February 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 997e3a: commit Test mutable confs
by GitHub 11 Feb '16

11 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 997e3abfb0f0a9db4c5c1832f4bb1c8b47f2c201 https://github.com/galaxyproject/usegalaxy-playbook/commit/997e3abfb0f0a9db… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml Log Message: ----------- commit Test mutable confs uploaded the backup version from PB to Test because of accidental overwrite and playbook reordered it

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[galaxyproject/usegalaxy-playbook] 5f5599: update Main's mutable confs
by GitHub 11 Feb '16

11 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5f5599998c9d8a379f31e0dd5e39d49a62c060cb https://github.com/galaxyproject/usegalaxy-playbook/commit/5f5599998c9d8a37… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update Main's mutable confs

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[galaxyproject/galaxy] 2ddf6e: Remove broken and hidden fix_errors tool.
by GitHub 10 Feb '16

10 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ddf6eed639957369e3891d8766fa9f5c3d48c32 https://github.com/galaxyproject/galaxy/commit/2ddf6eed639957369e3891d8766f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M config/tool_conf.xml.sample R tools/validation/fix_errors.py R tools/validation/fix_errors.xml R tools/validation/fix_errors_code.py R tools/validation/validate.py Log Message: ----------- Remove broken and hidden fix_errors tool. Commit: 8703f3bd9ef595fb3b77a7021c85174f8502efa5 https://github.com/galaxyproject/galaxy/commit/8703f3bd9ef595fb3b77a7021c85… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: R tools/plotting/plot_filter.py R tools/plotting/plotter.py Log Message: ----------- Remove unused files. Commit: 39da6c327857a028d3540ec7e7c3b9aa101ff132 https://github.com/galaxyproject/galaxy/commit/39da6c327857a028d3540ec7e7c3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/sr_mapping/srma_wrapper.xml M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py Log Message: ----------- Fix the remaining 2180 flake8 errors in tools/ . Commit: f8a6ee3354072d6edc8f7bf002d81e96285f17f0 https://github.com/galaxyproject/galaxy/commit/f8a6ee3354072d6edc8f7bf002d8… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M config/tool_conf.xml.sample M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py R tools/plotting/plot_filter.py R tools/plotting/plotter.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/sr_mapping/srma_wrapper.xml R tools/validation/fix_errors.py R tools/validation/fix_errors.xml R tools/validation/fix_errors_code.py R tools/validation/validate.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py Log Message: ----------- Merge pull request #1713 from nsoranzo/flake8_fixes Fix the remaining 2180 flake8 errors in tools/ . Compare: https://github.com/galaxyproject/galaxy/compare/1e46198becdb...f8a6ee335407

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[galaxyproject/galaxy] a4a104: API: allow filtering by date using string format Y...
by GitHub 10 Feb '16

10 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a4a104dcc2f020ed4100ed7edda75dd1d2857578 https://github.com/galaxyproject/galaxy/commit/a4a104dcc2f020ed4100ed7edda7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API: allow filtering by date using string format YYYY-MM-DDTHH:MM (by removing the 'T' from when parsing the filter), allow filtering by hybrid properties and not just columns; API, history contents: allow filtering, order, and limit/offset of contents (in the same format as histories) Commit: 1cb1c48975e915ab98a0776a6a37dca914c542d4 https://github.com/galaxyproject/galaxy/commit/1cb1c48975e915ab98a0776a6a37… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Managers, history contents: use text fn to wrap history_content_type filters; API, history contents: correct default order Commit: d4374bd0617d162db1a7b2803f1cc42880e0a9c7 https://github.com/galaxyproject/galaxy/commit/d4374bd0617d162db1a7b2803f1c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py Log Message: ----------- Managers, history contents: remove model_class column, remove content_type from allowed filters (does not work on postgres), general cleanup Commit: 31e252743e633ffb48c655a3a12f4640a90c155e https://github.com/galaxyproject/galaxy/commit/31e252743e633ffb48c655a3a12f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API, history contents: provide support for deleted and visible filters as bare keywords (e.g. 'deleted=True') Commit: 81b4eb484d55c30b386cce0af3141d6e5d4ee565 https://github.com/galaxyproject/galaxy/commit/81b4eb484d55c30b386cce0af314… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API, history contents: remove unreadable preceding binary operator, add blank line Commit: 120fef8cd09c4b158e5577833d89db60e7da3caf https://github.com/galaxyproject/galaxy/commit/120fef8cd09c4b158e5577833d89… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py Log Message: ----------- API, History contents: allow filtering by state, history_content_type Commit: d95c7c9d2b25d8b27d342f94c28d5c967c4af47a https://github.com/galaxyproject/galaxy/commit/d95c7c9d2b25d8b27d342f94c28d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API, history contents: split code path in index to prevent backwards incompatibility Commit: c423f1eaa5f17190bf79f5f97b4f8a41903f5e3b https://github.com/galaxyproject/galaxy/commit/c423f1eaa5f17190bf79f5f97b4f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py A test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- API, history_contents: allow filtering by update/create times, inclusion in type_id list; models: add type_id as sql property on HDCAs and HDAs; managers: allow count; testing Commit: 1561759919073caa77d25eec9930b0f2235a82a1 https://github.com/galaxyproject/galaxy/commit/1561759919073caa77d25eec9930… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: A .ci/first_startup.sh M .travis.yml M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.xml A config/plugins/interactive_environments/phinch/static/js/phinch.js A config/plugins/interactive_environments/phinch/templates/phinch.mako A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst M doc/source/project/issues.rst A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py A 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/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.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/linters/inputs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/install_manager.py M scripts/binary_compatibility.py M scripts/bootstrap_history.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/manage_repository.mako M templates/user/info.mako M templates/user/username.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M test-data/3.bam M test/api/test_workflows.py M test/api/workflows_format_2/converter.py A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py M tools/data_source/upload.xml M tools/phenotype_association/linkToDavid.xml M tox.ini Log Message: ----------- (merge conflicts with dev) Commit: 1e46198becdba27f98f7ce93bb27f21ae59392a1 https://github.com/galaxyproject/galaxy/commit/1e46198becdba27f98f7ce93bb27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py A test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Merge pull request #1602 from carlfeberhard/history.contents API, history contents: allow filters, limit/offset, and ordering Compare: https://github.com/galaxyproject/galaxy/compare/6a5d2653a706...1e46198becdb

