July 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] efc877: Adding showBootstrap feature for Phylocanvas viz
by GitHub 06 Jul '17

06 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: efc877ab29b86e897552e4822d0a05c6fa796902 https://github.com/galaxyproject/galaxy/commit/efc877ab29b86e897552e4822d0a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Adding showBootstrap feature for Phylocanvas viz Commit: 065ab584c7bd6fa15c3cadc2cc9ef2ef57921f3b https://github.com/galaxyproject/galaxy/commit/065ab584c7bd6fa15c3cadc2cc9e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.ptkscmp M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/queue_worker.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py R lib/galaxy/tools/toolbox/lineages/stock.py R lib/galaxy/tools/toolbox/lineages/tool_shed.py A lib/galaxy/util/tool_version.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/work/context.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/log_tempfile.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/tools/tool_version_manager.py M static/maps/layout/menu.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js M static/style/blue/base.css M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/js-app.mako M templates/user/logout.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/errors.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/list_published.mako R templates/webapps/galaxy/history/shared_grid.mako M templates/webapps/galaxy/mobile/form.mako M templates/webapps/galaxy/mobile/index.mako M templates/webapps/galaxy/root/tool_runner.mako M templates/webapps/reports/base_panels.mako M templates/webapps/tool_shed/admin/center.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/api/test_dataset_collections.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_config_options_users.py A test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Merging with dev Commit: 1ecaa06987325100fa9bb0334a9be2d212ee0d9e https://github.com/galaxyproject/galaxy/commit/1ecaa06987325100fa9bb0334a9b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #4284 from bgruening/enhancement_phylocanvas Enhancement for Phylocanvas plugin Compare: https://github.com/galaxyproject/galaxy/compare/9a65d9b2ab3f...1ecaa0698732

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[galaxyproject/galaxy] 0bc2d9: Uniform html titles
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0bc2d9c96abf0f0a85f6e804ff9c892649b28cb9 https://github.com/galaxyproject/galaxy/commit/0bc2d9c96abf0f0a85f6e804ff9c… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-02 (Sun, 02 Jul 2017) Changed paths: M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/js-app.mako M templates/user/logout.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/errors.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/list_published.mako M templates/webapps/galaxy/mobile/form.mako M templates/webapps/galaxy/mobile/index.mako M templates/webapps/galaxy/root/tool_runner.mako M templates/webapps/reports/base_panels.mako M templates/webapps/tool_shed/admin/center.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Uniform html titles Commit: 3f03774616634a6126405c1ff934f0f338197c8b https://github.com/galaxyproject/galaxy/commit/3f03774616634a6126405c1ff934… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-02 (Sun, 02 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library.py Log Message: ----------- Redundant Commit: e88986f3897aa661197bcaf22077e5f3cc515cef https://github.com/galaxyproject/galaxy/commit/e88986f3897aa661197bcaf22077… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-02 (Sun, 02 Jul 2017) Changed paths: M templates/js-app.mako Log Message: ----------- Accidental inclusion Commit: 9a65d9b2ab3fd8169ee196c068af2bf3ba3a66eb https://github.com/galaxyproject/galaxy/commit/9a65d9b2ab3fd8169ee196c068af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library.py M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/js-app.mako M templates/user/logout.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/base_panels.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/errors.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/list_published.mako M templates/webapps/galaxy/mobile/form.mako M templates/webapps/galaxy/mobile/index.mako M templates/webapps/galaxy/root/tool_runner.mako M templates/webapps/reports/base_panels.mako M templates/webapps/tool_shed/admin/center.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Merge pull request #4272 from erasche/uniform-titles Uniform titles Compare: https://github.com/galaxyproject/galaxy/compare/bec227436c00...9a65d9b2ab3f

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[galaxyproject/galaxy] caffea: Search collections by tags
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: caffea12536e085e6bfa094615066f76fdd87aff https://github.com/galaxyproject/galaxy/commit/caffea12536e085e6bfa09461506… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Search collections by tags Commit: 601c136247fedadb6bf889187346481fb533882d https://github.com/galaxyproject/galaxy/commit/601c136247fedadb6bf889187346… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js Log Message: ----------- Merge remote-tracking branch 'pvanheus/collection_tag_searchable' into dev Commit: bec227436c00f74e2999f766db34ea8019092a5e https://github.com/galaxyproject/galaxy/commit/bec227436c00f74e2999f766db34… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M static/maps/mvc/collection/collection-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-model.js Log Message: ----------- Client build as part of merge. Compare: https://github.com/galaxyproject/galaxy/compare/a42abc03e0b0...bec227436c00

