galaxy-commits May 2018

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[galaxyproject/galaxy] 03a815: Some more upload/sniff tests.
by GitHub 30 May '18

30 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 03a815a2c379186237a9978d0f3af32f1e69c933 https://github.com/galaxyproject/galaxy/commit/03a815a2c379186237a9978d0f3a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.tiff A test-data/1.tiff M test/api/test_tools_upload.py M test/base/populators.py Log Message: ----------- Some more upload/sniff tests. Commit: 27106c59e5d6d3583f1a11adec1ddd26d0114da1 https://github.com/galaxyproject/galaxy/commit/27106c59e5d6d3583f1a11adec1d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.tiff A test-data/1.tiff M test/api/test_tools_upload.py M test/base/populators.py Log Message: ----------- Merge pull request #6212 from jmchilton/tiff_tests Some more upload/sniff tests. Compare: https://github.com/galaxyproject/galaxy/compare/a79d6fae43be...27106c59e5d6 **NOTE:** This service 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] f99f86: Hyperlink DOIs against preferred resolver
by GitHub 30 May '18

30 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f99f8667bcfceea21101d0690d2ba6f5630d34cf https://github.com/galaxyproject/galaxy/commit/f99f8667bcfceea21101d0690d2b… Author: Katrin Leinweber <kalei(a)posteo.de> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M doc/source/admin/galaxy_options.rst M lib/galaxy/datatypes/test/example.iqtree M lib/galaxy/managers/citations.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M tools/sr_mapping/bfast_wrapper.xml Log Message: ----------- Hyperlink DOIs against preferred resolver Commit: a79d6fae43be20dbf79d57e8067a022f877b57be https://github.com/galaxyproject/galaxy/commit/a79d6fae43be20dbf79d57e8067a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M doc/source/admin/galaxy_options.rst M lib/galaxy/datatypes/test/example.iqtree M lib/galaxy/managers/citations.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M tools/sr_mapping/bfast_wrapper.xml Log Message: ----------- Merge pull request #6244 from katrinleinweber/resolve-DOIs-securely Hyperlink DOIs against preferred resolver Compare: https://github.com/galaxyproject/galaxy/compare/8fcc9332448a...a79d6fae43be **NOTE:** This service 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] 3b27d2: Strip busted history structure view -- we're goign...
by GitHub 30 May '18

30 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3b27d249b2876a8e88691dad2fe42213f8943893 https://github.com/galaxyproject/galaxy/commit/3b27d249b2876a8e88691dad2fe4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/mvc/history/history-structure-view.js M lib/galaxy/webapps/galaxy/controllers/history.py R templates/webapps/galaxy/history/structure.mako Log Message: ----------- Strip busted history structure view -- we're goign to start from scratch here Commit: 8d9a21c4e9eeab4f1b947b66688658941c482340 https://github.com/galaxyproject/galaxy/commit/8d9a21c4e9eeab4f1b947b666886… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Remove unused import. Commit: 8fcc9332448add1e55fd6b5831da80b336d63078 https://github.com/galaxyproject/galaxy/commit/8fcc9332448add1e55fd6b5831da… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/apps/extended.js R client/galaxy/scripts/mvc/history/history-structure-view.js M lib/galaxy/webapps/galaxy/controllers/history.py R templates/webapps/galaxy/history/structure.mako Log Message: ----------- Merge pull request #6241 from dannon/history_structure_cleanup Strip legacy history structure view Compare: https://github.com/galaxyproject/galaxy/compare/9b4697d3eda8...8fcc9332448a **NOTE:** This service 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] b17beb: Move smart_str() calls inside pbkdf2_bin()
by GitHub 30 May '18

30 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b17bebcb30cd131ee1aab0f9bebeae5a9f3e6b04 https://github.com/galaxyproject/galaxy/commit/b17bebcb30cd131ee1aab0f9bebe… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Move smart_str() calls inside pbkdf2_bin() Commit: 6b21a35319a2916e9d4fa552ac32d8766d0b7c4e https://github.com/galaxyproject/galaxy/commit/6b21a35319a2916e9d4fa552ac32… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Use unicodify() Commit: 7b5e1903f13de4a245a04d42254f68ac81bfeecd https://github.com/galaxyproject/galaxy/commit/7b5e1903f13de4a245a04d42254f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Make pbkdf2_bin() faster `digest` was needlessly recalculated as `bytearray(u)` in the internal loop, instead make `_pseudorandom()` return both the bytestring and the list of character ordinals. Commit: 2ebe88718aa4c4b6bafcfd7dfc0d29bccf9df614 https://github.com/galaxyproject/galaxy/commit/2ebe88718aa4c4b6bafcfd7dfc0d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Unicodify bytearrays Commit: 9b4697d3eda8243ada0908a03b2e8810642eec04 https://github.com/galaxyproject/galaxy/commit/9b4697d3eda8243ada0908a03b2e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M lib/galaxy/security/passwords.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #6242 from nsoranzo/python3 Password encoding improvements Compare: https://github.com/galaxyproject/galaxy/compare/d4cb7c614ecb...9b4697d3eda8 **NOTE:** This service 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] 6702fa: Remove defunct sharing column link
by GitHub 28 May '18

