arvados.git
6 years agoMerge branch '13076-r-autogen-api'
Fuad Muhic [Fri, 20 Apr 2018 08:20:12 +0000 (10:20 +0200)]
Merge branch '13076-r-autogen-api'

refs #13076

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

6 years agoarvbox pin pip to 9.0.3. Add LINES/COLUMNS to "arvbox shell", no issue #
Peter Amstutz [Thu, 19 Apr 2018 17:52:37 +0000 (13:52 -0400)]
arvbox pin pip to 9.0.3.  Add LINES/COLUMNS to "arvbox shell", no issue #

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

6 years agoMake the runin-reqs less stingy about RAM refs #13301
Peter Amstutz [Thu, 19 Apr 2018 20:05:28 +0000 (16:05 -0400)]
Make the runin-reqs less stingy about RAM refs #13301

Tests were failing because it turns out 4 MB isn't enough to run Python!

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

6 years ago13076: R SDK online docs include both README and method docs.
Peter Amstutz [Thu, 19 Apr 2018 19:47:23 +0000 (15:47 -0400)]
13076: R SDK online docs include both README and method docs.

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

6 years ago13076: Get rid of pkgdown, just call knitr
Peter Amstutz [Thu, 19 Apr 2018 18:24:11 +0000 (14:24 -0400)]
13076: Get rid of pkgdown, just call knitr

Converts README.Rmd to README.html for documentation.

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

6 years agoBump arvados-python-client version dependency.
Peter Amstutz [Wed, 18 Apr 2018 20:26:19 +0000 (16:26 -0400)]
Bump arvados-python-client version dependency.

Set threadsafe api object to use calling command.keepdocker and
command.put.

refs #13108

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

6 years agoarv-put: restore_signal_handlers conditional on install_sig_handlers
Peter Amstutz [Wed, 18 Apr 2018 20:23:29 +0000 (16:23 -0400)]
arv-put: restore_signal_handlers conditional on install_sig_handlers

arv-keepdocker: accept api object to use

refs #13108

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

6 years agoAdded script to generate html doc for .Rmd files.
Fuad Muhic [Tue, 17 Apr 2018 15:10:04 +0000 (17:10 +0200)]
Added script to generate html doc for .Rmd files.

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

6 years agofix cwltest junit-xml dependency refs #13108
Peter Amstutz [Tue, 17 Apr 2018 01:26:41 +0000 (21:26 -0400)]
fix cwltest junit-xml dependency refs #13108

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

6 years agoUpdated README and small fix for Subcollection docs.
Fuad Muhic [Mon, 16 Apr 2018 15:03:38 +0000 (17:03 +0200)]
Updated README and small fix for Subcollection docs.

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

6 years agoMethod documentation now shows headline properly.
Fuad Muhic [Mon, 16 Apr 2018 13:51:47 +0000 (15:51 +0200)]
Method documentation now shows headline properly.

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

6 years agoAdded documentation for hardcoded Arvados class project methods.
Fuad Muhic [Mon, 16 Apr 2018 13:16:47 +0000 (15:16 +0200)]
Added documentation for hardcoded Arvados class project methods.

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

6 years agoAdded auto-generated documentation for Arvados class.
Fuad Muhic [Mon, 16 Apr 2018 12:26:40 +0000 (14:26 +0200)]
Added auto-generated documentation for Arvados class.

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

6 years agoMerge branch '13108-acr-threading-fixes' refs #13108
Peter Amstutz [Fri, 13 Apr 2018 17:23:40 +0000 (13:23 -0400)]
Merge branch '13108-acr-threading-fixes' refs #13108

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

6 years ago13108: Fix import
Peter Amstutz [Fri, 13 Apr 2018 15:54:17 +0000 (11:54 -0400)]
13108: Fix import

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

6 years ago13108: Refactor signal handling
Peter Amstutz [Fri, 13 Apr 2018 15:41:54 +0000 (11:41 -0400)]
13108: Refactor signal handling

a-c-r handles SystemExit the same way as KeyboardInterrupt.

Bump version of cwltest (to get the terminate-on-timeout bugfix).

