arvados.git
5 years agoFix testing on master
Peter Amstutz [Mon, 15 Jul 2019 18:02:51 +0000 (14:02 -0400)]
Fix testing on master

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

5 years agoarvbox update go version, refactor creating cluster config.
Peter Amstutz [Mon, 15 Jul 2019 17:46:04 +0000 (13:46 -0400)]
arvbox update go version, refactor creating cluster config.

no issue #

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

5 years ago15319: Adds troubleshooting documentation to the Admin section.
Lucas Di Pentima [Mon, 15 Jul 2019 17:34:53 +0000 (14:34 -0300)]
15319: Adds troubleshooting documentation to the Admin section.

Explains both 15318 & 15319 features.

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

5 years ago14965: Fixes port waiting regex
Eric Biagiotti [Fri, 12 Jul 2019 20:46:08 +0000 (16:46 -0400)]
14965: Fixes port waiting regex

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

5 years agoMerge branch 'master' into 15319-api-useful-stacktraces
Lucas Di Pentima [Fri, 12 Jul 2019 19:53:10 +0000 (16:53 -0300)]
Merge branch 'master' into 15319-api-useful-stacktraces

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

5 years ago15219: Tests for exception backtraces being included on the json log.
Lucas Di Pentima [Fri, 12 Jul 2019 19:50:35 +0000 (16:50 -0300)]
15219: Tests for exception backtraces being included on the json log.

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

5 years ago14965: Clarifies decoding in pdh test
Eric Biagiotti [Fri, 12 Jul 2019 19:29:46 +0000 (15:29 -0400)]
14965: Clarifies decoding in pdh test

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

5 years agoMerge branch '13647-load-old-config'
Tom Clegg [Fri, 12 Jul 2019 19:05:06 +0000 (15:05 -0400)]
Merge branch '13647-load-old-config'

refs #13647

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

5 years ago14965: Tweak netstat usage.
Tom Clegg [Fri, 12 Jul 2019 18:49:15 +0000 (14:49 -0400)]
14965: Tweak netstat usage.

Only list listening sockets, since those are the ones we're looking
for. (-l, not -a)

Don't truncate IP/port numbers. (-W)

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

5 years ago13647: Fix default cluster config source. Comment flag usage.
Tom Clegg [Fri, 12 Jul 2019 18:06:09 +0000 (14:06 -0400)]
13647: Fix default cluster config source. Comment flag usage.

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

5 years ago14965: Report python 3 compatibility
Eric Biagiotti [Fri, 12 Jul 2019 17:42:11 +0000 (13:42 -0400)]
14965: Report python 3 compatibility

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

5 years ago14965: Cleans up test output by reducing resource warnings
Eric Biagiotti [Fri, 12 Jul 2019 17:35:11 +0000 (13:35 -0400)]
14965: Cleans up test output by reducing resource warnings

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

5 years ago15219: Logs exceptions with backtraces as part of the JSON log.
Lucas Di Pentima [Fri, 12 Jul 2019 15:27:05 +0000 (12:27 -0300)]
15219: Logs exceptions with backtraces as part of the JSON log.

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

5 years ago14965: Mocks FreshBase _poll_time to avoid comparing mock and int
Eric Biagiotti [Fri, 12 Jul 2019 14:18:39 +0000 (10:18 -0400)]
14965: Mocks FreshBase _poll_time to avoid comparing mock and int

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

5 years ago14965: Adds encoding to keep.put argument
Eric Biagiotti [Fri, 12 Jul 2019 14:11:41 +0000 (10:11 -0400)]
14965: Adds encoding to keep.put argument

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

5 years agoMerge branch '15421-include-param-doc' closes #15421
Peter Amstutz [Thu, 11 Jul 2019 21:22:28 +0000 (17:22 -0400)]
Merge branch '15421-include-param-doc' closes #15421

