arvados.git
7 years agoBump up rails package iteration.
Ward Vandewege [Fri, 6 Jan 2017 22:31:50 +0000 (17:31 -0500)]
Bump up rails package iteration.

refs #10838

7 years agoFix run-tests.sh --only option for the workbench suite.
Ward Vandewege [Fri, 6 Jan 2017 19:17:20 +0000 (14:17 -0500)]
Fix run-tests.sh --only option for the workbench suite.

refs #8345

7 years agoMerge branch '10793-cwl-continue-on-error' closes #10793
Peter Amstutz [Fri, 6 Jan 2017 18:41:11 +0000 (13:41 -0500)]
Merge branch '10793-cwl-continue-on-error' closes #10793

7 years ago10793: Ensure on_error is set if not present in job_order_object.
Peter Amstutz [Fri, 6 Jan 2017 18:40:32 +0000 (13:40 -0500)]
10793: Ensure on_error is set if not present in job_order_object.

7 years agoMerge branch '10838-fix-rails-package-postinst'
Ward Vandewege [Fri, 6 Jan 2017 18:39:55 +0000 (13:39 -0500)]
Merge branch '10838-fix-rails-package-postinst'

closes #10838

7 years agoIn our rails postinstall package script, preserve newlines when looking
Ward Vandewege [Fri, 6 Jan 2017 18:29:00 +0000 (13:29 -0500)]
In our rails postinstall package script, preserve newlines when looking
for the '^database:' line, so that we match every line of the rake
db:migrate:status output, not just the first one.

refs #10838

7 years agoMerge branch '10223-cr-set-output-name'
Lucas Di Pentima [Thu, 5 Jan 2017 22:05:36 +0000 (19:05 -0300)]
Merge branch '10223-cr-set-output-name'
Closes #10223

7 years ago10223: Added CR's output_name to FTS index
Lucas Di Pentima [Thu, 5 Jan 2017 21:23:03 +0000 (18:23 -0300)]
10223: Added CR's output_name to FTS index

7 years ago10223: Added test to check for missing full text search indexes
Lucas Di Pentima [Thu, 5 Jan 2017 20:59:28 +0000 (17:59 -0300)]
10223: Added test to check for missing full text search indexes

7 years ago10793: Fix to return tuple for alternate exit points --create/update-workflow and...
Peter Amstutz [Thu, 5 Jan 2017 20:29:57 +0000 (15:29 -0500)]
10793: Fix to return tuple for alternate exit points --create/update-workflow and --no-wait

7 years agoMerge branch '10808-admin-cancel-job'
Tom Clegg [Thu, 5 Jan 2017 17:42:22 +0000 (12:42 -0500)]
Merge branch '10808-admin-cancel-job'

refs #10808

7 years ago10808: Move comment.
Tom Clegg [Thu, 5 Jan 2017 17:42:04 +0000 (12:42 -0500)]
10808: Move comment.

7 years ago10793: Move output_callback to finally block to ensure it is always called.
Peter Amstutz [Thu, 5 Jan 2017 16:17:57 +0000 (11:17 -0500)]
10793: Move output_callback to finally block to ensure it is always called.

7 years ago10808: Exempt "change state to Cancelled" from "locked by uuid" protection.
Tom Clegg [Thu, 5 Jan 2017 15:55:53 +0000 (10:55 -0500)]
10808: Exempt "change state to Cancelled" from "locked by uuid" protection.

7 years ago10223: Added relevant explanation on the rollback command
Lucas Di Pentima [Thu, 5 Jan 2017 15:54:30 +0000 (12:54 -0300)]
10223: Added relevant explanation on the rollback command

7 years ago10793: Return output, status tuple from executor.
Peter Amstutz [Thu, 5 Jan 2017 15:45:30 +0000 (10:45 -0500)]
10793: Return output, status tuple from executor.

7 years ago10223: Test simplification: better name, assertion error description added, and use...
Lucas Di Pentima [Thu, 5 Jan 2017 15:43:17 +0000 (12:43 -0300)]
10223: Test simplification: better name, assertion error description added, and use of preexisting fixture.

