- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 963069: Simpler, more targeted fix for copy datasets dialo...
by GitHub 06 Aug '18

06 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 9630699c21875199fec75bc3f607d5b81a224348 https://github.com/galaxyproject/galaxy/commit/9630699c21875199fec75bc3f607… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Simpler, more targeted fix for copy datasets dialog tag copies (will refactor in dev) Commit: 6c7b9a3c7d4459b171fa806f2912d49e44ccd5bd https://github.com/galaxyproject/galaxy/commit/6c7b9a3c7d4459b171fa806f2912… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #6532 from dannon/fix-dataset-copy-tags [18.05] Fix dataset copy tags Compare: https://github.com/galaxyproject/galaxy/compare/66e74d0e475e...6c7b9a3c7d44 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 5a3e28: Better encapsulation when queueing jobs.
by GitHub 06 Aug '18

06 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a3e28db774a51197e7000b0cb493a5741b24474 https://github.com/galaxyproject/galaxy/commit/5a3e28db774a51197e7000b0cb49… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Better encapsulation when queueing jobs. No need for the runner to know all these internals of the JobWrapper when it is just taking attributes on the job or job wrapper and calling job wrapper methods with them. Provides nice symmetry between queue/finish now also. Commit: 1b5dff11a738c8d01b457dedda80e5f533ad1127 https://github.com/galaxyproject/galaxy/commit/1b5dff11a738c8d01b457dedda80… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/unit/jobs/test_job_wrapper.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Setup objectstore for datasets in job handler instead of web thread. This is good for a few reasons * It speeds up the bottleneck that is the job creation code in the web thread (the job handler is much easier to parallelize). Skipping the flush for all those datasets and skipping the disk write per dataset should really speed things up nicely when submitting large numbers of jobs and jobs with a large number of inputs. * This prevents a disk slow down from grinding the web response to a halt. We don't want the handler to freeze up either - but if something is going to freeze it is a better user experience and easier to recover from the job handler freezing while their are disk problems. * This allows per-job-handler object store configurations - simply configure different job handlers with different object store configurations. This is cool and important and I can imagine some awesome applications but I will wait for them to materialize. Commit: 36019f93085d4c5c51c14b3eafa936d779096513 https://github.com/galaxyproject/galaxy/commit/36019f93085d4c5c51c14b3eafa9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Restructure JobWrapper/TaskWrapper for more unified initialization... ... especially after changes to set object store id in the job handler. This fixes the parallelism tests for those changes. Commit: c9d17545d843df5e3989185433b8419036fe8208 https://github.com/galaxyproject/galaxy/commit/c9d17545d843df5e3989185433b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Config rebuild, and a few typos. Commit: 561e0099bc22ce5593a3ca2b363cceb8a05fd6c6 https://github.com/galaxyproject/galaxy/commit/561e0099bc22ce5593a3ca2b363c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/unit/jobs/test_job_wrapper.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #6550 from jmchilton/objectstore_setup Configure object store for datasets in job handler instead of web thread. Compare: https://github.com/galaxyproject/galaxy/compare/1f35d13db561...561e0099bc22 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d53366: Move back to paste's FileApp
by GitHub 04 Aug '18

04 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d53366c2f01be1c1648a061f978e8a2f73383117 https://github.com/galaxyproject/galaxy/commit/d53366c2f01be1c1648a061f978e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/web/framework/middleware/static.py Log Message: ----------- Move back to paste's FileApp I didn't figure out how to set the the max_age header using webob's FileApp. Fixes https://github.com/galaxyproject/galaxy/pull/6561#issuecomment-409973637 Commit: 4b89a73f224fe0d6e1d9010d5d5313683fb16d69 https://github.com/galaxyproject/galaxy/commit/4b89a73f224fe0d6e1d9010d5d53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-03 (Fri, 03 Aug 2018) Changed paths: M lib/galaxy/web/framework/middleware/static.py Log Message: ----------- Fix import order for I100 lint error Commit: da94441400e991aaac91daab6bd0ec07ffe382a8 https://github.com/galaxyproject/galaxy/commit/da94441400e991aaac91daab6bd0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-04 (Sat, 04 Aug 2018) Changed paths: M lib/galaxy/web/framework/middleware/static.py Log Message: ----------- Merge pull request #7 from dannon/fix_fileapp_max_age_cache Fix import order for I100 lint error Commit: 1f35d13db5615e8167e187f729bbc4aa3a7da5b0 https://github.com/galaxyproject/galaxy/commit/1f35d13db5615e8167e187f729bb… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-04 (Sat, 04 Aug 2018) Changed paths: M lib/galaxy/web/framework/middleware/static.py Log Message: ----------- Merge pull request #6567 from mvdbeek/fix_fileapp_max_age_cache Move back to paste's FileApp Compare: https://github.com/galaxyproject/galaxy/compare/feb4e2933baa...1f35d13db561 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 876fb1: Fix formatting in repo information display (spacin...