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

5 years ago14965: Simplifies previous fix to FuseMagicTest
Eric Biagiotti [Thu, 11 Jul 2019 21:07:10 +0000 (17:07 -0400)]
14965: Simplifies previous fix to FuseMagicTest

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

5 years ago14965: Fixes FuseMountTest encoding
Eric Biagiotti [Thu, 11 Jul 2019 21:06:00 +0000 (17:06 -0400)]
14965: Fixes FuseMountTest encoding

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

5 years ago14965: Fixes rmdir and rename op encoding
Eric Biagiotti [Thu, 11 Jul 2019 21:04:40 +0000 (17:04 -0400)]
14965: Fixes rmdir and rename op encoding

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

5 years agoMerge branch '15003-ensure-all-sample-keys'
Tom Clegg [Thu, 11 Jul 2019 21:02:38 +0000 (17:02 -0400)]
Merge branch '15003-ensure-all-sample-keys'

closes #15003

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

5 years ago13647: Add MungeLegacyConfigArgs.
Tom Clegg [Thu, 11 Jul 2019 21:00:45 +0000 (17:00 -0400)]
13647: Add MungeLegacyConfigArgs.

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

5 years agoarvbox rotates its TLS certificates when they expire
Peter Amstutz [Thu, 11 Jul 2019 20:59:36 +0000 (16:59 -0400)]
arvbox rotates its TLS certificates when they expire

no issue #

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

5 years ago15003: Ensure all map[string]* have sample keys.
Tom Clegg [Thu, 11 Jul 2019 19:51:09 +0000 (15:51 -0400)]
15003: Ensure all map[string]* have sample keys.

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

5 years agodoc: on the config migration page, make sure to include RAILS_ENV in the bundle
Ward Vandewege [Thu, 11 Jul 2019 19:47:59 +0000 (15:47 -0400)]
doc: on the config migration page, make sure to include RAILS_ENV in the bundle
commands for Workbench.

No issue #

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

5 years agodoc: on the config migration page, make sure to include RAILS_ENV in the bundle
Ward Vandewege [Thu, 11 Jul 2019 19:45:16 +0000 (15:45 -0400)]
doc: on the config migration page, make sure to include RAILS_ENV in the bundle
commands.

No issue #

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

5 years ago13647: Add comments.
Tom Clegg [Thu, 11 Jul 2019 19:22:22 +0000 (15:22 -0400)]
13647: Add comments.

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

5 years ago15421: Improve wording
Peter Amstutz [Thu, 11 Jul 2019 19:12:32 +0000 (15:12 -0400)]
15421: Improve wording

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

5 years agoMerge branch '15003-real-configs-flagged-unknown'
Tom Clegg [Thu, 11 Jul 2019 17:35:09 +0000 (13:35 -0400)]
Merge branch '15003-real-configs-flagged-unknown'

refs #15003

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

5 years ago13647: ARVADOS_CONFIG env var overrides default cluster config path.
Tom Clegg [Thu, 11 Jul 2019 17:32:23 +0000 (13:32 -0400)]
13647: ARVADOS_CONFIG env var overrides default cluster config path.

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

5 years agoMerge branch '15454-stop-building-debian8-and-ubuntu1404'
Ward Vandewege [Thu, 11 Jul 2019 17:20:23 +0000 (13:20 -0400)]
Merge branch '15454-stop-building-debian8-and-ubuntu1404'

closes #15454

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

5 years agoMerge branch '15318-ReqIds-on-api-errors'
Lucas Di Pentima [Thu, 11 Jul 2019 15:57:51 +0000 (12:57 -0300)]
Merge branch '15318-ReqIds-on-api-errors'
Closes #15318

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

5 years ago15003: Fix errant warnings on Workbench configs.
Tom Clegg [Thu, 11 Jul 2019 15:57:14 +0000 (11:57 -0400)]
15003: Fix errant warnings on Workbench configs.