7 years agoMerge branch '10808-file-cache-ownership'
Tom Clegg [Thu, 5 Jan 2017 15:09:13 +0000 (10:09 -0500)]
Merge branch '10808-file-cache-ownership'

refs #10808

7 years ago10793: Bump cwltool pin for workflow engine improvements. Propagate on-error
Peter Amstutz [Thu, 5 Jan 2017 14:59:53 +0000 (09:59 -0500)]
10793: Bump cwltool pin for workflow engine improvements.  Propagate on-error
behavior from command line to workflow runner job.

7 years ago10808: Avoid using the disk cache if a different user owns it (e.g., running a rake...
Tom Clegg [Wed, 4 Jan 2017 23:12:13 +0000 (18:12 -0500)]
10808: Avoid using the disk cache if a different user owns it (e.g., running a rake task or crunch-dispatch as root).

7 years ago10223: Merge branch 'master' into 10223-cr-set-output-name
Lucas Di Pentima [Wed, 4 Jan 2017 15:19:39 +0000 (12:19 -0300)]
10223: Merge branch 'master' into 10223-cr-set-output-name

7 years ago10223: Added support to CR output_name on cwl-runner. Updated test.
Lucas Di Pentima [Wed, 4 Jan 2017 14:25:20 +0000 (11:25 -0300)]
10223: Added support to CR output_name on cwl-runner. Updated test.

7 years agoFix run-tests.sh --skip option.
Tom Clegg [Wed, 4 Jan 2017 03:47:14 +0000 (22:47 -0500)]
Fix run-tests.sh --skip option.

No issue #

7 years agoMerge branch '8345-revert-llfuse-to-0.41.1'
Tom Clegg [Wed, 4 Jan 2017 01:57:40 +0000 (20:57 -0500)]
Merge branch '8345-revert-llfuse-to-0.41.1'

refs #8345

7 years ago8345: Revert llfuse to 0.41.1.
Tom Clegg [Tue, 3 Jan 2017 20:05:20 +0000 (15:05 -0500)]
8345: Revert llfuse to 0.41.1.

7 years ago8345: Compatibility with llfuse 0.41 and 1.x.
Tom Clegg [Tue, 3 Jan 2017 15:50:41 +0000 (10:50 -0500)]
8345: Compatibility with llfuse 0.41 and 1.x.

7 years ago8345: Add run-tests.sh --repeat option.
Tom Clegg [Sun, 1 Jan 2017 01:38:02 +0000 (20:38 -0500)]
8345: Add run-tests.sh --repeat option.

7 years agoMerge branch '10795-get-zero-block'
Tom Clegg [Tue, 3 Jan 2017 21:40:11 +0000 (16:40 -0500)]
Merge branch '10795-get-zero-block'

refs #10795

7 years ago10795: For md5(""), skip the request and just return an empty reader.
Tom Clegg [Tue, 3 Jan 2017 21:35:58 +0000 (16:35 -0500)]
10795: For md5(""), skip the request and just return an empty reader.

7 years ago10795: Remove test-selector code (use -check.f instead).
Tom Clegg [Tue, 3 Jan 2017 21:33:19 +0000 (16:33 -0500)]
10795: Remove test-selector code (use -check.f instead).

7 years agoMerge branch '10682-azure-stats'
Tom Clegg [Tue, 3 Jan 2017 20:50:35 +0000 (15:50 -0500)]
Merge branch '10682-azure-stats'

refs #10682

7 years ago10682: Add GetMetadataOps and GetPropertiesOps to Azure backend stats.
Tom Clegg [Tue, 3 Jan 2017 20:49:46 +0000 (15:49 -0500)]
10682: Add GetMetadataOps and GetPropertiesOps to Azure backend stats.

7 years ago10682: Add comments to statsTicker.
Tom Clegg [Tue, 3 Jan 2017 15:34:27 +0000 (10:34 -0500)]
10682: Add comments to statsTicker.

