas Di Pentima [Fri, 5 Apr 2019 12:26:15 +0000 (09:26 -0300)]
Merge branch 'master' into 14873-api-rails5-upgrade

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

5 years ago14873: Fixes permission benchmark test
Lucas Di Pentima [Thu, 4 Apr 2019 22:25:11 +0000 (19:25 -0300)]
14873: Fixes permission benchmark test

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

5 years ago14873: Changes perftest with benchmark because of unidentified errors.
Lucas Di Pentima [Thu, 4 Apr 2019 21:24:50 +0000 (18:24 -0300)]
14873: Changes perftest with benchmark because of unidentified errors.

Didn't want to dilate the migraton any longer because of this. If it's
critical we could investigate further.

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

5 years agocheck-exist uses default python (oops) refs #15040
Peter Amstutz [Thu, 4 Apr 2019 20:44:19 +0000 (16:44 -0400)]
check-exist uses default python (oops) refs #15040

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

5 years ago14873: Migrated functional tests to be integration tests.
Lucas Di Pentima [Thu, 4 Apr 2019 19:11:55 +0000 (16:11 -0300)]
14873: Migrated functional tests to be integration tests.

Making more than 1 request on functional tests produces issues hard
to debug. Instead, those kind of tests should be done as integration tests.

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

5 years agoRun check-exist.py in Docker container refs #15040
Peter Amstutz [Thu, 4 Apr 2019 15:13:04 +0000 (11:13 -0400)]
Run check-exist.py in Docker container refs #15040

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

5 years agoMerge branch '14484-collection-record-update'
Eric Biagiotti [Thu, 4 Apr 2019 14:54:49 +0000 (10:54 -0400)]
Merge branch '14484-collection-record-update'

refs #14484

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years agoPin networkx because 2.2 is the last version to support Python 2.7 and 3.4
Peter Amstutz [Thu, 4 Apr 2019 14:41:27 +0000 (10:41 -0400)]
Pin networkx because 2.2 is the last version to support Python 2.7 and 3.4

no issue #

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

5 years ago14873: Modifies failing tests for debugging purposes.
Lucas Di Pentima [Thu, 4 Apr 2019 13:50:44 +0000 (10:50 -0300)]
14873: Modifies failing tests for debugging purposes.

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

5 years agoFix stale cached container state after successful Cancel.
Tom Clegg [Thu, 4 Apr 2019 13:44:07 +0000 (09:44 -0400)]
Fix stale cached container state after successful Cancel.

Avoids needless retries between a successful Cancel and the next sync.

No issue #

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

5 years agoMerge branch '14796-dispatchcloud-install-docs'
Tom Clegg [Wed, 3 Apr 2019 21:11:25 +0000 (17:11 -0400)]
Merge branch '14796-dispatchcloud-install-docs'

refs #14796

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

5 years agoMerge remote-tracking branch 'origin/master' into 14484-collection-record-update
Eric Biagiotti [Wed, 3 Apr 2019 20:42:25 +0000 (16:42 -0400)]
Merge remote-tracking branch 'origin/master' into 14484-collection-record-update

refs #14484

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14796: Tweak example boot probe command.
Tom Clegg [Wed, 3 Apr 2019 20:24:35 +0000 (16:24 -0400)]
14796: Tweak example boot probe command.

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

5 years ago14796: Add Amazon EC2 configuration example.
Tom Clegg [Wed, 3 Apr 2019 20:23:17 +0000 (16:23 -0400)]
14796: Add Amazon EC2 configuration example.

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

5 years ago14484: Adds test for updating a collection with file stats and manifest changes
Eric Biagiotti [Wed, 3 Apr 2019 20:20:26 +0000 (16:20 -0400)]
14484: Adds test for updating a collection with file stats and manifest changes

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14484: Improves test coverage and attribute setting performance
Eric Biagiotti [Wed, 3 Apr 2019 20:01:26 +0000 (16:01 -0400)]
14484: Improves test coverage and attribute setting performance

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14796: Add arvados-dispatch-cloud (experimental) to install docs.
Tom Clegg [Wed, 3 Apr 2019 15:39:47 +0000 (11:39 -0400)]
14796: Add arvados-dispatch-cloud (experimental) to install docs.

