arvados.git
5 years agoMerge branch '13609-r-sdk-copy' refs #13609
Peter Amstutz [Thu, 2 Aug 2018 18:00:37 +0000 (14:00 -0400)]
Merge branch '13609-r-sdk-copy' refs #13609

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

5 years ago13609: Note that move/copy between collections isn't supported
Peter Amstutz [Thu, 2 Aug 2018 17:59:37 +0000 (13:59 -0400)]
13609: Note that move/copy between collections isn't supported

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

5 years ago13609: Spelling fix
Peter Amstutz [Thu, 2 Aug 2018 17:53:47 +0000 (13:53 -0400)]
13609: Spelling fix

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

5 years ago13609: Improve README fomatting a bit.
Peter Amstutz [Thu, 2 Aug 2018 17:52:35 +0000 (13:52 -0400)]
13609: Improve README fomatting a bit.

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

5 years ago13609: Update version to 0.0.5
Peter Amstutz [Thu, 2 Aug 2018 17:40:28 +0000 (13:40 -0400)]
13609: Update version to 0.0.5

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

5 years agoMerge branch '13934-guard-comment'
Tom Clegg [Thu, 2 Aug 2018 04:13:15 +0000 (00:13 -0400)]
Merge branch '13934-guard-comment'

closes #13934

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

5 years ago13934: Add comment to guard dispatch bugfix.
Tom Clegg [Wed, 1 Aug 2018 16:56:31 +0000 (12:56 -0400)]
13934: Add comment to guard dispatch bugfix.

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

5 years agoMerge branch '13497-controller'
Tom Clegg [Wed, 1 Aug 2018 13:14:14 +0000 (09:14 -0400)]
Merge branch '13497-controller'

refs #13497

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

5 years agoMerge branch '13198-keep-web-metrics'
Tom Clegg [Tue, 31 Jul 2018 18:04:39 +0000 (14:04 -0400)]
Merge branch '13198-keep-web-metrics'

refs #13198

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

5 years agoMerge branch '13892-deprecate-jobs-api' closes #13892
Peter Amstutz [Tue, 31 Jul 2018 17:51:05 +0000 (13:51 -0400)]
Merge branch '13892-deprecate-jobs-api' closes #13892

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

5 years ago13892: Make warning more obvious.
Peter Amstutz [Tue, 31 Jul 2018 17:26:14 +0000 (13:26 -0400)]
13892: Make warning more obvious.

Link to information about migrating for both users and admins.

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

5 years ago13892: Update disable_api_methods with the full list
Peter Amstutz [Tue, 31 Jul 2018 15:40:28 +0000 (11:40 -0400)]
13892: Update disable_api_methods with the full list

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

5 years ago13497: Link issues and commit hashes to redmine.
Tom Clegg [Tue, 31 Jul 2018 15:31:55 +0000 (11:31 -0400)]
13497: Link issues and commit hashes to redmine.

"#1234" and "commit:foo" markup doesn't work here like it did on the
redmine wiki where the content came from.

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

5 years ago13497: Add controller to upgrade notes.
Tom Clegg [Tue, 31 Jul 2018 15:26:36 +0000 (11:26 -0400)]
13497: Add controller to upgrade notes.

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

5 years ago13497: Add controller to install docs.
Tom Clegg [Mon, 30 Jul 2018 19:53:45 +0000 (15:53 -0400)]
13497: Add controller to install docs.

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

5 years ago13198: Add cache stats to metrics.
Tom Clegg [Mon, 30 Jul 2018 16:03:07 +0000 (12:03 -0400)]
13198: Add cache stats to metrics.

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

5 years agoMerge branch '13690-composer-user-guide' closes #13690
Peter Amstutz [Mon, 30 Jul 2018 16:53:54 +0000 (12:53 -0400)]
Merge branch '13690-composer-user-guide' closes #13690

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

5 years ago13690: Add/fix links
Peter Amstutz [Mon, 30 Jul 2018 14:35:37 +0000 (10:35 -0400)]
13690: Add/fix links

* Fix CWL user guide link
* Link from "Developing Workflows" to Composer tutorial
* More detail about what goes in "Docker Repository" field

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

5 years ago13690: Fill in some missing steps.
Peter Amstutz [Fri, 27 Jul 2018 17:57:11 +0000 (13:57 -0400)]
13690: Fill in some missing steps.

