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[galaxyproject/infrastructure-playbook] c64057: Automatically accept host keys when running Jenkin...
by GitHub 25 Oct '18

25 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c6405712b97d5f828083dcabfd6b3c1c0e9a9b86 https://github.com/galaxyproject/infrastructure-playbook/commit/c6405712b97… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M env/galaxy/files/jenkins/jenkins_server_user_ssh_config M env/galaxy/files/jenkins/jenkins_slave_user_ssh_config Log Message: ----------- Automatically accept host keys when running Jenkins jobs **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] e0721a: Merge pull request #6431 from nsoranzo/python3
by GitHub 25 Oct '18

25 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: e0721ac8545107bd0eb0194f131bbb687cfcc18f https://github.com/galaxyproject/galaxy/commit/e0721ac8545107bd0eb0194f131b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/framework/webapp.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge pull request #6431 from nsoranzo/python3 Do not encode a rendered Mako template Commit: fe003da510d71ad001bb63ed40e6ce45f4ca23c2 https://github.com/galaxyproject/galaxy/commit/fe003da510d71ad001bb63ed40e6… Author: Caleb Easterly <easte080(a)umn.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- fix linting errors Commit: 41f25b928afbf849e94c3c3b5ca222253d778abb https://github.com/galaxyproject/galaxy/commit/41f25b928afbf849e94c3c3b5ca2… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- fix a few tool_deps test errors Commit: 01ba96a7acda5f321e3f3f0975909615122a7880 https://github.com/galaxyproject/galaxy/commit/01ba96a7acda5f321e3f3f097590… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue Log Message: ----------- Merge pull request #6427 from dannon/citations_style_fix Citation style work Commit: 258fff927633bcafe844dec09c1d8e40979b9f73 https://github.com/galaxyproject/galaxy/commit/258fff927633bcafe844dec09c1d… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py Log Message: ----------- py3 compat: fixes test_vcf, test_sniff_compressed* Commit: fcdd1a42451f02fa97349b6213c44e55676071ad https://github.com/galaxyproject/galaxy/commit/fcdd1a42451f02fa97349b6213c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #6436 from bgruening/lint-fixes fix a few tool_deps test errors Commit: 82523528f2b90447df5c47cbfc54bf03f462961c https://github.com/galaxyproject/galaxy/commit/82523528f2b90447df5c47cbfc54… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/layout/panel.js Log Message: ----------- Merge pull request #6421 from jxtx/fix-panel-drag Fix panel drag resize. Commit: 8b90cd997fb485045ab4384d96149e89891b29aa https://github.com/galaxyproject/galaxy/commit/8b90cd997fb485045ab4384d9614… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Encode JSON encoder output Commit: 44300668d4e479b3f7f6e6928fd82c5517f1c556 https://github.com/galaxyproject/galaxy/commit/44300668d4e479b3f7f6e6928fd8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M test/unit/test_galaxy_mapping.py Log Message: ----------- Fix registry import in test_galaxy_mapping.py Commit: f93b3e09862bbda6d7a7c358f414d847bd6c2238 https://github.com/galaxyproject/galaxy/commit/f93b3e09862bbda6d7a7c358f414… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Unicodify _sniffnfix_pg9_hex output Commit: 59060783a9e169496548ae38766f04cd94eb54a3 https://github.com/galaxyproject/galaxy/commit/59060783a9e169496548ae38766f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- replace the administration header in admin menu with version closes #1201 Commit: 1e9e38703a53767d22ef4ce21e9dcf73ebe03a99 https://github.com/galaxyproject/galaxy/commit/1e9e38703a53767d22ef4ce21e9d… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add zoom support to workflow editor. Zoom levels are discrete from a pre-defined set. Uses css transforms and... math. Commit: 8be94009680ef9efaa081d56cedb78eff270d098 https://github.com/galaxyproject/galaxy/commit/8be94009680ef9efaa081d56cedb… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js Log Message: ----------- Fix incorrect variable reference Commit: d145d9ac92051ecb765d00330a6eb370c6319ac3 https://github.com/galaxyproject/galaxy/commit/d145d9ac92051ecb765d00330a6e… Author: Evan Bolyen <ebolyen(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/dataset_matcher.py M test/unit/tools/test_dataset_matcher.py Log Message: ----------- Allows DatasetMatcher to use multiple filters In particular this enables multiple add_value filters to be used with <options>'s option_filter_attribute. Commit: 433d4648706be8902f609a4cba1a0d941acb7a0d https://github.com/galaxyproject/galaxy/commit/433d4648706be8902f609a4cba1a… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M config/tool_conf.xml.sample M tools/data_source/intermine.xml Log Message: ----------- Update InterMine Commit: 5b0088ae43c748edaaccbaa363e0d0c86756a66a https://github.com/galaxyproject/galaxy/commit/5b0088ae43c748edaaccbaa363e0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Update InterMine Commit: 27a34151887a65bc24a44b33bf06280339f6e710 https://github.com/galaxyproject/galaxy/commit/27a34151887a65bc24a44b33bf06… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M templates/base/base_panels.mako M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- resolve missing closing div and three extra closing divs with net of two extra closing divs this used to work Commit: 1f9894069c7424dd202fbaeb562f9d71a86564d7 https://github.com/galaxyproject/galaxy/commit/1f9894069c7424dd202fbaeb562f… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M templates/base/base_panels.mako M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge pull request #6445 from martenson/mako-crazy fix TS: resolve missing closing div and three extra closing divs Commit: e398818ab6329888f8855cde7ffc9ebfd18a9abc https://github.com/galaxyproject/galaxy/commit/e398818ab6329888f8855cde7ffc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/util/json.py Log Message: ----------- Drop fix_json, doesn't seem to be necessary and fixes workflow unit tests Commit: bc712cae907ded706954deeb417e7c66e3a5f533 https://github.com/galaxyproject/galaxy/commit/bc712cae907ded706954deeb417e… Author: Alexandru Mahmoud <amahmou4(a)jhu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js Log Message: ----------- Changing menu tabs without hard refresh Commit: 073d04474913913e6e8fc20346297fc3a9ef2a3e https://github.com/galaxyproject/galaxy/commit/073d04474913913e6e8fc2034629… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: b062a8c4f312952441696da9cca825ca35549523 https://github.com/galaxyproject/galaxy/commit/b062a8c4f312952441696da9cca8… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py Log Message: ----------- Merge pull request #6442 from caleb-easterly/is_gzip_bz2 py3 compat: fixes test_vcf, test_sniff_compressed* Commit: ee267e95611652ed0a6068144f88320c9b602ae2 https://github.com/galaxyproject/galaxy/commit/ee267e95611652ed0a6068144f88… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6441 from jxtx/workflow-zoom Add zoom support to workflow editor. Commit: 9b2101e948942f6b239a2c45892c4535a13ec9f9 https://github.com/galaxyproject/galaxy/commit/9b2101e948942f6b239a2c45892c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Merge remote-tracking branch 'martenson/show-version-admin' into dev Commit: a51ad0fc5204ae138d024c19358be720359f09ab https://github.com/galaxyproject/galaxy/commit/a51ad0fc5204ae138d024c19358b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Client format and build from several upstream changes Commit: 75511506a8828e922c8b12f91af4637c5db3b778 https://github.com/galaxyproject/galaxy/commit/75511506a8828e922c8b12f91af4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/model/custom_types.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #6439 from mvdbeek/py3_db_interaction Python3: Encode return values of JSON encoder Commit: f7e43aa2212090f08e94ba9ad65ad7afbf4fcfd4 https://github.com/galaxyproject/galaxy/commit/f7e43aa2212090f08e94ba9ad65a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/util/json.py Log Message: ----------- Merge pull request #6446 from mvdbeek/drop_json_fix Python3: Drop fix_json, doesn't seem to be necessary and fixes workflow unit t… Commit: 72f9e9c587e043982a296f4885a88077a720fb1f https://github.com/galaxyproject/galaxy/commit/72f9e9c587e043982a296f4885a8… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- py3: fixes test_DatasetManager.py:DatasetManagerTestCase Commit: dc6774b7b2d0bd90705f289fe6cd82ba9e8eed9e https://github.com/galaxyproject/galaxy/commit/dc6774b7b2d0bd90705f289fe6cd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- CI - ignore node_modules anywhere, since we use them in multiple places and not always 'client' Commit: 1eae38854b53433a367ec2038e74e30ffa4bfab1 https://github.com/galaxyproject/galaxy/commit/1eae38854b53433a367ec2038e74… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/users.py Log Message: ----------- py3: replace e.message with str(e) Commit: 9eb1bfe3ff0a17629922156a0465694c3a31b88e https://github.com/galaxyproject/galaxy/commit/9eb1bfe3ff0a17629922156a0465… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Fix droptarget:drop trigger (wasn't passing the panel) Commit: 6d2ff7bad295d9850f2690e4cb81e06f851cc451 https://github.com/galaxyproject/galaxy/commit/6d2ff7bad295d9850f2690e4cb81… Author: Caleb Easterly <easte080(a)umn.edu> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- linting fix Commit: 5ad321e08540f6c1a046f397a5c18db16d240c56 https://github.com/galaxyproject/galaxy/commit/5ad321e08540f6c1a046f397a5c1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- Merge pull request #6452 from caleb-easterly/test_dataset_manager py3: fixes test_DatasetManager.py:DatasetManagerTestCase Commit: 54b6a8883d9549c0a84204f530332d695676afdb https://github.com/galaxyproject/galaxy/commit/54b6a8883d9549c0a84204f53033… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- py3: Fix the dynamic tool destination unit test Commit: 19e70b8aeb0c8d08b70d050b1dcf2d4d00480b4f https://github.com/galaxyproject/galaxy/commit/19e70b8aeb0c8d08b70d050b1dcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Merge pull request #6449 from dannon/node_modules_blacklist CI - ignore node_modules anywhere Commit: 9957d39b043dd9bc17b7e0c56c5e116ddc45f94f https://github.com/galaxyproject/galaxy/commit/9957d39b043dd9bc17b7e0c56c5e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #6454 from caleb-easterly/exceptions py3: replace e.message with str(e) Commit: a1bedf4be8835f84a14df9cc5e1231dd585302d5 https://github.com/galaxyproject/galaxy/commit/a1bedf4be8835f84a14df9cc5e12… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Lint doctests Commit: 256d901df20e6703094cf98f693b19ff79384c3e https://github.com/galaxyproject/galaxy/commit/256d901df20e6703094cf98f693b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/util/checkers.py Log Message: ----------- Use `with` statement Commit: c03dd53520a4b581af208c1e592ea135a4340016 https://github.com/galaxyproject/galaxy/commit/c03dd53520a4b581af208c1e592e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Correctly handle `bytearray`s in `smart_str()` Also: - Use `assert` in doctests - Speed up `unicodify()` on Unicode strings Commit: 7195c224321b0826a9b2297166ea6fa6ce1de007 https://github.com/galaxyproject/galaxy/commit/7195c224321b0826a9b2297166ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Encode chunk before comparing with gzip_magic Since commit 8d8299a19315aef2f2daef278a5e8d8c47da63bb , `text_type(util.gzip_magic)` generates the following exception: ``` UnicodeDecodeError: 'ascii' codec can't decode byte 0x8b in position 1: ordinal not in range(128) ``` Commit: 82028d95d0d58532821816d526e2b932ea8ee5ec https://github.com/galaxyproject/galaxy/commit/82028d95d0d58532821816d526e2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Remove needless check The `filename` file is the destination file and is always empty at this point. Introduced in commit 85ea42b79dcfc30622a55f1b9fc507bc822ae325 . Commit: 64c591a6069c43067ad1871dca06cc3c5a581903 https://github.com/galaxyproject/galaxy/commit/64c591a6069c43067ad1871dca06… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- More proper fix for some test_tool_deps.py unit tests Follow up to https://github.com/galaxyproject/galaxy/pull/6436/files#r199368686 Commit: b46d7c6276d09c160f37f22df8ed64461a96b407 https://github.com/galaxyproject/galaxy/commit/b46d7c6276d09c160f37f22df8ed… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Merge pull request #6451 from dannon/fixdragdrop Fix droptarget:drop trigger (drag/drop in the multiview) Commit: 59cc94256ca011ab68e25d3a9423166c3ad4ec1c https://github.com/galaxyproject/galaxy/commit/59cc94256ca011ab68e25d3a9423… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #6428 from mvdbeek/run_published_workflows Run workflows from published workflows menu Commit: 561330fea9eb1a79a52aa48d986218e1b89d8800 https://github.com/galaxyproject/galaxy/commit/561330fea9eb1a79a52aa48d9862… Author: Caleb Easterly <easte080(a)umn.edu> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- rewind change Commit: f65c77d385303703d1cfcd47140f84d56fadec2b https://github.com/galaxyproject/galaxy/commit/f65c77d385303703d1cfcd47140f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #6455 from nsoranzo/python3 Various Python 3 fixes Commit: cc0022d5d1cc985b23644b6ff6b3e60c29d9caa6 https://github.com/galaxyproject/galaxy/commit/cc0022d5d1cc985b23644b6ff6b3… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #6434 from caleb-easterly/test_tool_deps_py3 py3 compat Commit: 5745df2318d4907fb0fa40bc9032b44db853bca0 https://github.com/galaxyproject/galaxy/commit/5745df2318d4907fb0fa40bc9032… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- GIE static url; https://github.com/galaxyproject/galaxy/issues/6459 Commit: 21f42f5bb6f076b3b318f5f98657929d7f66102b https://github.com/galaxyproject/galaxy/commit/21f42f5bb6f076b3b318f5f98657… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/tools/parser/interface.py Log Message: ----------- fixes test/unit/jobs/test_job_output_checker.py Commit: fb0cc8bb1f8a786699f861256d5d25632b50af3f https://github.com/galaxyproject/galaxy/commit/fb0cc8bb1f8a786699f861256d5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/tools/parser/interface.py Log Message: ----------- Use stdioerrorlevel constants to indicate FATAL Commit: 0d59c9cd54d49fad31767f52c07c995ff963ce18 https://github.com/galaxyproject/galaxy/commit/0d59c9cd54d49fad31767f52c07c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: R lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M test/unit/jobs/test_job_output_checker.py Log Message: ----------- Refactor galaxy.jobs.error_level -> galaxy.tools.parser.error_level. Needed after 46170e9bcdcc2eb104ebab72a7afc9b7238bc314 to keep galaxy-lib from importing things outside of galaxy-lib but clearly a good refactoring on its own since it eliminates mid-file imports that were there to prevent circular dependencies from loading Galaxy. Commit: fb229c251f7487215a285967be8b7b331c1d21f2 https://github.com/galaxyproject/galaxy/commit/fb229c251f7487215a285967be8b… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: R lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M test/unit/jobs/test_job_output_checker.py Log Message: ----------- Merge pull request #6438 from caleb-easterly/test_job_output_checker_py3 fixes test/unit/jobs/test_job_output_checker.py; strange default? Commit: 7f0684e3d57f248b74ff5d6fd6f9a2537b07d726 https://github.com/galaxyproject/galaxy/commit/7f0684e3d57f248b74ff5d6fd6f9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M test/functional/test_toolbox.py Log Message: ----------- Fix test_toolbox for python 3 Commit: ae9b6057da7a0056191f27511e2a71fd1bd6dac2 https://github.com/galaxyproject/galaxy/commit/ae9b6057da7a0056191f27511e2a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M test/functional/test_data_managers.py Log Message: ----------- Fix test_data_managers for python 3 Commit: 37782cf5131eab2be8c08320bedf8365a475abbc https://github.com/galaxyproject/galaxy/commit/37782cf5131eab2be8c08320bedf… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #6460 from thobalose/ie_static_url GIE static url Commit: d85b65a2e5011e7187817c7f86db0c1e09a788d5 https://github.com/galaxyproject/galaxy/commit/d85b65a2e5011e7187817c7f86db… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Merge pull request #6453 from mvdbeek/fix_py3_dtd py3: Fix the dynamic tool destination unit test Commit: 6206f706794c997ae137381eabba7d0d88852c49 https://github.com/galaxyproject/galaxy/commit/6206f706794c997ae137381eabba… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M test/functional/test_data_managers.py M test/functional/test_toolbox.py Log Message: ----------- Merge pull request #6463 from mvdbeek/prepare_py3_api_tests Fix test_toolbox for python 3 Commit: 1f57706abffb933a1e5300f585ed19c1493b39d2 https://github.com/galaxyproject/galaxy/commit/1f57706abffb933a1e5300f585ed… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Log Message: ----------- Merge pull request #6464 from dannon/backport-gie-static [18.05] Backport of IE static url fix Commit: 14ef3b8643eb96a98b1f39391c1f385596d1cb42 https://github.com/galaxyproject/galaxy/commit/14ef3b8643eb96a98b1f39391c1f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt M .travis.yml A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md R client/galaxy/docs/galaxy-styles.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DataDialog.vue A client/galaxy/scripts/components/admin/DataTypes.vue M client/galaxy/scripts/galaxy.pages.js A client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js 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lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/relabel_from_file.xml M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/json.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M scripts/grt/export.py M static/style/blue/base.css R templates/admin/view_datatypes_registry.mako M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_tools.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_params.py M test/unit/test_galaxy_mapping.py M test/unit/test_security_helper.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into topic/daa Commit: 9a06474a30cb82122ee6a78c30eca601af9d6578 https://github.com/galaxyproject/galaxy/commit/9a06474a30cb82122ee6a78c30ec… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/diamond.daa Log Message: ----------- Merge pull request #6313 from bernt-matthias/topic/daa added daa (diamond alignment) datatype Commit: 6e11334fa7122858012c644038eb0bf58de7e6f2 https://github.com/galaxyproject/galaxy/commit/6e11334fa7122858012c644038eb… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Refactor cloud download api and use only one handle to the staging file. Commit: 57f5b42974929d4090429df87aca9973faae869f https://github.com/galaxyproject/galaxy/commit/57f5b42974929d4090429df87aca… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/workflows/test_extract_summary.py Log Message: ----------- py3: fix workflow extract summary Commit: af6b572eac2e2571e5f6f0b46945f7f76fce685b https://github.com/galaxyproject/galaxy/commit/af6b572eac2e2571e5f6f0b46945… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/tools/test_history_imp_exp.py Log Message: ----------- py3: Fix history/import export Commit: 048f7737dda50c8dc64fc211a5e59c971aa92041 https://github.com/galaxyproject/galaxy/commit/048f7737dda50c8dc64fc211a5e5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix job disocvery Commit: c52d1476122adf82b62e6e1045cd7155f34bb9f7 https://github.com/galaxyproject/galaxy/commit/c52d1476122adf82b62e6e1045cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/tools/test_evaluation.py Log Message: ----------- No need to explicitly compare to bytestring Commit: 492ee207e0ac9884178249251f1047181148c458 https://github.com/galaxyproject/galaxy/commit/492ee207e0ac9884178249251f10… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Cast odict.items() and odict.values() to list Commit: b773aedfa7670ee7fe13d43618f956a4bea3d5da https://github.com/galaxyproject/galaxy/commit/b773aedfa7670ee7fe13d43618f9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- py3: open job script in text mode Commit: c03a86caea4f7cb945a5a8ae539cb7d8ea3ccce8 https://github.com/galaxyproject/galaxy/commit/c03a86caea4f7cb945a5a8ae539c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- py3: fix test_job_param unit test Commit: 3af3591e626ddb7204cb958ef414e1fba203e843 https://github.com/galaxyproject/galaxy/commit/3af3591e626ddb7204cb958ef414… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/rule_helper.py Log Message: ----------- py3: fix rule-helper Commit: 25b93c78b6d2a68917bd0aad1e27f155f9d5600c https://github.com/galaxyproject/galaxy/commit/25b93c78b6d2a68917bd0aad1e27… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/config.py M test/unit/web/framework/test_webapp.py Log Message: ----------- Fix CORS unit test Commit: 05f8f2063a69e682bc5349933e44d751b2c9e477 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https://github.com/galaxyproject/galaxy/commit/db10b5b679217c36414dcf2a8018… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- py3: Fix has_limit Commit: cde7784606947eb452d1b3c98ca3eaca99b25ea8 https://github.com/galaxyproject/galaxy/commit/cde7784606947eb452d1b3c98ca3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/model/metadata.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- py3: Fix metadata setting Commit: 84dc5cd02ff0ceab8529cd9e11f825eaed2e3633 https://github.com/galaxyproject/galaxy/commit/84dc5cd02ff0ceab8529cd9e11f8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- py3: Get unicode strings from ElementTree on py3 Commit: c8f720d71c3d14c2e90d5ebcf0fa41d7bb2726b5 https://github.com/galaxyproject/galaxy/commit/c8f720d71c3d14c2e90d5ebcf0fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- py3: don't case payload to bytestring. Doesn't seem to affect py2 either Commit: f29ebb7389a8e695020e11ec4c4c759e89c0a062 https://github.com/galaxyproject/galaxy/commit/f29ebb7389a8e695020e11ec4c4c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- py3: fix generting conda env hash Commit: c16d8531b9948f71d9861692b40a005e7d8c2a21 https://github.com/galaxyproject/galaxy/commit/c16d8531b9948f71d9861692b40a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- py3: fix StringFunctionFilter Commit: 7e29d5d83b55846e0bbe5ec43ced2870b7bb1913 https://github.com/galaxyproject/galaxy/commit/7e29d5d83b55846e0bbe5ec43ced… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M test/unit/test_remote_shell.py Log Message: ----------- py3: fix paramiko shell runner by casting to unicode Commit: 962b1fe176e1120d5a093726d74271fda860884f https://github.com/galaxyproject/galaxy/commit/962b1fe176e1120d5a093726d742… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- py3: fix check_limits Commit: 6bad1027a7b22c833ca241214c93090badc66d37 https://github.com/galaxyproject/galaxy/commit/6bad1027a7b22c833ca241214c93… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- py3: fix collection mapping over Commit: 9d547dd5e439ea67193e94242b8354b5e6ec1b92 https://github.com/galaxyproject/galaxy/commit/9d547dd5e439ea67193e94242b83… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M templates/tagging_common.mako Log Message: ----------- py3: fix 'saved histories' menu Commit: e08c2b347e8e2c625c97f719bc6048e5e956ca9d https://github.com/galaxyproject/galaxy/commit/e08c2b347e8e2c625c97f719bc60… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py Log Message: ----------- Fix some datatype sniffers and `guess_ext()` doctests Commit: 09e39e90794234ae2cbcc2ea6b747888a5075dcd https://github.com/galaxyproject/galaxy/commit/09e39e90794234ae2cbcc2ea6b74… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- py3: Fix mako template rendering in multiple history view and workflow editor Commit: ea440345facd8c9e1cb6c6636970cacfa0544a6f https://github.com/galaxyproject/galaxy/commit/ea440345facd8c9e1cb6c6636970… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M templates/tagging_common.mako Log Message: ----------- py3: fix published workflows grid Commit: 252913b84a4de19d61294790d10ffca93944e520 https://github.com/galaxyproject/galaxy/commit/252913b84a4de19d61294790d10f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/model/orm/scripts.py Log Message: ----------- Fix SafeConfigParser import for Python 3 Commit: e9f3afa0f3d6451116283a592c680c47a986bbef https://github.com/galaxyproject/galaxy/commit/e9f3afa0f3d6451116283a592c68… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- py3: fix tool_shed.util.web_util.escape doctest Commit: 7cf76bc66aa9c8b95a74f699a934c4dd81debd57 https://github.com/galaxyproject/galaxy/commit/7cf76bc66aa9c8b95a74f699a934… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Fix documentation Commit: d5d245ff65841a33c8cb8a32a146a63b14663a7a https://github.com/galaxyproject/galaxy/commit/d5d245ff65841a33c8cb8a32a146… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- py3: Fix job_script writing Commit: 0c3a447f25d74132f5b449cac4c744f57af48198 https://github.com/galaxyproject/galaxy/commit/0c3a447f25d74132f5b449cac4c7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Import docker.types Might fix the last failing unit test? Commit: 84af674f9c84182094803a81091ff932873d80a5 https://github.com/galaxyproject/galaxy/commit/84af674f9c84182094803a81091f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/web/framework/decorators.py Log Message: ----------- Fix loading workflow in the editor under Python 3 Commit: a177fc6240c90985183807fc141b18e06e436cda https://github.com/galaxyproject/galaxy/commit/a177fc6240c90985183807fc141b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix login under Python 3 Commit: b49c4be21c6c090448d899857e53c1fed8be5d5a https://github.com/galaxyproject/galaxy/commit/b49c4be21c6c090448d899857e53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/tool_shed/util/readme_util.py Log Message: ----------- Misc Python 3 fixes Commit: d15b6cc7360d3e00780dc1b9ee39353707ba786f https://github.com/galaxyproject/galaxy/commit/d15b6cc7360d3e00780dc1b9ee39… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Code clarifications Commit: fddc7899c1f09bf20f36369883f091199db0edd0 https://github.com/galaxyproject/galaxy/commit/fddc7899c1f09bf20f36369883f0… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Let data managers also use conda python. Since data managers only return a json object, there is no need for them to use the galaxy python. Commit: 3f2b2f81fa2dfafee4c2a861b9d1f451b843bd23 https://github.com/galaxyproject/galaxy/commit/3f2b2f81fa2dfafee4c2a861b9d1… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Style fix Commit: 8e1813b53d00946f298baf1eea86599fb45f7973 https://github.com/galaxyproject/galaxy/commit/8e1813b53d00946f298baf1eea86… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use profile version to determine if data managers should preserve python env Commit: e33427a3b79073b1f78a91e848a154f27798ec6c https://github.com/galaxyproject/galaxy/commit/e33427a3b79073b1f78a91e848a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M .travis.yml M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/web_util.py M templates/tagging_common.mako M test/unit/test_remote_shell.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_history_imp_exp.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Merge pull request #6450 from mvdbeek/py3_workflow_and_tool_unit_fixes Fix all remaining unit tests under Python 3 Commit: 019f088543736cecf74febd414782d7a207acd9c https://github.com/galaxyproject/galaxy/commit/019f088543736cecf74febd41478… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Allow including paths in inputs json files. Commit: 6af48d90dbb64b9aa01b9876ae5b10cbe17e5f09 https://github.com/galaxyproject/galaxy/commit/6af48d90dbb64b9aa01b9876ae5b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- data_stype to data_style Commit: 0b98e3ed13fe24264b8a5037c1c345dd679c26af https://github.com/galaxyproject/galaxy/commit/0b98e3ed13fe24264b8a5037c1c3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/dataset_matcher.py M test/unit/tools/test_dataset_matcher.py Log Message: ----------- Merge pull request #6443 from ebolyen/multiple_filter_datasetmatcher Allows DatasetMatcher to use multiple filters Commit: 3e551cd9994e76820151bbd002ed782e36c23a69 https://github.com/galaxyproject/galaxy/commit/3e551cd9994e76820151bbd002ed… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Rename the cloud storage APIs from Download and Upload to Copy-from and Copy-To, respectively. Commit: 6c2bee5ea464a6740c7f8c93b3699c6f824a70a4 https://github.com/galaxyproject/galaxy/commit/6c2bee5ea464a6740c7f8c93b369… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Update cliff and other related dependencies cliff now has a universal wheel. Remove unused Pipfile.lock files. Skip broken lxml 4.2.2, see https://github.com/lxml/lxml/pull/265 . Fix more oscillating environment markers. Commit: 58c68d408f2eec0c787ad176dabb3330a322d582 https://github.com/galaxyproject/galaxy/commit/58c68d408f2eec0c787ad176dabb… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: A tool-data/intermine_simple_display.loc.sample Log Message: ----------- add missing intermine_simple_display.loc.sample Commit: 8df7cafe3ac6d700f2637f0c41d0dfba8a360076 https://github.com/galaxyproject/galaxy/commit/8df7cafe3ac6d700f2637f0c41d0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M config/datatypes_conf.xml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/intermine/intermine_simple.xml A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml Log Message: ----------- Merge pull request #6444 from blankenberg/intermine Intermine Enhancements Commit: d6578988002416f95e10ed3751e22b9ed287f565 https://github.com/galaxyproject/galaxy/commit/d6578988002416f95e10ed3751e2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #6466 from rhpvorderman/patch-2 Let data managers also use conda python. Commit: 3b3c18e0de83b535c2cd0235307eaeb821300196 https://github.com/galaxyproject/galaxy/commit/3b3c18e0de83b535c2cd0235307e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Merge pull request #6469 from nsoranzo/update_dependencies Update cliff and other related dependencies Commit: cfe6a9a67757150d7fce0d42f992cd1065cac9ee https://github.com/galaxyproject/galaxy/commit/cfe6a9a67757150d7fce0d42f992… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update documentation of the cloud copy from/to APIs reflecting previous refactoring. Commit: b61bb88daa3566c8b929d81e74f7cc9710875026 https://github.com/galaxyproject/galaxy/commit/b61bb88daa3566c8b929d81e74f7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Refactor api access to the cloud storage index. Commit: 068005fd6e1c6da73dd08a8c1f8e7c1fdbefe871 https://github.com/galaxyproject/galaxy/commit/068005fd6e1c6da73dd08a8c1f8e… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: A lib/galaxy/managers/cloud.py A lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #5835 from VJalili/cloud-api Copy data from a cloud-based storage to a Galaxy history Commit: a6173c023e4620430ffe3fc127750e0cb04355b1 https://github.com/galaxyproject/galaxy/commit/a6173c023e4620430ffe3fc12775… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/util/create_history_template.py Log Message: ----------- Fix bug noticed in sentry Commit: 9356ff88c3e6a786f494f2b2cba059fc24ea3f98 https://github.com/galaxyproject/galaxy/commit/9356ff88c3e6a786f494f2b2cba0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Rulebuilder: Special case auto URL schema detection for SRA inputs. @mblue9 has runs some tests and this prefix seems to serve the files considerably faster. Commit: ce866b9e2396da30f660206e10a7a375e244f583 https://github.com/galaxyproject/galaxy/commit/ce866b9e2396da30f660206e10a7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/util/create_history_template.py Log Message: ----------- Merge pull request #6474 from erasche/asdfasdf Fix bug noticed in sentry Commit: 60fc4baa4c3af7b32fd74dccd7aee1850196bc87 https://github.com/galaxyproject/galaxy/commit/60fc4baa4c3af7b32fd74dccd7ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #6351 from dpryan79/fixHandlerLogging Fix the --log-file option in the job handlers Commit: fb449b49906197fbb611833acf06ee13e5b34e48 https://github.com/galaxyproject/galaxy/commit/fb449b49906197fbb611833acf06… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M scripts/grt/upload.py Log Message: ----------- fix the logging init - properly initialiaze the logger - change level for some of the logs - add some debug and critical logs Commit: 390aedf8c8c28db739a78dc7c41e9275a735369b https://github.com/galaxyproject/galaxy/commit/390aedf8c8c28db739a78dc7c41e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M scripts/grt/grt.yml.sample M scripts/grt/upload.py Log Message: ----------- add all sample tool_conf data source tools to GRT sanitization Commit: ce09f53e24ff992d7f39fc94d01b75a1cbcee1fe https://github.com/galaxyproject/galaxy/commit/ce09f53e24ff992d7f39fc94d01b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-09 (Mon, 09 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6468 from jmchilton/allow_including_paths_in_inputs_json Allow including paths in inputs json files. Commit: 9f001807df651ec2792902aa82dd48ea0f937205 https://github.com/galaxyproject/galaxy/commit/9f001807df651ec2792902aa82dd… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Add more information to the dataset template Commit: 04db42343ce9840a078f0f0178a667e20c982b17 https://github.com/galaxyproject/galaxy/commit/04db42343ce9840a078f0f0178a6… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Address review comments Commit: 4bf2d60d6cdc1ef20a275aaf37d602c33005a865 https://github.com/galaxyproject/galaxy/commit/4bf2d60d6cdc1ef20a275aaf37d6… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Use horizontal <th> Commit: 8077d59fd9772ef6d1d9175e8edef4c8f95ace5a https://github.com/galaxyproject/galaxy/commit/8077d59fd9772ef6d1d9175e8ede… Author: Nadia Goué <nadia.goue(a)gmail.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Update common_startup_functions.sh Not to override tool_shed config file. Commit: 0860fdf134978f634707bf3f6aa18e1517f89bbb https://github.com/galaxyproject/galaxy/commit/0860fdf134978f634707bf3f6aa1… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #6480 from erasche/more-job-info Add more information to the dataset template Commit: ab760f5d27bb248a9c78d79a002b5ab2c68fa5d3 https://github.com/galaxyproject/galaxy/commit/ab760f5d27bb248a9c78d79a002b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- revert the datasource tool sanitation, set default # for export Commit: 6ca7db806b953a183fa192bcc0739540599348fa https://github.com/galaxyproject/galaxy/commit/6ca7db806b953a183fa192bcc073… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Fix for show params server error for https://github.com/galaxyproject/galaxy/pull/6480 Commit: c9df2ef9be73cf12644cb436cf7d4d23c7308174 https://github.com/galaxyproject/galaxy/commit/c9df2ef9be73cf12644cb436cf7d… Author: Qiang Gu <36086881+qiagu(a)users.noreply.github.com> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M test-data/configfile.json Log Message: ----------- Update configfile.json Commit: 038da2e3e65b8bb21fcf77a186f02db1aae563f2 https://github.com/galaxyproject/galaxy/commit/038da2e3e65b8bb21fcf77a186f0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-10 (Tue, 10 Jul 2018) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #6486 from blankenberg/show-param Fix for show params server error Commit: f25af28f6667fa3984fd64bd5c17d906c5e1510a https://github.com/galaxyproject/galaxy/commit/f25af28f6667fa3984fd64bd5c17… Author: Helena Rasche <erasche(a)users.noreply.github.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py Log Message: ----------- Merge pull request #6478 from martenson/telescope-logging GRT: fix the upload logging init Commit: f33770096c038d420696c822bd3ab8c397156f14 https://github.com/galaxyproject/galaxy/commit/f33770096c038d420696c822bd3a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6481 from nagoue/patch-1 Update common_startup_functions.sh Commit: 239c7c920634c1074505cb9a2ebb1b263b852c2d https://github.com/galaxyproject/galaxy/commit/239c7c920634c1074505cb9a2ebb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Optimize setting large numbers of HIDs for collection outputs. Commit: 6fc937a3d8b46f3620b73f3e057d9b6ba5422540 https://github.com/galaxyproject/galaxy/commit/6fc937a3d8b46f3620b73f3e057d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6374 from gregvonkuster/multi_dynamic_select Fix for rendering multiple dependent dynamic select lists Commit: 53709df8cfb8fd384d60d221786c4167d7aa9658 https://github.com/galaxyproject/galaxy/commit/53709df8cfb8fd384d60d221786c… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M test-data/configfile.json Log Message: ----------- Revert "Update configfile.json" This reverts commit c9df2ef9be73cf12644cb436cf7d4d23c7308174. Commit: 62482dd9fda547ba22391cd210518316a0bbbf76 https://github.com/galaxyproject/galaxy/commit/62482dd9fda547ba22391cd21051… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/WorkflowImport.vue Log Message: ----------- Use bootstrap vue classes for workflow import form Commit: d91ad7d6275cf004b670a11a23a6258e51500c89 https://github.com/galaxyproject/galaxy/commit/d91ad7d6275cf004b670a11a23a6… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- small improvement to the too xsd docs Commit: cabd6a11bed38eaa69175a8505c4f6071478bd5f https://github.com/galaxyproject/galaxy/commit/cabd6a11bed38eaa69175a8505c4… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- added <output> to snippet Commit: 5bac0eff82d5fa4931834082baeb220c701fd5b5 https://github.com/galaxyproject/galaxy/commit/5bac0eff82d5fa4931834082baeb… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Update galaxy.xsd Commit: b0693203a1ed4d755f6fac261dd98bdddb6da6b2 https://github.com/galaxyproject/galaxy/commit/b0693203a1ed4d755f6fac261dd9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Allow : in tag values for PJA setting. Based on #5457, certain paths to creating tag values with : must already work - just not when parsing from a raw string I guess. Commit: b45ce119401b6ef36a19c1bd21c84856ebc074e2 https://github.com/galaxyproject/galaxy/commit/b45ce119401b6ef36a19c1bd21c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Centralize logic for determining which tags get auto-propagated. Commit: 0280713c43442a412cf6294b57caf1c12160322f https://github.com/galaxyproject/galaxy/commit/0280713c43442a412cf6294b57ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Auto-propagate group tags - the way name tags are propagated. Commit: 0674af824d2ccfa8cdc924b6387e0112912bbb47 https://github.com/galaxyproject/galaxy/commit/0674af824d2ccfa8cdc924b6387e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6490 from bernt-matthias/topic/xsd-doc-discover-improvement small improvement to the too xsd docs regarding discovered_datasets Commit: 2cccf7c23fc57e4e633af2b1703d7d4a034f5850 https://github.com/galaxyproject/galaxy/commit/2cccf7c23fc57e4e633af2b1703d… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6491 from jmchilton/auto_group_tags Implement ``group:`` tags (toward multi-factor analysis with group tagging) Commit: 4da67218c166374016c239397db2c10f3a388e66 https://github.com/galaxyproject/galaxy/commit/4da67218c166374016c239397db2… Author: takadonet <philipmabon(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Added fix to ensure that original ftp files that have been uploaded are purged if set in galaxy.yml with flag ftp_upload_purge. Address issue #6492 Commit: c7c7691c98b2ef2cdeee5bf7661b9415e6eebf86 https://github.com/galaxyproject/galaxy/commit/c7c7691c98b2ef2cdeee5bf7661b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue A 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lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/web_util.py M manage_db.sh M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/api/common.py M scripts/bootstrap_history.py M scripts/check_python.py M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh A scripts/docker_swarm_manager.py M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/maintenance.sh A scripts/plugin_staging.py A static/images/fonts/FontAwesome.otf M static/images/fonts/fontawesome-webfont.eot A static/images/fonts/fontawesome-webfont.svg M static/images/fonts/fontawesome-webfont.ttf M static/images/fonts/fontawesome-webfont.woff A static/images/fonts/fontawesome-webfont.woff2 M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css M static/welcome.html.sample R templates/admin/impersonate.mako R templates/admin/view_data_tables_registry.mako R templates/admin/view_datatypes_registry.mako M templates/base/base_panels.mako M templates/display_common.mako M templates/ind_share_base.mako R templates/sharing_base.mako M templates/show_params.mako M templates/tagging_common.mako M templates/user/login.