radhika [Wed, 27 Jul 2016 16:13:15 +0000 (12:13 -0400)]
closes #9552
Merge branch '9552-compute-checksum-flag'
radhika [Wed, 27 Jul 2016 16:07:35 +0000 (12:07 -0400)]
Merge branch 'master' into 9552-compute-checksum-flag
Conflicts:
sdk/cwl/setup.py
Brett Smith [Tue, 26 Jul 2016 20:54:39 +0000 (16:54 -0400)]
9659: Bump CWL SDK's versioned dependency on PySDK.
The CWL SDK depends on the change made to arv-run in
27816b602e9da83a2565e6fe8f87f250555b1ba5. Update the version
dependency in setup.py to reflect this. Refs #9570, #9659.
radhika [Tue, 26 Jul 2016 18:47:32 +0000 (14:47 -0400)]
9552: update cwltool version, which offer compute_checksum flag.
Lucas Di Pentima [Tue, 26 Jul 2016 14:28:38 +0000 (11:28 -0300)]
Merge branch '9551-python-keep-services-env'
9551: Python SDK support for ARVADOS_KEEP_SERVICES environment variable. Closes #9551
Lucas Di Pentima [Tue, 26 Jul 2016 14:03:57 +0000 (11:03 -0300)]
9551: Replaced ARVADOS_KEEP_PROXY with ARVADOS_KEEP_SERVICES new var on tests. Added proxy URI validation test.
Lucas Di Pentima [Tue, 26 Jul 2016 13:34:12 +0000 (10:34 -0300)]
9551: Proxy URLs validation. Iteration optimization builind _keep_services list
Tom Clegg [Tue, 26 Jul 2016 12:59:48 +0000 (08:59 -0400)]
Merge branch '9550-keep-services-env'
closes #9550
Tom Clegg [Mon, 25 Jul 2016 20:41:25 +0000 (16:41 -0400)]
9550: Ignore extra spaces in ARVADOS_KEEP_SERVICES, and ensure each entry is an absolute URI.
Tom Clegg [Mon, 25 Jul 2016 19:54:41 +0000 (15:54 -0400)]
9550: Update comments.
Tom Clegg [Fri, 22 Jul 2016 13:59:32 +0000 (09:59 -0400)]
9550: Add service discovery override field to new SDK.
Tom Clegg [Fri, 22 Jul 2016 13:41:47 +0000 (09:41 -0400)]
9550: Allow overriding keep services discovery with ARVADOS_KEEP_SERVICES env var.
Lucas Di Pentima [Tue, 26 Jul 2016 12:39:17 +0000 (09:39 -0300)]
9551: Change proxy parameter priority over environment variables. Updated docstring to mention ARVADOS_KEEP_SERVICES.
Lucas Di Pentima [Mon, 25 Jul 2016 20:32:46 +0000 (17:32 -0300)]
9551: Added support for env var ARVADOS_KEEP_SERVICES as a special case of a proxy.
Tom Clegg [Thu, 21 Jul 2016 23:35:56 +0000 (19:35 -0400)]
Merge branch '9613-test-profile-save'
closes #9613
Tom Clegg [Thu, 21 Jul 2016 23:34:43 +0000 (19:34 -0400)]
9613: Touch up "find required field" loop.
Tom Clegg [Thu, 21 Jul 2016 19:50:00 +0000 (15:50 -0400)]
9613: Ensure submitted values are saved, and displayed on the edit form after it reloads.
Tom Clegg [Thu, 21 Jul 2016 19:25:28 +0000 (15:25 -0400)]
9613: Dry up user profile tests.
