Peter Amstutz [Wed, 15 Aug 2018 18:44:27 +0000 (14:44 -0400)]
13146: Update comment
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 15 Aug 2018 18:28:13 +0000 (14:28 -0400)]
13146: Support for query filters, "includes"
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Tue, 14 Aug 2018 19:38:54 +0000 (16:38 -0300)]
Merge branch '14028-wb-textile-html-sanitization'
Closes #14028
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 14 Aug 2018 18:01:28 +0000 (15:01 -0300)]
14028: Confirm that safe tags (like <b></b>) don't get cleaned by sanitize()
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Tue, 14 Aug 2018 17:49:17 +0000 (13:49 -0400)]
Merge branch 'jrandall/patch-4' refs #14017
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Tue, 14 Aug 2018 17:01:36 +0000 (14:01 -0300)]
14028: Sanitize RedCloth's output.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 14 Aug 2018 17:32:47 +0000 (14:32 -0300)]
14028: Add test exposing the bug
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Joshua C. Randall [Mon, 13 Aug 2018 12:01:10 +0000 (12:01 +0000)]
Make dispatcher Run loop use count=none and BatchSize limit
Arvados-DCO-1.1-Signed-off-by: Joshua C. Randall <jcrandall@alum.mit.edu>
Peter Amstutz [Mon, 13 Aug 2018 20:14:59 +0000 (16:14 -0400)]
Merge branch '13931-uri-unquote' refs #13931
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 13 Aug 2018 18:50:53 +0000 (14:50 -0400)]
13931: un-uriquote keep: URIs when converting to (collection, path) tuple
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Joshua C. Randall [Mon, 13 Aug 2018 14:47:03 +0000 (15:47 +0100)]
fix "submitted container [uuid]" log from a-c-r
fixes 14017
Arvados-DCO-1.1-Signed-off-by: Joshua C. Randall <jcrandall@alum.mit.edu>
Tom Clegg [Mon, 13 Aug 2018 14:10:36 +0000 (10:10 -0400)]
Note slow migration in upgrade notes.
refs #13752
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 13 Aug 2018 13:37:28 +0000 (09:37 -0400)]
Merge branch '13399-nb-squeue-check'
refs #13399
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 10 Aug 2018 18:28:17 +0000 (14:28 -0400)]
Fix version dependency on 'typing' refs #13931
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 10 Aug 2018 15:17:19 +0000 (11:17 -0400)]
Merge branch '13976-acr-keep-references' refs #13976
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 10 Aug 2018 14:30:55 +0000 (10:30 -0400)]
13976: Add code comment about only_real in upload_dependencies
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 10 Aug 2018 14:14:31 +0000 (10:14 -0400)]
13976: Filter out keep references with secondaryFiles from list of files to upload
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Thu, 9 Aug 2018 20:53:06 +0000 (16:53 -0400)]
13399: Don't block job submissions during release/renice batches.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 9 Aug 2018 19:27:57 +0000 (15:27 -0400)]
Merge branch 'wtsi-hgi-13558-debug-log-tag-req-id'
closes #13558
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 9 Aug 2018 19:06:28 +0000 (15:06 -0400)]
13558: Merge branch 'master' into wtsi-hgi-13558-debug-log-tag-req-id
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 9 Aug 2018 16:53:45 +0000 (12:53 -0400)]
Fix version of 'typing' dep refs #13931
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 9 Aug 2018 16:44:11 +0000 (12:44 -0400)]
13146: Shared endpoint wip
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Wed, 8 Aug 2018 20:13:30 +0000 (17:13 -0300)]
13976: Fix keep reference error
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Thu, 9 Aug 2018 14:47:28 +0000 (11:47 -0300)]
13976: Add CWL test exposing the bug
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Tom Clegg [Thu, 9 Aug 2018 14:18:05 +0000 (10:18 -0400)]
Merge branch '13939-unqualified-contents-orders'
fixes #13939
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Thu, 9 Aug 2018 13:38:32 +0000 (09:38 -0400)]
Merge branch '13752-index-all-filenames'
refs #13752
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Thu, 9 Aug 2018 13:30:09 +0000 (09:30 -0400)]
Merge branch '13931-cwltool-deps' refs #13931
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 9 Aug 2018 13:29:13 +0000 (09:29 -0400)]
13931: Reorganize for consistency.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Thu, 9 Aug 2018 13:28:22 +0000 (09:28 -0400)]
13931: package deps for centos7
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 8 Aug 2018 21:10:03 +0000 (17:10 -0400)]
13931: Fix "don't rebuild packages that already exist" logic
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 8 Aug 2018 20:50:36 +0000 (16:50 -0400)]
13931: Add dependencies required by latest cwltool
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Wed, 8 Aug 2018 20:46:29 +0000 (16:46 -0400)]
Merge branch '13198-keep-web-metrics'
refs #13198
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 7 Aug 2018 22:09:25 +0000 (18:09 -0400)]
13198: Remove old counters from status.json.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 7 Aug 2018 20:19:05 +0000 (16:19 -0400)]
Merge branch '13399-lock-starvation'
refs #13399
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 7 Aug 2018 20:17:34 +0000 (16:17 -0400)]
Merge branch '13931-cwl-size' refs #13931
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 7 Aug 2018 18:24:29 +0000 (14:24 -0400)]
13823: Accept ruamel.yaml 0.15.x, build 0.15.34.
ubuntu bionic ships 0.15.34, making it awkward to depend on an older
version.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Tue, 7 Aug 2018 17:32:08 +0000 (13:32 -0400)]
13931: Update tests for sizes being added
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Tue, 7 Aug 2018 17:24:14 +0000 (13:24 -0400)]
13823: Use pip instead of easy_install if easy_install3 is missing.
easy_install3 no longer exists in ubuntu:bionic.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 7 Aug 2018 17:07:28 +0000 (13:07 -0400)]
13823: Switch to stock fpm.
