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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
Tom Clegg [Thu, 12 Jul 2018 18:09:59 +0000 (14:09 -0400)]
13497: Fix Rails redirect targets.
Rails relies on the X-Forwarded-Proto request header, so we need to
set that in the test suite's Nginx config, like we do in the install
guide.
Also tidy up needlessly divergent proxy directives in Nginx test
config.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Lucas Di Pentima [Fri, 13 Jul 2018 14:43:01 +0000 (11:43 -0300)]
13803: Upgrade oj to latest on workbench
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 13 Jul 2018 14:34:48 +0000 (11:34 -0300)]
13803: Upgrade oj dependency on arvados-cli gem.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Fri, 13 Jul 2018 14:33:41 +0000 (11:33 -0300)]
13803: Upgrade oj gem on API server by removing arvados-cli dependency
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Fernando Monserrat [Thu, 12 Jul 2018 20:52:48 +0000 (17:52 -0300)]
13667: test fail on rpm package
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Thu, 12 Jul 2018 20:21:44 +0000 (17:21 -0300)]
13667: test fail on rpm package
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Thu, 12 Jul 2018 20:01:01 +0000 (17:01 -0300)]
13667: test fail on rpm package
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Thu, 12 Jul 2018 19:51:13 +0000 (16:51 -0300)]
13667: test fail on rpm package
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Thu, 12 Jul 2018 19:37:22 +0000 (16:37 -0300)]
13667: test fail on rpm package
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Peter Amstutz [Thu, 12 Jul 2018 18:18:14 +0000 (14:18 -0400)]
13799: More install doc refactor
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 12 Jul 2018 16:36:37 +0000 (12:36 -0400)]
Fix slow tests skipped even when not in --short mode.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 12 Jul 2018 15:34:56 +0000 (11:34 -0400)]
13799: Install doc refactor WIP
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fernando Monserrat [Thu, 12 Jul 2018 15:07:21 +0000 (12:07 -0300)]
13667: test fail on rpm package
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Tom Clegg [Thu, 12 Jul 2018 15:06:45 +0000 (11:06 -0400)]
13497: Fix bypassing controller in test suite after calling reset().
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Fernando Monserrat [Thu, 12 Jul 2018 14:06:05 +0000 (11:06 -0300)]
13667: remove PKG_VERSION in run-build-packages
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Peter Amstutz [Thu, 12 Jul 2018 13:57:30 +0000 (09:57 -0400)]
Merge branch '13690-composer-install' refs #13690
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fernando Monserrat [Wed, 11 Jul 2018 20:23:14 +0000 (17:23 -0300)]
13667: remove PKG_VERSION in run-build-packages
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Wed, 11 Jul 2018 20:10:00 +0000 (17:10 -0300)]
13667: test add PKG_VERSION in run-build-packages
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Wed, 11 Jul 2018 19:35:19 +0000 (16:35 -0300)]
13667: test add config-file for rpm
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Peter Amstutz [Wed, 11 Jul 2018 19:34:08 +0000 (15:34 -0400)]
Merge branch '13767-reserve-ram-doc' closes #13767
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 11 Jul 2018 19:29:42 +0000 (15:29 -0400)]
13767: Tweak text for ReserveExtraRAM to specify default value.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 11 Jul 2018 19:19:55 +0000 (15:19 -0400)]
13497: Merge branch 'master' into 13497-controller
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Wed, 11 Jul 2018 19:17:53 +0000 (15:17 -0400)]
Merge branch '12983-containerd' closes #12983
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 11 Jul 2018 19:15:38 +0000 (15:15 -0400)]
12983: Change break -> return to exit goroutine, add comment
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fernando Monserrat [Wed, 11 Jul 2018 18:37:49 +0000 (15:37 -0300)]
13667: test add config-file for rpm
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Peter Amstutz [Wed, 11 Jul 2018 17:32:03 +0000 (13:32 -0400)]
Merge branch '13780-sprockets' closes #13780
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 11 Jul 2018 13:27:12 +0000 (09:27 -0400)]
13497: 13779: Forward Host header, and don't follow redirects.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 11 Jul 2018 03:00:06 +0000 (23:00 -0400)]
Fix: subcommand not recognized in $0 when no CLI args are given.
refs #13779
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Fernando Monserrat [Tue, 10 Jul 2018 21:03:03 +0000 (18:03 -0300)]
13667: clean up version file generationx
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Peter Amstutz [Tue, 10 Jul 2018 20:16:44 +0000 (16:16 -0400)]
13690: Add Composer install documentation
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fernando Monserrat [Tue, 10 Jul 2018 19:53:08 +0000 (16:53 -0300)]
13667: fix variable in adding version file to ROR packages
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Tue, 10 Jul 2018 19:25:29 +0000 (16:25 -0300)]
13667: fix variable in adding version file to ROR packages
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Peter Amstutz [Tue, 10 Jul 2018 19:04:28 +0000 (15:04 -0400)]
13780: Update sprockets gem
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fernando Monserrat [Tue, 10 Jul 2018 18:50:42 +0000 (15:50 -0300)]
13667: fix variable in adding version file to ROR packages
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Lucas Di Pentima [Tue, 10 Jul 2018 18:50:27 +0000 (15:50 -0300)]
Merge branch '13501-subprocess32'
Closes #13501
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 10 Jul 2018 18:31:50 +0000 (15:31 -0300)]
Merge branch '13668-api-wb-package-version'
Closes #13668
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Tue, 10 Jul 2018 18:31:28 +0000 (14:31 -0400)]
12983: Tweak error regex
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 10 Jul 2018 18:27:38 +0000 (14:27 -0400)]
12983: Add another error message to the "broken node" blacklist.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Tue, 10 Jul 2018 18:12:32 +0000 (14:12 -0400)]
12983: Command line option takes duration. Add tests.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Tue, 10 Jul 2018 17:58:38 +0000 (14:58 -0300)]
13668: Updates VersionHelper on workbench to read packageVersion key
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 10 Jul 2018 17:47:52 +0000 (14:47 -0300)]
13668: Replaced package_version with packageVersion on discovery doc.