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

6 years agoMerge branch '12320-access-projects-from-by_id'
Fuad Muhic [Fri, 13 Apr 2018 07:59:02 +0000 (09:59 +0200)]
Merge branch '12320-access-projects-from-by_id'

closes #12320

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

6 years ago13108: crunch_script uses safeapi
Peter Amstutz [Fri, 13 Apr 2018 00:54:57 +0000 (20:54 -0400)]
13108: crunch_script uses safeapi

Also take workflow lock on update_pipeline_component to prevent update races.

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

6 years ago13108: Don't try to install signal handler in background thread
Peter Amstutz [Thu, 12 Apr 2018 20:22:52 +0000 (16:22 -0400)]
13108: Don't try to install signal handler in background thread

Fix Docker image upload failure due to arv-put trying to install a
signal handler somewhere other than the main thread.

Also install toplevel signal handler to convert SIGTERM to
KeyboardInterrupt.

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

6 years agorefs #13339 "Merge branch '13339-update-gemspecs-new-versioning'".
Fernando Monserrat [Thu, 12 Apr 2018 18:59:59 +0000 (15:59 -0300)]
refs #13339 "Merge branch '13339-update-gemspecs-new-versioning'".
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13339: fix git_hash variable
Fernando Monserrat [Thu, 12 Apr 2018 18:37:46 +0000 (15:37 -0300)]
13339: fix git_hash variable
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13339: fix git_latest_tag formatting
Fernando Monserrat [Thu, 12 Apr 2018 18:19:28 +0000 (15:19 -0300)]
13339: fix git_latest_tag formatting
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13339: fix git_latest_tag formatting
Fernando Monserrat [Thu, 12 Apr 2018 18:11:38 +0000 (15:11 -0300)]
13339: fix git_latest_tag formatting
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13339: fix typo assigning git_latest_tag
Fernando Monserrat [Thu, 12 Apr 2018 17:20:40 +0000 (14:20 -0300)]
13339: fix typo assigning git_latest_tag
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years agoOptimized API call to not return non project groups
Fuad Muhic [Thu, 12 Apr 2018 09:49:32 +0000 (11:49 +0200)]
Optimized API call to not return non project groups

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

6 years agoUpdate instructions to get arvados node manager Azure credentials to v2
Ward Vandewege [Thu, 12 Apr 2018 01:17:38 +0000 (21:17 -0400)]
Update instructions to get arvados node manager Azure credentials to v2
of the Azure cli.

No issue #

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

6 years agoMerge branch '13348-recursive-submit'
Tom Clegg [Wed, 11 Apr 2018 20:21:21 +0000 (16:21 -0400)]
Merge branch '13348-recursive-submit'

refs #13348
refs #13108

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

6 years ago13348: Don't submit child jobs/containers with submit=True.
Tom Clegg [Wed, 11 Apr 2018 19:54:15 +0000 (15:54 -0400)]
13348: Don't submit child jobs/containers with submit=True.

Fixes infinite recursion.

see a82b39e1849a67854cb3399a4660b77548edd580

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

6 years agoMerge branch '13108-cwl-parallel-submit' closes #13108
Peter Amstutz [Tue, 10 Apr 2018 19:38:18 +0000 (15:38 -0400)]
Merge branch '13108-cwl-parallel-submit' closes #13108

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

6 years ago13108: Add test for taskqueue
Peter Amstutz [Tue, 10 Apr 2018 18:19:05 +0000 (14:19 -0400)]
13108: Add test for taskqueue

Also tighten up code in a few places.

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

6 years agoUsers can only access groups with group_class set to project from by_id
Fuad Muhic [Tue, 10 Apr 2018 16:29:16 +0000 (18:29 +0200)]
Users can only access groups with group_class set to project from by_id
directory

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

6 years agoMerge branch '13142-dispatch-nfiles'
Tom Clegg [Tue, 10 Apr 2018 15:48:48 +0000 (11:48 -0400)]
Merge branch '13142-dispatch-nfiles'

refs #13142

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

6 years ago13142: Raise open files limit.
Tom Clegg [Wed, 28 Mar 2018 20:24:04 +0000 (16:24 -0400)]
13142: Raise open files limit.