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

5 years agoMerge branch '13920-arvados-gem-with-newer-rubies'
Lucas Di Pentima [Thu, 26 Jul 2018 20:41:33 +0000 (17:41 -0300)]
Merge branch '13920-arvados-gem-with-newer-rubies'
Closes #13920

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

5 years ago13920: Fixes google-api-client gem issue with ruby 2.3.7+
Lucas Di Pentima [Thu, 26 Jul 2018 19:45:23 +0000 (16:45 -0300)]
13920: Fixes google-api-client gem issue with ruby 2.3.7+

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

5 years ago13690: Walkthrough of Composer on Arvados
Peter Amstutz [Thu, 26 Jul 2018 18:31:53 +0000 (14:31 -0400)]
13690: Walkthrough of Composer on Arvados

* Creating a new git repository through Arvados to store the workflow
* Creating CommandLineTools for “sort” and “uniq”
* Creating a Workflow which uses “sort” and “uniq” to remove duplicate lines from a text file
* Submitting the Workflow to run on Arvados

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

5 years agoMerge branch '13910-arvados-gem-retrieval'
Lucas Di Pentima [Thu, 26 Jul 2018 18:28:18 +0000 (15:28 -0300)]
Merge branch '13910-arvados-gem-retrieval'
Closes #13910

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

5 years agoFix a few typos.
Ward Vandewege [Thu, 26 Jul 2018 16:22:12 +0000 (12:22 -0400)]
Fix a few typos.

refs #13791

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

5 years agoMerge branch 'master' of git.curoverse.com:arvados into 13609-r-sdk-copy
Fuad Muhic [Thu, 26 Jul 2018 15:18:24 +0000 (17:18 +0200)]
Merge branch 'master' of git.curoverse.com:arvados into 13609-r-sdk-copy

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

5 years agoImprove Collections create and move methods and update documentation
Fuad Muhic [Thu, 26 Jul 2018 14:09:14 +0000 (16:09 +0200)]
Improve Collections create and move methods and update documentation

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

5 years agoMerge branch '13791-monitoring-docs' closes #13791
Peter Amstutz [Thu, 26 Jul 2018 13:54:10 +0000 (09:54 -0400)]
Merge branch '13791-monitoring-docs' closes #13791

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

5 years ago13892: Add jobs API deprecation notice to arvados-cwl-runner
Peter Amstutz [Thu, 26 Jul 2018 13:42:49 +0000 (09:42 -0400)]
13892: Add jobs API deprecation notice to arvados-cwl-runner

Also document how to disable the jobs API so that a-c-r selects the
containers API automatically.

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

5 years agoMerge branch '12444-tmpdir-monitoring'
Lucas Di Pentima [Wed, 25 Jul 2018 20:38:09 +0000 (17:38 -0300)]
Merge branch '12444-tmpdir-monitoring'
Closes #12444

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

5 years ago13910: Fixes arvados gem dependency on arvados-cli & arvados-login-sync
Lucas Di Pentima [Wed, 25 Jul 2018 20:27:27 +0000 (17:27 -0300)]
13910: Fixes arvados gem dependency on arvados-cli & arvados-login-sync

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

5 years agoarvbox uses keep config file instead of cli switches. no issue #
Peter Amstutz [Wed, 25 Jul 2018 19:18:48 +0000 (15:18 -0400)]
arvbox uses keep config file instead of cli switches.  no issue #

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

5 years agoMerge branch '13570-crunch-ram-doc' closes #13570
Peter Amstutz [Wed, 25 Jul 2018 19:10:53 +0000 (15:10 -0400)]
Merge branch '13570-crunch-ram-doc' closes #13570

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

5 years ago13570: Doc tweaks
Peter Amstutz [Wed, 25 Jul 2018 19:09:38 +0000 (15:09 -0400)]
13570: Doc tweaks

* Capitalize "Keep"
* Clarify usage of cgroups
* Clarify "Available compute node types"

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

5 years agoImplement copy method, update move method and remove trailing
Fuad Muhic [Wed, 25 Jul 2018 09:54:08 +0000 (11:54 +0200)]
Implement copy method, update move method and remove trailing
whitespace in Arvados.R.

