galaxy-commits February 2018

galaxy-commits@lists.galaxyproject.org

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188 discussions

[galaxyproject/galaxy] f6ac13: Don't fail rest of multi-action queue when attempt...
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6ac13568f62731fb785e3aafafbf3aacf21a7a2 https://github.com/galaxyproject/galaxy/commit/f6ac13568f62731fb785e3aafafb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-18 (Sun, 18 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Don't fail rest of multi-action queue when attempting to purge a collection. Fixes https://github.com/galaxyproject/galaxy/issues/5117. Commit: 5e6a2572f8bfabd6c674ff218d8a3ee1f9f22615 https://github.com/galaxyproject/galaxy/commit/5e6a2572f8bfabd6c674ff218d8a… Author: Nicola Soranzo <nicola.soranzo(a)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/d964d594a5314b85def7676f5ae3… Author: John Chilton <jmchilton(a)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: e7f7d5e29a0fc746625d5c8634d8976d4c2b667c https://github.com/galaxyproject/galaxy/commit/e7f7d5e29a0fc746625d5c8634d8… Author: Dannon Baker <dannon.baker(a)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/af7b0ab1b65f5a54b8a8adda1c09… Author: John Chilton <jmchilton(a)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: 6a3ce34c09bd516a18bd7d8f04851e1155d6d174 https://github.com/galaxyproject/galaxy/commit/6a3ce34c09bd516a18bd7d8f0485… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Merge pull request #5443 from jmchilton/fix5117 [18.01] Don't silently fail rest of multi-action queue when attempting to purge a collection. Commit: 3cf84ea3da0ec4fa84d423a050f4ef82271bc0c5 https://github.com/galaxyproject/galaxy/commit/3cf84ea3da0ec4fa84d423a050f4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-20 (Tue, 20 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit.js M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/49a8a317e886...3cf84ea3da0e

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[galaxyproject/galaxy] f6ac13: Don't fail rest of multi-action queue when attempt...
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: f6ac13568f62731fb785e3aafafbf3aacf21a7a2 https://github.com/galaxyproject/galaxy/commit/f6ac13568f62731fb785e3aafafb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-18 (Sun, 18 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Don't fail rest of multi-action queue when attempting to purge a collection. Fixes https://github.com/galaxyproject/galaxy/issues/5117. Commit: 6a3ce34c09bd516a18bd7d8f04851e1155d6d174 https://github.com/galaxyproject/galaxy/commit/6a3ce34c09bd516a18bd7d8f0485… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Merge pull request #5443 from jmchilton/fix5117 [18.01] Don't silently fail rest of multi-action queue when attempting to purge a collection. Compare: https://github.com/galaxyproject/galaxy/compare/af7b0ab1b65f...6a3ce34c09bd

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[galaxyproject/galaxy] 0b516b: Remove defunct casperjs tests.
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b516b67e93d1e9642d000aa16e13769ec6d6b39 https://github.com/galaxyproject/galaxy/commit/0b516b67e93d1e9642d000aa16e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M run_tests.sh R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js Log Message: ----------- Remove defunct casperjs tests. Tests not converted are tracked on #3853. Commit: 49a8a317e886de73894d26f11d3912e79419108c https://github.com/galaxyproject/galaxy/commit/49a8a317e886de73894d26f11d39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M run_tests.sh R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js Log Message: ----------- Merge pull request #5567 from jmchilton/casperjs_remove Remove defunct casperjs tests. Compare: https://github.com/galaxyproject/galaxy/compare/0c7dcc37c966...49a8a317e886