See https://dev.arvados.org/issues/13142

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

6 years agoMerge branch '13105-wb-ignore-missing-remotes'
Lucas Di Pentima [Tue, 10 Apr 2018 15:34:55 +0000 (10:34 -0500)]
Merge branch '13105-wb-ignore-missing-remotes'
Closes #13105

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

6 years ago13105: discoveryDoc() call simplification.
Lucas Di Pentima [Tue, 10 Apr 2018 15:26:34 +0000 (10:26 -0500)]
13105: discoveryDoc() call simplification.

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

6 years agoArvados projects can be accessed from by_id directory in keep mount
Fuad Muhic [Tue, 10 Apr 2018 13:40:13 +0000 (15:40 +0200)]
Arvados projects can be accessed from by_id directory in keep mount

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

6 years agoMerge branch '13100-crunch-run-output'
Tom Clegg [Tue, 10 Apr 2018 13:21:26 +0000 (09:21 -0400)]
Merge branch '13100-crunch-run-output'

fixes #13100
fixes #11583
fixes #12606
refs #13048

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

6 years ago13105: Set remoteHosts and remoteHostsViaDNS default values when missing.
Lucas Di Pentima [Thu, 5 Apr 2018 19:04:28 +0000 (16:04 -0300)]
13105: Set remoteHosts and remoteHostsViaDNS default values when missing.

Also fix some discovery doc requests to use the SessionDB cache.

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

6 years ago13100: Merge branch 'master' into 13100-crunch-run-output
Tom Clegg [Mon, 9 Apr 2018 20:22:33 +0000 (16:22 -0400)]
13100: Merge branch 'master' into 13100-crunch-run-output

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

6 years ago13100: 12606: Test chain of relative symlinks.
Tom Clegg [Mon, 9 Apr 2018 15:26:26 +0000 (11:26 -0400)]
13100: 12606: Test chain of relative symlinks.

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

6 years ago13100: Handle output symlinks to writable collections.
Tom Clegg [Mon, 9 Apr 2018 15:13:30 +0000 (11:13 -0400)]
13100: Handle output symlinks to writable collections.

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

6 years ago13100: Handle writable collections mounted below output dir.
Tom Clegg [Mon, 9 Apr 2018 14:19:59 +0000 (10:19 -0400)]
13100: Handle writable collections mounted below output dir.

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

6 years ago13100: Update comment.
Tom Clegg [Mon, 9 Apr 2018 13:56:03 +0000 (09:56 -0400)]
13100: Update comment.

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

6 years ago13339: update gemspecs for new versioning
Fernando Monserrat [Fri, 6 Apr 2018 20:13:46 +0000 (17:13 -0300)]
13339: update gemspecs for new versioning
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13108: Add copyright notice to task_queue.py
Peter Amstutz [Fri, 6 Apr 2018 17:49:11 +0000 (13:49 -0400)]
13108: Add copyright notice to task_queue.py

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

6 years ago13108: Fix tests.
Peter Amstutz [Fri, 6 Apr 2018 17:37:08 +0000 (13:37 -0400)]
13108: Fix tests.

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

6 years ago13108: Refactor task queue into its own class.
Peter Amstutz [Fri, 6 Apr 2018 15:32:03 +0000 (11:32 -0400)]
13108: Refactor task queue into its own class.

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

6 years ago13108: Fix tracking tasks in flight
Peter Amstutz [Fri, 6 Apr 2018 15:21:56 +0000 (11:21 -0400)]
13108: Fix tracking tasks in flight

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

6 years ago13108: Rename parallel_submit_count to thread_count
Peter Amstutz [Fri, 6 Apr 2018 14:29:30 +0000 (10:29 -0400)]
13108: Rename parallel_submit_count to thread_count

Make sure it gets passed through to RunnerContainer.