Ward Vandewege [Thu, 21 Jul 2016 19:43:07 +0000 (15:43 -0400)]
Merge branch '9639-split-workbench-tests'
refs #9639
Ward Vandewege [Thu, 21 Jul 2016 19:02:21 +0000 (15:02 -0400)]
9639: Make it possible to run unit, functional and integration tests for
Workbench separately.
refs #9639
Tom Clegg [Thu, 21 Jul 2016 02:35:01 +0000 (22:35 -0400)]
9639: Relax unnecessarily strict time limit.
refs #9639
Tom Clegg [Wed, 20 Jul 2016 21:14:47 +0000 (17:14 -0400)]
9639: Delete all cached discovery docs, but do not delete the cache directory.
refs #9639
Tom Clegg [Wed, 20 Jul 2016 20:03:18 +0000 (16:03 -0400)]
9639: Avoid sharing rvm gemsets between concurrent builds.
refs #9639
radhika [Tue, 19 Jul 2016 20:03:23 +0000 (16:03 -0400)]
closes #9319
Merge branch '9319-all-processes-index'
radhika [Tue, 5 Jul 2016 23:13:13 +0000 (19:13 -0400)]
9319: /all_processes index page.
Tom Clegg [Tue, 19 Jul 2016 19:11:43 +0000 (15:11 -0400)]
9624: Fix format string.
closes #9624
Tom Clegg [Tue, 19 Jul 2016 13:30:27 +0000 (09:30 -0400)]
Merge branch '9613-user-profile-string-keys'
refs #9613
Brett Smith [Tue, 19 Jul 2016 13:07:02 +0000 (09:07 -0400)]
9262: Stop setting sbatch --priority in crunch-dispatch-slurm.
There are a few reasons we want to back this out:
* `--priority` is a relatively new feature of SLURM, added in 14.03,
and it's not clear how many users are running that.
* Setting `--priority` requires extra privileges, per the sbatch man
page, and it's not clear crunch-dispatch-slurm should run with
those.
* There are multiple ways to set the "priority" of a SLURM job.
There's also a niceness value. Which is correct to use is probably
ultimately going to depend on site rules or conventions. We need to
get more feedback on what people are doing before we implement
something. We might need configurations options along the lines of
"translate container priority into this option with this scaling
factor," or something like that.
Per discussion with Tom Clegg. Closes #9626.
Lucas Di Pentima [Mon, 18 Jul 2016 21:25:42 +0000 (18:25 -0300)]
Merge branch '9438-http-default-timeout'
9438: Added a new var DefaultSecureClient and assigned a 5 minute timeout to both InsecureHTTPClient and DefaultSecureClient.
refs #9438
Lucas Di Pentima [Mon, 18 Jul 2016 20:47:38 +0000 (17:47 -0300)]
9438: Eliminated redundant casting
Tom Clegg [Mon, 18 Jul 2016 03:24:11 +0000 (23:24 -0400)]
9613: Stop prepending ":" to profile keys.
Nico Cesar [Sun, 17 Jul 2016 13:37:09 +0000 (09:37 -0400)]
Merge branch '9614-cwl-no-websockets'
closes #9614
Peter Amstutz [Sat, 16 Jul 2016 20:21:58 +0000 (16:21 -0400)]
9614: Don't use websockets for event notification until it is more reliable.
Ward Vandewege [Fri, 15 Jul 2016 21:09:38 +0000 (17:09 -0400)]
Pin the html5lib package we build for centos6 and centos7 to version
0.
9999999, because newer versions have a dependency on a
python-setuptools 0.18.5 which we don't have in the build containers
(yet).
refs #9459
Brett Smith [Fri, 15 Jul 2016 20:14:56 +0000 (16:14 -0400)]
Merge branch '9459-arvbox-demo-version-arg-wip'
Refs #9459. Closes #9531.
Brett Smith [Thu, 30 Jun 2016 21:45:12 +0000 (17:45 -0400)]
9459: arvbox-demo accepts version arguments for Git checkouts.
Lucas Di Pentima [Fri, 15 Jul 2016 19:46:09 +0000 (16:46 -0300)]
9438: Added a new var DefaultSecureClient and assigned a 5 minute timeout to both InsecureHTTPClient and DefaultSecureClient
Peter Amstutz [Fri, 15 Jul 2016 19:16:17 +0000 (15:16 -0400)]
Bump version of setuptools used by run_tests.sh for cwl-runner dependency refs #9570
Peter Amstutz [Fri, 15 Jul 2016 18:30:50 +0000 (14:30 -0400)]
Merge branch '9369-arv-cwl-docs' closes #9369
Brett Smith [Fri, 15 Jul 2016 18:26:45 +0000 (14:26 -0400)]
9369: Copyedit CLI SDK install guide.