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/galaxy.panels.mako R templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako A test-data/1.tiff A test-data/filter1_in6.bed A test-data/filter1_test6.bed A test-data/rules/treated1fb.txt A test-data/rules/treated2fb.txt A test-data/rules/treated3fb.txt M test-data/rules/uniprot.json A test-data/rules/untreated1fb.txt A test-data/rules/untreated2fb.txt A test-data/rules/untreated3fb.txt A test-data/rules/untreated4fb.txt A test-data/sort_out1.bed A test-data/sort_out2.bed A test-data/sort_out3.tab A test-data/sort_out4.sam M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py A test/base/data/rules_dsl_spec.yml M test/base/populators.py A test/base/rules_test_data.py A test/base/workflow_fixtures.py M test/base/workflows_format_2/main.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml A test/functional/tools/collection_type_source_map_over.xml A test/functional/tools/empty_select.xml M test/functional/tools/for_workflows/cat_collection.xml A test/functional/tools/identifier_single_in_repeat.xml A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/job_properties.xml M test/functional/tools/multi_data_optional.xml A test/functional/tools/output_action_change_format_paired.xml R test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.py A test/unit/datatypes/test_datatypes_registry.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_params.py M test/unit/test_galaxy_mapping.py M test/unit/test_remote_shell.py A test/unit/test_rule_utils.py M test/unit/test_security_helper.py A test/unit/test_security_passwords.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml M tools/data_source/upload.py M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/cutWrapper.pl M tools/filters/sorter.py M tools/filters/sorter.xml M tools/filters/wig_to_bigwig.xml M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.py M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into upload_to_cloud Commit: 5b1b4314a3ac140779146286f4dc2cfd5fad6807 https://github.com/galaxyproject/galaxy/commit/5b1b4314a3ac140779146286f4dc… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Refactor the API end point from `upload` to `copy_to`. Commit: 97fd2088faa0eda1275448d7552a47c801ab9a4b https://github.com/galaxyproject/galaxy/commit/97fd2088faa0eda1275448d7552a… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Add cloud storage `copy_to` API. Commit: 7e8be2ff53e9f6f781618c2182d9b3d58675c47e https://github.com/galaxyproject/galaxy/commit/7e8be2ff53e9f6f781618c2182d9… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Add cloud-based storage `copy-to` manager. Commit: 30feac0c4ca4488caa4d7d00beee698a6e465cdf https://github.com/galaxyproject/galaxy/commit/30feac0c4ca4488caa4d7d00beee… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #6494 from phac-nml/fix_ftp_upload_purge Fix ftp_upload_purge in galaxy.yml Commit: 89c62229c5af00ecc05df596129a53473a96db38 https://github.com/galaxyproject/galaxy/commit/89c62229c5af00ecc05df596129a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- remove dead link I did not find the original post Commit: fa43f2c2b2e7f047b2d8a27b9bca313f67637c75 https://github.com/galaxyproject/galaxy/commit/fa43f2c2b2e7f047b2d8a27b9bca… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #6365 from moskalenko/dev Add period to the list of allowed characters in user names Commit: 2abb01b6cbb11f28a7f6a838c97b8540b62e45fb https://github.com/galaxyproject/galaxy/commit/2abb01b6cbb11f28a7f6a838c97b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/web/base/controller.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: b3f1a7cf9cdc29bcc52a6d7f5c35fc6ecfa02878 https://github.com/galaxyproject/galaxy/commit/b3f1a7cf9cdc29bcc52a6d7f5c35… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Doc style updates; copy-to return dict with copied datasets Commit: 4a8857e4f9daf15101270724375dad14c4897e6c https://github.com/galaxyproject/galaxy/commit/4a8857e4f9daf15101270724375d… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6078 from VJalili/upload_to_cloud Upload data to a cloud-based storage Commit: 59bd1ba20a16ecf50586abec4b637c133eefb2a7 https://github.com/galaxyproject/galaxy/commit/59bd1ba20a16ecf50586abec4b63… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M test/unit/managers/test_HistoryManager.py Log Message: ----------- Add unittest that catches https://github.com/galaxyproject/galaxy/issues/6495 Commit: 4610258b9c2fde78fb056bb9183eb67d12ec00a4 https://github.com/galaxyproject/galaxy/commit/4610258b9c2fde78fb056bb9183e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix job resume from history menu Commit: bc90d0a4359194fc79b5102f4e88a0cd9a36b1a8 https://github.com/galaxyproject/galaxy/commit/bc90d0a4359194fc79b5102f4e88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-13 (Fri, 13 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #6498 from mvdbeek/fix_resume_from_history_panel Fix resume from history panel Commit: 2097c9db787bc9803b391c9286a2a3f3561ba293 https://github.com/galaxyproject/galaxy/commit/2097c9db787bc9803b391c9286a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-14 (Sat, 14 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Remove redundant endpoint to edit user info Commit: e7bfd6c552ec6d65338bf9319cfcb9bca4e7264a https://github.com/galaxyproject/galaxy/commit/e7bfd6c552ec6d65338bf9319cfc… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-07-14 (Sat, 14 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml Log Message: ----------- Set detect_errors to aggressive As per the [documentation](https://docs.galaxyproject.org/en/master/dev/schema.html#too… leaving the tool without `detect_errors` and without a `profile` set to greater than or equal to `16.04` invokes the old behaviour where any output to `stderr` denotes failure. When provided with a BAM format input file and the `-g` option, `bedtools` outputs a warning to `stderr` stating that it will ignore the provided genome, triggering a tool failure. Commit: a72954dfba7c69195a6845b4111d4a350e69d54f https://github.com/galaxyproject/galaxy/commit/a72954dfba7c69195a6845b4111d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #6496 from martenson/remove-dead-link remove dead link Commit: f9ba8d3823854e00e321b7776056d381132b0346 https://github.com/galaxyproject/galaxy/commit/f9ba8d3823854e00e321b7776056… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_dataset_collections.py M test/api/test_tools_upload.py Log Message: ----------- Allow setting tags on targets & contents in data fetch API. Rebased with default argument handling improvements suggested by Marius. Commit: 489839cb638df8648041cc6197a61faf9cfc7a6a https://github.com/galaxyproject/galaxy/commit/489839cb638df8648041cc6197a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Integrate tagging into the rule builder. - Allow specifying name tags, group tags, and "general" tags on stand-alone datasets and collection content datasets. - Allow reusing the collection name as a name tag during upload for the whole collection. In this context I think the name tag is especially useful and will typically be the same name as the collection so the UI is kept simple by making it a checkbox. Commit: 6da93fc07102d98a5f996ec9694e1465e2d45c3c https://github.com/galaxyproject/galaxy/commit/6da93fc07102d98a5f996ec9694e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6476 from jmchilton/sra_special_case Rulebuilder: Special case auto URL schema detection for SRA inputs. Commit: 8a85270629b80b4c4b306a9130293f25dc7a2da6 https://github.com/galaxyproject/galaxy/commit/8a85270629b80b4c4b306a913029… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix and docs for advanced container options in job_conf.xml. These options were added in #2790 but you know how @jmchilton is about documentation. The bug fix is to fix selecting the first valid option if multiple ones are present instead of just the first option which may be invalid given the other configured destination parameters. Commit: d661d99b12ede64280dce8a597e7845abfd6dd10 https://github.com/galaxyproject/galaxy/commit/d661d99b12ede64280dce8a597e7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #6501 from guerler/admin_user_info Remove redundant/duplicate endpoint to edit user info Commit: f8210d89ace977ec8857ef7205a778b5af0b680a https://github.com/galaxyproject/galaxy/commit/f8210d89ace977ec8857ef7205a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M client/galaxy/scripts/components/WorkflowImport.vue M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix workflow import Selenium tests for #6489. Commit: 86922d65572ee32b1498ccf422f3f52eb2405386 https://github.com/galaxyproject/galaxy/commit/86922d65572ee32b1498ccf422f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/WorkflowImport.vue Log Message: ----------- Explicitly specify bootstrapvue (works currently either way, due to bundling and the way these are included, but it might not forever -- best to be explicit) Commit: 9f352f77c0c7a747295ab9aa8e96afee9b13304a https://github.com/galaxyproject/galaxy/commit/9f352f77c0c7a747295ab9aa8e96… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/WorkflowImport.vue M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #6489 from guerler/workflow_import Use bootstrap vue classes for workflow import form Commit: 66af9ce96111685e8fe22c48aa7d0e6471027c64 https://github.com/galaxyproject/galaxy/commit/66af9ce96111685e8fe22c48aa7d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/web/framework/base.py M tools/data_source/upload.py Log Message: ----------- Make upload tool python3 compatible Commit: 8ce663addbb9f8cde2bd411ab45f097cffa017e8 https://github.com/galaxyproject/galaxy/commit/8ce663addbb9f8cde2bd411ab45f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Consistently use webob.compat.cgi_FieldStorage This works around bugs in python3 cgi.FieldStorage. Commit: a729faab8ba5e82e33baa837e804afd747532a9d https://github.com/galaxyproject/galaxy/commit/a729faab8ba5e82e33baa837e804… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/web/framework/middleware/batch.py Log Message: ----------- Fix batch api middleware Commit: 28cca49747d29bacbb0751df34475a47cd045cd9 https://github.com/galaxyproject/galaxy/commit/28cca49747d29bacbb0751df3447… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile Log Message: ----------- Remove WebOb pin in Pipfile Commit: ca8547ce1d729249f8ff07962e8e96d4f017a556 https://github.com/galaxyproject/galaxy/commit/ca8547ce1d729249f8ff07962e8e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Inject `self` and `obj` into global scope The list comprehension code in `transform_lines` gets its own local scope, so just copying the local scope into the eval functions local scope doesn't work. Commit: c5fa023c26fafa53ea9da477243b13b3e6b85278 https://github.com/galaxyproject/galaxy/commit/c5fa023c26fafa53ea9da477243b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M config/plugins/webhooks/demo/tour_generator/__init__.py M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Use webob.compat's FieldStorage in the remaining codebase Commit: a65cd29c366035fb8b26e2274046e8c96e3cab33 https://github.com/galaxyproject/galaxy/commit/a65cd29c366035fb8b26e2274046… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Patch webob.compat.cgi_FieldStorage instead of overwrite it Commit: c6c34beb812a966c224c30c17e675d6dfd278248 https://github.com/galaxyproject/galaxy/commit/c6c34beb812a966c224c30c17e67… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M tox.ini Log Message: ----------- Add py34-unit to default tox tests Commit: 051bc950731365b580d3569be8c0481f8bcecf86 https://github.com/galaxyproject/galaxy/commit/051bc950731365b580d3569be8c0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #6503 from jmchilton/destination_container_target_fixes Fix and docs for advanced container options in job_conf.xml. Commit: 9d886c866da5a04e51e5ff6887867393a009257d https://github.com/galaxyproject/galaxy/commit/9d886c866da5a04e51e5ff688786… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Use six.moves for urlparse import Commit: 61fdb0ba831bc5dd9ed17b238730264e560bfbcd https://github.com/galaxyproject/galaxy/commit/61fdb0ba831bc5dd9ed17b238730… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Return a json blob containing redirect URI in OIDC login controller instead of redirecting users. Commit: 43c9c9624a4f5ed7f27c0bdc576dcf6467287633 https://github.com/galaxyproject/galaxy/commit/43c9c9624a4f5ed7f27c0bdc576d… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-16 (Mon, 16 Jul 2018) Changed paths: M config/openid_conf.xml.sample R openid/aol.xml Log Message: ----------- Remove deprecated AOL openid backend. Commit: 347e3124f4628cde3ad9f6ba169ecf1d2a0a0e4e https://github.com/galaxyproject/galaxy/commit/347e3124f4628cde3ad9f6ba169e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M config/plugins/webhooks/demo/tour_generator/__init__.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/tool_shed/api/repositories.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merge pull request #6467 from mvdbeek/fix_upload_tool_py3 Make upload tool python3 compatible Commit: 188015b138307f08ad75078466587183527e28c5 https://github.com/galaxyproject/galaxy/commit/188015b138307f08ad7507846658… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml Log Message: ----------- Merge pull request #6502 from pvanheus/patch-3 Fix bam to bigwig error detection. Commit: 2f9520e6a2394b528b3a31a541cc33fb70dee2fa https://github.com/galaxyproject/galaxy/commit/2f9520e6a2394b528b3a31a541cc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M config/openid_conf.xml.sample R openid/aol.xml Log Message: ----------- Merge pull request #6505 from VJalili/remove_deprecated_openid_backends Remove the deprecated AOL openid backend. Commit: 3c4eb54a9a877ff213f22315019ae17b33da5c09 https://github.com/galaxyproject/galaxy/commit/3c4eb54a9a877ff213f22315019a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #6394 from jmchilton/collection_opt Optimize setting large numbers of HIDs for collection outputs. Commit: 31d331379188e11fe95cdbfe5d8f1035dd511b63 https://github.com/galaxyproject/galaxy/commit/31d331379188e11fe95cdbfe5d8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Minor typo in new text (or -> of), and two bonus old typo fixes. Commit: 4719c4a3f1296d179e5e1dc107156ec5fae305ed https://github.com/galaxyproject/galaxy/commit/4719c4a3f1296d179e5e1dc10715… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_dataset_collections.py M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #6499 from jmchilton/upload_tags_api Allow setting tags on targets & contents in data fetch API. Commit: 26b5891908757648eed5ce9be3cccbe7104ad7d3 https://github.com/galaxyproject/galaxy/commit/26b5891908757648eed5ce9be3cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Client-format Commit: e8b437dfd8e07f88f48a5872ce18693343f33573 https://github.com/galaxyproject/galaxy/commit/e8b437dfd8e07f88f48a5872ce18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-17 (Tue, 17 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge branch 'rule_builder_tags' into dev Commit: 163018c35177a9356a7e6f789ee719f3be5d861e https://github.com/galaxyproject/galaxy/commit/163018c35177a9356a7e6f789ee7… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- keep default Galaxy dataset name of pasted content to Pasted Entry Commit: 6c668774f7cac2098bc32a3123471a0eb62f384c https://github.com/galaxyproject/galaxy/commit/6c668774f7cac2098bc32a312347… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-18 (Wed, 18 Jul 2018) Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 9f73bc89854420a4f28188fbcefad7999689ca6b https://github.com/galaxyproject/galaxy/commit/9f73bc89854420a4f28188fbcefa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M test/api/test_dataset_collections.py Log Message: ----------- Repsonse->response Commit: 5171b9bd497cb07c3e7ab940230c97916ab29f6a https://github.com/galaxyproject/galaxy/commit/5171b9bd497cb07c3e7ab940230c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M test/base/populators.py M test/integration/test_scripts.py Log Message: ----------- A couple more typos. Commit: e794443f488649c8bb1d1d0825e4a113dacee26c https://github.com/galaxyproject/galaxy/commit/e794443f488649c8bb1d1d0825e4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/data_fetch.xml M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_dataset_collections.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/populators.py M test/integration/test_scripts.py Log Message: ----------- Merge pull request #6294 from jmchilton/better_tool_tests Upload collections directly for tests. Commit: 0a2f77c4926c51f17541492d9ada6971f865e09e https://github.com/galaxyproject/galaxy/commit/0a2f77c4926c51f17541492d9ada… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tools.js Log Message: ----------- Minor formatting. Commit: adb082a805d28985d4e24c7700417f4822f8acfa https://github.com/galaxyproject/galaxy/commit/adb082a805d28985d4e24c770041… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js Log Message: ----------- Merge branch 'soft-page-change' into dev Commit: 8d687bc3b7e2e4496b464e28c0961ba9fe2ad691 https://github.com/galaxyproject/galaxy/commit/8d687bc3b7e2e4496b464e28c096… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Cache chrom_info generation when mapping over collections. Eliminates several SQL queries per job and 20ms off the time it takes to create a job (about 10% for simple jobs). Timings below based on a branch with other optimizations so this will probably represent a smaller percent of runtime in dev until it catches up but the idea is pretty self contained unlike some other work in local my branch. Before chrom_info cache: ``` galaxy.tools.actions INFO 2018-07-18 14:59:35,041 Collected inputs for tool execute (14.586 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,069 setup execute (28.450 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,071 Handled output named out_file1 for tool cat_data_and_sleep (1.082 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,077 Added output datasets to history (5.986 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,104 Flushed output datasets (27.165 ms) ... galaxy.tools.actions INFO 2018-07-18 14:59:35,183 Collected inputs for tool execute (9.299 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,210 setup execute (26.842 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,211 Handled output named out_file1 for tool cat_data_and_sleep (1.375 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,217 Added output datasets to history (5.168 ms) galaxy.tools.actions INFO 2018-07-18 14:59:35,244 Flushed output datasets (27.395 ms) ... galaxy.model.orm.engine_factory INFO 2018-07-18 14:59:36,033 Executed [417] SQL requests in for web request [/api/tools] (807.188749(s)ms) ``` ``` galaxy.tools.actions INFO 2018-07-18 14:58:20,505 Collected inputs for tool execute (8.643 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,533 setup execute (27.325 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,534 Handled output named out_file1 for tool cat_data_and_sleep (1.201 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,539 Added output datasets to history (4.913 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,565 Flushed output datasets (25.520 ms) ... galaxy.tools.actions INFO 2018-07-18 14:58:20,641 Collected inputs for tool execute (7.044 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,669 setup execute (27.744 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,670 Handled output named out_file1 for tool cat_data_and_sleep (0.990 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,674 Added output datasets to history (4.727 ms) galaxy.tools.actions INFO 2018-07-18 14:58:20,701 Flushed output datasets (26.265 ms) ... galaxy.model.orm.engine_factory INFO 2018-07-18 14:58:21,480 Executed [417] SQL requests in for web request [/api/tools] (796.465635(s)ms) ``` After chrom_info cache: ``` ... galaxy.tools.actions INFO 2018-07-18 14:56:21,486 Collected inputs for tool execute (9.792 ms) galaxy.tools.actions INFO 2018-07-18 14:56:21,487 setup execute (0.399 ms) galaxy.tools.actions INFO 2018-07-18 14:56:21,488 Handled output named out_file1 for tool cat_data_and_sleep (1.068 ms) galaxy.tools.actions INFO 2018-07-18 14:56:21,497 Added output datasets to history (9.218 ms) galaxy.tools.actions INFO 2018-07-18 14:56:21,522 Flushed output datasets (24.905 ms) ... galaxy.model.orm.engine_factory INFO 2018-07-18 14:56:22,352 Executed [381] SQL requests in for web request [/api/tools] (684.080839(s)ms) ``` ``` galaxy.tools.actions INFO 2018-07-18 14:55:27,979 Collected inputs for tool execute (8.400 ms) galaxy.tools.actions INFO 2018-07-18 14:55:27,979 setup execute (0.462 ms) galaxy.tools.actions INFO 2018-07-18 14:55:27,980 Handled output named out_file1 for tool cat_data_and_sleep (1.208 ms) galaxy.tools.actions INFO 2018-07-18 14:55:27,991 Added output datasets to history (10.558 ms) galaxy.tools.actions INFO 2018-07-18 14:55:28,016 Flushed output datasets (24.182 ms) ... galaxy.model.orm.engine_factory INFO 2018-07-18 14:55:28,838 Executed [381] SQL requests in for web request [/api/tools] (714.353323(s)ms) ``` Commit: 20f10fe6db8ceb73c843c2a5609ab5fa5cf2f4ba https://github.com/galaxyproject/galaxy/commit/20f10fe6db8ceb73c843c2a5609a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py A test-data/11.tabular A test-data/configfile.json A test/functional/tools/column_param_configfile.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6389 from qiagu/data_column_1 fix data_column cast error when multiple is false Commit: 1b52d247b4d12a5a000c72cf8c78f6856562d6af https://github.com/galaxyproject/galaxy/commit/1b52d247b4d12a5a000c72cf8c78… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-19 (Thu, 19 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Fix a bug in cloud storage api calling a non-existing function from manager. Commit: d2adf34f96e3ffc96ef5b0a63198ab525a5bc602 https://github.com/galaxyproject/galaxy/commit/d2adf34f96e3ffc96ef5b0a63198… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-19 (Thu, 19 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Use signed URLs to copy data from cloud to Galaxy, instead of staging them. Commit: 8f35166746f9f7b155bf98b37e41278d7f3a2389 https://github.com/galaxyproject/galaxy/commit/8f35166746f9f7b155bf98b37e41… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-19 (Thu, 19 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update error message of failing to copy from cloud to Galaxy. Commit: 13ae24ce01c22078a2d7a16a730bd9c99e301c98 https://github.com/galaxyproject/galaxy/commit/13ae24ce01c22078a2d7a16a730b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-19 (Thu, 19 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Add `SIGNED_URL_TTL` in cloud storage manager. Commit: 423c747a1f4fa898dcd80030c9402d8b6a232848 https://github.com/galaxyproject/galaxy/commit/423c747a1f4fa898dcd80030c940… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M client/galaxy/scripts/qunit/tests/masthead_tests.js Log Message: ----------- Fix failing qunit tests in dev. minor Commit: eeb6722fe7f7f96ee3e459a2a66ae052c1d3517c https://github.com/galaxyproject/galaxy/commit/eeb6722fe7f7f96ee3e459a2a66a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- More optimized HID generation - in one commit instead of two. Before HID optimization: galaxy.tools.actions INFO 2018-07-18 11:10:20,164 Added output datasets to history (14.193 ms) galaxy.tools.actions INFO 2018-07-18 11:10:20,416 Added output datasets to history (17.583 ms) galaxy.tools.actions INFO 2018-07-18 11:10:20,675 Added output datasets to history (19.875 ms) galaxy.model.orm.engine_factory INFO 2018-07-18 11:10:21,734 Executed [445] SQL requests in for web request [/api/tools] (1036.418676ms) After HID optimization: galaxy.tools.actions INFO 2018-07-18 11:13:41,855 Added output datasets to history (6.049 ms) galaxy.tools.actions INFO 2018-07-18 11:13:42,018 Added output datasets to history (7.192 ms) galaxy.tools.actions INFO 2018-07-18 11:13:42,184 Added output datasets to history (10.277 ms) galaxy.tools.actions INFO 2018-07-18 11:13:42,344 Added output datasets to history (5.800 ms) galaxy.model.orm.engine_factory INFO 2018-07-18 11:13:43,179 Executed [434] SQL requests in for web request [/api/tools] (818.706274ms) Commit: af4becedd2736e3bae7790d98367a341b021faff https://github.com/galaxyproject/galaxy/commit/af4becedd2736e3bae7790d98367… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- Rebuild CSS. If we're going to keep this file in the tree it should be updated against current sources then I believe. Commit: b39bebb6a694af2cd50cee8c416443e7dcb501cf https://github.com/galaxyproject/galaxy/commit/b39bebb6a694af2cd50cee8c4164… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #6515 from jmchilton/chrom_info_cache Cache chrom_info generation when mapping over collections. Commit: c7dd6c2a00f59c053ffbccfc5d6ca52f00fde0a8 https://github.com/galaxyproject/galaxy/commit/c7dd6c2a00f59c053ffbccfc5d6c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- Merge pull request #6521 from jmchilton/css_rebuild Rebuild CSS against latest dev Commit: 5a72bfdf8617b2a79beeab8f243f5b41b71cdef7 https://github.com/galaxyproject/galaxy/commit/5a72bfdf8617b2a79beeab8f243f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M client/galaxy/scripts/qunit/tests/masthead_tests.js Log Message: ----------- Merge pull request #6520 from jmchilton/failing_qunit_tests Fix failing qunit tests in dev. Commit: 3b629f02933cc20ee3af779f1dd90219f73cda5f https://github.com/galaxyproject/galaxy/commit/3b629f02933cc20ee3af779f1dd9… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #6516 from jmchilton/hid_opt More optimized HID generation - in one commit instead of two. Commit: a146aeac63fa9513f0232f69337a782a48a2e17f https://github.com/galaxyproject/galaxy/commit/a146aeac63fa9513f0232f69337a… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-20 (Fri, 20 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix lint issues: remove unused imports and add a missing blank line. Commit: 4d8b13d0e54f31679b9adcd58a045f01efee3f30 https://github.com/galaxyproject/galaxy/commit/4d8b13d0e54f31679b9adcd58a04… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/tools/data_fetch.py M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Handle pasted content in fetch API. Unlike upload 1.0, use different 'src' types to distinguish between URLs and pasted content - in the abstract this is better because it is more structured and practically this allows 'pasting' spreadsheets that start with URLs for instance (that is sometimes useful). Commit: 8c3d7f60f4911183f74b60c36caa949b38867bf3 https://github.com/galaxyproject/galaxy/commit/8c3d7f60f4911183f74b60c36caa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/web/stack/transport.py Log Message: ----------- Removal of unreachable exit() Commit: dd6b6436c845752c50d0f376300bcbadf8ea196e https://github.com/galaxyproject/galaxy/commit/dd6b6436c845752c50d0f376300b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/webapp.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Use cached database identity to avoid certain DB requests when creating jobs. When creating thousands of jobs for large database transactions - previously Galaxy would query the database thousands of times for the same history id, user id, and session id. Commit: 2d1471efb40c023c606286ab21527811b25bed2a https://github.com/galaxyproject/galaxy/commit/2d1471efb40c023c606286ab2152… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/web/stack/transport.py Log Message: ----------- Merge pull request #6529 from dannon/unreachable_code Removal of unreachable exit() Commit: 4f1e2bf4f862c87d65be59186a053fbd6bc83866 https://github.com/galaxyproject/galaxy/commit/4f1e2bf4f862c87d65be59186a05… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml Log Message: ----------- Merge branch 'release_18.05' into dev Commit: be4e4d3dae178243db0ca6b6ddd6f68bbe947d21 https://github.com/galaxyproject/galaxy/commit/be4e4d3dae178243db0ca6b6ddd6… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Rename API: from `copy-from` to `upload`, and update docs. Commit: a6cf909fd064bb37491c0b8e44090ef814dc51aa https://github.com/galaxyproject/galaxy/commit/a6cf909fd064bb37491c0b8e4409… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Rename API: from `copy-to` to `download`, and update docs. Commit: 3e7bfc8069c20057d0fc8fff81cd0c10fe8617f0 https://github.com/galaxyproject/galaxy/commit/3e7bfc8069c20057d0fc8fff81cd… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Append `job_errors` to cloud upload api error messages. Commit: 0dde5d3253e81af3beb13e515f765b9cdcb10771 https://github.com/galaxyproject/galaxy/commit/0dde5d3253e81af3beb13e515f76… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Update cloud storage Upload API and manager to take a list of objects. Commit: 99f9d72fd462b51e67e97157a0445fcd576ca660 https://github.com/galaxyproject/galaxy/commit/99f9d72fd462b51e67e97157a044… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- remove an extra blank line in cloud api. Commit: 46e18dc2230ae618c000e34dc56c9619b43d768c https://github.com/galaxyproject/galaxy/commit/46e18dc2230ae618c000e34dc56c… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Inlined upload_tool pointer. Commit: 559730c950d5bd51882acb072814846b5b52bcb8 https://github.com/galaxyproject/galaxy/commit/559730c950d5bd51882acb072814… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Add `input_args` to cloud upload API and manager. Commit: 1a8be699d9f4c08c5865fb327d8b2b265ad87ac8 https://github.com/galaxyproject/galaxy/commit/1a8be699d9f4c08c5865fb327d8b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Make static the `_configure_provider` method in cloud storage manager. Commit: 87959ecb8fb5250e0ddae3cd5bc51e819308087e https://github.com/galaxyproject/galaxy/commit/87959ecb8fb5250e0ddae3cd5bc5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Change the default value of `input_args` from empty dict to None. Commit: 87320ccd1275c1ae7dbbaf234e73a211f81325b8 https://github.com/galaxyproject/galaxy/commit/87320ccd1275c1ae7dbbaf234e73… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update method docs in cloud manager. Commit: e697ec51b4dab8db9827287e3dcb1ad911a7c088 https://github.com/galaxyproject/galaxy/commit/e697ec51b4dab8db9827287e3dcb… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug handling missing `input_args`. Commit: 6e3cb8888a4b0cd88d34d0a47b13b1cc268b0566 https://github.com/galaxyproject/galaxy/commit/6e3cb8888a4b0cd88d34d0a47b13… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Surround an object `get` in cloud storage manager in a try-catch block. Commit: e8cf719d4e4360c79814fd591c6aabd828b4b071 https://github.com/galaxyproject/galaxy/commit/e8cf719d4e4360c79814fd591c6a… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6519 from VJalili/improve_cloud_storage_api Improvements to Cloud Storage Manager Commit: 63c2ffd3bae58fc4d37edf6149b79cf51de8a37c https://github.com/galaxyproject/galaxy/commit/63c2ffd3bae58fc4d37edf6149b7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: A test/unit/test_model_copy.py Log Message: ----------- Implement simple history copy unit tests. Commit: fe3e284bf9d17c2274cfac8b80b3c11b5e52297b https://github.com/galaxyproject/galaxy/commit/fe3e284bf9d17c2274cfac8b80b3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M lib/galaxy/managers/hdcas.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Fix HDCA annotations. Backend for these simply did not work. Commit: 9780d069c8646fb4f02de848d62159680d95ae79 https://github.com/galaxyproject/galaxy/commit/9780d069c8646fb4f02de848d621… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py Log Message: ----------- Optimized dataset copying during histories. Use only one unqualified flush to prevent constant repeated invalidation off all SA just to get a single ID for a new object. For a simple history with 10 datasets - this reduces the copy() time in testing from 260 ms to 70ms. Some random times: Before optimization: 10 datasets - with a MetadataFile metadata parameter history copied (390.457 ms) history copied (398.501 ms) history copied (360.997 ms) 10 datasets - without a MetadataFile metadata parameter history copied (291.972 ms) history copied (276.479 ms) history copied (272.323 ms) 10 datasets - with a MetadataFile metadata parameter history copied (230.171 ms) history copied (218.215 ms) history copied (226.205 ms) 10 datasets - without a MetadataFile metadata parameter history copied (66.360 ms) history copied (70.126 ms) history copied (65.166 ms) Commit: 45b2b7f434fc1bd1e646c72c6024bacc482a8b8e https://github.com/galaxyproject/galaxy/commit/45b2b7f434fc1bd1e646c72c6024… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M 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config/plugins/visualizations/drawrna/src/drawrnajs/utils/spectrum.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/style.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/annoview.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/optspanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/seqpanel.js A config/plugins/visualizations/drawrna/src/drawrnajs/views/vispanel.js A config/plugins/visualizations/drawrna/src/script.js A config/plugins/visualizations/drawrna/static/logo.png A config/plugins/visualizations/drawrna/static/script.js A config/plugins/visualizations/example/config/example.xml A config/plugins/visualizations/example/package.json A config/plugins/visualizations/example/src/script.js A config/plugins/visualizations/example/static/logo.png A config/plugins/visualizations/example/static/script.js M config/plugins/visualizations/graphviz/config/graphviz.xml R config/plugins/visualizations/graphviz/static/js/jquery.qtip.js 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config/plugins/visualizations/hivtrace/static/hivtrace.js A config/plugins/visualizations/hivtrace/static/hivtrace.js.map A config/plugins/visualizations/hivtrace/static/logo.png A config/plugins/visualizations/hivtrace/static/vendor.js A config/plugins/visualizations/hivtrace/static/vendor.js.map A config/plugins/visualizations/hivtrace/templates/index.mako A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml A config/plugins/visualizations/jqplot/jqplot_bar/package.json A config/plugins/visualizations/jqplot/jqplot_bar/src/script.js A config/plugins/visualizations/jqplot/jqplot_bar/static/logo.png A config/plugins/visualizations/jqplot/jqplot_bar/static/script.css A config/plugins/visualizations/jqplot/jqplot_bar/static/script.js A config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml A config/plugins/visualizations/jqplot/jqplot_box/static/logo.png A config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml A config/plugins/visualizations/jqplot/jqplot_histogram/static/logo.png A config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml A config/plugins/visualizations/jqplot/jqplot_line/static/logo.png A config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml A config/plugins/visualizations/jqplot/jqplot_scatter/static/logo.png A config/plugins/visualizations/msa/config/msa.xml A config/plugins/visualizations/msa/package.json A config/plugins/visualizations/msa/src/msa.js A config/plugins/visualizations/msa/static/logo.png A config/plugins/visualizations/msa/static/script.js A config/plugins/visualizations/ngl/config/ngl.xml A config/plugins/visualizations/ngl/package.json A config/plugins/visualizations/ngl/src/ngl.js A config/plugins/visualizations/ngl/src/viewer.js A config/plugins/visualizations/ngl/static/logo.png A config/plugins/visualizations/ngl/static/ngl.js A config/plugins/visualizations/nvd3/nvd3_bar/.babelrc A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml A config/plugins/visualizations/nvd3/nvd3_bar/package.json A config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar/static/logo.png A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js A config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml A config/plugins/visualizations/nvd3/nvd3_bar_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml A config/plugins/visualizations/nvd3/nvd3_histogram/static/logo.png A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml A config/plugins/visualizations/nvd3/nvd3_horizontal/static/logo.png A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml A config/plugins/visualizations/nvd3/nvd3_line/static/logo.png A config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml A config/plugins/visualizations/nvd3/nvd3_line_focus/static/logo.png A config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml A config/plugins/visualizations/nvd3/nvd3_pie/static/logo.png A config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml A config/plugins/visualizations/nvd3/nvd3_scatter/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/static/logo.png A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/static/logo.png A config/plugins/visualizations/phylocanvas/config/phylocanvas.xml A config/plugins/visualizations/phylocanvas/package.json A config/plugins/visualizations/phylocanvas/src/script.js A config/plugins/visualizations/phylocanvas/static/logo.png A config/plugins/visualizations/phylocanvas/static/script.js M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png A config/plugins/visualizations/pv/config/pv.xml A config/plugins/visualizations/pv/package.json A config/plugins/visualizations/pv/src/pv.js A config/plugins/visualizations/pv/static/logo.png A config/plugins/visualizations/pv/static/pv.js A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js A config/plugins/visualizations/scatterplot/src/numeric-column-stats.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/src/worker-stats.js A config/plugins/visualizations/scatterplot/static/8850628034555be072a0e4f882d4d8e5.js A config/plugins/visualizations/scatterplot/static/logo.png R config/plugins/visualizations/scatterplot/static/numeric-column-stats.js R config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js A config/plugins/visualizations/scatterplot/static/scatterplot.js R config/plugins/visualizations/scatterplot/static/worker-stats.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R config/plugins/visualizations/scatterplot/webpack.config.js M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/unipept/templates/unipept.mako A config/plugins/visualizations/venn/config/venn.xml A config/plugins/visualizations/venn/package.json A config/plugins/visualizations/venn/src/script.js A config/plugins/visualizations/venn/src/venn.js A config/plugins/visualizations/venn/static/logo.png A config/plugins/visualizations/venn/static/script.css A config/plugins/visualizations/venn/static/script.js M config/plugins/webhooks/demo/search/script.js M config/plugins/webhooks/demo/tour_generator/__init__.py M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample M config/tool_destinations.yml.sample M config/tool_shed.yml.sample M config/user_preferences_extra_conf.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M create_db.sh M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml A display_applications/intermine/intermine_simple.xml M doc/parse_gx_xsd.py M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/nginx.md M doc/source/admin/reports_options.