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

5 years ago14873: Adds JSONB columns to discovery doc.
Lucas Di Pentima [Wed, 3 Apr 2019 00:45:30 +0000 (21:45 -0300)]
14873: Adds JSONB columns to discovery doc.

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

5 years ago14873: Removes byebug debug call on test.
Lucas Di Pentima [Tue, 2 Apr 2019 23:26:17 +0000 (20:26 -0300)]
14873: Removes byebug debug call on test.

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

5 years ago14873: Fixes JSON custom types.
Lucas Di Pentima [Tue, 2 Apr 2019 22:13:25 +0000 (19:13 -0300)]
14873: Fixes JSON custom types.

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

5 years ago14873: Custom JSON attributes that default to [] or {} when nil.
Lucas Di Pentima [Tue, 2 Apr 2019 21:36:08 +0000 (18:36 -0300)]
14873: Custom JSON attributes that default to [] or {} when nil.

Previously we used the 'serialize' call to declare a JSONB column as a Hash
or Array and this had the side effect to default to an empty hash or array
when assigning nil (whether was reading from the database or passed as a param).
JSONB columns shouldn't be now declared as serialized because Rails would serialize
their contents twice, but not declaring them makes us lose their side effect.

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

5 years ago14873: Fixes nested params behavior on controller tests.
Lucas Di Pentima [Tue, 2 Apr 2019 21:30:11 +0000 (18:30 -0300)]
14873: Fixes nested params behavior on controller tests.

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

5 years ago14873: Updates test for fix deprecation warning.
Lucas Di Pentima [Tue, 2 Apr 2019 18:37:07 +0000 (15:37 -0300)]
14873: Updates test for fix deprecation warning.

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

5 years agoGive up if test services don't come up.
Tom Clegg [Tue, 2 Apr 2019 18:18:17 +0000 (14:18 -0400)]
Give up if test services don't come up.

refs #15044

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

5 years agoRemove dependency on jq.
Tom Clegg [Tue, 2 Apr 2019 18:11:55 +0000 (14:11 -0400)]
Remove dependency on jq.

refs #15044

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

5 years agoMerge branch '15044-test-fixes'
Tom Clegg [Tue, 2 Apr 2019 17:28:10 +0000 (13:28 -0400)]
Merge branch '15044-test-fixes'

closes #15044

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

5 years ago15044: Sanity-check test services when bringing them up.
Tom Clegg [Tue, 2 Apr 2019 17:24:45 +0000 (13:24 -0400)]
15044: Sanity-check test services when bringing them up.

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

5 years ago14873: Reverts previous fixture changes.
Lucas Di Pentima [Tue, 2 Apr 2019 16:23:44 +0000 (13:23 -0300)]
14873: Reverts previous fixture changes.

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

5 years ago14484: Update collection model to overwrite file stats if a change is attempted
Eric Biagiotti [Tue, 2 Apr 2019 15:49:29 +0000 (11:49 -0400)]
14484: Update collection model to overwrite file stats if a change is attempted

Also updates tests and documentation

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago15044: Require newer mocha.
Tom Clegg [Tue, 2 Apr 2019 14:20:45 +0000 (10:20 -0400)]
15044: Require newer mocha.

Without this, old dev environments will not necessarily support the
non-deprecated usage (require 'mocha/minitest').

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

5 years agoMerge branch 'arvbox-cert-docs' no issue #
Peter Amstutz [Mon, 1 Apr 2019 18:58:40 +0000 (14:58 -0400)]
Merge branch 'arvbox-cert-docs' no issue #

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

5 years ago14844: Adds collections controller tests and updates collection model tests
Eric Biagiotti [Mon, 1 Apr 2019 18:49:42 +0000 (14:49 -0400)]
14844: Adds collections controller tests and updates collection model tests

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years agoUpdate arvbox docs to describe how to install root cert
Peter Amstutz [Mon, 1 Apr 2019 16:28:12 +0000 (12:28 -0400)]
Update arvbox docs to describe how to install root cert

Remove slurm from arvbox

Arvbox cluster ids now always start with 'x' to be consistent with
cluster identifier guidelines for "experimental/local-only/private clusters"

no issue #

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

5 years ago14484: Moves the file count and total size callback to after_validation
Eric Biagiotti [Mon, 1 Apr 2019 15:37:33 +0000 (11:37 -0400)]
14484: Moves the file count and total size callback to after_validation

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years agoMerge branch '14758-keepproxy-panic'
Tom Clegg [Mon, 1 Apr 2019 15:16:58 +0000 (11:16 -0400)]
Merge branch '14758-keepproxy-panic'

fixes #14758

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

5 years ago14758: Fix panic on error reading request body.
Tom Clegg [Mon, 1 Apr 2019 14:40:43 +0000 (10:40 -0400)]
14758: Fix panic on error reading request body.

