Eric Biagiotti [Wed, 6 Feb 2019 16:40:17 +0000 (11:40 -0500)]
Merge branch 'master' into 13306-arvados-cwl-runner-py3-support
refs #13306
3
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <eric.biagiotti@gmail.com>
Eric Biagiotti [Wed, 6 Feb 2019 16:40:04 +0000 (11:40 -0500)]
13306: Removing unneeded import statements
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <eric.biagiotti@gmail.com>
Ward Vandewege [Tue, 5 Feb 2019 22:14:05 +0000 (17:14 -0500)]
Make the python-arvados-cwl-runner package expose the cwltool executable, make
it conflict with the python-cwltool (and cwltool) packages, and add a note to
the upgrade documentation to that effect. Also document the Centos7 specific
upgrade from python33 to rh-python35 as part of story 9945.
refs #9945
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Eric Biagiotti [Tue, 5 Feb 2019 18:25:14 +0000 (13:25 -0500)]
Merge branch '13306-arvados-cwl-runner-py3-support'
refs #13306
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <eric.biagiotti@gmail.com>
Eric Biagiotti [Tue, 5 Feb 2019 17:55:54 +0000 (12:55 -0500)]
13306: Adds declaration of py2/3 support to arvados cwl and python sdks
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <eric.biagiotti@gmail.com>
Eric Biagiotti [Tue, 5 Feb 2019 16:53:07 +0000 (11:53 -0500)]
13306: fixes test_with_arvados.sh pip executable with python2
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <eric.biagiotti@gmail.com>
Tom Clegg [Tue, 5 Feb 2019 15:41:51 +0000 (10:41 -0500)]
Merge branch '14806-crunch1-unescape-manifest'
fixes #14806
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Tom Clegg [Tue, 5 Feb 2019 15:41:31 +0000 (10:41 -0500)]
14806: Merge branch 'master'
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Ward Vandewege [Tue, 5 Feb 2019 13:36:07 +0000 (08:36 -0500)]
We have reset the package iterations to -1, make the
run-build-docker-jobs-image.sh script reflect that.
refs #9945
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Mon, 4 Feb 2019 22:21:22 +0000 (17:21 -0500)]
Do not try to test packages that were not built.
refs #9945
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Tom Clegg [Mon, 4 Feb 2019 21:43:14 +0000 (16:43 -0500)]
14806: Fix test suite to work even if PERL5LIB is set.
PERL5LIB has precedence over PERLLIB.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 4 Feb 2019 18:17:44 +0000 (13:17 -0500)]
arvbox support for python3 refs #13306
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Tom Clegg [Mon, 4 Feb 2019 20:58:57 +0000 (15:58 -0500)]
14806: Handle escaped chars when parsing docker image manifest.
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>
Peter Amstutz [Mon, 4 Feb 2019 20:13:34 +0000 (15:13 -0500)]
13306: fix crunchv1 bug
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 4 Feb 2019 20:13:12 +0000 (15:13 -0500)]
13306: test_with_arvbox can select api
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 4 Feb 2019 19:22:58 +0000 (14:22 -0500)]
13306: select between "conformance" and "integration" in test_with_arvbox.sh
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Mon, 4 Feb 2019 18:27:09 +0000 (13:27 -0500)]
13306: test_with_arvbox.sh can test either python2 or python3
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Ward Vandewege [Mon, 4 Feb 2019 17:41:29 +0000 (12:41 -0500)]
The libpam-arvados package on Centos7 has a dependency on the python-pam package.
refs #9945
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Mon, 4 Feb 2019 15:35:51 +0000 (10:35 -0500)]
Merge branch '9945-make-python-package-dependency-free'
closes #9945
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Mon, 4 Feb 2019 15:19:35 +0000 (10:19 -0500)]
9945: Merge branch 'master' into 9945-make-python-package-dependency-free
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Mon, 4 Feb 2019 13:36:00 +0000 (08:36 -0500)]
9945: Backwards compatibility fix for libpam-arvados
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Peter Amstutz [Fri, 1 Feb 2019 22:03:52 +0000 (17:03 -0500)]
arvbox certificates can have DNS in subjectAltName
no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Eric Biagiotti [Fri, 1 Feb 2019 18:45:25 +0000 (13:45 -0500)]
13306: Improved py2/3 str compatibility
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <eric.biagiotti@gmail.com>
Eric Biagiotti [Fri, 1 Feb 2019 18:33:14 +0000 (13:33 -0500)]
13306: Additional dict item iteration improvements
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <eric.biagiotti@gmail.com>
Ward Vandewege [Fri, 1 Feb 2019 15:39:16 +0000 (10:39 -0500)]
9945: Merge branch 'master' into 9945-make-python-package-dependency-free
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Peter Amstutz [Thu, 31 Jan 2019 17:54:10 +0000 (12:54 -0500)]
13306: Fix 12213-keepref test
Test itself was buggy and seems to have been relying on undefined
behavior, py3 exposed the bug.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Eric Biagiotti [Thu, 31 Jan 2019 17:16:42 +0000 (12:16 -0500)]
13306: Fixes futurize mistakes regarding PathMapper items()
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <eric.biagiotti@gmail.com>
Ward Vandewege [Wed, 30 Jan 2019 21:14:52 +0000 (16:14 -0500)]
9945: More changes based on review comments.