Peter Amstutz [Fri, 15 Jul 2016 18:11:37 +0000 (14:11 -0400)]
9369: Remove cwl install from Python SDK page. Remove "sudo -i" from
pip/python install instructions. Fixup use of ~$ prompt in example
instructions.
Peter Amstutz [Fri, 15 Jul 2016 17:11:49 +0000 (13:11 -0400)]
Merge branch 'master' into 9369-arv-cwl-docs
Peter Amstutz [Fri, 15 Jul 2016 17:11:07 +0000 (13:11 -0400)]
Merge branch '9570-cwl-runner-fixes' closes #9570 (again)
Brett Smith [Fri, 15 Jul 2016 15:03:56 +0000 (11:03 -0400)]
9369: Copyedits throughout the CWL documentation.
Peter Amstutz [Fri, 15 Jul 2016 14:00:22 +0000 (10:00 -0400)]
9369: Add note about Javascript eval timeout.
Peter Amstutz [Fri, 15 Jul 2016 13:52:02 +0000 (09:52 -0400)]
9570: Raise exception on workflow failure.
Peter Amstutz [Fri, 15 Jul 2016 13:41:29 +0000 (09:41 -0400)]
9369: bwa-mem-input-local hashbang uses cwltool.
Peter Amstutz [Thu, 14 Jul 2016 20:57:27 +0000 (16:57 -0400)]
9570: Use special path mapper for staging files to output dir.
Peter Amstutz [Thu, 14 Jul 2016 20:40:24 +0000 (16:40 -0400)]
9570: Call normalizeFilesDirs to make sure basename is there.
Peter Amstutz [Thu, 14 Jul 2016 20:34:19 +0000 (16:34 -0400)]
9570: Just add keep: to input keep locators in cwl-runner.
Peter Amstutz [Thu, 14 Jul 2016 19:40:05 +0000 (15:40 -0400)]
9570: Adjust Directory objects, too.
Peter Amstutz [Thu, 14 Jul 2016 19:01:39 +0000 (15:01 -0400)]
9570: Remove spurious print statement.
Peter Amstutz [Thu, 14 Jul 2016 18:54:18 +0000 (14:54 -0400)]
9570: Bump cwltool dependency
Peter Amstutz [Thu, 14 Jul 2016 17:57:09 +0000 (13:57 -0400)]
9570: Update cwl-runner for latest cwltool. Ensure use_container,
tmpdir_prefix and on_error are set.
Tom Clegg [Thu, 14 Jul 2016 20:47:38 +0000 (16:47 -0400)]
Merge branch 'fix-python-sdk-mac' of https://github.com/adambom/arvados
No issue #
Adam Savitzky [Thu, 14 Jul 2016 20:38:38 +0000 (13:38 -0700)]
Monkey patch socket constants on apple only
Peter Amstutz [Thu, 14 Jul 2016 19:21:30 +0000 (15:21 -0400)]
Remove spurious print introduced in
6884eed, refs #9570
Peter Amstutz [Thu, 14 Jul 2016 17:34:25 +0000 (13:34 -0400)]
9369: Add section about Docker. Change cluster references to qr1hi. Fix path to use /home/example.