Also, enhanced package version caching on api server & workbench.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Tue, 10 Jul 2018 13:49:17 +0000 (09:49 -0400)]
12983: Periodically check for containerd
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fernando Monserrat [Tue, 10 Jul 2018 15:19:10 +0000 (12:19 -0300)]
13667: fix variable in adding version file to ROR packages
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fernando Monserrat [Tue, 10 Jul 2018 14:49:30 +0000 (11:49 -0300)]
13667: Add version file to ROR packages
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>
Fuad Muhic [Tue, 10 Jul 2018 14:20:09 +0000 (16:20 +0200)]
Merge branch '13330-cwl-intermediate-collections-cleanup'
closes #13330
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Tue, 10 Jul 2018 10:48:03 +0000 (12:48 +0200)]
Merge branch 'master' of git.curoverse.com:arvados into 13330-cwl-intermediate-collections-cleanup
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Fuad Muhic [Tue, 10 Jul 2018 10:33:43 +0000 (12:33 +0200)]
Update get_intermediate_collection_info and add owner_uuid to save_new
method in arvcontainer.py and arvjob.py
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Lucas Di Pentima [Mon, 9 Jul 2018 21:01:19 +0000 (18:01 -0300)]
13668: Adds package version to workbench. Reports versions on dialog.
API & Workbench package versions are displayed on the 'Show version' &
'Report problem' dialogs.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 9 Jul 2018 20:24:56 +0000 (17:24 -0300)]
13668: Adds support for package version on API server.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 9 Jul 2018 18:33:37 +0000 (15:33 -0300)]
13501: Adds subprocess32 install dependency on python-client for keepdocker.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 9 Jul 2018 18:09:34 +0000 (15:09 -0300)]
13501: Replaces subprocess with subprocess32 on keepdocker.
Reverted subprocess32 usage on arvados_version.py files so that package
building scripts don't break.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 9 Jul 2018 17:05:22 +0000 (14:05 -0300)]
13501: Replaces subprocess with subprocess32 on arvados-cwl-runner
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Mon, 9 Jul 2018 16:41:24 +0000 (12:41 -0400)]
Merge branch '13766-libyaml-workaround' refs #13766
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 9 Jul 2018 14:11:38 +0000 (10:11 -0400)]
13767: Update crunch-dispatch-slurm install docs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Fuad Muhic [Mon, 9 Jul 2018 13:08:59 +0000 (15:08 +0200)]
Remove _get_intermediate_collection_info method and create function
with same name
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>
Peter Amstutz [Mon, 9 Jul 2018 12:48:16 +0000 (08:48 -0400)]
Merge branch '13681-wb-acr-submit-ram' closes #13681
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 6 Jul 2018 19:41:46 +0000 (15:41 -0400)]
13681: Fix workbench for workflows that don't have "hints"
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 6 Jul 2018 17:48:34 +0000 (13:48 -0400)]
13681: Revert to yaml.round_trip_dump instead of json.dumps().
Also style tweaks.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 5 Jul 2018 20:28:13 +0000 (16:28 -0400)]
13681: Add new test file
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 5 Jul 2018 19:15:16 +0000 (15:15 -0400)]
13681: Update documentation for arv:WorkflowRunnerResources
Also bring default allocation for cwl-runner launched by workbench in
line with a-c-r command line (1 GiB / 1 core).
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 5 Jul 2018 19:03:41 +0000 (15:03 -0400)]
13681: Can use --submit-runner-ram with --create/update-workflow
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 5 Jul 2018 18:39:13 +0000 (14:39 -0400)]
13681: Implement WorkflowRunnerResources hint
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 6 Jul 2018 22:12:29 +0000 (18:12 -0400)]
13766: upload_workflow dumps to json
Workaround for incompatibility between Python ruamel.yaml and Ruby
Psych/libyaml over ":" appearing in unquoted strings in "flow style"
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Fri, 6 Jul 2018 20:04:19 +0000 (17:04 -0300)]
13501: Replaces subprocess module with subprocess32 on nodemanager.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Fri, 6 Jul 2018 14:39:49 +0000 (10:39 -0400)]
Merge branch '13692-acr-error' closes #13692
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 5 Jul 2018 21:25:43 +0000 (17:25 -0400)]
Fix "order" param docs for groups#contents.
No issue #
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 5 Jul 2018 21:03:11 +0000 (17:03 -0400)]
13692: Make Python SDK error reporting more user friendly.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
projects / arvados.git / log