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/bug_reports.rst A doc/source/admin/special_topics/gdpr_compliance.rst M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/performance_tracking.rst M doc/source/conf.py A doc/source/conf.versioning.py M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/project/organization.rst A doc/source/releases/18.01.rst M doc/source/releases/18.01_announce.rst A doc/source/releases/18.05.rst A doc/source/releases/18.05_announce.rst M doc/source/releases/index.rst M extract_dataset_parts.sh M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py A lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/managers.py A lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml A lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/fasta_to_fai.xml M lib/galaxy/datatypes/converters/fasta_to_len.py R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.py A lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py R lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.afg A lib/galaxy/datatypes/test/1.arff A lib/galaxy/datatypes/test/1.fastqsanger.bz2 A lib/galaxy/datatypes/test/1.fastqsanger.gz A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz A lib/galaxy/datatypes/test/1.hdt A lib/galaxy/datatypes/test/1.obo A lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.phyloxml A lib/galaxy/datatypes/test/1.stockholm A lib/galaxy/datatypes/test/1.tiff A lib/galaxy/datatypes/test/1.ttl A lib/galaxy/datatypes/test/1.xmfa A lib/galaxy/datatypes/test/2.tabular A lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.txt A lib/galaxy/datatypes/test/Acanium.hmm A lib/galaxy/datatypes/test/diamond.daa A lib/galaxy/datatypes/test/empty.txt M lib/galaxy/datatypes/test/example.iqtree A lib/galaxy/datatypes/test/test.blib M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A 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static/scripts/viz/trackster/slotting.js R static/scripts/viz/trackster/tracks.js R static/scripts/viz/trackster/util.js R static/scripts/viz/visualization.js R static/scripts/viz/viz_views.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css M static/welcome.html.sample R templates/admin/impersonate.mako R templates/admin/view_data_tables_registry.mako R templates/admin/view_datatypes_registry.mako M templates/base/base_panels.mako M templates/display_common.mako M templates/ind_share_base.mako M templates/js-app.mako R templates/sharing_base.mako M templates/show_params.mako M templates/tagging_common.mako M templates/user/login.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M 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test/base/workflow_fixtures.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/tools/collection_paired_conditional_structured_like.xml A test/functional/tools/collection_paired_structured_like.xml A test/functional/tools/collection_type_source_map_over.xml A test/functional/tools/column_param_configfile.xml A test/functional/tools/empty_select.xml A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/for_workflows/cat_collection.xml A test/functional/tools/identifier_single_in_repeat.xml A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/job_properties.xml M test/functional/tools/multi_data_optional.xml M test/functional/tools/multi_output_recurse.xml A test/functional/tools/output_action_change_format_paired.xml R test/functional/tools/paired_collection_map_over_structured_like.xml R test/functional/tools/sam_to_bam_native.xml A test/functional/tools/sam_to_unsorted_bam.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_data_manager_table_reload.py A test/integration/test_scripts.py A test/integration/test_shed_tool_tests.py M test/integration/test_upload_configuration_options.py A test/integration/uses_shed.py R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml M test/unit/config/1607_root_filters/config/galaxy.ini M test/unit/config/1607_root_samples/config/galaxy.ini M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.py A test/unit/datatypes/test_datatypes_registry.py A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_params.py M test/unit/managers/test_HistoryManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_remote_shell.py A test/unit/test_rule_utils.py M test/unit/test_security_helper.py A test/unit/test_security_passwords.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_validation.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/cutWrapper.pl M tools/filters/sorter.py M tools/filters/sorter.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.py M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into select_tag_parameter Commit: d417e9b239309707274011d4199b8f827fcc0f6d https://github.com/galaxyproject/galaxy/commit/d417e9b239309707274011d4199b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Flush out collection tag parameters a bit. - Switch select_tag to group_tag as a parameter name - since it is restricted to group_tags and we don't call data parameters select_data. - Add minimal XSD documentation for this new parameter type. - Add example tools - for single and multiple tags. - Add API tests for these tools and the tag handling. Commit: d5a057fe37b57343bcc023509e00a3c633aab32a https://github.com/galaxyproject/galaxy/commit/d5a057fe37b57343bcc023509e00… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Merge pull request #6517 from VJalili/authn_controller2 Return a json blob containing redirect URI in OIDC login controller Commit: e5c532298d5db34da04d8f046ebe44abddbbaa64 https://github.com/galaxyproject/galaxy/commit/e5c532298d5db34da04d8f046ebe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Make tag order stable when using group_tag parameters. Commit: 6677e7b91385d027989613bdc621108da76e8425 https://github.com/galaxyproject/galaxy/commit/6677e7b91385d027989613bdc621… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Fix failing import/export test for group_tag changes. Commit: a9d3a82f1bf8bbb9c8fb12bf4edec90105b59dba https://github.com/galaxyproject/galaxy/commit/a9d3a82f1bf8bbb9c8fb12bf4ede… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Notify user if newer tool versions are available Commit: 84159d37cc44146716cc0f59df0a149aa5b0539e https://github.com/galaxyproject/galaxy/commit/84159d37cc44146716cc0f59df0a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #6533 from guerler/new_tool_version Notify if newer tool version is available Commit: f1ab39a0a01a4faaef215a3b914ebf31e430513b https://github.com/galaxyproject/galaxy/commit/f1ab39a0a01a4faaef215a3b914e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/data_fetch.py M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Merge pull request #6523 from jmchilton/fetch_api_pasted Handle pasted content in fetch API. Commit: b0b12e4706999ddce317769b660e4d9a32a8a2bb https://github.com/galaxyproject/galaxy/commit/b0b12e4706999ddce317769b660e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/managers/hdcas.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M test/unit/test_galaxy_mapping.py A test/unit/test_model_copy.py Log Message: ----------- Merge pull request #6531 from jmchilton/history_copy_opts Optimizations for history copying. Commit: 43a0482f1ca4b5e48d1ec576ff0c4875bae87fe3 https://github.com/galaxyproject/galaxy/commit/43a0482f1ca4b5e48d1ec576ff0c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Minor (comment-only) wording tweaks. Commit: 4955add0a343bd0b1b09a3cde11d9ffc8621baf9 https://github.com/galaxyproject/galaxy/commit/4955add0a343bd0b1b09a3cde11d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/webapp.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #6524 from jmchilton/cached_identity Use cached database identity to avoid many DB requests when creating jobs. Commit: d06b221905cc4eb935939c6a29685c0dff125bf8 https://github.com/galaxyproject/galaxy/commit/d06b221905cc4eb935939c6a2968… Author: Andrey Tovchigrechko <tovchigrechkoa(a)medimmune.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Convert tool parameter XML attribute 'hidden' into the correct boolean Python type. Previously it was converted into string, and in the logical predicates any non-empty value would always evaluate to True. This fix allows using the 'hidden' attribute in parameterized XML macros with 'true' or 'false' passed as a macros parameter. This in turns allows hiding some form fields (after setting default values) based on choices picked in conditional switches. Commit: 3fd7b87fb96ebb4503f4b8c2c456aaced9a5c482 https://github.com/galaxyproject/galaxy/commit/3fd7b87fb96ebb4503f4b8c2c456… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6539 from andreyto/at_hidden_par_conv Convert tool parameter XML attribute 'hidden' into the correct boolean Python type Commit: f56c0bbac2c9769a69bc03d0092cf2dfc09ceb81 https://github.com/galaxyproject/galaxy/commit/f56c0bbac2c9769a69bc03d0092c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case for nested collection input to flatten in a workflow. Also exercises delayed workflow scheduling because of the dynamic discovery of the input collection. xref #5867 Commit: 10b17fb48a257246a401ce560b371edb41c8237c https://github.com/galaxyproject/galaxy/commit/10b17fb48a257246a401ce560b37… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #6541 from jmchilton/flatten_bug Test case for nested collection input to flatten in a workflow. 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: 6e8a7fddb1727a7b6f4c3ae4817d38fe73f2079b https://github.com/galaxyproject/galaxy/commit/6e8a7fddb1727a7b6f4c3ae4817d… 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: 42ddfbde4c429b6bd3a19f901f0f3bf7db1d85ba https://github.com/galaxyproject/galaxy/commit/42ddfbde4c429b6bd3a19f901f0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M test/base/data/rules_dsl_spec.yml Log Message: ----------- Fill out, polish the rule spec a little more. Drop use of startsWith in favor of indexOf for PhantomJS testing. Commit: 6cd8650b5a5530835e6d396e81d6f481ca6b141a https://github.com/galaxyproject/galaxy/commit/6cd8650b5a5530835e6d396e81d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove stray debug statement left in 18.05. Commit: 4d83746cc2f83c1208abcefbce3e66a00f01076a https://github.com/galaxyproject/galaxy/commit/4d83746cc2f83c1208abcefbce3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Allow loading tag metadata from existing objects in rule builder. This should allow nesting and filtering from tags - including group tags. Commit: 58072302539dd7c5283ee11c13512a19a9bf99fb https://github.com/galaxyproject/galaxy/commit/58072302539dd7c5283ee11c1351… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-27 (Fri, 27 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/util/rules_dsl.py M test/api/test_tools.py M test/base/data/rules_dsl_spec.yml M test/base/populators.py M test/base/rules_test_data.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Implement rule builder rule to quickly grab group tag value. Should make it a lot easier to nested and filter on group tag values. Commit: fe5e1f1686dd60e6357594c4541b894a29f04984 https://github.com/galaxyproject/galaxy/commit/fe5e1f1686dd60e6357594c4541b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-27 (Fri, 27 Jul 2018) Changed paths: M test/base/driver_util.py A test/integration/test_objectstore_jobs.py Log Message: ----------- Integration test for the interaction of nested object stores and jobs. - Test hierarchical store uses its first disk store for new files and not the remaining entries. - Test basic functionality of writing to the distributed object store. - Test all job outputs get placed in the same object store. Commit: 38e5816b06d0804324dfe2a9c642859d990cfdb9 https://github.com/galaxyproject/galaxy/commit/38e5816b06d0804324dfe2a9c642… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-28 (Sat, 28 Jul 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Redirect unindentifed routes in admin panel Fix Commit: 06a4c603d3b27c4fea948907476a3290acd58690 https://github.com/galaxyproject/galaxy/commit/06a4c603d3b27c4fea948907476a… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- Remove the sharing of toolbox in GRT This has been broken for a while and was never super useful data to obtain. Fixes #6534 Commit: 524df1a3b71510bcf1c9fe95617627f3bef7a1a7 https://github.com/galaxyproject/galaxy/commit/524df1a3b71510bcf1c9fe956176… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- Merge pull request #6553 from erasche/grt-remove-toolbox Remove the sharing of toolbox in GRT 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: b829e0cc93b17842f64d0636a59eec5401753133 https://github.com/galaxyproject/galaxy/commit/b829e0cc93b17842f64d0636a59e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M test/base/driver_util.py A test/integration/test_objectstore_jobs.py Log Message: ----------- Merge pull request #6546 from jmchilton/objectstore_jobs_test Integration test for the interaction of nested object stores and jobs. Commit: 111b40ac37a1fb5cc4746c0987d5d73eb4105d0a https://github.com/galaxyproject/galaxy/commit/111b40ac37a1fb5cc4746c0987d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Fix linting issue introduced in #6553. Commit: 1a73b1f2adf828834a386245d131139fe979b4d2 https://github.com/galaxyproject/galaxy/commit/1a73b1f2adf828834a386245d131… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6554 from jmchilton/fix_lint_ Fix linting issue introduced in #6553. 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: 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: 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: 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. 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: 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. 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. 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: 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: 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. 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 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 Commit: af755a098061f8db55db5ecc398c3410f180f9e1 https://github.com/galaxyproject/galaxy/commit/af755a098061f8db55db5ecc398c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Minor import cleanup, formatting. 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 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. Commit: 7882a067c8cbcf564aff605b91beea8d7849fb00 https://github.com/galaxyproject/galaxy/commit/7882a067c8cbcf564aff605b91be… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/objectstore/__init__.py A test/integration/objectstore_selection_job_conf.xml A test/integration/objectstore_selection_job_resource_parameters_conf.xml A test/integration/objectstore_selection_rules/__init__.py A test/integration/objectstore_selection_rules/rules.py A test/integration/test_objectstore_selection.py Log Message: ----------- Allow configuring object stores on a per-job-destination basis. Setup a hierarchical objectstore with ids - these ids can be zero weight for objectstores that should only be used on a per-job-destination basis. Job destinations can then set object_store_id as a param to force a particular object store from the hierarchical configuration to be used. This can be set in job_conf.xml directly for static mappings or combined with dynamic job destinations for dynamic mapping to object stores. Dynamic job destinations can dispatch on cluster conditions, user, user preferences, etc.. Additionally, job resource parameters can be used with dynamic job destinations to allow user input on the object store to use. An integration test case is included that tests and demonstrates all these different pieces. It sets up a Galaxy with a job and object store configuration that routes one tool to a specific disk store (called "static"), and routes another tool dynamically using job resource parameters that allow the user to pick between "slow, cheap" and "fast, expensive" storage options (for the test it is all just disk stores used - but you can imagine choosing between EBS and S3 or something this way). I'd be happy to see something more formal than job resource parameters or user preferences developed to help users route job outputs to particular object stores - this is just a demonstration of what can be done today after these changes using extension points already being used by admins and users. Commit: d1423b6e18cbf054799027d6c6700b1b1186d6a9 https://github.com/galaxyproject/galaxy/commit/d1423b6e18cbf054799027d6c670… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/util/rules_dsl.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py M test/unit/test_rule_utils.py Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 5a914b9fa71ff2c00d7ba1a7c1dc3ccbb8437eae https://github.com/galaxyproject/galaxy/commit/5a914b9fa71ff2c00d7ba1a7c1dc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Keep all user-selected tags, including duplicates Commit: 95e8a3491280cc26d435bebc1cf03488d7db3b88 https://github.com/galaxyproject/galaxy/commit/95e8a3491280cc26d435bebc1cf0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Correct copy-pasted docstring Commit: 55436c38008c3d1b261b7d9dfc728cc968bd6622 https://github.com/galaxyproject/galaxy/commit/55436c38008c3d1b261b7d9dfc72… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml M test/functional/tools/samples_tool_conf.xml M test/unit/test_objectstore.py M test/unit/tools/test_wrappers.py Log Message: ----------- Merge pull request #5457 from mvdbeek/select_tag_parameter Allow selecting subset of collection by group tag Commit: 1d0f51a05e5e5fb73940d7dae284bf9c00a4054c https://github.com/galaxyproject/galaxy/commit/1d0f51a05e5e5fb73940d7dae284… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix upload file selector value resetting Fix Commit: f992980d458edeebc0501ac036c2ee5c6fba7989 https://github.com/galaxyproject/galaxy/commit/f992980d458edeebc0501ac036c2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6573 from guerler/fix_upload_naming [18.05] Fix upload file selector value resetting Commit: ec60327f983ced46fa2a8489c359100960b72d5b https://github.com/galaxyproject/galaxy/commit/ec60327f983ced46fa2a8489c359… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/utils/uploadbox.js Log Message: ----------- Client rebuild to include uploadbox value fix in release branch. Commit: 4f3cd889f1cb2371519cabbc975dfffee6ec9b71 https://github.com/galaxyproject/galaxy/commit/4f3cd889f1cb2371519cabbc975d… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Typo and wording fixes for dependency resolvers docs Commit: a7e159dd8b8c584772defb6becb56f5450172dad https://github.com/galaxyproject/galaxy/commit/a7e159dd8b8c584772defb6becb5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Merge pull request #6575 from afgane/dev Typo and wording fixes for dependency resolvers docs Commit: 4072d68e0d6d182a4249df143ab4fcba3e8f35cf https://github.com/galaxyproject/galaxy/commit/4072d68e0d6d182a4249df143ab4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M client/galaxy/scripts/apps/admin.js Log Message: ----------- Redirect without using backbone Commit: d7398672a1a3432ae11b0c41b291e45e77bbd183 https://github.com/galaxyproject/galaxy/commit/d7398672a1a3432ae11b0c41b291… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6574 from dannon/release_18.05 [18.05] Client rebuild to include uploadbox value fix in release branch. Commit: c2246d8b8a17fdf126aefb5f6b53eb680bb58848 https://github.com/galaxyproject/galaxy/commit/c2246d8b8a17fdf126aefb5f6b53… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/base/rules_test_data.py Log Message: ----------- Fix last consistently failing Selenium test. Commit: 75e50d3fdd98a75cc0c109616293608bdab5eac3 https://github.com/galaxyproject/galaxy/commit/75e50d3fdd98a75cc0c109616293… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/base/rules_test_data.py Log Message: ----------- Merge pull request #6578 from jmchilton/selenium_fixes_44 Fix last consistently failing Selenium test. Commit: 84597a12356aaa5b5d59ba95c30691739fed2300 https://github.com/galaxyproject/galaxy/commit/84597a12356aaa5b5d59ba95c306… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/build_list.xml A lib/galaxy/tools/extract_dataset.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_parsing.py Log Message: ----------- Lists-as-tuples collection operations. Commit: 7eb0be96cf3dba5099f28fd001c5f2b87ddacf38 https://github.com/galaxyproject/galaxy/commit/7eb0be96cf3dba5099f28fd001c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 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: 272c6b071d5c5db526cb3da8cc174dd4785a0d6e https://github.com/galaxyproject/galaxy/commit/272c6b071d5c5db526cb3da8cc17… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case to clarify workflow API a bit in simple cases. Commit: 9874e5db0cbf1967a90d3ad74820af1790602981 https://github.com/galaxyproject/galaxy/commit/9874e5db0cbf1967a90d3ad74820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow uniform access to job state for WorkflowInvocationSteps. Use the concept of job_source_type and job_source_id used by IDs to summarize the state and list out individual jobs in the response as a shortcut. This information used to be readily accessible before 18.01. Commit: b878835ea388cc7ea15c0bf9d56738732d44b8e2 https://github.com/galaxyproject/galaxy/commit/b878835ea388cc7ea15c0bf9d567… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Add a legacy_job_state mode to restore 17.09 workflow invocation behavior. Commit: 5d85c32da24396a4853d09cf5fccb12481f1ccee https://github.com/galaxyproject/galaxy/commit/5d85c32da24396a4853d09cf5fcc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Merge pull request #6551 from guerler/fix_admin_routes Redirect unidentified routes in admin panel Commit: 683ef6eceea208c5c244bb9fe895b5e591dcb8df https://github.com/galaxyproject/galaxy/commit/683ef6eceea208c5c244bb9fe895… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Improve robustness of tour Selenium test. Give the URL upload jobs a bit more time to complete. https://github.com/galaxyproject/galaxy/issues/6581 might also improve this - I'm not sure. Commit: 4d1ce0f431d337a45964eee3aa3813be1f4e41c6 https://github.com/galaxyproject/galaxy/commit/4d1ce0f431d337a45964eee3aa38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Cancel jobs when exiting test_history decorator. Should reduce the probability of a test interferring with other tests. Commit: 136255c0ad7a2aca6584f4c1fa3d10ea5e4a632e https://github.com/galaxyproject/galaxy/commit/136255c0ad7a2aca6584f4c1fa3d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M run_tests.sh M test/base/populators.py Log Message: ----------- Allow test_history context to annotate whether new histories are needed by test. Usually tests should have new histories but we should still capture this information so we can target tests are particular histories for debugging interactively and so we could potentially reduce the number of new histories created when testing remote Galaxies (there have been complaints about this in the past). Commit: 36e1d6cfce946b46f5904af3cc924cb0f21970ee https://github.com/galaxyproject/galaxy/commit/36e1d6cfce946b46f5904af3cc92… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M test/api/test_tools.py M test/base/populators.py Log Message: ----------- More use of test_history contextmanager in test_tools. Commit: e3435eb23d62815f5a08aca7dbaf68991b05ab60 https://github.com/galaxyproject/galaxy/commit/e3435eb23d62815f5a08aca7dbaf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: R client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/qunit/tests/ui_tests.js Log Message: ----------- Remove backbone thumbnail element Commit: 03702d0a61733682cd80ee3d4849cd094c00d0d1 https://github.com/galaxyproject/galaxy/commit/03702d0a61733682cd80ee3d4849… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove unused thumbnail styles Commit: 2f87087ba2a88d71d539f888401d79167997a4ea https://github.com/galaxyproject/galaxy/commit/2f87087ba2a88d71d539f888401d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Use object store to check for existence of extra_files_path This should fix https://github.com/galaxyproject/galaxy/issues/6585 Commit: 9910ea47d9b353fe61fc510469a0599210009a25 https://github.com/galaxyproject/galaxy/commit/9910ea47d9b353fe61fc510469a0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh M test/api/test_tools.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #6586 from jmchilton/toward_test_history_cleaning Smarter Test Histories (Part I) Commit: 1ddaf4a64d6307fd477653d3bba7353a30e88eb2 https://github.com/galaxyproject/galaxy/commit/1ddaf4a64d6307fd477653d3bba7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #6588 from mvdbeek/extra_path_nested_object_store_issue [18.05] Use object store to check for existence of extra_files_path Commit: 0ea1430136c51c5558f17e4a051e8d1a58009fd3 https://github.com/galaxyproject/galaxy/commit/0ea1430136c51c5558f17e4a051e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Commit: 0b1d804cf675fb47f4132363f32b27680becbdf8 https://github.com/galaxyproject/galaxy/commit/0b1d804cf675fb47f4132363f32b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue R client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6587 from guerler/remove_bb_thumbnail Remove backbone version of thumbnail element Commit: 2839475967320b7d95ade125e542625c6d54c1b9 https://github.com/galaxyproject/galaxy/commit/2839475967320b7d95ade125e542… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Update ucsc genome-test server URL. Commit: 1cd36e3f815b6ad06da7a1aa1ee2c56d67edc36c https://github.com/galaxyproject/galaxy/commit/1cd36e3f815b6ad06da7a1aa1ee2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Bump version; 'patch' since it should be the exact same, as much as anything over the net ever could be\? Commit: 07d41517460eedf514071cd1b66c7d958ad23037 https://github.com/galaxyproject/galaxy/commit/07d41517460eedf514071cd1b66c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Show workflow parameters in worklfow editor below title header Commit: bd921368413002f6b57e0c6ee229b2ff06e7482d https://github.com/galaxyproject/galaxy/commit/bd921368413002f6b57e0c6ee229… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt A pytest.ini M run_tests.sh M scripts/plugin_staging.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Setup pytest python3 API testing Commit: 1b3f5550548741370e70ff2b25bc404e84d2594e https://github.com/galaxyproject/galaxy/commit/1b3f5550548741370e70ff2b25bc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Bump docker image version Commit: 7342a7ebbc404c275fb0635c1628eecb92b56ff5 https://github.com/galaxyproject/galaxy/commit/7342a7ebbc404c275fb0635c1628… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Avoid prepopulating database twice Commit: 4e3a981003f9bd0c99a604327e17f37e16f07f33 https://github.com/galaxyproject/galaxy/commit/4e3a981003f9bd0c99a604327e17… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Temporarily run tests with image published in my channel Commit: 661b3101c635fc376d9c16878fd8b23122ab4950 https://github.com/galaxyproject/galaxy/commit/661b3101c635fc376d9c16878fd8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: A .ci/jenkins/api-py3/run_tests.sh Log Message: ----------- Add py3 build script for jenkins Commit: 39e1877ccedd36242bc93696d897f62d5c8f0126 https://github.com/galaxyproject/galaxy/commit/39e1877ccedd36242bc93696d897… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Explicitly create a python 3 virtualenv Commit: 5b02f5ccedd87a9d529d19a49950df57cc29a8cf https://github.com/galaxyproject/galaxy/commit/5b02f5ccedd87a9d529d19a49950… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Bump docker image version Commit: eb1cb57f424d7ab286658699d2313621ed9e1d4e https://github.com/galaxyproject/galaxy/commit/eb1cb57f424d7ab286658699d231… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Fix up Dockerfile for bdbag installation Commit: 091ba0f32c75b6046938c95b0521b3271d9c3a72 https://github.com/galaxyproject/galaxy/commit/091ba0f32c75b6046938c95b0521… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Use 18.09.0 tag Commit: 327ec3d4e9e9d0ab15ae07c2cd0596d6a8abbe90 https://github.com/galaxyproject/galaxy/commit/327ec3d4e9e9d0ab15ae07c2cd05… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M .ci/jenkins/api-py3/run_tests.sh Log Message: ----------- Do use python 3 Commit: a6b78e7a614aaf3e8254fdea32723f6f06678b5e https://github.com/galaxyproject/galaxy/commit/a6b78e7a614aaf3e8254fdea3272… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/base/populators.py Log Message: ----------- Decode bytestring returned by source_string Commit: d659d91d331eb434221940a1cddbd5458d75d8b3 https://github.com/galaxyproject/galaxy/commit/d659d91d331eb434221940a1cddb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/web/framework/middleware/batch.py Log Message: ----------- Decode body when using json.loads in batch middleware Commit: 61fa9711dc406dc15b434630aff3c3497f18fd52 https://github.com/galaxyproject/galaxy/commit/61fa9711dc406dc15b434630aff3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/base/populators.py M test/base/rules_test_data.py Log Message: ----------- More resource_string fixes Commit: 03f80f8aef781908f4290f613de9ee78f58b632c https://github.com/galaxyproject/galaxy/commit/03f80f8aef781908f4290f613de9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Patch LargeBinary to cast strings to bytestring I don't fully understand the issue, and we might be accumulating technical debt here. What I'm seeing without this commit is this when I run for instance the VisualizationsApiTestCase.test_create API test. ``` Traceback (most recent call last): File "/galaxy/lib/galaxy/web/framework/decorators.py", line 283, in decorator rval = func(self, trans, *args, **kwargs) File "/galaxy/lib/galaxy/webapps/galaxy/api/visualizations.py", line 55, in index visualizations = self.get_visualizations_by_user(trans, user) File "/galaxy/lib/galaxy/web/base/controller.py", line 664, in get_visualizations_by_user return query.all() File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/query.py", line 2737, in all return list(self) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 98, in instances util.raise_from_cause(err) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/util/compat.py", line 187, in reraise raise value File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 79, in instances rows = [proc(row) for row in fetch] File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 79, in <listcomp> rows = [proc(row) for row in fetch] File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 493, in _instance loaded_instance, populate_existing, populators) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 604, in _populate_full populator(state, dict_, row) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/strategies.py", line 1782, in load_scalar_from_joined_new_row dict_[key] = _instance(row) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 493, in _instance loaded_instance, populate_existing, populators) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/orm/loading.py", line 593, in _populate_full dict_[key] = getter(row) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/sql/type_api.py", line 1204, in process return process_value(impl_processor(value), dialect) File "/galaxy_venv3/lib/python3.5/site-packages/sqlalchemy/sql/sqltypes.py", line 902, in process value = bytes(value) TypeError: string argument without an encoding ``` I think LargeBinary isn't meant to store strings the way we do this (we dump JSON as bytestring), and somehow on python 3 we get unicode strings back from the database, which blows up here. I suspect this might be configured on the connection level (see http://docs.sqlalchemy.org/en/latest/dialects/postgresql.html#unicode) but not blowing up here seems like a good default. Commit: 2527038ffce1f7f1b987f9318671bc4fec567ec0 https://github.com/galaxyproject/galaxy/commit/2527038ffce1f7f1b987f9318671… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Mount in run_tests script at container runtime This allows changing variables in the script without rebuilding the container Commit: 3d9c0b154ab744345808d36c8af38972524ab2c3 https://github.com/galaxyproject/galaxy/commit/3d9c0b154ab744345808d36c8af3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/api/test_workflows.py M test/base/data/test_workflow_with_runtime_input.ga M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml Log Message: ----------- Make random_lines1 consistent on py2 and py3 (again) Turns out integers are used as is in `random.seed()`, but strings are hashed (in the version 1 protocol), and the hashing isn't stable. So instead we hack around this by using `ord()` on each character and concatenating the digits. Yucky, but probably better than using numpy and putting this tool on the list of tools that inherit galaxy's environment (or adding a requirement tag and resolving with conda ...). Commit: 4602d413cc80e7478eaa8de164aa8fde014de500 https://github.com/galaxyproject/galaxy/commit/4602d413cc80e7478eaa8de164aa… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Implement dataset permissions api Commit: 409d5fcc8057309df71e2baa1b9bd37b16a5883a https://github.com/galaxyproject/galaxy/commit/409d5fcc8057309df71e2baa1b9b… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- remove unnecessary doc Commit: fe5794916496364dbabfd97f7ad3fba6d91f7336 https://github.com/galaxyproject/galaxy/commit/fe5794916496364dbabfd97f7ad3… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- fix linting Commit: 19523352ced554868fa6979dfe37161be7c864dd https://github.com/galaxyproject/galaxy/commit/19523352ced554868fa6979dfe37… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- Correct documentation URL Commit: f7176dcfc9c63c7230c3ddc127e4e7718be49b9e https://github.com/galaxyproject/galaxy/commit/f7176dcfc9c63c7230c3ddc127e4… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- Allow exception to bubble up naturally Commit: 6067fee3d44e6106217012ed9d7f029691e5d99f https://github.com/galaxyproject/galaxy/commit/6067fee3d44e6106217012ed9d7f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/managers/datasets.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Remove unused dataset deserializer stuff. An unfinished thread left in the code base. It was a fine idea but I don't think anyone is left to pick it up and run with it. Commit: 18148a9656242369220d2ba1f0f10d89f2d44f2e https://github.com/galaxyproject/galaxy/commit/18148a9656242369220d2ba1f0f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Refactor dataset_is_private_to_user to consume dataset instead of LibraryDataset. More consistent with other methods in that file and allows for use without knowledge of how to go from a LD -> Dataset. Commit: 49693814a9702a855d7df166d27c7a6f4f1faba1 https://github.com/galaxyproject/galaxy/commit/49693814a9702a855d7df166d27c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/lddas.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/users.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py A test/api/test_roles.py M test/api/test_tools.py M test/base/api.py M test/base/populators.py Log Message: ----------- Unified dataset permission API. There was an existing library dataset permission API and one proposed for HDAs in #6461. This tries to reconcile the two approaches and move toward managers. - Proper treatment of "master_api_key" throughout the manager layers related to this. - Use PUT instead of POST, since that is more appropriate for updates I believe. - Use a similar URL pattern for library datasets, history contents, and dataset APIs. - Generalize the dataset API to allow HDA or LDDA inputs (the proposal for the new API in #6461 added an HDA-only option to the dataset API - this isn't how that API layer is meant to be used I believe). - Add an HDA only endpoint in the history contents API for this functionality to mirror the library dataset API. - Use consistent and backward compatible payload parsing for these endpoints. - Use consistent serialization for the result of these changes. - Generalize the HDA variant of this to allow different actions - such as make public and make private that were available in the library dataset variant. - Test cases for the new API endpoints, the roles API, tests for permissions during collection creation and running tools with both dataset and collection inputs. Commit: c6b593b1ca6efa0ef60b1e9fdbed10022bf9fc4e https://github.com/galaxyproject/galaxy/commit/c6b593b1ca6efa0ef60b1e9fdbed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M test/api/test_jobs.py Log Message: ----------- Migrate API tests in test_jobs.py to use test_history context. More configurable, better error reporting, cleans up jobs, etc.. Commit: b2fed75059767aece3c0a75c630c9f30e31f0078 https://github.com/galaxyproject/galaxy/commit/b2fed75059767aece3c0a75c630c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-11 (Sat, 11 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Flip testing image back to galaxy namespace Commit: 00e8d4ee76c65652e6a0b208f44d957c79db40b1 https://github.com/galaxyproject/galaxy/commit/00e8d4ee76c65652e6a0b208f44d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- Quote Filter1 input and output Commit: 819ee07af36d10734b32474fa832ce9e09e1b376 https://github.com/galaxyproject/galaxy/commit/819ee07af36d10734b32474fa832… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Respect unavilable peek when serializing HDA Also call display_peek() just once. That fixes the following exception that occurs when running the Filter1 tool through the API: ``` galaxy.datatypes.tabular ERROR 2018-08-12 22:53:42,939 make_html_peek_rows failed on HDA 64 Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/tabular.py", line 186, in make_html_peek_rows dataset.set_peek() File "/Users/mvandenb/src/galaxy/lib/galaxy/model/__init__.py", line 2264, in set_peek return self.datatype.set_peek(self) File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/tabular.py", line 57, in set_peek super(TabularData, self).set_peek(dataset, line_count=line_count, WIDTH=WIDTH, skipchars=skipchars, line_wrap=False) File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/data.py", line 813, in set_peek dataset.peek = get_file_peek(dataset.file_name, WIDTH=WIDTH, skipchars=skipchars, line_wrap=line_wrap) File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/data.py", line 1029, in get_file_peek with compression_utils.get_fileobj(file_name, "U") as temp: File "/Users/mvandenb/src/galaxy/lib/galaxy/util/compression_utils.py", line 29, in get_fileobj return get_fileobj_raw(filename, mode, compressed_formats)[1] File "/Users/mvandenb/src/galaxy/lib/galaxy/util/compression_utils.py", line 58, in get_fileobj_raw return compressed_format, io.open(filename, mode, encoding='utf-8') FileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpan_4qaow/tmpfzus9jhv/tmplqjtbp5c/database/files/000/dataset_40.dat' ``` This is because we serialize the HDA just after the job has been created, meaning the file may not exist yet. Commit: f4343d876f13e55e92ca228582b4430dcd01e4aa https://github.com/galaxyproject/galaxy/commit/f4343d876f13e55e92ca228582b4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Clarify set_peek setting when finishing job Commit: 3f032f6c383b108946f77f8fd6b7a02e98d474e1 https://github.com/galaxyproject/galaxy/commit/3f032f6c383b108946f77f8fd6b7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M scripts/functional_tests.