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

5 years ago14287: Merge branch 'master' into 14287-federated-list
Tom Clegg [Thu, 11 Jul 2019 15:13:12 +0000 (11:13 -0400)]
14287: Merge branch 'master' into 14287-federated-list

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

5 years ago13647: Return recognizable error when no clusters are defined.
Tom Clegg [Thu, 11 Jul 2019 15:06:12 +0000 (11:06 -0400)]
13647: Return recognizable error when no clusters are defined.

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

5 years ago14965: Fixes mkdir name encoding
Eric Biagiotti [Thu, 11 Jul 2019 14:37:24 +0000 (10:37 -0400)]
14965: Fixes mkdir name encoding

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

5 years ago13647: Load one example value from old keepstore config.
Tom Clegg [Wed, 10 Jul 2019 20:10:50 +0000 (16:10 -0400)]
13647: Load one example value from old keepstore config.

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

5 years ago13647: Suppress "exit status 1" after config-check diff output.
Tom Clegg [Wed, 10 Jul 2019 20:10:52 +0000 (16:10 -0400)]
13647: Suppress "exit status 1" after config-check diff output.

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

5 years agoStop building debian8 and ubuntu1404.
Ward Vandewege [Thu, 11 Jul 2019 13:51:03 +0000 (09:51 -0400)]
Stop building debian8 and ubuntu1404.

refs #15454

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

5 years ago15003: Fix errant warnings on PostgreSQL params and InternalURLs.
Tom Clegg [Wed, 10 Jul 2019 19:09:10 +0000 (15:09 -0400)]
15003: Fix errant warnings on PostgreSQL params and InternalURLs.

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

5 years agoUse go 1.12 in package building (part 2).
Ward Vandewege [Wed, 10 Jul 2019 18:37:19 +0000 (14:37 -0400)]
Use go 1.12 in package building (part 2).

refs #

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

5 years agoMerge branch '13913-crunchstat-summary-tmpdir'
Tom Morris [Wed, 10 Jul 2019 15:34:03 +0000 (11:34 -0400)]
Merge branch '13913-crunchstat-summary-tmpdir'

Fixes #13913

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

5 years agoWe require go 1.12, update the run-tests.sh version check.
Ward Vandewege [Wed, 10 Jul 2019 13:47:08 +0000 (09:47 -0400)]
We require go 1.12, update the run-tests.sh version check.

Also use go 1.12 in package building.

No issue #

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

5 years agoOur workbench and api server packages now have a runtime dependency on
Ward Vandewege [Tue, 9 Jul 2019 22:23:12 +0000 (18:23 -0400)]
Our workbench and api server packages now have a runtime dependency on
arvados-server for configuration validation.

Our workbench package now also has a build-time dependency on arvados-server,
because it needs some configuration while precompiling assets.

closes #15449
refs #14812

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

5 years agoFix arvbox demo build. Add Services.Controller to config.yml
Peter Amstutz [Tue, 9 Jul 2019 21:29:40 +0000 (17:29 -0400)]
Fix arvbox demo build.  Add Services.Controller to config.yml

no issue #

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

5 years ago15318: Updates go components' tests to consider the req-ids.
Lucas Di Pentima [Tue, 9 Jul 2019 21:23:51 +0000 (18:23 -0300)]
15318: Updates go components' tests to consider the req-ids.

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

5 years agoMerge branch '15380-full-text-search-docs'
Eric Biagiotti [Tue, 9 Jul 2019 20:34:14 +0000 (16:34 -0400)]
Merge branch '15380-full-text-search-docs'

refs #15380

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

5 years ago15421: Elaborate a little more on what include= is useful for
Peter Amstutz [Tue, 9 Jul 2019 19:51:06 +0000 (15:51 -0400)]
15421: Elaborate a little more on what include= is useful for

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

5 years ago14965: Fixes token expiry time mock, byte data, and open mock
Eric Biagiotti [Tue, 9 Jul 2019 19:47:25 +0000 (15:47 -0400)]
14965: Fixes token expiry time mock, byte data, and open mock

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

5 years ago15421: Document "includes" parameter to group contents endpoint
Peter Amstutz [Tue, 9 Jul 2019 19:42:46 +0000 (15:42 -0400)]
15421: Document "includes" parameter to group contents endpoint

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

5 years ago15318: Updates tests.
Lucas Di Pentima [Tue, 9 Jul 2019 19:38:04 +0000 (16:38 -0300)]
15318: Updates tests.