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[galaxyproject/galaxy] c2897c: Replace ShedToolLineage with enhanced StockLineage
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2897c211b1d9a3743171e3e9b05c235b79c50f7 https://github.com/galaxyproject/galaxy/commit/c2897c211b1d9a3743171e3e9b05… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/lineages/stock.py R lib/galaxy/tools/toolbox/lineages/tool_shed.py A lib/galaxy/util/tool_version.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/tools/tool_version_manager.py M test/unit/tools/test_toolbox.py Log Message: ----------- Replace ShedToolLineage with enhanced StockLineage This means we don't rely on the Tool Shed metadata anymore and instead deduce the tool lineage via the tool_id, which contains the version. Version comparison then happens via LooseVersions. This works for toolshed and non-toolshed tools, restoring proper grouping in the tool panel and version switches, even for tool shed tools whose lineage is broken. Commit: 0017d167f100f84df95967a05b0551250828f7a4 https://github.com/galaxyproject/galaxy/commit/0017d167f100f84df95967a05b05… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M test/unit/shed_unit/test_tool_panel_manager.py Log Message: ----------- Use correct tool version for ToolPanelManager.test_add_twice test to pass Commit: db5d0095a6a426efcd587eca6808f350a6e126cf https://github.com/galaxyproject/galaxy/commit/db5d0095a6a426efcd587eca6808… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Fix grouping tests by setting up correct versions Commit: aabb933fdf69719adcb6fb9e9ba82d795a3b9b74 https://github.com/galaxyproject/galaxy/commit/aabb933fdf69719adcb6fb9e9ba8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/lineages/stock.py M test/unit/tools/test_toolbox.py Log Message: ----------- Keep StockLineage versions sorted Commit: 77e016bbbd5de566484d1c74c4f5679354edf360 https://github.com/galaxyproject/galaxy/commit/77e016bbbd5de566484d1c74c4f5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Remove unused next/previous version methods Commit: 6864187725b0af03e2196d12722f78f71d84977e https://github.com/galaxyproject/galaxy/commit/6864187725b0af03e2196d12722f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M lib/galaxy/tools/__init__.py M test/unit/tools_support.py Log Message: ----------- ToolVersion to StockLineage, drop ToolVersionCache remnant from unittests (thx @nsoranzo!). Commit: 81e73969dce5102dec799e3ca8b2a3056969f6a3 https://github.com/galaxyproject/galaxy/commit/81e73969dce5102dec799e3ca8b2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/galaxy/util/tool_version.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove duplication between ToolLineage and TVM Getting tool versions and tool ids is now done through the tool lineage. Also assume that the lineage can always be found for a given loaded tool in the ToolVersionListGrid class. Thanks @nsoranzo for these suggestions! Commit: 0830ea2e4172e3be51ae081f9578c2c582f12a7e https://github.com/galaxyproject/galaxy/commit/0830ea2e4172e3be51ae081f9578… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/util/tool_version.py Log Message: ----------- Remove unused `get_version_from_guid` function Commit: db5e41c186d4c4b452ee4b7e83a0b26474d72873 https://github.com/galaxyproject/galaxy/commit/db5e41c186d4c4b452ee4b7e83a0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unused tool_id variable Commit: 0257248152db3edb493bfd4420f105a19000ae89 https://github.com/galaxyproject/galaxy/commit/0257248152db3edb493bfd4420f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py R lib/galaxy/tools/toolbox/lineages/stock.py Log Message: ----------- Rename StockLineage to ToolLineage and merge stock.py contents into interface.py Commit: 68981c16cc708514e879941f152be9a60f7ad290 https://github.com/galaxyproject/galaxy/commit/68981c16cc708514e879941f152b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove unused lineage_ids from Tool class Commit: e9658e8adb5d0bf0f8db42faa4d14cb50d4c90ce https://github.com/galaxyproject/galaxy/commit/e9658e8adb5d0bf0f8db42faa4d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M lib/galaxy/tools/toolbox/lineages/factory.py Log Message: ----------- Clarify when and why tool version is being registered Commit: 41d739bdb4d1ac622fb7fd78f8b3dbc9acd978ad https://github.com/galaxyproject/galaxy/commit/41d739bdb4d1ac622fb7fd78f8b3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-23 (Fri, 23 Jun 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Move tool.tool_version to tool.lineage This change makes it obvious that a Lineage object will be returned. Also removes two unused methods from ToolLineageVersion. Commit: 84e0e7e01e732b28dedebdf8a3fbea8225fece9a https://github.com/galaxyproject/galaxy/commit/84e0e7e01e732b28dedebdf8a3fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-06-24 (Sat, 24 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Access tool.lineage only if tool was loaded Commit: a42abc03e0b018546137471f302e28a39f3f7b2b https://github.com/galaxyproject/galaxy/commit/a42abc03e0b018546137471f302e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py R lib/galaxy/tools/toolbox/lineages/stock.py R lib/galaxy/tools/toolbox/lineages/tool_shed.py A lib/galaxy/util/tool_version.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/tools/tool_version_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #4119 from mvdbeek/version_switch_fix Merge ShedToolLineage and StockLineage to ToolLineage Compare: https://github.com/galaxyproject/galaxy/compare/516f7bff63fe...a42abc03e0b0