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py Log Message: ----------- Rework and simplify data manager testing We don't rely on TwillTestCase anymore, that is now exclusively used by ShedTwillTestCase. Then I've just re-used the infrastructure of ToolsTestCase for discovering tests, while making sure that we do use an admin API key during testing. Commit: e21d94298d5d215a0f4f31dae26848388c593590 https://github.com/galaxyproject/galaxy/commit/e21d94298d5d215a0f4f31dae268… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Look in self.tool_dir if repository_dir is not available Commit: c2ab74985148781f9a7eae16dec2fde89a0c154d https://github.com/galaxyproject/galaxy/commit/c2ab74985148781f9a7eae16dec2… Author: Anup Kumar <anup.rulez(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add download option to workflow editor menu Commit: 4550a7152c1be518effac678b807da9748b997eb https://github.com/galaxyproject/galaxy/commit/4550a7152c1be518effac678b807… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Workflow parameter positioning tweaks, keeps display to the right and minimally large. Commit: e853762fdbb20c7d9396223f17b2cd728d29dd68 https://github.com/galaxyproject/galaxy/commit/e853762fdbb20c7d9396223f17b2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6592 from guerler/fix_workflow_parameters Resolve overlap of workflow parameter container with gear-icon in editor header Commit: 3d0763f71c795549e6c133f2734cf7ae5337c296 https://github.com/galaxyproject/galaxy/commit/3d0763f71c795549e6c133f2734c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M tools/stats/filtering.xml Log Message: ----------- Merge pull request #6594 from mvdbeek/respect_unavailable_display_peek Respect unavailable display peek Commit: 5de98d84709bceba887f040760763abf5500b096 https://github.com/galaxyproject/galaxy/commit/5de98d84709bceba887f04076076… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add trr datatype Commit: 0c2dc3aafb684fc13458ba682eb1c46fa6054d7e https://github.com/galaxyproject/galaxy/commit/0c2dc3aafb684fc13458ba682eb1… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: A lib/galaxy/datatypes/test/em.trr Log Message: ----------- add trr example file Commit: 572b9ced2dada0c5a99d52f6de3886ad85b9d368 https://github.com/galaxyproject/galaxy/commit/572b9ced2dada0c5a99d52f6de38… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- no edam format know yet Commit: e42829f03604c8ba0d4a467027c3c3eb689e8395 https://github.com/galaxyproject/galaxy/commit/e42829f03604c8ba0d4a467027c3… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- register datatype Commit: 51c6e2f6ba6b654b7f234c0440cfaa95ac2735b4 https://github.com/galaxyproject/galaxy/commit/51c6e2f6ba6b654b7f234c0440cf… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add a step in PSA pipeline to determine if ID token exists. Commit: 405a08522e8f54341478dde5c88868e33ed55ec7 https://github.com/galaxyproject/galaxy/commit/405a08522e8f54341478dde5c888… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- check for missing ID and refresh tokens. Commit: 0ed0bdf203c6d088487c24e42fd50951039f7e74 https://github.com/galaxyproject/galaxy/commit/0ed0bdf203c6d088487c24e42fd5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add some comments explaining when some OIDC-related errors can happen. Commit: ae3d41924ac844d22c454fbd01d49a9ac3ee3b74 https://github.com/galaxyproject/galaxy/commit/ae3d41924ac844d22c454fbd01d4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/util/encoding_util.py Log Message: ----------- py3: Fix repository installation I'm very surprised this actually worked. I suppose we called my system's `hg` ?! Commit: 4d5ea3d724cf1a7fac1c6a2f9eeac133c47c2a06 https://github.com/galaxyproject/galaxy/commit/4d5ea3d724cf1a7fac1c6a2f9eea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: A .ci/jenkins/integration-py3/run_tests.sh M run_tests.sh Log Message: ----------- Start testing integration tests on python 3 Commit: b47c246e0c688be2f9474c36e1d12b786deb2ac0 https://github.com/galaxyproject/galaxy/commit/b47c246e0c688be2f9474c36e1d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix showing, creating and downloading HTML files Commit: 37b5120197d8a8bf39b52585408998252e601d82 https://github.com/galaxyproject/galaxy/commit/37b5120197d8a8bf39b525854089… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/renamed_temporary_file.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M test/integration/test_data_manager_table_reload.py M test/integration/tool_sheds_conf.xml M test/integration/uses_shed.py Log Message: ----------- py3: fix installing and running data managers Commit: 167e0e912907821943bd93eab2c0986a3d31136c https://github.com/galaxyproject/galaxy/commit/167e0e912907821943bd93eab2c0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Fix dictify_outputs The hack of setting `.__len` doesn't work on python 3. Subclassing OrderedDict and providing list-like access using integers should have the same effect. Commit: 14b1e1acd4eedce4a86b96094a496cbb76dd4239 https://github.com/galaxyproject/galaxy/commit/14b1e1acd4eedce4a86b96094a49… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/util/none_like.py Log Message: ----------- py3: Fix optional dataset bool value This fixes cheetah like `#if $input.dataset: ... #end if`. Which is a little weird, but fastqc uses this pattern. Commit: 344f68ea6d9c48a2a6f9dd56dd434633167d8f8e https://github.com/galaxyproject/galaxy/commit/344f68ea6d9c48a2a6f9dd56dd43… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M scripts/galaxy-main Log Message: ----------- py3: Fix uwsgi mule startup Commit: 0b30a94bbe34fb40eaf6fc97c816fcbe0586d078 https://github.com/galaxyproject/galaxy/commit/0b30a94bbe34fb40eaf6fc97c816… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/uploads.py Log Message: ----------- py3: Fix new direct API-backed uploads Commit: dc4a4b0eb5c9a07d9048e893b9fa48b43eb58c09 https://github.com/galaxyproject/galaxy/commit/dc4a4b0eb5c9a07d9048e893b9fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M scripts/secret_decoder_ring.py Log Message: ----------- py3: fix secret decoder script Commit: 293ce5a4720c7fc2ec26d44985750188e3762e6b https://github.com/galaxyproject/galaxy/commit/293ce5a4720c7fc2ec26d4498575… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M test/base/driver_util.py M test/integration/test_mules_as_job_handlers.py Log Message: ----------- py3: Fix mules test cases We're now just copying the current python path. Also the handler names have actually changed, I think this hasn't been updated after a late change (it is now as it should be, based on the documentation). Commit: cfce2468451e52c72bf7f0544c1bc7e209cc9224 https://github.com/galaxyproject/galaxy/commit/cfce2468451e52c72bf7f0544c1b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Fix GRT export test Commit: 620375c9d045e0085e2b260a97b3fdd5912fb45a https://github.com/galaxyproject/galaxy/commit/620375c9d045e0085e2b260a97b3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M test/integration/test_mules_as_job_handlers.py Log Message: ----------- Do test mules on Jenkins, I don't see why this shouldn't work Commit: 6e7a66cdc0b9f467341af77d4d2fd5eadc9f409d https://github.com/galaxyproject/galaxy/commit/6e7a66cdc0b9f467341af77d4d2f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Fix repository dependency manager Commit: dd7e4c601a3f31ce9c4fa06afc8234a39f0a5804 https://github.com/galaxyproject/galaxy/commit/dd7e4c601a3f31ce9c4fa06afc82… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Deal with docker localhost quirks Commit: fc06e78743086d3078d18e3928512cf62915bfb9 https://github.com/galaxyproject/galaxy/commit/fc06e78743086d3078d18e392851… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- py3: Fix Maf datatype Commit: dfba132d11b0f6f6d15cb9fc8c79e0645640489e https://github.com/galaxyproject/galaxy/commit/dfba132d11b0f6f6d15cb9fc8c79… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/util/__init__.py Log Message: ----------- Fix stdout/stderr exception handling Commit: 164a7d7f04be50e2ecd8edc64646a8e947680f4a https://github.com/galaxyproject/galaxy/commit/164a7d7f04be50e2ecd8edc64646… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6596 from bgruening/export_wf_galaxy_wf_editor Add download option to workflow editor menu Commit: 853b2d03abcfe563b12c817db84d871fbc291725 https://github.com/galaxyproject/galaxy/commit/853b2d03abcfe563b12c817db84d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: A .ci/jenkins/api-py3/run_tests.sh A .ci/jenkins/integration-py3/run_tests.sh M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/__init__.py M lib/galaxy/util/none_like.py M lib/galaxy/util/renamed_temporary_file.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/uploads.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/util/encoding_util.py A pytest.ini M run_tests.sh M scripts/galaxy-main M scripts/plugin_staging.py M scripts/secret_decoder_ring.py M test/api/test_workflows.py M test/base/data/test_workflow_with_runtime_input.ga M test/base/driver_util.py M test/base/populators.py M test/base/rules_test_data.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh M test/integration/test_data_manager_table_reload.py M test/integration/test_mules_as_job_handlers.py M test/integration/test_scripts.py M test/integration/tool_sheds_conf.xml M test/integration/uses_shed.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml Log Message: ----------- Merge pull request #6565 from mvdbeek/setup_py3_test_job Setup py3 test job Commit: 6cbb574553a882b7573d86f25bede17e7293cc76 https://github.com/galaxyproject/galaxy/commit/6cbb574553a882b7573d86f25bed… Author: Matthew Spelchak <mrs11teen(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M doc/source/admin/special_topics/interactive_environments.rst Log Message: ----------- Fix Location of Plugin Static Content Commit: 55756ba12de6f40db077576d3bae961aea6f190d https://github.com/galaxyproject/galaxy/commit/55756ba12de6f40db077576d3bae… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #6582 from jmchilton/selenium_fixes_45 Improve robustness of tour Selenium test. Commit: 7e445be502a64213c96cb233200aa0f53a2821f4 https://github.com/galaxyproject/galaxy/commit/7e445be502a64213c96cb233200a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M doc/source/admin/special_topics/interactive_environments.rst Log Message: ----------- Merge pull request #6602 from phac-nml/ie_documentation_fix [18.05] Fix Location of Plugin Static Content In Documentation for 18.05 Commit: ef0a51537e56e3257532df258494a00a8f7c2506 https://github.com/galaxyproject/galaxy/commit/ef0a51537e56e3257532df258494… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/verify/interactor.py M scripts/functional_tests.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py Log Message: ----------- Merge pull request #6595 from mvdbeek/modernize_data_manager_testing_strip_twill Modernize data manager testing and strip twill Commit: 318fc0994903d3598d9a62e1c8718cb7cde53bfe https://github.com/galaxyproject/galaxy/commit/318fc0994903d3598d9a62e1c871… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/em.trr Log Message: ----------- Merge pull request #6597 from bgruening/trr add trr datatype Commit: 709e49f104e2cba5d180bffb0ed0fee175f5ffba https://github.com/galaxyproject/galaxy/commit/709e49f104e2cba5d180bffb0ed0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Merge pull request #6591 from dannon/ucsc-test-server-domain [18.05] Update UCSC genome-test server URLs Commit: 3e6fa40ec84206558aa11679170fd747ff2f20b3 https://github.com/galaxyproject/galaxy/commit/3e6fa40ec84206558aa11679170f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Fix some lint issues in psa_authnz.py. Commit: 5624323a337a5d6176d3bb9be3bef599e65167b1 https://github.com/galaxyproject/galaxy/commit/5624323a337a5d6176d3bb9be3be… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: A .ci/jenkins/framework-py3/run_tests.sh M run_tests.sh Log Message: ----------- Add framework_py3 test target Commit: fc464f975878867ddc8ef90818db9faab31c7368 https://github.com/galaxyproject/galaxy/commit/fc464f975878867ddc8ef90818db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M test/functional/tools/metadata_biom1.xml Log Message: ----------- Allow 4 lines diff to acount for the prefix of python2 unicode strings Commit: 58067b4c896df7f2f48f3c7b6f4c92f9c6d6f265 https://github.com/galaxyproject/galaxy/commit/58067b4c896df7f2f48f3c7b6f4c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix count_lines function for compressed datatypes that inherit from Text Commit: 79ec064214030badbc64694213db0ce4865b5e64 https://github.com/galaxyproject/galaxy/commit/79ec064214030badbc64694213db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- py3: Fix Biom1 datatype Commit: 37132212fe5e1fdf7f43e41c59eac051bfb8f389 https://github.com/galaxyproject/galaxy/commit/37132212fe5e1fdf7f43e41c59ea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/jobs/splitters/multi.py Log Message: ----------- py3: Fix file splitting for parallelism Commit: f831c616cb418f72baa1aae420b47a49a0aacc3c https://github.com/galaxyproject/galaxy/commit/f831c616cb418f72baa1aae420b4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- py3: fix paths_as_file functionality Commit: 70640071224745f61d756ed1475b5a03c85f4f40 https://github.com/galaxyproject/galaxy/commit/70640071224745f61d756ed1475b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Don't log error to provide arguments to __new__ for types that don't take arguments This is just very verbose and unneeded. Commit: ea0e3ffeb779fee900aa8dbc33773a921e39ec9c https://github.com/galaxyproject/galaxy/commit/ea0e3ffeb779fee900aa8dbc3377… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- py3: Fix dataset dataset collection Commit: a927413df22ff3454cf6c691f851cf54673eefb7 https://github.com/galaxyproject/galaxy/commit/a927413df22ff3454cf6c691f851… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M test/functional/tools/parallelism.xml M test/functional/tools/parallelism_optional.xml Log Message: ----------- Use exit code and quote file parameters for paralellism test tools Commit: b041e41155ac18252c46364ac409a9695d9f8bfb https://github.com/galaxyproject/galaxy/commit/b041e41155ac18252c46364ac409… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Write configfile in binary mode This fixes the unicode_stream tool on docker. Commit: b29311fdab1a08a70eee7fad69f77bc72d8e88bc https://github.com/galaxyproject/galaxy/commit/b29311fdab1a08a70eee7fad69f7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Get ID token, if expired, refresh it. Commit: 27db877816bdba5f91ada327c63b7a7717341e18 https://github.com/galaxyproject/galaxy/commit/27db877816bdba5f91ada327c63b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove the `get_access_token` as it hides a base method. Commit: f0a8c541d8c83e6e6bbd7731ba4197cae549b47a https://github.com/galaxyproject/galaxy/commit/f0a8c541d8c83e6e6bbd7731ba41… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add a comment explaining a PSA pipeline step. Commit: 9d7f50c6c074a9d3e39763180d6e270f7290164f https://github.com/galaxyproject/galaxy/commit/9d7f50c6c074a9d3e39763180d6e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add doc string for `contains_required_data` function. Commit: 79decc3ba77c5fbcaf36a0cbb9aace16512bcf9d https://github.com/galaxyproject/galaxy/commit/79decc3ba77c5fbcaf36a0cbb9aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Use OrderedDict to collect implicit collections This should fix randomly failing tests that rely on the order of the implcit collection elements, like `test_map_over_two_collections_unlinked`. Commit: 899353d631b1a3fa0b38730009f9dfc6e97b761f https://github.com/galaxyproject/galaxy/commit/899353d631b1a3fa0b38730009f9… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add dcd datatype Commit: c430d4a6509375c5aaf658f149b3038aa8f34883 https://github.com/galaxyproject/galaxy/commit/c430d4a6509375c5aaf658f149b3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Fix selenium test setup Commit: 3957ed91e2d25faae9100c85bc19b9a1c5b3d68e https://github.com/galaxyproject/galaxy/commit/3957ed91e2d25faae9100c85bc19… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M templates/display_common.mako M templates/legacy/grid_base.mako M templates/tagging_common.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Fix errors found during selenium testing Commit: ae9effa61005504c51ca11adbbf6b70f95fab3b8 https://github.com/galaxyproject/galaxy/commit/ae9effa61005504c51ca11adbbf6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: A .ci/jenkins/selenium-py3/run_tests.sh Log Message: ----------- Add selenium py3 jenkins setup Commit: fb86e96bffecaef3861ce68db963c22aee193d54 https://github.com/galaxyproject/galaxy/commit/fb86e96bffecaef3861ce68db963… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Skip decoding to unicode strings in grids At this point we should not have bytestrings anymore (we might, but if we do we should fix that instead). Commit: 7559b90a692a72da2556c61b65c8615ddff822a5 https://github.com/galaxyproject/galaxy/commit/7559b90a692a72da2556c61b65c8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M test/base/driver_util.py M test/functional/test_toolbox.py A test/functional/test_toolbox_pytest.py Log Message: ----------- Setup a simple pytest tool test Commit: b9ca3b7c339628ac017ffc27a91659dce87c4a96 https://github.com/galaxyproject/galaxy/commit/b9ca3b7c339628ac017ffc27a916… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M test/api/test_jobs.py Log Message: ----------- Merge pull request #6593 from jmchilton/toward_test_history_cleaning Migrate API tests in test_jobs.py to use test_history context. Commit: d9f394793897a4429664027cbdaacbb8fca6d4e2 https://github.com/galaxyproject/galaxy/commit/d9f394793897a4429664027cbdaa… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: A .ci/jenkins/framework-py3/run_tests.sh A .ci/jenkins/selenium-py3/run_tests.sh M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/web/framework/helpers/grids.py M run_tests.sh M templates/display_common.mako M templates/legacy/grid_base.mako M templates/tagging_common.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/base/driver_util.py M test/functional/test_toolbox.py A test/functional/test_toolbox_pytest.py M test/functional/tools/metadata_biom1.xml M test/functional/tools/parallelism.xml M test/functional/tools/parallelism_optional.xml Log Message: ----------- Merge pull request #6605 from mvdbeek/enable_and_fix_framework_py3_test Enable and fix framework py3 tests Commit: 9e07d9cc062bf8a21bfab72c2505191e1d3c86e4 https://github.com/galaxyproject/galaxy/commit/9e07d9cc062bf8a21bfab72c2505… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: A test/functional/conftest.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/test_toolbox_pytest.py Log Message: ----------- Handle driver shutdown, show all test in pytest This is pretty hackish as fixtures can't be used during test discovery. To properly shut down the driver I've added a conftest.py file that will be called when quitting pytest. We might be able to handle this a little better if we wrote a full plugin, but for now this works. Also now reports all test indexes, so you can select e.g test 2 of a tool. Commit: 2b275b7df033c323cec93c34a8089a4820fce768 https://github.com/galaxyproject/galaxy/commit/2b275b7df033c323cec93c34a808… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M test/functional/test_toolbox_pytest.py Log Message: ----------- Start counting test numbers at 1 and use _test_n That allows for nicer select syntax like ```` pytest test/functional/test_toolbox_pytest.py -k '(random_lines1 or Cut1) and _test_1' ``` Commit: dac763a665703e84bd7cd29f63de60dd75fd305c https://github.com/galaxyproject/galaxy/commit/dac763a665703e84bd7cd29f63de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Keep unicode tags Should fix ``` selenium.webdriver.remote.remote_connection DEBUG 2018-08-16 19:17:13,852 Finished Request galaxy.web.framework.decorators ERROR 2018-08-16 19:17:13,858 Uncaught exception in exposed API method: Traceback (most recent call last): File "/galaxy/lib/galaxy/web/framework/decorators.py", line 157, in decorator rval = func(self, trans, *args, **kwargs) File "/galaxy/lib/galaxy/web/framework/decorators.py", line 77, in decorator return func(self, trans, *args, **kwargs) File "/galaxy/lib/galaxy/webapps/galaxy/controllers/history.py", line 317, in list return self.stored_list_grid(trans, **kwargs) File "/galaxy/lib/galaxy/web/framework/helpers/grids.py", line 139, in __call__ query = column.filter(trans, trans.user, query, column_filter) File "/galaxy/lib/galaxy/web/framework/helpers/grids.py", line 664, in filter query = query.filter(self.get_filter(trans, user, column_filter)) File "/galaxy/lib/galaxy/web/framework/helpers/grids.py", line 703, in get_filter raw_tags = trans.app.tag_handler.parse_tags(column_filter.encode("utf-8")) File "/galaxy/lib/galaxy/managers/tags.py", line 260, in parse_tags raw_tags = reg_exp.split(tag_str) TypeError: cannot use a string pattern on a bytes-like object ``` Commit: 43f539ce729f8c0be06ff0d5d8cf6f26db52a148 https://github.com/galaxyproject/galaxy/commit/43f539ce729f8c0be06ff0d5d8cf… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Cloud: raise an exception if a history with decoded id does not exist. Commit: 85f76945777b09958488672ef1a7c456d2bc5980 https://github.com/galaxyproject/galaxy/commit/85f76945777b09958488672ef1a7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Fix one more case of tag encoding Commit: c63e4fde41c4c72a45a8d2999833804481c9c9a2 https://github.com/galaxyproject/galaxy/commit/c63e4fde41c4c72a45a8d2999833… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- register dcd datatype Commit: 98e4dab4ef48617bd8e03590d19d009c730284ab https://github.com/galaxyproject/galaxy/commit/98e4dab4ef48617bd8e03590d19d… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: A lib/galaxy/datatypes/test/test_glucose_vacuum.dcd Log Message: ----------- add dcd example file Commit: f8833cc4b34784a033e8d0910ae09eeddab5105c https://github.com/galaxyproject/galaxy/commit/f8833cc4b34784a033e8d0910ae0… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- PEP corrections Commit: d05e8e0cb10cd75310c59a903eed8f4e0cab7fa2 https://github.com/galaxyproject/galaxy/commit/d05e8e0cb10cd75310c59a903eed… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- file open fix Commit: 2c6900930c2454979fcc96e9159bdbbe44bafc3b https://github.com/galaxyproject/galaxy/commit/2c6900930c2454979fcc96e9159b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Merge pull request #6610 from mvdbeek/fix_selenium_py3_tests Fix remaining selenium py3 test failures Commit: f5bd245faaaa90693d8a5739f60bc863f545762f https://github.com/galaxyproject/galaxy/commit/f5bd245faaaa90693d8a5739f60b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M cron/build_chrom_db.py M cron/parse_builds_3_sites.py M doc/source/admin/special_topics/interactive_environments.rst M tools/data_source/ucsc_tablebrowser_test.xml Log Message: ----------- Merge branch 'release_18.05' into dev Commit: bf206c870b793edda71aaa5655baeca070e3729a https://github.com/galaxyproject/galaxy/commit/bf206c870b793edda71aaa5655ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py M lib/galaxy/util/permutations.py Log Message: ----------- Reorder inputs before multiplications This should be a stable order. Ideally this would be configurable to the user or tool auther, but for now this is based on the order within which data paramaters appear in tool.inputs, which depends on the order in the XML/YML. If this isn't stable the order of the input combinations may change, and elements will jump in the collection structure. For instance the reverse:forward output for a pair:pair in inputA multiplied by pair:pair in input B may end up in forward:reverse if re-run. Commit: 9138651bdd92e0eb1fe2ea2b2099b5b2f04f655d https://github.com/galaxyproject/galaxy/commit/9138651bdd92e0eb1fe2ea2b2099… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Serialize JobParamters with sort_keys=True This wasn't a bigger issue on python 2 for the same reason that the input ordering in the previous commit didn't matter. I hope it'll make the test_workflow_rerun_with_use_cached_job test that is marked as flakey stable as well. Commit: 2d60d9af0132c4975ae636d161097140b72e6fbc https://github.com/galaxyproject/galaxy/commit/2d60d9af0132c4975ae636d16109… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Wait for first workflow when testing cache That should make the test less flakey. While in theory we should be able to replace scheduled workflow jobs with cached jobs, this is not what we're testing here, and I assume it doesn't work for now. Commit: 7160b7f4e48e0c611758aea890771fea07a059ec https://github.com/galaxyproject/galaxy/commit/7160b7f4e48e0c611758aea89077… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- No kwargs for rsplit on python 2 Commit: 3fc40c16a3fc9cda2284cf9e5cca91373797a52c https://github.com/galaxyproject/galaxy/commit/3fc40c16a3fc9cda2284cf9e5cca… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- use seek. logic improved. Commit: 33794fa318e49b8eeef2e65ce59a8a5bf361db3a https://github.com/galaxyproject/galaxy/commit/33794fa318e49b8eeef2e65ce59a… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test_charmm.vel Log Message: ----------- add vel datatype,register and example Commit: 85f347e1c6597523b0e8718d7a93d4dc27cac2f9 https://github.com/galaxyproject/galaxy/commit/85f347e1c6597523b0e8718d7a93… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/util/permutations.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6609 from mvdbeek/fix_random_implicit_collection_order Order data parameters before unlinked multiplication Commit: f8b797c06092695c5e5431be49d806b94e900780 https://github.com/galaxyproject/galaxy/commit/f8b797c06092695c5e5431be49d8… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- no edam format yet. soon. Commit: e9846ae9766e29bbbb8b16ff8e5b6b654333e168 https://github.com/galaxyproject/galaxy/commit/e9846ae9766e29bbbb8b16ff8e5b… Author: Chris Barnett <chris.barnett(a)uct.ac.za> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- edam data Commit: 3c7eeecee52d5babf8039fd48ab161555086f84f https://github.com/galaxyproject/galaxy/commit/3c7eeecee52d5babf8039fd48ab1… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test_charmm.vel A lib/galaxy/datatypes/test/test_glucose_vacuum.dcd Log Message: ----------- Merge pull request #6613 from chrisbarnettster/cbb_md_dcd add dcd datatype for molecular dynamics Commit: e07cc9a96009bafb47c27199cc231213ce2c3514 https://github.com/galaxyproject/galaxy/commit/e07cc9a96009bafb47c27199cc23… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: A test/functional/conftest.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/test_toolbox_pytest.py Log Message: ----------- Merge pull request #6608 from mvdbeek/more_pytest_improvements Handle driver shutdown, show all tests in pytest Commit: 78a8c865a13b98bd3dc93a2b0dade86d2d6e43bf https://github.com/galaxyproject/galaxy/commit/78a8c865a13b98bd3dc93a2b0dad… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/tools/evaluation.py M lib/galaxy/web/framework/webapp.py Log Message: ----------- Revert unnecessary changes Commit: 5bddd24d8b8994f9f59d0f7ba541321c8146a166 https://github.com/galaxyproject/galaxy/commit/5bddd24d8b8994f9f59d0f7ba541… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-20 (Mon, 20 Aug 2018) Changed paths: M test/api/test_jobs.py Log Message: ----------- Remove unreachable return statement Commit: 4a3ed12f0af3f9b26dc9cb5b66eabb26f9dc542e https://github.com/galaxyproject/galaxy/commit/4a3ed12f0af3f9b26dc9cb5b66ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M .gitignore Log Message: ----------- Ignore .pytest_cache/ , assets/ and run_integration_tests.html Commit: df8abbe3ef13c0b288becba07af4a05b8f6dc668 https://github.com/galaxyproject/galaxy/commit/df8abbe3ef13c0b288becba07af4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/web/framework/middleware/batch.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/util/encoding_util.py M scripts/secret_decoder_ring.py M test/base/populators.py M test/base/rules_test_data.py M test/integration/test_scripts.py Log Message: ----------- Prefer `unicodify()` for binary-to-text conversion which supports non-utf-8 encodings. Commit: 5d1ced2678737e1ceebb727c3b81d4546ee6588b https://github.com/galaxyproject/galaxy/commit/5d1ced2678737e1ceebb727c3b81… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/util/checkers.py Log Message: ----------- Do not open text file in binary mode Commit: f54246e1a1d157ba43783dc2a86f40aeb5c7b7f2 https://github.com/galaxyproject/galaxy/commit/f54246e1a1d157ba43783dc2a86f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml M lib/galaxy/web/framework/middleware/batch.py M test/api/test_authenticate.py Log Message: ----------- Use `encode()` method instead of `bytearray()` to encode a Unicode string to a binary one. Commit: 72f020726593bcd6026cba5a127ff615df49968f https://github.com/galaxyproject/galaxy/commit/72f020726593bcd6026cba5a127f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Remove unused `binary_chars` parameter of `smart_str()` Commit: d265b8a88ada5d2e57efbc03740c697ab5c7464f https://github.com/galaxyproject/galaxy/commit/d265b8a88ada5d2e57efbc03740c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Raise an exception if `unicodify()` fails the conversion Commit: 61041a7c6b09664b2fa9d8d479de4251647cec87 https://github.com/galaxyproject/galaxy/commit/61041a7c6b09664b2fa9d8d479de… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Raise `AttributeError` exception in `DatasetCollectionWrapper.__getattr__()` Commit: cd11a8c19ab672d8326cb474d7833cf532ae82cc https://github.com/galaxyproject/galaxy/commit/cd11a8c19ab672d8326cb474d783… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Use `NamedTemporaryFile` opened in text mode Commit: 670d8b1623b1ba16f2b23cc661e581600556ae61 https://github.com/galaxyproject/galaxy/commit/670d8b1623b1ba16f2b23cc661e5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: R test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge TwillTestCase in ShedTwillTestCase Commit: ff15f3679818dc8f0ea4610ed28cc5957ac68901 https://github.com/galaxyproject/galaxy/commit/ff15f3679818dc8f0ea4610ed28c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/framework-py3/run_tests.sh M .ci/jenkins/integration-py3/run_tests.sh M run_tests.sh Log Message: ----------- Run Py2 API and integration tests with pytest Remove `-api_py3`, `--framework_py3` and `--integration_py3` options of `run_tests.sh`. To run the tests under Python3 it is enough to prepend `GALAXY_VIRTUAL_ENV=.venv3` (or add `--python3` when using `--dockerize`). Commit: c501fb1647b21720dfbaeedb062084813095284e https://github.com/galaxyproject/galaxy/commit/c501fb1647b21720dfbaeedb0620… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/util/bunch.py M lib/galaxy/util/expressions.py M lib/galaxy/util/none_like.py Log Message: ----------- Alias `__nonzero__` to `__bool__` Commit: 05999f9767b9ad906a719f2e103c96e64e1b41a7 https://github.com/galaxyproject/galaxy/commit/05999f9767b9ad906a719f2e103c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/web/stack/__init__.py Log Message: ----------- Unicodify all farm elements Commit: ff0d28c35c2c7c5371f2101e72c00259ebd4950b https://github.com/galaxyproject/galaxy/commit/ff0d28c35c2c7c5371f2101e72c0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/util/template.py M test/functional/tools/unicode_stream.xml Log Message: ----------- Fix unicode_stream framework tests on Docker This fixes the following traceback: ``` ( unicode_stream ) > Test-1 ... galaxy.tools DEBUG 2018-08-21 09:40:59,052 Validated and populated state for tool request (0.098 ms) galaxy.tools.actions INFO 2018-08-21 09:40:59,076 Handled output named out_file1 for tool unicode_stream (1.337 ms) galaxy.tools.actions INFO 2018-08-21 09:40:59,080 Added output datasets to history (4.399 ms) galaxy.tools.actions INFO 2018-08-21 09:40:59,084 Verified access to datasets for Job[unflushed,tool_id=unicode_stream] (0.058 ms) galaxy.tools.actions INFO 2018-08-21 09:40:59,086 Setup for job Job[unflushed,tool_id=unicode_stream] complete, ready to flush (5.220 ms) galaxy.tools.actions INFO 2018-08-21 09:40:59,127 Flushed transaction for job Job[id=354,tool_id=unicode_stream] (40.627 ms) galaxy.tools.execute DEBUG 2018-08-21 09:40:59,127 Tool [unicode_stream] created job [354] (56.506 ms) galaxy.tools.execute DEBUG 2018-08-21 09:40:59,132 Executed 1 job(s) for tool unicode_stream request: (79.434 ms) galaxy.jobs.mapper DEBUG 2018-08-21 09:40:59,556 (354) Mapped job to destination id: local galaxy.jobs.handler DEBUG 2018-08-21 09:40:59,561 (354) Dispatching to local runner galaxy.jobs DEBUG 2018-08-21 09:40:59,571 (354) Working directory for job is: /tmp/tmp3drfmr6x/tmp_ywd33ar/tmpbzo4a1d9/database/job_working_directory_azry9a1y/000/354 galaxy.jobs DEBUG 2018-08-21 09:40:59,574 (354) Persisting job destination (destination id: local) galaxy.jobs.runners DEBUG 2018-08-21 09:40:59,589 Job [354] queued (27.361 ms) galaxy.jobs.handler INFO 2018-08-21 09:40:59,604 (354) Job dispatched galaxy.jobs.runners ERROR 2018-08-21 09:40:59,715 (354) Failure preparing job Traceback (most recent call last): File "/galaxy/lib/galaxy/jobs/runners/__init__.py", line 187, in prepare_job job_wrapper.prepare() File "/galaxy/lib/galaxy/jobs/__init__.py", line 874, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File "/galaxy/lib/galaxy/tools/evaluation.py", line 435, in build raise e File "/galaxy/lib/galaxy/tools/evaluation.py", line 431, in build self.__build_config_files() File "/galaxy/lib/galaxy/tools/evaluation.py", line 504, in __build_config_files self.__write_workdir_file(config_filename, config_text, param_dict, is_template=is_template) File "/galaxy/lib/galaxy/tools/evaluation.py", line 578, in __write_workdir_file f.write(value) UnicodeEncodeError: 'ascii' codec can't encode characters in position 0-5: ordinal not in range(128) galaxy.tools.error_reports DEBUG 2018-08-21 09:40:59,869 Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7f92efb81668> generated response None FAIL ``` which is due to the fact that the default encoding in the Docker image is `ANSI_X3.4-1968`. Also update `unicode_stream` test tool to IUC best practices. Commit: 99517c6fdf3d07bf98dad6f88946bca4fb82fea1 https://github.com/galaxyproject/galaxy/commit/99517c6fdf3d07bf98dad6f88946… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M .ci/jenkins/api-py3/run_tests.sh M .ci/jenkins/framework-py3/run_tests.sh M .ci/jenkins/integration-py3/run_tests.sh M .gitignore M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/evaluation.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/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/bunch.py M lib/galaxy/util/checkers.py M lib/galaxy/util/expressions.py M lib/galaxy/util/none_like.py M lib/galaxy/util/template.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/util/encoding_util.py M run_tests.sh M scripts/secret_decoder_ring.py M test/api/test_authenticate.py M test/api/test_jobs.py M test/base/populators.py M test/base/rules_test_data.py M test/functional/tools/unicode_stream.xml R test/functional/twilltestcase.py M test/integration/test_scripts.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #6616 from nsoranzo/followup_on_6561 Py3 testing cleanups Commit: aa0df987bbe4790eb830b86b3dc2f2db2b8edd85 https://github.com/galaxyproject/galaxy/commit/aa0df987bbe4790eb830b86b3dc2… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update doc string. Commit: 46dc4db25a5c44788ff454650e91b383fb506837 https://github.com/galaxyproject/galaxy/commit/46dc4db25a5c44788ff454650e91… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Merge pull request #6611 from VJalili/patch_cloud_upload Raise an exception if a history with decoded id does not exist. Commit: 626195335ee70dbc2d0568603e0627744d07d529 https://github.com/galaxyproject/galaxy/commit/626195335ee70dbc2d0568603e06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M test/base/driver_util.py M test/base/integration_util.py A test/integration/delay_job_conf.xml A test/integration/delay_rules/__init__.py A test/integration/delay_rules/rules.py A test/integration/test_job_recovery.py M test/integration/test_job_resubmission.py Log Message: ----------- Integration test for job recovery (before and after handler has picked it up). Commit: 6cce9830a7c77b22d8baaa889b34b53faf933b67 https://github.com/galaxyproject/galaxy/commit/6cce9830a7c77b22d8baaa889b34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M templates/display_common.mako Log Message: ----------- [minor] Fix incorrect import in display_common.mako. Broke a few Selenium tests, not sure which commit broke this but it was fairly recent because these tests were passing two weeks ago. Commit: fc167c068c9d3b5fcdcce4514801ea2626c7d6d3 https://github.com/galaxyproject/galaxy/commit/fc167c068c9d3b5fcdcce4514801… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M templates/display_common.mako Log Message: ----------- Merge pull request #6622 from jmchilton/selenium_fixes_46 [minor] Fix incorrect import in display_common.mako. Commit: c852de734dbc8d95ac925c103f4cad563d3f9e53 https://github.com/galaxyproject/galaxy/commit/c852de734dbc8d95ac925c103f4c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M cron/build_chrom_db.py Log Message: ----------- Fix cron/build_chrom_db.py Fix the following errors: ``` $ python cron/build_chrom_db.py tool-data/shared/ucsc/chrom/ tool-data/shared/ucsc/builds.txt Retrieving hg38 Failed to retrieve hg38: Problem parsing line '' Retrieving hg19 Failed to retrieve hg19: Problem parsing line '' ... ``` Broken in commit 9b8e76f9d9df0ae0ba6238d44a8f07b97fe34d6f . Commit: 926f0abde2c5ae6caf0727d890c2f90a34587cec https://github.com/galaxyproject/galaxy/commit/926f0abde2c5ae6caf0727d890c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Update UCSC builds Commit: 2d4b717aaff3fc8a76852af8a16744f1085fa8cc https://github.com/galaxyproject/galaxy/commit/2d4b717aaff3fc8a76852af8a167… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case to clarify workflow API a bit in simple cases. Commit: c593bd1772dc6d8780153115641d556bea347bc9 https://github.com/galaxyproject/galaxy/commit/c593bd1772dc6d8780153115641d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow uniform access to job state for WorkflowInvocationSteps. Use the concept of job_source_type and job_source_id used by IDs to summarize the state and list out individual jobs in the response as a shortcut. This information used to be readily accessible before 18.01. Commit: 35ebdc5b1029bbe782c2852b5f6b094d97dbd7ea https://github.com/galaxyproject/galaxy/commit/35ebdc5b1029bbe782c2852b5f6b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Add a legacy_job_state mode to restore 17.09 workflow invocation behavior. Commit: 53b8f08752edc35839f1ed9a8bc6355a528c99b4 https://github.com/galaxyproject/galaxy/commit/53b8f08752edc35839f1ed9a8bc6… Author: Helena Rasche <erasche(a)users.noreply.github.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/lddas.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/users.py M lib/galaxy/security/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py A test/api/test_roles.py M test/api/test_tools.py M test/base/api.py M test/base/populators.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #6568 from jmchilton/dataset-permissions-api-2 Unified dataset permission API. Commit: 498e7d576bb40e7f2eea47b1d787638a2c507965 https://github.com/galaxyproject/galaxy/commit/498e7d576bb40e7f2eea47b1d787… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/objectstore/__init__.py A test/integration/objectstore_selection_job_conf.xml A test/integration/objectstore_selection_job_resource_parameters_conf.xml A test/integration/objectstore_selection_rules/__init__.py A test/integration/objectstore_selection_rules/rules.py A test/integration/test_objectstore_selection.py Log Message: ----------- Merge pull request #6552 from jmchilton/per_destination_object_store Allow configuring object stores on a per-job-destination basis. Commit: 89f237216d7d5c2030c2d620af0f95c6318ac14c https://github.com/galaxyproject/galaxy/commit/89f237216d7d5c2030c2d620af0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M cron/build_chrom_db.