The deferred inline func panics if status != 200 && err == nil.

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

5 years agoMerge branch '15050-limit-cdl-containers' closes #15050
Peter Amstutz [Mon, 1 Apr 2019 15:08:53 +0000 (11:08 -0400)]
Merge branch '15050-limit-cdl-containers' closes #15050

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

5 years agoAdd another nil check to Azure driver.
Tom Clegg [Sun, 31 Mar 2019 19:25:11 +0000 (15:25 -0400)]
Add another nil check to Azure driver.

refs #15007

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

5 years ago15050: After waking up, check if the container was cancelled
Peter Amstutz [Fri, 29 Mar 2019 20:27:04 +0000 (16:27 -0400)]
15050: After waking up, check if the container was cancelled

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

5 years ago15044: Fix sensitivity to group existence on the testing host.
Tom Clegg [Fri, 29 Mar 2019 19:22:44 +0000 (15:22 -0400)]
15044: Fix sensitivity to group existence on the testing host.

Also fix some ruby warnings.

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

5 years ago14484: Moves test for grouping pdhs to its own file
Eric Biagiotti [Fri, 29 Mar 2019 19:08:36 +0000 (15:08 -0400)]
14484: Moves test for grouping pdhs to its own file

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14484: Moves pdh grouping into a lib module
Eric Biagiotti [Fri, 29 Mar 2019 18:46:30 +0000 (14:46 -0400)]
14484: Moves pdh grouping into a lib module

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago15050: Need to make sure to raise the semaphore when we're done
Peter Amstutz [Fri, 29 Mar 2019 18:28:01 +0000 (14:28 -0400)]
15050: Need to make sure to raise the semaphore when we're done

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

5 years ago15050: Limit number of containers that crunch-dispatch-local runs at a time
Peter Amstutz [Fri, 29 Mar 2019 18:06:22 +0000 (14:06 -0400)]
15050: Limit number of containers that crunch-dispatch-local runs at a time

So I can do some testing with submitting a huge number of containers
and not melt my machine.

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

5 years ago14484: Adds tests for Collection model and makes file attributes readonly
Eric Biagiotti [Fri, 29 Mar 2019 17:54:28 +0000 (13:54 -0400)]
14484: Adds tests for Collection model and makes file attributes readonly

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago15044: Don't kill run-tests's keepproxy server in sdk/python tests.
Tom Clegg [Fri, 29 Mar 2019 17:36:51 +0000 (13:36 -0400)]
15044: Don't kill run-tests's keepproxy server in sdk/python tests.

This was causing an apps/workbench test
(CollectionUploadTest#test_Upload_non-empty_files) to fail when
running after sdk/python tests.

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

5 years agoFix assigning APIHost in NewClientFromConfig refs #15045
Peter Amstutz [Fri, 29 Mar 2019 15:44:51 +0000 (11:44 -0400)]
Fix assigning APIHost in NewClientFromConfig refs #15045

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

5 years ago15044: Specify test database collation.
Tom Clegg [Thu, 28 Mar 2019 20:21:26 +0000 (16:21 -0400)]
15044: Specify test database collation.

apps/workbench/test/controllers/projects_controller_test.rb:546 fails
with other collations.

Remove obsolete websocket comment.

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

5 years ago15044: Fix unnecessarily unsafe yaml load.
Tom Clegg [Thu, 28 Mar 2019 20:01:28 +0000 (16:01 -0400)]
15044: Fix unnecessarily unsafe yaml load.

...and eliminate the associated warnings in test logs.

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

5 years ago15044: Fix workbench test args in interactive mode.
Tom Clegg [Thu, 28 Mar 2019 19:58:10 +0000 (15:58 -0400)]
15044: Fix workbench test args in interactive mode.