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

5 years ago14965: Fixes replace test encoding
Eric Biagiotti [Tue, 9 Jul 2019 19:26:07 +0000 (15:26 -0400)]
14965: Fixes replace test encoding

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

5 years ago14965: Fixes magic directory test data
Eric Biagiotti [Tue, 9 Jul 2019 19:24:18 +0000 (15:24 -0400)]
14965: Fixes magic directory test data

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

5 years ago15318: Adds X-Request-Id value to every error response. Fixes test.
Lucas Di Pentima [Tue, 9 Jul 2019 19:15:32 +0000 (16:15 -0300)]
15318: Adds X-Request-Id value to every error response. Fixes test.

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

5 years ago15318: Updates test to expect X-Request-Id value on error messages.
Lucas Di Pentima [Tue, 9 Jul 2019 19:09:53 +0000 (16:09 -0300)]
15318: Updates test to expect X-Request-Id value on error messages.

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

5 years ago14965: Fixes crunchstat test assertion
Eric Biagiotti [Tue, 9 Jul 2019 18:44:06 +0000 (14:44 -0400)]
14965: Fixes crunchstat test assertion

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

5 years ago14965: Fixes netstat regex string
Eric Biagiotti [Tue, 9 Jul 2019 18:43:02 +0000 (14:43 -0400)]
14965: Fixes netstat regex string

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

5 years agoFix up test gold standard references for new output
Tom Morris [Tue, 9 Jul 2019 18:04:41 +0000 (14:04 -0400)]
Fix up test gold standard references for new output

refs #13913

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

5 years agoAdd a simple temp disk utilization based recommendation.
Tom Morris [Wed, 3 Jul 2019 17:52:34 +0000 (13:52 -0400)]
Add a simple temp disk utilization based recommendation.

refs #13913

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

5 years agoGraph temp disk usage
Tom Morris [Tue, 23 Apr 2019 00:48:53 +0000 (20:48 -0400)]
Graph temp disk usage

Plots temp disk space used as well as total available.

Also adds support for multiple metrics per graph and
groups CPU and network stats by category.

refs #13913

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

5 years ago14965: Add sanity check for netstat.
Tom Clegg [Tue, 9 Jul 2019 17:42:27 +0000 (13:42 -0400)]
14965: Add sanity check for netstat.

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

5 years ago14965: Adds net-tools to arvbox for run-test-server.py netstat update
Eric Biagiotti [Tue, 9 Jul 2019 15:29:56 +0000 (11:29 -0400)]
14965: Adds net-tools to arvbox for run-test-server.py netstat update

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

5 years ago14965: Use netstat instead of lsof to check for listening process.
Tom Clegg [Tue, 9 Jul 2019 14:50:06 +0000 (10:50 -0400)]
14965: Use netstat instead of lsof to check for listening process.

`lsof -t -i tcp:1234` hangs if a zombie process exists on the system.

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

5 years ago14965: Run py3 tests in the python3 virtualenv.
Tom Clegg [Tue, 9 Jul 2019 14:49:44 +0000 (10:49 -0400)]
14965: Run py3 tests in the python3 virtualenv.