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge pull request #6623 from nsoranzo/ucsc_builds Fix cron/build_chrom_db.py and update UCSC builds Commit: 5f4dd9be92e3d9446d25b34fd83e7e8cc61e8c67 https://github.com/galaxyproject/galaxy/commit/5f4dd9be92e3d9446d25b34fd83e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Update some run_tests.sh docs for recent changes. Commit: 7360a90695db121008acc7df51c9bcab7824a4c2 https://github.com/galaxyproject/galaxy/commit/7360a90695db121008acc7df51c9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M .travis.yml Log Message: ----------- Remove check_python_dependencies job from Travis No need to run it on every pull request and merge. It can be run locally via: ``` $ tox -e check_python_dependencies ``` Commit: 636e8c66785cf4757b502d7fab2e80607612d324 https://github.com/galaxyproject/galaxy/commit/636e8c66785cf4757b502d7fab2e… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #6629 from jmchilton/run_test_update Update some run_tests.sh docs for recent changes. Commit: e824fbeec16c68b144a3f1dcddcdae2609619ac7 https://github.com/galaxyproject/galaxy/commit/e824fbeec16c68b144a3f1dcddcd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py Log Message: ----------- Sort local test data if output is sort="true" This means if you run planemo test --update_test_data, your test will actually work, instead of needing to sort it manually. The other benefit is that you can see the expected test data without sorting, e.g sorted HTML files are most likely not valid after sorting. Commit: 23cfb4600115ad9d6c2fee239b73aa7dc72ea92b https://github.com/galaxyproject/galaxy/commit/23cfb4600115ad9d6c2fee239b73… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M test/base/driver_util.py M test/integration/uses_shed.py Log Message: ----------- Allow setting CONDA_PREFIX using GALAXY_TEST_CONDA_PREFIX in testing Commit: 0d85a6c5c089934df6cfc8c0d5ae9af31678aa81 https://github.com/galaxyproject/galaxy/commit/0d85a6c5c089934df6cfc8c0d5ae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/tools/verify/test_data.py Log Message: ----------- Use first resolved test data file Commit: 000026a46a620607defde16fa518cace953b1ca9 https://github.com/galaxyproject/galaxy/commit/000026a46a620607defde16fa518… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/jobs/output_checker.py Log Message: ----------- Report stderr whenever a job fails, and report more The 250 character level is usually not enough to figure out what's going on, and I think if we want to see the stderr if a job fails because of stderr problems, we probably also want to see a peek of the stderr if a job fails because of the exit code. Commit: 5c889cd5e18e60818a922816884f56cb35262a2e https://github.com/galaxyproject/galaxy/commit/5c889cd5e18e60818a922816884f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #6630 from nsoranzo/remove_check_python_dependencies_from_travis Remove check_python_dependencies job from Travis Commit: a2d99e30c727e7050c1fd6218603b7b2941c8c4d https://github.com/galaxyproject/galaxy/commit/a2d99e30c727e7050c1fd6218603… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Update all dependencies Also merge dev dependencies in default Pipfile. Commit: ac29abb6266fb9b83c985b27804db607c503ef51 https://github.com/galaxyproject/galaxy/commit/ac29abb6266fb9b83c985b27804d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Fix metadata elements reset when creating Metadata files This is a fallout out from 9780d069c8646fb4f02de848d62159680d95ae79 Commit: ea42956c6c3a02435a9a0f6f43ae653cb9d9bd00 https://github.com/galaxyproject/galaxy/commit/ea42956c6c3a02435a9a0f6f43ae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/roles.py Log Message: ----------- Catch all exception types when decoding an id Under Python 3 `codecs.decode()` raises a `binascii.Error` exception instead of a `TypeError`. Fix the following traceback produced by the `test/api/test_roles.py::RolesApiTestCase::test_show_error_codes` API test under Python 3: ``` galaxy.web.framework.decorators ERROR 2018-08-22 22:17:47,960 Uncaught exception in exposed API method: Traceback (most recent call last): File "/galaxy_venv3/lib/python3.5/encodings/hex_codec.py", line 19, in hex_decode return (binascii.a2b_hex(input), len(input)) binascii.Error: Odd-length string The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/galaxy/lib/galaxy/web/framework/decorators.py", line 157, in decorator rval = func(self, trans, *args, **kwargs) File "/galaxy/lib/galaxy/webapps/galaxy/api/roles.py", line 39, in show decoded_role_id = trans.security.decode_id(role_id) File "/galaxy/lib/galaxy/web/security/__init__.py", line 84, in decode_id return int(unicodify(id_cipher.decrypt(codecs.decode(obj_id, 'hex'))).lstrip("!")) binascii.Error: decoding with 'hex' codec failed (Error: Odd-length string) ``` See https://jenkins.galaxyproject.org/job/docker-api-py3/140/testReport/junit/t… Commit: 43dbfdc7b1290f493584901ae00dd08ea1b0396a https://github.com/galaxyproject/galaxy/commit/43dbfdc7b1290f493584901ae00d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/jobs/output_checker.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/test_data.py M test/base/driver_util.py M test/integration/uses_shed.py Log Message: ----------- Merge pull request #6632 from mvdbeek/testing_framework_improvements Testing framework improvements Commit: f6a55ee2eef2fe85cc8d7ed198c1610be5607165 https://github.com/galaxyproject/galaxy/commit/f6a55ee2eef2fe85cc8d7ed198c1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Tweak conda_* setting in test driver Thanks @nsoranzo! Commit: 6ad304976ecb41d428e55a7a33614dd5e76edb2d https://github.com/galaxyproject/galaxy/commit/6ad304976ecb41d428e55a7a3361… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Merge pull request #6633 from mvdbeek/testing_framework_followup Tweak conda_* setting in test driver Commit: 6220a557f7661a3f658450530bf485914b657f5e https://github.com/galaxyproject/galaxy/commit/6220a557f7661a3f658450530bf4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt R lib/galaxy/dependencies/pipfiles/develop/Pipfile R lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/webapps/galaxy/api/roles.py Log Message: ----------- Merge pull request #6628 from nsoranzo/update_deps Update all dependencies Commit: dfdf3dd5eac4f6ae182ddf3d50490dc73a4dd614 https://github.com/galaxyproject/galaxy/commit/dfdf3dd5eac4f6ae182ddf3d5049… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Merge pull request #6631 from mvdbeek/fix_metadata_element_rest Fix metadata elements reset when creating Metadata files Commit: 3879a019490a05f9e26e3651e6de52d0586d5963 https://github.com/galaxyproject/galaxy/commit/3879a019490a05f9e26e3651e6de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_workflows.py Log Message: ----------- Add API endpoint to index all invocations for a user or history. Refactor toward managers to allow unified serialization of invocations and such. Add test case. Commit: ded2311799a772914ddb9c732d59ba2f4de572b4 https://github.com/galaxyproject/galaxy/commit/ded2311799a772914ddb9c732d59… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Handle job_wrapper.working_directory correctly during job recovery. Commit: 107c89a0a994a50fd37589fbd2b4d104064c7336 https://github.com/galaxyproject/galaxy/commit/107c89a0a994a50fd37589fbd2b4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6580 from jmchilton/wf_invocation_update Add API endpoint to fetch a history's workflow invocations. Commit: 5e74154c930326f4c7a69f7dbd33ea88189fb257 https://github.com/galaxyproject/galaxy/commit/5e74154c930326f4c7a69f7dbd33… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Optimize initial validation of collection input parameters. Commit: 49eae728916af02a6fbd3ce9d69599c08d4e58b9 https://github.com/galaxyproject/galaxy/commit/49eae728916af02a6fbd3ce9d695… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Fix for workflow extraction cleanup routine. Workflow extraction would be incorrect if you had parameters ordered and named as e.g. "somename" and "somename_2" in the input root. When these parameters are both dataset inputs, this would cause a server error. Commit: 0b64442ed3d06bd7fdf9f0fbb53520d28e9332b9 https://github.com/galaxyproject/galaxy/commit/0b64442ed3d06bd7fdf9f0fbb535… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: A test/functional/known_broken_tools.txt M test/functional/test_toolbox_pytest.py Log Message: ----------- Skip tool tests in test/functional/known_broken_tools.txt Commit: 300ab73c10332968a98eb5f77a85abc66a3f4686 https://github.com/galaxyproject/galaxy/commit/300ab73c10332968a98eb5f77a85… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M pytest.ini M test/functional/test_toolbox_pytest.py Log Message: ----------- Mark skipped tests instead of not collecting them Also marks tests as tool or data_manager, so `pytest -m <tool|data_manager>` can be used to select a subset of tests. Commit: 6f299202313c3b40d357468e9ba0e9b32f858038 https://github.com/galaxyproject/galaxy/commit/6f299202313c3b40d357468e9ba0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Use pytest for -framework, -installed, -data_manager, -migrated tests Commit: 546b90a6985cc6a8e4d87482778c8ac275c9903f https://github.com/galaxyproject/galaxy/commit/546b90a6985cc6a8e4d87482778c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Add additional test target for tools in tool_conf.xml.main Commit: e73257f8ed2556a94a6e58efff62ed1873709f42 https://github.com/galaxyproject/galaxy/commit/e73257f8ed2556a94a6e58efff62… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M test/functional/test_toolbox_pytest.py Log Message: ----------- Set conda_auto_init and conda_auto_install to true for pytest driver Commit: 7f807ce971e8d743dca0f0438e5ce078f742ec65 https://github.com/galaxyproject/galaxy/commit/7f807ce971e8d743dca0f0438e5c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Fix shell syntax Commit: 9099e73a3e00658082891fae7ea3de0774cce2ad https://github.com/galaxyproject/galaxy/commit/9099e73a3e00658082891fae7ea3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M .coveragerc Log Message: ----------- Add include-ignored, otherwise spams stderr out Commit: d476fcc072dbcb8e3b19f511dc43ae731e7c97e0 https://github.com/galaxyproject/galaxy/commit/d476fcc072dbcb8e3b19f511dc43… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M lib/galaxy/jobs/runners/util/kill.py Log Message: ----------- Fix LocalShell on python3 Commit: 1c64cdd674fcbfc0f077f5d31947dd9b6c6e9149 https://github.com/galaxyproject/galaxy/commit/1c64cdd674fcbfc0f077f5d31947… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M pytest.ini M run_tests.sh M tox.ini Log Message: ----------- Use pytest to run unit and doctests Commit: 1152a19fd2cd5d6589becde3c7ebdd6435a33cff https://github.com/galaxyproject/galaxy/commit/1152a19fd2cd5d6589becde3c7eb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Use pytest-cov for testing coverage Commit: 66c64ccfe46cfd91bcffabaf2b4bddd7b86cef91 https://github.com/galaxyproject/galaxy/commit/66c64ccfe46cfd91bcffabaf2b4b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py Log Message: ----------- Adapt dynamic_tool_destination unit tests to pytest as driver The log capturing seems to be a bit different Commit: d9a2c5a970aafabe101842991a34074701f8854c https://github.com/galaxyproject/galaxy/commit/d9a2c5a970aafabe101842991a34… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Don't test tools in tool_conf.xml.sample as part of -framework This replicates what the FrameworkToolsGalaxyTestDriver does. Commit: 2560919bd04d6f27e14fcf9f580aea66244afa30 https://github.com/galaxyproject/galaxy/commit/2560919bd04d6f27e14fcf9f580a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py M test/base/driver_util.py M test/base/integration_util.py A test/integration/delay_job_conf.xml A test/integration/delay_rules/__init__.py A test/integration/delay_rules/rules.py A test/integration/test_job_recovery.py M test/integration/test_job_resubmission.py Log Message: ----------- Merge pull request #6620 from jmchilton/job_recovery_test Integration test for job recovery. Commit: aa0becad0be33ee7fe1d430c64f1d89f475ca6e2 https://github.com/galaxyproject/galaxy/commit/aa0becad0be33ee7fe1d430c64f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M run_tests.sh Log Message: ----------- Simplify tool_conf selection in run_tests.sh Drops -with_framework_test_tools altogether. Thanks @nsoranzo. Commit: a3fc0b9f324f3aa2a4824b260f3057a36471857a https://github.com/galaxyproject/galaxy/commit/a3fc0b9f324f3aa2a4824b260f30… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/build_list.xml A lib/galaxy/tools/extract_dataset.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #6312 from jmchilton/tuple_operations Lists-as-tuples collection operations Commit: 0e69ca8bfbc3c93bd18a22a32cd77494d55e915e https://github.com/galaxyproject/galaxy/commit/0e69ca8bfbc3c93bd18a22a32cd7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/rules_dsl.py M test/api/test_tools.py M test/base/data/rules_dsl_spec.yml M test/base/populators.py M test/base/rules_test_data.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #6545 from jmchilton/rule_builder_use_group_tags Allow Consuming Tags in the Apply Rules Tool Commit: 296105ee395194c48d962671a8c367469ea74907 https://github.com/galaxyproject/galaxy/commit/296105ee395194c48d962671a8c3… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- row ids that are all numeric become ints... 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static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports/run_stats.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Add static for 2a148ff1ec37c68e280c431fceee88ee0510e017 Commit: 85751ebb163eb5474d6ba18b7bf9d75097d53e15 https://github.com/galaxyproject/galaxy/commit/85751ebb163eb5474d6ba18b7bf9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Add tag and group tag rule to history level rule builder Commit: 1e7ce13b4773ffeaea169b03963a2a252187dfee https://github.com/galaxyproject/galaxy/commit/1e7ce13b4773ffeaea169b03963a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py Log Message: ----------- Reuse HDA copy method in HDAManager Should benefit from smarter flush strategy in HDA.copy() Commit: d1f9ab88e4637d00c6c5c3c2290f6a19dd369456 https://github.com/galaxyproject/galaxy/commit/d1f9ab88e4637d00c6c5c3c2290f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Always copy HDAs when creating a new collection from exisitng datasets, and allow setting tags Commit: 91438996df29caac56bb7a6fe8dc25e52815caf8 https://github.com/galaxyproject/galaxy/commit/91438996df29caac56bb7a6fe8dc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py Log Message: ----------- Test creation of collection from existing dataset, with a new tag Commit: eb4b878f3f5e9a898d5048c917ce2d379d7bf20f https://github.com/galaxyproject/galaxy/commit/eb4b878f3f5e9a898d5048c917ce… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/hdas.py Log Message: ----------- Simplify hda manager usage Commit: 5dd63dd6d077e9836f126d97a3c50b8a25ea66cc https://github.com/galaxyproject/galaxy/commit/5dd63dd6d077e9836f126d97a3c5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Include tags in element_identifier when building collection from datasets Commit: ce892a028cb9d65aa19f8a4333626b421a184ec9 https://github.com/galaxyproject/galaxy/commit/ce892a028cb9d65aa19f8a433362… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Restore hiding of dataset instances Commit: d4a80e61e13fbeeda43a65874910d85cfc1c8b29 https://github.com/galaxyproject/galaxy/commit/d4a80e61e13fbeeda43a65874910… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Adapt unit tests to copying HDAs when creating collections Commit: a9cb290754f09a1ea3073e8858df6f9a9e45b147 https://github.com/galaxyproject/galaxy/commit/a9cb290754f09a1ea3073e8858df… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflows.py Log Message: ----------- Adjust API tests to copying HDAs when creating collection Commit: 711016ab9aac78c96fa65cd04f9421fbb6473b49 https://github.com/galaxyproject/galaxy/commit/711016ab9aac78c96fa65cd04f94… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Treat LDDA as HDA when creating collection This avoids copying the LDDA to HDA and then copying the HDA again. Commit: 34cfdcac6a583c84c8641ac8e26243769d09598d https://github.com/galaxyproject/galaxy/commit/34cfdcac6a583c84c8641ac8e262… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py Log Message: ----------- Test for proper 403 response Coincidentally fixed by e013f2fbd1596b103ef195afcba8cbd787c49b33. Commit: c00ae9f81b953df7909aa591e411ebd6298a6f7c https://github.com/galaxyproject/galaxy/commit/c00ae9f81b953df7909aa591e411… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Default to not copying source HDAs when creating new collections via API Commit: 9409322a730d431344d4438e379e61559632812d https://github.com/galaxyproject/galaxy/commit/9409322a730d431344d4438e379e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Revert "Adapt unit tests to copying HDAs when creating collections" This reverts commit 408a003f171be73e4b347579ee6f662a18fc1990. Commit: b13cce0a1340a5f9b7a77ab7eda1ceb0930ed161 https://github.com/galaxyproject/galaxy/commit/b13cce0a1340a5f9b7a77ab7eda1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflows.py Log Message: ----------- Revert "Adjust API tests to copying HDAs when creating collection" This reverts commit f120390a63700ff0ec6c09185aad26b91ad8f842. Commit: cfd8379917703ce03b631fd48b5a2bcecc30bbea https://github.com/galaxyproject/galaxy/commit/cfd8379917703ce03b631fd48b5a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py Log Message: ----------- Send copy_elements=True in new create collection test Commit: 43ee13a0ce43ae5b29ffa1e317df1db645cb93a8 https://github.com/galaxyproject/galaxy/commit/43ee13a0ce43ae5b29ffa1e317df… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Default to copying HDAs when creating collections via the UI Commit: 50a524496a4ed52184967ede53094e5c8243d93d https://github.com/galaxyproject/galaxy/commit/50a524496a4ed52184967ede5309… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Add unit test for copy_element option Commit: ddb0c74b9bd9f534691a93911f10903da3609927 https://github.com/galaxyproject/galaxy/commit/ddb0c74b9bd9f534691a93911f10… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Original HDA must be owned by user if hiding source elements Commit: 366701cfb23d8de31eac3c4312c6accca2e74ef1 https://github.com/galaxyproject/galaxy/commit/366701cfb23d8de31eac3c4312c6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/tags.py M lib/galaxy/util/__init__.py A test/unit/managers/test_TagManager.py Log Message: ----------- Strip unicode control characters from tags Leaving them in can trip up postgresql: ``` Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 283, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/history_contents.py", line 396, in create return self.__create_dataset_collection(trans, history, payload, **kwd) File "lib/galaxy/webapps/galaxy/api/history_contents.py", line 525, in __create_dataset_collection **create_params File "lib/galaxy/managers/collections.py", line 108, in create copy_elements=copy_elements, File "lib/galaxy/managers/collections.py", line 181, in create_dataset_collection copy_elements=copy_elements) File "lib/galaxy/managers/collections.py", line 217, in _element_identifiers_to_elements copy_elements=copy_elements) File "lib/galaxy/managers/collections.py", line 389, in __load_elements copy_elements=copy_elements) File "lib/galaxy/managers/collections.py", line 434, in __load_element self.tag_manager.apply_item_tags(user=trans.user, item=element, tags_str=tag_str) File "lib/galaxy/managers/tags.py", line 182, in apply_item_tags self.apply_item_tag(user, item, name, value) File "lib/galaxy/managers/tags.py", line 154, in apply_item_tag tag = self._get_or_create_tag(lc_name) File "lib/galaxy/managers/tags.py", line 233, in _get_or_create_tag tag = self.get_tag_by_name(scrubbed_tag_str) File "lib/galaxy/managers/tags.py", line 205, in get_tag_by_name return self.sa_session.query(galaxy.model.Tag).filter_by(name=tag_name.lower()).first() File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2789, in first ret = list(self[0:1]) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2581, in __getitem__ return list(res) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2889, in __iter__ return self._execute_and_instances(context) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2912, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute return meth(self, multiparams, params) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement compiled_sql, distilled_params File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context context) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1416, in _handle_dbapi_exception util.reraise(*exc_info) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context context) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute cursor.execute(statement, parameters) ValueError: A string literal cannot contain NUL (0x00) characters. ``` Commit: af99f49d82d917b681157ec8f5a4506c6a37cab6 https://github.com/galaxyproject/galaxy/commit/af99f49d82d917b681157ec8f5a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Merge pull request #6636 from blankenberg/11yowffix Fix for workflow extraction cleanup routine. Commit: 03c485ee45e96784b269896a23223d233c566b89 https://github.com/galaxyproject/galaxy/commit/03c485ee45e96784b269896a2322… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/admin.toolshed.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/communication-server-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js M static/scripts/legacy/grid/grid-model.js M static/scripts/legacy/grid/grid-template.js M static/scripts/legacy/grid/grid-view.js M static/scripts/mocha/test.js M static/scripts/mocha/tests/rules_tests.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M 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static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-utils.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/chart/chart-client.js M static/scripts/mvc/visualization/chart/components/model.js M static/scripts/mvc/visualization/chart/components/screenshot.js M static/scripts/mvc/visualization/chart/utilities/datasets.js M static/scripts/mvc/visualization/chart/utilities/jobs.js M static/scripts/mvc/visualization/chart/utilities/series.js M static/scripts/mvc/visualization/chart/views/description.js M static/scripts/mvc/visualization/chart/views/editor.js M static/scripts/mvc/visualization/chart/views/groups.js M static/scripts/mvc/visualization/chart/views/menu.js M static/scripts/mvc/visualization/chart/views/settings.js M static/scripts/mvc/visualization/chart/views/viewer.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports/run_stats.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Merge pull request #6639 from bwlang/patch-2 [18.05] row ids that are all numeric become ints... Commit: 660a51495b52cf886db31dbcc807e54c5b787469 https://github.com/galaxyproject/galaxy/commit/660a51495b52cf886db31dbcc807… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6606 from VJalili/refresh_token Refresh an expired OIDC ID token Commit: ca26c3d5aff4d92192bfef744348c94b6e41ea7e https://github.com/galaxyproject/galaxy/commit/ca26c3d5aff4d92192bfef744348… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py Log Message: ----------- Optimize permission loading and checking collection parameters. We were checking permissions twice it seems like to me, only do it once. Avoid loading dataset permissions for each individual dataset in a collection - work with summary sets of role ids. Commit: 51b4def4ec005b136707bff38611ed09ba6db2ff https://github.com/galaxyproject/galaxy/commit/51b4def4ec005b136707bff38611… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M scripts/galaxy-main Log Message: ----------- Allow running scripts/galaxy-main without Galaxy on $PYTHONPATH Commit: 4ed9df9a947563a5fca4e07caad1b6a19cd6a845 https://github.com/galaxyproject/galaxy/commit/4ed9df9a947563a5fca4e07caad1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M scripts/galaxy-main Log Message: ----------- Set config builder attributes before they're referenced in app_kwds() Commit: 167ab6b54eb330ad44b8c7900d52514a1c90d1cb https://github.com/galaxyproject/galaxy/commit/167ab6b54eb330ad44b8c7900d52… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix color of workflow panel background Commit: 7fa539162791e5e1eca836616b31381f2ad62b05 https://github.com/galaxyproject/galaxy/commit/7fa539162791e5e1eca836616b31… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Merge pull request #6415 from FredericBGA/supplying_name_pasted_data Allow supplying name of pasted data Commit: 73b6e81a0ab2f646de7d3709bcbf9e4284a1c439 https://github.com/galaxyproject/galaxy/commit/73b6e81a0ab2f646de7d3709bcbf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py Log Message: ----------- Eliminate more queries in history.add_dataset(s) by using cached IDs. Commit: 74bb5434a0e9020673f1d4acaab98a6bd9865268 https://github.com/galaxyproject/galaxy/commit/74bb5434a0e9020673f1d4acaab9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Eliminate old and invalid tool optimization comment. Commit: 3121d9f0a468d23f6619e3496cf46c627560d90c https://github.com/galaxyproject/galaxy/commit/3121d9f0a468d23f6619e3496cf4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6643 from guerler/fix_panel_background Fix color of workflow panel background Commit: e0d1208834deb7762564d5ae1cdc84da682dde5f https://github.com/galaxyproject/galaxy/commit/e0d1208834deb7762564d5ae1cdc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- document the sniff_compressed_dynamic_datatypes_default config and include in sample Commit: 2adae6c4ca77067f2f45f3f101218d411fec7e25 https://github.com/galaxyproject/galaxy/commit/2adae6c4ca77067f2f45f3f10121… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M test/api/test_history_contents.py M test/unit/managers/test_HistoryContentsManager.py A test/unit/managers/test_TagManager.py Log Message: ----------- Merge pull request #6572 from mvdbeek/add_group_tags_to_history_rule_builder Add tagging rule to history level rule builder, copy HDAs when building collection Commit: c0c587abdf23b8d5a01222cace7cc81f4b3d82f4 https://github.com/galaxyproject/galaxy/commit/c0c587abdf23b8d5a01222cace7c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: A scripts/page_to_raw.py Log Message: ----------- Add page_to_raw to decode ids in the database. Commit: a23e5d77a54710662a784d7ec1454e3af54c3097 https://github.com/galaxyproject/galaxy/commit/a23e5d77a54710662a784d7ec145… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Allow pages to read both encoded and unencoded ids out of the database. Always save unencoded version, with the additional benefit of using a simpler, smaller placeholder. Commit: b8fa78358c07fc2b0eaa53f2e02a2674cc522ef1 https://github.com/galaxyproject/galaxy/commit/b8fa78358c07fc2b0eaa53f2e02a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Remove outdated comment; I refactored to handle this. Commit: b34414adc8a5afad30d4822dfbc794cfc3bad9ff https://github.com/galaxyproject/galaxy/commit/b34414adc8a5afad30d4822dfbc7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- switch the default to sniff compressed datatypes Commit: b2fe48a6be69bd5c05357ae0a8a7fe07f8d314db https://github.com/galaxyproject/galaxy/commit/b2fe48a6be69bd5c05357ae0a8a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Allow history_id to be specified instead of history in check_elements. Commit: f9d791c228d1dfafdaaae404ae1ec6fb94f51555 https://github.com/galaxyproject/galaxy/commit/f9d791c228d1dfafdaaae404ae1e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M scripts/page_to_raw.py Log Message: ----------- Refactoring, drop BS4. It's faster, for sure, but this leaves us with fewer moving parts and this isn't a script anyone's going to run often. Hopefully. Commit: 9f14fcb1005452bae314eeebb324351a98510204 https://github.com/galaxyproject/galaxy/commit/9f14fcb1005452bae314eeebb324… Author: Maria Doyle <maria.doyle(a)petermac.org> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add Seurat datatype: rdata.seurat Commit: feaaecf2199f78e42668418ab4eb5c8f68ff0e8d https://github.com/galaxyproject/galaxy/commit/feaaecf2199f78e42668418ab4eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Strip API keys option from admin panel left side -- this is all in the user management grid now. I don't know if this got added back in a bad merge or if it was erroneously left in. Commit: 223c3988083c5397626bd33908376bc007bc28bc https://github.com/galaxyproject/galaxy/commit/223c3988083c5397626bd3390837… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- drop admin api keys navigator from selenium configs (which may break other tests, we should wait to see) Commit: f01726dc6f27492a20007ca51d4dda82f1eb43c8 https://github.com/galaxyproject/galaxy/commit/f01726dc6f27492a20007ca51d4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Almost there, one more (preexisting) bug to fix. This adds validation on save and correct processing to the page writer. Commit: eb8d80b6d248eaeb7218ce0ad324be93634ca805 https://github.com/galaxyproject/galaxy/commit/eb8d80b6d248eaeb7218ce0ad324… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M scripts/page_to_raw.py Log Message: ----------- Handle item name fetching, enforce accessible Commit: 2fa6dedf4e22351b88bb0706992928c306137cea https://github.com/galaxyproject/galaxy/commit/2fa6dedf4e22351b88bb07069929… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Only display encoded ids in editor as well. Commit: 4fa1cc38eacbc20622f81bbe7505df0d21480b72 https://github.com/galaxyproject/galaxy/commit/4fa1cc38eacbc20622f81bbe7505… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: R scripts/page_to_raw.py A scripts/pages_identifier_conversion.py Log Message: ----------- Rename page 'fixer' script Commit: 0acdc8a1a3eecae23b1dfe0876cf15d0ab41aa05 https://github.com/galaxyproject/galaxy/commit/0acdc8a1a3eecae23b1dfe0876cf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- adjust test definitions for compressed handling so it tests the new defaults Commit: dd0a6884ba7b20788fdec5b38e3715596b2ac177 https://github.com/galaxyproject/galaxy/commit/dd0a6884ba7b20788fdec5b38e37… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M lib/galaxy/managers/collections.py M test/selenium_tests/test_collection_builders.py Log Message: ----------- Fixes... Commit: 5d22d73f303298fdef98c5ab8c8e8e91bae65bb3 https://github.com/galaxyproject/galaxy/commit/5d22d73f303298fdef98c5ab8c8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- client-format Commit: f8273572f7aaf08cc94c06d8569b26089c231fa4 https://github.com/galaxyproject/galaxy/commit/f8273572f7aaf08cc94c06d8569b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js Log Message: ----------- Fix (unrelated to the changes in this PR -- bonus bug) name injection for embedded objects. Commit: 5ffff7f1b455a6a0f95377f715421ee8229b56f5 https://github.com/galaxyproject/galaxy/commit/5ffff7f1b455a6a0f95377f71542… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M static/scripts/bundled/extended.bundled.js M static/scripts/galaxy.pages.js Log Message: ----------- Client build. Looks like we accidentally committed the map references? Leaving that in place, but we had agreed to drop them. Commit: eab6dd858168a5a5cf396b79d4415a265082e9d7 https://github.com/galaxyproject/galaxy/commit/eab6dd858168a5a5cf396b79d441… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M scripts/pages_identifier_conversion.py Log Message: ----------- Add dry run mode for script to test Commit: 7c339c9bffb58a71053e8d6dd20122498061f7ec https://github.com/galaxyproject/galaxy/commit/7c339c9bffb58a71053e8d6dd201… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Use uses_test_history for selected upload tests Commit: d437875513c4d88f5096952a63eca62a96ed68bb https://github.com/galaxyproject/galaxy/commit/d437875513c4d88f5096952a63ec… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #29 from mvdbeek/martenson-rename-and-document-config-value Use uses_test_history for selected upload tests Commit: bb95452882726e4f6c3f26c76abfe7b22bafadb4 https://github.com/galaxyproject/galaxy/commit/bb95452882726e4f6c3f26c76abf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-29 (Wed, 29 Aug 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M test/galaxy_selenium/navigation.yml Log Message: ----------- Merge pull request #6651 from dannon/admin_apikeys_fixup Strip API keys option from admin panel left side Commit: e1b32368028cf9360ecef6400c6ce26f1bb0adc8 https://github.com/galaxyproject/galaxy/commit/e1b32368028cf9360ecef6400c6c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- fix tests for the bed.gz dtaatype compressed beds are not part of the datatypes_conf.xml.sample Commit: 4a21ac30ea51aba6df2d98076a67caaa2e3feed0 https://github.com/galaxyproject/galaxy/commit/4a21ac30ea51aba6df2d98076a67… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Merge branch 'rename-and-document-config-value' of github.com:martenson/galaxy into rename-and-document-config-value Commit: 9b5724d62d614d8f1e721f169ed76d0c5c6a789c https://github.com/galaxyproject/galaxy/commit/9b5724d62d614d8f1e721f169ed7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- add back the unstable flags for bed.gz datasets I expect the datatypes_conf.xml bed compress default will change in near future Commit: 25ae4e6e26a27696fa47ea656fa36889f435e2f2 https://github.com/galaxyproject/galaxy/commit/25ae4e6e26a27696fa47ea656fa3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-08-30 (Thu, 30 Aug 2018) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix get_fileobj() call in Eland.set_meta() Broken in commit 59f44cf2be48abd4bed0f7c6ddf7cc0aee5ad1f5 . Commit: 3a77b64aeb71c027d8f8d7ca56574b63ff83afb3 https://github.com/galaxyproject/galaxy/commit/3a77b64aeb71c027d8f8d7ca5657… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-31 (Fri, 31 Aug 2018) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #6659 from nsoranzo/fix_Eland_set_meta Fix get_fileobj() call in Eland.set_meta() Commit: 410ec1927c34fbb4a61969e1fe188babd9a8f82b https://github.com/galaxyproject/galaxy/commit/410ec1927c34fbb4a61969e1fe18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-31 (Fri, 31 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/upload-view.js M lib/galaxy/managers/collections.py M test/selenium_tests/test_collection_builders.py Log Message: ----------- Merge pull request #6656 from jmchilton/collect_builder_fixes Assorted fixes for #6572 Commit: 3c5991632246d5fd404b269507642f819abf7d68 https://github.com/galaxyproject/galaxy/commit/3c5991632246d5fd404b26950764… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Allow group tag selection also for multiple="true" inputs Commit: 77706a8e62f6c7ffafc923b9f94f3359089e8ee9 https://github.com/galaxyproject/galaxy/commit/77706a8e62f6c7ffafc923b9f94f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.authnz.rst M doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.rst R doc/source/lib/galaxy.external_services.result_handlers.rst R doc/source/lib/galaxy.external_services.rst R doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.rst R doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst A doc/source/lib/galaxy.tools.error_reports.plugins.rst A doc/source/lib/galaxy.tools.error_reports.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.verify.rst R doc/source/lib/galaxy.util.backports.rst R doc/source/lib/galaxy.util.log.rst A doc/source/lib/galaxy.util.logging.rst A doc/source/lib/galaxy.util.path.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.plugins.rst R doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst A doc/source/lib/galaxy.webapps.reports.framework.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.workflow.resources.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/tool_shed.util.rst Log Message: ----------- Update application documentation With ``` make -C doc/ updaterst ``` Commit: ad02c53154a3d3046a814b838cffdf0a79ac9a13 https://github.com/galaxyproject/galaxy/commit/ad02c53154a3d3046a814b838cff… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/error_report.yml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/tool_shed.yml.sample M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst M doc/source/admin/config.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/releases/16.04_announce.rst M doc/source/releases/16.10.rst M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/search.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/uwsgi_schema.yml M run_tests.sh M scripts/api/README M scripts/slideshow/example.md M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/base/workflows_format_2/interface.py Log Message: ----------- Fix many links Commit: 59c1ed2266504a2bd03e80e9f4ec72664148524f https://github.com/galaxyproject/galaxy/commit/59c1ed2266504a2bd03e80e9f4ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/galaxy.yml.sample M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/admin/galaxy_options.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Various doc fixes Commit: ea34aa84be9be03489e541b928ea57adfb087e80 https://github.com/galaxyproject/galaxy/commit/ea34aa84be9be03489e541b928ea… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py R lib/galaxy/datatypes/test/em.trr A lib/galaxy/datatypes/test/md.cpt A lib/galaxy/datatypes/test/md.trr A lib/galaxy/datatypes/test/md.xtc M lib/galaxy/datatypes/text.py Log Message: ----------- adding 4 new GROMACS datatypes: cpt, xtc, top, and gro shrinking test files Commit: 6a730bc5821c94d25411cb51a7033ab56064617b https://github.com/galaxyproject/galaxy/commit/6a730bc5821c94d25411cb51a703… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- linting Commit: 3c7d7d9d49d49781f822a36c3bdbd860ddc0e8f0 https://github.com/galaxyproject/galaxy/commit/3c7d7d9d49d49781f822a36c3bdb… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- tightening up the sniffer functions Commit: 0d97c55cc7256ccff7285d57dd5ed3ec64616887 https://github.com/galaxyproject/galaxy/commit/0d97c55cc7256ccff7285d57dd5e… Author: sb635 <sb635(a)bmd6.physik.privat> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add refs for trr/xtc/cpt binary magic numbers Commit: 56d55399ebe2ecd614a7ba5a146739f58e917541 https://github.com/galaxyproject/galaxy/commit/56d55399ebe2ecd614a7ba5a1467… Author: sb635 <sb635(a)bmd6.physik.privat> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- removing top and gro sniffers, at least for now Commit: e59219deabe89cbf3a98f984bf54d314157d6599 https://github.com/galaxyproject/galaxy/commit/e59219deabe89cbf3a98f984bf54… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- created new GmxBinary class from which xtc, trr, cpt inherit Commit: 5d15063f7de0b7b07f7bad5d7dbbb31f5e872855 https://github.com/galaxyproject/galaxy/commit/5d15063f7de0b7b07f7bad5d7dbb… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove __init__() from GmxBinary subclasses Commit: 09d349cbfff5623a52f23ccd480b4975759f8d8b https://github.com/galaxyproject/galaxy/commit/09d349cbfff5623a52f23ccd480b… Author: Simon Bray <32272674+simonbray(a)users.noreply.github.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- default for magic_number None not 0 Commit: ed641aceb9d117aee7a83de9bbcd7a7876d20703 https://github.com/galaxyproject/galaxy/commit/ed641aceb9d117aee7a83de9bbcd… Author: simonbray <sbray1371(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove __init__ from GmxBinary Commit: 76d89d020f56e202939a26b06972e3bce489dd3b https://github.com/galaxyproject/galaxy/commit/76d89d020f56e202939a26b06972… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/test/em.trr A lib/galaxy/datatypes/test/md.cpt A lib/galaxy/datatypes/test/md.trr A lib/galaxy/datatypes/test/md.xtc Log Message: ----------- Merge pull request #6655 from simonbray/dev Adding 4 new GROMACS datatypes: cpt, xtc, top, and gro Commit: b9d07aed22c59c2aeb92e30d18953bc6fecea0a6 https://github.com/galaxyproject/galaxy/commit/b9d07aed22c59c2aeb92e30d1895… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-03 (Mon, 03 Sep 2018) Changed paths: M config/error_report.yml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/tool_shed.yml.sample M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst M doc/source/admin/config.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.authnz.rst M doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.rst R doc/source/lib/galaxy.external_services.result_handlers.rst R doc/source/lib/galaxy.external_services.rst R doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.rst R doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.rst R doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst A doc/source/lib/galaxy.tools.error_reports.plugins.rst A doc/source/lib/galaxy.tools.error_reports.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.verify.rst R doc/source/lib/galaxy.util.backports.rst R doc/source/lib/galaxy.util.log.rst A doc/source/lib/galaxy.util.logging.rst A doc/source/lib/galaxy.util.path.