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[galaxyproject/galaxy] 167eb5: Modify show_param input walking to account for mul...
by GitHub 10 Feb '16

10 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 167eb50dd39cd362126ca6fecf2d1d20b111464b https://github.com/galaxyproject/galaxy/commit/167eb50dd39cd362126ca6fecf2d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Modify show_param input walking to account for multiple data parmaeters. xref https://github.com/galaxyproject/galaxy/pull/1561 fixes https://github.com/galaxyproject/galaxy/issues/1660 Commit: 6a5d2653a706fd82979d83f245ec4fbb89de71ff https://github.com/galaxyproject/galaxy/commit/6a5d2653a706fd82979d83f245ec… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #1670 from jmchilton/input_param_walking_fix Modify show_param input walking to account for multiple data parameters. Compare: https://github.com/galaxyproject/galaxy/compare/74c3ff0f5618...6a5d2653a706

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[galaxyproject/galaxy] bf4e73: Update david identifier types
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf4e736c3ca8e129ff8c75f8261c08f303c76080 https://github.com/galaxyproject/galaxy/commit/bf4e736c3ca8e129ff8c75f8261c… Author: pavanvidem <videmp(a)informatik.uni-freiburg.de> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M tools/phenotype_association/linkToDavid.xml Log Message: ----------- Update david identifier types David identifier types seem to be changed. Some of them are no more available on david web server. Commit: 776180ab80b352a60713fbf6576adbfc4934ed85 https://github.com/galaxyproject/galaxy/commit/776180ab80b352a60713fbf6576a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- show all available information for current library and the opened folder Commit: 65d9ec9cab2b6e46fa7a067948bba69e3255c1ff https://github.com/galaxyproject/galaxy/commit/65d9ec9cab2b6e46fa7a067948bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1705 from martenson/fix-location-info [16.01] libraries - fix location info Commit: db9c0b89ab56d5ba0b272bb7ddaa220ed3b48c14 https://github.com/galaxyproject/galaxy/commit/db9c0b89ab56d5ba0b272bb7ddaa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge release_16.01 into dev Commit: 22e84e4814b09a3fff4fcd8c44b7f83394ebc640 https://github.com/galaxyproject/galaxy/commit/22e84e4814b09a3fff4fcd8c44b7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- repack client after merge conflicts Commit: 74c3ff0f56184fa32f53fdde8928ce65bd079f1a https://github.com/galaxyproject/galaxy/commit/74c3ff0f56184fa32f53fdde8928… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1708 from martenson/dev merge 16.01 into dev Compare: https://github.com/galaxyproject/galaxy/compare/5e7dd07db653...74c3ff0f5618