Peter Amstutz [Thu, 14 Jul 2016 17:32:02 +0000 (13:32 -0400)]
9369: Update CLI install documentation to include arvados-cwl-runner (& arvados-python-client)
Adam Savitzky [Wed, 13 Jul 2016 22:54:54 +0000 (15:54 -0700)]
Patch socket configuration for Apple systems
Peter Amstutz [Wed, 13 Jul 2016 21:32:32 +0000 (17:32 -0400)]
9369: Update tutorial to CWL v1.0
Nico Cesar [Wed, 13 Jul 2016 21:18:52 +0000 (17:18 -0400)]
Merge branch '9459-test_with_arvbox_tweaks'
refs #9459
Nico Cesar [Tue, 12 Jul 2016 19:32:25 +0000 (15:32 -0400)]
9459: added test_in_arvbox.sh and arvbox the docker tag parameter.
refs #9459
Tom Clegg [Wed, 13 Jul 2016 19:17:18 +0000 (15:17 -0400)]
Merge branch '9567-keep-web-session-test'
refs #9567
Tom Clegg [Wed, 13 Jul 2016 19:14:14 +0000 (15:14 -0400)]
9567: Use longer timeouts for keep-web download tests.
Tom Clegg [Wed, 13 Jul 2016 19:05:38 +0000 (15:05 -0400)]
9567: Print log messages from keep et al. as they appear, even in jenkins where stdout is not a tty.
Peter Amstutz [Wed, 13 Jul 2016 18:45:39 +0000 (14:45 -0400)]
Fix tests. refs #9570
Peter Amstutz [Wed, 13 Jul 2016 16:51:21 +0000 (12:51 -0400)]
Merge branch '9486-retry-instance-limit-exceeded' closes #9486
Peter Amstutz [Wed, 13 Jul 2016 16:49:57 +0000 (12:49 -0400)]
Merge branch '9570-cwl-v1.0' closes #9570
Peter Amstutz [Wed, 13 Jul 2016 15:36:03 +0000 (11:36 -0400)]
9570: Set docker_outdir consistently.
Peter Amstutz [Wed, 13 Jul 2016 15:05:34 +0000 (11:05 -0400)]
9570: Update version pin and add reminder to setup.py to do it in the future.
Peter Amstutz [Wed, 13 Jul 2016 13:53:48 +0000 (09:53 -0400)]
9570: Fix secondaryFile staging to ensure that all files are in the same
collection.
Peter Amstutz [Tue, 12 Jul 2016 22:14:53 +0000 (18:14 -0400)]
9570: Fix for Pathmapper API change. Most tests pass or exit unsupported
feature.
Peter Amstutz [Tue, 12 Jul 2016 19:55:34 +0000 (15:55 -0400)]
9570: Support Directory and file literal features. Support
success/temporary/permanent exit codes.
Brett Smith [Tue, 12 Jul 2016 14:19:37 +0000 (10:19 -0400)]
9369: Copyedits throughout the CWL docs.
Peter Amstutz [Mon, 11 Jul 2016 20:02:49 +0000 (16:02 -0400)]
9570: Pass tests except related to directory features
Peter Amstutz [Mon, 11 Jul 2016 19:31:45 +0000 (15:31 -0400)]
9570: CWL v1.0 support wip
Peter Amstutz [Mon, 11 Jul 2016 19:30:47 +0000 (15:30 -0400)]
9570: Add support to crunchrunner for redirecting stderr to support CWL 1.0.
Tom Clegg [Thu, 7 Jul 2016 18:32:03 +0000 (14:32 -0400)]
9567: Avoid ruamel.yaml >0.11.11. refs #9567
Tom Clegg [Thu, 7 Jul 2016 15:43:35 +0000 (11:43 -0400)]
Merge branch '9456-less-clear-trash'
closes #9456
Tom Clegg [Thu, 7 Jul 2016 15:43:17 +0000 (11:43 -0400)]
9456: Do not clear trash lists between runs when the list of keep services has not changed.
Tom Clegg [Thu, 7 Jul 2016 15:23:59 +0000 (11:23 -0400)]
Merge branch '9528-slurm-parsable'
closes #9528
Tom Clegg [Thu, 7 Jul 2016 02:11:56 +0000 (22:11 -0400)]
9528: Drop sbatch --parsable flag. It fails in older versions of slurm,
and we don't need to parse the output anyway.