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.plugins.rst R doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.stack.rst M doc/source/lib/galaxy.webapps.galaxy.api.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst A doc/source/lib/galaxy.webapps.reports.framework.rst M doc/source/lib/galaxy.webapps.reports.rst M doc/source/lib/galaxy.webapps.rst A doc/source/lib/galaxy.workflow.resources.rst M doc/source/lib/galaxy.workflow.rst M doc/source/lib/tool_shed.util.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.10.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/search.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/uwsgi_schema.yml M run_tests.sh M scripts/api/README M scripts/slideshow/example.md M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/base/workflows_format_2/interface.py Log Message: ----------- Merge pull request #6662 from nsoranzo/doc_fixes2 Various link and documentation fixes Commit: 3ca449fa73fcc18389876756814fdaa5bb6e2aed https://github.com/galaxyproject/galaxy/commit/3ca449fa73fcc18389876756814f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #6661 from mvdbeek/group_tags_for_multiple_true_inputs Allow group tag selection also for multiple="true" inputs Commit: bc1526ab2dd5044f3ea274c176fcb43b490b0c63 https://github.com/galaxyproject/galaxy/commit/bc1526ab2dd5044f3ea274c176fc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #6644 from jmchilton/add_datasets Small Optimizations to Adding Datasets to History Commit: f2072310afac4ab6052bade41cdadb03210963d4 https://github.com/galaxyproject/galaxy/commit/f2072310afac4ab6052bade41cda… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Swap placeholder template string back to a single line. Commit: a3799350ff81d56bcc7db6a5cc8a53470bbe72fe https://github.com/galaxyproject/galaxy/commit/a3799350ff81d56bcc7db6a5cc8a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Fix hda security check. Commit: 4ec42d28362cdc6252206a8b9d2f4cc9361c4def https://github.com/galaxyproject/galaxy/commit/4ec42d28362cdc6252206a8b9d2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-04 (Tue, 04 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Enforce PAGE_MAXRAW, otherwise we have no way to differentiate between potentially all-integer 16 character identifiers. I can't think of a better way to do this, unfortunately. Commit: c867c6863fbbb75f473f209fea7a805e2da63a47 https://github.com/galaxyproject/galaxy/commit/c867c6863fbbb75f473f209fea7a… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M tools/genomespace/genomespace_importer.py Log Message: ----------- Upgraded genomespaceclient to newer version This fixes issue reported in: https://github.com/galaxyproject/usegalaxy-playbook/issues/100 Also related to PR: https://github.com/galaxyproject/galaxy/pull/6660 Commit: 64652c28cf7ea88195b1c9008c46137c3bb3644a https://github.com/galaxyproject/galaxy/commit/64652c28cf7ea88195b1c9008c46… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Drop wait from cached job tests Commit: 8148bd91deb4d4f9b621b6e3097ae0f01ba81abd https://github.com/galaxyproject/galaxy/commit/8148bd91deb4d4f9b621b6e3097a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M .coveragerc M lib/galaxy/jobs/runners/util/kill.py M pytest.ini M run_tests.sh A test/functional/known_broken_tools.txt M test/functional/test_toolbox_pytest.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M tox.ini Log Message: ----------- Merge pull request #6638 from mvdbeek/move_tests_to_pytest_setup Move tests to pytest setup Commit: 09f6e1f9ee08f4da770d18e2fb33e6434c64ba90 https://github.com/galaxyproject/galaxy/commit/09f6e1f9ee08f4da770d18e2fb33… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 85cab90689f07fd17b15f7d52efc5e0cae720056 https://github.com/galaxyproject/galaxy/commit/85cab90689f07fd17b15f7d52efc… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update bx-python to 0.8.2 to include https://github.com/bxlab/bx-python/pull/35 . Fix https://github.com/galaxyproject/galaxy/issues/6379 and https://github.com/galaxyproject/galaxy/issues/6598 . Commit: 8affe206df782658dbc388d5ffe1c5c1d6a136ef https://github.com/galaxyproject/galaxy/commit/8affe206df782658dbc388d5ffe1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/secure_hash_message_digest.py Log Message: ----------- py3: fix secure_hash_message_digest.py Commit: df5cab38ae35a38e1d7486d8c2fc0c8f452ed32e https://github.com/galaxyproject/galaxy/commit/df5cab38ae35a38e1d7486d8c2fc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/wc_gnu.xml Log Message: ----------- Fix wc_gnu test 1; list comprehensions are function objects on py3 and can't access outer local namespace Commit: 6352a0ef3ea5d80771276bcf4b928dda3acdbc08 https://github.com/galaxyproject/galaxy/commit/6352a0ef3ea5d80771276bcf4b92… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/util/ucsc.py Log Message: ----------- Fix wiggle2simple1 Commit: 36c74bbafa972f0e76ad8bf7befa23090eb8d92e https://github.com/galaxyproject/galaxy/commit/36c74bbafa972f0e76ad8bf7befa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/tools/util/maf_utilities.py Log Message: ----------- Fix maf_utilities comparison Commit: 6c7203b83d19d1f79bd6b1790ce24e9507931257 https://github.com/galaxyproject/galaxy/commit/6c7203b83d19d1f79bd6b1790ce2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/plotting/boxplot.xml Log Message: ----------- py3: Fix qual_stats_boxplot Commit: 6405aeb86c2240e010fadcd4e4758feccabba218 https://github.com/galaxyproject/galaxy/commit/6405aeb86c2240e010fadcd4e475… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/stats/aggregate_binned_scores_in_intervals.xml Log Message: ----------- Comment out tests with unavailable test data Commit: 8190c3fc4389299c8d9484bf3b3409b5cea51921 https://github.com/galaxyproject/galaxy/commit/8190c3fc4389299c8d9484bf3b34… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/join.py Log Message: ----------- Fix the join1 tool Commit: 3fcf1e336dd2e32b0199388528078ce19ab7d98b https://github.com/galaxyproject/galaxy/commit/3fcf1e336dd2e32b019938852807… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/solid_tools/solid_qual_stats.py Log Message: ----------- Fix solid_qual_stats.py Commit: 2d732715ff50241fcddfab58795306a3880bd3c3 https://github.com/galaxyproject/galaxy/commit/2d732715ff50241fcddfab587953… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/stats/grouping.py Log Message: ----------- Fix grouping tool Commit: 8889bd0a3d93266893a21dedefa9f93b8e51e8ef https://github.com/galaxyproject/galaxy/commit/8889bd0a3d93266893a21dedefa9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/senatag.py Log Message: ----------- Fix various things about the hgv_ldtools tool Unfortnately this doens't produce the test-data output on python 3 and so I added a requiremtn on python 2. (I think the result is probably correct but not deterministic). Commit: 9949053f430fcd44cdff6434f934146eecaa1d1f https://github.com/galaxyproject/galaxy/commit/9949053f430fcd44cdff6434f934… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_limit_to_species.py Log Message: ----------- Fix maf_limit_to_species.py if no species is given Commit: 2827dbf669ff2e9e2a7938aad0b81c94220c813d https://github.com/galaxyproject/galaxy/commit/2827dbf669ff2e9e2a7938aad0b8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_interval.py Log Message: ----------- Fix maf_to_interval.py Commit: 548b9c8c89121935e5557d98e6e8ec87327714bf https://github.com/galaxyproject/galaxy/commit/548b9c8c89121935e5557d98e6e8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_bed.py Log Message: ----------- Fix maf_to_bed.py Commit: 2d36e8955e020958334088d6ba5853c1027d8b75 https://github.com/galaxyproject/galaxy/commit/2d36e8955e020958334088d6ba58… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Fix recursion issue in gff_filter_by_feature_count Commit: 918634f1fbbfafecbe9a25e869f82ea2df7e8edf https://github.com/galaxyproject/galaxy/commit/918634f1fbbfafecbe9a25e869f8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Switch rpy2 to 2.9.4, 2.7.8 can't be resolved Commit: 491fe4251e97335505243f460f6a3bdf99df1556 https://github.com/galaxyproject/galaxy/commit/491fe4251e97335505243f460f6a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/uniq.xml Log Message: ----------- Fix uniq tests on OSX Commit: 77b43946f616b2e29b0550a21255a2c970dbd4dc https://github.com/galaxyproject/galaxy/commit/77b43946f616b2e29b0550a21255… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/next_gen_conversion/solid2fastq.xml Log Message: ----------- Fix solid2fastq tests Commit: 18ac62c1fd5952a94e5c6eaf4c3e357335a47ff2 https://github.com/galaxyproject/galaxy/commit/18ac62c1fd5952a94e5c6eaf4c3e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/wig_to_bigwig.xml Log Message: ----------- Fix wig_to_bigwig tool tests Commit: da4906dc56175cabd72a7d4b9b2ecce93bcad740 https://github.com/galaxyproject/galaxy/commit/da4906dc56175cabd72a7d4b9b2e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/functional/known_broken_tools.txt Log Message: ----------- Add GeneBed_Maf_Fasta2 to no test list Commit: c1dffec4ecdda1494a6169e3239c82dadbeda50c https://github.com/galaxyproject/galaxy/commit/c1dffec4ecdda1494a6169e3239c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/tailWrapper.xml Log Message: ----------- Quote tail wrapper inputs and outputs, drop interpreter attribute Commit: 05f18d029bb1308ab37e575f6972e8e18792e8b5 https://github.com/galaxyproject/galaxy/commit/05f18d029bb1308ab37e575f6972… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml Log Message: ----------- Fix linkToGProfile test Commit: 4acfd9a770518b33191a395dc1c606b82b67879a https://github.com/galaxyproject/galaxy/commit/4acfd9a770518b33191a395dc1c6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/sff_extractor.xml Log Message: ----------- Fix sffextractor tests by requiring python 2.7 Commit: f22f0ebb2f95415573a42c0b4a783dde8aeb8c04 https://github.com/galaxyproject/galaxy/commit/f22f0ebb2f95415573a42c0b4a78… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_split_by_species.xml Log Message: ----------- Sort maf_split_by_species test output Commit: e8d0ce39cf60b8311d9b749189a29025ad476144 https://github.com/galaxyproject/galaxy/commit/e8d0ce39cf60b8311d9b749189a2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml Log Message: ----------- Fix random order of fasta headers in maf_to_bed Commit: aee261daf7f87289063a91371fd66ffcb3c595b8 https://github.com/galaxyproject/galaxy/commit/aee261daf7f87289063a91371fd6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_fasta_multiple_sets.py Log Message: ----------- Fix random header order in MAF to FASTA Commit: 36196bd2be7b350c0aae85c44cd1fcb8a1b1c737 https://github.com/galaxyproject/galaxy/commit/36196bd2be7b350c0aae85c44cd1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/maf/maf_to_interval.xml Log Message: ----------- Specify maf ftype in maf_to_interval.xml Commit: 906951f28e075829444c8c222000e4af82a86ef9 https://github.com/galaxyproject/galaxy/commit/906951f28e075829444c8c222000… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/solid_tools/solid_qual_stats.xml Log Message: ----------- Single-quote paths in solid_qual_stats and fix test by using sim_size -- we have different float precision between py2 and py3. Commit: 72f95ba9c4bb940c892b8f6b37a1d91471d013c9 https://github.com/galaxyproject/galaxy/commit/72f95ba9c4bb940c892b8f6b37a1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/bed_to_bigbed.xml Log Message: ----------- Test bed_to_bigbed using compare="sim_size" Commit: 8e7088b1a0744df3c35871d24b91dfd76fe310c3 https://github.com/galaxyproject/galaxy/commit/8e7088b1a0744df3c35871d24b91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6670 from nsoranzo/release_18.05_bx-python_0.8.2 [18.05] Update bx-python to 0.8.2 Commit: d645d80443c23d89fc65f3bb33caf4be9c9c7f21 https://github.com/galaxyproject/galaxy/commit/d645d80443c23d89fc65f3bb33ca… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update bx-python to 0.8.2 to include https://github.com/bxlab/bx-python/pull/35 . Fix https://github.com/galaxyproject/galaxy/issues/6379 and https://github.com/galaxyproject/galaxy/issues/6598 . Commit: 8b757f22d1489deb09a863cfc701f4ce1ea0c1f3 https://github.com/galaxyproject/galaxy/commit/8b757f22d1489deb09a863cfc701… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/functional/known_broken_tools.txt Log Message: ----------- Exclude bed_to_bigbed and wig_to_bigwig from tests They work, but required hg17.len to be present. Commit: 91b02cc6a80ea267743779ffcf4483ada5338cf9 https://github.com/galaxyproject/galaxy/commit/91b02cc6a80ea267743779ffcf44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: A .ci/jenkins/main-tools-py3/run_tests.sh A .ci/jenkins/main-tools/run_tests.sh Log Message: ----------- Add .ci/jenkins/main* for testing tools in tool_conf.xml.main Commit: 309c13b5ba42dc3ee27982202b3ed320d9ecb214 https://github.com/galaxyproject/galaxy/commit/309c13b5ba42dc3ee27982202b3e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Log Message: ----------- Merge branch 'release_18.05' into dev Commit: 7f220276cc2fb500447b0f320b3d4985855def01 https://github.com/galaxyproject/galaxy/commit/7f220276cc2fb500447b0f320b3d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/filters/joinWrapper.py Log Message: ----------- py3: Fix comp1 tool Commit: c939e7bb616103fb4d79067cf3d8159e276524ea https://github.com/galaxyproject/galaxy/commit/c939e7bb616103fb4d79067cf3d8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Bump version of Summary Statistics for rpy2 version update Commit: 9b488ff291a7d5c2204ed20b3f71769fe58d7e30 https://github.com/galaxyproject/galaxy/commit/9b488ff291a7d5c2204ed20b3f71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/selenium_tests/test_collection_builders.py Log Message: ----------- One last Selenium fix for collection interface change. Commit: cf9d7c53f0637425fa3af6153d432aa240838cb2 https://github.com/galaxyproject/galaxy/commit/cf9d7c53f0637425fa3af6153d43… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M scripts/pages_identifier_conversion.py Log Message: ----------- Restructure to allow individual successful conversions to commit, only rolling back individual fails instead of the entire transaction. This is going to be necessary for complicated deployments like main, where we have ~95% working fine but the otehr 5% were busted to start with (and won't parse), etc. Also swap dryrun to difflib display. Commit: ae7b4fda89764ccae189141c75d1609a751b3add https://github.com/galaxyproject/galaxy/commit/ae7b4fda89764ccae189141c75d1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M test/selenium_tests/test_collection_builders.py Log Message: ----------- Merge pull request #6672 from jmchilton/selenium_fixes_47 One last Selenium fix for collection interface change. Commit: 7f1f8a7a4eda4b753bcedcc25b11a9abe34175c6 https://github.com/galaxyproject/galaxy/commit/7f1f8a7a4eda4b753bcedcc25b11… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: A .ci/jenkins/main-tools-py3/run_tests.sh A .ci/jenkins/main-tools/run_tests.sh M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/ucsc.py M test/functional/known_broken_tools.txt M tools/filters/bed_to_bigbed.xml M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extractor.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wc_gnu.xml M tools/filters/wig_to_bigwig.xml M tools/maf/maf_limit_to_species.py M tools/maf/maf_split_by_species.xml M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml M tools/phenotype_association/senatag.py M tools/plotting/boxplot.xml M tools/solid_tools/solid_qual_stats.py M tools/solid_tools/solid_qual_stats.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/grouping.py M tools/stats/gsummary.xml Log Message: ----------- Merge pull request #6627 from mvdbeek/test_more_tools Test tools shipped with Galaxy Commit: 923ed2ed493a9575473b58da52d80de2d58ab41a https://github.com/galaxyproject/galaxy/commit/923ed2ed493a9575473b58da52d8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-05 (Wed, 05 Sep 2018) Changed paths: M scripts/galaxy-main Log Message: ----------- Simplify importing from galaxy lib Commit: e14b871eb9ce577a8ee107728e4acb41028ddaa1 https://github.com/galaxyproject/galaxy/commit/e14b871eb9ce577a8ee107728e4a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Add test for scripts/galaxy-main Commit: d7a245608ead868c8104f2e6dbbbc9fc9ef20dcc https://github.com/galaxyproject/galaxy/commit/d7a245608ead868c8104f2e6dbbb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Fix lint Commit: 6787dbc9ee90662e2bf52b596d787ea0d66f88bd https://github.com/galaxyproject/galaxy/commit/6787dbc9ee90662e2bf52b596d78… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M scripts/galaxy-main M test/integration/test_scripts.py Log Message: ----------- Merge pull request #6642 from natefoo/galaxy-main-import Allow running scripts/galaxy-main without Galaxy on sys.path Commit: 6a266a19a947e853b37ce20eee9fc1f775b5f550 https://github.com/galaxyproject/galaxy/commit/6a266a19a947e853b37ce20eee9f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflow_fixtures.py M test/base/workflows_format_2/converter.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_workflow_run.py Log Message: ----------- More tests for runtime workflow parameters. Commit: 89405fae9435bfc344f10c4155736d2810df84cd https://github.com/galaxyproject/galaxy/commit/89405fae9435bfc344f10c415573… Author: Helena Rasche <erasche(a)users.noreply.github.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6648 from mblue9/add_seurat_datatype Add Seurat datatype: rdata.seurat Commit: 31d850b64484dd4f418a27c9313a954f89e37d7d https://github.com/galaxyproject/galaxy/commit/31d850b64484dd4f418a27c9313a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py Log Message: ----------- Make discovery of cachable jobs more robust We update the actually used version once the job inputs are ready. This allows finding jobs when a dataset is being new / being updated while the job is new. This is also more accurate since we record the dataset versino that is actually being used when the tool is being evaluated. This should allow chaching when simultaneously running workflows that share steps. Commit: a0982c1b900111d0b2a4add372f0caef0686a000 https://github.com/galaxyproject/galaxy/commit/a0982c1b900111d0b2a4add372f0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Only create HDA history if HDA columns have changed This creates fewer versions because we ignore relationship changes. Commit: 7806a84d1c22ba6f8b580fee78cb6bf594967936 https://github.com/galaxyproject/galaxy/commit/7806a84d1c22ba6f8b580fee78cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/base/workflow_fixtures.py M test/selenium_tests/test_workflow_run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Implement runtime parameters in nested workflows. Commit: fc75d4f9fbf8c6406d80873570392e925e40f56c https://github.com/galaxyproject/galaxy/commit/fc75d4f9fbf8c6406d8087357039… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M test/api/test_workflows.py M test/base/workflow_fixtures.py Log Message: ----------- Test case - verify step parameters replace after workflow invoke pauses. Commit: 5c54793ddfbd86875322280ab74041152e6c8a40 https://github.com/galaxyproject/galaxy/commit/5c54793ddfbd86875322280ab740… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-06 (Thu, 06 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6669 from mvdbeek/fix_cache_tests Increase robustness and accuracy of job search / cache use Commit: da18624067c819d4940658d9a5675c84977a2b3d https://github.com/galaxyproject/galaxy/commit/da18624067c819d4940658d9a567… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/workflow_fixtures.py M test/base/workflows_format_2/converter.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_workflow_run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #6664 from jmchilton/runtime_parameters Implement runtime parameters for subworkflows. Commit: 3824a8948a43a8a0def879df73087ce190182b3f https://github.com/galaxyproject/galaxy/commit/3824a8948a43a8a0def879df7308… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #6635 from jmchilton/permission_opts Optimize tool execution permission checking Commit: 69252d711a1d7112e3340a25d5b3b821cb027e39 https://github.com/galaxyproject/galaxy/commit/69252d711a1d7112e3340a25d5b3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M run_tests.sh Log Message: ----------- Tell pytest not to execute Python code in node_modules for web proxy. Causes test execution to fail for me. Commit: 1ba4b47d7335c097a189a15859c58ddac1e2dadd https://github.com/galaxyproject/galaxy/commit/1ba4b47d7335c097a189a15859c5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #6676 from jmchilton/pytest_fix Tell pytest not to execute Python code in node_modules for web proxy. Commit: 3efda23b4fe84f1a61d83aba07186e46c81990ce https://github.com/galaxyproject/galaxy/commit/3efda23b4fe84f1a61d83aba0718… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Restore logging block in galaxy config schema. Commit: ee0c8327e4b2f848c9f9d3c0003cc49781c149f4 https://github.com/galaxyproject/galaxy/commit/ee0c8327e4b2f848c9f9d3c0003c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Serialize select field options This fixes the empty select list in the beta install interface. Commit: 3571df4e4d8324a84eaeb16cd840098165fb2ffd https://github.com/galaxyproject/galaxy/commit/3571df4e4d8324a84eaeb16cd840… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Use PAGE_MAXRAW in both places (refactor this after it all works perfectly) Commit: 8f979b4da16ff4e1498aa1110b45dbb8d62921f1 https://github.com/galaxyproject/galaxy/commit/8f979b4da16ff4e1498aa1110b45… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflow_fixtures.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Workflow replacement parameters polish. - Selenium test case demonstrating their use in simple workflows. - API test demonstrating they work with nested workflows from the run perspective. - Update run variant of workflow to_dict to parse out replacement parameters to display on the backend and tweak the client to just accept these. - Parse out replacement parameters for subworkflows recursively, include in new run output attribute - nested workflow replacement parameters work now. - Selenium test case demosntrating subworkflow replacement parameters are rendered and used when submitted. Commit: fa64299fd1f32e58185259a35612c0f203accb72 https://github.com/galaxyproject/galaxy/commit/fa64299fd1f32e58185259a35612… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Drop redundant decode; this is handled in either path of the logic above. Commit: eba93525afbfa16234754efee081caf028e0cc0d https://github.com/galaxyproject/galaxy/commit/eba93525afbfa16234754efee081… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Minor refactoring/dedupe Commit: ba22818ff45ee639fb1a199a6dff5085a28f8365 https://github.com/galaxyproject/galaxy/commit/ba22818ff45ee639fb1a199a6dff… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge pull request #6668 from gvlproject/genomespaceclient_upgrade Upgraded genomespaceclient to newer version Commit: d6f01741a111180f5a4f3a4af56d017250dca124 https://github.com/galaxyproject/galaxy/commit/d6f01741a111180f5a4f3a4af56d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Escape parenthesis in output names Otherwise this leads to: ``` webpack-internal:///0:1468 Uncaught Error: Syntax error, unrecognized expression: .callout.with (parenthesis) at Function.Sizzle.error (webpack-internal:///0:1468) at Sizzle.tokenize (webpack-internal:///0:2125) at Function.Sizzle (webpack-internal:///0:838) at Function.jQuery.find (webpack-internal:///453:290) at jQuery.fn.init.find (webpack-internal:///0:2792) at jQuery.fn.init.jQuery.fn.find (webpack-internal:///453:677) at child.eval (webpack-internal:///760:322) at Function.each (webpack-internal:///0:371) at Object.eval (webpack-internal:///760:319) at Function.each (webpack-internal:///0:371) ``` Commit: 1ee673306c59f7a97a072b47046151ccd53273a5 https://github.com/galaxyproject/galaxy/commit/1ee673306c59f7a97a072b470461… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M scripts/pages_identifier_conversion.py Log Message: ----------- Skip the commit attempt, just flush on success Commit: 95462754c09facf8ae767b88767003b2d00c1da1 https://github.com/galaxyproject/galaxy/commit/95462754c09facf8ae767b887670… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Merge pull request #6677 from mvdbeek/fix_shed_tool_conf_selection Serialize select field options, fixes beta install Commit: 7d7a875af398c440040e78dcc2516aae1c6eb041 https://github.com/galaxyproject/galaxy/commit/7d7a875af398c440040e78dcc251… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5919 from erasche/fix-config-validate [18.01] Allow schema to validate Commit: f5194910f724554df3b2ac17ff489c0c986cc1ac https://github.com/galaxyproject/galaxy/commit/f5194910f724554df3b2ac17ff48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Merge pull request #6680 from mvdbeek/subworkflow_escape_names Fix wf-editor when loading subworkflow with parenthesis in label Commit: 64bb339a31e8e2559bbb4ba81e8f27f65d1fe412 https://github.com/galaxyproject/galaxy/commit/64bb339a31e8e2559bbb4ba81e8f… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #6641 from martenson/rename-and-document-config-value document config for sniffing compressed files, enable by default Commit: 8695a0d9bc4481ebf49ec9fc13db1c066243b12c https://github.com/galaxyproject/galaxy/commit/8695a0d9bc4481ebf49ec9fc13db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M lib/galaxy/tools/cache.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Keep newly broken tool in toolbox That's handy when developing tools and you messed up something so bad the tool isn't valid anymore. We retrieve the non-broken previous version from the tool cache. Commit: 947389887b011fc277ac776b3f6c21c3dd6df96d https://github.com/galaxyproject/galaxy/commit/947389887b011fc277ac776b3f6c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Add unit test that exercises reloading for broken tools Commit: dc49c3ea0ebd64ac2d1b51a67e7c18df06255804 https://github.com/galaxyproject/galaxy/commit/dc49c3ea0ebd64ac2d1b51a67e7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-08 (Sat, 08 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py Log Message: ----------- Provide visual feedback if tool is broken Commit: 9d5146017c77f3a2c29bb4c7dec5885849f67c66 https://github.com/galaxyproject/galaxy/commit/9d5146017c77f3a2c29bb4c7dec5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Expose version parameter for workflows, allows retrieving non-latest versions Commit: f49da14e45feed1273c705112a6d75a484ba9548 https://github.com/galaxyproject/galaxy/commit/f49da14e45feed1273c705112a6d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Move recovery functionality for getting perticular workflow versions into StoredWorkflow Commit: e18433127f244b332325e6a7bf9e914f9e0391e6 https://github.com/galaxyproject/galaxy/commit/e18433127f244b332325e6a7bf9e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Order list of workflows related to a StoredWorkflow This will put the newest workflows first. Commit: c652cf4b078ae69e36292f1ba1ef72a899ff0b4f https://github.com/galaxyproject/galaxy/commit/c652cf4b078ae69e36292f1ba1ef… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Allow loading non-latest workflows into editor There is no UI-element so far, but you can append &version=<N> to the editor URL to load any arbitrary version of a workflow. Commit: 3d8db3a91f9b5dff0b5940fc0f40f5d5b19f051a https://github.com/galaxyproject/galaxy/commit/3d8db3a91f9b5dff0b5940fc0f40… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Inform user that workflow loading has failed This sends the user back to the worflow index page. Commit: 56411c3c116d160fc4c95b718e52a27b13c5bd98 https://github.com/galaxyproject/galaxy/commit/56411c3c116d160fc4c95b718e52… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Hack around routes returning 'None' for parameter Commit: f1e94f84739c929429c0079f245baa10afacc155 https://github.com/galaxyproject/galaxy/commit/f1e94f84739c929429c0079f245b… Author: charesredhat <cstrittmatter(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Added Workflow version change control to the top bar Commit: 98a2526cec43129e143c3201e908dee943194353 https://github.com/galaxyproject/galaxy/commit/98a2526cec43129e143c3201e908… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Show current version in version selection Commit: 85d80ec20ba7bf9985c3139aa47a75e974aafa5d https://github.com/galaxyproject/galaxy/commit/85d80ec20ba7bf9985c3139aa47a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-09 (Sun, 09 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Always pass in a version when loading the wf-editor Commit: 85adb0a371b0079b929e360e7fa35e97b2cd09d8 https://github.com/galaxyproject/galaxy/commit/85adb0a371b0079b929e360e7fa3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move version selection to right-hand most location Commit: d377b00388f8c8060853ef77f8be6187968e78b4 https://github.com/galaxyproject/galaxy/commit/d377b00388f8c8060853ef77f8be… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Indicate which version is currently on display Commit: ec320d2bad5c327b625e66a13a22c941cac96c5d https://github.com/galaxyproject/galaxy/commit/ec320d2bad5c327b625e66a13a22… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Update `cloud` objectstore to adhere with cloudbridge v1 interface. Commit: d0e2820b4f2e35e5a15c96296c656e7c03ee44df https://github.com/galaxyproject/galaxy/commit/d0e2820b4f2e35e5a15c96296c65… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Log exception message failing to create bucket in cloud objectstore. Commit: a52b8a436523a6de040001d45f9773699e58445b https://github.com/galaxyproject/galaxy/commit/a52b8a436523a6de040001d45f97… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/objectstore/cloud.py Log Message: ----------- Catch a cloudbridge exception if a given bucket does not exist. Commit: 0956604e557bf1a3857fa870beee7f7f6f36d929 https://github.com/galaxyproject/galaxy/commit/0956604e557bf1a3857fa870beee… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update cloud manager to adhere with v1 cloudbridge interface. Commit: 94fe62803b18151f4aa7830c27704fe6ab65cefb https://github.com/galaxyproject/galaxy/commit/94fe62803b18151f4aa7830c2770… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Update cloudbridge version in conditional requirements. Commit: ae41b22113332d7cb11db4d64b9037da473d90ba https://github.com/galaxyproject/galaxy/commit/ae41b22113332d7cb11db4d64b90… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update dependencies using `make update-dependencies`. Commit: c95d995e9d980ced74ef0697b14c786a72369680 https://github.com/galaxyproject/galaxy/commit/c95d995e9d980ced74ef0697b14c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Fix pyinotify environment marker Remove outdated pin on boto. Commit: 11274995ca5a84f750000be724d770e77d9de990 https://github.com/galaxyproject/galaxy/commit/11274995ca5a84f750000be724d7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Rename bucket to bucket_name in cloud API and manager. Commit: 240074224f07d1a047e5560627e3f19fb02ae0e7 https://github.com/galaxyproject/galaxy/commit/240074224f07d1a047e5560627e3… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Rename bucket_obj to bucket. Commit: efec721676d2b27c91afb655c7c6630ed838a39e https://github.com/galaxyproject/galaxy/commit/efec721676d2b27c91afb655c7c6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Move version selection out of editor.mako Also adds an API that lists workflow versions for a workflow id. Commit: d42fb41cb0599488b17008849b79dc064f7e54f9 https://github.com/galaxyproject/galaxy/commit/d42fb41cb0599488b17008849b79… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6681 from mvdbeek/continue_reloading_if_tool_is_broken Keep newly broken tool in toolbox Commit: d349d4763d61d540a9704ba5b184189fa0fb2d1e https://github.com/galaxyproject/galaxy/commit/d349d4763d61d540a9704ba5b184… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflow_fixtures.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #6678 from jmchilton/subworkflow_parameters Workflow replacement parameters polish. Commit: 9217680ab6af2d0d96a1ce8be520ed010767cdfb https://github.com/galaxyproject/galaxy/commit/9217680ab6af2d0d96a1ce8be520… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js M lib/galaxy/webapps/galaxy/controllers/page.py A scripts/pages_identifier_conversion.py M static/scripts/bundled/extended.bundled.js M static/scripts/galaxy.pages.js M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge pull request #6647 from dannon/page_fixes [18.05] Pages - fixes for encoded ids in the database Commit: 3e4bbfbbc29f84ae30cd5905e7a43376915cbf47 https://github.com/galaxyproject/galaxy/commit/3e4bbfbbc29f84ae30cd5905e7a4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6683 from mvdbeek/expose_workflow_versions Expose workflow versions Commit: b8fe2fe294f11f8700cda2dd6bbdd1d796cada2c https://github.com/galaxyproject/galaxy/commit/b8fe2fe294f11f8700cda2dd6bbd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js M lib/galaxy/webapps/galaxy/controllers/page.py A scripts/pages_identifier_conversion.py M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge branch 'release_18.05' into dev Commit: ebc5858f02e07585860b4adc26ccaff300e1154c https://github.com/galaxyproject/galaxy/commit/ebc5858f02e07585860b4adc26cc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/managers/cloud.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Merge pull request #6660 from VJalili/upgrade_cloudbridge Upgrade CloudBridge to v1.0.1 Commit: be04959cf311e0f495f5a10e84f6f1933594a38d https://github.com/galaxyproject/galaxy/commit/be04959cf311e0f495f5a10e84f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.09.rc1 Commit: c8cb164ab8ad4fe5d7ea9768e3f7e58051200525 https://github.com/galaxyproject/galaxy/commit/c8cb164ab8ad4fe5d7ea9768e3f7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-10 (Mon, 10 Sep 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #6687 from dannon/version-18.09 Update version to 18.09.rc1 Commit: 4fc9fe2150690c04d4d6071994126a05b250379b https://github.com/galaxyproject/galaxy/commit/4fc9fe2150690c04d4d607199412… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Fix target update for rule collection builder after input selection Commit: a937bc5539414624fe42c49607416f14dadd425b https://github.com/galaxyproject/galaxy/commit/a937bc5539414624fe42c4960741… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Client build. Commit: 471162eadb4408318db534c6d24f7685bedb29eb https://github.com/galaxyproject/galaxy/commit/471162eadb4408318db534c6d24f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/extract_dataset.xml Log Message: ----------- [18.09] Fix new extract dataset to perserve collection element identifier. Commit: ba4e7d199b4bc080dcd741710d2241147bdbe745 https://github.com/galaxyproject/galaxy/commit/ba4e7d199b4bc080dcd741710d22… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Make gro and top datatypes tabular subclasses I think that was the intention in https://github.com/galaxyproject/galaxy/commit/56d55399ebe2ecd614a7ba5a1467… Commit: 80266129fe3d3d4b9657da0a3c5e8232bfa2a46b https://github.com/galaxyproject/galaxy/commit/80266129fe3d3d4b9657da0a3c5e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/extract_dataset.xml Log Message: ----------- Merge pull request #6692 from jmchilton/1809_fix_extract_name [18.09] Fix new extract dataset tool to preserve collection element identifier. Commit: 2a79ae0ce1bbefe8a0340edb4882a00f07fc6de2 https://github.com/galaxyproject/galaxy/commit/2a79ae0ce1bbefe8a0340edb4882… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Merge pull request #6691 from jmchilton/backport_6326 [18.05] Backport #6326 Commit: 1f8c234c2be8baac9db94e17f4727e6c3c6c55ef https://github.com/galaxyproject/galaxy/commit/1f8c234c2be8baac9db94e17f472… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Make top datatype inherit from Text. Commit: 17157dd0633b4deb91a39bbc76288dd2968423f5 https://github.com/galaxyproject/galaxy/commit/17157dd0633b4deb91a39bbc7628… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #9 from blankenberg/gro2 Make top datatype inherit from Text. Commit: 9657cd6b32ed0768d2c73dd9d63c38432afb4b71 https://github.com/galaxyproject/galaxy/commit/9657cd6b32ed0768d2c73dd9d63c… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6695 from mvdbeek/fix_gro_top_datatypes [18.09] Make gro and top datatypes tabular subclasses Commit: bddabe3029335a7db51a0ef1c6a7508937db33fa https://github.com/galaxyproject/galaxy/commit/bddabe3029335a7db51a0ef1c6a7… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add missing route for API endpoint. Commit: 1dacc35332cf956ed5631fe8c6fa8e231dab663e https://github.com/galaxyproject/galaxy/commit/1dacc35332cf956ed5631fe8c6fa… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6703 from davebx/updates_api [18.05] Add missing route for API endpoint. Commit: 7e2a77e8af152a501f124a6d0f702a66502e0dd3 https://github.com/galaxyproject/galaxy/commit/7e2a77e8af152a501f124a6d0f70… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch additional permutations of Slurm cgroup creation warnings Commit: f7c1d31dbc6f23eb4fba37b82aeb2808fd69224f https://github.com/galaxyproject/galaxy/commit/f7c1d31dbc6f23eb4fba37b82aeb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- unquote the tool_version in the tools API if the tool version includes '+', which is a recommended way of versioning per https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_x… this would fail the comparison down the line in the toolbox.get_tool() method this commit also downgrades the unquote_plus to unquote for tool_id for similar reasons since it also contains the version Commit: 1b6d422afdd0c1f7291a0999bfc54284b90972d2 https://github.com/galaxyproject/galaxy/commit/1b6d422afdd0c1f7291a0999bfc5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- unquote similarly to previous commit but in the workflow controller Commit: b4b49dc2028da2064fd34d7345b23b47150a1039 https://github.com/galaxyproject/galaxy/commit/b4b49dc2028da2064fd34d7345b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Add self help to error reporting interface. Commit: 88bf3435775e94217bccfc46a5215311dea321aa https://github.com/galaxyproject/galaxy/commit/88bf3435775e94217bccfc46a521… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Import Backbone consistently across the app Commit: f513594c31a3738420889b3f5e36d39796946587 https://github.com/galaxyproject/galaxy/commit/f513594c31a3738420889b3f5e36… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6707 from martenson/unqoute_tool_version [18.05] unquote the tool_version in the tools API Commit: 84d66bea6008dc534aa6a2331e824005b204da19 https://github.com/galaxyproject/galaxy/commit/84d66bea6008dc534aa6a2331e82… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- h2!