Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: c5fa911b10e90229940bf65467a1610f3b23ee2c https://github.com/galaxyproject/galaxy/commit/c5fa911b10e90229940bf65467a16... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-01-09 (Tue, 09 Jan 2018) Changed paths: M client/galaxy/scripts/utils/localization.js M config/galaxy.ini.sample M config/user_preferences_extra_conf.yml.sample Log Message: ----------- draft configurable locale Commit: 8ecddefd09ce70cab2f275d95832a0901fd4dd94 https://github.com/galaxyproject/galaxy/commit/8ecddefd09ce70cab2f275d95832a... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M doc/source/conf.py Log Message: ----------- WIP for linking doc versions Commit: 141ac1eabc64b11444a31bbd7c8c0d91436a9d29 https://github.com/galaxyproject/galaxy/commit/141ac1eabc64b11444a31bbd7c8c0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M doc/source/conf.py A doc/source/conf.versioning.py Log Message: ----------- Move simpleversioning config to a separate file that can be written to conf.py by Jenkins Commit: 59c6d6957e6bfd3500c2967cb9a86d8c87731a4f https://github.com/galaxyproject/galaxy/commit/59c6d6957e6bfd3500c2967cb9a86... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Fix string slicing error Commit: 98e369c9a730090fb99975d9904484c749a6ea50 https://github.com/galaxyproject/galaxy/commit/98e369c9a730090fb99975d990448... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Use $TARGET_GIT_BRANCH instead of $GIT_BRANCH (which is a lie for matrix configs) Commit: 4bdebe018648bc28a3029368849c82cc786ae650 https://github.com/galaxyproject/galaxy/commit/4bdebe018648bc28a3029368849c8... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Conditional fixes for the documentation message box Commit: d238b0f25bba2319d414f3de4a48dc1a887b6051 https://github.com/galaxyproject/galaxy/commit/d238b0f25bba2319d414f3de4a48d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-01-18 (Thu, 18 Jan 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Fix linting error and avoid double import Commit: 1c2bd5ff284925ccadc8957bb2dc40eba33f988f https://github.com/galaxyproject/galaxy/commit/1c2bd5ff284925ccadc8957bb2dc4... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/utils/localization.js M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- use session to store current locale Commit: 8d1a499e42bd7c71ec9b5e727a28a8ef9b3973ed https://github.com/galaxyproject/galaxy/commit/8d1a499e42bd7c71ec9b5e727a28a... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M Makefile M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/library/library-dataset-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/tours.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/nls/zh/locale.js M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample R config/galaxy.ini.sample A config/galaxy.yml.sample M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst M doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst M doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst R doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/msa.py A lib/galaxy/datatypes/test/infernal_model.cm M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/library_datasets.py M lib/galaxy/model/migrate/check.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/path/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py A lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py A lib/galaxy/webapps/galaxy/uwsgi_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/modules.py M scripts/common_startup.sh M scripts/common_startup_functions.sh A scripts/common_startup_variables.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/get_uwsgi_args.py A scripts/maintenance.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/nls/zh/locale.js M templates/webapps/galaxy/history/display_structured.mako M test/api/test_workflows.py M test/base/driver_util.py M test/docker/base/run_test_wrapper.sh A test/functional/tools/multi_output_recurse.xml M test/functional/tools/samples_tool_conf.xml A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py M test/unit/tools/test_collect_primary_datasets.py M tools/data_source/microbial_import_code.py Log Message: ----------- ini -> yml Commit: 3f2f5e6af4890d5edd1001844bf2c5eb9275daa6 https://github.com/galaxyproject/galaxy/commit/3f2f5e6af4890d5edd1001844bf2c... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- doc/schema Commit: 3ae47e611d2582c543d42a69d0c320634a70150f https://github.com/galaxyproject/galaxy/commit/3ae47e611d2582c543d42a69d0c32... 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test-data/random-file A test-data/sam_with_header.sam Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into dev Commit: 007e3cc2db247096cf06b59d4c7583112dacd7fa https://github.com/galaxyproject/galaxy/commit/007e3cc2db247096cf06b59d4c758... Author: Jim Johnson <jj@umn.edu> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py Log Message: ----------- Add Proteomics datatypes proBAM and proBED Add datatypes proBAM and proBED for genomic alignment and annotation of proteomic analysis results. Commit: 04c16f7e046945be3780b8431c492a9fac0d294a https://github.com/galaxyproject/galaxy/commit/04c16f7e046945be3780b8431c492... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Add nodeenv to dev requirements Commit: 8e4eab6e6cc6686f7bfdf7b86e29d725183a7397 https://github.com/galaxyproject/galaxy/commit/8e4eab6e6cc6686f7bfdf7b86e29d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-01-24 (Wed, 24 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Install node and yarn in common_startup.sh using nodeenv and the venv's npm. Commit: 1de0ef437b32619a06b23411d26520e89793877b https://github.com/galaxyproject/galaxy/commit/1de0ef437b32619a06b23411d2652... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/handlers.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M test/unit/jobs/test_mapper.py Log Message: ----------- Fix MRO issues Make Mixins new style classes Commit: d3895db861a003206dce0be833174493923dcc23 https://github.com/galaxyproject/galaxy/commit/d3895db861a003206dce0be833174... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Python3: dict_keys doesn't support indexing Commit: 15cd09d2c5e73e8721c9369bee518d68da3c8e44 https://github.com/galaxyproject/galaxy/commit/15cd09d2c5e73e8721c9369bee518... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Use newer psycopg2 library Commit: 31ec21d89fb91c00f368a46fe071d250a108c26f https://github.com/galaxyproject/galaxy/commit/31ec21d89fb91c00f368a46fe071d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Switch to Cheetah3 Commit: 326f743d3a5582fe6f3c6c78a1f1d7cb6331c9b7 https://github.com/galaxyproject/galaxy/commit/326f743d3a5582fe6f3c6c78a1f1d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Write integrated tool panel xml in one go Commit: fb9ebf980923858a1a4cbeb588d22a2b9820ff9a https://github.com/galaxyproject/galaxy/commit/fb9ebf980923858a1a4cbeb588d22... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Switch to Fabric3 for py2/3 support Commit: 00526c9928c3e1fdbdfe0f70d02549b632b82ef7 https://github.com/galaxyproject/galaxy/commit/00526c9928c3e1fdbdfe0f70d0254... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/configuration.py Log Message: ----------- Python3 fixes Commit: 973bfbafb980cfd15b545b2b0b4d873440bf1203 https://github.com/galaxyproject/galaxy/commit/973bfbafb980cfd15b545b2b0b4d8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/web/security/__init__.py Log Message: ----------- Use Crypto's get_random_bytes instead of rolling our own Commit: fbd33a57e0033a1547c3bf6f9812dd574cdb36d2 https://github.com/galaxyproject/galaxy/commit/fbd33a57e0033a1547c3bf6f9812d... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/web/framework/helpers/__init__.py Log Message: ----------- Remove dependency on WebHelpers Workaround babel bug when locale is not set Commit: e87d1aa79d84a08721d76ae2b6cb234351b6356b https://github.com/galaxyproject/galaxy/commit/e87d1aa79d84a08721d76ae2b6cb2... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M .ci/jenkins/selenium-compose/run_tests.sh M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/Makefile M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M scripts/common_startup.sh M test/manual/launch_and_run.sh Log Message: ----------- More Python3 print function fixes Commit: 6f6a671d36ff4f7ebe258c04aef6155384a4736e https://github.com/galaxyproject/galaxy/commit/6f6a671d36ff4f7ebe258c04aef61... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Make id encoding/decoding py3 compatible Commit: 0ce2d97c4dd65e5b2827c29dfa0aece4e6432666 https://github.com/galaxyproject/galaxy/commit/0ce2d97c4dd65e5b2827c29dfa0ae... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Create the virtualenv using the python that passed check_python This will make it easier to support Python3. Commit: d32f0d2eb111dee6951e021b98b41c051f07e46f https://github.com/galaxyproject/galaxy/commit/d32f0d2eb111dee6951e021b98b41... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.05.dev Commit: c1e78ae75c8849639f0db889a1f722e2473f12dd https://github.com/galaxyproject/galaxy/commit/c1e78ae75c8849639f0db889a1f72... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Log Message: ----------- Merge branch 'version-18.01' into version-18.05.dev Commit: 6a2e6be733b8349842689c38fb11fbf734fc518b https://github.com/galaxyproject/galaxy/commit/6a2e6be733b8349842689c38fb11f... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M .ci/jenkins/api/run_tests.sh Log Message: ----------- Add --skip_flakey_fails flag to CI script for API tests xref. https://github.com/galaxyproject/galaxy/pull/5286#issuecomment-358404551 and following comments. Commit: 83bf0ccce71c1244b362323efde0c89f2a4c8b60 https://github.com/galaxyproject/galaxy/commit/83bf0ccce71c1244b362323efde0c... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #5386 from martenson/version-18.05.dev Version 18.05.dev Commit: c31a0341714efa85a75df13da06ba34925673de5 https://github.com/galaxyproject/galaxy/commit/c31a0341714efa85a75df13da06ba... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M .ci/jenkins/api/run_tests.sh Log Message: ----------- Merge pull request #5388 from nsoranzo/skip_flakey_fails_for_api_tests Add --skip_flakey_fails flag to CI script for API tests Commit: 2854643057dd7d8517594299cf4c2d022c3fe78a https://github.com/galaxyproject/galaxy/commit/2854643057dd7d8517594299cf4c2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #5375 from natefoo/nodeenv Install node and yarn on startup if running a non-release branch Commit: df597db60ef479a8499b7a3b34591527c5d86dd7 https://github.com/galaxyproject/galaxy/commit/df597db60ef479a8499b7a3b34591... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M run_tests.sh Log Message: ----------- remove dead link urls are not forever... Commit: 046cb8f35956c45e5c88786b1e9c081cd5584efe https://github.com/galaxyproject/galaxy/commit/046cb8f35956c45e5c88786b1e9c0... Author: John Chilton <jmchilton@gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #5392 from martenson/remove-spam remove dead link Commit: 792a07148915ccc94d44f415db206e53addb12db https://github.com/galaxyproject/galaxy/commit/792a07148915ccc94d44f415db206... Author: John Chilton <jmchilton@gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M .ci/jenkins/selenium-compose/run_tests.sh M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/Makefile M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/handlers.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M scripts/common_startup.sh M test/manual/launch_and_run.sh M test/unit/jobs/test_mapper.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #5359 from mvdbeek/py3_fixes Various Python3 related fixes Commit: 28f5aca05695bab1a3608fbbcc93bd3f09c1eb28 https://github.com/galaxyproject/galaxy/commit/28f5aca05695bab1a3608fbbcc93b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Log Message: ----------- Merge branch 'release_18.01' into dev Commit: da002bdf44ff9c3809c15990e5f086d029c34533 https://github.com/galaxyproject/galaxy/commit/da002bdf44ff9c3809c15990e5f08... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M config/galaxy.yml.sample M doc/source/admin/dependency_resolvers.rst M doc/source/admin/galaxy_options.rst M lib/galaxy/dataset_collections/structure.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_tools.py M test/api/test_workflows.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml Log Message: ----------- Merge branch 'release_18.01' into dev Commit: db287a227441f78d457462a16ff59c4ebac23d94 https://github.com/galaxyproject/galaxy/commit/db287a227441f78d457462a16ff59... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 847d801c61702d826c948688b9305427d2f32ca2 https://github.com/galaxyproject/galaxy/commit/847d801c61702d826c948688b9305... Author: John Chilton <jmchilton@gmail.com> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Cleanup per-destination container override in job config. - Python 3 fix to martialize iterator into list. - Restrict XML query to just container elements - this is much more correct. Both fixes thanks to @nsoranzo. Commit: 9489fe471155c92028216ebf02056ed6389fddd4 https://github.com/galaxyproject/galaxy/commit/9489fe471155c92028216ebf02056... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #5427 from jmchilton/py3_fix Python 3 fix for reading container elements from job_conf. Commit: 5958d173c44e20e8860f90498f01cf2e6f510cf9 https://github.com/galaxyproject/galaxy/commit/5958d173c44e20e8860f90498f01c... 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R static/scripts/utils/ajax-queue.js R static/scripts/utils/async-save-text.js R static/scripts/utils/config.js R static/scripts/utils/deferred.js R static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R 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 Log Message: ----------- Remove static/scripts/* from the dev branch, add to .gitignore. These will be manually added back to release branches along with any other artifacts for distribution. This slight release-time burden will (per feedback from multiple developers) make it easier to manage changes to -dev. Commit: 29a1bf05e68a54c4fc9242e86ec5d27c8ac1db1a https://github.com/galaxyproject/galaxy/commit/29a1bf05e68a54c4fc9242e86ec5d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M .gitignore Log Message: ----------- Remove redundant subdir rules. Commit: a76614486be3dd0ad85f0007d604655dde02d6e9 https://github.com/galaxyproject/galaxy/commit/a76614486be3dd0ad85f0007d6046... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'release_18.01' into dev Commit: bc50c14490e4f81144e5bc59f76e6abe2d93a8fa https://github.com/galaxyproject/galaxy/commit/bc50c14490e4f81144e5bc59f76e6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Drop py26 XML parsing variant Commit: 49872e7612070df9aee607897fb4cf5cb9cb2242 https://github.com/galaxyproject/galaxy/commit/49872e7612070df9aee607897fb4c... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/util/logging/__init__.py M lib/galaxy/web/stack/message.py Log Message: ----------- Use six.create_bound_method() instead of types.MethodType() On Python2 the MethodType constructor requires the object's class to be passed. Commit: f43a3268b11841f65d3de195611bc6b0a940544c https://github.com/galaxyproject/galaxy/commit/f43a3268b11841f65d3de195611bc... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py M templates/webapps/galaxy/dataset/security_common.mako Log Message: ----------- Use builtin set Commit: 39104af3b42e6d253391a9b73f6912cf4423e783 https://github.com/galaxyproject/galaxy/commit/39104af3b42e6d253391a9b73f691... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Define file_types instead of types.FileType and pull up TarFile Commit: 046f3265dd50ec6ff53470a96a4dfdb0193d7c17 https://github.com/galaxyproject/galaxy/commit/046f3265dd50ec6ff53470a96a4df... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Fix loading custom JSONType Commit: 0be36ef4fce3b50bec37d199af2a404f3372ed65 https://github.com/galaxyproject/galaxy/commit/0be36ef4fce3b50bec37d199af2a4... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Use string.ascii_letters instead of string.letters for Py2/3 compat Update <sanitizer> documentation. Commit: 553d165087335528892232b17706b398bb3bf941 https://github.com/galaxyproject/galaxy/commit/553d165087335528892232b17706b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M templates/galaxy_client_app.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Python3 exception syntax fixes in templates/ Commit: 52586fcca2ef6ef6926fcd25b6c6f1b9ed598a6e https://github.com/galaxyproject/galaxy/commit/52586fcca2ef6ef6926fcd25b6c6f... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/datatypes/phylip.py Log Message: ----------- Fix relative import to be Python3-compatible Commit: 386526d928be1de57268163db1814640baa13459 https://github.com/galaxyproject/galaxy/commit/386526d928be1de57268163db1814... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Replace distutils.version with packaging.version distutils under Python3 has this bug: https://bugs.python.org/issue14894 which causes this traceback: ``` Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) File "lib/galaxy/app.py", line 125, in __init__ self._configure_toolbox() File "lib/galaxy/config.py", line 930, in _configure_toolbox self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self) File "lib/galaxy/tools/__init__.py", line 232, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1056, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 84, in __init__ self._load_tool_panel() File "lib/galaxy/tools/toolbox/base.py", line 358, in _load_tool_panel self.__add_tool_to_tool_panel(section_val, section, section=True) File "lib/galaxy/tools/toolbox/base.py", line 278, in __add_tool_to_tool_panel related_tool = self._lineage_in_panel(panel_dict, tool=tool) File "lib/galaxy/tools/toolbox/base.py", line 961, in _lineage_in_panel lineage_tool_versions = reversed(tool_lineage.get_versions()) File "lib/galaxy/tools/toolbox/lineages/interface.py", line 77, in get_versions return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 55, in tool_ids return ["%s/%s" % (tool_id, version) for version in self.tool_versions] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 49, in tool_versions return sorted(self._tool_versions, key=LooseVersion) File "/usr/lib/python3.4/distutils/version.py", line 58, in __lt__ c = self._cmp(other) File "/usr/lib/python3.4/distutils/version.py", line 343, in _cmp if self.version < other.version: TypeError: unorderable types: str() < int() ``` when a tool version contains a letter in the "wrong" place (e.g. in the first position). Fix https://github.com/galaxyproject/galaxy/issues/5408 . Commit: c7b6afbcd25fdeef9d7a59df95e3ace3136e0fa9 https://github.com/galaxyproject/galaxy/commit/c7b6afbcd25fdeef9d7a59df95e3a... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: A scripts/dump_library_paths.py Log Message: ----------- Add a script for dumping library file paths for backup Commit: b4cdce925bf485ecdb24868bacdcffe2f4e7a717 https://github.com/galaxyproject/galaxy/commit/b4cdce925bf485ecdb24868bacdcf... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/history/options-menu.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/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/page_tests.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/webhooks.rst A lib/galaxy/dependencies/conda-file.sh M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M scripts/common_startup.sh M test/api/test_webhooks.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- Merge branch 'release_18.01' into dev I removed the conflicted file that was modified in dev after removal in 18.01 Commit: a1662e37059e6956cdca3cb3eb235fd7b890b5c4 https://github.com/galaxyproject/galaxy/commit/a1662e37059e6956cdca3cb3eb235... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: R lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- remove lib/galaxy/dependencies/conda-environment.txt the file is no longer valid and has been replaced by conda-file.sh I believe Commit: b1df43a1f83a2b3026e23758843017d428e56a64 https://github.com/galaxyproject/galaxy/commit/b1df43a1f83a2b3026e2375884301... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: R lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- Merge pull request #5440 from martenson/remove-condaenv-txt remove lib/galaxy/dependencies/conda-environment.txt Commit: 5a31ac84ce129d03aea5fcbd73edaa4d67c465e5 https://github.com/galaxyproject/galaxy/commit/5a31ac84ce129d03aea5fcbd73eda... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: A scripts/dump_library_paths.py Log Message: ----------- Merge pull request #5436 from natefoo/dump-library-paths A script for dumping library file paths for backup Commit: 988cab4db7ef83714cf6f0c57f73f4255e3f075d https://github.com/galaxyproject/galaxy/commit/988cab4db7ef83714cf6f0c57f73f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/logging/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/stack/message.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/tool_shed/util/xml_util.py M templates/galaxy_client_app.mako M templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Merge pull request #5422 from nsoranzo/python3 Mixed Python3 fixes Commit: 245394acb694020c0f9f78185749fbccf45ec587 https://github.com/galaxyproject/galaxy/commit/245394acb694020c0f9f78185749f... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__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/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 6b2150b1feaca405d2e718bace5cb743b8a60376 https://github.com/galaxyproject/galaxy/commit/6b2150b1feaca405d2e718bace5cb... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py A lib/galaxy/web/framework/helpers/tags.py Log Message: ----------- Restore WebHelpers functions used in visualization makos Broken in commit fbd33a57e0033a1547c3bf6f9812dd574cdb36d2 . Reported by @guerler. Commit: 2be7eb8cfa0640dbec5954de006bab3c10f700f2 https://github.com/galaxyproject/galaxy/commit/2be7eb8cfa0640dbec5954de006ba... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M .travis.yml M tox.ini Log Message: ----------- Add py34-first_startup and py34-unit tox environments Also: - rename `first_startup` to `py27-first_startup` - rename other tox environments to use hyphens only to delimit factors - use the more specific ``` setenv = GALAXY_VIRTUAL_ENV={envdir} ``` instead of passing `--no-create-venv` to run unit tests inside the tox virtualenv (xref. commit 744835bbfe8bb07041600326af2f2f5d203365f5). Previously, `.venv` would be used if present. Commit: 6346b9e30949cd72a57eb683abd9bbaf431dd732 https://github.com/galaxyproject/galaxy/commit/6346b9e30949cd72a57eb683abd9b... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 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 .gitignore Log Message: ----------- Ignore the future default Python3 virtualenv Commit: f2c6e083a15eab453ea7c94565464575b0356ae1 https://github.com/galaxyproject/galaxy/commit/f2c6e083a15eab453ea7c94565464... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- twill and pygithub3 are not Python3-compatible Commit: 0a44e77a89f6533c7ceaad99ffb9942517989ea4 https://github.com/galaxyproject/galaxy/commit/0a44e77a89f6533c7ceaad99ffb99... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/tool_shed/util/repository_util.py Log Message: ----------- Fix missing space Commit: 0b60de76b93edbfeae5560a3a531d27e31e027f6 https://github.com/galaxyproject/galaxy/commit/0b60de76b93edbfeae5560a3a531d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-04 (Sun, 04 Feb 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 .gitignore M .travis.yml M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/tool_shed/util/repository_util.py M tox.ini Log Message: ----------- Merge pull request #5453 from nsoranzo/python3 Preparations for testing under Python3 Commit: f8d21f098af23db441ad4b81e1a25f2f8bd148b3 https://github.com/galaxyproject/galaxy/commit/f8d21f098af23db441ad4b81e1a25... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py A lib/galaxy/web/framework/helpers/tags.py Log Message: ----------- Merge pull request #5451 from nsoranzo/webhelpers_removal_followup Restore WebHelpers functions used in visualization makos Commit: 3864a1763ffa101384314090066c671bca5ba23d https://github.com/galaxyproject/galaxy/commit/3864a1763ffa101384314090066c6... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/tools/execute.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 Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 4347d5f83debc78a86c6be2fc4809cd99714124b https://github.com/galaxyproject/galaxy/commit/4347d5f83debc78a86c6be2fc4809... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Pass query params separately to visit_url() and visit_galaxy_url() For proper encoding. Commit: 204bb0e8fdf5ff10696e03c51c6805a62de79813 https://github.com/galaxyproject/galaxy/commit/204bb0e8fdf5ff10696e03c51c680... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M .gitignore R static/scripts/admin.toolshed.js R static/scripts/bundled/admin.bundled.js R static/scripts/bundled/analysis.bundled.js R static/scripts/bundled/extended.bundled.js R static/scripts/bundled/libs.bundled.js R static/scripts/bundled/login.bundled.js R static/scripts/galaxy.interactive_environments.js R static/scripts/galaxy.js R static/scripts/galaxy.library.js R static/scripts/galaxy.pages.js R static/scripts/i18n.js R static/scripts/layout/generic-nav-view.js R static/scripts/layout/masthead.js R static/scripts/layout/menu.js R static/scripts/layout/modal.js R static/scripts/layout/page.js R static/scripts/layout/panel.js R static/scripts/layout/router.js R static/scripts/layout/scratchbook.js R static/scripts/legacy/grid/grid-model.js R static/scripts/legacy/grid/grid-template.js R static/scripts/legacy/grid/grid-view.js R static/scripts/libs/backbone.js R static/scripts/libs/bbi/bigwig.js R static/scripts/libs/bbi/jquery-ajax-native.js R static/scripts/libs/bbi/jszlib.js R static/scripts/libs/bbi/spans.js R static/scripts/libs/bibtexParse.js R static/scripts/libs/bootstrap-tour.js R static/scripts/libs/bootstrap.js R static/scripts/libs/d3.js R static/scripts/libs/farbtastic.js R static/scripts/libs/jquery.sparklines.js R static/scripts/libs/jquery/jquery-ui.js R static/scripts/libs/jquery/jquery.autocomplete.js R static/scripts/libs/jquery/jquery.complexify.js R static/scripts/libs/jquery/jquery.cookie.js R static/scripts/libs/jquery/jquery.dynatree.js R static/scripts/libs/jquery/jquery.event.drag.js R static/scripts/libs/jquery/jquery.event.drop.js R static/scripts/libs/jquery/jquery.event.hover.js R static/scripts/libs/jquery/jquery.form.js R static/scripts/libs/jquery/jquery.js R static/scripts/libs/jquery/jquery.migrate.js R static/scripts/libs/jquery/jquery.mousewheel.js R static/scripts/libs/jquery/jquery.rating.js R static/scripts/libs/jquery/jquery.wymeditor.js R static/scripts/libs/jquery/jstorage.js R static/scripts/libs/jquery/jstree.js R static/scripts/libs/jquery/select2.js R static/scripts/libs/raven.js R static/scripts/libs/require.js R static/scripts/libs/toastr.js R static/scripts/libs/underscore.js R static/scripts/mvc/annotation.js R static/scripts/mvc/base-mvc.js R static/scripts/mvc/base/controlled-fetch-collection.js R static/scripts/mvc/collection/base-creator.js R static/scripts/mvc/collection/collection-li-edit.js R static/scripts/mvc/collection/collection-li.js R static/scripts/mvc/collection/collection-model.js R static/scripts/mvc/collection/collection-view-edit.js R static/scripts/mvc/collection/collection-view.js R static/scripts/mvc/collection/list-collection-creator.js R static/scripts/mvc/collection/list-of-pairs-collection-creator.js R static/scripts/mvc/collection/pair-collection-creator.js R static/scripts/mvc/dataset/data.js R static/scripts/mvc/dataset/dataset-choice.js R static/scripts/mvc/dataset/dataset-edit-attributes.js R static/scripts/mvc/dataset/dataset-error.js R static/scripts/mvc/dataset/dataset-li-edit.js R static/scripts/mvc/dataset/dataset-li.js R static/scripts/mvc/dataset/dataset-list.js R static/scripts/mvc/dataset/dataset-model.js R static/scripts/mvc/dataset/states.js R static/scripts/mvc/form/form-data.js R static/scripts/mvc/form/form-input.js R static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-repeat.js R static/scripts/mvc/form/form-section.js R static/scripts/mvc/form/form-view.js R static/scripts/mvc/form/form-wrapper.js R static/scripts/mvc/grid/grid-model.js R static/scripts/mvc/grid/grid-shared.js R static/scripts/mvc/grid/grid-template.js R static/scripts/mvc/grid/grid-view.js R static/scripts/mvc/history/copy-dialog.js R static/scripts/mvc/history/hda-li-edit.js R static/scripts/mvc/history/hda-li.js R static/scripts/mvc/history/hda-model.js R static/scripts/mvc/history/hdca-li-edit.js R static/scripts/mvc/history/hdca-li.js R static/scripts/mvc/history/hdca-model.js R static/scripts/mvc/history/history-content-model.js R static/scripts/mvc/history/history-contents.js R static/scripts/mvc/history/history-item-li.js R static/scripts/mvc/history/history-list.js R static/scripts/mvc/history/history-model.js R static/scripts/mvc/history/history-preferences.js R static/scripts/mvc/history/history-structure-view.js R static/scripts/mvc/history/history-view-annotated.js R static/scripts/mvc/history/history-view-edit-current.js R static/scripts/mvc/history/history-view-edit.js R static/scripts/mvc/history/history-view.js R static/scripts/mvc/history/job-dag.js R static/scripts/mvc/history/job-states-model.js R static/scripts/mvc/history/multi-panel.js R static/scripts/mvc/history/options-menu.js R static/scripts/mvc/job/job-li.js R static/scripts/mvc/job/job-model.js R static/scripts/mvc/job/job-params.js R static/scripts/mvc/lazy/lazy-limited.js R static/scripts/mvc/library/library-dataset-view.js R static/scripts/mvc/library/library-folder-view.js R static/scripts/mvc/library/library-folderlist-view.js R static/scripts/mvc/library/library-folderrow-view.js R static/scripts/mvc/library/library-foldertoolbar-view.js R static/scripts/mvc/library/library-library-view.js R static/scripts/mvc/library/library-librarylist-view.js R static/scripts/mvc/library/library-libraryrow-view.js R static/scripts/mvc/library/library-librarytoolbar-view.js R static/scripts/mvc/library/library-model.js R static/scripts/mvc/library/library-util.js R static/scripts/mvc/list/list-item.js R static/scripts/mvc/list/list-view.js R static/scripts/mvc/tag.js R static/scripts/mvc/tool/tool-form-base.js R static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form.js R static/scripts/mvc/tool/tool-genomespace.js R static/scripts/mvc/tool/tools.js R static/scripts/mvc/toolshed/categories-view.js R