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

5 years ago13570: Add formulas. Add link from cwl-style to crunch discussion.
Peter Amstutz [Tue, 24 Jul 2018 20:19:40 +0000 (16:19 -0400)]
13570: Add formulas.  Add link from cwl-style to crunch discussion.

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

5 years ago12444: Allow crunch-run to provide tmpdir to crunchstat
Lucas Di Pentima [Tue, 24 Jul 2018 20:15:21 +0000 (17:15 -0300)]
12444: Allow crunch-run to provide tmpdir to crunchstat

Also, get the temp dir from $TMPDIR if not provided, fix the 'used'
space calculation, and report which dir is being monitored.

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

5 years ago13791: Tweak doc ordering.
Peter Amstutz [Tue, 24 Jul 2018 19:09:18 +0000 (15:09 -0400)]
13791: Tweak doc ordering.

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

5 years ago13791: More detail about monitoring
Peter Amstutz [Tue, 24 Jul 2018 19:02:52 +0000 (15:02 -0400)]
13791: More detail about monitoring

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

5 years ago12444: Adds tmpdir stats to crunchstat reporting
Lucas Di Pentima [Tue, 24 Jul 2018 14:31:29 +0000 (11:31 -0300)]
12444: Adds tmpdir stats to crunchstat reporting

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

5 years agoMerge branch '13888-cli-dependency-on-api'
Lucas Di Pentima [Tue, 24 Jul 2018 17:07:31 +0000 (14:07 -0300)]
Merge branch '13888-cli-dependency-on-api'
Closes #13888

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

5 years ago13570: Add section describing RAM allocation behavior.
Peter Amstutz [Tue, 24 Jul 2018 15:53:51 +0000 (11:53 -0400)]
13570: Add section describing RAM allocation behavior.

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

5 years ago13888: Adds arvados-cli dependency back on API server
Lucas Di Pentima [Tue, 24 Jul 2018 15:43:22 +0000 (12:43 -0300)]
13888: Adds arvados-cli dependency back on API server

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

5 years agoArvbox fix correct permissions to stop one-shot services. no issue #
Peter Amstutz [Mon, 23 Jul 2018 18:33:02 +0000 (14:33 -0400)]
Arvbox fix correct permissions to stop one-shot services. no issue #

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

5 years ago13791: Admin documentation for monitoring wip
Peter Amstutz [Mon, 23 Jul 2018 15:29:28 +0000 (11:29 -0400)]
13791: Admin documentation for monitoring wip

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

5 years ago13791: Health check endpoint docs wip
Peter Amstutz [Mon, 23 Jul 2018 13:31:51 +0000 (09:31 -0400)]
13791: Health check endpoint docs wip

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

5 years agoMerge branch '13546-crunch1-timeout' refs #13546
Peter Amstutz [Mon, 23 Jul 2018 13:33:44 +0000 (09:33 -0400)]
Merge branch '13546-crunch1-timeout' refs #13546

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

5 years agoMerge branch '13879-arvados-server' closes #13879
Peter Amstutz [Fri, 20 Jul 2018 20:52:52 +0000 (16:52 -0400)]
Merge branch '13879-arvados-server' closes #13879

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

5 years ago13879: Fix cut and paste typo.
Peter Amstutz [Fri, 20 Jul 2018 20:51:03 +0000 (16:51 -0400)]
13879: Fix cut and paste typo.

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

5 years ago13546: crunch-job has timeout on srun_sync
Peter Amstutz [Fri, 20 Jul 2018 20:42:56 +0000 (16:42 -0400)]
13546: crunch-job has timeout on srun_sync

* Add global timeout to srun_sync, default 15 minutes, terminates
  job if a call to srun_sync exceeds the timeout.

