Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: db47c876ee69bd034b7e131daf0a7fd5672d2221 https://github.com/galaxyproject/galaxy/commit/db47c876ee69bd034b7e131daf0a7... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove prepopulation of column selector Commit: fc7beca6d1d379ddfc1ea4769edfc8c22d74fb10 https://github.com/galaxyproject/galaxy/commit/fc7beca6d1d379ddfc1ea4769edfc... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Create input element combining text and select options Commit: 2e8c9489bfd149d12b9498ea89c5633a07509d48 https://github.com/galaxyproject/galaxy/commit/2e8c9489bfd149d12b9498ea89c56... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix value handling, remove redundant value check Commit: 9fbdcd1d5ee84887c28eed727fec77d402ef95fa https://github.com/galaxyproject/galaxy/commit/9fbdcd1d5ee84887c28eed727fec7... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Relax validation conditions Commit: ff874dc4e4f4d21bb133b2730058393c7ae7a66a https://github.com/galaxyproject/galaxy/commit/ff874dc4e4f4d21bb133b27300583... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Properly switch between states, transfer current value Commit: 9fff4f1615aa7ce02561d681ae20397b22b17f02 https://github.com/galaxyproject/galaxy/commit/9fff4f1615aa7ce02561d681ae203... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove redundant initial value checks, value can only be empty Commit: 1db1c0c77122edd183ab6f0bf5da24c94c83b476 https://github.com/galaxyproject/galaxy/commit/1db1c0c77122edd183ab6f0bf5da2... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Revise condition, check explicitly for none Commit: 608f3dc9d3ed59a21fba221f590240ecfdc1294a https://github.com/galaxyproject/galaxy/commit/608f3dc9d3ed59a21fba221f59024... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add check for column index values Commit: f4f275f82aa9b1e19aafe0525b4006876905ef96 https://github.com/galaxyproject/galaxy/commit/f4f275f82aa9b1e19aafe0525b400... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add dataset state check to column input Commit: a144eb1fb40eee0920e8153b3e51304c10130003 https://github.com/galaxyproject/galaxy/commit/a144eb1fb40eee0920e8153b3e513... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix integer test Commit: 29337d2b7b1d51c44ff621049483037fd9d48d1a https://github.com/galaxyproject/galaxy/commit/29337d2b7b1d51c44ff6210494830... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Simplify legal value length check Commit: 05ce42d229db08c6af7425f1afe1eea625dfd1da https://github.com/galaxyproject/galaxy/commit/05ce42d229db08c6af7425f1afe1e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Provide value for column index if not an integer Commit: 9febc519944dcfb5c8907b8a302fd6aff6f0f79f https://github.com/galaxyproject/galaxy/commit/9febc519944dcfb5c8907b8a302fd... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Identify implicit conversions, check reference context for datasets Commit: 1baafd07ffbaa42bd5071a659ccb82203591afa0 https://github.com/galaxyproject/galaxy/commit/1baafd07ffbaa42bd5071a659ccb8... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Move implicit dataset tagging to dataset state check Check attribute Commit: dae6cc7f4cb403cdee44c532f314f639d8e9f96b https://github.com/galaxyproject/galaxy/commit/dae6cc7f4cb403cdee44c532f314f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix indent Commit: f305c0b0ab9182af0578078c622d024a57b9b05d https://github.com/galaxyproject/galaxy/commit/f305c0b0ab9182af0578078c622d0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Reinsert legal value check handler Commit: c7e794745b1b7699a7ac34caaa684f298f562dbc https://github.com/galaxyproject/galaxy/commit/c7e794745b1b7699a7ac34caaa684... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-19 (Mon, 19 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Validate value before matching dataset Commit: 81a418fe98ee2f26b35bae81060398431b9a096e https://github.com/galaxyproject/galaxy/commit/81a418fe98ee2f26b35bae8106039... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove explicit integer validation Commit: 187c540cd4aac7e1059fdaa6aaf56c87913f1d09 https://github.com/galaxyproject/galaxy/commit/187c540cd4aac7e1059fdaa6aaf56... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-21 (Wed, 21 Mar 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix test case Commit: 04fee6070bfa94a3788c89dc0cc1414469db20e6 https://github.com/galaxyproject/galaxy/commit/04fee6070bfa94a3788c89dc0cc14... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/releases/18.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml 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 tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into select_to_text Commit: ade62bc3b15b25e76d7114c5ee9051cd5f575700 https://github.com/galaxyproject/galaxy/commit/ade62bc3b15b25e76d7114c5ee905... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Revise select display matching Commit: 8290da24eaf0994c018b055ba9bbc73876540f7c https://github.com/galaxyproject/galaxy/commit/8290da24eaf0994c018b055ba9bbc... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix indentation Commit: 241ade62cd740bf62d2348859493ed7326799597 https://github.com/galaxyproject/galaxy/commit/241ade62cd740bf62d2348859493e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Align validation order for consistency Commit: 2b3557ffce38a97080c9921846e06131aa43e2e9 https://github.com/galaxyproject/galaxy/commit/2b3557ffce38a97080c9921846e06... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Fix test case verifying we check column values before tool execution. Commit: 91e97b60968d6813bd7a28d0d60e778b288ac385 https://github.com/galaxyproject/galaxy/commit/91e97b60968d6813bd7a28d0d60e7... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Refactor code for clarity Commit: 840e436ea1f181ebe0c8478145e2cd0e97dc1778 https://github.com/galaxyproject/galaxy/commit/840e436ea1f181ebe0c8478145e2c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-03-26 (Mon, 26 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add strict workflow building mode check to drill downs Commit: bf5d472e28505438c5f345ad29989b80fe3aae80 https://github.com/galaxyproject/galaxy/commit/bf5d472e28505438c5f345ad29989... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-27 (Tue, 27 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py M test/api/test_tools.py Log Message: ----------- Merge pull request #5702 from guerler/select_to_text Relax validation condition for dynamic parameters Compare: https://github.com/galaxyproject/galaxy/compare/61adffbd614c...bf5d472e2850