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Lucas Di Pentima [Wed, 30 Jan 2019 20:53:42 +0000 (17:53 -0300)]
Merge branch '14770-wb-acr-bad-param'
Closes #14770
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 30 Jan 2019 20:18:30 +0000 (17:18 -0300)]
Merge branch '14738-tag-editor-fix-es5'
Closes #14738
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Ward Vandewege [Tue, 29 Jan 2019 21:53:43 +0000 (16:53 -0500)]
9945: address more review comments.
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Lucas Di Pentima [Tue, 29 Jan 2019 22:48:15 +0000 (19:48 -0300)]
14738: Replaces double with single quotes for code style.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 29 Jan 2019 20:39:26 +0000 (17:39 -0300)]
14738: Enhances code readability when concatenating strings.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 29 Jan 2019 19:25:02 +0000 (16:25 -0300)]
14738: Fixes the double-slash usage on requests to prevent 301 from controller
When a request is made to controller using double slashes, for example to
http://apiserver//arvados/v1/collections, arvados controller returns a 301
that breaks CORS.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 29 Jan 2019 09:30:10 +0000 (06:30 -0300)]
Merge branch '14718-api-login-salted-token'
Closes #14718
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 28 Jan 2019 22:03:10 +0000 (19:03 -0300)]
14718: Updates controller test to support josh_id's return_to new format.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Mon, 28 Jan 2019 21:58:06 +0000 (18:58 -0300)]
14718: Validates remote cluster id parameter on login endpoint & callback.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Ward Vandewege [Wed, 23 Jan 2019 15:12:59 +0000 (10:12 -0500)]
9945: address a bunch of review comments.
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Lucas Di Pentima [Mon, 28 Jan 2019 20:12:33 +0000 (17:12 -0300)]
14718: Changes the way remote param is packed into return_to.
Also:
* Escapes the remote param for security reasons.
* Adds comments.
* Updates tests.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Eric Biagiotti [Mon, 28 Jan 2019 15:34:10 +0000 (10:34 -0500)]
Merge branch 'master' into 13306-arvados-cwl-runner-py3-support
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Mon, 28 Jan 2019 15:14:30 +0000 (10:14 -0500)]
13306: Removing debug echo
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Lucas Di Pentima [Sat, 26 Jan 2019 00:04:58 +0000 (21:04 -0300)]
14718: Issue salted token when passing 'remote' param to login.
When logging in with a 'remote' parameter, it's encoded into the return_to
param passed to the SSO server so that it's received back after the user
is authenticated.
When the omniauth callback receives a remote parameter inside the return_to
url, it returns the salted version of the client token.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Eric Biagiotti [Fri, 25 Jan 2019 18:03:12 +0000 (13:03 -0500)]
13306: Adding support for building the dev docker jobs image with py3
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Lucas Di Pentima [Thu, 24 Jan 2019 18:48:54 +0000 (15:48 -0300)]
14770: Fixes parameter on acr call.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Eric Biagiotti [Thu, 24 Jan 2019 14:38:25 +0000 (09:38 -0500)]
13306: Unicode fix for docker image generation in py3 environment
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Thu, 24 Jan 2019 14:37:13 +0000 (09:37 -0500)]
13306: Unicode fixes for the conformance tests
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Lucas Di Pentima [Tue, 22 Jan 2019 16:40:02 +0000 (13:40 -0300)]
Merge branch '14482-rubysdk-empty-dir'
Closes #14482
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Ward Vandewege [Tue, 22 Jan 2019 01:46:50 +0000 (20:46 -0500)]
9945: use virtualenv for our python packages
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Thu, 20 Dec 2018 16:52:01 +0000 (11:52 -0500)]
9945: run-library changes
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Ward Vandewege [Sun, 20 Jan 2019 18:12:45 +0000 (13:12 -0500)]
9945: there is a new rvm gpg key
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege@veritasgenetics.com>
Lucas Di Pentima [Fri, 18 Jan 2019 23:24:43 +0000 (20:24 -0300)]
14482: Stricter token regexes.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Eric Biagiotti [Fri, 18 Jan 2019 16:08:13 +0000 (11:08 -0500)]
13306: Removing old_div to simplify division operations
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Lucas Di Pentima [Thu, 17 Jan 2019 23:53:58 +0000 (20:53 -0300)]
14482: Manifest validation including 8-bit escaped chars; with tests.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Eric Biagiotti [Thu, 17 Jan 2019 21:03:03 +0000 (16:03 -0500)]
13306: Removing list wrapping added by futurize to PathMapper objects
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Because cwltool.PathMapper objects have a function called items(), futurize incorrectly added the results of calls to items() to a list object (thinking it was a call to dict.items()). In fact, cwltool.PathMapper.items() already returns a list.