by GitHub 02 Aug '18

02 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 876fb17ab03716fe5c0ad8fe38f50264e7cbb9c8 https://github.com/galaxyproject/galaxy/commit/876fb17ab03716fe5c0ad8fe38f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix formatting in repo information display (spacing) Commit: a0dd200026ab6d57ffb6478634918451d11e56fd https://github.com/galaxyproject/galaxy/commit/a0dd200026ab6d57ffb647863491… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Simplify navigation/state management in toolshed admin app. Discard and recreate views always -- simpler, safer, and basically the same speed since many of these did a full re-initialization anyway. Commit: b26ab71ce1282659d4390d4ad90e55250f6840f7 https://github.com/galaxyproject/galaxy/commit/b26ab71ce1282659d4390d4ad90e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Minor formatting. Commit: feb4e2933baa6ffcd906fdbef4ac1575716b4748 https://github.com/galaxyproject/galaxy/commit/feb4e2933baa6ffcd906fdbef4ac… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Merge pull request #6564 from dannon/ts-admin-fixes Misc Admin TS Panel Fixes Compare: https://github.com/galaxyproject/galaxy/compare/389a1d6563f0...feb4e2933baa **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 632cde: Replace paste.httpexception with webob.exc classes
by GitHub 02 Aug '18

02 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 632cdeae86c70d8ca66e78643c82c130501e0ca6 https://github.com/galaxyproject/galaxy/commit/632cdeae86c70d8ca66e78643c82… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/tools/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Replace paste.httpexception with webob.exc classes Commit: 27a354f97ec40e99343caa1f1f1e7da94a721c53 https://github.com/galaxyproject/galaxy/commit/27a354f97ec40e99343caa1f1f1e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Fix make_file method of patched cgi_FieldStorage This copies the behavior from webob.compat.cgi_FieldStorage, except we use a NamedTemporaryFile instead of TemporaryFile. Commit: deba605e7eaaa418fe9fed3f1e0f6a9e15223718 https://github.com/galaxyproject/galaxy/commit/deba605e7eaaa418fe9fed3f1e0f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Pass bytestring to hash function Commit: 6b86ed56f35e1b51e27053169e80c5b4b7b9ddf2 https://github.com/galaxyproject/galaxy/commit/6b86ed56f35e1b51e27053169e80… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py Log Message: ----------- Fix binary file check Commit: cb7ebd73494153b1950ec87a39d12e874c183a13 https://github.com/galaxyproject/galaxy/commit/cb7ebd73494153b1950ec87a39d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/web/base/controller.py M test/unit/tools/test_history_imp_exp.py Log Message: ----------- py3: Fix history import/export tool - Open history tarfile in binary mode - Fix base64 encoding in history import tool - test history export more extensively Commit: 1dc4cf224108db9756a96b9d50a71f9f099a00f2 https://github.com/galaxyproject/galaxy/commit/1dc4cf224108db9756a96b9d50a7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Fix cgi_FieldStorage monkey patch self.__file is defined in cgi.FieldStorage, so that is the class that needs to be patched. Followup to a65cd29c366035fb8b26e2274046e8c96e3cab33 Commit: 8093d6b61046f7b09381c520d5c95dda54f7ed71 https://github.com/galaxyproject/galaxy/commit/8093d6b61046f7b09381c520d5c9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_dataset_collections.py Log Message: ----------- py3: Fix dataset collection test Commit: a88ce7cfd21646f3dbd04ef41f8e1755da793713 https://github.com/galaxyproject/galaxy/commit/a88ce7cfd21646f3dbd04ef41f8e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/util/checkers.py Log Message: ----------- py3: fix check_html Commit: dc9e5c5a83877599991274298fca3316263a4b36 https://github.com/galaxyproject/galaxy/commit/dc9e5c5a83877599991274298fca… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/authenticate.py