Tom Clegg [Thu, 7 Jul 2016 14:37:33 +0000 (10:37 -0400)]
Revert "Bump cwltool dependency. Previously pinned version was broken."
This reverts commit
d8900c1b1410b97ad24aba69d9f8fa1f042afc90.
No issue #
Tom Clegg [Thu, 7 Jul 2016 14:16:34 +0000 (10:16 -0400)]
Bump cwltool dependency. Previously pinned version was broken.
cwltool==1.0.
20160630171631 depends on
schema-salad==1.12.
20160610104117, which contains an errant .py file
with syntax errors. Installing with pip emits an error message and
succeeds. Installing as an fpm->deb package emits the same error
message and fails.
Linking and byte-compiling packages for runtime python2.7...
File "/usr/lib/python2.7/dist-packages/schema_salad/ref_resolver_BACKUP_28804.py", line 222
<<<<<<<
973dceb3aeef33920968fa257c7b04885a3a716d
^
SyntaxError: invalid syntax
No issue #
Tom Clegg [Wed, 6 Jul 2016 16:05:11 +0000 (12:05 -0400)]
Merge branch '9542-websocket-queries'
refs #9542
Tom Clegg [Wed, 6 Jul 2016 15:47:45 +0000 (11:47 -0400)]
9542: Avoid retrieving huge result sets from postgres.
Tom Clegg [Tue, 5 Jul 2016 20:50:39 +0000 (16:50 -0400)]
Respect running_job_log_records_to_fetch in JobsController#logs.
Fixes flaky test
WebsocketTest#test_test_running_job_with_too_many_previous_log_records
(see https://ci.curoverse.com/job/arvados-api-server/3092/consoleText)
No issue #
Tom Clegg [Tue, 5 Jul 2016 18:47:05 +0000 (14:47 -0400)]
8016: Rename Poll to PollPeriod. Amends
c63c699aa9948f6a672536ba08e664471fb0d654.
refs #8016
Tom Clegg [Tue, 5 Jul 2016 17:28:51 +0000 (13:28 -0400)]
Merge branch '8016-crunchrun-crunchstat'
closes #8016
radhika [Mon, 4 Jul 2016 21:23:10 +0000 (17:23 -0400)]
closes #9498
Merge branch '9498-containers-in-project-tab'
radhika [Tue, 28 Jun 2016 19:58:27 +0000 (15:58 -0400)]
9498: show top-level container requests in project#Pipelines_and_processes tab.
Tom Clegg [Mon, 4 Jul 2016 21:08:37 +0000 (17:08 -0400)]
8016: Clarify comments/docs and cpuSample initialization.
Tom Clegg [Mon, 4 Jul 2016 21:07:54 +0000 (17:07 -0400)]
8016: Rename Poll to PollPeriod.
Tom Clegg [Mon, 4 Jul 2016 21:06:48 +0000 (17:06 -0400)]
8016: Fix race in test case.
Brett Smith [Fri, 1 Jul 2016 20:55:43 +0000 (16:55 -0400)]
Add libgnutls28-dev to arvados/jobs.
This is necessary to build pycurl, and with it the Python Arvados SDK,
and support arvados_sdk_version in Crunch. I'm guessing we lost it
when we switched the base from arvados/debian:7 to debian:jessie.
No issue #.
Peter Amstutz [Fri, 24 Jun 2016 14:18:22 +0000 (10:18 -0400)]
9486: Add InstanceLimitExceeded to is_cloud_exception
Peter Amstutz [Fri, 1 Jul 2016 19:38:59 +0000 (15:38 -0400)]
9369: tweaks
Peter Amstutz [Thu, 30 Jun 2016 17:31:46 +0000 (13:31 -0400)]
9369: arvados-cwl-runner documentation and examples, add deprecation notices to pipeline documentation
Tom Clegg [Fri, 1 Jul 2016 17:53:21 +0000 (13:53 -0400)]
Merge branch '9437-keep-index-ns'
refs #9437
See https://dev.arvados.org/issues/9437#note-3 and #note-4
projects / arvados.git / log