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

5 years agoArvbox won't create application.yml if arvados_config.rb exists.
Peter Amstutz [Mon, 8 Jul 2019 20:40:42 +0000 (16:40 -0400)]
Arvbox won't create application.yml if arvados_config.rb exists.

refs #14812

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

5 years agoMerge branch '14812-wb1-new-config' refs #14812
Peter Amstutz [Tue, 9 Jul 2019 14:00:13 +0000 (10:00 -0400)]
Merge branch '14812-wb1-new-config' refs #14812

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

5 years ago14812: Documentation fixes
Peter Amstutz [Tue, 9 Jul 2019 13:59:02 +0000 (09:59 -0400)]
14812: Documentation fixes

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

5 years ago14812: Add note about config migration to upgrading notes
Peter Amstutz [Mon, 8 Jul 2019 20:07:23 +0000 (16:07 -0400)]
14812: Add note about config migration to upgrading notes

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

5 years ago14812: Update API install documentation for new config as well.
Peter Amstutz [Mon, 8 Jul 2019 19:56:48 +0000 (15:56 -0400)]
14812: Update API install documentation for new config as well.

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

5 years ago14812: Add documentation about migrating Workbench config.
Peter Amstutz [Mon, 8 Jul 2019 19:04:52 +0000 (15:04 -0400)]
14812: Add documentation about migrating Workbench config.

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

5 years ago"arvbox clone" doesn't clone data, just dependencies. no issue #
Peter Amstutz [Mon, 8 Jul 2019 18:04:49 +0000 (14:04 -0400)]
"arvbox clone" doesn't clone data, just dependencies.  no issue #

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

5 years ago14812: Delete legacy load_config.rb
Peter Amstutz [Mon, 8 Jul 2019 17:34:39 +0000 (13:34 -0400)]
14812: Delete legacy load_config.rb

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

5 years agoMerge branch '15358-fetch-text-encoding' closes #15358
Peter Amstutz [Mon, 8 Jul 2019 15:24:19 +0000 (11:24 -0400)]
Merge branch '15358-fetch-text-encoding' closes #15358

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

5 years ago14812: Remove obsolete defaults from development section
Peter Amstutz [Mon, 8 Jul 2019 15:20:36 +0000 (11:20 -0400)]
14812: Remove obsolete defaults from development section

Fix tests

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

5 years ago14812: Improve error reporting
Peter Amstutz [Mon, 8 Jul 2019 15:06:05 +0000 (11:06 -0400)]
14812: Improve error reporting

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

5 years ago14287: Add GOPATH/bin to PATH.
Tom Clegg [Thu, 4 Jul 2019 15:19:16 +0000 (11:19 -0400)]
14287: Add GOPATH/bin to PATH.

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

5 years ago14287: Remove extra panic after error running goimports.
Tom Clegg [Thu, 4 Jul 2019 13:24:43 +0000 (09:24 -0400)]
14287: Remove extra panic after error running goimports.

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

5 years ago14287: Install goimports if needed.
Tom Clegg [Thu, 4 Jul 2019 13:18:24 +0000 (09:18 -0400)]
14287: Install goimports if needed.

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

5 years ago14812: Sync config defaults (off by one line)
Peter Amstutz [Wed, 3 Jul 2019 20:35:08 +0000 (16:35 -0400)]
14812: Sync config defaults (off by one line)

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

5 years ago14812: We can't log the error, might as well make it fatal.
Peter Amstutz [Wed, 3 Jul 2019 20:18:11 +0000 (16:18 -0400)]
14812: We can't log the error, might as well make it fatal.

Rails.logger isn't initialized at this point.

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

5 years ago14965: Fix for default command args test
Eric Biagiotti [Wed, 3 Jul 2019 19:35:48 +0000 (15:35 -0400)]
14965: Fix for default command args test

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

5 years ago14812: Fix a couple more tests
Peter Amstutz [Wed, 3 Jul 2019 19:02:55 +0000 (15:02 -0400)]
14812: Fix a couple more tests

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

5 years ago14865: Reverts change to read op and fixes StringFile
Eric Biagiotti [Wed, 3 Jul 2019 18:42:56 +0000 (14:42 -0400)]
14865: Reverts change to read op and fixes StringFile

Changed the StringFile readfrom function to return utf-8 encoded bytes. This is what the fuse read op is expecting in Pyhton 3.