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[galaxyproject/usegalaxy-playbook] a4c8ea: Update Main
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a4c8ea1ba6e8c288d378065e99edfad9d8a15303 https://github.com/galaxyproject/usegalaxy-playbook/commit/a4c8ea1ba6e8c288… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] 25952e: Map static content by default for Reports and Tool...
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: 25952e81e7cc7c2985379f039915d40bc8142d98 https://github.com/galaxyproject/galaxy/commit/25952e81e7cc7c2985379f039915… Author: Nate Coraor <nate(a)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: 13e72e84c523bda22bda792bbebf4720d28542d5 https://github.com/galaxyproject/galaxy/commit/13e72e84c523bda22bda792bbebf… Author: Nicola Soranzo <nsoranzo(a)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/0d029b39ac9ae6bc21a6c1834fe6… Author: Nicola Soranzo <nicola.soranzo(a)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: 5e6a2572f8bfabd6c674ff218d8a3ee1f9f22615 https://github.com/galaxyproject/galaxy/commit/5e6a2572f8bfabd6c674ff218d8a… Author: Nicola Soranzo <nicola.soranzo(a)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/d964d594a5314b85def7676f5ae3… Author: John Chilton <jmchilton(a)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: e7f7d5e29a0fc746625d5c8634d8976d4c2b667c https://github.com/galaxyproject/galaxy/commit/e7f7d5e29a0fc746625d5c8634d8… Author: Dannon Baker <dannon.baker(a)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/af7b0ab1b65f5a54b8a8adda1c09… Author: John Chilton <jmchilton(a)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: 39f245433c57581d65d5486c5755ab86c6cb9065 https://github.com/galaxyproject/galaxy/commit/39f245433c57581d65d5486c5755… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 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: 91bb57bfb55bcc4e6124bd54f3a32ed07b7e5fb0 https://github.com/galaxyproject/galaxy/commit/91bb57bfb55bcc4e6124bd54f3a3… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- fixed flake8 errors Commit: a456c645f0a115f12c66544f13921010449869f0 https://github.com/galaxyproject/galaxy/commit/a456c645f0a115f12c66544f1392… Author: nekrut <anton(a)nekrut.org> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- removing stray whitespace Commit: 2978145fbf4c73732f0930758c2822e1f1ea6ce8 https://github.com/galaxyproject/galaxy/commit/2978145fbf4c73732f0930758c28… Author: nekrut <anton(a)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: 0f4510298e7417b67bf533a1c427e28290baa69d https://github.com/galaxyproject/galaxy/commit/0f4510298e7417b67bf533a1c427… Author: Martin Cech <marten(a)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: c786adf01c07fe5b3608250f9f26b8d6d255a27c https://github.com/galaxyproject/galaxy/commit/c786adf01c07fe5b3608250f9f26… Author: Martin Cech <marten(a)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: fa283b525f4412fbc3d05ad10feb7176b52a27f3 https://github.com/galaxyproject/galaxy/commit/fa283b525f4412fbc3d05ad10feb… Author: Nate Coraor <nate(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/a63b0e7f857a...fa283b525f44

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[galaxyproject/galaxy]
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy

1 0

[galaxyproject/galaxy] c5fa91: draft configurable locale
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: c5fa911b10e90229940bf65467a1610f3b23ee2c https://github.com/galaxyproject/galaxy/commit/c5fa911b10e90229940bf65467a1… Author: Anthony Bretaudeau <anthony.bretaudeau(a)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/8ecddefd09ce70cab2f275d95832… Author: Nate Coraor <nate(a)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/141ac1eabc64b11444a31bbd7c8c… Author: Nate Coraor <nate(a)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/59c6d6957e6bfd3500c2967cb9a8… Author: Nate Coraor <nate(a)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/98e369c9a730090fb99975d99044… Author: Nate Coraor <nate(a)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/4bdebe018648bc28a3029368849c… Author: Nate Coraor <nate(a)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/d238b0f25bba2319d414f3de4a48… Author: Nate Coraor <nate(a)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/1c2bd5ff284925ccadc8957bb2dc… Author: Anthony Bretaudeau <anthony.bretaudeau(a)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/8d1a499e42bd7c71ec9b5e727a28… Author: Anthony Bretaudeau <anthony.bretaudeau(a)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/3f2f5e6af4890d5edd1001844bf2… Author: Anthony Bretaudeau <anthony.bretaudeau(a)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/3ae47e611d2582c543d42a69d0c3… Author: Jim Johnson <jj(a)umn.edu> Date: 2018-01-22 (Mon, 22 Jan 2018) Changed paths: A .ci/autopep8.sh A .ci/check_py3_compatibility.sh M .ci/first_startup.sh M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt R .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh R .ci/flake8_wrapper_imports.sh A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M 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A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test-data/neostore.zip A test-data/new_element_sort_order.txt A test-data/new_labels_1.txt A test-data/new_labels_2.txt A test-data/new_labels_bad_1.txt A test-data/new_labels_bad_2.txt A 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/007e3cc2db247096cf06b59d4c75… Author: Jim Johnson <jj(a)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/04c16f7e046945be3780b8431c49… Author: Nate Coraor <nate(a)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/8e4eab6e6cc6686f7bfdf7b86e29… Author: Nate Coraor <nate(a)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/1de0ef437b32619a06b23411d265… Author: mvdbeek <m.vandenbeek(a)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/d3895db861a003206dce0be83317… Author: mvdbeek <m.vandenbeek(a)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/15cd09d2c5e73e8721c9369bee51… Author: mvdbeek <m.vandenbeek(a)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/31ec21d89fb91c00f368a46fe071… Author: mvdbeek <m.vandenbeek(a)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/326f743d3a5582fe6f3c6c78a1f1… 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973bfbafb980cfd15b545b2b0b4d873440bf1203 https://github.com/galaxyproject/galaxy/commit/973bfbafb980cfd15b545b2b0b4d… Author: mvdbeek <m.vandenbeek(a)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/fbd33a57e0033a1547c3bf6f9812… Author: Nicola Soranzo <nicola.soranzo(a)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/e87d1aa79d84a08721d76ae2b6cb… Author: Nicola Soranzo <nicola.soranzo(a)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/6f6a671d36ff4f7ebe258c04aef6… Author: Nicola Soranzo <nicola.soranzo(a)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/0ce2d97c4dd65e5b2827c29dfa0a… Author: Nicola Soranzo <nicola.soranzo(a)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/d32f0d2eb111dee6951e021b98b4… Author: Martin Cech <marten(a)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/c1e78ae75c8849639f0db889a1f7… Author: Martin Cech <marten(a)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/6a2e6be733b8349842689c38fb11… Author: Nicola Soranzo <nicola.soranzo(a)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/83bf0ccce71c1244b362323efde0… Author: Nicola Soranzo <nsoranzo(a)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/c31a0341714efa85a75df13da06b… Author: Martin Cech <marten(a)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/2854643057dd7d8517594299cf4c… Author: Dannon Baker <dannon.baker(a)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/df597db60ef479a8499b7a3b3459… Author: Martin Cech <marten(a)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/046cb8f35956c45e5c88786b1e9c… Author: John Chilton <jmchilton(a)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/792a07148915ccc94d44f415db20… Author: John Chilton <jmchilton(a)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/28f5aca05695bab1a3608fbbcc93… Author: Dannon Baker <dannon.baker(a)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/da002bdf44ff9c3809c15990e5f0… Author: Nicola Soranzo <nicola.soranzo(a)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/db287a227441f78d457462a16ff5… Author: Nicola Soranzo <nicola.soranzo(a)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/847d801c61702d826c948688b930… Author: John Chilton <jmchilton(a)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/9489fe471155c92028216ebf0205… Author: Nicola Soranzo <nsoranzo(a)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. 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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: ----------- 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/29a1bf05e68a54c4fc9242e86ec5… Author: Dannon Baker <dannon.baker(a)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/a76614486be3dd0ad85f0007d604… Author: Nicola Soranzo <nicola.soranzo(a)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/bc50c14490e4f81144e5bc59f76e… Author: mvdbeek <m.vandenbeek(a)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/49872e7612070df9aee607897fb4… Author: Nicola Soranzo <nicola.soranzo(a)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/f43a3268b11841f65d3de195611b… Author: mvdbeek <m.vandenbeek(a)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/39104af3b42e6d253391a9b73f69… Author: mvdbeek <m.vandenbeek(a)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/046f3265dd50ec6ff53470a96a4d… Author: mvdbeek <m.vandenbeek(a)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/0be36ef4fce3b50bec37d199af2a… Author: mvdbeek <m.vandenbeek(a)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/553d165087335528892232b17706… Author: mvdbeek <m.vandenbeek(a)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/52586fcca2ef6ef6926fcd25b6c6… Author: Nicola Soranzo <nicola.soranzo(a)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/386526d928be1de57268163db181… Author: Nicola Soranzo <nicola.soranzo(a)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/c7b6afbcd25fdeef9d7a59df95e3… Author: Nate Coraor <nate(a)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/b4cdce925bf485ecdb24868bacdc… Author: Martin Cech <marten(a)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/a1662e37059e6956cdca3cb3eb23… Author: Martin Cech <marten(a)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/b1df43a1f83a2b3026e237588430… Author: Dannon Baker <dannon.baker(a)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/5a31ac84ce129d03aea5fcbd73ed… Author: John Chilton <jmchilton(a)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/988cab4db7ef83714cf6f0c57f73… Author: Dannon Baker <dannon.baker(a)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/245394acb694020c0f9f78185749… Author: Nicola Soranzo <nicola.soranzo(a)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/6b2150b1feaca405d2e718bace5c… Author: Nicola Soranzo <nicola.soranzo(a)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/2be7eb8cfa0640dbec5954de006b… Author: Nicola Soranzo <nicola.soranzo(a)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/6346b9e30949cd72a57eb683abd9… Author: Nicola Soranzo <nicola.soranzo(a)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/f2c6e083a15eab453ea7c9456546… Author: Nicola Soranzo <nicola.soranzo(a)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/0a44e77a89f6533c7ceaad99ffb9… Author: Nicola Soranzo <nicola.soranzo(a)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/0b60de76b93edbfeae5560a3a531… Author: Dannon Baker <dannon.baker(a)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/f8d21f098af23db441ad4b81e1a2… Author: Dannon Baker <dannon.baker(a)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/3864a1763ffa101384314090066c… Author: Nicola Soranzo <nicola.soranzo(a)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/4347d5f83debc78a86c6be2fc480… Author: Nicola Soranzo <nicola.soranzo(a)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/204bb0e8fdf5ff10696e03c51c68… Author: Martin Cech <marten(a)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 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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/dfe25ac131582a5315369ef8ba4e… Author: Dannon Baker <dannon.baker(a)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/02fa48f85cdaa1ed0722f050b695… Author: Dannon Baker <dannon.baker(a)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/490f67f3a0e70f9d90898163ea42… Author: John Chilton <jmchilton(a)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/3a7414acaca59dc602ab3ea8092d… Author: Dannon Baker <dannon.baker(a)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/77bcca49a393ab4a181efae7c55f… Author: Nicola Soranzo <nicola.soranzo(a)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/b114f3f7b9d483509e7d684aa8be… Author: mvdbeek <m.vandenbeek(a)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/b2be7b51814a4354307e8f0a0df0… Author: mvdbeek <m.vandenbeek(a)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/f9664a0863b24ff738aefcbe520f… Author: mvdbeek <m.vandenbeek(a)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/fd373501c78dee268844e82fa1a5… Author: mvdbeek <m.vandenbeek(a)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/e306a447c080f8d252a9a7fe49f4… Author: mvdbeek <m.vandenbeek(a)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/b3ea83929fc67f656c30aed865d2… Author: Nicola Soranzo <nicola.soranzo(a)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/c3bb2859039338c513e1f9ac871d… Author: Anthony Bretaudeau <abretaud(a)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/4dbfd50f064256f2af8f7e3b08dd… Author: Anthony Bretaudeau <abretaud(a)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 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 config/tool_shed.yml.sample M doc/Makefile M doc/source/admin/dependency_resolvers.rst M doc/source/admin/framework_dependencies.rst M doc/source/admin/galaxy_options.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/webhooks.rst M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/util.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.py A lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.phylip R lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/conda-file.sh 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/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/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/dictifiable.py M lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/util/logging/__init__.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/__init__.py A 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 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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 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/d14bae73f72cd454ef41bb1815cf… Author: mvdbeek <m.vandenbeek(a)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/43d572558a5dc5747dac0a7fc824… Author: John Chilton <jmchilton(a)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/29acb11df5c971a2bc99ae534e36… Author: Peter Cock <p.j.a.cock(a)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/12f72412abe1e1675f5755c77bda… Author: Dannon Baker <dannon.baker(a)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/45ab11cca78809a0bc779ddeff41… Author: Dannon Baker <dannon.baker(a)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/65e2e0b48f59948a7df46f1d3440… Author: Nate Coraor <nate(a)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/db45db89b396b0f70f600f078aef… Author: Dannon Baker <dannon.baker(a)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/d1f120108735cdf15b6c782d5bb2… Author: E. Rasche <hxr(a)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/3f80a43bda5e7d32cf9f1317666e… Author: Dannon Baker <dannon.baker(a)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/8ce7f96353f3d31e6b41bd19c611… Author: Dannon Baker <dannon.baker(a)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/55ca8132a38c67d7e30e6ee59f14… Author: Nate Coraor <nate(a)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/0ca7afb343d865a7d1bd4cc6b517… Author: Nicola Soranzo <nsoranzo(a)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/6f2a0cceb03b4277f9ed4e8761cc… Author: Nicola Soranzo <nicola.soranzo(a)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/10ff797ac77da470cf2078059b32… Author: Nicola Soranzo <nicola.soranzo(a)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/1ea41622632aeefdac7138ad5156… Author: Nicola Soranzo <nicola.soranzo(a)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/b6fe83409ad57e15adcb1b270102… Author: John Chilton <jmchilton(a)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/d0b4503e0cc2e3d083330da08672… Author: Marius van den Beek <m.vandenbeek(a)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/587f20cf9c0b6d250bee403cf3ba… Author: Björn Grüning <bjoern(a)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/0367a356d528b3ca395eec1f3de5… Author: Björn Grüning <bjoern(a)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/ca66882fcec96ff29c6dc147146f… Author: guerler <aysam.guerler(a)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/daf500f80cfa2bdb36b74acadca6… Author: guerler <aysam.guerler(a)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/80ee52b2d12f361f58cc2724372e… Author: guerler <aysam.guerler(a)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/bc5eecf6a8efe0f299b740046a5e… Author: guerler <aysam.guerler(a)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/c7bf80599e19f2a165a4406b0039… Author: guerler <aysam.guerler(a)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/26f72481aaa20c0a57d491c6086d… Author: guerler <aysam.guerler(a)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/feab8314b0bf309804e23de61de4… Author: guerler <aysam.guerler(a)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/0049d5a760ec19383fa97f2ca72a… Author: guerler <aysam.guerler(a)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/b16c6027dfdff5208adaeae76006… Author: guerler <aysam.guerler(a)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/39c0eb37ba73b127e36260279491… Author: guerler <aysam.guerler(a)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/b6db962284d06918a1ff1dc61b73… Author: guerler <aysam.guerler(a)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/1829c4a8bcb0a428593530cf9016… Author: guerler <aysam.guerler(a)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/33ae04a04fca19f9c251efb2acac… Author: guerler <aysam.guerler(a)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 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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/6ec649c04d4200a38066fb8cca95… Author: guerler <aysam.guerler(a)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/48518d84f7d06903e2f2ad22ce24… Author: guerler <aysam.guerler(a)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/76fac9181f1a9f85913be6e6daea… Author: guerler <aysam.guerler(a)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/9be959396ec4c401e2ee8af83a60… Author: guerler <aysam.guerler(a)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/123e9febb856731df4a0d990349a… Author: guerler <aysam.guerler(a)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 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<aysam.guerler(a)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/1eccb2a6434fc6e098626066b739… Author: guerler <aysam.guerler(a)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/911b667f383b801ac22f8fb87bae… Author: guerler <aysam.guerler(a)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/4bcc9e6c2e79110bfde3c472debe… Author: guerler <aysam.guerler(a)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/d1798f376d2633d6d25955b238b3… Author: guerler <aysam.guerler(a)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 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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/964c82329c3a8bdc2c47ab5f2412… Author: guerler <aysam.guerler(a)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/778f92155ca6e19a3755fac7423d… Author: guerler <aysam.guerler(a)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/4b158e3f7a39f8019fc1af81e88e… Author: guerler <aysam.guerler(a)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/8c3babfd1823137879797ce8af93… Author: guerler <aysam.guerler(a)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/0451024aa08cbd7d4b96b01c9ef3… Author: guerler <aysam.guerler(a)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/2b50fe94af3d12649ed76251cf1e… Author: guerler <aysam.guerler(a)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/f56cb32fb722640fa63b943293eb… Author: guerler <aysam.guerler(a)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/d871196c5e70ee089d357a0c2523… Author: guerler <aysam.guerler(a)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/5e8bd49b126b91cdbf2b2c29988e… Author: guerler <aysam.guerler(a)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/83c27b629a2e6d17a8ce955f3de1… Author: guerler <aysam.guerler(a)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/e011371096401673c2774ac6e320… Author: guerler <aysam.guerler(a)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/a0fa19048a49c662afa0a6e068ae… Author: Dannon Baker <dannon.baker(a)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/2b0fbe80ebc8814d2d6bba8bae0d… Author: Dannon Baker <dannon.baker(a)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/73486849e03f3bbe6daaebd7953b… Author: Dannon Baker <dannon.baker(a)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/1e9c8cf57a7f9a3978416bc0ba70… Author: Dannon Baker <dannon.baker(a)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/2b0074be26c725a708aa4150ac7e… Author: Dannon Baker <dannon.baker(a)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/039bdfb2d460fc3dc0b01d1cf2d6… Author: Dannon Baker <dannon.baker(a)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/172f9317d2c25246a04f0297347d… Author: Dannon Baker <dannon.baker(a)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/660df78c7cb2d4e8858686191d54… Author: Dannon Baker <dannon.baker(a)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/04c71f33e3f802233da60ae1eab3… Author: Dannon Baker <dannon.baker(a)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/65590f1350245753f04fcc132775… Author: Dannon Baker <dannon.baker(a)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/939bbff6d81fcde264323819f548… Author: Dannon Baker <dannon.baker(a)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/ae0da08047a06231578de3ec98e8… Author: Dannon Baker <dannon.baker(a)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/d9c445796f43dc1a2d1d811c21d5… Author: Dannon Baker <dannon.baker(a)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/5848c991caf5dd271d16cb346d28… Author: Dannon Baker <dannon.baker(a)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/3329bf8907410b7eb8fec45a40fa… Author: Dannon Baker <dannon.baker(a)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/f65d42d4fd298ed34110425f8852… Author: Dannon Baker <dannon.baker(a)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/b6b31e0853bc486065fd3d7b917a… Author: Dannon Baker <dannon.baker(a)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/16405ce19aa14c5a2a744fc3d0d1… Author: guerler <aysam.guerler(a)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/8518432e265ed90b377409d621b5… Author: guerler <aysam.guerler(a)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/49618cf061f1873d2e5c83f4771e… Author: guerler <aysam.guerler(a)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/a0ad05494cbe109a58932b1a51cf… Author: guerler <aysam.guerler(a)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/be3d22215c6b91d8d1111a525663… Author: guerler <aysam.guerler(a)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/ebb8f05c6d99ecb6d151c5b83b47… Author: guerler <aysam.guerler(a)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/f9107934b8373aac40673bcfe912… Author: guerler <aysam.guerler(a)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/21e065052e714acc4708c94cc0b8… Author: guerler <aysam.guerler(a)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/2b3c517161f701bfcf2a549ee3db… Author: Dannon Baker <dannon.baker(a)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/dea41ef60c245f8bc4dbe25a8f85… Author: Dannon