M test/api/test_authenticate.py Log Message: ----------- py3: Fix authenticate api test Commit: a760ecdaf0e56a9eee9a02ace9dc7a97906dda02 https://github.com/galaxyproject/galaxy/commit/a760ecdaf0e56a9eee9a02ace9dc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Cast to bytestring for is_binary check Commit: 02d9415ece13452e5c23ee8078d644c34a6b40cd https://github.com/galaxyproject/galaxy/commit/02d9415ece13452e5c23ee8078d6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- py3: Fix raw dataset display Commit: 330aaf8683587484efdbd02f93ba04e82c568859 https://github.com/galaxyproject/galaxy/commit/330aaf8683587484efdbd02f93ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- py3: Fix catching malformed IDs Commit: bbf739a3dfb28a9d0a5350f4d640c1113b2e977a https://github.com/galaxyproject/galaxy/commit/bbf739a3dfb28a9d0a5350f4d640… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/webapps/galaxy/api/tool_data.py M test/api/test_tool_data.py Log Message: ----------- py3: Fix tool_data API Commit: 8f7363549987536748c4a7e88dd88a60280b9089 https://github.com/galaxyproject/galaxy/commit/8f7363549987536748c4a7e88dd8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_jobs.py Log Message: ----------- py3: Fix upload jobs API tests Commit: 27a30b762d8663b0d1c6a6c0b21d44f35791884d https://github.com/galaxyproject/galaxy/commit/27a30b762d8663b0d1c6a6c0b21d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_libraries.py Log Message: ----------- py3: Fix library tests Commit: 33c0b58ae0db139aa9b0f0c619e01a40eba06c03 https://github.com/galaxyproject/galaxy/commit/33c0b58ae0db139aa9b0f0c619e0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- py3: Send bytestring in various datatatypes' display_data methods Commit: c2c2117e497365ab59483aad660d82bdd8c714e8 https://github.com/galaxyproject/galaxy/commit/c2c2117e497365ab59483aad660d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- py3: Cast map objects to lists when serializing tools to json Commit: 057938c30d57da3afce259a08d064e837e0d5ede https://github.com/galaxyproject/galaxy/commit/057938c30d57da3afce259a08d06… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/webhooks.py Log Message: ----------- py3: Fix getting first webhook Commit: 187457a461a7d28878e1ece803a843c868f7c174 https://github.com/galaxyproject/galaxy/commit/187457a461a7d28878e1ece803a8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- py3: Don't rely on order of outputs, instead match by output name Commit: f3bc18c85a8d450f2b3bed3e28c03ed5ea65576b https://github.com/galaxyproject/galaxy/commit/f3bc18c85a8d450f2b3bed3e28c0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/base/populators.py Log Message: ----------- py3: Use reponse.text instead of reponse.content for decoded text Commit: 9ea589d5e737bcca173040682513b2e913675da4 https://github.com/galaxyproject/galaxy/commit/9ea589d5e737bcca173040682513… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M tools/filters/random_lines_two_pass.py Log Message: ----------- Make random_lines reproducible between py2 and py3 random.seed has changed in python 3, and while there's backwards compatibility using `version=1`, random.randint and random.sample have also changed. The most striaghtforward change without adding additional dependencies then was to copy those methods from the python 2.7 source code. Commit: 7fe1079a52822d99e687d9cd966ee4d5e5f828b9 https://github.com/galaxyproject/galaxy/commit/7fe1079a52822d99e687d9cd966e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/webapp.py M templates/tagging_common.mako Log Message: ----------- py3: Fix the remaining mako issues Commit: 11f92221223fe191cf2c4141e6dfc3b3630affa7 https://github.com/galaxyproject/galaxy/commit/11f92221223fe191cf2c4141e6df… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/unit/tools/test_execution.py Log Message: ----------- Fix redirection unit test Commit: fab5d69d58e70ab85ce160a4b963a1d0bd4f3677 