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[galaxyproject/galaxy] 422add: Fix problem in collection download tests related t...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 422add1c480ff0726cd691bccb7a28ec479dcee0 https://github.com/galaxyproject/galaxy/commit/422add1c480ff0726cd691bccb7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M test/api/test_dataset_collections.py Log Message: ----------- Fix problem in collection download tests related to ID references. DatasetsCollectionElement ids were being confused with HDA ids. Commit: 516f7bff63fe8339ec29ce544a509a228d903304 https://github.com/galaxyproject/galaxy/commit/516f7bff63fe8339ec29ce544a50… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M test/api/test_dataset_collections.py Log Message: ----------- Merge pull request #4281 from jmchilton/test_fixes Fix problem in collection download tests related to ID references. Compare: https://github.com/galaxyproject/galaxy/compare/3529897b8888...516f7bff63fe

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[galaxyproject/galaxy] c90b94: Instead of setting the tags from a list, workflow ...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: c90b94311e5427da95a36a9661c1d0eb19e16fc2 https://github.com/galaxyproject/galaxy/commit/c90b94311e5427da95a36a9661c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py Log Message: ----------- Instead of setting the tags from a list, workflow PJAs will now append tags, so propagating tags will work alongside this feature. Commit: 01510af8f57508877dda205cb0afdc144bfa73c2 https://github.com/galaxyproject/galaxy/commit/01510af8f57508877dda205cb0af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Consistent spacing (not a fan of the rule, but consistency is better) Commit: 472ff8ce520a6327179dd54c301db763ea7e979b https://github.com/galaxyproject/galaxy/commit/472ff8ce520a6327179dd54c301d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Fix for when item.tags is undefined Commit: fc613d2d60c126b3b37c9ebe3ddbd9cc58803643 https://github.com/galaxyproject/galaxy/commit/fc613d2d60c126b3b37c9ebe3ddb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py Log Message: ----------- Merge pull request #4188 from dannon/workflow_pja_add_not_set_tags [17.05] Hashtags w/ workflow-defined tags fix Compare: https://github.com/galaxyproject/galaxy/compare/d0893b91ae28...fc613d2d60c1

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[galaxyproject/galaxy] 562489: Fix #3990, don't chown non-galaxy files
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 562489ad013a3322c584b7665a0381ba39590fbd https://github.com/galaxyproject/galaxy/commit/562489ad013a3322c584b7665a03… Author: dpryan79 <dpryan79(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix #3990, don't chown non-galaxy files Commit: 3529897b88889b98e61efcec8e50fa56395281b4 https://github.com/galaxyproject/galaxy/commit/3529897b88889b98e61efcec8e50… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4186 from dpryan79/fix3990 Fix #3990, don't chown non-galaxy files Compare: https://github.com/galaxyproject/galaxy/compare/dab07a67151e...3529897b8888