7 years ago10682: Track Azure backend errors by type.
Tom Clegg [Mon, 2 Jan 2017 19:54:43 +0000 (14:54 -0500)]
10682: Track Azure backend errors by type.

7 years ago10682: Add backend stats for Azure volumes.
Tom Clegg [Mon, 2 Jan 2017 18:57:31 +0000 (13:57 -0500)]
10682: Add backend stats for Azure volumes.

7 years ago10223: Added output_name column to container_request. When being finalized, if output...
Lucas Di Pentima [Mon, 2 Jan 2017 21:14:33 +0000 (18:14 -0300)]
10223: Added output_name column to container_request. When being finalized, if output_name is set then the output
collection will be named accordingly. If there is a unique index violation, a date is added to its name.
Also, added output_name to CR search index.

7 years ago10682: Avoid invoking special "test mode" behavior in Azure SDK.
Tom Clegg [Mon, 2 Jan 2017 20:13:45 +0000 (15:13 -0500)]
10682: Avoid invoking special "test mode" behavior in Azure SDK.

Restores compatibility with latest azure-sdk-for-go.

refs #10682

7 years agorun-build-packages-all-targets.sh: Make sure to build all packages once not twice.
Ward Vandewege [Sat, 31 Dec 2016 21:35:38 +0000 (16:35 -0500)]
run-build-packages-all-targets.sh: Make sure to build all packages once not twice.

No issue #

7 years agoMerge branch '10786-remove-centos6-from-build-directory'
Ward Vandewege [Sat, 31 Dec 2016 21:34:44 +0000 (16:34 -0500)]
Merge branch '10786-remove-centos6-from-build-directory'

closes #10786

7 years agoRemove additional CentOS6 files.
Ward Vandewege [Sat, 31 Dec 2016 20:27:51 +0000 (15:27 -0500)]
Remove additional CentOS6 files.

refs #10786

7 years agoRemove CentOS6 support from the build directory.
Ward Vandewege [Thu, 29 Dec 2016 15:33:29 +0000 (10:33 -0500)]
Remove CentOS6 support from the build directory.

refs #10786

7 years agoMerge branch 'master' into 10786-remove-centos6-from-build-directory
Ward Vandewege [Sat, 31 Dec 2016 20:20:11 +0000 (15:20 -0500)]
Merge branch 'master' into 10786-remove-centos6-from-build-directory

7 years agoMerge branch '10467-client-disconnect' closes #10467
Tom Clegg [Fri, 30 Dec 2016 22:06:55 +0000 (17:06 -0500)]
Merge branch '10467-client-disconnect' closes #10467

7 years agoMerge branch '10790-crunch-job-log-timeout' refs #10790
Peter Amstutz [Fri, 30 Dec 2016 21:12:35 +0000 (16:12 -0500)]
Merge branch '10790-crunch-job-log-timeout' refs #10790

7 years ago10790: Increase timeout reading from arv-put.
Peter Amstutz [Fri, 30 Dec 2016 20:48:23 +0000 (15:48 -0500)]
10790: Increase timeout reading from arv-put.

7 years agoMerge branch '10538-trash-delete' closes #10538
Tom Clegg [Fri, 30 Dec 2016 20:17:02 +0000 (15:17 -0500)]
Merge branch '10538-trash-delete' closes #10538

7 years ago10538: Mention fixture names in comments when not using fixture finders.
Tom Clegg [Fri, 30 Dec 2016 20:16:31 +0000 (15:16 -0500)]
10538: Mention fixture names in comments when not using fixture finders.

7 years ago10467: Use BlockReader and BlockWriter interfaces instead of passing methods to get...
Tom Clegg [Fri, 30 Dec 2016 19:58:00 +0000 (14:58 -0500)]
10467: Use BlockReader and BlockWriter interfaces instead of passing methods to get/putWithPipe.

7 years ago10467: Remove debug printfs.
Tom Clegg [Fri, 30 Dec 2016 19:41:12 +0000 (14:41 -0500)]
10467: Remove debug printfs.