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

5 years agoMerge branch '15026-cloudtest'
Tom Clegg [Wed, 3 Jul 2019 18:26:15 +0000 (14:26 -0400)]
Merge branch '15026-cloudtest'

closes #15026

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

5 years ago15026: Fix infinite loop in -destroy-existing.
Tom Clegg [Wed, 3 Jul 2019 18:24:49 +0000 (14:24 -0400)]
15026: Fix infinite loop in -destroy-existing.

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

5 years ago15026: Avoid special chars in default instanceSetID.
Tom Clegg [Wed, 3 Jul 2019 18:23:59 +0000 (14:23 -0400)]
15026: Avoid special chars in default instanceSetID.

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

5 years agoUnify string quotation on python example scripts on doc site.
Lucas Di Pentima [Wed, 3 Jul 2019 18:14:08 +0000 (15:14 -0300)]
Unify string quotation on python example scripts on doc site.
No issue #

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

5 years ago15358: Add encoding option to CollectionFsAccess.open() and use in fetch_text()
Peter Amstutz [Wed, 3 Jul 2019 18:03:33 +0000 (14:03 -0400)]
15358: Add encoding option to CollectionFsAccess.open() and use in fetch_text()

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

5 years ago14812: Tweak config export
Peter Amstutz [Wed, 3 Jul 2019 16:56:58 +0000 (12:56 -0400)]
14812: Tweak config export

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

5 years ago14812: Fix email defaults
Peter Amstutz [Wed, 3 Jul 2019 16:50:52 +0000 (12:50 -0400)]
14812: Fix email defaults

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

5 years ago14812: Move TrustAllContent to Collections
Peter Amstutz [Wed, 3 Jul 2019 14:58:54 +0000 (10:58 -0400)]
14812: Move TrustAllContent to Collections

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

5 years ago15380: Improves list filter search documentation
Eric Biagiotti [Wed, 3 Jul 2019 14:01:45 +0000 (10:01 -0400)]
15380: Improves list filter search documentation

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

5 years ago14812: Remove commented debug line
Peter Amstutz [Wed, 3 Jul 2019 13:29:44 +0000 (09:29 -0400)]
14812: Remove commented debug line

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

5 years ago14812: Migrate previously missed config items
Peter Amstutz [Wed, 3 Jul 2019 13:20:43 +0000 (09:20 -0400)]
14812: Migrate previously missed config items

Remove defaults from application.defaults.yml that now come from
arvados-server

Migrate comments describing configuration items

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

5 years ago14287: Merge list results from multiple backends.
Tom Clegg [Wed, 3 Jul 2019 13:10:38 +0000 (09:10 -0400)]
14287: Merge list results from multiple backends.

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

5 years ago14287: Shut down RailsAPI before trying to reinstall.
Tom Clegg [Tue, 2 Jul 2019 14:10:41 +0000 (10:10 -0400)]
14287: Shut down RailsAPI before trying to reinstall.

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

5 years ago14812: Fix lib/config tests
Peter Amstutz [Tue, 2 Jul 2019 17:42:17 +0000 (13:42 -0400)]
14812: Fix lib/config tests

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

5 years ago14965: Fixes unlink operation encoding
Eric Biagiotti [Tue, 2 Jul 2019 16:11:05 +0000 (12:11 -0400)]
14965: Fixes unlink operation encoding

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

5 years ago14965: Fixes test for checking the arvmount version
Eric Biagiotti [Tue, 2 Jul 2019 15:59:26 +0000 (11:59 -0400)]
14965: Fixes test for checking the arvmount version

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

5 years agoTweak arvbox build order, API server depends on arvados-server
Peter Amstutz [Mon, 1 Jul 2019 21:50:31 +0000 (17:50 -0400)]
Tweak arvbox build order, API server depends on arvados-server

refs #14812

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

5 years ago14812: Tweak install order because API server depends on arvados-server
Peter Amstutz [Mon, 1 Jul 2019 21:49:23 +0000 (17:49 -0400)]
14812: Tweak install order because API server depends on arvados-server

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