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[galaxyproject/galaxy] 55956f: Expose 4 more rows from the galaxy_user table to h...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55956fe2ca49fe9a1d1a8fc52b221e6fc05e07a6 https://github.com/galaxyproject/galaxy/commit/55956fe2ca49fe9a1d1a8fc52b22… Author: Tim Thompson <tim.thompson(a)xdbio.com> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Expose 4 more rows from the galaxy_user table to help out sys admins doing user management via the API Commit: e320fd4a2009aa4c155d0cbbdd549a9f07295108 https://github.com/galaxyproject/galaxy/commit/e320fd4a2009aa4c155d0cbbdd54… Author: XDtim <tim.thompson(a)xdbio.com> Date: 2017-07-03 (Mon, 03 Jul 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Impliment review comments from @nsoranzo Commit: 57d5b485b505f64fa9035a1c739c4030ae8951d9 https://github.com/galaxyproject/galaxy/commit/57d5b485b505f64fa9035a1c739c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-04 (Tue, 04 Jul 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge remote-tracking branch 'XDtim/dev' into users_api Commit: d9607684ef7d880e213d4e08d07ed2582875e286 https://github.com/galaxyproject/galaxy/commit/d9607684ef7d880e213d4e08d07e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py A test/integration/test_config_options_users.py Log Message: ----------- Tweak exposing user attributes to use an include list instead of exclude list. This allows for the addition of new dictifiable attributes on user like in 55956fe2ca49fe9a1d1a8fc52b221e6fc05e07a6 without exposing these attributes to non-admin users. Commit: dab07a67151e59ae989c6dd07ea272a03acdb36b https://github.com/galaxyproject/galaxy/commit/dab07a67151e59ae989c6dd07ea2… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/users.py A test/integration/test_config_options_users.py Log Message: ----------- Merge pull request #4274 from jmchilton/users_api Expose more user properties to admins via the API. Compare: https://github.com/galaxyproject/galaxy/compare/9eb3c0f40a42...dab07a67151e

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[galaxyproject/galaxy] 0ff61d: Fix Registry.get_datatype_by_extension() to return...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77 https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. Commit: c8eff858d68cdbea85524c4e366cc479ba556dcd https://github.com/galaxyproject/galaxy/commit/c8eff858d68cdbea85524c4e366c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Remove float style from color picker label Commit: bd2d52800e7776ead1c8c7af53995d13cd288397 https://github.com/galaxyproject/galaxy/commit/bd2d52800e7776ead1c8c7af5399… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #4233 from guerler/fix_color_picker_release [17.05] Remove float style from color picker label Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233 https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4230 from nsoranzo/release_16.07_backport_4224 [16.07] Backport #4224 Commit: fada8d2a60e625cf16fce7e20715422f86d6f40c https://github.com/galaxyproject/galaxy/commit/fada8d2a60e625cf16fce7e20715… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: bfb3ce6e79074c42803444701e814c65631ac0cd https://github.com/galaxyproject/galaxy/commit/bfb3ce6e79074c42803444701e81… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: test/functional/tools/sample_datatypes_conf.xml Commit: d0893b91ae281a17b3ae1bc210f197c6f259103c https://github.com/galaxyproject/galaxy/commit/d0893b91ae281a17b3ae1bc210f1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: 9eb3c0f40a425b74adc03ee0e72442a292225c98 https://github.com/galaxyproject/galaxy/commit/9eb3c0f40a425b74adc03ee0e724… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/style/less/ui.less M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_17.05' into dev Conflicts: static/style/blue/base.css test/functional/tools/sample_datatypes_conf.xml Compare: https://github.com/galaxyproject/galaxy/compare/7baf86f7c137...9eb3c0f40a42

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[galaxyproject/galaxy] 0ff61d: Fix Registry.get_datatype_by_extension() to return...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77 https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233 https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4230 from nsoranzo/release_16.07_backport_4224 [16.07] Backport #4224 Commit: fada8d2a60e625cf16fce7e20715422f86d6f40c https://github.com/galaxyproject/galaxy/commit/fada8d2a60e625cf16fce7e20715… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: bfb3ce6e79074c42803444701e814c65631ac0cd https://github.com/galaxyproject/galaxy/commit/bfb3ce6e79074c42803444701e81… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: test/functional/tools/sample_datatypes_conf.xml Commit: d0893b91ae281a17b3ae1bc210f197c6f259103c https://github.com/galaxyproject/galaxy/commit/d0893b91ae281a17b3ae1bc210f1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Compare: https://github.com/galaxyproject/galaxy/compare/bd2d52800e77...d0893b91ae28

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