7 years ago10467: Remove unneeded errorReadCloser, make getter/putter interfaces more like Write...
Tom Clegg [Fri, 30 Dec 2016 19:39:52 +0000 (14:39 -0500)]
10467: Remove unneeded errorReadCloser, make getter/putter interfaces more like WriterTo/ReaderFrom.

7 years agoMerge branch '10497-cwl-job-logs' closes #10497
Peter Amstutz [Fri, 30 Dec 2016 19:12:27 +0000 (14:12 -0500)]
Merge branch '10497-cwl-job-logs' closes #10497

7 years agoMerge branch '10722-cwl-subworkflow' closes #10722
Peter Amstutz [Fri, 30 Dec 2016 19:12:16 +0000 (14:12 -0500)]
Merge branch '10722-cwl-subworkflow' closes #10722

7 years ago10538: Clarify error message.
Tom Clegg [Fri, 30 Dec 2016 18:39:07 +0000 (13:39 -0500)]
10538: Clarify error message.

7 years ago10538: Clear up default_trash_interval logic
Tom Clegg [Fri, 30 Dec 2016 18:38:26 +0000 (13:38 -0500)]
10538: Clear up default_trash_interval logic

7 years ago10538: Fix misspelled IsTrash -> IsTrashed
Tom Clegg [Fri, 30 Dec 2016 18:37:41 +0000 (13:37 -0500)]
10538: Fix misspelled IsTrash -> IsTrashed

7 years ago10497: Replace \d\d\d\d with \d{4}
Peter Amstutz [Fri, 30 Dec 2016 18:34:27 +0000 (13:34 -0500)]
10497: Replace \d\d\d\d with \d{4}

7 years ago8345: Build python27-python-contextlib2 for centos7.
Tom Clegg [Fri, 30 Dec 2016 15:28:38 +0000 (10:28 -0500)]
8345: Build python27-python-contextlib2 for centos7.

refs #8345

7 years agoFix version# of centos7 llfuse backport.
Tom Clegg [Fri, 30 Dec 2016 00:52:10 +0000 (19:52 -0500)]
Fix version# of centos7 llfuse backport.

No issue #

7 years agoBring back ca-certificates to package-testing images.
Tom Clegg [Thu, 29 Dec 2016 19:57:45 +0000 (14:57 -0500)]
Bring back ca-certificates to package-testing images.

No issue #

7 years agoMerge branch '8345-llfuse-1.0' closes #8345
Tom Clegg [Thu, 29 Dec 2016 16:03:59 +0000 (11:03 -0500)]
Merge branch '8345-llfuse-1.0' closes #8345

7 years agoMerge branch 'master' into 8345-llfuse-1.0
Tom Clegg [Thu, 29 Dec 2016 16:02:34 +0000 (11:02 -0500)]
Merge branch 'master' into 8345-llfuse-1.0

Conflicts:
build/package-test-dockerfiles/debian7/Dockerfile
build/run-build-packages.sh

7 years agoObey --only-build arg in "test packages" mode.
Tom Clegg [Thu, 29 Dec 2016 15:45:55 +0000 (10:45 -0500)]
Obey --only-build arg in "test packages" mode.

7 years agoUpdate package-test images to ruby 2.3
Tom Clegg [Thu, 29 Dec 2016 15:37:27 +0000 (10:37 -0500)]
Update package-test images to ruby 2.3

7 years agoMerge branch '10785-remove-debian7'
Ward Vandewege [Thu, 29 Dec 2016 13:36:37 +0000 (08:36 -0500)]
Merge branch '10785-remove-debian7'

closes #10785

7 years ago8345: Build python27-python-contextlib2 for centos6.
Tom Clegg [Thu, 29 Dec 2016 07:47:40 +0000 (02:47 -0500)]
8345: Build python27-python-contextlib2 for centos6.

7 years ago8345: Upgrade to llfuse 1.0
Tom Clegg [Mon, 18 Apr 2016 16:40:21 +0000 (12:40 -0400)]
8345: Upgrade to llfuse 1.0

7 years ago8345: Revert change to getattr() @catch_exceptions setup.
Tom Clegg [Thu, 10 Mar 2016 20:04:10 +0000 (15:04 -0500)]
8345: Revert change to getattr() @catch_exceptions setup.