* Default can be adjusted by setting CRUNCH_SRUN_SYNC_TIMEOUT in the
  environment of crunch_dispatch.rb (value is in seconds)

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

5 years agoMerge branch '13851-wb-multisite-search'
Lucas Di Pentima [Fri, 20 Jul 2018 17:00:47 +0000 (14:00 -0300)]
Merge branch '13851-wb-multisite-search'
Closes #13851

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

5 years agoMerge branch '13493-federation-proxy'
Tom Clegg [Fri, 20 Jul 2018 15:11:36 +0000 (11:11 -0400)]
Merge branch '13493-federation-proxy'

refs #13493

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

5 years ago13493: Merge branch 'master' into 13493-federation-proxy
Tom Clegg [Fri, 20 Jul 2018 14:25:45 +0000 (10:25 -0400)]
13493: Merge branch 'master' into 13493-federation-proxy

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

5 years ago13879: Arvbox support for arvados-controller
Peter Amstutz [Thu, 19 Jul 2018 22:15:03 +0000 (18:15 -0400)]
13879: Arvbox support for arvados-controller

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

5 years agoMerge branch '13788-concurrent-map-write'
Tom Clegg [Thu, 19 Jul 2018 20:56:25 +0000 (16:56 -0400)]
Merge branch '13788-concurrent-map-write'

fixes #13788

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

5 years agoMerge branch '13198-keep-web-metrics'
Tom Clegg [Thu, 19 Jul 2018 20:15:47 +0000 (16:15 -0400)]
Merge branch '13198-keep-web-metrics'

refs #13198

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

5 years agoReflect the new name and url for the public evaluation and trial instance,
Ward Vandewege [Thu, 19 Jul 2018 19:55:18 +0000 (15:55 -0400)]
Reflect the new name and url for the public evaluation and trial instance,
Arvados Playground.

No issue #

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

5 years ago13788: Fix concurrent map write.
Tom Clegg [Thu, 19 Jul 2018 19:26:02 +0000 (15:26 -0400)]
13788: Fix concurrent map write.

Reading multiple pages into the same ContainerList was reusing
embedded maps that had been passed to other goroutines.

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

5 years ago13851: Reverted use of discoveryDoc() on findAPI()
Lucas Di Pentima [Thu, 19 Jul 2018 18:10:44 +0000 (15:10 -0300)]
13851: Reverted use of discoveryDoc() on findAPI()

Also checking adding a '/' to baseURL on discoveryDoc when needed.

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

5 years agoMerge branch '13868-invalid-node-size' refs #13868
Peter Amstutz [Thu, 19 Jul 2018 16:09:44 +0000 (12:09 -0400)]
Merge branch '13868-invalid-node-size' refs #13868

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

5 years ago13868: Fallback behavior when arvados_node_size tag is missing
Peter Amstutz [Thu, 19 Jul 2018 15:12:05 +0000 (11:12 -0400)]
13868: Fallback behavior when arvados_node_size tag is missing

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

5 years agoMerge branch '13645-fix-arvados-api-host-insecure'
Fuad Muhic [Thu, 19 Jul 2018 14:59:19 +0000 (16:59 +0200)]
Merge branch '13645-fix-arvados-api-host-insecure'

refs #13645

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

5 years agorefs #13667 "Merge branch '13667-add-version-file'".
Fernando Monserrat [Thu, 19 Jul 2018 14:47:18 +0000 (11:47 -0300)]
refs #13667 "Merge branch '13667-add-version-file'".
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

5 years agoMerge branch '13399-nice-logs'
Tom Clegg [Thu, 19 Jul 2018 01:44:23 +0000 (21:44 -0400)]
Merge branch '13399-nice-logs'

refs #13399

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

5 years agoMerge branch '13804-no-shutdown-wanted-nodes' refs #13804
Peter Amstutz [Wed, 18 Jul 2018 18:02:40 +0000 (14:02 -0400)]
Merge branch '13804-no-shutdown-wanted-nodes' refs #13804

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

5 years agoremove trailing white space from all files
Fuad Muhic [Wed, 18 Jul 2018 10:43:20 +0000 (12:43 +0200)]
remove trailing white space from all files

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

5 years agoadd tests for exec and getConnection methods in HttpRequest class
Fuad Muhic [Wed, 18 Jul 2018 10:36:41 +0000 (12:36 +0200)]
add tests for exec and getConnection methods in HttpRequest class

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

5 years ago13399: Link to wiki in warning message.
Tom Clegg [Tue, 17 Jul 2018 21:04:05 +0000 (17:04 -0400)]
13399: Link to wiki in warning message.

