Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2d33cc28664f1b5a592576fd149264ccf0a023b7 https://github.com/galaxyproject/galaxy/commit/2d33cc28664f1b5a592576fd14926... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add client routes for pages edit attribute form Commit: 8001299333ec7f71efc6233562a5b2f641686c64 https://github.com/galaxyproject/galaxy/commit/8001299333ec7f71efc6233562a5b... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/controllers/page.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix url to pages edit controller endpoint Commit: 56cab82eb23f2022af128f1ba6828f8f0bd41206 https://github.com/galaxyproject/galaxy/commit/56cab82eb23f2022af128f1ba6828... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Remove debug statement Commit: c038d09f0de31f8ad6d4e2b21b6ede74a9c61cf4 https://github.com/galaxyproject/galaxy/commit/c038d09f0de31f8ad6d4e2b21b6ed... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Add support to build form and save new attributes Commit: 408a2d212f163656dfe9a42151f64b6b07fbd37a https://github.com/galaxyproject/galaxy/commit/408a2d212f163656dfe9a42151f64... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Move message exception handler to base controller Commit: 8d4fbc02010f38bbb433b22faa39aeb65ec7d8d6 https://github.com/galaxyproject/galaxy/commit/8d4fbc02010f38bbb433b22faa39a... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Use shared message exception handler Commit: a4544284af192a3ade610bbcededa20d4b3f76a0 https://github.com/galaxyproject/galaxy/commit/a4544284af192a3ade610bbcededa... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Revise create page endpoint Commit: e42dc9c8ca5a932315e2e37e66e2ad9919a74539 https://github.com/galaxyproject/galaxy/commit/e42dc9c8ca5a932315e2e37e66e2a... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add client side route to analysis app Commit: 8f76f7a0b24217af9808e36c7f69354441ae4ff8 https://github.com/galaxyproject/galaxy/commit/8f76f7a0b24217af9808e36c7f693... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Redirect grid operation to client route Commit: ea164310a23781c95ae493af376c25a821ecc782 https://github.com/galaxyproject/galaxy/commit/ea164310a23781c95ae493af376c2... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py R templates/webapps/galaxy/page/create.mako Log Message: ----------- Remove page create mako Commit: 2bfb088ddb52250f88e774299d1f770fbded4926 https://github.com/galaxyproject/galaxy/commit/2bfb088ddb52250f88e774299d1f7... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Fix input help text, user is required to enter unique identifier Commit: cdf384a8f55c3315c26f09d83b530f7ac6448457 https://github.com/galaxyproject/galaxy/commit/cdf384a8f55c3315c26f09d83b530... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Add direct link to view page, analogous to other objects in grids Commit: 08940ad9af56717ec62026db094d90e4599c02e0 https://github.com/galaxyproject/galaxy/commit/08940ad9af56717ec62026db094d9... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Fix create form title Commit: 90dd81913522db8bc6962845574775e2b5599146 https://github.com/galaxyproject/galaxy/commit/90dd81913522db8bc696284557477... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Add blank line to forms controller Commit: a985cf5784f1e04f08ea4e8d86126ee15c3b8274 https://github.com/galaxyproject/galaxy/commit/a985cf5784f1e04f08ea4e8d86126... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M CITATION 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/dependencies/pinned-requirements.txt M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.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/DEFAULT_JOB_FILE_TEMPLATE.sh 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/model/metadata.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/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/deps/resolvers/modules.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/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.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/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/config.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/common_startup.sh M scripts/common_startup_functions.sh 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 templates/display_base.mako M templates/display_common.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_custom_builds.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_published_histories_grid.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_management.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' into replace_page_edit_form Commit: 4a916413c2c9fb19e8ad350771ed4de53200630a https://github.com/galaxyproject/galaxy/commit/4a916413c2c9fb19e8ad350771ed4... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Touch up identifier error message and help Revise help info for identifier Fix Commit: 075c0a76843170db53a80d98f5618d96a52556a5 https://github.com/galaxyproject/galaxy/commit/075c0a76843170db53a80d98f5618... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unused id parsing Commit: a8f59a46a92e29cc054933450da7dc23dda28945 https://github.com/galaxyproject/galaxy/commit/a8f59a46a92e29cc054933450da7d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.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 lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/webapp.py M static/maps/galaxy.interactive_environments.js.map M static/maps/mvc/workflow/workflow-model.js.map M static/maps/onload.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/galaxy.interactive_environments.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 Log Message: ----------- Merge branch 'dev' into replace_page_edit_form Commit: 297cb2da4b62067c1582301aa6ebd6b05237edf9 https://github.com/galaxyproject/galaxy/commit/297cb2da4b62067c1582301aa6ebd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R templates/webapps/galaxy/page/create.mako Log Message: ----------- Merge branch 'replace_page_edit_form' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f4941e54224d...297cb2da4b62