https://github.com/galaxyproject/galaxy/commit/fab5d69d58e70ab85ce160a4b963… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- fix is_binary Commit: a2a155777dadda2fc576d078e5f9c8a488931e56 https://github.com/galaxyproject/galaxy/commit/a2a155777dadda2fc576d078e5f9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- py3: Fix redirection Commit: 4a9faf78c198ad92430a2e0666dcb92f0469fcb8 https://github.com/galaxyproject/galaxy/commit/4a9faf78c198ad92430a2e0666dc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Fix webob.compat make_file patching for py2 Commit: 418f1220c8f6b21bcf3b4ddcf9d19f29bdb2c373 https://github.com/galaxyproject/galaxy/commit/418f1220c8f6b21bcf3b4ddcf9d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- py3: Fix DataParameter test data upload Commit: bb26a3a7ac361b2bc094285184775990de99f7ee https://github.com/galaxyproject/galaxy/commit/bb26a3a7ac361b2bc09428518477… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py Log Message: ----------- py3: fix safe_eval Commit: d13697b66b5dfb6a38221036fa777f477f2d1dca https://github.com/galaxyproject/galaxy/commit/d13697b66b5dfb6a38221036fa77… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- py3: Fix mulled resolver Commit: e91d892a9bb3bec5b16389ff1435cd90195cea7a https://github.com/galaxyproject/galaxy/commit/e91d892a9bb3bec5b16389ff1435… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/util/hash_util.py Log Message: ----------- py3: fix sha1 hashing Commit: 63da35889d45459de83a8c66e4fbb7060d92e72c https://github.com/galaxyproject/galaxy/commit/63da35889d45459de83a8c66e4fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/base/populators.py Log Message: ----------- py3: Fix exception handling in wait_on method Commit: fd5e8cdd288846a375c34ae6ca83f051cfdea45b https://github.com/galaxyproject/galaxy/commit/fd5e8cdd288846a375c34ae6ca83… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- py3: fix test_scripts integration test Commit: 8ccd5ed137797e31ed2fac34fa68244f770c6514 https://github.com/galaxyproject/galaxy/commit/8ccd5ed137797e31ed2fac34fa68… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- py3: Fix upload_configuration_options integration test Commit: 049e4d0fa37c66c41961d609337649791271c883 https://github.com/galaxyproject/galaxy/commit/049e4d0fa37c66c41961d6093376… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M test/api/test_libraries.py Log Message: ----------- py3: Fix test_fetch_zip_to_folder test Commit: b7163c0597fac16a34b53d607ae7e8485869022a https://github.com/galaxyproject/galaxy/commit/b7163c0597fac16a34b53d607ae7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/workflow/steps.py M test/base/data/test_workflow_topoambigouity.ga M test/base/data/test_workflow_topoambigouity_auto_laidout.ga Log Message: ----------- Explicitly sort workflow step edges This seems to be necessary so that the workflow_stability test passes under python 2 and python3, but does change the result under python 2, hence the updated workflows (produced by uploading and downloading the workflow to an instance running with this commit). Commit: 389a1d6563f06fc5b8b4ae42fa1824053f3897d4 https://github.com/galaxyproject/galaxy/commit/389a1d6563f06fc5b8b4ae42fa18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/test.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/steps.py M templates/tagging_common.mako M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tool_data.py M test/api/test_tools.py M test/base/data/test_workflow_topoambigouity.ga M test/base/data/test_workflow_topoambigouity_auto_laidout.ga M test/base/populators.py M test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M tools/filters/random_lines_two_pass.py Log Message: ----------- Merge pull request #6561 from mvdbeek/start_py3_api_tests Fix all py3 api tests Compare: https://github.com/galaxyproject/galaxy/compare/b7dba0b82d49...389a1d6563f0 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 955283: More Selenium test fixes.