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

5 years ago13399: Recognize held jobs with priority between 1 and 20K.
Tom Clegg [Tue, 17 Jul 2018 19:32:45 +0000 (15:32 -0400)]
13399: Recognize held jobs with priority between 1 and 20K.

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

5 years ago13399: If slurm refuses to renice past 10K, stop trying.
Tom Clegg [Tue, 3 Jul 2018 21:03:11 +0000 (17:03 -0400)]
13399: If slurm refuses to renice past 10K, stop trying.

Fixes log spam.

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

5 years agoMerge branch 'master' into 13804-no-shutdown-wanted-nodes
Peter Amstutz [Tue, 17 Jul 2018 20:55:52 +0000 (16:55 -0400)]
Merge branch 'master' into 13804-no-shutdown-wanted-nodes

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

5 years ago13804: Update comments for comments for "consecutive_idle_count"
Peter Amstutz [Tue, 17 Jul 2018 20:53:31 +0000 (16:53 -0400)]
13804: Update comments for comments for "consecutive_idle_count"

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

5 years agoMerge branch '13803-oj-gem-malloc-bug'
Lucas Di Pentima [Tue, 17 Jul 2018 19:19:23 +0000 (16:19 -0300)]
Merge branch '13803-oj-gem-malloc-bug'
Closes #13803

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

5 years ago13804: Fix tests
Peter Amstutz [Tue, 17 Jul 2018 18:47:01 +0000 (14:47 -0400)]
13804: Fix tests

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

5 years ago13198: Document metrics endpoints.
Tom Clegg [Tue, 17 Jul 2018 18:17:47 +0000 (14:17 -0400)]
13198: Document metrics endpoints.

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

5 years agoFix typo.
Ward Vandewege [Tue, 17 Jul 2018 17:14:44 +0000 (13:14 -0400)]
Fix typo.

No issue #

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

5 years agoMerge branch '13822-nm-delayed-daemon' refs #13822
Peter Amstutz [Tue, 17 Jul 2018 15:40:38 +0000 (11:40 -0400)]
Merge branch '13822-nm-delayed-daemon' refs #13822

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

5 years ago13198: Track & serve keep-web metrics.
Tom Clegg [Tue, 17 Jul 2018 15:38:45 +0000 (11:38 -0400)]
13198: Track & serve keep-web metrics.

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

5 years agoMerge branch 'master' into 13822-nm-delayed-daemon
Peter Amstutz [Tue, 17 Jul 2018 14:26:29 +0000 (10:26 -0400)]
Merge branch 'master' into 13822-nm-delayed-daemon

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

5 years ago13804: Smarter shutdown behavior WIP
Peter Amstutz [Tue, 17 Jul 2018 13:51:23 +0000 (09:51 -0400)]
13804: Smarter shutdown behavior WIP

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

5 years ago13803: Fix behavior change on Oj 3.x
Lucas Di Pentima [Mon, 16 Jul 2018 23:43:38 +0000 (20:43 -0300)]
13803: Fix behavior change on Oj 3.x

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

5 years ago13804: Try to cancel pending shutdowns if nodes are needed
Peter Amstutz [Mon, 16 Jul 2018 21:19:53 +0000 (17:19 -0400)]
13804: Try to cancel pending shutdowns if nodes are needed

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

5 years ago13803: Re-enable Oj's rails optimizations & fix time format test failures.
Lucas Di Pentima [Mon, 16 Jul 2018 20:52:52 +0000 (17:52 -0300)]
13803: Re-enable Oj's rails optimizations & fix time format test failures.

There's one failing test pending on collection controller: when asking for
the index with select="" the followin exception is being masked by
load_limit_offset_order_params():

JSON::ParserError: Empty input at line 1, column 1 [parse.c:928]

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

5 years ago13804: Node must report as "idle" two consecutive times
Peter Amstutz [Mon, 16 Jul 2018 20:05:02 +0000 (16:05 -0400)]
13804: Node must report as "idle" two consecutive times

Gives idle nodes 1 poll period to be allocated by slurm before
becoming candidates for shutdown.