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[galaxyproject/galaxy] 8d6e9d: Sets mappable metadata as list (e.g. column_names)...
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d6e9d1d775c49148b2ecd0cecc49ad5a59372bd https://github.com/galaxyproject/galaxy/commit/8d6e9d1d775c49148b2ecd0cecc4… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/output.py Log Message: ----------- Sets mappable metadata as list (e.g. column_names) from a tool wrapper Commit: fbc4fa16781f91d1f3fdfd92062352c440eeac4b https://github.com/galaxyproject/galaxy/commit/fbc4fa16781f91d1f3fdfd920623… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/parameters/output.py Log Message: ----------- put old line back Commit: 5f9e1e67c239583d35d8a7e06ad515f5323c6cc4 https://github.com/galaxyproject/galaxy/commit/5f9e1e67c239583d35d8a7e06ad5… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Fixes flake8 error Commit: 134dd40fadcb8eab1c9e60d729f414166c74befe https://github.com/galaxyproject/galaxy/commit/134dd40fadcb8eab1c9e60d729f4… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Passing metadata through update Commit: 8ab40d502578597408686f0de7481554cc9d2ef4 https://github.com/galaxyproject/galaxy/commit/8ab40d502578597408686f0de748… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh A .ci/first_startup.sh M .ci/flake8_blacklist.txt A .ci/flake8_py3_wrapper.sh M .ci/flake8_wrapper.sh A .ci/py3_sources.txt M .gitignore M .travis.yml M CONTRIBUTING.md M CONTRIBUTORS.md A Makefile M README.rst A client/.docker-build.sh A 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test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py A test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py A test/unit/web/framework/__init__.py A test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_render.py M test/unit/workflows/test_run_parameters.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/data_source/data_source.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/cutWrapper.xml M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wig_to_bigwig.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_importer.xml M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into metadata_list_fix Commit: 061828aac6cb663eb48767204c9e6c604c5ef14a https://github.com/galaxyproject/galaxy/commit/061828aac6cb663eb48767204c9e… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Passing metadata through update Commit: d370d3b012d9dc7e7976a94939506c6e8e7907a2 https://github.com/galaxyproject/galaxy/commit/d370d3b012d9dc7e7976a9493950… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- passing metadata through as list: revert value setting Commit: 5e7dd07db6532f54605c771aab706249511969a0 https://github.com/galaxyproject/galaxy/commit/5e7dd07db6532f54605c771aab70… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #961 from yhoogstrate/metadata_list_fix Sets mappable list-type metadata (e.g. column_names) from a tool wrapper Compare: https://github.com/galaxyproject/galaxy/compare/34376b1d8f25...5e7dd07db653

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[galaxyproject/galaxy] 83bb8c: Visualization plugins: add routes that more closel...
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83bb8cbc11c242ebb0ee2c9338d284c2c0d306e3 https://github.com/galaxyproject/galaxy/commit/83bb8cbc11c242ebb0ee2c9338d2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Visualization plugins: add routes that more closely match potential static assets in order to allow easier, relative hrefs (for both new and saved visualizations); Grids: allow operations to use named routes by adding kwarg '__route_name__' Commit: a89125cb76384462571275bbd68be77bfe6336f3 https://github.com/galaxyproject/galaxy/commit/a89125cb76384462571275bbd68b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Fix to 83bb8cb: remove debugging Commit: 683c49c185be37435bb7e4736799a2ccb3145f56 https://github.com/galaxyproject/galaxy/commit/683c49c185be37435bb7e4736799… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Visualization plugins: switch the registry to using the new urls, add similar url changes for interactive_environments urls Commit: 0718558a16b7f202818f698247fba5c1c21c32a9 https://github.com/galaxyproject/galaxy/commit/0718558a16b7f202818f698247fb… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Visualization plugins: remove print statement Commit: 34376b1d8f25ef51aba1f7ec0081a5b24eb8153a https://github.com/galaxyproject/galaxy/commit/34376b1d8f25ef51aba1f7ec0081… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Merge pull request #1615 from carlfeberhard/plugin-urls Visualization plugins: add routes that more closely match potential s… Compare: https://github.com/galaxyproject/galaxy/compare/db1bb2f19142...34376b1d8f25

