Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5733667ec66f2a710de86c6a0f88939c96169bd https://github.com/galaxyproject/galaxy/commit/d5733667ec66f2a710de86c6a0f88... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add PostgresqlArchive class Commit: 750486d96b58dca3ef9c27c064be0f321e50e657 https://github.com/galaxyproject/galaxy/commit/750486d96b58dca3ef9c27c064be0... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add the postgresql datatype to the config Commit: baa6d2be46cad6c326bfd7d4ff34e8e4e1bbc800 https://github.com/galaxyproject/galaxy/commit/baa6d2be46cad6c326bfd7d4ff34e... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/onload.js M client/toolshed/scripts/mvc/groups/group-model.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py 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/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/api/data_manager_example_execute.py M scripts/api/display.py M scripts/api/search.py R scripts/binary_compatibility.py M scripts/data_libraries/build_lucene_index.py M scripts/dump_tour.py M scripts/edam_mapping.py M scripts/fetch_eggs.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/manage_tool_dependencies.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/paster.py M scripts/rst2html.py M scripts/summarize_timings.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M static/maps/galaxy.interactive_environments.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/workflow/workflow-model.js.map M static/maps/onload.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/onload.js M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/mvc/groups/group-listrow-view.js.map M static/toolshed/maps/mvc/groups/group-model.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js M static/toolshed/scripts/mvc/groups/group-model.js R templates/webapps/galaxy/history/rename.mako R templates/webapps/galaxy/visualization/create.mako M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/twilltestcase.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_stock_tours.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_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py A test/unit/__init__.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_HistoryManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.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/workflow_support.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into postgresql_datatype Commit: f4b944206cb5f1f52ecffe9462e14b673ceb92f8 https://github.com/galaxyproject/galaxy/commit/f4b944206cb5f1f52ecffe9462e14... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix detection of pg database Commit: 5fd482809d66c1ba0dfadec6876eed8aa9b1b659 https://github.com/galaxyproject/galaxy/commit/5fd482809d66c1ba0dfadec6876ee... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: A lib/galaxy/datatypes/test/postgresql_fake.tar.bz2 Log Message: ----------- add example dataset Commit: 2bf3481e7de2be9159cdd6e90e25d96196dc6c39 https://github.com/galaxyproject/galaxy/commit/2bf3481e7de2be9159cdd6e90e25d... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix pep8 Commit: 43b86e019e72f8e8d8958483d80e48cf87aa9afe https://github.com/galaxyproject/galaxy/commit/43b86e019e72f8e8d8958483d80e4... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix test Commit: dd7366d31eb0ecc24ec9c046b27a8d1f865ad5ce https://github.com/galaxyproject/galaxy/commit/dd7366d31eb0ecc24ec9c046b27a8... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge branch 'postgresql_datatype' of https://github.com/bgruening/galaxy into postgresql_datatype Commit: 5a6c3e797cabf795e82408078f00ce35c628e7f5 https://github.com/galaxyproject/galaxy/commit/5a6c3e797cabf795e82408078f00c... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- address Erics comments Commit: 6497329e1cafaa3803c46a97e0c28fd443edb0aa https://github.com/galaxyproject/galaxy/commit/6497329e1cafaa3803c46a97e0c28... Author: Eric Rasche <hxr@hx42.org> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/postgresql_fake.tar.bz2 Log Message: ----------- Merge pull request #4730 from bgruening/postgresql_datatype add postgresql datatype Compare: https://github.com/galaxyproject/galaxy/compare/f0972b15b0fe...6497329e1caf