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

6 years ago13108: Rename runnable_queue -> task_queue
Peter Amstutz [Fri, 6 Apr 2018 12:44:23 +0000 (08:44 -0400)]
13108: Rename runnable_queue -> task_queue

Execute synchronously when parallel_submit_count == 1

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

6 years ago13108: Collect outputs in separate threads as well
Peter Amstutz [Thu, 5 Apr 2018 22:20:24 +0000 (18:20 -0400)]
13108: Collect outputs in separate threads as well

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

6 years ago13108: Work queue submit wip
Peter Amstutz [Thu, 5 Apr 2018 21:10:25 +0000 (17:10 -0400)]
13108: Work queue submit wip

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

6 years ago13108: Simplify locking, add methods for recording process status
Peter Amstutz [Thu, 5 Apr 2018 20:32:19 +0000 (16:32 -0400)]
13108: Simplify locking, add methods for recording process status

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

6 years agoFix comment. 1.1.4
Ward Vandewege [Thu, 5 Apr 2018 20:00:31 +0000 (16:00 -0400)]
Fix comment.

No issue #

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

6 years ago13100: Use collection FS for output and logs.
Tom Clegg [Thu, 5 Apr 2018 06:31:10 +0000 (02:31 -0400)]
13100: Use collection FS for output and logs.

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

6 years ago13108: Use ThreadSafeApiCache
Peter Amstutz [Thu, 5 Apr 2018 19:45:58 +0000 (15:45 -0400)]
13108: Use ThreadSafeApiCache

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

6 years ago13108: Handle multiple instances of arv-keepdocker uploading same docker image
Peter Amstutz [Thu, 5 Apr 2018 19:28:09 +0000 (15:28 -0400)]
13108: Handle multiple instances of arv-keepdocker uploading same docker image

Use cooperative locking with flock to minimize interference.

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

6 years agoMerge branch '13201-less-validate' closes #13201
Peter Amstutz [Thu, 5 Apr 2018 17:25:44 +0000 (13:25 -0400)]
Merge branch '13201-less-validate' closes #13201

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

6 years agoMerge branch '12085-anm-metrics'
Lucas Di Pentima [Thu, 5 Apr 2018 15:15:43 +0000 (12:15 -0300)]
Merge branch '12085-anm-metrics'
Closes #12085

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

6 years ago13201: Fix tests.
Peter Amstutz [Thu, 5 Apr 2018 14:47:39 +0000 (10:47 -0400)]
13201: Fix tests.

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

6 years ago12085: Unconditionally remove the idle time counter of paired missing nodes.
Lucas Di Pentima [Thu, 5 Apr 2018 14:37:49 +0000 (11:37 -0300)]
12085: Unconditionally remove the idle time counter of paired missing nodes.

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

6 years ago12085: When an idle node disappears from the cloud node list, clear its counter.
Lucas Di Pentima [Tue, 3 Apr 2018 16:50:35 +0000 (13:50 -0300)]
12085: When an idle node disappears from the cloud node list, clear its counter.

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

6 years ago12085: Add node_quota status & count different cloud errors separately.
Lucas Di Pentima [Mon, 2 Apr 2018 21:04:08 +0000 (18:04 -0300)]
12085: Add node_quota status & count different cloud errors separately.

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

6 years ago12085: Idle node times tracking, with tests.
Lucas Di Pentima [Wed, 28 Mar 2018 18:51:14 +0000 (15:51 -0300)]
12085: Idle node times tracking, with tests.

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

6 years ago12085: Boot failures counting, with tests.
Lucas Di Pentima [Tue, 27 Mar 2018 13:58:37 +0000 (10:58 -0300)]
12085: Boot failures counting, with tests.

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

6 years ago12085: Test actor & cloud errors counting.
Lucas Di Pentima [Thu, 22 Mar 2018 20:34:22 +0000 (17:34 -0300)]
12085: Test actor & cloud errors counting.

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

6 years ago12085: Counters support for status tracker.
Lucas Di Pentima [Thu, 22 Mar 2018 14:25:46 +0000 (11:25 -0300)]
12085: Counters support for status tracker.

Also:
* Expose configured max_nodes settings
* Count number of cloud errors
* Add related tests

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

6 years ago13201: disable redundant validation.
Peter Amstutz [Wed, 4 Apr 2018 18:55:07 +0000 (14:55 -0400)]
13201: disable redundant validation.