static/scripts/mvc/toolshed/repo-queue-view.js R static/scripts/mvc/toolshed/repo-status-view.js R static/scripts/mvc/toolshed/repositories-view.js R static/scripts/mvc/toolshed/repository-queue-view.js R static/scripts/mvc/toolshed/repository-view.js R static/scripts/mvc/toolshed/shed-list-view.js R static/scripts/mvc/toolshed/toolshed-model.js R static/scripts/mvc/toolshed/util.js R static/scripts/mvc/toolshed/workflows-view.js R static/scripts/mvc/tours.js R static/scripts/mvc/ui/error-modal.js R static/scripts/mvc/ui/icon-button.js R static/scripts/mvc/ui/popup-menu.js R static/scripts/mvc/ui/ui-buttons.js R static/scripts/mvc/ui/ui-color-picker.js R static/scripts/mvc/ui/ui-drilldown.js R static/scripts/mvc/ui/ui-frames.js R static/scripts/mvc/ui/ui-list.js R static/scripts/mvc/ui/ui-misc.js R static/scripts/mvc/ui/ui-modal.js R static/scripts/mvc/ui/ui-options.js R static/scripts/mvc/ui/ui-popover.js R static/scripts/mvc/ui/ui-portlet.js R static/scripts/mvc/ui/ui-select-content.js R static/scripts/mvc/ui/ui-select-default.js R static/scripts/mvc/ui/ui-select-ftp.js R static/scripts/mvc/ui/ui-select-genomespace.js R static/scripts/mvc/ui/ui-select-library.js R static/scripts/mvc/ui/ui-select.js R static/scripts/mvc/ui/ui-slider.js R static/scripts/mvc/ui/ui-table.js R static/scripts/mvc/ui/ui-tabs.js R static/scripts/mvc/ui/ui-thumbnails.js R static/scripts/mvc/upload/collection/collection-row.js R static/scripts/mvc/upload/collection/collection-view.js R static/scripts/mvc/upload/composite/composite-row.js R static/scripts/mvc/upload/composite/composite-view.js R static/scripts/mvc/upload/default/default-row.js R static/scripts/mvc/upload/default/default-view.js R static/scripts/mvc/upload/upload-button.js R static/scripts/mvc/upload/upload-extension.js R static/scripts/mvc/upload/upload-ftp.js R static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-settings.js R static/scripts/mvc/upload/upload-view.js R static/scripts/mvc/user/user-custom-builds.js R static/scripts/mvc/user/user-model.js R static/scripts/mvc/user/user-preferences.js R static/scripts/mvc/user/user-quotameter.js R static/scripts/mvc/visualization/visualization-model.js R static/scripts/mvc/webhooks.js R static/scripts/mvc/workflow/workflow-canvas.js R static/scripts/mvc/workflow/workflow-connector.js R static/scripts/mvc/workflow/workflow-forms.js R static/scripts/mvc/workflow/workflow-icons.js R static/scripts/mvc/workflow/workflow-manager.js R static/scripts/mvc/workflow/workflow-model.js R static/scripts/mvc/workflow/workflow-node.js R static/scripts/mvc/workflow/workflow-terminals.js R static/scripts/mvc/workflow/workflow-view-data.js R static/scripts/mvc/workflow/workflow-view-node.js R static/scripts/mvc/workflow/workflow-view-terminals.js R static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js R static/scripts/nls/de/locale.js R static/scripts/nls/es/locale.js R static/scripts/nls/fr/locale.js R static/scripts/nls/ja/locale.js R static/scripts/nls/locale.js R static/scripts/nls/zh/locale.js R static/scripts/onload.js R static/scripts/polyfills.js R static/scripts/reports/run_stats.js R static/scripts/toolshed/groups/group-detail-view.js R static/scripts/toolshed/groups/group-list-view.js R static/scripts/toolshed/groups/group-listrow-view.js R static/scripts/toolshed/groups/group-model.js R static/scripts/toolshed/toolshed.groups.js R static/scripts/ui/autocom_tagging.js R static/scripts/ui/editable-text.js R static/scripts/ui/fa-icon-button.js R static/scripts/ui/filter-control.js R static/scripts/ui/hoverhighlight.js R static/scripts/ui/loading-indicator.js R static/scripts/ui/mode-button.js R static/scripts/ui/pagination.js R static/scripts/ui/peek-column-selector.js R static/scripts/ui/popupmenu.js R static/scripts/ui/scroll-panel.js R static/scripts/ui/search-input.js R static/scripts/utils/add-logging.js R static/scripts/utils/ajax-queue.js R static/scripts/utils/async-save-text.js R static/scripts/utils/config.js R static/scripts/utils/deferred.js R static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R 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 Log Message: ----------- Merge pull request #5434 from dannon/static_scripts_dev_removal Remove static/scripts/* from the dev branch, add to .gitignore. Commit: dfe25ac131582a5315369ef8ba4e94abff7bff94 https://github.com/galaxyproject/galaxy/commit/dfe25ac131582a5315369ef8ba4e9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Client format Commit: 02fa48f85cdaa1ed0722f050b6953d6bbe7113c7 https://github.com/galaxyproject/galaxy/commit/02fa48f85cdaa1ed0722f050b6953... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M client/galaxy/scripts/galaxy.js Log Message: ----------- Define locale var, log global usage of $ Commit: 490f67f3a0e70f9d90898163ea42e7d273c790ba https://github.com/galaxyproject/galaxy/commit/490f67f3a0e70f9d90898163ea42e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #5458 from nsoranzo/ts_tests_query_params Pass query params separately to visit_url() and visit_galaxy_url() Commit: 3a7414acaca59dc602ab3ea8092df2be9ce34258 https://github.com/galaxyproject/galaxy/commit/3a7414acaca59dc602ab3ea8092df... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/style/less/ui/icon-btn.less M lib/galaxy/config.py M lib/galaxy/managers/collections.py M lib/galaxy/util/facts.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Commit: 77bcca49a393ab4a181efae7c55fc06ee7494543 https://github.com/galaxyproject/galaxy/commit/77bcca49a393ab4a181efae7c55fc... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M lib/galaxy/web/security/__init__.py Log Message: ----------- Python3: make encoded id JSON-serializable Fix the following traceback when visiting the Galaxy homepage: ``` Error - <class 'TypeError'>: b'f5cd946f78fsbc0d' is not JSON serializable URL: http://127.0.0.1:8080/ File 'lib/galaxy/web/framework/middleware/error.py', line 157 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv3/lib/python3.4/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv3/lib/python3.4/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File 'lib/galaxy/web/framework/base.py', line 137 in __call__ return self.handle_request(environ, start_response) File 'lib/galaxy/web/framework/base.py', line 216 in handle_request body = method(trans, **kwargs) File 'lib/galaxy/webapps/galaxy/controllers/root.py', line 112 in index return self.template(trans, 'analysis', options=js_options) File 'lib/galaxy/web/base/controller.py', line 325 in template masthead=masthead File 'lib/galaxy/web/framework/webapp.py', line 920 in fill_template return self.fill_template_mako(filename, **kwargs) File 'lib/galaxy/web/framework/webapp.py', line 934 in fill_template_mako return template.render(**data) File '/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv3/lib/python3.4/site-packages/mako/template.py', line 445 in render return runtime._render(self, self.callable_, args, data) File '/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv3/lib/python3.4/site-packages/mako/runtime.py', line 829 in _render **_kwargs_for_callable(callable_, data)) File '/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv3/lib/python3.4/site-packages/mako/runtime.py', line 864 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv3/lib/python3.4/site-packages/mako/runtime.py', line 890 in _exec_template callable_(context, *args, **kwargs) File '/usr/users/ga002/soranzon/software/nsoranzo_galaxy/database/compiled_templates/js-app.mako.py', line 75 in render_body __M_writer(str( h.dumps( options ) )) File 'lib/galaxy/util/json.py', line 79 in safe_dumps dumped = json.dumps(*args, allow_nan=False, **kwargs) File '/usr/lib/python3.4/json/__init__.py', line 237 in dumps **kw).encode(obj) File '/usr/lib/python3.4/json/encoder.py', line 192 in encode chunks = self.iterencode(o, _one_shot=True) File '/usr/lib/python3.4/json/encoder.py', line 250 in iterencode return _iterencode(o, 0) File '/usr/lib/python3.4/json/encoder.py', line 173 in default raise TypeError(repr(o) + " is not JSON serializable") TypeError: b'f5cd946f78fsbc0d' is not JSON serializable ``` Commit: b114f3f7b9d483509e7d684aa8be54e769fddbf7 https://github.com/galaxyproject/galaxy/commit/b114f3f7b9d483509e7d684aa8be5... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/tag_collection_from_file.xml A test-data/new_tags_1.txt Log Message: ----------- Add tool that tags collection elements from a file This tags collection elements (but not collections). Commit: b2be7b51814a4354307e8f0a0df0c8885ef73bb0 https://github.com/galaxyproject/galaxy/commit/b2be7b51814a4354307e8f0a0df0c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M lib/galaxy/managers/taggable.py Log Message: ----------- Sort tags when serializing them Commit: f9664a0863b24ff738aefcbe520f033e5f53e76d https://github.com/galaxyproject/galaxy/commit/f9664a0863b24ff738aefcbe520f0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M test/base/interactor.py Log Message: ----------- Make presence of tags testable Commit: fd373501c78dee268844e82fa1a56a108d34cf23 https://github.com/galaxyproject/galaxy/commit/fd373501c78dee268844e82fa1a56... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add tag from file tool to samples_tool_conf.xml Commit: e306a447c080f8d252a9a7fe49f4d36f6a8de4a9 https://github.com/galaxyproject/galaxy/commit/e306a447c080f8d252a9a7fe49f4d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-06 (Tue, 06 Feb 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py M lib/galaxy/tools/tag_collection_from_file.xml Log Message: ----------- Switch tag tool to use select and add remove mode Commit: b3ea83929fc67f656c30aed865d26a5575cc19c7 https://github.com/galaxyproject/galaxy/commit/b3ea83929fc67f656c30aed865d26... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M test/functional/twilltestcase.py Log Message: ----------- Unicodify the return value of TwillTestCase.last_page() inside the check_page_for_string() method. Fix the following stacktrace during ToolShed tests: ``` Traceback (most recent call last): File "/usr/lib/python2.7/unittest/case.py", line 329, in run testMethod() File "/galaxy/test/shed_functional/functional/test_1160_tool_help_images.py", line 79, in test_0010_load_tool_page self.load_display_tool_page(repository, tool_path, changeset_revision, strings_displayed=[image_path], strings_not_displayed=[]) File "/galaxy/test/shed_functional/base/twilltestcase.py", line 1122, in load_display_tool_page self.check_for_strings(strings_displayed, strings_not_displayed) File "/galaxy/test/functional/twilltestcase.py", line 39, in check_for_strings self.check_page_for_string(string) File "/galaxy/test/functional/twilltestcase.py", line 69, in check_page_for_string if page.find(patt) == -1: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 8760: ordinal not in range(128) ``` Commit: c3bb2859039338c513e1f9ac871dc569d5469e5c https://github.com/galaxyproject/galaxy/commit/c3bb2859039338c513e1f9ac871dc... Author: Anthony Bretaudeau <abretaud@irisa.fr> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge pull request #2 from dannon/i18n Minor tweaks to i18n work Commit: 4dbfd50f064256f2af8f7e3b08ddbb8a2b352aac https://github.com/galaxyproject/galaxy/commit/4dbfd50f064256f2af8f7e3b08ddb... Author: Anthony Bretaudeau <abretaud@irisa.fr> Date: 2018-02-07 (Wed, 07 Feb 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/api/run_tests.sh M .ci/jenkins/selenium-compose/run_tests.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.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/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/history.less M client/galaxy/style/less/ui/icon-btn.less M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A 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lib/galaxy/web/framework/helpers/tags.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/message.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/xml_util.py M run_tests.sh M 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static/scripts/viz/viz_views.js M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/galaxy_client_app.mako M templates/user/register.mako M templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/api/test_tools.py M test/api/test_webhooks.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/integration_util.py M test/base/workflows_format_2/converter.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/job_environment_default.xml A test/functional/tools/job_environment_default_legacy.xml A test/functional/tools/job_environment_explicit_shared_home.xml A test/functional/tools/mulled_example_explicit.xml A test/functional/tools/mulled_example_simple.xml A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css A test/integration/dockerized_job_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/manual/launch_and_run.sh M test/selenium_tests/test_tool_describing_tours.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_evaluation.py M tox.ini Log Message: ----------- Merge branch 'dev' into i18n Commit: d14bae73f72cd454ef41bb1815cf1dfc9256db5d https://github.com/galaxyproject/galaxy/commit/d14bae73f72cd454ef41bb1815cf1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/managers/tags.py M lib/galaxy/tools/tag_collection_from_file.xml M test-data/new_tags_1.txt Log Message: ----------- Flush once per tag Not sure this is the right thing to do (maybe there is a better way to get an ID?), but it avoids ``` IntegrityError: (psycopg2.IntegrityError) duplicate key value violates unique constraint "tag_name_key" DETAIL: Key (name)=(group) already exists. [SQL: 'INSERT INTO tag (type, parent_id, name) VALUES (%(type)s, %(parent_id)s, %(name)s) RETURNING tag.id'] [parameters: {'parent_id': None, 'type': 0, 'name': u'group'}] galaxy.tools.execute WARNING 2018-02-06 15:22:38,808 [p:2122,w:1,m:0] [uWSGIWorker1Core1] There was a failure executing a job for tool [__TAG_FROM_FILE__] - Error executing tool: (psycopg2.IntegrityError) duplicate key value violates unique constraint "tag_name_key" ``` Commit: 43d572558a5dc5747dac0a7fc824bef3af4a809a https://github.com/galaxyproject/galaxy/commit/43d572558a5dc5747dac0a7fc824b... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/web/security/__init__.py M test/functional/twilltestcase.py Log Message: ----------- Merge pull request #5461 from nsoranzo/python3 Python3: make encoded id JSON-serializable Commit: 29acb11df5c971a2bc99ae534e36cffa046e2a6c https://github.com/galaxyproject/galaxy/commit/29acb11df5c971a2bc99ae534e36c... Author: Peter Cock <p.j.a.cock@googlemail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Show parameter name in DataToolParameter exception Goal is to replace this kind of output in a failed test run: RunToolException: Error creating a job for these tool inputs - Specify a dataset of the required format / build. with: RunToolException: Error creating a job for these tool inputs - Specify a dataset of the required format / build in parameter 'XXX'. Commit: 12f72412abe1e1675f5755c77bda08707116db67 https://github.com/galaxyproject/galaxy/commit/12f72412abe1e1675f5755c77bda0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/utils/localization.js M config/galaxy.yml.sample M config/user_preferences_extra_conf.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/config_schema.yml M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Merge pull request #5282 from abretaud/i18n [WIP] Global and profile-bound language configuration Commit: 45ab11cca78809a0bc779ddeff411f0ae2bbf311 https://github.com/galaxyproject/galaxy/commit/45ab11cca78809a0bc779ddeff411... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Initial work towards slow request logging into sentry Commit: 65e2e0b48f59948a7df46f1d3440ffd127757be3 https://github.com/galaxyproject/galaxy/commit/65e2e0b48f59948a7df46f1d3440f... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/parser/xml.py M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'origin/release_18.01' into dev Commit: db45db89b396b0f70f600f078aef1f833b760745 https://github.com/galaxyproject/galaxy/commit/db45db89b396b0f70f600f078aef1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M config/galaxy.yml.sample M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Make sloreq_threshold configurable Commit: d1f120108735cdf15b6c782d5bb2f66ffce274c4 https://github.com/galaxyproject/galaxy/commit/d1f120108735cdf15b6c782d5bb2f... Author: E. Rasche <hxr@hx42.org> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M config/galaxy.yml.sample M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #5479 from dannon/slow_request_timing_sentry Slow request timing in sentry Commit: 3f80a43bda5e7d32cf9f1317666e5fa618f38bd6 https://github.com/galaxyproject/galaxy/commit/3f80a43bda5e7d32cf9f1317666e5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M config/galaxy.yml.sample M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Add configuration for slow request timing to schema, regenerate Commit: 8ce7f96353f3d31e6b41bd19c611c33a57411cb6 https://github.com/galaxyproject/galaxy/commit/8ce7f96353f3d31e6b41bd19c611c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M doc/source/admin/galaxy_options.rst Log Message: ----------- Rebuild rst for new configuration options Commit: 55ca8132a38c67d7e30e6ee59f1497d58f6158df https://github.com/galaxyproject/galaxy/commit/55ca8132a38c67d7e30e6ee59f149... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge remote-tracking branch 'origin/release_18.01' into dev Commit: 0ca7afb343d865a7d1bd4cc6b5170f9bf03a0cf3 https://github.com/galaxyproject/galaxy/commit/0ca7afb343d865a7d1bd4cc6b5170... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-02-08 (Thu, 08 Feb 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 #5487 from dannon/slow_request_timing_sentry Add configuration for slow request timing to schema, regenerate Commit: 6f2a0cceb03b4277f9ed4e8761cc011e230fa08e https://github.com/galaxyproject/galaxy/commit/6f2a0cceb03b4277f9ed4e8761cc0... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M Makefile M config/reports.yml.sample M doc/source/admin/reports_options.rst Log Message: ----------- Unify config-rebuild Makefile targets Rebuild reports sample and RST from schema with the new Makefile target. Commit: 10ff797ac77da470cf2078059b3235cee04570ff https://github.com/galaxyproject/galaxy/commit/10ff797ac77da470cf2078059b323... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M client/package.json M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_18.01' into dev Conflicts: scripts/common_startup.sh Commit: 1ea41622632aeefdac7138ad515659a594887908 https://github.com/galaxyproject/galaxy/commit/1ea41622632aeefdac7138ad51565... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Python3: Update pulsar-galaxy-lib dependency to 0.8.3 Commit: b6fe83409ad57e15adcb1b270102827e5e5fc084 https://github.com/galaxyproject/galaxy/commit/b6fe83409ad57e15adcb1b2701028... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-08 (Thu, 08 Feb 2018) Changed paths: M Makefile M config/reports.yml.sample M doc/source/admin/reports_options.rst Log Message: ----------- Merge pull request #5488 from nsoranzo/unify_makefile_targets Unify config-rebuild Makefile targets Commit: d0b4503e0cc2e3d083330da08672b6ca35d5c4b2 https://github.com/galaxyproject/galaxy/commit/d0b4503e0cc2e3d083330da08672b... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-02-09 (Fri, 09 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #5494 from nsoranzo/update_pulsar_galaxy_lib Python3: Update pulsar-galaxy-lib dependency to 0.8.3 Commit: 587f20cf9c0b6d250bee403cf3baab85e1272dcf https://github.com/galaxyproject/galaxy/commit/587f20cf9c0b6d250bee403cf3baa... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #5465 from peterjc/patch-5 Show parameter name in DataToolParameter exception Commit: 0367a356d528b3ca395eec1f3de57563cba19c2e https://github.com/galaxyproject/galaxy/commit/0367a356d528b3ca395eec1f3de57... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #5360 from jj-umn/dev Add Proteomics datatypes proBAM and proBED Commit: ca66882fcec96ff29c6dc147146f20c6584670a6 https://github.com/galaxyproject/galaxy/commit/ca66882fcec96ff29c6dc147146f2... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A client/galaxy/scripts/mvc/visualization/client/components/model.js A client/galaxy/scripts/mvc/visualization/client/components/screenshot.js A client/galaxy/scripts/mvc/visualization/client/views/description.js A client/galaxy/scripts/mvc/visualization/client/views/editor.js A client/galaxy/scripts/mvc/visualization/client/views/groups.js A client/galaxy/scripts/mvc/visualization/client/views/settings.js A client/galaxy/scripts/mvc/visualization/client/views/viewer.js A client/galaxy/scripts/mvc/visualization/client/views/viewport.js A client/galaxy/scripts/mvc/visualization/visualization-client.js A client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Move charts client to core Commit: daf500f80cfa2bdb36b74acadca6a9eb7a61975c https://github.com/galaxyproject/galaxy/commit/daf500f80cfa2bdb36b74acadca6a... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Add routes to analysis app Commit: 80ee52b2d12f361f58cc2724372ec88fad3d9a76 https://github.com/galaxyproject/galaxy/commit/80ee52b2d12f361f58cc2724372ec... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Redirect link in history panel to visualization client Commit: bc5eecf6a8efe0f299b740046a5e5ab77ab95b5b https://github.com/galaxyproject/galaxy/commit/bc5eecf6a8efe0f299b740046a5e5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/style/less/ui.less Log Message: ----------- Augment thumbnail styles for default icon Commit: c7bf80599e19f2a165a4406b00391e64035ad116 https://github.com/galaxyproject/galaxy/commit/c7bf80599e19f2a165a4406b00391... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Check for visualization logo to be displayed in thumbnail selector Commit: 26f72481aaa20c0a57d491c6086d573b82dbeeec https://github.com/galaxyproject/galaxy/commit/26f72481aaa20c0a57d491c6086d5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/registry.py R static/scripts/packed M static/style/blue/base.css Log Message: ----------- Augment registry response Commit: feab8314b0bf309804e23de61de4a5e550c55a71 https://github.com/galaxyproject/galaxy/commit/feab8314b0bf309804e23de61de4a... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add routes to build app Commit: 0049d5a760ec19383fa97f2ca72afa6352486d3c https://github.com/galaxyproject/galaxy/commit/0049d5a760ec19383fa97f2ca72af... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-thumbnails.js Log Message: ----------- Augment thumbnail viewer Commit: b16c6027dfdff5208adaeae760062cffa2aaad0a https://github.com/galaxyproject/galaxy/commit/b16c6027dfdff5208adaeae760062... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml Log Message: ----------- Augment xmls Commit: 39c0eb37ba73b127e36260279491bc1408943c3c https://github.com/galaxyproject/galaxy/commit/39c0eb37ba73b127e36260279491b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Add regular attribute to config parser Commit: b6db962284d06918a1ff1dc61b73b534712f2821 https://github.com/galaxyproject/galaxy/commit/b6db962284d06918a1ff1dc61b73b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Revise initial viewer, fix logo display Commit: 1829c4a8bcb0a428593530cf901645f01ef2b056 https://github.com/galaxyproject/galaxy/commit/1829c4a8bcb0a428593530cf90164... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/api/visualizations.py Log Message: ----------- Move dictionary generator from registry to plugin Commit: 33ae04a04fca19f9c251efb2acac36fb521a93a0 https://github.com/galaxyproject/galaxy/commit/33ae04a04fca19f9c251efb2acac3... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Add static url to response Commit: 80222ba4116476c04a7a4c08c4af76e43374b97a https://github.com/galaxyproject/galaxy/commit/80222ba4116476c04a7a4c08c4af7... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-client.js M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Parse entry point in dictionary Commit: 9b6b757503efd1877e5addc185cdf12c03eacde2 https://github.com/galaxyproject/galaxy/commit/9b6b757503efd1877e5addc185cdf... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/mvc/visualization/client/components/model.js R client/galaxy/scripts/mvc/visualization/client/components/screenshot.js R client/galaxy/scripts/mvc/visualization/client/views/description.js R client/galaxy/scripts/mvc/visualization/client/views/editor.js R client/galaxy/scripts/mvc/visualization/client/views/groups.js R client/galaxy/scripts/mvc/visualization/client/views/settings.js R client/galaxy/scripts/mvc/visualization/client/views/viewer.js R client/galaxy/scripts/mvc/visualization/client/views/viewport.js R client/galaxy/scripts/mvc/visualization/visualization-client.js M client/webpack.config.js M config/plugins/visualizations/charts/config/charts.xml A config/plugins/visualizations/common/templates/chart_entry_point.mako M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add chart type common mako and bundle to visualization framework Commit: 6ec649c04d4200a38066fb8cca951dda5de22a92 https://github.com/galaxyproject/galaxy/commit/6ec649c04d4200a38066fb8cca951... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A client/galaxy/scripts/apps/chart.js A client/galaxy/scripts/mvc/visualization/chart/chart-client.js A client/galaxy/scripts/mvc/visualization/chart/components/model.js A client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js A client/galaxy/scripts/mvc/visualization/chart/views/description.js A client/galaxy/scripts/mvc/visualization/chart/views/editor.js A client/galaxy/scripts/mvc/visualization/chart/views/groups.js A client/galaxy/scripts/mvc/visualization/chart/views/settings.js A client/galaxy/scripts/mvc/visualization/chart/views/viewer.js A client/galaxy/scripts/mvc/visualization/chart/views/viewport.js Log Message: ----------- Add shared chart client Commit: 48518d84f7d06903e2f2ad22ce24ebb617de82ae https://github.com/galaxyproject/galaxy/commit/48518d84f7d06903e2f2ad22ce24e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M config/plugins/visualizations/common/templates/chart_entry_point.mako Log Message: ----------- Load dataset for chart visualization plugin Commit: 76fac9181f1a9f85913be6e6daea72da0ced549a https://github.com/galaxyproject/galaxy/commit/76fac9181f1a9f85913be6e6daea7... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako Log Message: ----------- Add name to response dictionary Commit: 9be959396ec4c401e2ee8af83a600a8b7cfac3bf https://github.com/galaxyproject/galaxy/commit/9be959396ec4c401e2ee8af83a600... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/style/less/base.less A client/galaxy/style/less/charts.less M config/plugins/visualizations/common/templates/chart_entry_point.mako A config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M static/style/blue/base.css Log Message: ----------- Move json config to xml Commit: 123e9febb856731df4a0d990349adfbf1288b923 https://github.com/galaxyproject/galaxy/commit/123e9febb856731df4a0d990349ad... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml Log Message: ----------- Fix support for data groups form in client Commit: 1c30571677865173452478dfb429792e580051f3 https://github.com/galaxyproject/galaxy/commit/1c30571677865173452478dfb4297... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Add conditional parameters to visualizations xml config Commit: fd9ac30d890a179e7184ceb62d9d8d0c333f8ad5 https://github.com/galaxyproject/galaxy/commit/fd9ac30d890a179e7184ceb62d9d8... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Add optional specifiers Commit: 664bf8bba5a4954926fba840aea43a06019ef163 https://github.com/galaxyproject/galaxy/commit/664bf8bba5a4954926fba840aea43... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js Log Message: ----------- More client side cleanup, revise import styles Commit: 1eccb2a6434fc6e098626066b739f2fa7c5f56a4 https://github.com/galaxyproject/galaxy/commit/1eccb2a6434fc6e098626066b739f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js Log Message: ----------- Use plugin object instead of chart definition Use plugin instead of definition Commit: 911b667f383b801ac22f8fb87bae81bd52051b19 https://github.com/galaxyproject/galaxy/commit/911b667f383b801ac22f8fb87bae8... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Fix conditional parameter description in xml Commit: 4bcc9e6c2e79110bfde3c472debe427ca3097f21 https://github.com/galaxyproject/galaxy/commit/4bcc9e6c2e79110bfde3c472debe4... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js Log Message: ----------- Remove unused split function Commit: d1798f376d2633d6d25955b238b38a7de1fb4d5e https://github.com/galaxyproject/galaxy/commit/d1798f376d2633d6d25955b238b38... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R config/plugins/visualizations/charts/config/charts.xml R config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/static/client/app.css R config/plugins/visualizations/charts/static/client/app.js R config/plugins/visualizations/charts/static/client/components/model.js R config/plugins/visualizations/charts/static/client/components/screenshot.js R config/plugins/visualizations/charts/static/client/views/description.js R config/plugins/visualizations/charts/static/client/views/editor.js R config/plugins/visualizations/charts/static/client/views/groups.js R config/plugins/visualizations/charts/static/client/views/settings.js R config/plugins/visualizations/charts/static/client/views/viewer.js R config/plugins/visualizations/charts/static/client/views/viewport.js R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js R 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config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js R config/plugins/visualizations/charts/templates/charts.mako R config/plugins/visualizations/charts/webpack.config.js A config/plugins/visualizations/nvd3/package.json A config/plugins/visualizations/nvd3/static/bundle.js A config/plugins/visualizations/nvd3/static/bundle.js.map A config/plugins/visualizations/nvd3/static/entry.js A config/plugins/visualizations/nvd3/static/plugin/nv.d3.css A config/plugins/visualizations/nvd3/static/plugin/nv.d3.js A config/plugins/visualizations/nvd3/static/utilities/jobs.js A config/plugins/visualizations/nvd3/static/utilities/tabular-datasets.js A config/plugins/visualizations/nvd3/static/utilities/tabular-utilities.js A config/plugins/visualizations/nvd3/static/utilities/utils.js A config/plugins/visualizations/nvd3/webpack.config.js Log Message: ----------- Add bundle for nvd3 Commit: 964c82329c3a8bdc2c47ab5f2412e8c23be12ef6 https://github.com/galaxyproject/galaxy/commit/964c82329c3a8bdc2c47ab5f2412e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R config/plugins/visualizations/nvd3/package.json R config/plugins/visualizations/nvd3/static/bundle.js R config/plugins/visualizations/nvd3/static/bundle.js.map R config/plugins/visualizations/nvd3/static/entry.js R config/plugins/visualizations/nvd3/static/plugin/nv.d3.css R config/plugins/visualizations/nvd3/static/plugin/nv.d3.js R config/plugins/visualizations/nvd3/static/utilities/jobs.js R config/plugins/visualizations/nvd3/static/utilities/tabular-datasets.js R config/plugins/visualizations/nvd3/static/utilities/tabular-utilities.js R config/plugins/visualizations/nvd3/static/utilities/utils.js R config/plugins/visualizations/nvd3/webpack.config.js Log Message: ----------- Fix entry name Commit: 778f92155ca6e19a3755fac7423dec9ac5a033cb https://github.com/galaxyproject/galaxy/commit/778f92155ca6e19a3755fac7423de... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3bar/package.json A config/plugins/visualizations/nvd3bar/static/bundle.js A config/plugins/visualizations/nvd3bar/static/bundle.js.map A config/plugins/visualizations/nvd3bar/static/logo.png A config/plugins/visualizations/nvd3bar/static/nvd3.js A config/plugins/visualizations/nvd3bar/static/plugin/nv.d3.css A config/plugins/visualizations/nvd3bar/static/plugin/nv.d3.js A config/plugins/visualizations/nvd3bar/static/utilities/jobs.js A config/plugins/visualizations/nvd3bar/static/utilities/tabular-datasets.js A config/plugins/visualizations/nvd3bar/static/utilities/tabular-utilities.js A config/plugins/visualizations/nvd3bar/static/utilities/utils.js A config/plugins/visualizations/nvd3bar/webpack.config.js Log Message: ----------- Add webpack config and bundle files Commit: 4b158e3f7a39f8019fc1af81e88e32b2e2adeb7d https://github.com/galaxyproject/galaxy/commit/4b158e3f7a39f8019fc1af81e88e3... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Add macro support to visualization xmls Commit: 8c3babfd1823137879797ce8af932c45741b8b18 https://github.com/galaxyproject/galaxy/commit/8c3babfd1823137879797ce8af932... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml A config/plugins/visualizations/nvd3bar/config/nvd3shared.xml Log Message: ----------- Add shared parameters Commit: 0451024aa08cbd7d4b96b01c9ef35d72554290fd https://github.com/galaxyproject/galaxy/commit/0451024aa08cbd7d4b96b01c9ef35... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M config/plugins/visualizations/nvd3bar/config/nvd3shared.xml M lib/galaxy/util/xml_macros.py Log Message: ----------- Disable base name sanitization of macro imports for now Commit: 2b50fe94af3d12649ed76251cf1ec3ca4cc3a147 https://github.com/galaxyproject/galaxy/commit/2b50fe94af3d12649ed76251cf1ec... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3bar/config/nvd3bar.xml M config/plugins/visualizations/nvd3bar/config/nvd3shared.xml A config/plugins/visualizations/nvd3scatter/config/nvd3scatter.xml A config/plugins/visualizations/nvd3scatter/static/logo.png Log Message: ----------- Add scatter plot configuration Commit: f56cb32fb722640fa63b943293eb146b819070c4 https://github.com/galaxyproject/galaxy/commit/f56cb32fb722640fa63b943293eb1... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml A config/plugins/visualizations/nvd3_bar/config/nvd3_shared.xml A config/plugins/visualizations/nvd3_bar/package.json A config/plugins/visualizations/nvd3_bar/static/logo.png A config/plugins/visualizations/nvd3_bar/static/nvd3.js A config/plugins/visualizations/nvd3_bar/static/plugin/nv.d3.css A config/plugins/visualizations/nvd3_bar/static/plugin/nv.d3.js A config/plugins/visualizations/nvd3_bar/static/utilities/jobs.js A config/plugins/visualizations/nvd3_bar/static/utilities/tabular-datasets.js A config/plugins/visualizations/nvd3_bar/static/utilities/tabular-utilities.js A config/plugins/visualizations/nvd3_bar/static/utilities/utils.js A config/plugins/visualizations/nvd3_bar/webpack.config.js A config/plugins/visualizations/nvd3_horizontal/config/nvd3_horizontal.xml A config/plugins/visualizations/nvd3_horizontal/static/logo.png A config/plugins/visualizations/nvd3_horizontal_stacked/config.js A config/plugins/visualizations/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml A config/plugins/visualizations/nvd3_horizontal_stacked/static/logo.png A config/plugins/visualizations/nvd3_scatter/config/nvd3_scatter.xml A config/plugins/visualizations/nvd3_scatter/static/logo.png R config/plugins/visualizations/nvd3bar/config/nvd3bar.xml R config/plugins/visualizations/nvd3bar/config/nvd3shared.xml R config/plugins/visualizations/nvd3bar/package.json R config/plugins/visualizations/nvd3bar/static/bundle.js R config/plugins/visualizations/nvd3bar/static/bundle.js.map R config/plugins/visualizations/nvd3bar/static/logo.png R config/plugins/visualizations/nvd3bar/static/nvd3.js R config/plugins/visualizations/nvd3bar/static/plugin/nv.d3.css R config/plugins/visualizations/nvd3bar/static/plugin/nv.d3.js R config/plugins/visualizations/nvd3bar/static/utilities/jobs.js R config/plugins/visualizations/nvd3bar/static/utilities/tabular-datasets.js R config/plugins/visualizations/nvd3bar/static/utilities/tabular-utilities.js R config/plugins/visualizations/nvd3bar/static/utilities/utils.js R config/plugins/visualizations/nvd3bar/webpack.config.js R config/plugins/visualizations/nvd3scatter/config/nvd3scatter.xml R config/plugins/visualizations/nvd3scatter/static/logo.png Log Message: ----------- Use underscores to specify nvd3 types Commit: d871196c5e70ee089d357a0c252321bd6e06f920 https://github.com/galaxyproject/galaxy/commit/d871196c5e70ee089d357a0c25232... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3_bar_stacked/config/nvd3_bar_stacked.xml A config/plugins/visualizations/nvd3_bar_stacked/static/logo.png R config/plugins/visualizations/nvd3_horizontal_stacked/config.js Log Message: ----------- Add config for stacked bars Commit: 5e8bd49b126b91cdbf2b2c29988e1395bb4a6670 https://github.com/galaxyproject/galaxy/commit/5e8bd49b126b91cdbf2b2c29988e1... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3_histogram/config/nvd3_histogram.xml A config/plugins/visualizations/nvd3_histogram/static/logo.png A config/plugins/visualizations/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml A config/plugins/visualizations/nvd3_histogram_discrete/static/logo.png A config/plugins/visualizations/nvd3_line/config/nvd3_line.xml A config/plugins/visualizations/nvd3_line/static/logo.png A config/plugins/visualizations/nvd3_line_focus/config/nvd3_line_focus.xml A config/plugins/visualizations/nvd3_line_focus/static/logo.png A config/plugins/visualizations/nvd3_pie/config/nvd3_pie.xml A config/plugins/visualizations/nvd3_pie/static/logo.png A config/plugins/visualizations/nvd3_stackedarea/config/nvd3_stackedarea.xml A config/plugins/visualizations/nvd3_stackedarea/static/logo.png A config/plugins/visualizations/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml A config/plugins/visualizations/nvd3_stackedarea_full/static/logo.png A config/plugins/visualizations/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml A config/plugins/visualizations/nvd3_stackedarea_stream/static/logo.png Log Message: ----------- Add remaining configuration files for nvd3 visualizations Commit: 83c27b629a2e6d17a8ce955f3de1586fce6581da https://github.com/galaxyproject/galaxy/commit/83c27b629a2e6d17a8ce955f3de15... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako Log Message: ----------- Fix chart entry point mako Commit: e011371096401673c2774ac6e3201323ab7c0baf https://github.com/galaxyproject/galaxy/commit/e011371096401673c2774ac6e3201... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml Log Message: ----------- Fix indention Commit: a0fa19048a49c662afa0a6e068aeeebe322c8a6d https://github.com/galaxyproject/galaxy/commit/a0fa19048a49c662afa0a6e068aee... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Fix bug with non-static-serving viz urls that was causing a browser crash Commit: 2b0fbe80ebc8814d2d6bba8bae0dcab9922a418d https://github.com/galaxyproject/galaxy/commit/2b0fbe80ebc8814d2d6bba8bae0dc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js M client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Client formatting. Commit: 73486849e03f3bbe6daaebd7953b39a6b3a65d67 https://github.com/galaxyproject/galaxy/commit/73486849e03f3bbe6daaebd7953b3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Fix scratchbook link click function, remove some unused vars. Commit: 1e9c8cf57a7f9a3978416bc0ba706f0cd7a858fd https://github.com/galaxyproject/galaxy/commit/1e9c8cf57a7f9a3978416bc0ba706... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/chart.js Log Message: ----------- Extend instead of overwrite window.bundleEntries Commit: 2b0074be26c725a708aa4150ac7e723b86889ee9 https://github.com/galaxyproject/galaxy/commit/2b0074be26c725a708aa4150ac7e7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js M client/galaxy/scripts/mvc/visualization/visualization-view.js Log Message: ----------- Remove unused imports, vars, some minor refactoring for clarity. Commit: 039bdfb2d460fc3dc0b01d1cf2d601e9270e8378 https://github.com/galaxyproject/galaxy/commit/039bdfb2d460fc3dc0b01d1cf2d60... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-thumbnails.js Log Message: ----------- Minor var cleanup in ui-thumbnails Commit: 172f9317d2c25246a04f0297347d1ce08a9420b6 https://github.com/galaxyproject/galaxy/commit/172f9317d2c25246a04f0297347d1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/editor.js Log Message: ----------- Minor refactoring trying to fix chart viz launch Commit: 660df78c7cb2d4e8858686191d54788e43bfa7aa https://github.com/galaxyproject/galaxy/commit/660df78c7cb2d4e8858686191d547... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/package.json Log Message: ----------- Grunt is not used here Commit: 04c71f33e3f802233da60ae1eab333c82bb5ba42 https://github.com/galaxyproject/galaxy/commit/04c71f33e3f802233da60ae1eab33... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/package.json R config/plugins/visualizations/nvd3_bar/static/plugin/nv.d3.css R config/plugins/visualizations/nvd3_bar/static/plugin/nv.d3.js R config/plugins/visualizations/nvd3_bar/webpack.config.js Log Message: ----------- Incremental step swapping to parcel for viz building -- simpler, faster, zero config (ish). Commit: 65590f1350245753f04fcc132775fef54d86b172 https://github.com/galaxyproject/galaxy/commit/65590f1350245753f04fcc132775f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- nvd3 formatting Commit: 939bbff6d81fcde264323819f548efcadac9b463 https://github.com/galaxyproject/galaxy/commit/939bbff6d81fcde264323819f548e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3_bar/dist/nvd3.js A config/plugins/visualizations/nvd3_bar/package-lock.json M config/plugins/visualizations/nvd3_bar/package.json M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Add a few package dependencies, convert to es6 imports, and build to dist. Commit: ae0da08047a06231578de3ec98e8e7662c7c03a5 https://github.com/galaxyproject/galaxy/commit/ae0da08047a06231578de3ec98e8e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R config/plugins/visualizations/nvd3_bar/package-lock.json Log Message: ----------- Remove package-lock Commit: d9c445796f43dc1a2d1d811c21d50915eac40f78 https://github.com/galaxyproject/galaxy/commit/d9c445796f43dc1a2d1d811c21d50... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/dist/nvd3.js M config/plugins/visualizations/nvd3_bar/package.json Log Message: ----------- transpile es6 for nvd3 Commit: 5848c991caf5dd271d16cb346d286b6c1e1f0a58 https://github.com/galaxyproject/galaxy/commit/5848c991caf5dd271d16cb346d286... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3_bar/.babelrc Log Message: ----------- Add .babelrc with env preset. Commit: 3329bf8907410b7eb8fec45a40fa5ce3072d0c38 https://github.com/galaxyproject/galaxy/commit/3329bf8907410b7eb8fec45a40fa5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/dist/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Add d3 for correct imports in nvd3 chart Commit: f65d42d4fd298ed34110425f88523d868b94b834 https://github.com/galaxyproject/galaxy/commit/f65d42d4fd298ed34110425f88523... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/scatterplot/package.json 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 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 Log Message: ----------- Initial parcel building for scatterplot Commit: b6b31e0853bc486065fd3d7b917aa80fdbde18ff https://github.com/galaxyproject/galaxy/commit/b6b31e0853bc486065fd3d7b917aa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R config/plugins/visualizations/scatterplot/webpack.config.js Log Message: ----------- Remove unused webpack config Commit: 16405ce19aa14c5a2a744fc3d0d15cd03bc5c385 https://github.com/galaxyproject/galaxy/commit/16405ce19aa14c5a2a744fc3d0d15... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js Log Message: ----------- Directly export charts client as view Commit: 8518432e265ed90b377409d621b5b64170fd86d3 https://github.com/galaxyproject/galaxy/commit/8518432e265ed90b377409d621b5b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/package.json Log Message: ----------- Move packed nvd3 build to static directory Commit: 49618cf061f1873d2e5c83f4771ef1b7951aa33b https://github.com/galaxyproject/galaxy/commit/49618cf061f1873d2e5c83f4771ef... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3_bar/package.json M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Remove require libs from common mako endpoint Commit: a0ad05494cbe109a58932b1a51cfc814719093e1 https://github.com/galaxyproject/galaxy/commit/a0ad05494cbe109a58932b1a51cfc... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3_bar/static/utilities/tabular-datasets.js M config/plugins/visualizations/nvd3_bar/static/utilities/tabular-utilities.js M config/plugins/visualizations/nvd3_bar/static/utilities/utils.js M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Load nvd3 plugins into bundle Commit: be3d22215c6b91d8d1111a525663c32eb7b1bdd1 https://github.com/galaxyproject/galaxy/commit/be3d22215c6b91d8d1111a525663c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/nvd3_bar/config/nvd3_shared.xml Log Message: ----------- Fix Commit: ebb8f05c6d99ecb6d151c5b83b470f7b7bea5f8c https://github.com/galaxyproject/galaxy/commit/ebb8f05c6d99ecb6d151c5b83b470... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3_bar/package.json A config/plugins/visualizations/nvd3_bar/src/utilities/datasets.js A config/plugins/visualizations/nvd3_bar/src/utilities/helpers.js A config/plugins/visualizations/nvd3_bar/src/utilities/jobs.js A config/plugins/visualizations/nvd3_bar/src/utilities/utils.js R config/plugins/visualizations/nvd3_bar/static/utilities/jobs.js R config/plugins/visualizations/nvd3_bar/static/utilities/tabular-datasets.js R config/plugins/visualizations/nvd3_bar/static/utilities/tabular-utilities.js R config/plugins/visualizations/nvd3_bar/static/utilities/utils.js Log Message: ----------- Fixes for nvd3 viewer, import styles, link entry function Commit: f9107934b8373aac40673bcfe91233f1c48677c5 https://github.com/galaxyproject/galaxy/commit/f9107934b8373aac40673bcfe9123... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/chart.js A client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js A client/galaxy/scripts/mvc/visualization/chart/utilities/helpers.js A client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js A client/galaxy/scripts/mvc/visualization/chart/utilities/utils.js R config/plugins/visualizations/nvd3_bar/src/utilities/datasets.js R config/plugins/visualizations/nvd3_bar/src/utilities/helpers.js R config/plugins/visualizations/nvd3_bar/src/utilities/jobs.js R config/plugins/visualizations/nvd3_bar/src/utilities/utils.js Log Message: ----------- Prepare shared chart utility features Commit: 21e065052e714acc4708c94cc0b8923ab55160ca https://github.com/galaxyproject/galaxy/commit/21e065052e714acc4708c94cc0b89... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R client/galaxy/scripts/mvc/visualization/chart/utilities/utils.js Log Message: ----------- Remove unused utils helper Commit: 2b3c517161f701bfcf2a549ee3dbf03c5a7e4598 https://github.com/galaxyproject/galaxy/commit/2b3c517161f701bfcf2a549ee3dbf... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/package.json A config/plugins/visualizations/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- D3 / NVD3 compatability changes, use from node_modules. Still need to add zoom customization. Commit: dea41ef60c245f8bc4dbe25a8f85c9d03c95c586 https://github.com/galaxyproject/galaxy/commit/dea41ef60c245f8bc4dbe25a8f85c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/common/templates/chart_entry_point.mako Log Message: ----------- Drop d3 from inline chart_entry_point libs; we should look at the rest of these, too, probably. Commit: 2683cc527550dfc27fae0885efc4ac9615302772 https://github.com/galaxyproject/galaxy/commit/2683cc527550dfc27fae0885efc4a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/nvd3_bar/static/nvd3.css Log Message: ----------- Add bundled nvd3 css; this got dropped during rebases. Commit: df90cc78addf1b2adc711347c54c399373f241c2 https://github.com/galaxyproject/galaxy/commit/df90cc78addf1b2adc711347c54c3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/src/nvd3.js Log Message: ----------- Fix tooltips to use new nvd3 chart generator. Commit: 62e4e0da8664490b20e3b090bd211d1cc3fe40d4 https://github.com/galaxyproject/galaxy/commit/62e4e0da8664490b20e3b090bd211... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/helpers.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- Client cleanup, no functional change. Commit: fa3d12a33cb6185cd9988a9e9d74d16993510995 https://github.com/galaxyproject/galaxy/commit/fa3d12a33cb6185cd9988a9e9d74d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R config/plugins/visualizations/nvd3_bar/dist/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Build final nvd3.js with included deps Commit: 719383fbea2d7cadf347967fb40e344a6be46e94 https://github.com/galaxyproject/galaxy/commit/719383fbea2d7cadf347967fb40e3... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/package.json M config/plugins/visualizations/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Fix y-axis label for nvd3, fix duration Commit: 525bc13d8dadbf5164f60967bdd2f01c2fc13ef6 https://github.com/galaxyproject/galaxy/commit/525bc13d8dadbf5164f60967bdd2f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3_scatter/config/nvd3_scatter.xml Log Message: ----------- Add entry function for scatter plot Commit: 171dcc1e24f84c2f7818105ec29788d767ce1aac https://github.com/galaxyproject/galaxy/commit/171dcc1e24f84c2f7818105ec2978... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Add zooming feature Commit: 21fb51782cc38e8ead0833417cf4bf0f6d091b73 https://github.com/galaxyproject/galaxy/commit/21fb51782cc38e8ead0833417cf4b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Remove duration, interference with zooming Commit: 159a8c72bc69c8c19d4dd6e039d801a6740d4921 https://github.com/galaxyproject/galaxy/commit/159a8c72bc69c8c19d4dd6e039d80... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/src/nvd3.js Log Message: ----------- Add another fallback value for tooltips Commit: de7cac90537b4bd9fa9500cb55b314408a5a1f06 https://github.com/galaxyproject/galaxy/commit/de7cac90537b4bd9fa9500cb55b31... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml Log Message: ----------- Remove zoomable flag for barcharts Commit: 00a105ef6a28add188b9356572e89392b3517099 https://github.com/galaxyproject/galaxy/commit/00a105ef6a28add188b9356572e89... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js R client/galaxy/scripts/mvc/visualization/chart/utilities/helpers.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M config/plugins/visualizations/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3_bar/static/nvd3.js Log Message: ----------- Revise shared utilities Commit: 91c4641c886c1f1015218abb34f541aff7a82bdd https://github.com/galaxyproject/galaxy/commit/91c4641c886c1f1015218abb34f54... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: 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 R config/plugins/visualizations/nvd3_bar/.babelrc R config/plugins/visualizations/nvd3_bar/config/nvd3_bar.xml R config/plugins/visualizations/nvd3_bar/config/nvd3_shared.xml R config/plugins/visualizations/nvd3_bar/package.json R config/plugins/visualizations/nvd3_bar/src/nvd3.js R config/plugins/visualizations/nvd3_bar/static/logo.png R config/plugins/visualizations/nvd3_bar/static/nvd3.css R config/plugins/visualizations/nvd3_bar/static/nvd3.js R config/plugins/visualizations/nvd3_bar_stacked/config/nvd3_bar_stacked.xml R config/plugins/visualizations/nvd3_bar_stacked/static/logo.png M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Allow plugins to be placed into first level sub directories Commit: 055e0fa167d77c94c03166bea65fe432867af226 https://github.com/galaxyproject/galaxy/commit/055e0fa167d77c94c03166bea65fe... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml 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 R config/plugins/visualizations/nvd3_histogram/config/nvd3_histogram.xml R config/plugins/visualizations/nvd3_histogram/static/logo.png R config/plugins/visualizations/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml R config/plugins/visualizations/nvd3_histogram_discrete/static/logo.png R config/plugins/visualizations/nvd3_horizontal/config/nvd3_horizontal.xml R config/plugins/visualizations/nvd3_horizontal/static/logo.png R config/plugins/visualizations/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml R config/plugins/visualizations/nvd3_horizontal_stacked/static/logo.png R config/plugins/visualizations/nvd3_line/config/nvd3_line.xml R config/plugins/visualizations/nvd3_line/static/logo.png R config/plugins/visualizations/nvd3_line_focus/config/nvd3_line_focus.xml R config/plugins/visualizations/nvd3_line_focus/static/logo.png R config/plugins/visualizations/nvd3_pie/config/nvd3_pie.xml R config/plugins/visualizations/nvd3_pie/static/logo.png R config/plugins/visualizations/nvd3_scatter/config/nvd3_scatter.xml R config/plugins/visualizations/nvd3_scatter/static/logo.png R config/plugins/visualizations/nvd3_stackedarea/config/nvd3_stackedarea.xml R config/plugins/visualizations/nvd3_stackedarea/static/logo.png R config/plugins/visualizations/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml R config/plugins/visualizations/nvd3_stackedarea_full/static/logo.png R config/plugins/visualizations/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml R config/plugins/visualizations/nvd3_stackedarea_stream/static/logo.png Log Message: ----------- Move nvd3 plugins into subdirectory Commit: 83467ca9efa5266c9968be5a598fb5fdd5c3c82e https://github.com/galaxyproject/galaxy/commit/83467ca9efa5266c9968be5a598fb... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml Log Message: ----------- Fix remaining nvd3 plugins Commit: 1014b5d5d31232212946e781fd92745133fe5865 https://github.com/galaxyproject/galaxy/commit/1014b5d5d31232212946e781fd927... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M config/plugins/visualizations/common/templates/chart_entry_point.mako A config/plugins/visualizations/ngl/config/ngl.xml 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 Log Message: ----------- Add ngl viewer Commit: b33ec3b3ca9cf346ae07673d60178d5fff2e7c79 https://github.com/galaxyproject/galaxy/commit/b33ec3b3ca9cf346ae07673d60178... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/ngl/package.json 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 Log Message: ----------- Add pv protein viewer Commit: 43d45dfee465e55657cbd3c4058541146b03aadf https://github.com/galaxyproject/galaxy/commit/43d45dfee465e55657cbd3c405854... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: 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 Log Message: ----------- Add venn diagram Commit: 97cab84b0846342f7d723203172f9c697af6066b https://github.com/galaxyproject/galaxy/commit/97cab84b0846342f7d723203172f9... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: 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 Log Message: ----------- Add biojs msa Commit: 820d0b4135e528ce3127daae6fc5d45b0e55dee3 https://github.com/galaxyproject/galaxy/commit/820d0b4135e528ce3127daae6fc5d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/drawrna/config/drawrna.xml A config/plugins/visualizations/drawrna/package.json A config/plugins/visualizations/drawrna/src/drawrnajs/drawrna.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/layout.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/base.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/connection.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/getnaview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/loop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/naview.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/radloop.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/region.js A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/radiate/getradiate.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/link.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/linkcol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/ncanno.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residue.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/residuecol.js A config/plugins/visualizations/drawrna/src/drawrnajs/models/structure.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/.Rhistory A config/plugins/visualizations/drawrna/src/drawrnajs/utils/lasso.js A config/plugins/visualizations/drawrna/src/drawrnajs/utils/parsedbr.js A 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 Log Message: ----------- Add drawrna, with existing code until npm dependency works Commit: c4ca8aba1ff56a540662eba7cefb3c25c9718180 https://github.com/galaxyproject/galaxy/commit/c4ca8aba1ff56a540662eba7cefb3... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/drawrna/static/script.js 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 Log Message: ----------- Add phylocanvas, using npm module Commit: d834a3c96865a6b74e1a4c2ce9b692e22d0b65aa https://github.com/galaxyproject/galaxy/commit/d834a3c96865a6b74e1a4c2ce9b69... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/cytoscape/config/cytoscape.xml A config/plugins/visualizations/cytoscape/package.json A config/plugins/visualizations/cytoscape/src/script.js A config/plugins/visualizations/cytoscape/static/logo.png A config/plugins/visualizations/cytoscape/static/script.js Log Message: ----------- Add cytoscape Commit: bedbd06a3983b27e9dc44ab07c5df3cfbd5cfc94 https://github.com/galaxyproject/galaxy/commit/bedbd06a3983b27e9dc44ab07c5df... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: 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 Log Message: ----------- Add jqplot bar Commit: a19088a68c8d361d39f9b1f9df46de96139ca477 https://github.com/galaxyproject/galaxy/commit/a19088a68c8d361d39f9b1f9df46d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml Log Message: ----------- Remove color picker for jqplot Commit: 4f9e0d92394d4b7b5a3e39505a0e52ffc6a7464e https://github.com/galaxyproject/galaxy/commit/4f9e0d92394d4b7b5a3e39505a0e5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml Log Message: ----------- Add legend option to tabular plugins Commit: a770cbcea305aa98d5d4d0583fa5d4de537a580b https://github.com/galaxyproject/galaxy/commit/a770cbcea305aa98d5d4d0583fa5d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/jqplot/jqplot_bar/src/script.js M 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 Log Message: ----------- Add remaining jqplot plugins Commit: 35ac99bfe5bccb103965f4f2d73a670a2b04dd80 https://github.com/galaxyproject/galaxy/commit/35ac99bfe5bccb103965f4f2d73a6... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml A config/plugins/visualizations/heatmap/heatmap_cluster/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml A config/plugins/visualizations/heatmap/heatmap_default/package.json A config/plugins/visualizations/heatmap/heatmap_default/src/colorsets.js A config/plugins/visualizations/heatmap/heatmap_default/src/script.js A config/plugins/visualizations/heatmap/heatmap_default/static/logo.png A config/plugins/visualizations/heatmap/heatmap_default/static/script.js Log Message: ----------- Add heatmap plugin Commit: 7f896c84d76ef9879aa70227e15dea6c9390f573 https://github.com/galaxyproject/galaxy/commit/7f896c84d76ef9879aa70227e15de... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_default/package.json Log Message: ----------- Use version 3 of d3 for heatmap Commit: e829579be3e34e6f0ff1c15327959e818f34cad8 https://github.com/galaxyproject/galaxy/commit/e829579be3e34e6f0ff1c15327959... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A config/plugins/visualizations/example/config/config.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 Log Message: ----------- Add example plugin Commit: adea33ad935e641ac8acca1646c1e035fd0b9ed8 https://github.com/galaxyproject/galaxy/commit/adea33ad935e641ac8acca1646c1e... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: R config/plugins/visualizations/example/config/config.js M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/example/package.json M config/plugins/visualizations/example/src/script.js M config/plugins/visualizations/example/static/script.js Log Message: ----------- Fix example Commit: a64b0835a23019995617f4c8679e4d293777b24c https://github.com/galaxyproject/galaxy/commit/a64b0835a23019995617f4c8679e4... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js M config/plugins/visualizations/example/config/example.xml Log Message: ----------- Fix vis saving Commit: 75b9d5f00487c124327ab73c1e7051e8f4a2d1cf https://github.com/galaxyproject/galaxy/commit/75b9d5f00487c124327ab73c1e705... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js Log Message: ----------- Load visualization with default values into the viewer before displaying editor Commit: 3df3f6fe02916f310a901e5dda7b16d64c65ee72 https://github.com/galaxyproject/galaxy/commit/3df3f6fe02916f310a901e5dda7b1... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-thumbnails.js A client/galaxy/scripts/mvc/visualization/chart/utilities/series.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/style/less/ui.less Log Message: ----------- Load visualization on single click, highlight on hover, add series module Commit: 0f3aacdd919dd2a3d12702d522ed62e652e5ffe3 https://github.com/galaxyproject/galaxy/commit/0f3aacdd919dd2a3d12702d522ed6... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix highlighting for suggested thumbnails Commit: 67e911b4be3b5d6b1fee686bab3928fd71332ea4 https://github.com/galaxyproject/galaxy/commit/67e911b4be3b5d6b1fee686bab392... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/style/less/ui.less Log Message: ----------- Remove highlighting Commit: ff84aa42706621fee4a6658745bb0fa1a19c19e1 https://github.com/galaxyproject/galaxy/commit/ff84aa42706621fee4a6658745bb0... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/cytoscape/config/cytoscape.xml M config/plugins/visualizations/cytoscape/src/script.js M config/plugins/visualizations/drawrna/src/script.js M static/style/blue/base.css Log Message: ----------- Use default load function for chart plugins Commit: 77340dded76f75148450c1bdcf47f356a770d330 https://github.com/galaxyproject/galaxy/commit/77340dded76f75148450c1bdcf47f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/cytoscape/static/script.js M config/plugins/visualizations/drawrna/static/script.js M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/example/static/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/ngl/src/ngl.js M config/plugins/visualizations/ngl/static/ngl.js M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/phylocanvas/src/script.js M config/plugins/visualizations/pv/config/pv.xml M config/plugins/visualizations/pv/src/pv.js M config/plugins/visualizations/pv/static/pv.js M config/plugins/visualizations/venn/config/venn.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js Log Message: ----------- Use default load handler Commit: 1afea3eec0c94d0d4bac660ac5674f7d6855b102 https://github.com/galaxyproject/galaxy/commit/1afea3eec0c94d0d4bac660ac5674... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/drawrna/config/drawrna.xml Log Message: ----------- Fix drawrnajs caller Commit: a6529c51d3ca0b0554e1bc4cebf7fdd8383288c7 https://github.com/galaxyproject/galaxy/commit/a6529c51d3ca0b0554e1bc4cebf7f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M config/plugins/visualizations/common/templates/chart_entry_point.mako Log Message: ----------- Show viewer before initiating load process Commit: 3a0c8b5634f1af656ad5c87a1181d030cae33a8c https://github.com/galaxyproject/galaxy/commit/3a0c8b5634f1af656ad5c87a1181d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Check len of tree elements Commit: 82a1f6e49e016372aa1a5a615f305900953bdd88 https://github.com/galaxyproject/galaxy/commit/82a1f6e49e016372aa1a5a615f305... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js Log Message: ----------- Improve resilience of dataset loader Commit: cea4db4a53ca25d4d92a9bed2b181cee65d838d7 https://github.com/galaxyproject/galaxy/commit/cea4db4a53ca25d4d92a9bed2b181... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js Log Message: ----------- Fix visualization name parsing when saving visualizations Commit: 4af913f7dfb55e1ddc028296063d1cab046cf956 https://github.com/galaxyproject/galaxy/commit/4af913f7dfb55e1ddc028296063d1... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M test/api/test_visualizations.py Log Message: ----------- Fix visualization type Commit: 3c7b621b3b320d98025caa7981c70afe864c472f https://github.com/galaxyproject/galaxy/commit/3c7b621b3b320d98025caa7981c70... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml Log Message: ----------- Fix entry function specifier for heatmaps Commit: 2507034e936db38024a8b9f70a359d3f28c94e1c https://github.com/galaxyproject/galaxy/commit/2507034e936db38024a8b9f70a359... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Remove unused components from config parser Commit: a77cf155e66cecaf2aaa3bcdf87a6c2bae236b63 https://github.com/galaxyproject/galaxy/commit/a77cf155e66cecaf2aaa3bcdf87a6... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Fix spacing Commit: e2d339936cb229096ab7e502831a2e90187cdd25 https://github.com/galaxyproject/galaxy/commit/e2d339936cb229096ab7e502831a2... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/qunit/tests/ui_tests.js Log Message: ----------- Fix tests Commit: 8f2f7e088a24f7541d07ca630714636a563d57e6 https://github.com/galaxyproject/galaxy/commit/8f2f7e088a24f7541d07ca6307146... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/page.js M templates/js-app.mako Log Message: ----------- Add embedding features to analysis app Commit: 6b21b258311c3cb923ea40fa374e1e9cb908639d https://github.com/galaxyproject/galaxy/commit/6b21b258311c3cb923ea40fa374e1... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/layout/page.js Log Message: ----------- Fix page template Commit: a109ca9e9bc9b77738acb0438406d7f07e1997dd https://github.com/galaxyproject/galaxy/commit/a109ca9e9bc9b77738acb0438406d... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/layout/page.js Log Message: ----------- Fix panel hiding options Commit: 50c8cb382618f4ac587439154c7f2bd8afb9d161 https://github.com/galaxyproject/galaxy/commit/50c8cb382618f4ac587439154c7f2... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Parse panel hiding options for scratchbook embedding Commit: 3ba5b2816ca2c33874c52dc48dfceaf32530e6b0 https://github.com/galaxyproject/galaxy/commit/3ba5b2816ca2c33874c52dc48dfce... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Fix scratchbook parameter parsing Commit: cb5c30c32ae42ff6d122c395d8fe50fac559aa88 https://github.com/galaxyproject/galaxy/commit/cb5c30c32ae42ff6d122c395d8fe5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-view.js M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml Log Message: ----------- Sort visualizations alphabetically Commit: c09d9c81b46e60a65b08840ac1cd52287c1cea9d https://github.com/galaxyproject/galaxy/commit/c09d9c81b46e60a65b08840ac1cd5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml Log Message: ----------- Fix horizontal bar diagram settings Commit: c132eb1c325802134cb40bd7b3f02811679b7671 https://github.com/galaxyproject/galaxy/commit/c132eb1c325802134cb40bd7b3f02... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Fix msa configuration settings Commit: 8c6b6b42a66da9fcc4c8747e1a8e850b22ed4033 https://github.com/galaxyproject/galaxy/commit/8c6b6b42a66da9fcc4c8747e1a8e8... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/phylocanvas/static/script.js Log Message: ----------- Fix phylocanvas loader Commit: 6c5fa30128fabbc9274f39e42396c354ebbd332b https://github.com/galaxyproject/galaxy/commit/6c5fa30128fabbc9274f39e42396c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix hovering styles Commit: 45b9e9529fbb9934c732549f0d767f40964d8b65 https://github.com/galaxyproject/galaxy/commit/45b9e9529fbb9934c732549f0d767... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/viewport.js Log Message: ----------- New ui Commit: 0004d40be9990895f756fc8f164cec535caaa887 https://github.com/galaxyproject/galaxy/commit/0004d40be9990895f756fc8f164ce... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Hide unused tabs Commit: 8cf35768fdcf27301f4d739d66e967698ad5893d https://github.com/galaxyproject/galaxy/commit/8cf35768fdcf27301f4d739d66e96... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/style/less/charts.less M config/plugins/visualizations/common/templates/chart_entry_point.mako M static/style/blue/base.css Log Message: ----------- Fix margins, refactor app Commit: 269be966a9da235d94d3058b7786c2326697b8c6 https://github.com/galaxyproject/galaxy/commit/269be966a9da235d94d3058b7786c... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Add editor buttons Commit: 79fc30c8e49238792abcdc7e9b9299b313a09639 https://github.com/galaxyproject/galaxy/commit/79fc30c8e49238792abcdc7e9b929... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Avoid settings reload on visualization refresh Commit: c30a3806a25253ea8ca5bf4a3c7d166d16c2e462 https://github.com/galaxyproject/galaxy/commit/c30a3806a25253ea8ca5bf4a3c7d1... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Add transparent operation buttons Commit: 77813a7aecebf05ab086659d434b5ca2624cb466 https://github.com/galaxyproject/galaxy/commit/77813a7aecebf05ab086659d434b5... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js R client/galaxy/scripts/mvc/visualization/chart/views/viewport.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Add export options and message view Commit: b098ba7952d7db9028b2af503ddd9482ff99425f https://github.com/galaxyproject/galaxy/commit/b098ba7952d7db9028b2af503ddd9... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Fix styles and naming Commit: 2257c2ff172f665ebf5dd0e9b2343b0eb1ac9bfe https://github.com/galaxyproject/galaxy/commit/2257c2ff172f665ebf5dd0e9b2343... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Limit message width, fix icon styles Commit: 18773ebd8f7f0f8f87c1e5460bb5935742ff62fe https://github.com/galaxyproject/galaxy/commit/18773ebd8f7f0f8f87c1e5460bb59... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: A client/galaxy/scripts/mvc/visualization/chart/views/menu.js Log Message: ----------- Add menu options Commit: 72de8cc85fe1e8e6d667a858186cf6ca6d51ff73 https://github.com/galaxyproject/galaxy/commit/72de8cc85fe1e8e6d667a858186cf... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/description.js Log Message: ----------- Fix description style Commit: 4fa486082c2ee231fe09b584ed62a11d9146bdcd https://github.com/galaxyproject/galaxy/commit/4fa486082c2ee231fe09b584ed62a... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Fix margin style Commit: f2335fe46192187316458d785918b920b61cf293 https://github.com/galaxyproject/galaxy/commit/f2335fe46192187316458d785918b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js Log Message: ----------- Instantly refresh visualizations on setting changes Commit: 9ae6cb1c6e91ed6903b5955df859529ad9ea0a8f https://github.com/galaxyproject/galaxy/commit/9ae6cb1c6e91ed6903b5955df8595... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Fix config parser Commit: 0ff4f7419e7dfbd77c36fd2c362d9e3e8c5a4e89 https://github.com/galaxyproject/galaxy/commit/0ff4f7419e7dfbd77c36fd2c362d9... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Add label to scratchbook Commit: bd9167400e243392d29cefc235db3bde9bc8a2d8 https://github.com/galaxyproject/galaxy/commit/bd9167400e243392d29cefc235db3... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/style/less/charts.less M static/style/blue/base.css Log Message: ----------- Reduce top padding Commit: 0b30336c213207d58a8e4d24ec871da7289012b6 https://github.com/galaxyproject/galaxy/commit/0b30336c213207d58a8e4d24ec871... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js Log Message: ----------- Cleanup redrawing triggering, remove unused message handlers Commit: 491fa33e8572b5936a4706a25a43b8a58161215a https://github.com/galaxyproject/galaxy/commit/491fa33e8572b5936a4706a25a43b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/venn/config/venn.xml Log Message: ----------- Show list for all visualization types Commit: 39ad58066b6ebabc00657f7b0421f787c93a6570 https://github.com/galaxyproject/galaxy/commit/39ad58066b6ebabc00657f7b0421f... Author: guerler <aysam.guerler@gmail.com> Date: 2018-02-11 (Sun, 11 Feb 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- Repack style sheets Commit: 6d00958d43eab15bf2c94bc9088dfa5f162ce3c9 https://github.com/galaxyproject/galaxy/commit/6d00958d43eab15bf2c94bc9088df... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/tag_collection_from_file.xml A test-data/new_tags_1.txt M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5462 from mvdbeek/tag_collection_from_files Tool that adds/sets tags for collection elements from a file Commit: 2e51d0576a59c3400d1e107c6e85c0cecaba8c28 https://github.com/galaxyproject/galaxy/commit/2e51d0576a59c3400d1e107c6e85c... Author: Dave B <dave@bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Close tempfile handles. Commit: e13740a3f6f91a86af0b19ce5121b4bd7f628182 https://github.com/galaxyproject/galaxy/commit/e13740a3f6f91a86af0b19ce5121b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M Makefile Log Message: ----------- Drop short-lived 'make client-production' warning from build scripts, since we're not including these moving forward. Commit: e58aaef95997f37974a501e69c4c00fba80d72e8 https://github.com/galaxyproject/galaxy/commit/e58aaef95997f37974a501e69c4c0... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M Makefile Log Message: ----------- Merge pull request #5508 from dannon/no-more-client-commits Drop short-lived 'make client-production' warning from build scripts,… Commit: e6535d33bfd76d18d7904ad42dabb5835ca9c5b3 https://github.com/galaxyproject/galaxy/commit/e6535d33bfd76d18d7904ad42dabb... Author: Dave B <dave@bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Implement Nicola's suggestion for cleaner solution. Commit: 8fa28994fc38c82b873a295df59b937a5ad95a35 https://github.com/galaxyproject/galaxy/commit/8fa28994fc38c82b873a295df59b9... Author: Dave B <dave@bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Remove unnecessary try/catch. Commit: 201d76568f75eeeebde3b9e585f54dd14332fca7 https://github.com/galaxyproject/galaxy/commit/201d76568f75eeeebde3b9e585f54... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/tool_shed/tools/tool_validator.py M templates/webapps/galaxy/workflow/sharing.mako M test/unit/tools/test_tool_validation.py Log Message: ----------- Merge branch 'release_18.01' into dev Commit: 007ae8f9377666ab84599aee20fce2a63cc03fbc https://github.com/galaxyproject/galaxy/commit/007ae8f9377666ab84599aee20fce... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Default slow request tracking to disabled; this is only used in Galaxy and should fix TS/reports error. Commit: 39fd5fdc05e81918df322d1b84b444864d67174d https://github.com/galaxyproject/galaxy/commit/39fd5fdc05e81918df322d1b84b44... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-12 (Mon, 12 Feb 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Merge pull request #5513 from dannon/fix_non_gxy_sentry_middleware Default slow request tracking to disabled; Commit: 7663de745f5df827f7873960c9ec341eb88e86a2 https://github.com/galaxyproject/galaxy/commit/7663de745f5df827f7873960c9ec3... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/execute.py Log Message: ----------- Remove unused methods. Commit: 54659b085f78dabfc987d8292e6d4750ecc83dd7 https://github.com/galaxyproject/galaxy/commit/54659b085f78dabfc987d8292e6d4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/visualization/chart/chart-client.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/qunit/tests/ui_tests.js Log Message: ----------- Client format Commit: be7f503448a6ffd5f5a63d27e6c54601dd558271 https://github.com/galaxyproject/galaxy/commit/be7f503448a6ffd5f5a63d27e6c54... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/example/package.json M config/plugins/visualizations/example/src/script.js M config/plugins/visualizations/example/static/script.js Log Message: ----------- Fix example plugin imports Commit: 6c68e8e980c7155dee8389e25d90b25864aa2bd7 https://github.com/galaxyproject/galaxy/commit/6c68e8e980c7155dee8389e25d90b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: R config/plugins/visualizations/graphviz/static/js/jquery.qtip.js R config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js R config/plugins/visualizations/graphviz/static/js/tip_followscroll.js M config/plugins/visualizations/graphviz/templates/graphviz.mako Log Message: ----------- Graphviz cleanup Commit: 5d4301ab3c73de38125a43f3a5f3e0c38a0d28cd https://github.com/galaxyproject/galaxy/commit/5d4301ab3c73de38125a43f3a5f3e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar/package.json M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js Log Message: ----------- Fix imports in nvd3.js, include underscore in package bundle Commit: fafcfbb5774033098ca5a6745b86d97d7cc5e177 https://github.com/galaxyproject/galaxy/commit/fafcfbb5774033098ca5a6745b86d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js Log Message: ----------- Remove duplicate key for nvd3_line lineChart. Commit: a82f4a1ae10457071ffad01956f27dd74a8b5574 https://github.com/galaxyproject/galaxy/commit/a82f4a1ae10457071ffad01956f27... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar/package.json M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js Log Message: ----------- Document jquery entanglement Commit: 320f1fccac8daac11b5411d36c947b707857575b https://github.com/galaxyproject/galaxy/commit/320f1fccac8daac11b5411d36c947... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_default/src/script.js Log Message: ----------- Incremental cleanup in heatmap default viz Commit: 997e31b88100ef38294632bf138c5994fd006316 https://github.com/galaxyproject/galaxy/commit/997e31b88100ef38294632bf138c5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_default/src/script.js Log Message: ----------- More heatmap cleanup, trying to fix heatmap_cluster Commit: 15d8afeddd3d7b1cd19595a1af2e7c3d275cc24c https://github.com/galaxyproject/galaxy/commit/15d8afeddd3d7b1cd19595a1af2e7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_default/package.json M config/plugins/visualizations/heatmap/heatmap_default/src/script.js M config/plugins/visualizations/heatmap/heatmap_default/static/script.js Log Message: ----------- Swap d3-3 back to d3 with a version pin. Commit: d5c089acc7467d9dd218485acb9f8c02594f9cff https://github.com/galaxyproject/galaxy/commit/d5c089acc7467d9dd218485acb9f8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/chart-client.js Log Message: ----------- Remove unused import, add required backbone import, document $, Galaxy globals Commit: cd1ed9bb56ecaff61b09e48f183f3bf3f93595b9 https://github.com/galaxyproject/galaxy/commit/cd1ed9bb56ecaff61b09e48f183f3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/components/model.js Log Message: ----------- Add backbone import to components/model in viz Commit: c18eafce90fd247e914c922561017198f6ab3a0c https://github.com/galaxyproject/galaxy/commit/c18eafce90fd247e914c922561017... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js Log Message: ----------- Fix some conflicting var defs (use let for scope control) in chart utils Commit: 13c40b1cffaf26b05468a00baa36f7e5b35df0a8 https://github.com/galaxyproject/galaxy/commit/13c40b1cffaf26b05468a00baa36f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- Cleanup in viz/utils/jobs, clarify scope in a few places and remove unused vars Commit: e9b26b4bd00052d8b75578a30f1aee7cc2f6be1a https://github.com/galaxyproject/galaxy/commit/e9b26b4bd00052d8b75578a30f1ae... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js Log Message: ----------- Document conflicting global d3 in series, minor refactoring. Commit: 8a721f6f37741d07fbe709112fa03c51b4697a49 https://github.com/galaxyproject/galaxy/commit/8a721f6f37741d07fbe709112fa03... Author: Nuwan Goonasekera <nuwan.ag@gmail.com> Date: 2018-02-13 (Tue, 13 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- Fix for: https://github.com/galaxyproject/galaxy/issues/5527 Commit: 83cf06e3614b5463e3aaac74f314e3d04ad46f9a https://github.com/galaxyproject/galaxy/commit/83cf06e3614b5463e3aaac74f314e... Author: anup kumar <anup.rulez@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Fix the bug Commit: 5b66429cb44836b1a56fb76c5e644b814ef5fd5c https://github.com/galaxyproject/galaxy/commit/5b66429cb44836b1a56fb76c5e644... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M config/plugins/visualizations/heatmap/heatmap_default/static/script.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js Log Message: ----------- Rebuild heatmap, nvd3 after refactoring. Commit: 25952e81e7cc7c2985379f039915d40bc8142d98 https://github.com/galaxyproject/galaxy/commit/25952e81e7cc7c2985379f039915d... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Map static content by default for Reports and Tool Shed webapps. Commit: 0b137669d7d2d8df2c63a6436ddb812001a82327 https://github.com/galaxyproject/galaxy/commit/0b137669d7d2d8df2c63a6436ddb8... 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config/plugins/visualizations/scatterplot/src/worker-stats.js A config/plugins/visualizations/scatterplot/static/8850628034555be072a0e4f882d4d8e5.js 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 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 lib/galaxy/util/xml_macros.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py R static/scripts/packed M static/style/blue/base.css M templates/js-app.mako M test/api/test_visualizations.py Log Message: ----------- Merge pull request #5505 from guerler/revise_charts_ui Integration of charts into the generic visualization framework Commit: 043fe35e9521c20987cd995de90aaf1f01e94e63 https://github.com/galaxyproject/galaxy/commit/043fe35e9521c20987cd995de90aa... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/onload.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/workflows.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 lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_18.01' into dev_merge_0 Commit: 3de8593e19641ad1078dbb53a870876ec32c80e1 https://github.com/galaxyproject/galaxy/commit/3de8593e19641ad1078dbb53a8708... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M client/galaxy/scripts/onload.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/mapping.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/workflows.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 lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #5540 from jmchilton/dev_merge_0 Merge release_18.01 into dev. Commit: 99e1305c53cde3f0244819fe495655ec61f13a9a https://github.com/galaxyproject/galaxy/commit/99e1305c53cde3f0244819fe49565... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-14 (Wed, 14 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Rev SQLAlchemy from 1.0.15 to 1.2.2. It'd be nice to use [selectinload](http://docs.sqlalchemy.org/en/latest/orm/loading_relationships.html#sqlalche...) when optimizing postgres calls. xref https://github.com/galaxyproject/starforge/pull/191 Commit: aed2b4a239ebbcd4081426599023867eed94f63b https://github.com/galaxyproject/galaxy/commit/aed2b4a239ebbcd40814265990238... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py Log Message: ----------- remove unused import Commit: a35d5a535eebb36d647353faac66c37417a8aeb7 https://github.com/galaxyproject/galaxy/commit/a35d5a535eebb36d647353faac66c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #5538 from jmchilton/rev_sqlalchemy Rev SQLAlchemy from 1.0.15 to 1.2.2. Commit: 41a31967540e74857c25257ec8cc738900cbad6c https://github.com/galaxyproject/galaxy/commit/41a31967540e74857c25257ec8cc7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/tools/repositories.py Log Message: ----------- Merge pull request #5506 from davebx/close_temp_files Close tempfile handles. Commit: 78ee5f8451e022515e75e9ca5888bf598d2d3414 https://github.com/galaxyproject/galaxy/commit/78ee5f8451e022515e75e9ca5888b... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #5450 from jmchilton/collection_mapping_cleanup Remove unused mapping code. Commit: 298ef7ee1951cf64fe42b4cc44ce83b4257aace6 https://github.com/galaxyproject/galaxy/commit/298ef7ee1951cf64fe42b4cc44ce8... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/tool/tool-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- Merge pull request #5528 from gvlproject/genomespace_18.01_bugfix Fix for GenomeSpace importer/exporter Commit: 92826fe5e763a0938cf4710955be4d1e4e5cf967 https://github.com/galaxyproject/galaxy/commit/92826fe5e763a0938cf4710955be4... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Merge pull request #5531 from bgruening/bugfix_#5522 Fix search overlay JS errors Commit: a54681e8c67c3bc9b1dff993a1445c23d87275dd https://github.com/galaxyproject/galaxy/commit/a54681e8c67c3bc9b1dff993a1445... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M doc/source/conf.py A doc/source/conf.versioning.py Log Message: ----------- Merge pull request #5334 from natefoo/doc-versioning Documentation version selection Commit: f7b505e68dad6cee53ba884dce258f659d7da33a https://github.com/galaxyproject/galaxy/commit/f7b505e68dad6cee53ba884dce258... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-15 (Thu, 15 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_variables.less M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/history.py A test/functional/tools/fail_writing_work_dir_file.xml M test/functional/tools/samples_tool_conf.xml M test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge branch 'release_18.01' into dev Commit: d30811eea38f3bb535d52cb86dbb0db0aca5009d https://github.com/galaxyproject/galaxy/commit/d30811eea38f3bb535d52cb86dbb0... Author: Matthias Bernt <m.bernt@ufz.de> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- fixed stale link Commit: c9c2e968daba29d15e574f148bbdcb06ee59ce3f https://github.com/galaxyproject/galaxy/commit/c9c2e968daba29d15e574f148bbdc... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #5548 from bernt-matthias/topic/fix-obo-link fixed stale link Commit: 13e72e84c523bda22bda792bbebf4720d28542d5 https://github.com/galaxyproject/galaxy/commit/13e72e84c523bda22bda792bbebf4... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Merge pull request #5534 from natefoo/17.09-static-map-fix [17.09] Map static content by default for Reports and Tool Shed webapps Commit: 0d029b39ac9ae6bc21a6c1834fe6e05280d8e0d0 https://github.com/galaxyproject/galaxy/commit/0d029b39ac9ae6bc21a6c1834fe6e... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/reports.yml.sample M config/tool_shed.yml.sample Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: 19eee525a166b6c9abf03e5a91fd69a356447c20 https://github.com/galaxyproject/galaxy/commit/19eee525a166b6c9abf03e5a91fd6... Author: nekrut <anton@nekrut.org> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- added fasta.gz Commit: 0c2c9ba49e70f19cd4ec9f4c93bf19af14fa348e https://github.com/galaxyproject/galaxy/commit/0c2c9ba49e70f19cd4ec9f4c93bf1... Author: nekrut <anton@nekrut.org> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- fixed flake8 errors Commit: 84e818577a162b507fa4f1a69006fdee20ad8e5f https://github.com/galaxyproject/galaxy/commit/84e818577a162b507fa4f1a69006f... Author: nekrut <anton@nekrut.org> Date: 2018-02-16 (Fri, 16 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- removing stray whitespace Commit: 5e6a2572f8bfabd6c674ff218d8a3ee1f9f22615 https://github.com/galaxyproject/galaxy/commit/5e6a2572f8bfabd6c674ff218d8a3... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Allow LDAP options not starting with OPT_ Fix https://github.com/galaxyproject/galaxy/issues/5486 Commit: d964d594a5314b85def7676f5ae39c949420f4f0 https://github.com/galaxyproject/galaxy/commit/d964d594a5314b85def7676f5ae39... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- [18.01] Do not reload page when deleting collections. Fixes #5499 reported by @mvdbeek (thanks for catching that). Commit: 4390cd4142605efbf062126fdf0082940d7dfe30 https://github.com/galaxyproject/galaxy/commit/4390cd4142605efbf062126fdf008... Author: nekrut <anton@nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/fastagz_to_fasta.xml Log Message: ----------- fixed name of fastagz->fasta converter Commit: 6359262b3ce3632bd859278201bcd9e6e893fba9 https://github.com/galaxyproject/galaxy/commit/6359262b3ce3632bd859278201bcd... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/fastagz_to_fasta.xml Log Message: ----------- fix copypasta Commit: 55a405f18a1b493c7e0249f8e56b12b254603d3c https://github.com/galaxyproject/galaxy/commit/55a405f18a1b493c7e0249f8e56b1... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- fix more fasta copypasta Commit: e7f7d5e29a0fc746625d5c8634d8976d4c2b667c https://github.com/galaxyproject/galaxy/commit/e7f7d5e29a0fc746625d5c8634d89... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Merge pull request #5558 from jmchilton/deletion_cleanup_1 [18.01] Do not reload page when deleting collections. Commit: af7b0ab1b65f5a54b8a8adda1c095fc9a8c2e912 https://github.com/galaxyproject/galaxy/commit/af7b0ab1b65f5a54b8a8adda1c095... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #5556 from nsoranzo/release_18.01_fix_5486 [18.01] Allow LDAP options not starting with OPT_ Commit: 69f784b4583774f491666bf245524627bb54c757 https://github.com/galaxyproject/galaxy/commit/69f784b4583774f491666bf245524... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js M config/reports.yml.sample M config/tool_shed.yml.sample M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into usegalaxy Commit: 229ad3c3888c1c312e3d5d59cfd2ec795cc6de8f https://github.com/galaxyproject/galaxy/commit/229ad3c3888c1c312e3d5d59cfd2e... 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static/scripts/mvc/workflow/workflow-view.js R static/scripts/mvc/workflow/workflow.js R static/scripts/nls/de/locale.js R static/scripts/nls/es/locale.js R static/scripts/nls/fr/locale.js R static/scripts/nls/ja/locale.js R static/scripts/nls/locale.js R static/scripts/nls/zh/locale.js R static/scripts/onload.js R static/scripts/packed R static/scripts/polyfills.js R static/scripts/reports/run_stats.js R static/scripts/toolshed/groups/group-detail-view.js R static/scripts/toolshed/groups/group-list-view.js R static/scripts/toolshed/groups/group-listrow-view.js R static/scripts/toolshed/groups/group-model.js R static/scripts/toolshed/toolshed.groups.js R static/scripts/ui/autocom_tagging.js R static/scripts/ui/editable-text.js R static/scripts/ui/fa-icon-button.js R static/scripts/ui/filter-control.js R static/scripts/ui/hoverhighlight.js R static/scripts/ui/loading-indicator.js R static/scripts/ui/mode-button.js R static/scripts/ui/pagination.js R static/scripts/ui/peek-column-selector.js R static/scripts/ui/popupmenu.js R static/scripts/ui/scroll-panel.js R static/scripts/ui/search-input.js R static/scripts/utils/add-logging.js R static/scripts/utils/ajax-queue.js R static/scripts/utils/async-save-text.js R static/scripts/utils/config.js R static/scripts/utils/deferred.js R static/scripts/utils/graph.js R static/scripts/utils/levenshtein.js R static/scripts/utils/localization.js R static/scripts/utils/metrics-logger.js R static/scripts/utils/natural-sort.js R static/scripts/utils/query-string-parsing.js R static/scripts/utils/uploadbox.js R static/scripts/utils/utils.js R static/scripts/viz/bbi-data-manager.js R static/scripts/viz/circster.js R static/scripts/viz/phyloviz.js R static/scripts/viz/sweepster.js R static/scripts/viz/trackster.js R static/scripts/viz/trackster/filters.js R static/scripts/viz/trackster/painters.js R 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/base.css M templates/galaxy_client_app.mako M templates/js-app.mako M templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/new_tags_1.txt M test/api/test_visualizations.py M test/base/interactor.py M test/functional/tools/samples_tool_conf.xml M test/functional/twilltestcase.py M test/manual/launch_and_run.sh M test/shed_functional/base/twilltestcase.py M test/unit/jobs/test_mapper.py M test/unit/managers/test_HistoryManager.py M tox.ini Log Message: ----------- Merge branch 'upstream/pr-5553' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/a63b0e7f857a...229ad3c3888c