Eric Biagiotti [Thu, 17 Jan 2019 20:55:24 +0000 (15:55 -0500)]
13306: Updating dict items as lists to improve py2 performance
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Thu, 17 Jan 2019 20:40:08 +0000 (15:40 -0500)]
13306: Fixing previous commit to use viewvalues instead of listvalues
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Thu, 17 Jan 2019 19:00:05 +0000 (14:00 -0500)]
13306: Updating dict values as a list to improve py2 performance
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Thu, 17 Jan 2019 18:49:39 +0000 (13:49 -0500)]
13306: Updating dict keys as a list to ensure py2/3 compatibility
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Lucas Di Pentima [Thu, 17 Jan 2019 16:43:25 +0000 (13:43 -0300)]
Merge branch '14539-pysdk-empty-dir'
Closes #14539
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Eric Biagiotti [Thu, 17 Jan 2019 16:21:04 +0000 (11:21 -0500)]
13306: Updating dict value iteration to be more efficient with py2
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Thu, 17 Jan 2019 16:11:35 +0000 (11:11 -0500)]
13306: Adds test for when get_current_container results in a 404
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Thu, 17 Jan 2019 15:04:03 +0000 (10:04 -0500)]
13306: Removes a log handler added during a test, breaking subsequent tests.
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Thu, 17 Jan 2019 15:02:43 +0000 (10:02 -0500)]
13306: Prevents multiple RunTimeStatusLoggingHandlers from being added
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Lucas Di Pentima [Thu, 17 Jan 2019 09:55:40 +0000 (06:55 -0300)]
14539: Simplifies a bit further the regexp replacement on escape() function.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Thu, 17 Jan 2019 09:48:53 +0000 (06:48 -0300)]
14539: Removes pointless code comment.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 16 Jan 2019 22:34:34 +0000 (19:34 -0300)]
14539: Fixes and simplifies the escape() function. Updates test.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Wed, 16 Jan 2019 21:33:49 +0000 (18:33 -0300)]
14539: Fixes literal backslash escaping.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Eric Biagiotti [Wed, 16 Jan 2019 01:52:36 +0000 (20:52 -0500)]
13306: Removing unneeded try/except statements in the acr submit tests
Removed the try/except statements and moved the asserts checking if the call to arvados_cwl.main exited properly to the bottom of the tests. In other words, the tests should be using specific call asserts to establish if it ran correctly and checking the exited value should be a last resort to report an unhandled case.
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Lucas Di Pentima [Tue, 15 Jan 2019 21:27:29 +0000 (18:27 -0300)]
14482: Allow unescaped " " on stream and file token regexes (WIP)
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Tue, 15 Jan 2019 18:40:34 +0000 (13:40 -0500)]
Merge branch '14324-cdc-azure' refs #14324
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Tue, 15 Jan 2019 18:33:58 +0000 (15:33 -0300)]
14482: Adds failing test about partially unescaped file tokens.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Tue, 15 Jan 2019 18:29:30 +0000 (13:29 -0500)]
14324: Embed test public key instead of reading from file
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Lucas Di Pentima [Tue, 15 Jan 2019 17:34:38 +0000 (14:34 -0300)]
Merge branch 'master' into 14482-rubysdk-empty-dir
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Lucas Di Pentima [Tue, 15 Jan 2019 17:25:39 +0000 (14:25 -0300)]
14539: Encode \t & \n chars on file/dir names on collection's manifest.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Eric Biagiotti [Tue, 15 Jan 2019 16:57:45 +0000 (11:57 -0500)]
13306: Updating get_current_container to raise when not a 404
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Tue, 15 Jan 2019 16:09:11 +0000 (11:09 -0500)]
13306: Updating depreciated assertEquals
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Tue, 15 Jan 2019 15:52:04 +0000 (10:52 -0500)]
13306: Updating depreciated warn function
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Tue, 15 Jan 2019 14:46:50 +0000 (09:46 -0500)]
13306: Updates ArvCwlExecutor to properly convert objects to JSON in unicode
json.dumps produces a str object in python 2 (bytestring) and a str object in python 3 (unicode), resulting in incompatibility when writing to the file (expects unicode). In order to prevent using py2 and py3 specific code, the solution is to call encode, which will force the string to be bytes in both languages, then decode to unicode from there.