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

6 years agoapi server: get_anonymous_user_token script
Ward Vandewege [Thu, 5 Apr 2018 02:19:32 +0000 (22:19 -0400)]
api server: get_anonymous_user_token script

* bugfix: always return the token (the script would sometimes fail with
an error message that it couldn't call api_token on a Hash)
* new feature: allow supplying of the token to be created via a command
line argument.

No issue #

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

6 years ago"refs #13200" "Merge branch '13200-python-pkg-version'".
Fernando Monserrat [Wed, 4 Apr 2018 22:28:58 +0000 (19:28 -0300)]
"refs #13200" "Merge branch '13200-python-pkg-version'".
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13200: fix SETUP_DIR on python packages
Fernando Monserrat [Wed, 4 Apr 2018 22:10:22 +0000 (19:10 -0300)]
13200: fix SETUP_DIR on python packages
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13200: remove_version from python packages
Fernando Monserrat [Wed, 4 Apr 2018 21:58:42 +0000 (18:58 -0300)]
13200: remove_version from python packages
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13200: Consolidate package version behavior in arvados_version for all the python...
Fernando Monserrat [Wed, 4 Apr 2018 21:42:08 +0000 (18:42 -0300)]
13200: Consolidate package version behavior in arvados_version for all the python packages
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13200: Consolidate package version behavior in arvados_version
Peter Amstutz [Wed, 4 Apr 2018 20:57:27 +0000 (16:57 -0400)]
13200: Consolidate package version behavior in arvados_version

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

6 years ago13200: Fix python versioning for arvados-python-client and arvados-cwl-runner
Peter Amstutz [Wed, 4 Apr 2018 20:05:31 +0000 (16:05 -0400)]
13200: Fix python versioning for arvados-python-client and arvados-cwl-runner

New behavior:

1) If ARVADOS_BUILDING_VERSION is set, write that to _version.py

2) Else, try to import arvados_version, get version based on git
  tags+timestamp and write that to _version.py.  arvados_version.py is
  present in the source tree but not included in the package, so if we
  get ImportError, do nothing.

If neither (1) or (2) succeeds, take that to mean we're installing a
source package.  Leave _version.py alone.

Read the version back from _version.py and use that.

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

6 years agoFix more ineffassign warnings in our golang code.
Ward Vandewege [Wed, 4 Apr 2018 19:23:45 +0000 (15:23 -0400)]
Fix more ineffassign warnings in our golang code.

refs #

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

6 years agokeepproxy: bugfix: do not swallow error if Readall succeeds but PutB fails.
Ward Vandewege [Wed, 4 Apr 2018 19:21:20 +0000 (15:21 -0400)]
keepproxy: bugfix: do not swallow error if Readall succeeds but PutB fails.
Found by ineffassign.

No issue #

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

6 years agoFix one gofmt and more ineffassign warnings in our golang tests.
Ward Vandewege [Tue, 3 Apr 2018 21:53:23 +0000 (17:53 -0400)]
Fix one gofmt and more ineffassign warnings in our golang tests.

No issue #

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

6 years agoFix a whole bunch of ineffassign warnings in our golang tests.
Ward Vandewege [Tue, 3 Apr 2018 21:25:02 +0000 (17:25 -0400)]
Fix a whole bunch of ineffassign warnings in our golang tests.

No issue #

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

6 years agoUpdate debian version in sdk/python/README.rst
Ward Vandewege [Tue, 3 Apr 2018 20:45:46 +0000 (16:45 -0400)]
Update debian version in sdk/python/README.rst

No issue #

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

6 years agoAdd missing test for error code in keepclient test.
Ward Vandewege [Tue, 3 Apr 2018 15:42:57 +0000 (11:42 -0400)]
Add missing test for error code in keepclient test.