Baker <dannon.baker(a)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/2683cc527550dfc27fae0885efc4… Author: Dannon Baker <dannon.baker(a)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/df90cc78addf1b2adc711347c54c… Author: Dannon Baker <dannon.baker(a)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/62e4e0da8664490b20e3b090bd21… Author: Dannon Baker <dannon.baker(a)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/fa3d12a33cb6185cd9988a9e9d74… Author: Dannon Baker <dannon.baker(a)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/719383fbea2d7cadf347967fb40e… Author: guerler <aysam.guerler(a)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/525bc13d8dadbf5164f60967bdd2… Author: guerler <aysam.guerler(a)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/171dcc1e24f84c2f7818105ec297… Author: guerler <aysam.guerler(a)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/21fb51782cc38e8ead0833417cf4… Author: guerler <aysam.guerler(a)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/159a8c72bc69c8c19d4dd6e039d8… Author: guerler <aysam.guerler(a)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/de7cac90537b4bd9fa9500cb55b3… Author: guerler <aysam.guerler(a)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/00a105ef6a28add188b9356572e8… Author: guerler <aysam.guerler(a)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/91c4641c886c1f1015218abb34f5… Author: guerler <aysam.guerler(a)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/055e0fa167d77c94c03166bea65f… Author: guerler <aysam.guerler(a)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/83467ca9efa5266c9968be5a598f… Author: guerler <aysam.guerler(a)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/1014b5d5d31232212946e781fd92… Author: guerler <aysam.guerler(a)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/b33ec3b3ca9cf346ae07673d6017… Author: guerler <aysam.guerler(a)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/43d45dfee465e55657cbd3c40585… Author: guerler <aysam.guerler(a)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/97cab84b0846342f7d723203172f… Author: guerler <aysam.guerler(a)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/820d0b4135e528ce3127daae6fc5… Author: guerler <aysam.guerler(a)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/c4ca8aba1ff56a540662eba7cefb… Author: guerler <aysam.guerler(a)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/d834a3c96865a6b74e1a4c2ce9b6… Author: guerler <aysam.guerler(a)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/bedbd06a3983b27e9dc44ab07c5d… Author: guerler <aysam.guerler(a)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/a19088a68c8d361d39f9b1f9df46… Author: guerler <aysam.guerler(a)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/4f9e0d92394d4b7b5a3e39505a0e… Author: guerler <aysam.guerler(a)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/a770cbcea305aa98d5d4d0583fa5… Author: guerler <aysam.guerler(a)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/35ac99bfe5bccb103965f4f2d73a… Author: guerler <aysam.guerler(a)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/7f896c84d76ef9879aa70227e15d… Author: guerler <aysam.guerler(a)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/e829579be3e34e6f0ff1c1532795… Author: guerler <aysam.guerler(a)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/adea33ad935e641ac8acca1646c1… Author: guerler <aysam.guerler(a)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/a64b0835a23019995617f4c8679e… Author: guerler <aysam.guerler(a)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 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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/0f3aacdd919dd2a3d12702d522ed… Author: guerler <aysam.guerler(a)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/67e911b4be3b5d6b1fee686bab39… Author: guerler <aysam.guerler(a)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/ff84aa42706621fee4a6658745bb… Author: guerler 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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/1afea3eec0c94d0d4bac660ac567… Author: guerler <aysam.guerler(a)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/a6529c51d3ca0b0554e1bc4cebf7… Author: guerler <aysam.guerler(a)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/3a0c8b5634f1af656ad5c87a1181… Author: guerler <aysam.guerler(a)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/82a1f6e49e016372aa1a5a615f30… Author: guerler <aysam.guerler(a)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/cea4db4a53ca25d4d92a9bed2b18… Author: guerler <aysam.guerler(a)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/4af913f7dfb55e1ddc028296063d… Author: guerler <aysam.guerler(a)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/3c7b621b3b320d98025caa7981c7… Author: guerler <aysam.guerler(a)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/2507034e936db38024a8b9f70a35… Author: guerler <aysam.guerler(a)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/a77cf155e66cecaf2aaa3bcdf87a… Author: guerler <aysam.guerler(a)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 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https://github.com/galaxyproject/galaxy/commit/cb5c30c32ae42ff6d122c395d8fe… Author: guerler <aysam.guerler(a)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/c09d9c81b46e60a65b08840ac1cd… Author: guerler <aysam.guerler(a)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 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----------- Fix description style Commit: 4fa486082c2ee231fe09b584ed62a11d9146bdcd https://github.com/galaxyproject/galaxy/commit/4fa486082c2ee231fe09b584ed62… Author: guerler <aysam.guerler(a)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/f2335fe46192187316458d785918… Author: guerler <aysam.guerler(a)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/9ae6cb1c6e91ed6903b5955df859… Author: guerler <aysam.guerler(a)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/0ff4f7419e7dfbd77c36fd2c362d… Author: guerler <aysam.guerler(a)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/bd9167400e243392d29cefc235db… Author: guerler <aysam.guerler(a)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 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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/39ad58066b6ebabc00657f7b0421… Author: guerler <aysam.guerler(a)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/6d00958d43eab15bf2c94bc9088d… Author: John Chilton <jmchilton(a)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/2e51d0576a59c3400d1e107c6e85… Author: Dave B <dave(a)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/e13740a3f6f91a86af0b19ce5121… Author: Dannon Baker <dannon.baker(a)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/e58aaef95997f37974a501e69c4c… Author: Martin Cech <marten(a)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/e6535d33bfd76d18d7904ad42dab… Author: Dave B <dave(a)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/8fa28994fc38c82b873a295df59b… Author: Dave B <dave(a)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/201d76568f75eeeebde3b9e585f5… Author: Martin Cech <marten(a)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/007ae8f9377666ab84599aee20fc… Author: Dannon Baker <dannon.baker(a)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/39fd5fdc05e81918df322d1b84b4… Author: Martin Cech <marten(a)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/7663de745f5df827f7873960c9ec… Author: John Chilton <jmchilton(a)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/54659b085f78dabfc987d8292e6d… Author: Dannon Baker <dannon.baker(a)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/be7f503448a6ffd5f5a63d27e6c5… Author: Dannon Baker <dannon.baker(a)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/6c68e8e980c7155dee8389e25d90… Author: Dannon Baker <dannon.baker(a)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/5d4301ab3c73de38125a43f3a5f3… Author: Dannon Baker <dannon.baker(a)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/fafcfbb5774033098ca5a6745b86… Author: Dannon Baker <dannon.baker(a)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/a82f4a1ae10457071ffad01956f2… Author: Dannon Baker <dannon.baker(a)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/320f1fccac8daac11b5411d36c94… Author: Dannon Baker <dannon.baker(a)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/997e31b88100ef38294632bf138c… Author: Dannon Baker <dannon.baker(a)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/15d8afeddd3d7b1cd19595a1af2e… Author: Dannon Baker <dannon.baker(a)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/d5c089acc7467d9dd218485acb9f… Author: Dannon Baker <dannon.baker(a)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/cd1ed9bb56ecaff61b09e48f183f… Author: Dannon Baker <dannon.baker(a)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/c18eafce90fd247e914c92256101… Author: Dannon Baker <dannon.baker(a)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/13c40b1cffaf26b05468a00baa36… Author: Dannon Baker <dannon.baker(a)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/e9b26b4bd00052d8b75578a30f1a… Author: Dannon Baker <dannon.baker(a)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/8a721f6f37741d07fbe709112fa0… Author: Nuwan Goonasekera <nuwan.ag(a)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/83cf06e3614b5463e3aaac74f314… Author: anup kumar <anup.rulez(a)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/5b66429cb44836b1a56fb76c5e64… Author: Dannon Baker <dannon.baker(a)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/25952e81e7cc7c2985379f039915… Author: Nate Coraor <nate(a)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. 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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/043fe35e9521c20987cd995de90a… Author: John Chilton <jmchilton(a)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/3de8593e19641ad1078dbb53a870… Author: John Chilton <jmchilton(a)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/99e1305c53cde3f0244819fe4956… Author: John Chilton <jmchilton(a)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_relationship… when optimizing postgres calls. xref https://github.com/galaxyproject/starforge/pull/191 Commit: aed2b4a239ebbcd4081426599023867eed94f63b https://github.com/galaxyproject/galaxy/commit/aed2b4a239ebbcd4081426599023… Author: Martin Cech <marten(a)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/a35d5a535eebb36d647353faac66… Author: Dannon Baker <dannon.baker(a)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/41a31967540e74857c25257ec8cc… Author: Dannon Baker <dannon.baker(a)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/78ee5f8451e022515e75e9ca5888… Author: Martin Cech <marten(a)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/298ef7ee1951cf64fe42b4cc44ce… Author: Martin Cech <marten(a)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/92826fe5e763a0938cf4710955be… Author: Martin Cech <marten(a)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 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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/d30811eea38f3bb535d52cb86dbb… Author: Matthias Bernt <m.bernt(a)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/c9c2e968daba29d15e574f148bbd… Author: Nicola Soranzo <nsoranzo(a)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/13e72e84c523bda22bda792bbebf… Author: Nicola Soranzo <nsoranzo(a)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/0d029b39ac9ae6bc21a6c1834fe6… Author: Nicola Soranzo <nicola.soranzo(a)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/19eee525a166b6c9abf03e5a91fd… Author: nekrut <anton(a)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/0c2c9ba49e70f19cd4ec9f4c93bf… Author: nekrut <anton(a)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/84e818577a162b507fa4f1a69006… Author: nekrut <anton(a)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/5e6a2572f8bfabd6c674ff218d8a… Author: Nicola Soranzo <nicola.soranzo(a)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/d964d594a5314b85def7676f5ae3… Author: John Chilton <jmchilton(a)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/4390cd4142605efbf062126fdf00… Author: nekrut <anton(a)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/6359262b3ce3632bd859278201bc… Author: Martin Cech <marten(a)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/55a405f18a1b493c7e0249f8e56b… Author: Martin Cech <marten(a)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/e7f7d5e29a0fc746625d5c8634d8… Author: Dannon Baker <dannon.baker(a)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/af7b0ab1b65f5a54b8a8adda1c09… Author: John Chilton <jmchilton(a)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/69f784b4583774f491666bf24552… Author: Nate Coraor <nate(a)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/229ad3c3888c1c312e3d5d59cfd2… Author: Nate 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static/maps/utils/ajax-queue.js.map R static/maps/utils/async-save-text.js.map R static/maps/utils/config.js.map R static/maps/utils/deferred.js.map R static/maps/utils/graph.js.map R static/maps/utils/levenshtein.js.map R static/maps/utils/localization.js.map R static/maps/utils/metrics-logger.js.map R static/maps/utils/natural-sort.js.map R static/maps/utils/query-string-parsing.js.map R static/maps/utils/uploadbox.js.map R static/maps/utils/utils.js.map R static/maps/viz/bbi-data-manager.js.map R static/maps/viz/circster.js.map R static/maps/viz/phyloviz.js.map R static/maps/viz/sweepster.js.map R static/maps/viz/trackster.js.map R static/maps/viz/trackster/filters.js.map R static/maps/viz/trackster/painters.js.map R static/maps/viz/trackster/slotting.js.map R static/maps/viz/trackster/tracks.js.map R static/maps/viz/trackster/util.js.map R static/maps/viz/visualization.js.map R static/maps/viz/viz_views.js.map R static/scripts/admin.toolshed.js R 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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/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