7 years ago8345: Fix dirent timestamps.
Tom Clegg [Wed, 9 Mar 2016 18:50:41 +0000 (13:50 -0500)]
8345: Fix dirent timestamps.

7 years ago8345: Pin llfuse to <1.0
Tom Clegg [Tue, 8 Mar 2016 21:40:22 +0000 (16:40 -0500)]
8345: Pin llfuse to <1.0

7 years ago8345: fix whitespace
Tom Clegg [Mon, 7 Mar 2016 20:26:14 +0000 (15:26 -0500)]
8345: fix whitespace

7 years agoupdates test_mount to use st_mtime_ns instead of st_mtime
Joshua Randall [Wed, 10 Feb 2016 12:04:25 +0000 (12:04 +0000)]
updates test_mount to use st_mtime_ns instead of st_mtime

7 years agoupdates setattr for llfuse-python 0.42
Joshua Randall [Tue, 9 Feb 2016 21:41:40 +0000 (21:41 +0000)]
updates setattr for llfuse-python 0.42

7 years agoadds backports specific to centos6
Joshua Randall [Fri, 5 Feb 2016 18:37:17 +0000 (18:37 +0000)]
adds backports specific to centos6

7 years agoadds missing fix for llfuse 0.42+
Joshua Randall [Fri, 5 Feb 2016 11:45:10 +0000 (11:45 +0000)]
adds missing fix for llfuse 0.42+

llfuse.capi._notify_queue => llfuse._notify_queue

7 years agoupdates llfuse requirement and API to >=0.42
Joshua Randall [Wed, 3 Feb 2016 11:48:55 +0000 (11:48 +0000)]
updates llfuse requirement and API to >=0.42

7 years agoRemove debian7 from the build directory.
Ward Vandewege [Wed, 28 Dec 2016 23:14:56 +0000 (18:14 -0500)]
Remove debian7 from the build directory.

refs #10785

7 years ago10467: local directory driver: skip disk IO if client disconnects before lock is...
Tom Clegg [Wed, 28 Dec 2016 21:44:32 +0000 (16:44 -0500)]
10467: local directory driver: skip disk IO if client disconnects before lock is acquired.

7 years ago10722: Issue better error when 'id' is missing.
Peter Amstutz [Wed, 28 Dec 2016 20:50:20 +0000 (15:50 -0500)]
10722: Issue better error when 'id' is missing.

7 years ago10497: Add logname (crunch-run, stdout, stderr) to container log tail
Peter Amstutz [Wed, 28 Dec 2016 18:24:11 +0000 (13:24 -0500)]
10497: Add logname (crunch-run, stdout, stderr) to container log tail

7 years ago10497: Filter crunchstat lines to make more space for useful logs.
Peter Amstutz [Wed, 28 Dec 2016 18:07:18 +0000 (13:07 -0500)]
10497: Filter crunchstat lines to make more space for useful logs.

7 years ago10497: Increase number of log lines shown by runner. Turn off 'debug' mode on crunch...
Peter Amstutz [Wed, 28 Dec 2016 16:13:56 +0000 (11:13 -0500)]
10497: Increase number of log lines shown by runner.  Turn off 'debug' mode on crunch script.

7 years ago10497: Don't prefix every line of log from job.
Peter Amstutz [Wed, 28 Dec 2016 15:55:46 +0000 (10:55 -0500)]
10497: Don't prefix every line of log from job.

7 years ago10497: Add --no-log-timestamps to eliminate redundant timestamps when running in...
Peter Amstutz [Wed, 28 Dec 2016 15:31:49 +0000 (10:31 -0500)]
10497: Add --no-log-timestamps to eliminate redundant timestamps when running in Arvados job or container.

Conflicts:
sdk/cwl/setup.py

7 years ago10497: Print last 25 lines of log when job fails.
Peter Amstutz [Mon, 19 Dec 2016 21:26:29 +0000 (16:26 -0500)]
10497: Print last 25 lines of log when job fails.