No issue #

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

6 years agoAdd missing file refs #13301
Peter Amstutz [Tue, 3 Apr 2018 13:15:51 +0000 (09:15 -0400)]
Add missing file refs #13301

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

6 years agoMerge branch '12414-delete-trashed-project-contents'
Lucas Di Pentima [Mon, 2 Apr 2018 19:58:48 +0000 (16:58 -0300)]
Merge branch '12414-delete-trashed-project-contents'
Closes #12414

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

6 years agoMerge branch '13301-cwl-resource-scatter' closes #13301
Peter Amstutz [Mon, 2 Apr 2018 19:55:53 +0000 (15:55 -0400)]
Merge branch '13301-cwl-resource-scatter' closes #13301

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

6 years ago12414: Test fixes
Lucas Di Pentima [Mon, 2 Apr 2018 19:11:56 +0000 (16:11 -0300)]
12414: Test fixes

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

6 years ago12414: Enhance sweep process test to ensure no unwanted deletions happen
Lucas Di Pentima [Mon, 2 Apr 2018 18:53:40 +0000 (15:53 -0300)]
12414: Enhance sweep process test to ensure no unwanted deletions happen

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

6 years agorefs #13200 Merge branch '13200-new-package-versioning-jb'
Fernando Monserrat [Mon, 2 Apr 2018 18:33:04 +0000 (15:33 -0300)]
refs #13200 Merge branch '13200-new-package-versioning-jb'
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years agoAdd RunInSingleContainer dynamic resource request tests
Peter Amstutz [Mon, 2 Apr 2018 18:30:54 +0000 (14:30 -0400)]
Add RunInSingleContainer dynamic resource request tests

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

6 years ago12414: Add tests for projects (and their contents) deletion.
Lucas Di Pentima [Mon, 2 Apr 2018 15:57:29 +0000 (12:57 -0300)]
12414: Add tests for projects (and their contents) deletion.

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

6 years ago13200: remove verbose bash on run-build-packages.sh
Fernando Monserrat [Wed, 28 Mar 2018 17:56:09 +0000 (14:56 -0300)]
13200: remove verbose bash on run-build-packages.sh
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13200: remove verbose bash on build packages
Fernando Monserrat [Wed, 28 Mar 2018 14:35:33 +0000 (11:35 -0300)]
13200: remove verbose bash on build packages
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13200: Fix format gitinfo on all the services
Fernando Monserrat [Mon, 26 Mar 2018 14:54:12 +0000 (11:54 -0300)]
13200: Fix format gitinfo on all the services
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13200: format gitinfo on all the services
Fernando Monserrat [Mon, 26 Mar 2018 14:37:43 +0000 (11:37 -0300)]
13200: format gitinfo on all the services
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13200: format gitinfo on all the services
Fernando Monserrat [Mon, 26 Mar 2018 13:44:11 +0000 (10:44 -0300)]
13200: format gitinfo on all the services
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years agoTrying some str formatting
Javier Bértoli [Fri, 23 Mar 2018 21:50:23 +0000 (18:50 -0300)]
Trying some str formatting

refs #13200
Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@veritasgenetics.com>

6 years agoTrying some str formatting
Javier Bértoli [Fri, 23 Mar 2018 21:39:14 +0000 (18:39 -0300)]
Trying some str formatting

refs #13200
Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@veritasgenetics.com>

6 years agoAdd functions to return the python version for packaging
Javier Bértoli [Fri, 23 Mar 2018 20:02:57 +0000 (17:02 -0300)]
Add functions to return the python version for packaging

refs #13200
Arvados-DCO-1.1-Signed-off-by: Javier Bértoli <jbertoli@veritasgenetics.com>

6 years ago13200:rollback tests
Fernando Monserrat [Fri, 23 Mar 2018 19:54:08 +0000 (16:54 -0300)]
13200:rollback tests
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13200:test update on version in gittaggers on sdk python
Fernando Monserrat [Fri, 23 Mar 2018 19:49:06 +0000 (16:49 -0300)]
13200:test update on version in gittaggers on sdk python
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>

6 years ago13200:test update on version in gittaggers on sdk python
Fernando Monserrat [Fri, 23 Mar 2018 19:45:20 +0000 (16:45 -0300)]
13200:test update on version in gittaggers on sdk python
Arvados-DCO-1.1-Signed-off-by: Fernando Monserrat <fmonserrat@veritasgenetics.com>