=h3 Commit: 32223161c7ca735647d53ebfe4b90f1cd4051051 https://github.com/galaxyproject/galaxy/commit/32223161c7ca735647d53ebfe4b9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js Log Message: ----------- Merge pull request #6711 from dannon/error_help [18.09] Add self help to error reporting interface Commit: 3d508a01d3d58908b667e428f125df91d8c599c1 https://github.com/galaxyproject/galaxy/commit/3d508a01d3d58908b667e428f125… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Improvements from @nsoranzo Commit: 6993dbb6fcd112e077fbad66deae716a53247d07 https://github.com/galaxyproject/galaxy/commit/6993dbb6fcd112e077fbad66deae… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6705 from natefoo/slurm-cgroup-enospc [18.05] Catch additional permutations of Slurm cgroup creation warnings Commit: dfff5c966342b38603514d8bfd3ed8e5b6e0bed9 https://github.com/galaxyproject/galaxy/commit/dfff5c966342b38603514d8bfd3e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom Log Message: ----------- Add Loom datatype and remove rdata.seurat. Commit: f06da87189ccabd209f60509dd438bc690fc5523 https://github.com/galaxyproject/galaxy/commit/f06da87189ccabd209f60509dd43… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove comment Commit: 2209c3171de52dbe83683d2644b0ec6befbaa763 https://github.com/galaxyproject/galaxy/commit/2209c3171de52dbe83683d2644b0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Minor cleanup. Commit: 037ddfeab5decd47d4d2bd8771e975dc1857703a https://github.com/galaxyproject/galaxy/commit/037ddfeab5decd47d4d2bd8771e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Fix active content setting for views with explicitly defined models Commit: df4fbe6b92457fa910f014bbd3a8dd84c25d3969 https://github.com/galaxyproject/galaxy/commit/df4fbe6b92457fa910f014bbd3a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js Log Message: ----------- Swap badge-default to badge-primary Commit: b2193bddc2aea250a189171ae61ed992b0449c84 https://github.com/galaxyproject/galaxy/commit/b2193bddc2aea250a189171ae61e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/docs/bootstrap.md Log Message: ----------- Drop badge-default from docs, correctly refer to secondary. Commit: a9273218424c1687bedf112591f2bbf735d32aa8 https://github.com/galaxyproject/galaxy/commit/a9273218424c1687bedf112591f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Client format. Commit: 0040c36d4561155af3f32262d186e186349d989d https://github.com/galaxyproject/galaxy/commit/0040c36d4561155af3f32262d186… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/docs/bootstrap.md M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6726 from dannon/badge-default-fix [18.09] Badge default fix Commit: 96593cb444063d6cc6819dd77d7b2fb89c250054 https://github.com/galaxyproject/galaxy/commit/96593cb444063d6cc6819dd77d7b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Import cleanup and documentation for dataset-li-edit. Commit: 072d40f3e9a9050f034f440b76c8b84536bc0ead https://github.com/galaxyproject/galaxy/commit/072d40f3e9a9050f034f440b76c8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- remove html tags and newlines from the help text this should improve the toolsearch for certain keywords and also make the search index smaller Commit: b7f16228575215c9be134d1bbc1cf9e37b700488 https://github.com/galaxyproject/galaxy/commit/b7f16228575215c9be134d1bbc1c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- replace the replacement for newline from empty string to space, that should avoid unwanted word merges Commit: 11b5157825ee318b763f6c48b674b968f114aebb https://github.com/galaxyproject/galaxy/commit/11b5157825ee318b763f6c48b674… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Use standard faIconButton for visualize. Commit: 17d67e24c072c8953e482aff41e9b1faed78b4d3 https://github.com/galaxyproject/galaxy/commit/17d67e24c072c8953e482aff41e9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- use bleach isntead of custom regex thanks @nsoranzo Commit: 54d137edab3fb33beac87c23cd35fb19dd7f44fa https://github.com/galaxyproject/galaxy/commit/54d137edab3fb33beac87c23cd35… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Remove deprecated `decode_param_names` parameter It has been deprecated since WebOb 1.1 and ignored since WebOb 1.2 . Commit: 8ed19a3a09df9b66266f66bc53e504c781ae524d https://github.com/galaxyproject/galaxy/commit/8ed19a3a09df9b66266f66bc53e5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/interactor.py Log Message: ----------- `async` is a reserved keyword in Python 3.7 - Remove unused `async` parameter of `stage_data_async()` method. - Rename `async` parameter of `quick_load()` method. Fix https://github.com/galaxyproject/galaxy/issues/6717 . xref. https://github.com/galaxyproject/galaxy/issues/1715 Commit: 8982212d396c1ab216c5c9ea0656e5231e05d745 https://github.com/galaxyproject/galaxy/commit/8982212d396c1ab216c5c9ea0656… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/util/xml_macros.py M scripts/loc_files/create_all_fasta_loc.py Log Message: ----------- Replace deprecated `xml.etree.ElementTree.Element.getiterator()` with `iter()` Commit: f0708488aa08393cfdf3ab3e0e45e37982d050d0 https://github.com/galaxyproject/galaxy/commit/f0708488aa08393cfdf3ab3e0e45… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M pytest.ini Log Message: ----------- pytest: disable test collection of classes starting with `Test` Fix warnings like: ``` /home/travis/build/galaxyproject/galaxy/lib/galaxy/tools/verify/test_data.py:29: PytestWarning: cannot collect test class 'TestDataResolver' because it has a __init__ constructor class TestDataResolver(object): ``` appearing e.g. in https://travis-ci.org/galaxyproject/galaxy/jobs/428114139 . See pytest documentation: https://docs.pytest.org/en/latest/reference.html#confval-python_classes Commit: 2874e87debcc1940e1f1143a7af4dacb38c95585 https://github.com/galaxyproject/galaxy/commit/2874e87debcc1940e1f1143a7af4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Merge pull request #6728 from martenson/fix-toolhelp-parsing [18.09] remove html tags and newlines from the help text Commit: 0974b130ef922e3177de27f6365ccd624bf194a7 https://github.com/galaxyproject/galaxy/commit/0974b130ef922e3177de27f6365c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/base.py M pytest.ini M scripts/loc_files/create_all_fasta_loc.py Log Message: ----------- Merge pull request #6730 from nsoranzo/release_18.09_backport_6722 [18.09] Partial backport of #6722 Commit: 6233a408cc93152a379651db3cc143d368f78dda https://github.com/galaxyproject/galaxy/commit/6233a408cc93152a379651db3cc1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst Log Message: ----------- Release notes templated; still needs manual curation Commit: 376516610ef6ac28cef7a9558adab1a88d8c0c12 https://github.com/galaxyproject/galaxy/commit/376516610ef6ac28cef7a9558ada… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Bugfix - missing tests for data source sniffing. Ensure #6334 is fixed I think. Commit: aca30f0b158a9ab0647747b957f55ea6716a4d18 https://github.com/galaxyproject/galaxy/commit/aca30f0b158a9ab0647747b957f5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Merge pull request #6733 from jmchilton/1809_sniff_test [18.09] Fix missing tests for data source sniffing. Commit: 8462df83c9b3d5bdba93025f25dd182b7f22ea34 https://github.com/galaxyproject/galaxy/commit/8462df83c9b3d5bdba93025f25dd… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.loom Log Message: ----------- Merge pull request #6723 from blankenberg/18.09-loom [18.09] Add Loom datatype and remove rdata.seurat Commit: 18d99deb951a8d429be5695fac539c93e4c90e3e https://github.com/galaxyproject/galaxy/commit/18d99deb951a8d429be5695fac53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Decode tool id and version in the client, not in the API using `decodeUriComponent` from `decode-uri-component` JS package. Revert https://github.com/galaxyproject/galaxy/pull/6707 Remove unused `_get_tool()` method in `lib/galaxy/webapps/galaxy/api/workflows.py` . Rebuild client with: ``` make client-production-maps ``` Commit: 7f38e61caebe8e56ab1f6cf6d5b577c6b020c9d3 https://github.com/galaxyproject/galaxy/commit/7f38e61caebe8e56ab1f6cf6d5b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: R lib/galaxy/dependencies/requirements.txt Log Message: ----------- Remove again lib/galaxy/dependencies/requirements.txt It was reintroduced (empty) by mistake in https://github.com/galaxyproject/galaxy/pull/4474 . Commit: 35754dc49a7d29a12fe10c444ce69c1af47b0a2b https://github.com/galaxyproject/galaxy/commit/35754dc49a7d29a12fe10c444ce6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Fix symlinking during plugin staging Remove also broken symlinks before creating the new ones. Commit: 5121275c1d5e7c724edbc3cef531f3401aea5225 https://github.com/galaxyproject/galaxy/commit/5121275c1d5e7c724edbc3cef531… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Remove stray debug statement. Commit: 1cdcb80fe88cd076f5c966b0b6a4acab37841877 https://github.com/galaxyproject/galaxy/commit/1cdcb80fe88cd076f5c966b0b6a4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #6739 from jmchilton/remove_debug [18.09] Remove stray debug statement. Commit: 806beaca9b4b51322214e68619407e8a0545a19d https://github.com/galaxyproject/galaxy/commit/806beaca9b4b51322214e6861940… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Test that newest version will be returned if tool id or version don't match Commit: c8552970dd7c2eeb9d765911843ed3e866b84ce3 https://github.com/galaxyproject/galaxy/commit/c8552970dd7c2eeb9d765911843e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort by tool version when picking a tool with an unavailable version Commit: 94082a878dca784eb57c6be1fd552a63f85bcfad https://github.com/galaxyproject/galaxy/commit/94082a878dca784eb57c6be1fd55… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Unit test that fails if we don't return the latest version upon version mismatch Commit: 3ea9d086bfe295a210d6f249ef2c39d8a65ef042 https://github.com/galaxyproject/galaxy/commit/3ea9d086bfe295a210d6f249ef2c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort rval so that newest tool appears last in rval Commit: f6f526a0a50a98143d4845f8907067b6f42e1dea https://github.com/galaxyproject/galaxy/commit/f6f526a0a50a98143d4845f89070… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Use tool_version instead of version parameter To be consistent with other routes that accept this parameter. Commit: 5635a05a2a70c3e8887c32b1a8675f124808fd49 https://github.com/galaxyproject/galaxy/commit/5635a05a2a70c3e8887c32b1a867… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py Log Message: ----------- Look up collection_type if collection_type_source is set We do this in the wf-editor and in the backend, so this works for subworkflows. This should make quite some tools more usable in a workflow scenario. Should fix - https://github.com/galaxyproject/galaxy/issues/6514 - https://github.com/galaxyproject/galaxy/issues/6012 - https://github.com/galaxyproject/galaxy/issues/6569 - https://github.com/galaxyproject/galaxy/issues/1889 and perhaps more issues related to this. Commit: f7fe3418d63683a998425b99f4688872fef07b09 https://github.com/galaxyproject/galaxy/commit/f7fe3418d63683a998425b99f468… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Reset collection_type if collection_type_source has been removed Commit: a52ee84aede53ff2cb5a3e667e4ef03df1fd3acb https://github.com/galaxyproject/galaxy/commit/a52ee84aede53ff2cb5a3e667e4e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Drop invalid connections if type_source is unavailable Commit: 29f07f0b0ad49b86b50c34e9890eb2117e067a2b https://github.com/galaxyproject/galaxy/commit/29f07f0b0ad49b86b50c34e9890e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #6741 from jmchilton/backport_type_source [18.09] Backport #6732 Commit: 3017568e77cf950b8b611a16ea7ce9fcc2159e81 https://github.com/galaxyproject/galaxy/commit/3017568e77cf950b8b611a16ea7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Drop unnecessary history in test_show_with_wrong_tool_version_in_tool_id test Commit: 840041744505402ab5af4f39b84ba76599cb8588 https://github.com/galaxyproject/galaxy/commit/840041744505402ab5af4f39b84b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M scripts/plugin_staging.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js Log Message: ----------- Merge pull request #6737 from nsoranzo/release_18.05_revert_6707 [18.05] Decode tool id and version in the client, not in the API Commit: 420f43645af9b37c32eb126f89c4266f36f6edb0 https://github.com/galaxyproject/galaxy/commit/420f43645af9b37c32eb126f89c4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/uwsgi_schema.yml M scripts/get_uwsgi_args.py Log Message: ----------- map the favicon in uwsgi config Commit: 4ce8086c2052a1abee4824456ddfd48ee5cb7c6a https://github.com/galaxyproject/galaxy/commit/4ce8086c2052a1abee4824456ddf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/package.json R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M scripts/plugin_staging.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: b45c3531dedc71b4ea8142fe5aa9f17f10bfb997 https://github.com/galaxyproject/galaxy/commit/b45c3531dedc71b4ea8142fe5aa9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- dispose of tooltip when the delete is being called Commit: 33eb06c9b872f75fd22e06297a2043f8685d1df2 https://github.com/galaxyproject/galaxy/commit/33eb06c9b872f75fd22e06297a20… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/uwsgi_schema.yml Log Message: ----------- remove something that should have never been where it was look at me, I do not know what I am doing Commit: 4aa2b8f919f28b798ba9a2401c602990287338b6 https://github.com/galaxyproject/galaxy/commit/4aa2b8f919f28b798ba9a2401c60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Disentangle this/self/frames in scratchbook's events. Commit: 077f3088ece5c8617b044d53764aebff1768b34f https://github.com/galaxyproject/galaxy/commit/077f3088ece5c8617b044d53764a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Correct visualization link to use router or scratchbook as appropriate. Commit: 3f29d32898efd121f315b2147e917584e9dec28f https://github.com/galaxyproject/galaxy/commit/3f29d32898efd121f315b2147e91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Strip unused function, cleanup. Commit: 0018ab989b117c953dd2b02e1e06cc80af1ddff2 https://github.com/galaxyproject/galaxy/commit/0018ab989b117c953dd2b02e1e06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Add event hook for non-bb-view center panel id setting, use it for dataset visualization. Commit: b64754dee94c571112c79ccb15fe515545337e15 https://github.com/galaxyproject/galaxy/commit/b64754dee94c571112c79ccb15fe… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/webapps/config_manage.py M scripts/get_uwsgi_args.py Log Message: ----------- Merge pull request #6743 from martenson/fix-favicon-uwsgi [18.09] fix favicon.ico for uwsgi deployments Commit: d17ea03442448472f1e5e5d4e12e73459f1736e7 https://github.com/galaxyproject/galaxy/commit/d17ea03442448472f1e5e5d4e12e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Minor formatting tweaks. Commit: 7a22f38a2e5229ebca109836396b17bf8785af37 https://github.com/galaxyproject/galaxy/commit/7a22f38a2e5229ebca109836396b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #6744 from martenson/dispose-tooltip-on-delete [18.09] dispose of dataset tooltip when the delete is being called Commit: f5dcf60561703086a070a2b59ad3918df68cbd0e https://github.com/galaxyproject/galaxy/commit/f5dcf60561703086a070a2b59ad3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Fix and test anonymous error reports Fixes https://github.com/galaxyproject/galaxy/issues/6675 Commit: 87ecf1428e841bced376e504d1d468319a7853c9 https://github.com/galaxyproject/galaxy/commit/87ecf1428e841bced376e504d1d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Use pre-fetched dataset id Commit: b5e221929687809adfb30cad8280767f3a8412c5 https://github.com/galaxyproject/galaxy/commit/b5e221929687809adfb30cad8280… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Fix page editor height for flex panels. Commit: 56f5bf743a50afadc74e253bc95fcef4bb6d599d https://github.com/galaxyproject/galaxy/commit/56f5bf743a50afadc74e253bc95f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Make newer unit tests more robust with a looped wait... ... instead of raw sleep. Commit: d014469f070e62a0b3dc8bdbd93128e4c7a308f8 https://github.com/galaxyproject/galaxy/commit/d014469f070e62a0b3dc8bdbd931… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #6742 from mvdbeek/fix_error_reporting [18.05] Fix and test anonymous error reports Commit: 5eb7e5ce6f16e4e6978e44637b419ff3fb1b8e87 https://github.com/galaxyproject/galaxy/commit/5eb7e5ce6f16e4e6978e44637b41… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: d312c48ea76876bd4219f544b8c03e2e909ac6f5 https://github.com/galaxyproject/galaxy/commit/d312c48ea76876bd4219f544b8c0… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6748 from jmchilton/1809_robust_sleep [18.09] Make newer unit tests more robust with a looped wait... Commit: f65e616c1afe6d9ec0bb9680fa90ee8e9d311900 https://github.com/galaxyproject/galaxy/commit/f65e616c1afe6d9ec0bb9680fa90… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Use mapped-over collectionType when inferring collectionType through format_source Commit: 02c177152bd7dbef02d4ea5d40449745e913b38b https://github.com/galaxyproject/galaxy/commit/02c177152bd7dbef02d4ea5d4044… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6740 from mvdbeek/backport_tool_version_select_fixes [18.05] Backport tool version select fixes Commit: 3ffbf5b4b6138177ed7581d7845432bec138ee23 https://github.com/galaxyproject/galaxy/commit/3ffbf5b4b6138177ed7581d78454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Append mapped-over collection type to output collection type So if for instance the connected input is a regular input with a list:list input and the output is a paired collection we set the output collection type to list:list:paired. Commit: eb37ad3752f5dbe4806e74f85b4fcee63ab407fa https://github.com/galaxyproject/galaxy/commit/eb37ad3752f5dbe4806e74f85b4f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Only reset the right hand side of a connection on disconnect Commit: 30728899054dde65ddd9fe99dc8424166ee0c5ad https://github.com/galaxyproject/galaxy/commit/30728899054dde65ddd9fe99dc84… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 287648f5d9f95ccd1b625037e30de0ab3e62e7f5 https://github.com/galaxyproject/galaxy/commit/287648f5d9f95ccd1b625037e30d… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Merge pull request #6725 from dannon/fix_active_highlight [18.09] Fix active highlight Commit: 9b5045a05c882c652935d9daaf589a10d776190c https://github.com/galaxyproject/galaxy/commit/9b5045a05c882c652935d9daaf58… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge pull request #6747 from dannon/fix_page_editor_height [18.09] Fix page editor height for flex panels. Commit: 7eac08979b1f474254e9a6a0b2005d365e09c143 https://github.com/galaxyproject/galaxy/commit/7eac08979b1f474254e9a6a0b200… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Undo auto-propagation of group tags. @mvdbeek and I discussed this in the Galaxy project gitter a few weeks ago and decided the propagation is too aggressive and should likely be done manually at the end of a workflow for now - using for instance the set tags collection operation tool. Commit: f3298953d41cb0e2b37812242a88d226a890e8aa https://github.com/galaxyproject/galaxy/commit/f3298953d41cb0e2b37812242a88… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Don't skip build on release/master moving forward. Commit: bd5d12049b238c4475f267fbbf63bd3a124b0a58 https://github.com/galaxyproject/galaxy/commit/bd5d12049b238c4475f267fbbf63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Swap nodeenv to a pinned requirement. Commit: 4d6d984fbd8d66b30c7da3cd5022903f11218b09 https://github.com/galaxyproject/galaxy/commit/4d6d984fbd8d66b30c7da3cd5022… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/README.md Log Message: ----------- Update client/README Commit: 3f8c2beff252587cd1347142ab84ad20afd57b03 https://github.com/galaxyproject/galaxy/commit/3f8c2beff252587cd1347142ab84… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Swap to a production w/ sourcemaps build by default for autobuilder (though, of course, folks can manually do whatever -- seems like the most sensible default though) Commit: 0fb115e046b3a492db6b592d8b38459104d696bf https://github.com/galaxyproject/galaxy/commit/0fb115e046b3a492db6b592d8b38… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6750 from jmchilton/1809_tags_walkback [18.09] Undo auto-propagation of group tags. Commit: e10180dea108785a017b7be37b7ff5d85a2eebf1 https://github.com/galaxyproject/galaxy/commit/e10180dea108785a017b7be37b7f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- (minor) client-format Commit: 8a4fe72f6710270ca453b75d61e8dbc96feadcc5 https://github.com/galaxyproject/galaxy/commit/8a4fe72f6710270ca453b75d61e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge branch 'collection_type_source_followup' into release_18.09 Commit: 679603b7c9a2b1f8c136dcc29d2eb41174bd6b31 https://github.com/galaxyproject/galaxy/commit/679603b7c9a2b1f8c136dcc29d2e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py Log Message: ----------- Catch any failures encountered while pausing/stopping jobs whose inputs are terminal and non-ok, so that it doesn't interrupt processing other jobs. That was discovered because attempting to delete purged job outputs on failure was raising ObjectNotFound since dataset object store assignment is done later now. So also, catch that ObjectNotFound. Commit: 1a19043789498f1d45725840b0761939d5dad2a5 https://github.com/galaxyproject/galaxy/commit/1a19043789498f1d45725840b076… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-09-23 (Sun, 23 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add graph DOT datatype Commit: 8d025aa4ed75f63924d9e11f9d0c65ca3aca7be0 https://github.com/galaxyproject/galaxy/commit/8d025aa4ed75f63924d9e11f9d0c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-09-23 (Sun, 23 Sep 2018) Changed paths: M config/plugins/visualizations/graphviz/config/graphviz.xml Log Message: ----------- add graph_dot datatype to graphvis Commit: 25fc1617030d392f85abb65ccd95f913561919e2 https://github.com/galaxyproject/galaxy/commit/25fc1617030d392f85abb65ccd95… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Update RN with new merges. Commit: ac65832cb5e4fa7a3e57af3722a09c7dfa4ac2ea https://github.com/galaxyproject/galaxy/commit/ac65832cb5e4fa7a3e57af3722a0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/visualizations/graphviz/config/graphviz.xml Log Message: ----------- Merge pull request #6760 from bgruening/graph_dot [18.09] Add graph dot datatype and enable it in visualisations Commit: 8c05e2f5f1677950a3279ffa30ccbf8949aa35e4 https://github.com/galaxyproject/galaxy/commit/8c05e2f5f1677950a3279ffa30cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add grapdot datatype. Commit: 611764b81a761c034bfd040b76818187a555807e https://github.com/galaxyproject/galaxy/commit/611764b81a761c034bfd040b7681… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Remove cruft releated to upgrading from 17.05 Galaxies. These interact poorly with recent changes in 18.09 and in nearly all cases should no longer be needed at this point. Commit: ea7359b08b21a9e0febe6cd98a9fd4488c133546 https://github.com/galaxyproject/galaxy/commit/ea7359b08b21a9e0febe6cd98a9f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Merge pull request #6761 from jmchilton/remove_upgrade_cruft [18.09] Remove upgrade cruft related to datatypes. Commit: 6ac5966c5e1a95e93c5923a4eddf5fa971518bd6 https://github.com/galaxyproject/galaxy/commit/6ac5966c5e1a95e93c5923a4eddf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add removal of upgrade logic specific to datatypes from 17.05 Commit: 546459f3536ca7b1504550794e8d1d77e68985d0 https://github.com/galaxyproject/galaxy/commit/546459f3536ca7b1504550794e8d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Wrap onclick functions with a tooltip de-tipper for faIconButtons. Commit: 35b72ff508a860ed297780345d213c9155f014aa https://github.com/galaxyproject/galaxy/commit/35b72ff508a860ed297780345d21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Remove now-unnecessary tooltip dispose Commit: 3146c57b310fedc525aa6a5b8ab87d8bacf2784d https://github.com/galaxyproject/galaxy/commit/3146c57b310fedc525aa6a5b8ab8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Blur buttons onclick Commit: 7c290b1743b03c1eb1711df8218f5733a8f791c8 https://github.com/galaxyproject/galaxy/commit/7c290b1743b03c1eb1711df8218f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Set a reasonable nearby focus instead of blur, to prevent tabindex loss. Commit: 34d54558b3dc40d54a507128b8a45b691151f863 https://github.com/galaxyproject/galaxy/commit/34d54558b3dc40d54a507128b8a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Simplify wrapping logic, fix context. Commit: 7320752138dc186b96f53746b1811dcc2c212dc1 https://github.com/galaxyproject/galaxy/commit/7320752138dc186b96f53746b181… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Client formatting. Commit: de6dc00236ad2947d3bef479b5d7df5c3bef7ba4 https://github.com/galaxyproject/galaxy/commit/de6dc00236ad2947d3bef479b5d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Don't attempt len(None), ensure stdout/stderr are strings in Job(Like).set_streams(). Commit: a0ad5adf6fc02c6a0864308f8d6f8a612a83f308 https://github.com/galaxyproject/galaxy/commit/a0ad5adf6fc02c6a0864308f8d6f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Increase the maximum number of stderr lines that will be scanned for slurm warnings to strip to 3. Commit: a89184aa707a477f14905bd44b368006c7cae427 https://github.com/galaxyproject/galaxy/commit/a89184aa707a477f14905bd44b36… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6766 from natefoo/remove-more-slurm-warnings [18.09] Increase the maximum number of stderr lines that will be scanned for slurm warnings Commit: 529ed61c3b48e2d8a830e6a890d93b16a4f42ea4 https://github.com/galaxyproject/galaxy/commit/529ed61c3b48e2d8a830e6a890d9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6765 from natefoo/job-stdout-none-fix [18.09] Don't attempt len(None), ensure stdout/stderr are strings in Job(Like).set_streams(). Commit: 0698a71861afadb7f16be765223819178d294c30 https://github.com/galaxyproject/galaxy/commit/0698a71861afadb7f16be7652238… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Another few stragglers. Commit: 9f688b2f9141683e02ea9aa759a15ebd46174042 https://github.com/galaxyproject/galaxy/commit/9f688b2f9141683e02ea9aa759a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py Log Message: ----------- Merge pull request #6755 from natefoo/job-object-store-fixes [18.09] Catch any failures encountered while pausing/stopping jobs whose inputs are terminal and non-ok Commit: d3db21fa82a834d0d9fa90106b3fa2b4911708dc https://github.com/galaxyproject/galaxy/commit/d3db21fa82a834d0d9fa90106b3f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6755 Commit: 300d316ad1bcd0ec1a7b762e859232bbe8c9548c https://github.com/galaxyproject/galaxy/commit/300d316ad1bcd0ec1a7b762e8592… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Resilience of success message handling Commit: 46dd1801cbc11cb24bb7fdd0d8a4f8e71fa9ef9e https://github.com/galaxyproject/galaxy/commit/46dd1801cbc11cb24bb7fdd0d8a4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge pull request #6768 from martenson/backport_resilience_of_success_message_handling [18.09] backport of: Resilience of success message handling Commit: 2d9b803025828869c50a70db25fb7654caa17368 https://github.com/galaxyproject/galaxy/commit/2d9b803025828869c50a70db25fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Use UserRoleAssociation to get private roles If I understand this correctly this should work even if the user email changes. Commit: 6cb4c32eb4e613b4d90680450d11804779e5b4a5 https://github.com/galaxyproject/galaxy/commit/6cb4c32eb4e613b4d90680450d11… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6768 Commit: 5a97e4fcea77426eab0a7ca22402cdf8b638f79b https://github.com/galaxyproject/galaxy/commit/5a97e4fcea77426eab0a7ca22402… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #6771 from mvdbeek/fix_private_role_none [18.05] Use UserRoleAssociation to get private roles Commit: eb1980ec087d7a2c3da6d138155f6c11895a8b26 https://github.com/galaxyproject/galaxy/commit/eb1980ec087d7a2c3da6d138155f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M client/README.md M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #6753 from dannon/client-build-startup-changes [18.09] Client build startup changes Commit: 71b561512db9819b68f9685d3e43317ba43790b2 https://github.com/galaxyproject/galaxy/commit/71b561512db9819b68f9685d3e43… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6559 from jmchilton/wf_api_legacy [18.01] Restore the ability to track jobs for a WF invocation step. Commit: cf62a1dafd90df9b65f811bed74d1d173542babc https://github.com/galaxyproject/galaxy/commit/cf62a1dafd90df9b65f811bed74d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: c3d4be2e2cb1ccbdfc68ea14ebf3fb71bdec2e97 https://github.com/galaxyproject/galaxy/commit/c3d4be2e2cb1ccbdfc68ea14ebf3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: 04d2d2ef4672d3ee5f24d7dffe68a7f24238a7f0 https://github.com/galaxyproject/galaxy/commit/04d2d2ef4672d3ee5f24d7dffe68… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6772 from dannon/release_18.09 [18.09] Merge forward from 18.01, 18.05 Commit: 364e7e1f1fc54565982cea2fa47062b610d7b5ae https://github.com/galaxyproject/galaxy/commit/364e7e1f1fc54565982cea2fa470… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Update name of Workflow when updating StoredWorkflow name Fixes https://github.com/galaxyproject/galaxy/issues/6773. Commit: ee47fdb50cef70dd2b940c42594611863e51bde7 https://github.com/galaxyproject/galaxy/commit/ee47fdb50cef70dd2b940c425946… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6753, 6771 Commit: 0743c7ba04fa6e61e2c48386a49a61f41d1eb493 https://github.com/galaxyproject/galaxy/commit/0743c7ba04fa6e61e2c48386a49a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- All extracted datasets should be visible Commit: bf0370c1929def91bc69e1ab252dc0e8bfc2a387 https://github.com/galaxyproject/galaxy/commit/bf0370c1929def91bc69e1ab252d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix __encode_invocation signature and passthrough to manager that I busted in merging 18.05 forward Commit: da3b6a1566dc0bb2665b2781cdb3c76551d68613 https://github.com/galaxyproject/galaxy/commit/da3b6a1566dc0bb2665b2781cdb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- encode_invocation defers to manager and doesn't require trans passing anymore Commit: becb922dc1e8c2d48e03a2badcb940ab1661e247 https://github.com/galaxyproject/galaxy/commit/becb922dc1e8c2d48e03a2badcb9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py A test/unit/test_utils.py Log Message: ----------- Strip all control characters from rules Similar to 366701cfb23d8de31eac3c4312c6accca2e74ef1, which is valid on its own, but here we just apply it to all rules. Commit: b44379c3d9da4b7916b3c5a4fdf5eff39ee2267d https://github.com/galaxyproject/galaxy/commit/b44379c3d9da4b7916b3c5a4fdf5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #6780 from mvdbeek/visible_extracted_datasets [18.09] All extracted datasets should be visible Commit: f54cba043354aa8fac339052462f7302613ca24a https://github.com/galaxyproject/galaxy/commit/f54cba043354aa8fac339052462f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6782 from dannon/fix-bad-workflow-invocation-merge [18.09] Fix __encode_invocation signature Commit: 53b062f804c6d495b187656c84597f953210a2b0 https://github.com/galaxyproject/galaxy/commit/53b062f804c6d495b187656c8459… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Add bam upload test `test_upload_bam_file` fails on release_18.09 but passes on 18.05. Commit: 57fe3a741a9c3ac9c09513e21d44984ba046322e https://github.com/galaxyproject/galaxy/commit/57fe3a741a9c3ac9c09513e21d44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Fix metadata spontaneuosly reverting Similar to https://github.com/galaxyproject/galaxy/pull/6631/files. This fixes https://github.com/galaxyproject/galaxy/issues/6769 Commit: c5a325d01535d9b46e28165c531a119d5f51b2d6 https://github.com/galaxyproject/galaxy/commit/c5a325d01535d9b46e28165c531a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py A test/unit/test_utils.py Log Message: ----------- Merge pull request #6785 from mvdbeek/escape_all_rules [18.09] Strip all control characters from rules Commit: b0dff4444085668cc3359b73d9d4d13b6da74cf6 https://github.com/galaxyproject/galaxy/commit/b0dff4444085668cc3359b73d9d4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py Log Message: ----------- allow making all datasets within history public, when sharing this is a one-off operation so notable behavior is that if you create a new dataset in the shared history, it still won't be public when there are default permissions set on history Commit: 70e325574cb82be62b1be8090e714ce44441686b https://github.com/galaxyproject/galaxy/commit/70e325574cb82be62b1be8090e71… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Use with statement for all file uploads Commit: e4399021520440a8f58e33dbae161f031f8da9eb https://github.com/galaxyproject/galaxy/commit/e4399021520440a8f58e33dbae16… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/web/base/controller.py Log Message: ----------- show warning to user if some of the items within were not published Commit: 5a98515df88b68483ad59bb7208a57f1a7f71664 https://github.com/galaxyproject/galaxy/commit/5a98515df88b68483ad59bb7208a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #6789 from mvdbeek/fix_bam_upload [18.09] Fix bam upload resulting in 'auto' datatype Commit: 29a3b6bbfbde469e59f6a896dc8a4f76a8d3ea3d https://github.com/galaxyproject/galaxy/commit/29a3b6bbfbde469e59f6a896dc8a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6793 from martenson/fix-sharing-by-link [18.09] allow making all datasets within history public, when sharing Commit: 106fb79c8b7bd8d2faa69f9bd007efe504183012 https://github.com/galaxyproject/galaxy/commit/106fb79c8b7bd8d2faa69f9bd007… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Drop incorrect flex designation for panel inner; these are generally single line styles with floats. Fixes header for "Published History" view, etc. Commit: 71df0e44652fca8755869248935dc2bdeba39208 https://github.com/galaxyproject/galaxy/commit/71df0e44652fca8755869248935d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/yarn.lock M static/style/blue/base.css Log Message: ----------- New integrity hashes for yarn? Typo, artifacts (which will be gone soon!) Commit: c51178578dcf67c8dbe16d3d8320f660e0c80027 https://github.com/galaxyproject/galaxy/commit/c51178578dcf67c8dbe16d3d8320… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Four more PRs Commit: fd6af5eb0e0ba79679f8395d9333cf3e7331ba05 https://github.com/galaxyproject/galaxy/commit/fd6af5eb0e0ba79679f8395d9333… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- No memory leaks here Commit: d0b6bc6ddc7391527e98a4ece4e33396229c2d25 https://github.com/galaxyproject/galaxy/commit/d0b6bc6ddc7391527e98a4ece4e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M templates/webapps/galaxy/page/editor.mako Log Message: ----------- panel-body will always be full height Commit: ff65263ab2ee1351bbed11709d8536de694a5776 https://github.com/galaxyproject/galaxy/commit/ff65263ab2ee1351bbed11709d85… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6789 Commit: 814c7f926dfe8d2aa344b5b17c83dcef757334d9 https://github.com/galaxyproject/galaxy/commit/814c7f926dfe8d2aa344b5b17c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Drop unused peek method (this used unencoded ids) Commit: f3ba9e2b9e924cd94bc35e7bf5d5cfabb8e2fe48 https://github.com/galaxyproject/galaxy/commit/f3ba9e2b9e924cd94bc35e7bf5d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #6796 from dannon/peek_drop [16.01] Drop unused peek method Commit: 482f1ea35971d6a0fe979e793119d207eca4b438 https://github.com/galaxyproject/galaxy/commit/482f1ea35971d6a0fe979e793119… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 Commit: 8a1616aaf8160a4a7a7446b0cad072897c6eb568 https://github.com/galaxyproject/galaxy/commit/8a1616aaf8160a4a7a7446b0cad0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 Commit: 809ae58c52ed912a3256600ccf21456fac853782 https://github.com/galaxyproject/galaxy/commit/809ae58c52ed912a3256600ccf21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: fa7f2a4f5c18ff6f3255a5230adc65508b5c9694 https://github.com/galaxyproject/galaxy/commit/fa7f2a4f5c18ff6f3255a5230adc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 Commit: c4150d200214aed7a150c44cc780d825b2628e83 https://github.com/galaxyproject/galaxy/commit/c4150d200214aed7a150c44cc780… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 Commit: 40cecf6ff42134256bb53fcc7cb96c5a94262a63 https://github.com/galaxyproject/galaxy/commit/40cecf6ff42134256bb53fcc7cb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 Commit: ac46d21ece75c4fce57836758f566eda8c878166 https://github.com/galaxyproject/galaxy/commit/ac46d21ece75c4fce57836758f56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 Commit: 9bc37c03b6572072bffabc797ea44f7816890103 https://github.com/galaxyproject/galaxy/commit/9bc37c03b6572072bffabc797ea4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: 1e7677c3b2d7a5063a7340255140c3c8aa42129a https://github.com/galaxyproject/galaxy/commit/1e7677c3b2d7a5063a7340255140… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: ab660686c26241ec4959711603919b80442d32a0 https://github.com/galaxyproject/galaxy/commit/ab660686c26241ec495971160391… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/identifier_in_conditional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test for single and multi-input identifiers test_identifier_map_over_input_in_conditional fails at the moment (same issue as in https://github.com/galaxyproject/galaxy/issues/6182) Commit: 5bc3b2e16c315b97b18e794e4338f22ffd964dbf https://github.com/galaxyproject/galaxy/commit/5bc3b2e16c315b97b18e794e4338… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Provide a useful exception message for object store exceptions. Commit: a29c1e47a79a7e2f8dd1924ca4e79b27fea60a97 https://github.com/galaxyproject/galaxy/commit/a29c1e47a79a7e2f8dd1924ca4e7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Merge pull request #6799 from natefoo/better-object-store-logging [18.09] Provide a useful exception message for object store exceptions Commit: 73f8f3129b07cbe96c10da161a547bf2008706e2 https://github.com/galaxyproject/galaxy/commit/73f8f3129b07cbe96c10da161a54… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/tools/parameters/wrapped.py Log Message: ----------- Partially fix missing element identifier This makes sure that any toplevel `|__identifier__` is passed on to nested inputs. Commit: f8d9a9e33a994a97c537ef15f1993fbe5d5866ea https://github.com/galaxyproject/galaxy/commit/f8d9a9e33a994a97c537ef15f199… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/util/__init__.py Log Message: ----------- Attempt to recover wrapper datasets Otherwise we create new wrappers that lack the element identifier. Commit: c6d915b8f2d470517dfa6504fa635c69cc546b64 https://github.com/galaxyproject/galaxy/commit/c6d915b8f2d470517dfa6504fa63… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Parse length to integer When using the little up/down button we get strings instead of integers, and those fail the rule validation. Fixes https://github.com/galaxyproject/galaxy/issues/6800 Commit: 2d78dbb9ec1d4d1ba7240d384b27bb6bb83c24b5 https://github.com/galaxyproject/galaxy/commit/2d78dbb9ec1d4d1ba7240d384b27… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Build client Commit: 565f611389e434b6df57d39ad5c01ae037e46e76 https://github.com/galaxyproject/galaxy/commit/565f611389e434b6df57d39ad5c0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M config/plugins/webhooks/demo/tour_generator/__init__.py M templates/show_params.