Upstream has --python-disable-dependency now, so we don't need to use
a fork.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 7 Aug 2018 17:06:50 +0000 (13:06 -0400)]
13823: Upgrade ws4py to version that ships in ubuntu 1804.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Colin Nolan [Mon, 30 Jul 2018 15:57:59 +0000 (16:57 +0100)]
Corrects logic to determine if audit logging is enabled.
Arvados-DCO-1.1-Signed-off-by: Colin Nolan <colin.nolan@sanger.ac.uk>
Joshua C. Randall [Fri, 13 Jul 2018 16:20:18 +0000 (16:20 +0000)]
fix ruby syntax of audit logging disabled check
`max_audit_log_delete_batch > 0 && max_audit_log_age == 0`
Arvados-DCO-1.1-Signed-off-by: Joshua C. Randall <jcrandall@alum.mit.edu>
Colin Nolan [Tue, 7 Aug 2018 14:36:56 +0000 (15:36 +0100)]
Allow audit logging to be disabled.
Audit logs not written if `max_audit_log_delete_batch > 0 and max_audit_log_age == 0`.
Arvados-DCO-1.1-Signed-off-by: Colin Nolan <colin.nolan@sanger.ac.uk>
Tom Clegg [Mon, 6 Aug 2018 23:33:03 +0000 (19:33 -0400)]
13823: Build packages for ubuntu1804.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 6 Aug 2018 21:22:48 +0000 (17:22 -0400)]
13752: Remove column size limit.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 6 Aug 2018 20:59:10 +0000 (16:59 -0400)]
13931: Add keep size test to test list and fix Dockerfile for dev jobs image
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 6 Aug 2018 20:07:06 +0000 (16:07 -0400)]
13399: Don't spam logs about low priority jobs that are running.
Once a job has started, its priority relative to other jobs doesn't
matter to us anyway, and we already skip low-priority jobs in the
"renice" procedure, so there's no reason to warn about this.
Also change "mysterious low priority" reporting threshold from 1Mi to
20K to match the other "nice/hold race" code.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 6 Aug 2018 19:54:35 +0000 (15:54 -0400)]
13931: Update cwltool for add_sizes fix
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 6 Aug 2018 18:14:04 +0000 (14:14 -0400)]
13931: Support for getting file sizes of files in Keep
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 6 Aug 2018 18:13:16 +0000 (14:13 -0400)]
13931: Add test that file sizes are available.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 6 Aug 2018 16:59:30 +0000 (12:59 -0400)]
13399: Adjust locking strategy to avoid starvation.
Don't acquire the slurm lock to call scancel or sbatch.
Don't acquire the slurm lock again immediately after updating the
queue and broadcasting. Instead, give readers a chance to reacquire
the lock after Wait().
Acquire a shared lock instead of an exclusive lock in HasUUID() or
SetPriority() when the protected operation is a read.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Mon, 6 Aug 2018 14:26:27 +0000 (10:26 -0400)]
13752: Dump structure with postgresql 9.6.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 6 Aug 2018 12:56:58 +0000 (08:56 -0400)]
Merge branch '13399-renice-too-low-priority-jobs' refs #13399
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Sat, 4 Aug 2018 15:05:45 +0000 (11:05 -0400)]
13399: Don't try to bury jobs below very-low-priority jobs.
Non-zero priorities below 20K are probably the result of renicing jobs
that have priority=0 because they are in admin-hold state.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Fri, 3 Aug 2018 18:31:13 +0000 (14:31 -0400)]
Merge branch '13961-separate-polling' refs #13961
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 3 Aug 2018 18:29:05 +0000 (14:29 -0400)]
13961: Use poll_time as fallback
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 3 Aug 2018 17:01:49 +0000 (13:01 -0400)]
13961: Separate config for cloudlist_poll_time, nodelist_poll_time, wishlist_poll_time
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Fri, 3 Aug 2018 14:54:19 +0000 (11:54 -0300)]
Merge branch '12762-safeyaml-warning'
Closes #12762
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Thu, 2 Aug 2018 18:59:36 +0000 (15:59 -0300)]
12762: Suppress SafeYAML warnings by setting its default mode.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
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>
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>
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>
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>
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>
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>
Tom Clegg [Wed, 1 Aug 2018 17:40:05 +0000 (13:40 -0400)]
13939: In groups#contents, apply unprefixed orders to all tables.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Wed, 1 Aug 2018 17:13:50 +0000 (13:13 -0400)]
13939: Test orders with no table name qualifier.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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>
projects / arvados.git / log