28 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 6702fa45cda22b3cc2d820d1075f2b02ae65abe5 https://github.com/galaxyproject/galaxy/commit/6702fa45cda22b3cc2d820d1075f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove defunct sharing column link Commit: 02feb1735086c8aca9feff740139bdebc1bc91d5 https://github.com/galaxyproject/galaxy/commit/02feb1735086c8aca9feff740139… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Fix broken collection_type_source tool and test. The tool wouldn't load after 8af243c176fd9c261277327750aaa71806add4ef and that caused the relevant tests to "SKIP" instead of failing outright. ./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_map_over_collection_type_source Commit: 221897be04bff63a0ca91646bbb1d82d4cf3ea84 https://github.com/galaxyproject/galaxy/commit/221897be04bff63a0ca91646bbb1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-26 (Sat, 26 May 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #6177 from guerler/remove_defunct_link [18.05] Remove defunct sharing column link Commit: c9641e1f13847fc7713a359076597217bf7c664a https://github.com/galaxyproject/galaxy/commit/c9641e1f13847fc7713a35907659… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-05-27 (Sun, 27 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Merge pull request #6227 from jmchilton/collection_type_source_regression [18.05] Fix broken collection_type_source tool and test. Compare: https://github.com/galaxyproject/galaxy/compare/e91f91b5f217...c9641e1f1384 **NOTE:** This service 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] 6702fa: Remove defunct sharing column link
by GitHub 28 May '18

28 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6702fa45cda22b3cc2d820d1075f2b02ae65abe5 https://github.com/galaxyproject/galaxy/commit/6702fa45cda22b3cc2d820d1075f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove defunct sharing column link Commit: 02feb1735086c8aca9feff740139bdebc1bc91d5 https://github.com/galaxyproject/galaxy/commit/02feb1735086c8aca9feff740139… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Fix broken collection_type_source tool and test. The tool wouldn't load after 8af243c176fd9c261277327750aaa71806add4ef and that caused the relevant tests to "SKIP" instead of failing outright. ./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_map_over_collection_type_source Commit: 221897be04bff63a0ca91646bbb1d82d4cf3ea84 https://github.com/galaxyproject/galaxy/commit/221897be04bff63a0ca91646bbb1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-26 (Sat, 26 May 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #6177 from guerler/remove_defunct_link [18.05] Remove defunct sharing column link Commit: c9641e1f13847fc7713a359076597217bf7c664a https://github.com/galaxyproject/galaxy/commit/c9641e1f13847fc7713a35907659… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-05-27 (Sun, 27 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Merge pull request #6227 from jmchilton/collection_type_source_regression [18.05] Fix broken collection_type_source tool and test. Commit: d4cb7c614ecb2cc3193de89a87a1fe9661975d21 https://github.com/galaxyproject/galaxy/commit/d4cb7c614ecb2cc3193de89a87a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-28 (Mon, 28 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/820712144000...d4cb7c614ecb **NOTE:** This service 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] 02feb1: Fix broken collection_type_source tool and test.
by GitHub 27 May '18

27 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 02feb1735086c8aca9feff740139bdebc1bc91d5 https://github.com/galaxyproject/galaxy/commit/02feb1735086c8aca9feff740139… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Fix broken collection_type_source tool and test. The tool wouldn't load after 8af243c176fd9c261277327750aaa71806add4ef and that caused the relevant tests to "SKIP" instead of failing outright. ./run_tests.sh -api test/api/test_tools.py:ToolsTestCase.test_map_over_collection_type_source Commit: c9641e1f13847fc7713a359076597217bf7c664a https://github.com/galaxyproject/galaxy/commit/c9641e1f13847fc7713a35907659… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-05-27 (Sun, 27 May 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Merge pull request #6227 from jmchilton/collection_type_source_regression [18.05] Fix broken collection_type_source tool and test. Compare: https://github.com/galaxyproject/galaxy/compare/221897be04bf...c9641e1f1384 **NOTE:** This service 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] 6702fa: Remove defunct sharing column link
by GitHub 26 May '18

26 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 6702fa45cda22b3cc2d820d1075f2b02ae65abe5 https://github.com/galaxyproject/galaxy/commit/6702fa45cda22b3cc2d820d1075f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Remove defunct sharing column link Commit: 221897be04bff63a0ca91646bbb1d82d4cf3ea84 https://github.com/galaxyproject/galaxy/commit/221897be04bff63a0ca91646bbb1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-26 (Sat, 26 May 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #6177 from guerler/remove_defunct_link [18.05] Remove defunct sharing column link Compare: https://github.com/galaxyproject/galaxy/compare/e91f91b5f217...221897be04bf **NOTE:** This service 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/usegalaxy-playbook] 25a9f2: update Main
by GitHub 25 May '18

25 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 25a9f268e6490ce921abb6ab8450a3b099100a6e https://github.com/galaxyproject/usegalaxy-playbook/commit/25a9f268e6490ce9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- update Main Commit: c0abca426a077788ad3db798d8a6ff347c9e1e65 https://github.com/galaxyproject/usegalaxy-playbook/commit/c0abca426a077788… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/266133080d84...… **NOTE:** This service 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] fdfba9: Fix file type error in RuleCollectionBuilder.
by GitHub 25 May '18

25 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fdfba9dac102cdd62db92b28a57a6d96ce2b52c6 https://github.com/galaxyproject/galaxy/commit/fdfba9dac102cdd62db92b28a57a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix file type error in RuleCollectionBuilder. Commit: 820712144000f05e088791159ffbd80b14e40999 https://github.com/galaxyproject/galaxy/commit/820712144000f05e088791159ffb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6231 from jmchilton/fix_file_type Fix file type error in RuleCollectionBuilder. Compare: https://github.com/galaxyproject/galaxy/compare/13b5883dd605...820712144000 **NOTE:** This service 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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galaxy-commits May 2018