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

5 years ago15044: Improve error reporting in test case.
Tom Clegg [Thu, 28 Mar 2019 18:58:10 +0000 (14:58 -0400)]
15044: Improve error reporting in test case.

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

5 years ago15044: Listen on localhost instead of default dual-stack [::].
Tom Clegg [Thu, 28 Mar 2019 17:27:52 +0000 (13:27 -0400)]
15044: Listen on localhost instead of default dual-stack [::].

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

5 years ago15044: Test gofmt as a separate suite, instead of refusing to run Go tests.
Tom Clegg [Thu, 28 Mar 2019 15:12:44 +0000 (11:12 -0400)]
15044: Test gofmt as a separate suite, instead of refusing to run Go tests.

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

5 years ago15044: Always use the en_US.UTF-8 locale. Add sanity check.
Tom Clegg [Thu, 28 Mar 2019 18:12:37 +0000 (14:12 -0400)]
15044: Always use the en_US.UTF-8 locale. Add sanity check.

Some tests are sensitive to charset and collation.

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

5 years ago14873: Removes debug data on fixture.
Lucas Di Pentima [Thu, 28 Mar 2019 21:10:21 +0000 (18:10 -0300)]
14873: Removes debug data on fixture.

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

5 years ago14873: Fixes unit tests.
Lucas Di Pentima [Thu, 28 Mar 2019 21:06:37 +0000 (18:06 -0300)]
14873: Fixes unit tests.

JSONB columns shouldn't be declared as 'serialized' because their content
get encoded twice.
When not declaring them as serialized, their default values (eg: [], {})
should be explicitly set.
Fixes on fixtures when default JSONB values are not defined on the schema.

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

5 years agoMerge branch 'master' into 14873-api-rails5-upgrade
Lucas Di Pentima [Wed, 27 Mar 2019 18:20:05 +0000 (15:20 -0300)]
Merge branch 'master' into 14873-api-rails5-upgrade

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

5 years ago15044: Fix error messages.
Tom Clegg [Thu, 28 Mar 2019 14:37:13 +0000 (10:37 -0400)]
15044: Fix error messages.

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

5 years ago15044: Fix interactive command handling.
Tom Clegg [Wed, 27 Mar 2019 20:46:04 +0000 (16:46 -0400)]
15044: Fix interactive command handling.

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

5 years ago15044: Override unusable nginx defaults. Test nginx startup success.
Tom Clegg [Wed, 27 Mar 2019 20:42:25 +0000 (16:42 -0400)]
15044: Override unusable nginx defaults. Test nginx startup success.

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

5 years agoMerge branch '14998-hoststat-total'
Tom Clegg [Thu, 28 Mar 2019 17:44:05 +0000 (13:44 -0400)]
Merge branch '14998-hoststat-total'

fixes #14998

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

5 years ago14998: Report total_* (hierarchy) stats if available.
Tom Clegg [Tue, 19 Mar 2019 19:49:49 +0000 (15:49 -0400)]
14998: Report total_* (hierarchy) stats if available.

Otherwise, host stats only include the root cgroup.

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

5 years agoprepare.py in fed tests uses default python refs #15040
Peter Amstutz [Thu, 28 Mar 2019 16:56:44 +0000 (12:56 -0400)]
prepare.py in fed tests uses default python refs #15040

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

5 years ago14484: Updates collection documentation to include the new file stats
Eric Biagiotti [Thu, 28 Mar 2019 16:45:20 +0000 (12:45 -0400)]
14484: Updates collection documentation to include the new file stats

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14484: Fixes performance test by changing file_size_total to bigint
Eric Biagiotti [Thu, 28 Mar 2019 14:44:42 +0000 (10:44 -0400)]
14484: Fixes performance test by changing file_size_total to bigint

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years agorun prepare.py in fed tests in docker container refs #15040
Peter Amstutz [Thu, 28 Mar 2019 14:17:50 +0000 (10:17 -0400)]
run prepare.py in fed tests in docker container refs #15040

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

5 years ago14484: Fixes tests that intentionally pass in invalid manifests
Eric Biagiotti [Wed, 27 Mar 2019 21:28:31 +0000 (17:28 -0400)]
14484: Fixes tests that intentionally pass in invalid manifests

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14484: Adds test for pdh grouping functionality in the container model
Eric Biagiotti [Wed, 27 Mar 2019 20:56:47 +0000 (16:56 -0400)]
14484: Adds test for pdh grouping functionality in the container model

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14484: Simplifies pdh transaction grouping, keeps SQL in the migration
Eric Biagiotti [Wed, 27 Mar 2019 20:35:14 +0000 (16:35 -0400)]
14484: Simplifies pdh transaction grouping, keeps SQL in the migration

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years agorun-tests.sh: don't prepopulate cmd if running in an emacs buffer.
Tom Clegg [Wed, 27 Mar 2019 20:34:36 +0000 (16:34 -0400)]
run-tests.sh: don't prepopulate cmd if running in an emacs buffer.