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[galaxyproject/galaxy] 9e0b34: Remove deprecated symbolic link added in 15.03.
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9e0b348559211a0c6b26e37ccfa9bd9413516aae https://github.com/galaxyproject/galaxy/commit/9e0b348559211a0c6b26e37ccfa9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: R lib/galaxy/metadata Log Message: ----------- Remove deprecated symbolic link added in 15.03. Was added for running jobs - so this may break running jobs if people upgrade from 15.03 (or earlier) to 16.04 (or later) directly. Commit: f21cde984b866ca910d8b447be24a35c796b82cb https://github.com/galaxyproject/galaxy/commit/f21cde984b866ca910d8b447be24… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Style fix - use more Pythonic name than linePieces. Commit: 2d86e00a5af20420a31e67cea5c567e41997b0e2 https://github.com/galaxyproject/galaxy/commit/2d86e00a5af20420a31e67cea5c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py Log Message: ----------- Cleanup some relative imports in galaxy.datatypes. Commit: 3861cffdc5c1b385d848f91fdf49213f661432b6 https://github.com/galaxyproject/galaxy/commit/3861cffdc5c1b385d848f91fdf49… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Rename galaxy.model.datatypes_registry... ... to make it clear it shouldn't be accessed outside that module. Commit: ba0d06f6ba165f2fd3d5d2742b1ada152bcd73b0 https://github.com/galaxyproject/galaxy/commit/ba0d06f6ba165f2fd3d5d2742b1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Eliminate more use of relative imports in datatypes modules. Commit: 3217bc78323271db4661e4aea308497d4f58fc81 https://github.com/galaxyproject/galaxy/commit/3217bc78323271db4661e4aea308… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M test/unit/tools/test_column_parameters.py M test/unit/tools_support.py Log Message: ----------- Don't construct a DatatypesRegistry just for tests in galaxy.model. Construct the model in the tests, this should cause galaxy.model to import much faster. Commit: 1f4b32903270926389a9993b3938c169f105371d https://github.com/galaxyproject/galaxy/commit/1f4b32903270926389a9993b3938… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/tools/exception_handling.py A lib/galaxy/util/ucsc.py M tools/filters/wiggle_to_simple.py M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Refactor galaxy.tools.exception_handling... ... so datatype module doesn't need to import something from galaxy.tools - which causes a bunch of more things to be imported because galaxy.tools at the top-level has so many imports. Commit: 4d9498c4c6b181779439e8211fd20c20568c40cb https://github.com/galaxyproject/galaxy/commit/4d9498c4c6b181779439e8211fd2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Elimiante runtime sniff -> registry dependency. It only existed for testing, so only require it in tests. Commit: ae493bfde0d693ae8f1560319053230496cf932d https://github.com/galaxyproject/galaxy/commit/ae493bfde0d693ae8f1560319053… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Eliminate import of registry from galaxy.model. Commit: 5756f6059720d39a75e5786283b232787a60f14e https://github.com/galaxyproject/galaxy/commit/5756f6059720d39a75e5786283b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/model/__init__.py A lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/util/none_like.py Log Message: ----------- Relocate galaxy.datatypes.metadata to galaxy.model.metadata. This eliminates the last dependency in galaxy.model on galaxy.datatypes - establishing a strict ordering of dependencies (galaxy.datatypes depends on galaxy.model and not vice versa). The galaxy.datatypes.metadata interface needs to remain in place for tool shed datatypes and is perfectly reasonable to use from within the datatypes module - it now depends on galaxy.model.metadata and exports the same interfac. In the longer run, this is a better, more explict design and should eliminate certain classes of problems with circular dependencies. Fixes #1552 Commit: df5a3a6da7749b47e50a2faffb5c8f8a8a282230 https://github.com/galaxyproject/galaxy/commit/df5a3a6da7749b47e50a2faffb5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: R scripts/set_metadata.py R set_metadata.sh Log Message: ----------- Eliminate legacy set metadata entry points. Commit: 499357e508035e7c9ffb5d711e0f355e960e1e05 https://github.com/galaxyproject/galaxy/commit/499357e508035e7c9ffb5d711e0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M tools/data_source/data_source.py M tools/data_source/upload.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Remove unneeded galaxy.model import in upload.py... ... and document the ability to remove from other data sources. Commit: 448aee9f004befa8ebc02de2ca726dca8e4c22c9 https://github.com/galaxyproject/galaxy/commit/448aee9f004befa8ebc02de2ca72… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M tools/data_source/upload.py Log Message: ----------- Fix for multi-byte char problem in PR #1556... ... caught by @nsoranzo of course. Commit: db1bb2f19142e8a9a0a08ffeb9d4295a4f153fcb https://github.com/galaxyproject/galaxy/commit/db1bb2f19142e8a9a0a08ffeb9d4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py R lib/galaxy/metadata M lib/galaxy/model/__init__.py A lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/util/none_like.py A lib/galaxy/util/ucsc.py R scripts/set_metadata.py R set_metadata.sh M test/unit/tools/test_column_parameters.py M test/unit/tools_support.py M tools/data_source/data_source.py M tools/data_source/upload.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Merge pull request #1556 from jmchilton/datatype_imports Code design and legacy cleanup of datatypes and metadata. Compare: https://github.com/galaxyproject/galaxy/compare/e6dc96def3b9...db1bb2f19142

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[galaxyproject/galaxy] 776180: show all available information for current library...
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 776180ab80b352a60713fbf6576adbfc4934ed85 https://github.com/galaxyproject/galaxy/commit/776180ab80b352a60713fbf6576a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- show all available information for current library and the opened folder Commit: 65d9ec9cab2b6e46fa7a067948bba69e3255c1ff https://github.com/galaxyproject/galaxy/commit/65d9ec9cab2b6e46fa7a067948bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1705 from martenson/fix-location-info [16.01] libraries - fix location info Compare: https://github.com/galaxyproject/galaxy/compare/bf4e736c3ca8...65d9ec9cab2b

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