7 years agoMerge branch '10782-container-retry' closes #10782
Peter Amstutz [Wed, 28 Dec 2016 17:39:59 +0000 (12:39 -0500)]
Merge branch '10782-container-retry' closes #10782

7 years ago10782: Bugfix, on retry only update container_uuid on container requests
Peter Amstutz [Wed, 28 Dec 2016 17:05:07 +0000 (12:05 -0500)]
10782: Bugfix, on retry only update container_uuid on container requests
associated with the container in the first place.  Update container retry test.

7 years agoFix crunch script to construct toolpath before it is turned into a File object. refs...
Peter Amstutz [Wed, 28 Dec 2016 15:54:37 +0000 (10:54 -0500)]
Fix crunch script to construct toolpath before it is turned into a File object. refs #10497

7 years agoMerge branch '10497-cwl-better-errors' refs #10497
Peter Amstutz [Wed, 28 Dec 2016 15:30:24 +0000 (10:30 -0500)]
Merge branch '10497-cwl-better-errors' refs #10497

7 years agoArvbox common.sh script won't fail if bundler gem not cached on disk.
Peter Amstutz [Wed, 28 Dec 2016 15:29:30 +0000 (10:29 -0500)]
Arvbox common.sh script won't fail if bundler gem not cached on disk.
Don't push docker images if build fails.  no issue #

7 years ago10497: Add pathlib2 to backports
Peter Amstutz [Wed, 28 Dec 2016 15:05:17 +0000 (10:05 -0500)]
10497: Add pathlib2 to backports

7 years ago10497: Pop cwl:tool parameter from job order
Peter Amstutz [Tue, 27 Dec 2016 22:06:17 +0000 (17:06 -0500)]
10497: Pop cwl:tool parameter from job order

7 years ago10497: Update ruamel.yaml, schema salad, and cwltool
Peter Amstutz [Tue, 27 Dec 2016 20:05:48 +0000 (15:05 -0500)]
10497: Update ruamel.yaml, schema salad, and cwltool

7 years ago10497: Use SourceLine in context manager in PathMapper. Remove unnecessary import.
Peter Amstutz [Wed, 21 Dec 2016 15:34:53 +0000 (10:34 -0500)]
10497: Use SourceLine in context manager in PathMapper.  Remove unnecessary import.

7 years ago10497: Improve up front feature checking and error reporting.
Peter Amstutz [Mon, 19 Dec 2016 20:33:40 +0000 (15:33 -0500)]
10497: Improve up front feature checking and error reporting.

7 years ago10497: Add source line reporting to errors and fix tests to work with CommentedMap...
Peter Amstutz [Mon, 19 Dec 2016 18:39:46 +0000 (13:39 -0500)]
10497: Add source line reporting to errors and fix tests to work with CommentedMap/Seq behavior.

7 years ago10497: Update cwltool & schema salad versions.
Peter Amstutz [Fri, 16 Dec 2016 21:34:59 +0000 (16:34 -0500)]
10497: Update cwltool & schema salad versions.

7 years agoLoad keep-balance config from default location if -config arg not given.
Tom Clegg [Wed, 28 Dec 2016 15:21:25 +0000 (10:21 -0500)]
Load keep-balance config from default location if -config arg not given.

No issue #

7 years agoArvbox use --local to install bundler if gem is available, also recognize .tar.bz2 in
Peter Amstutz [Tue, 13 Dec 2016 14:36:47 +0000 (09:36 -0500)]
Arvbox use --local to install bundler if gem is available, also recognize .tar.bz2 in
pip cache.  no issue #

7 years agoFix use of unquoted user input in regexp.
Tom Clegg [Wed, 28 Dec 2016 05:52:29 +0000 (00:52 -0500)]
Fix use of unquoted user input in regexp.

7 years ago10538: Add /arvados/v1/collections/{uuid}/trash endpoint.
Tom Clegg [Wed, 28 Dec 2016 05:26:42 +0000 (00:26 -0500)]
10538: Add /arvados/v1/collections/{uuid}/trash endpoint.