No issue #

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

5 years agotest mode creates certificate so that setting up SSO can succeed
Peter Amstutz [Wed, 27 Mar 2019 20:04:05 +0000 (16:04 -0400)]
test mode creates certificate so that setting up SSO can succeed

also added "arvbox update"

no issue #

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

5 years ago14873: Adds headers to controller tests' requests.
Lucas Di Pentima [Wed, 27 Mar 2019 18:09:52 +0000 (15:09 -0300)]
14873: Adds headers to controller tests' requests.

API server logs used to report 'format: html' when running functional tests.
With these additions, it now reports 'json', but this is not enough to fix
the issue about nested arrays being flattened when running tests.

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

5 years ago14873: Gets rid of yet another deprecation warning.
Lucas Di Pentima [Wed, 27 Mar 2019 18:07:09 +0000 (15:07 -0300)]
14873: Gets rid of yet another deprecation warning.

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

5 years ago14873: Skips indexes which 'columns' attribute isn't an Array.
Lucas Di Pentima [Wed, 27 Mar 2019 18:02:11 +0000 (15:02 -0300)]
14873: Skips indexes which 'columns' attribute isn't an Array.

ActiveRecord::Base.connection.indexes(table) didn't seem to return these
previous to rails 5.0 upgrade.

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

5 years ago14484: Makes quotation marks consistent
Eric Biagiotti [Wed, 27 Mar 2019 17:50:26 +0000 (13:50 -0400)]
14484: Makes quotation marks consistent

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14484: Updates the migration to use the sdk for manifest parsing
Eric Biagiotti [Wed, 27 Mar 2019 17:27:06 +0000 (13:27 -0400)]
14484: Updates the migration to use the sdk for manifest parsing

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years agoAccept :py3 modifier for any Python suite in interactive mode.
Tom Clegg [Wed, 27 Mar 2019 15:15:15 +0000 (11:15 -0400)]
Accept :py3 modifier for any Python suite in interactive mode.

(even ones that aren't normally run with python3 by jenkins)

refs #14939

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

5 years ago14873: Marks past migrations with version 4.2
Lucas Di Pentima [Wed, 27 Mar 2019 02:41:10 +0000 (23:41 -0300)]
14873: Marks past migrations with version 4.2

Rails 5 migration API changes, so to be able to run past migrations
with newer rails, it's required to mark them.
This isn't documented on the Rails 5.0 upgrade notes, but it's mentioned on some
blogs, like this one:

https://blog.bigbinary.com/2016/03/01/migrations-are-versioned-in-rails-5.html

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

5 years ago14873: Fixes parameter handling (WIP)
Lucas Di Pentima [Wed, 27 Mar 2019 01:38:43 +0000 (22:38 -0300)]
14873: Fixes parameter handling (WIP)

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

5 years ago14484: Adds file count and size callback to the collection model
Eric Biagiotti [Tue, 26 Mar 2019 21:02:56 +0000 (17:02 -0400)]
14484: Adds file count and size callback to the collection model

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14873: Fixes integration tests.
Lucas Di Pentima [Tue, 26 Mar 2019 20:46:42 +0000 (17:46 -0300)]
14873: Fixes integration tests.

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

5 years agono issue # Remove jessie-updates from sources.list as it is no longer supported
Fernando Monserrat [Tue, 26 Mar 2019 20:29:45 +0000 (17:29 -0300)]
no issue # Remove jessie-updates from sources.list as it is no longer supported
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

5 years agoarvbox nginx redirects http to https
Peter Amstutz [Tue, 26 Mar 2019 20:09:31 +0000 (16:09 -0400)]
arvbox nginx redirects http to https

no issue #

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

5 years ago14484: Fixes grouping bug by simplifying nested pdhs arrays
Eric Biagiotti [Tue, 26 Mar 2019 18:50:18 +0000 (14:50 -0400)]
14484: Fixes grouping bug by simplifying nested pdhs arrays

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14873: Fixes deprecation warnings on integration tests.
Lucas Di Pentima [Tue, 26 Mar 2019 18:33:15 +0000 (15:33 -0300)]
14873: Fixes deprecation warnings on integration tests.