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Lucas Di Pentima [Tue, 15 Jan 2019 14:31:43 +0000 (11:31 -0300)]
14538: Update comment.
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Eric Biagiotti [Tue, 15 Jan 2019 13:30:53 +0000 (08:30 -0500)]
13306: Adding py2/3 unicode support to the test_job tests
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Peter Amstutz [Mon, 14 Jan 2019 19:13:20 +0000 (14:13 -0500)]
14324: Fix API throttling header fallbacks. Add gocheck_test
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Eric Biagiotti [Mon, 14 Jan 2019 18:04:55 +0000 (13:04 -0500)]
13306: test_submit additional fixes for py2 unicode support
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Lucas Di Pentima [Mon, 14 Jan 2019 17:16:32 +0000 (14:16 -0300)]
Merge branch 'master' into 14539-pysdk-empty-dir
Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>
Peter Amstutz [Mon, 14 Jan 2019 16:00:12 +0000 (11:00 -0500)]
Fix arvbox demo for workbench2 no issue #
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Eric Biagiotti [Fri, 11 Jan 2019 21:38:47 +0000 (16:38 -0500)]
13306: test_submit fixes for py2 unicode support
Makes the stdout passed to cwltool python version dependent for the submit tests. Also adds unicode specifications to calls to the log.
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Peter Amstutz [Fri, 11 Jan 2019 19:04:06 +0000 (14:04 -0500)]
14324: Fix tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Eric Biagiotti [Fri, 11 Jan 2019 18:55:49 +0000 (13:55 -0500)]
13306: Adding py2 and py3 compatible byte objects for literals
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Fri, 11 Jan 2019 16:22:24 +0000 (11:22 -0500)]
13306: Updated use of built in 'sorted' and a test_util bytestring
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Fri, 11 Jan 2019 15:12:52 +0000 (10:12 -0500)]
13306: Added py2 and 3 compatible 'next' for test_job.TestWorkflow.test_run
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Peter Amstutz [Fri, 11 Jan 2019 15:08:37 +0000 (10:08 -0500)]
14324: Use logrus in Azure driver. Fix Sirupsen->sirupsen in imports
"It's in the past been possible to import Logrus as both upper- and
lower-case. Due to the Go package environment, this caused issues in
the community and we needed a standard. Some environments experienced
problems with the upper-case variant, so the lower-case was
decided. Everything using logrus will need to use the lower-case:
github.com/sirupsen/logrus. Any package that isn't, should be
changed."
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Eric Biagiotti [Thu, 10 Jan 2019 18:54:41 +0000 (13:54 -0500)]
13306: Fixed test_submit.TestCreateTemplate encoding
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Peter Amstutz [Thu, 10 Jan 2019 18:33:50 +0000 (13:33 -0500)]
14324: Remove context from interface, use Stop() instead
Remove 'Context' passed into methods of the InstanceSet interface,
instead the AzureInstanceSet creates its own cancellable background
context. The Stop() method now cancels the context and waits for any
outstanding cloud driver work to complete before returning.
* Fix test
* Document how to run individual test cases against real cloud
* ManageBlobs runs periodically in the background
* Logging cleaned up
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Eric Biagiotti [Thu, 10 Jan 2019 14:57:49 +0000 (09:57 -0500)]
13306: Fix for test_job.TestJob.test_done and test_done_use_existing_collection
Had to mock a key for the CollectionReader due to 'list' being added to arvjob.py line 249 during stage2 of finalize. The 'list' call interrupts the on demand mocking of the CollectionReader object.
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Thu, 10 Jan 2019 14:38:37 +0000 (09:38 -0500)]
13306: Fix for sdk/cwl tests.test_job.TestJob.test_run
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Thu, 10 Jan 2019 14:16:37 +0000 (09:16 -0500)]
13306: Fixed formatting for newly introduced imports
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Eric Biagiotti [Thu, 10 Jan 2019 14:06:42 +0000 (09:06 -0500)]
13306: Changes to arvados-cwl-runner code after running futurize --stage2
Arvados-DCO-1.1-Signed-off-by: Eric Biagiotti <ebiagiotti@veritasgenetics.com>
Peter Amstutz [Wed, 9 Jan 2019 21:13:56 +0000 (16:13 -0500)]
14324: Azure driver for crunch-dispatch-cloud
* Adds context parameter to methods of InstanceSet interface that may block
* Fix tests
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Wed, 9 Jan 2019 16:35:55 +0000 (11:35 -0500)]
14324: Azure driver WIP
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 31 Aug 2018 20:41:07 +0000 (16:41 -0400)]
13964: Fail on missing node-token tag
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
Peter Amstutz [Fri, 31 Aug 2018 20:27:08 +0000 (16:27 -0400)]
13964: Forget the node token once the key fingerprint is known
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>
projects / arvados.git / log