by GitHub 02 Aug '18

02 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9552830121a900a3ac3ae7926a0299718a4b1f10 https://github.com/galaxyproject/galaxy/commit/9552830121a900a3ac3ae7926a02… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/Sharing.vue M test/base/populators.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py Log Message: ----------- More Selenium test fixes. A lot broke while we weren't running the tests against PRs. Commit: b7dba0b82d4997f54bf609c9dd67ff269608ca29 https://github.com/galaxyproject/galaxy/commit/b7dba0b82d4997f54bf609c9dd67… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/Sharing.vue M test/base/populators.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #6562 from jmchilton/selenium_fixes_43 More Selenium test fixes. Compare: https://github.com/galaxyproject/galaxy/compare/1510eb112f15...b7dba0b82d49 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 5b4331: Fix console error when viewing empty queue.
by GitHub 01 Aug '18

01 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5b43316036e4e4815ca5253df3b73ed60dac2735 https://github.com/galaxyproject/galaxy/commit/5b43316036e4e4815ca5253df3b7… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js Log Message: ----------- Fix console error when viewing empty queue. Commit: 99b2e28a9e38434755641a904688d9d79738f061 https://github.com/galaxyproject/galaxy/commit/99b2e28a9e38434755641a904688… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Additional fixes to API installation. - Fix tool display on repository details page. - Fix tool panel selection globally and per-tool. Commit: 4b88cf1bed8484ee82fcff71f83aaa064fe80595 https://github.com/galaxyproject/galaxy/commit/4b88cf1bed8484ee82fcff71f83a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Fix repoqueue display in titlebar (needs more refactoring, but this fixes the display) Commit: 6044ccdc144a72cded27a99e2f93dda70dee3244 https://github.com/galaxyproject/galaxy/commit/6044ccdc144a72cded27a99e2f93… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: R client/galaxy/scripts/mvc/toolshed/repo-queue-view.js Log Message: ----------- Clear unused repo-queue-view Commit: 60ca265a3791ec0d7051a7bec6cf0df945cbd7cd https://github.com/galaxyproject/galaxy/commit/60ca265a3791ec0d7051a7bec6cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js Log Message: ----------- Cleanup repository-queue-view Commit: 2c6e92a3ea7ebe8a47d157411dc73b0270d1dba2 https://github.com/galaxyproject/galaxy/commit/2c6e92a3ea7ebe8a47d157411dc7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Use correct backbone, standardize JS in workflows-view Commit: 53b9d216204a3f86eb1715a184af112de6a8499e https://github.com/galaxyproject/galaxy/commit/53b9d216204a3f86eb1715a184af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/repo-status-view.js Log Message: ----------- Cleanup/standardization in repo-status-view Commit: d5d3731c22a111b0f1d98f2c41de654c7c647372 https://github.com/galaxyproject/galaxy/commit/d5d3731c22a111b0f1d98f2c41de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Clean up and standardization in repository-view.js Commit: 1714059b64087ac97f978e36452eff4a6bfa0d21 https://github.com/galaxyproject/galaxy/commit/1714059b64087ac97f978e36452e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/categories-view.js Log Message: ----------- Toolshed JS cleanup in categories-view Commit: b8ce606d4057dd2b44480e6003e3ecdd81198b24 https://github.com/galaxyproject/galaxy/commit/b8ce606d4057dd2b44480e6003e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/repositories-view.js Log Message: ----------- Toolshed client cleanup in repositories-view Commit: 2fc02a054a099a783ebe7ad0756e07afb05effaf https://github.com/galaxyproject/galaxy/commit/2fc02a054a099a783ebe7ad0756e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/shed-list-view.js Log Message: ----------- Toolshed client cleanup in shed-list-view Commit: 9ef81bd290edcab301d2fa655526c9cfa538b123 https://github.com/galaxyproject/galaxy/commit/9ef81bd290edcab301d2fa655526… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/toolshed-model.js Log Message: ----------- Toolshed client cleanup in toolshed-model Commit: 88e4c6aa311fecd0b29c78c0028f445731841750 https://github.com/galaxyproject/galaxy/commit/88e4c6aa311fecd0b29c78c0028f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/util.js Log Message: ----------- Toolshed client cleanup in ts-util Commit: 1ebb0bf8d0a96f7fdba8df10c633fb02527044b2 https://github.com/galaxyproject/galaxy/commit/1ebb0bf8d0a96f7fdba8df10c633… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js