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Fix remaining selenium py3 erorrs Commit: de794dd9051b5b9788cd6db7db81ccbe62eec4fa https://github.com/galaxyproject/galaxy/commit/de794dd9051b5b9788cd6db7db81… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6774 from mvdbeek/fix_old_wf_name [18.05] Update name of Workflow when updating StoredWorkflow name Commit: f0131eff8b0c8886135fc4f9854e0060352a0e6e https://github.com/galaxyproject/galaxy/commit/f0131eff8b0c8886135fc4f9854e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: 2e7adfbee4835f1374dffe7ba49760cfc19fdb0e https://github.com/galaxyproject/galaxy/commit/2e7adfbee4835f1374dffe7ba497… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-29 (Sat, 29 Sep 2018) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py Log Message: ----------- Cast to bytestring in md5 function Commit: 702870c17c9f27707db3c2f003356fe1b52529e0 https://github.com/galaxyproject/galaxy/commit/702870c17c9f27707db3c2f00335… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M scripts/common_startup_functions.sh Log Message: ----------- Allow starting Galaxy under gunicorn when using galaxy.ini and starting Galaxy with `APP_WEBSERVER=gunicorn sh run.sh`. Additional gunicorn cmdline arguments can be passed using `GUNICORN_CMD_ARGS`. In a first pass this will allow running planemo {server, test} under python 3, as Paste has some problems under python 3: ``` galaxy.web.stack INFO 2018-09-29 22:16:00,216 Galaxy server instance 'main' is running Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1055, in run invoke(command, command_name, options, args[1:]) File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke exit_code = runner.run(args) File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 226, in run result = self.command() File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 676, in command serve() File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 653, in serve server(app) File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper **context.local_conf) File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call val = callable(*args, **kw) File "/home/travis/.planemo/gx_venv_3_release_18.09/lib/python3.6/site-packages/paste/httpserver.py", line 1353, in server_runner for name, value in kwargs.items(): RuntimeError: dictionary changed size during iteration ``` That said gunicorn is a nice pure-python alternative to paste going forward. Commit: a47887639d50b2e5da55d9121b8d8e55509a9cd3 https://github.com/galaxyproject/galaxy/commit/a47887639d50b2e5da55d9121b8d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M config/plugins/webhooks/demo/tour_generator/__init__.py M lib/galaxy/web/framework/helpers/__init__.py M templates/show_params.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Merge pull request #6803 from mvdbeek/finish_py3_selenium [18.09] Fix remaining selenium py3 errors Commit: e226edc5ade76dd0ec2e3d8db2e799567e8c11d7 https://github.com/galaxyproject/galaxy/commit/e226edc5ade76dd0ec2e3d8db2e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/util/__init__.py M test/api/test_tools.py A test/functional/tools/identifier_in_conditional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6798 from mvdbeek/fix_element_identifier_for_non_multiple_true_mapover_in_conditionals [18.09] Fix element identifier for non multiple true mapover in conditionals Commit: 9f1e78d92f96499bc8409d7f5f1cfe0a652a1b92 https://github.com/galaxyproject/galaxy/commit/9f1e78d92f96499bc8409d7f5f1c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Drop gulp plugin staging task from default (probably temporarily?), since it's all done in python at server start now. Commit: 96d77b0791592b35fb6e4201d011f5c223060cfe https://github.com/galaxyproject/galaxy/commit/96d77b0791592b35fb6e4201d011… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-30 (Sun, 30 Sep 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- More PRs, stub out proposed features. Commit: d3ab953be3c553cfd71347322538c3adab6d7515 https://github.com/galaxyproject/galaxy/commit/d3ab953be3c553cfd71347322538… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/style/scss/base.scss M client/yarn.lock M static/style/blue/base.css M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge pull request #6791 from dannon/flex-style-fixes [18.09] Flex-related style fixes Commit: b64c82921e02d3be5de21a8a971c44279650399c https://github.com/galaxyproject/galaxy/commit/b64c82921e02d3be5de21a8a971c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M scripts/common_startup_functions.sh Log Message: ----------- Need quotes around export? Commit: 3d772dc03bf0ffa1c6d010596488c5cd3a26901d https://github.com/galaxyproject/galaxy/commit/3d772dc03bf0ffa1c6d010596488… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6791 Commit: 2aad3b2ced20189ab4e500bd501797a876089ee9 https://github.com/galaxyproject/galaxy/commit/2aad3b2ced20189ab4e500bd5017… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #6802 from mvdbeek/fix_int_parsing_rules [18.05] Cast rule.length to int when parsing rules Commit: 87463f4be6334849b0e121bd534fada090aeb1d8 https://github.com/galaxyproject/galaxy/commit/87463f4be6334849b0e121bd534f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: 7622d128094d16775c8eb426b6debace070193ad https://github.com/galaxyproject/galaxy/commit/7622d128094d16775c8eb426b6de… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Merge pull request #6808 from dannon/no_plugin_staging_gulp [18.09] Drop gulp plugin staging task from default tasks Commit: 176364ac80130ca439006c4b75fd393ac850681b https://github.com/galaxyproject/galaxy/commit/176364ac80130ca439006c4b75fd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Move gunicorn to dev-requirements Commit: 1a3e9ae17327f3d77fc6f64ec85c4165d4c680ef https://github.com/galaxyproject/galaxy/commit/1a3e9ae17327f3d77fc6f64ec85c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M scripts/common_startup_functions.sh Log Message: ----------- Merge pull request #6805 from mvdbeek/gunicorn_run_sh_support [18.09] Allow starting Galaxy under gunicorn when using galaxy.ini Commit: b7187f0e62e172dd7d2db1bbd51f9c3f9a5058c5 https://github.com/galaxyproject/galaxy/commit/b7187f0e62e172dd7d2db1bbd51f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Don't delete referenced Datasets when purging users. Commit: 74d82096d8eef3cbd05b52cf956d0dc654d05533 https://github.com/galaxyproject/galaxy/commit/74d82096d8eef3cbd05b52cf956d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/ui/fa-icon-button.js Log Message: ----------- Merge pull request #6745 from dannon/more-generic-tooltip-handling-for-fa-buttons [18.09] Generic tooltip hide for onclick faIconButtons Commit: f6a5cae8e1af10003e3553cb27b2512977bc0c8e https://github.com/galaxyproject/galaxy/commit/f6a5cae8e1af10003e3553cb27b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #6809 from natefoo/purge-user-fix [18.05] Don't delete referenced Datasets when purging users Commit: ce3d43221a8d4e843a25c49c679a4ab75fd3756c https://github.com/galaxyproject/galaxy/commit/ce3d43221a8d4e843a25c49c679a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- More Prs for the release notes. Commit: b5a2fafa07fcf1580989d51dd64f335387a568b8 https://github.com/galaxyproject/galaxy/commit/b5a2fafa07fcf1580989d51dd64f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-01 (Mon, 01 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- do not rule out numbers that are accessed with shift modifier closes #5370 I think there are more problems with this code: - it assumes too much about the keyboard used and puts unnecessary restrictions on the user - the implementation should be refactored to use KeyboardEvent.key instead of the deprecated charCode Commit: 266ebdb225a6e3aec28bbd2a4b356c1e83f49429 https://github.com/galaxyproject/galaxy/commit/266ebdb225a6e3aec28bbd2a4b35… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- cast row count to integer in filter first/last N rows rule Commit: e54dd1d19c0e7e36ec4e8bd9b0d5b21f298b0d17 https://github.com/galaxyproject/galaxy/commit/e54dd1d19c0e7e36ec4e8bd9b0d5… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- build client Commit: 87d2c20dbfc86bf0dd5136e274b6e960d2543a91 https://github.com/galaxyproject/galaxy/commit/87d2c20dbfc86bf0dd5136e274b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #6814 from shiltemann/rulebuilder-fix [18.05] Fix apply rules bug in filter first/last N rows. Commit: b5f7955c5addba2664b6375aa87c9873b2949fad https://github.com/galaxyproject/galaxy/commit/b5f7955c5addba2664b6375aa87c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Announce Python 3 Beta Support Commit: 4a345b99c3cc1ee21b648386dafb4c15edcbb856 https://github.com/galaxyproject/galaxy/commit/4a345b99c3cc1ee21b648386dafb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M lib/galaxy/util/compression_utils.py A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar A test/unit/test_compression_util.py Log Message: ----------- Fix security problems when extracting untrusted tar files. Fixes GX-2018-0006. Commit: 1c4a4ed8cb60ab67d8b1cf71f231d4cf4acfb077 https://github.com/galaxyproject/galaxy/commit/1c4a4ed8cb60ab67d8b1cf71f231… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/util/compression_utils.py M lib/galaxy/webapps/galaxy/controllers/admin.py A test-data/safetar_with_symlink.tar A test-data/testdir.tar A test-data/unsafe.tar A test-data/unsafe.zip A test-data/unsafe_relative_symlink.tar A test/unit/test_compression_util.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/release_18.05' into release_18.09 Commit: 90718843096f115324be8a086d7a6089e0086703 https://github.com/galaxyproject/galaxy/commit/90718843096f115324be8a086d7a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add deprecation notice for username being null Commit: 8ea455303ab76cf94e5c7acdf22d14d75260b188 https://github.com/galaxyproject/galaxy/commit/8ea455303ab76cf94e5c7acdf22d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #6810 from martenson/fix-nonUS-keyboards [18.09] do not rule out numbers that are accessed with shift modifier Commit: afffd9bdaa66b4fcadbd790a25387654c23e4aa6 https://github.com/galaxyproject/galaxy/commit/afffd9bdaa66b4fcadbd790a2538… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add final PR. Commit: eacec03d10c00503fdbb4da107254c06082507bb https://github.com/galaxyproject/galaxy/commit/eacec03d10c00503fdbb4da10725… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Update.... Commit: 4d165a567139abc3b4ad3baac422c9c0ebbaf554 https://github.com/galaxyproject/galaxy/commit/4d165a567139abc3b4ad3baac422… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge branch '18.09_release_notes' of github.com:jmchilton/galaxy into 18.09_release_notes Commit: 386229d1ce58522be4bece11b8f9473f5dce56b9 https://github.com/galaxyproject/galaxy/commit/386229d1ce58522be4bece11b8f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Re-add removed PRs (bad merge I think) Commit: fdaf9ac8641cfa5fa0aad706310aec2b31692ac1 https://github.com/galaxyproject/galaxy/commit/fdaf9ac8641cfa5fa0aad706310a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Link up workflow PRs Commit: 98a9c86badd87a4db4a815490c06c717b67fced0 https://github.com/galaxyproject/galaxy/commit/98a9c86badd87a4db4a815490c06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-06 (Sat, 06 Oct 2018) Changed paths: M lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Allow testing tags in input collections. Commit: 9044e614f03b4d0daa3e67e32be15d7d3f1268f1 https://github.com/galaxyproject/galaxy/commit/9044e614f03b4d0daa3e67e32be1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade concurrently; this fixes a 'null' return from webpack run vi aconcurrently, which can fail the build in some situations. Commit: 58ea67eb457ce154e1d119e94c07a81a1e617ba4 https://github.com/galaxyproject/galaxy/commit/58ea67eb457ce154e1d119e94c07… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-07 (Sun, 07 Oct 2018) Changed paths: M lib/galaxy/tools/tag_collection_from_file.xml M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6823 from jmchilton/tag_input_tests [18.09] Allow testing tags in input collections. Commit: b99fedefa81b3ca59c27eb64ea9a7e9865cd9db8 https://github.com/galaxyproject/galaxy/commit/b99fedefa81b3ca59c27eb64ea9a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Update to latest galaxy-lib Includes: - change channel priority ( https://github.com/galaxyproject/galaxy-lib/pull/132 ) - channel cleanup ( https://github.com/galaxyproject/galaxy-lib/pull/136 ) Commit: c83c5cb78475c96d8e49510619c76f737cca5c8e https://github.com/galaxyproject/galaxy/commit/c83c5cb78475c96d8e49510619c7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Change conda channel priority: conda-forge > bioconda xref. https://github.com/bioconda/bioconda-utils/issues/330 Commit: 9b6833b5a04cea06d245086b7b74a24a524b0064 https://github.com/galaxyproject/galaxy/commit/9b6833b5a04cea06d245086b7b74… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- make config-rebuild Commit: 5205ed7eebe4b9a2a25d0f19abd5fd732f42e302 https://github.com/galaxyproject/galaxy/commit/5205ed7eebe4b9a2a25d0f19abd5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Merge pull request #6828 from dannon/null_exit_bug_fix [18.09] Upgrade concurrently for 'null' return fix Commit: 381d6ad83183a822baebca44622e506d088f10b1 https://github.com/galaxyproject/galaxy/commit/381d6ad83183a822baebca44622e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add two recently merged PRs. Commit: 02410b270d025e5fb8cb4e2036fb627051c7850a https://github.com/galaxyproject/galaxy/commit/02410b270d025e5fb8cb4e2036fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Register job monitor as postfork function This should fix https://github.com/galaxyproject/galaxy/issues/6831, and might fix https://github.com/galaxyproject/galaxy/issues/6261. Commit: 6b62a57047f8877ba36e0767aaee04879bbc20c0 https://github.com/galaxyproject/galaxy/commit/6b62a57047f8877ba36e0767aaee… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-08 (Mon, 08 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Should fix bug Jen saw with history panel being masked at bottom Commit: a43a60656a49ad0b53574dce61738764cf466287 https://github.com/galaxyproject/galaxy/commit/a43a60656a49ad0b53574dce6173… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-09 (Tue, 09 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M lib/galaxy/dependencies/conda-file.sh M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6830 from nsoranzo/release_18.09_channel_priority_update [18.09] Update conda channel priority: conda-forge > bioconda Commit: 5844bdc7aa0a90d992c3b36e041abb8d103e3b95 https://github.com/galaxyproject/galaxy/commit/5844bdc7aa0a90d992c3b36e041a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Add integration test for remote shell CLI runners This tests both the SecureShell and Paramiko shell plugins and the Slurm and Torque CLI runner. Commit: 57a1f19b069597bde97852b3e0d0a3e1c0068bc4 https://github.com/galaxyproject/galaxy/commit/57a1f19b069597bde97852b3e0d0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Fix slurm cli plugin by avoiding `shell=True` in subprocess Fixes the remaining issue in https://github.com/galaxyproject/galaxy/issues/6831#issuecomment-428097520 Commit: fc28e0bd83a2df59f11b80f0119e67da1326887f https://github.com/galaxyproject/galaxy/commit/fc28e0bd83a2df59f11b80f0119e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py Log Message: ----------- Use long-form options Commit: 5e12e509bf20d7e4f4464a60f04c7479cb4e232d https://github.com/galaxyproject/galaxy/commit/5e12e509bf20d7e4f4464a60f04c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Fix selection of job plugin and image Thanks @nsoranzo. Commit: b08c6219c3fe771e00d0b6d8b9adb1c97e38e9a6 https://github.com/galaxyproject/galaxy/commit/b08c6219c3fe771e00d0b6d8b9ad… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Simplify ssh key handling in integration test Commit: ac3e1ca1d0d7bb85cc00e2e113f70e3576f0b048 https://github.com/galaxyproject/galaxy/commit/ac3e1ca1d0d7bb85cc00e2e113f7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M test/integration/test_cli_runners.py Log Message: ----------- Use Crypto to generate SSH keys Also remove key files in `stop_ssh_docker()`. Commit: cd62461e8486bd4e44aee51907f7d515718ef3d8 https://github.com/galaxyproject/galaxy/commit/cd62461e8486bd4e44aee51907f7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6839 from dannon/unified-panel-style-tweaks [18.09] Unified panel style bottom padding fix Commit: a1f7634fd7dca45902a2d3f67d2279db3aa2270d https://github.com/galaxyproject/galaxy/commit/a1f7634fd7dca45902a2d3f67d22… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Updated volume kwds. Commit: fe6c1738c0ea3ee35fa34fec8a2c2e8eb97ec044 https://github.com/galaxyproject/galaxy/commit/fe6c1738c0ea3ee35fa34fec8a2c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako Log Message: ----------- Merge pull request #6851 from martenson/backport-gie-kwds [18.05] Updated volume kwds for GIEs Commit: fd0b24ecd2bff2f8baa636304e45eb2dbdcaf3a9 https://github.com/galaxyproject/galaxy/commit/fd0b24ecd2bff2f8baa636304e45… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Merge pull request #6845 from mvdbeek/fix_slurm_cli_on_secure_shell [18.05] Fix slurm cli on secure shell Commit: c1383bc2d55cb6565fbd63eb4088c734a805700e https://github.com/galaxyproject/galaxy/commit/c1383bc2d55cb6565fbd63eb4088… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Small fixes Commit: c6193ca4406450cdaa01b9c27bcfb871c916544c https://github.com/galaxyproject/galaxy/commit/c6193ca4406450cdaa01b9c27bcf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M scripts/bootstrap_history.py Log Message: ----------- Update DEVTEAM, rebuild, include a few new PRs. Commit: 7cb2eb57aca559c86b3d938912d8f7bde5da9f74 https://github.com/galaxyproject/galaxy/commit/7cb2eb57aca559c86b3d938912d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge branch '18.09_release_notes' of github.com:galaxyproject/galaxy into 18.09_release_notes Commit: baa992d217032b809d321cb800cd2f41af401c63 https://github.com/galaxyproject/galaxy/commit/baa992d217032b809d321cb800cd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Merge pull request #6836 from mvdbeek/fix_job_monitor_thread [18.01] Register job monitor thread as postfork function Commit: d33006cf33f71f4992eebefb7c3065606088aea1 https://github.com/galaxyproject/galaxy/commit/d33006cf33f71f4992eebefb7c30… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Final docs update Commit: d42b899b7805f722a77153c4e33fffcfad846ce0 https://github.com/galaxyproject/galaxy/commit/d42b899b7805f722a77153c4e33f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M scripts/bootstrap_history.py Log Message: ----------- Embellish 18.09 release notes Commit: 9251484e7236cd881cb4df64265a3cee2e654d83 https://github.com/galaxyproject/galaxy/commit/9251484e7236cd881cb4df64265a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: A doc/source/releases/18.09.rst A doc/source/releases/18.09_announce.rst A doc/source/releases/19.01_announce.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6731 from galaxyproject/18.09_release_notes [18.09] 18.09 release notes Commit: d791a2c80f3290d66c2252f29981a16a4459661b https://github.com/galaxyproject/galaxy/commit/d791a2c80f3290d66c2252f29981… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Revert selective metadata flushing - seems to break upload changes. Commit: 20f60a5a44842dda8ffe7b97d1b60b6c5ecfdd9d https://github.com/galaxyproject/galaxy/commit/20f60a5a44842dda8ffe7b97d1b6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- update paramiko dep Commit: 2c14c2afc4d39626096c3d15828b8c3001aab40f https://github.com/galaxyproject/galaxy/commit/2c14c2afc4d39626096c3d15828b… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6859 from martenson/paramiko-update [18.09] update paramiko dep Commit: a8fa5a1d4a6c801fc230c037129671978955916c https://github.com/galaxyproject/galaxy/commit/a8fa5a1d4a6c801fc230c0371296… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/util/monitors.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: d22f652f918f7a49d80ede8652d335d41c478546 https://github.com/galaxyproject/galaxy/commit/d22f652f918f7a49d80ede8652d3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M config/plugins/interactive_environments/neo/templates/neo.mako M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/util/monitors.py M test/functional/tools/job_environment_default.xml M test/functional/tools/job_environment_default_legacy.xml M test/functional/tools/job_environment_explicit_shared_home.xml A test/integration/test_cli_runners.py M test/integration/test_job_environments.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 19f716de9141080ecf3043fe3aeac391c55b8158 https://github.com/galaxyproject/galaxy/commit/19f716de9141080ecf3043fe3aea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Fix ``LocalShell`` doctest Broken in commit 57a1f19b069597bde97852b3e0d0a3e1c0068bc4 . Commit: 4805304e0bf3b1612c3cd425d94d33990f076d6a https://github.com/galaxyproject/galaxy/commit/4805304e0bf3b1612c3cd425d94d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Merge pull request #6863 from nsoranzo/release_18.09_fix_LocalShell_doctest [18.09] Fix ``LocalShell`` doctest Commit: f3da0864b45a3aa307c7fe9eeb8c5d26dd9c8527 https://github.com/galaxyproject/galaxy/commit/f3da0864b45a3aa307c7fe9eeb8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for regression #6856. Commit: 01f1f1b95fba671a2d92d7111676229a7ed5d58a https://github.com/galaxyproject/galaxy/commit/01f1f1b95fba671a2d92d7111676… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6858 from jmchilton/fix_metadata_revert [18.09] Revert selective metadata flushing - breaks multiple uploads/outputs. Commit: 8edb7499c8d336d727fa751a2097d0356cf5bcbe https://github.com/galaxyproject/galaxy/commit/8edb7499c8d336d727fa751a2097… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Keep xlsx files compressed Fixes https://github.com/galaxyproject/galaxy/issues/6849 Commit: 0c7cc50e73827ac65eabf10400c90a644a15f10b https://github.com/galaxyproject/galaxy/commit/0c7cc50e73827ac65eabf10400c9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M lib/galaxy/datatypes/upload_util.py Log Message: ----------- Only warn about multi-file zips if we don't keep the compressed archive Commit: 03073ed1249d2403994013d9f4486f85d7a23e80 https://github.com/galaxyproject/galaxy/commit/03073ed1249d2403994013d9f448… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/upload_util.py Log Message: ----------- Merge pull request #6867 from mvdbeek/fix_xlsx_unpacking [18.09] Keep xlsx files compressed Commit: b9a01761b03e4ad4c06e86a1250c2f33e62ae0be https://github.com/galaxyproject/galaxy/commit/b9a01761b03e4ad4c06e86a1250c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Do not traceback when uploading a TS repo with no changes Fix the following traceback when executing `planemo shed_update`: ``` galaxy.web.framework.decorators ERROR 2018-10-15 18:07:38,736 [p:30249,w:1,m:0] [uWSGIWorker1Core1] Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 154, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/tool_shed/api/repositories.py", line 1116, in create_changeset_revision new_repo_alert File "lib/tool_shed/util/repository_content_util.py", line 64, in upload_tar undesirable_files_removed) File "lib/tool_shed/util/commit_util.py", line 225, in handle_directory_changes message=commit_message) File "lib/tool_shed/util/hg_util.py", line 65, in commit_changeset raise Exception(error_message) Exception: Error committing '/opt/galaxy/database/community_files/000/repo_1' to repository: Command '['hg', 'commit', '-u', u'earlhaminst', '-m', u'planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 22231ebc4e5e990c61243a3609b3347cf63fa024', '/opt/galaxy/database/community_files/000/repo_1']' returned non-zero exit status 1 Output was: nothing changed 127.0.0.1 - - [15/Oct/2018:18:07:38 +0100] "POST /api/repositories/adb5f5c93f827949/changeset_revision HTTP/1.1" 500 - "-" "python-requests/2.18.4" ``` Commit: d4e2f6d59e15bc06b35824201be30e95209596fb https://github.com/galaxyproject/galaxy/commit/d4e2f6d59e15bc06b35824201be3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #6875 from nsoranzo/release_18.09_fix_commit_changeset [18.09] Do not traceback when uploading a TS repo with no changes Commit: 126ee5fe2bb6d8c1c2874545cd5a583389d45bca https://github.com/galaxyproject/galaxy/commit/126ee5fe2bb6d8c1c2874545cd5a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Create composite file archives in new_file_path instead of TMP Commit: d19effdf3c042538ffa0ba1351a2f3433ad19fd1 https://github.com/galaxyproject/galaxy/commit/d19effdf3c042538ffa0ba1351a2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- One last batch of PRs. Commit: 89fbe9c9344d1e8ad88fe88a0685cf85aa1edcb3 https://github.com/galaxyproject/galaxy/commit/89fbe9c9344d1e8ad88fe88a0685… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Merge pull request #6890 from dannon/18.09_release_notes_updates [18.09] One last batch of PRs added to RN Commit: 9735146f2848beca367ac84c066d10a4b5008a25 https://github.com/galaxyproject/galaxy/commit/9735146f2848beca367ac84c066d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- add discovered tool vulnerabilities to RN Commit: fa212c3c31b78f885b7aff2681430bc9e54fec89 https://github.com/galaxyproject/galaxy/commit/fa212c3c31b78f885b7aff268143… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- specify which gemini tools were fixed Commit: 0aca12ce96f0c2a860453a15022bbd5e693493ed https://github.com/galaxyproject/galaxy/commit/0aca12ce96f0c2a860453a15022b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6892 from martenson/security-notes [18.09] add discovered tool vulnerabilities to RN Commit: 46e56417dddfa88c9b093c612eb006c9f471579d https://github.com/galaxyproject/galaxy/commit/46e56417dddfa88c9b093c612eb0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Use hasattr instead of relying on value Commit: 3411852fedf31c93ec506aa4f8f8a922d4b57ad7 https://github.com/galaxyproject/galaxy/commit/3411852fedf31c93ec506aa4f8f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-21 (Sun, 21 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #6885 from mvdbeek/create_in_new_file_path [18.05] Create composite file archives in new_file_path instead of TMP Commit: 794d1e03be57fdc0cde02bab79f8404c0eed7626 https://github.com/galaxyproject/galaxy/commit/794d1e03be57fdc0cde02bab79f8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Fix messed up printing of shed_tool_conf.xml file This drops xml_to_string from lib/tool_shed/util/xml_util.py and uses xml_to_string form lib/galaxy/utils/__init__.py. Also reduces plain string manipulation of xml structures. Uses xml.dom.minidom to make xml pretty if necessary. Commit: 88b840d2c6cc18184c71772d96301a9f9a71cbdc https://github.com/galaxyproject/galaxy/commit/88b840d2c6cc18184c71772d9630… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6893 from martenson/backport-6884 [18.09] check presence of attribute in addition to value Commit: 4dd2ecb13f1cac23730debd107dd150e46c47568 https://github.com/galaxyproject/galaxy/commit/4dd2ecb13f1cac23730debd107dd… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Fix ``make config-validate`` Commit: 194358703450ff8fef553d92531fc6e6a0938612 https://github.com/galaxyproject/galaxy/commit/194358703450ff8fef553d92531f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6908 from nsoranzo/release_18.09_config_validate [18.09] Fix ``make config-validate`` Commit: 8a39f27b3c8d20c5adf933f6a3782525b3925432 https://github.com/galaxyproject/galaxy/commit/8a39f27b3c8d20c5adf933f6a378… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Fix toolshed tests Commit: a4655432604a758f2725c5badc120f4836ffcbda https://github.com/galaxyproject/galaxy/commit/a4655432604a758f2725c5badc12… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Drop threading lock and global try/except The Lock wasn't actually preventing anything, and I don't think anything would need ot be protected here. mkdtemp should be thread-safe. We also remove the try/except Statement. I think it'd be better to expose any exceptions here instead of producing broken capsules and logging an exception. Commit: 57a4e50d8cfe038632bbe25ed6cbb69662491f2e https://github.com/galaxyproject/galaxy/commit/57a4e50d8cfe038632bbe25ed6cb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Fix capsule export in docker testing Found this by removing the blank try/except in the previous commit. This only affects testing when python can't determine the correct locale and falls back to ASCII. Commit: ecb56d80a103dc3b11091beb3de06a086ed48953 https://github.com/galaxyproject/galaxy/commit/ecb56d80a103dc3b11091beb3de0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 3f172cc9880e58396e7f71b7480bea9e7163dda4 https://github.com/galaxyproject/galaxy/commit/3f172cc9880e58396e7f71b7480b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Fix job stopping from DRMAA jobs broken in a1c58a708829d79859426ecb7c39b5c5f69ad735 and improve logging around it. Commit: 36383785697bed5db7e99461c3483f19836a016b https://github.com/galaxyproject/galaxy/commit/36383785697bed5db7e99461c348… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #6912 from natefoo/fix-drmaa-job-stop [18.09] Fix stopping DRMAA jobs Commit: 328c410fdcad8a870816dea307499fef31c812e7 https://github.com/galaxyproject/galaxy/commit/328c410fdcad8a870816dea30749… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-23 (Tue, 23 Oct 2018) Changed paths: M lib/galaxy/tools/data/__init__.py M lib/galaxy/util/__init__.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge pull request #6904 from mvdbeek/fix_weird_xml [18.09] Fix pretty printing of shed_tool_conf.xml file Commit: c862d55ec8fe99e950df7984127461eaedd6f438 https://github.com/galaxyproject/galaxy/commit/c862d55ec8fe99e950df79841274… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Use with statement when handling NamedTemporaryFile Commit: 91a9dbaf5cf093ff72f39d9ea606bef59ecfc45a https://github.com/galaxyproject/galaxy/commit/91a9dbaf5cf093ff72f39d9ea606… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Revert unncessary double logging of exception Commit: 843474e5e375a2359979a8f9ae46fb0e58ac148b https://github.com/galaxyproject/galaxy/commit/843474e5e375a2359979a8f9ae46… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge pull request #6915 from mvdbeek/6904_followup [18.09] Small followup to #6904 Commit: 6a072ab29d842f79ea0ba46f0f0bc30aa43fd577 https://github.com/galaxyproject/galaxy/commit/6a072ab29d842f79ea0ba46f0f0b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Four more RN PRs. Commit: 5a71a744edeea3691b04cbd18680eadea90f78bc https://github.com/galaxyproject/galaxy/commit/5a71a744edeea3691b04cbd18680… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add client artifact note Commit: b6e716b289e36ec62cdada07e356552e1388f618 https://github.com/galaxyproject/galaxy/commit/b6e716b289e36ec62cdada07e356… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Correct javascript caps Commit: 17f4f7955f84830f87c21c0027d487a291da66c4 https://github.com/galaxyproject/galaxy/commit/17f4f7955f84830f87c21c0027d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- s/sources/artifacts Commit: 3263aba44a95e2a5e50e5050893628ba618fd306 https://github.com/galaxyproject/galaxy/commit/3263aba44a95e2a5e50e50508936… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add a warning to the 18.09 release notes informing admins that job handling will block until old `new` state jobs have been migrated to a terminal state. Commit: 43d978729593818c5abf2b9a09bd7cb2852f0ffd https://github.com/galaxyproject/galaxy/commit/43d978729593818c5abf2b9a09bd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6923 from dannon/18.09_final_notes [18.09] Final release notes updates Commit: 9b24afc5922bdefca5a19b802a7e84896c748aca https://github.com/galaxyproject/galaxy/commit/9b24afc5922bdefca5a19b802a7e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.09 Compare: https://github.com/galaxyproject/galaxy/compare/ea085b07a0ef...9b24afc5922b **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]
by GitHub 25 Oct '18

25 Oct '18

Branch: refs/tags/v18.09 Home: https://github.com/galaxyproject/galaxy **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] 6a072a: Four more RN PRs.
by GitHub 25 Oct '18

25 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a072ab29d842f79ea0ba46f0f0bc30aa43fd577 https://github.com/galaxyproject/galaxy/commit/6a072ab29d842f79ea0ba46f0f0b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Four more RN PRs. Commit: 5a71a744edeea3691b04cbd18680eadea90f78bc https://github.com/galaxyproject/galaxy/commit/5a71a744edeea3691b04cbd18680… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add client artifact note Commit: b6e716b289e36ec62cdada07e356552e1388f618 https://github.com/galaxyproject/galaxy/commit/b6e716b289e36ec62cdada07e356… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Correct javascript caps Commit: 17f4f7955f84830f87c21c0027d487a291da66c4 https://github.com/galaxyproject/galaxy/commit/17f4f7955f84830f87c21c0027d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- s/sources/artifacts Commit: 3263aba44a95e2a5e50e5050893628ba618fd306 https://github.com/galaxyproject/galaxy/commit/3263aba44a95e2a5e50e50508936… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add a warning to the 18.09 release notes informing admins that job handling will block until old `new` state jobs have been migrated to a terminal state. Commit: 43d978729593818c5abf2b9a09bd7cb2852f0ffd https://github.com/galaxyproject/galaxy/commit/43d978729593818c5abf2b9a09bd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6923 from dannon/18.09_final_notes [18.09] Final release notes updates Commit: 5076f1d2d198cef9300751183289156a0360299b https://github.com/galaxyproject/galaxy/commit/5076f1d2d198cef9300751183289… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge branch 'release_18.09' into dev Commit: 9b24afc5922bdefca5a19b802a7e84896c748aca https://github.com/galaxyproject/galaxy/commit/9b24afc5922bdefca5a19b802a7e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.09 Commit: 56d8c634b02088ecb9d5744254004a7d951c4e5d https://github.com/galaxyproject/galaxy/commit/56d8c634b02088ecb9d574425400… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/210cdc998a8f...56d8c634b020 **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] 9b24af: Update version to 18.09
by GitHub 25 Oct '18

25 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 9b24afc5922bdefca5a19b802a7e84896c748aca https://github.com/galaxyproject/galaxy/commit/9b24afc5922bdefca5a19b802a7e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.09 **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] 6a072a: Four more RN PRs.
by GitHub 25 Oct '18

25 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 6a072ab29d842f79ea0ba46f0f0bc30aa43fd577 https://github.com/galaxyproject/galaxy/commit/6a072ab29d842f79ea0ba46f0f0b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Four more RN PRs. Commit: 5a71a744edeea3691b04cbd18680eadea90f78bc https://github.com/galaxyproject/galaxy/commit/5a71a744edeea3691b04cbd18680… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add client artifact note Commit: b6e716b289e36ec62cdada07e356552e1388f618 https://github.com/galaxyproject/galaxy/commit/b6e716b289e36ec62cdada07e356… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Correct javascript caps Commit: 17f4f7955f84830f87c21c0027d487a291da66c4 https://github.com/galaxyproject/galaxy/commit/17f4f7955f84830f87c21c0027d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- s/sources/artifacts Commit: 3263aba44a95e2a5e50e5050893628ba618fd306 https://github.com/galaxyproject/galaxy/commit/3263aba44a95e2a5e50e50508936… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Add a warning to the 18.09 release notes informing admins that job handling will block until old `new` state jobs have been migrated to a terminal state. Commit: 43d978729593818c5abf2b9a09bd7cb2852f0ffd https://github.com/galaxyproject/galaxy/commit/43d978729593818c5abf2b9a09bd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge pull request #6923 from dannon/18.09_final_notes [18.09] Final release notes updates Compare: https://github.com/galaxyproject/galaxy/compare/843474e5e375...43d978729593 **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/usegalaxy-playbook] 280a8e: Update Test and Main
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 280a8e9fb4c53baa86c3e99949ac7b7d27c09335 https://github.com/galaxyproject/usegalaxy-playbook/commit/280a8e9fb4c53baa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test and Main **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] 949dcf: Do not log exceptions twice
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 949dcfdbc34331de7f0aa321e67e1255a7627306 https://github.com/galaxyproject/galaxy/commit/949dcfdbc34331de7f0aa321e67e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/cloud.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/util/readme_util.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M test/base/populators.py M tools/data_source/upload.py Log Message: ----------- Do not log exceptions twice `logging.exception()` already adds the the exception information after the supplied message. Also: the `message` attribute of `Exception` class has been dropped in Python 3, always use `str(e)`. xref. https://github.com/galaxyproject/galaxy/issues/1715 Commit: 210cdc998a8f8929362d881bfaded32ac1e45aef https://github.com/galaxyproject/galaxy/commit/210cdc998a8f8929362d881bfade… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/cloud.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py M lib/galaxy/objectstore/cloud.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/util/readme_util.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M test/base/populators.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #6916 from nsoranzo/fix_exception_logging Do not log exception info twice Compare: https://github.com/galaxyproject/galaxy/compare/2dcd126e82fc...210cdc998a8f **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] cd92dd: add isa-rwal to default pipfile
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd92dd2819ef3e789e0f25e9b1c99dcc8404d486 https://github.com/galaxyproject/galaxy/commit/cd92dd2819ef3e789e0f25e9b1c9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile Log Message: ----------- add isa-rwal to default pipfile it is in pinned already Commit: 4a82c43270670d4d4cc7bd30e6301c4a3516f48c https://github.com/galaxyproject/galaxy/commit/4a82c43270670d4d4cc7bd30e630… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- make update-dependencies Commit: 2dcd126e82fc6db51c8ab9cacb39abd496504d51 https://github.com/galaxyproject/galaxy/commit/2dcd126e82fc6db51c8ab9cacb39… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6906 from martenson/isa-req add isa-rwal to default pipfile Compare: https://github.com/galaxyproject/galaxy/compare/014b9d76f76c...2dcd126e82fc **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] 5dfb74: Allow ``remove_value`` filter on data tables
by GitHub 24 Oct '18

24 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5dfb743ae160f873db670bff26d3ba19d85d4ce9 https://github.com/galaxyproject/galaxy/commit/5dfb743ae160f873db670bff26d3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Allow ``remove_value`` filter on data tables The `RemoveValueFilter.filter_options()` method was expecting `options` to be a list of lists, where each inner list contains exactly 3-elements (name, value, selected), which is the format returned by the `data_meta` filter. In fact, the only known use of the `remove_falue` filter is in the tool `tools/maf/maf_to_interval.xml`, to filter dataset metadata. This commit generalises the filter to look for a column of the dynamic options named `value`, and use it during the filtering. Fix https://github.com/galaxyproject/tools-iuc/issues/2151 Commit: 26680e0ca1ace0ad8c857ab712f60d2fc4bf8c1b https://github.com/galaxyproject/galaxy/commit/26680e0ca1ace0ad8c857ab712f6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: A test/functional/tools/remove_value.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test for remove_value form dynamic options Unfortunately you can select an invalid value (in the API, not the UI) and Galaxy will replace the invalid value with the first valid value. Commit: 7c81daa073dea39785144b9228b53b2cd9f6fdbe https://github.com/galaxyproject/galaxy/commit/7c81daa073dea39785144b9228b5… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Fix assertion in ``RemoveValueFilter`` Commit: 19c98b27455862e7f50570bbc147a28667182e31 https://github.com/galaxyproject/galaxy/commit/19c98b27455862e7f50570bbc147… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M test/functional/tools/remove_value.xml Log Message: ----------- Fix tests and name tool more appropriately Commit: 014b9d76f76c2eb959266bc271ad0539a1ab0f6d https://github.com/galaxyproject/galaxy/commit/014b9d76f76c2eb959266bc271ad… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py A test/functional/tools/remove_value.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6914 from nsoranzo/remove_value Allow ``remove_value`` filter on data tables Compare: https://github.com/galaxyproject/galaxy/compare/51ca8dc0f5d4...014b9d76f76c **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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