1 0

[galaxyproject/usegalaxy-playbook] 5b7f1b: update test
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5b7f1bd7b85a21272bf4b1d9b1e9497f62bf1cc9 https://github.com/galaxyproject/usegalaxy-playbook/commit/5b7f1bd7b85a2127… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- update test

1 0

[galaxyproject/galaxy] 5e6a25: Allow LDAP options not starting with OPT_
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 5e6a2572f8bfabd6c674ff218d8a3ee1f9f22615 https://github.com/galaxyproject/galaxy/commit/5e6a2572f8bfabd6c674ff218d8a… Author: Nicola Soranzo <nicola.soranzo(a)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: af7b0ab1b65f5a54b8a8adda1c095fc9a8c2e912 https://github.com/galaxyproject/galaxy/commit/af7b0ab1b65f5a54b8a8adda1c09… Author: John Chilton <jmchilton(a)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_ Compare: https://github.com/galaxyproject/galaxy/compare/e7f7d5e29a0f...af7b0ab1b65f

1 0

[galaxyproject/galaxy] b84da7: Allow per-request SQL debugging via URL parameter.
by GitHub 20 Feb '18

20 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b84da7a07a7b53f7770d6dc015ff0829305e3075 https://github.com/galaxyproject/galaxy/commit/b84da7a07a7b53f7770d6dc015ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-18 (Sun, 18 Feb 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py A lib/galaxy/web/framework/middleware/sqldebug.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Allow per-request SQL debugging via URL parameter. This has been super helpful in debugging the SQL generated by Galaxy for recent PRs. To use this simply enable the middleware, use your browser's network logger to find the URL of interest, copy the URL into the browser address bar and add ``?debug_sql=1`` to it. You will then see the sql in the logs only for that request and for every statement in that request. Simply turning all logging on results in a deluge of logging I've never been able to grok and that is very hard to ping to particular request. Slow request logging is great but it doesn't make this kind of per-query full profile of the SQL generated as easy as this approach and isn't great at debugging performance problems when the result from a large number of small requests (you'd have to set a very low threshold to make sure you are logging every query and then it is no different from the full log). Commit: 0c7dcc37c96617a6a98d1f061c051bee678e8c67 https://github.com/galaxyproject/galaxy/commit/0c7dcc37c96617a6a98d1f061c05… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-19 (Mon, 19 Feb 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py A lib/galaxy/web/framework/middleware/sqldebug.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5539 from jmchilton/per_request_sql_debugging Add middleware and instrumentation to allow per-request SQL debugging. Compare: https://github.com/galaxyproject/galaxy/compare/ca7cbaf2bffb...0c7dcc37c966

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galaxy-commits February 2018