Log Message: ----------- Formatting, and remove some debug cruft. Commit: c86ab4b338d6ed82e968ea7831673c242efe6333 https://github.com/galaxyproject/galaxy/commit/c86ab4b338d6ed82e968ea783167… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js R client/galaxy/scripts/mvc/toolshed/repo-queue-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js Log Message: ----------- Merge pull request #5 from dannon/ts_api_fixes Ts api fixes Commit: 8027ab3c24e356801e1a7c23c42929221134d66d https://github.com/galaxyproject/galaxy/commit/8027ab3c24e356801e1a7c23c429… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js Log Message: ----------- Fix tool panel switcher button. Commit: 1510eb112f156904d4cc27281cdccd0218819b86 https://github.com/galaxyproject/galaxy/commit/1510eb112f156904d4cc27281cdc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-01 (Wed, 01 Aug 2018) Changed paths: M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/mvc/toolshed/categories-view.js R client/galaxy/scripts/mvc/toolshed/repo-queue-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/toolshed-model.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M lib/galaxy/webapps/galaxy/api/toolshed.py Log Message: ----------- Merge pull request #6544 from davebx/ts_api_fixes Fixes for API installation bugs. Compare: https://github.com/galaxyproject/galaxy/compare/1d0313c286d4...1510eb112f15 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d8bd5f: Many selenium tests fixes for recent dev changes.
by GitHub 30 Jul '18

30 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d8bd5f4690319374a04d4d4dd2fe179618312fa5 https://github.com/galaxyproject/galaxy/commit/d8bd5f4690319374a04d4d4dd2fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py M test/selenium_tests/test_history_panel_collections.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Many selenium tests fixes for recent dev changes. Commit: 1d0313c286d4501518a85ecf4361bbc2d7c8c44f https://github.com/galaxyproject/galaxy/commit/1d0313c286d4501518a85ecf4361… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py M test/selenium_tests/test_history_panel_collections.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge pull request #6557 from jmchilton/admin_selenium_fixes Many selenium tests fixes for recent dev changes. Compare: https://github.com/galaxyproject/galaxy/compare/68cb2bb82b60...1d0313c286d4 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ce4792: Restore log_destination = stdout configuration opt...
by GitHub 30 Jul '18

30 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce4792e103c43afcb3d50ad3f6252e28365474c4 https://github.com/galaxyproject/galaxy/commit/ce4792e103c43afcb3d50ad3f625… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Restore log_destination = stdout configuration option. Implementation in 17.09 was here https://github.com/galaxyproject/galaxy/blob/release_17.09/lib/galaxy/confi…. This option set to stdout is used by the test framework output Galaxy logs to stdout. As far as I can tell log_destination was removed in 18.01 and the effect was to sort of default to stdout - but when we fixed log_destination for files and backported recently https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… - test output became written to a file called "stdout". This commit should restore the 17.09 behavior for both files and stdout configuration of this logging. Commit: 68cb2bb82b6023cee3609cc99043a224ef70f44a https://github.com/galaxyproject/galaxy/commit/68cb2bb82b6023cee3609cc99043… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #6555 from jmchilton/restore_log_destination_stdout Restore log_destination = stdout configuration option. Compare: https://github.com/galaxyproject/galaxy/compare/1a73b1f2adf8...68cb2bb82b60 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 5f19b8: Fix empty handling rule.
by GitHub 30 Jul '18

30 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 5f19b8752dfd940efd156de1a0c1a4e6e914800b https://github.com/galaxyproject/galaxy/commit/5f19b8752dfd940efd156de1a0c1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Fix empty handling rule. Commit: 66e74d0e475ef6fd6f6de125b41f9990e274fbfb https://github.com/galaxyproject/galaxy/commit/66e74d0e475ef6fd6f6de125b41f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Merge pull request #6542 from jmchilton/1805_fix_empty_handling_rule_on_backend [18.05] Fix "filter empty" rule in Python rule handling framework. Compare: https://github.com/galaxyproject/galaxy/compare/a88bf0a2bee1...66e74d0e475e **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0