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

5 years ago13198: Test case for keep-web metrics.
Tom Clegg [Mon, 16 Jul 2018 19:01:42 +0000 (15:01 -0400)]
13198: Test case for keep-web metrics.

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

5 years ago13822: Don't call list_sizes() in cloud client constructor.
Peter Amstutz [Mon, 16 Jul 2018 18:54:35 +0000 (14:54 -0400)]
13822: Don't call list_sizes() in cloud client constructor.

Also make subscribe() call to SetupActor asynchronous.

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

5 years ago13803: Remove oj_mimic_json gem.
Lucas Di Pentima [Mon, 16 Jul 2018 18:47:14 +0000 (15:47 -0300)]
13803: Remove oj_mimic_json gem.

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

5 years ago13493: Update CORS OPTIONS test.
Tom Clegg [Mon, 16 Jul 2018 15:40:55 +0000 (11:40 -0400)]
13493: Update CORS OPTIONS test.

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

5 years ago13198: Move metrics to httpserver package.
Tom Clegg [Mon, 16 Jul 2018 14:42:23 +0000 (10:42 -0400)]
13198: Move metrics to httpserver package.

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

5 years ago13493: Fix proxy-redirect implementation.
Tom Clegg [Mon, 16 Jul 2018 13:55:51 +0000 (09:55 -0400)]
13493: Fix proxy-redirect implementation.

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

5 years agoMerge branch '13799-install-doc-sections' refs #13799
Peter Amstutz [Mon, 16 Jul 2018 13:50:27 +0000 (09:50 -0400)]
Merge branch '13799-install-doc-sections' refs #13799

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

5 years ago13493: Merge branch 'master' into 13493-federation-proxy
Tom Clegg [Mon, 16 Jul 2018 13:46:23 +0000 (09:46 -0400)]
13493: Merge branch 'master' into 13493-federation-proxy

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

5 years agoMerge branch '13497-controller'
Tom Clegg [Fri, 13 Jul 2018 20:31:11 +0000 (16:31 -0400)]
Merge branch '13497-controller'

refs #13497

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

5 years ago13497: Merge branch 'master' into 13497-controller
Tom Clegg [Fri, 13 Jul 2018 20:30:48 +0000 (16:30 -0400)]
13497: Merge branch 'master' into 13497-controller

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

5 years ago13667: clean up
Fernando Monserrat [Fri, 13 Jul 2018 19:10:56 +0000 (16:10 -0300)]
13667: clean up
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

5 years ago13667: test fail on rpm package
Fernando Monserrat [Fri, 13 Jul 2018 18:01:03 +0000 (15:01 -0300)]
13667: test fail on rpm package
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

5 years ago13497: Add comments on odd Nginx config. Less confusing vhost name.
Tom Clegg [Fri, 13 Jul 2018 17:24:07 +0000 (13:24 -0400)]
13497: Add comments on odd Nginx config. Less confusing vhost name.

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

5 years ago13667: test fail on rpm package
Fernando Monserrat [Fri, 13 Jul 2018 15:44:55 +0000 (12:44 -0300)]
13667: test fail on rpm package
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

5 years ago13497: Improve nginx logging in test suite.
Tom Clegg [Fri, 13 Jul 2018 14:51:43 +0000 (10:51 -0400)]
13497: Improve nginx logging in test suite.

Include request scheme://host:port, elapsed time, and upstream server
type.

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

5 years ago13497: Avoid misdirecting POST to GET when request has double slash.
Tom Clegg [Thu, 12 Jul 2018 20:50:59 +0000 (16:50 -0400)]
13497: Avoid misdirecting POST to GET when request has double slash.

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

5 years ago13497: Use X-Forwarded-Proto as scheme for keep-web redirect URLs.
Tom Clegg [Thu, 12 Jul 2018 20:43:37 +0000 (16:43 -0400)]
13497: Use X-Forwarded-Proto as scheme for keep-web redirect URLs.

This avoids relying on the downstream proxy to rewrite redirects.

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