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

5 years ago14484: Changes file token to match the one used in collection.rb model
Eric Biagiotti [Tue, 26 Mar 2019 17:56:10 +0000 (13:56 -0400)]
14484: Changes file token to match the one used in collection.rb model

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14484: Adds migration for collection file count and total size
Eric Biagiotti [Tue, 26 Mar 2019 16:47:06 +0000 (12:47 -0400)]
14484: Adds migration for collection file count and total size

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14484: Fixes bug in pdh transaction grouping
Eric Biagiotti [Tue, 26 Mar 2019 16:46:15 +0000 (12:46 -0400)]
14484: Fixes bug in pdh transaction grouping

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14873: Upgrades 'pg' gem & solves an issue related to a new internal table.
Lucas Di Pentima [Tue, 26 Mar 2019 16:18:00 +0000 (13:18 -0300)]
14873: Upgrades 'pg' gem & solves an issue related to a new internal table.

Rails 5 includes an undocumented internal table called 'ar_internal_metadata'
used to record the environment that the current system is on, so that it can
avoid accidental database wipes when in production.
Our code iterates over the tables so this one needs to be skipped.

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

5 years agoMerge branch '14807-prod-blockers'
Tom Clegg [Tue, 26 Mar 2019 14:28:19 +0000 (10:28 -0400)]
Merge branch '14807-prod-blockers'

refs #14807

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

5 years ago14484: Adds functionality and test for pdh grouping in the container model
Eric Biagiotti [Mon, 25 Mar 2019 22:30:40 +0000 (18:30 -0400)]
14484: Adds functionality and test for pdh grouping in the container model

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14484: Updates the db structure after db:migrate
Eric Biagiotti [Mon, 25 Mar 2019 20:17:37 +0000 (16:17 -0400)]
14484: Updates the db structure after db:migrate

Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>

5 years ago14807: Move "fallback to ARVADOS_*" logic out to lib/service.
Tom Clegg [Mon, 25 Mar 2019 14:47:37 +0000 (10:47 -0400)]
14807: Move "fallback to ARVADOS_*" logic out to lib/service.

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

5 years ago14873: Removes legacy setting as all controllers were migrated.
Lucas Di Pentima [Mon, 25 Mar 2019 14:44:49 +0000 (11:44 -0300)]
14873: Removes legacy setting as all controllers were migrated.

When needing to stop the callback chain, instead of returning false
now we need to call: throw(:abort)
The removed setting allowed the old behavior, and it isn't neede anymore.

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

5 years ago14873: Adds new abstract class ApplicationRecord.
Lucas Di Pentima [Mon, 25 Mar 2019 14:33:30 +0000 (11:33 -0300)]
14873: Adds new abstract class ApplicationRecord.

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

5 years ago14783: Fixes more deprecation warnings from functional tests.
Lucas Di Pentima [Fri, 22 Mar 2019 21:25:14 +0000 (18:25 -0300)]
14783: Fixes more deprecation warnings from functional tests.

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

5 years ago14807: Add lib/service test.
Tom Clegg [Fri, 22 Mar 2019 20:20:29 +0000 (16:20 -0400)]
14807: Add lib/service test.

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

5 years ago14807: Fix go vet warnings about %s args.
Tom Clegg [Fri, 22 Mar 2019 19:25:47 +0000 (15:25 -0400)]
14807: Fix go vet warnings about %s args.

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

5 years ago14873: Fixes deprecation notes on functional tests.
Lucas Di Pentima [Fri, 22 Mar 2019 18:56:02 +0000 (15:56 -0300)]
14873: Fixes deprecation notes on functional tests.

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

5 years ago14807: Pass token to service handlers explicitly, not via context.
Tom Clegg [Fri, 22 Mar 2019 18:44:03 +0000 (14:44 -0400)]
14807: Pass token to service handlers explicitly, not via context.

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