- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 2e2d46: Update Japanese translation
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e2d46491ff4ced0a5b9c7999c442b8b29bd4fc5 https://github.com/galaxyproject/galaxy/commit/2e2d46491ff4ced0a5b9c7999c44… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/nls/ja/locale.js Log Message: ----------- Update Japanese translation Commit: 26ef9b02c814cca93b2278be6e462f7d6b8dca2d https://github.com/galaxyproject/galaxy/commit/26ef9b02c814cca93b2278be6e46… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/nls/ja/locale.js Log Message: ----------- Update Localization Edit history Annotaion was used in locale.js But it must be 'Edit history annotation' . It is written in client/galaxy/scripts/mvc/history/history-view-edit.js Commit: 76fa748c47901195379bfd2bb40f9ee5080cdf90 https://github.com/galaxyproject/galaxy/commit/76fa748c47901195379bfd2bb40f… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/nls/ja/locale.js Log Message: ----------- Localization Admin Commit: 68e6cdbe81cd5d310e770248fcd6aeef05ff5123 https://github.com/galaxyproject/galaxy/commit/68e6cdbe81cd5d310e770248fcd6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/nls/ja/locale.js Log Message: ----------- Merge pull request #4304 from manabuishii/nls_ja_locale Update Japanese translation Compare: https://github.com/galaxyproject/galaxy/compare/641a268d7137...68e6cdbe81cd

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[galaxyproject/galaxy] 8df7b3: Update __init__.py
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8df7b309a977eed9d5926a28afe90a1cf4f07580 https://github.com/galaxyproject/galaxy/commit/8df7b309a977eed9d5926a28afe9… Author: cche <cche(a)users.noreply.github.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Update __init__.py Commit: e4ab9b08c885eb5c6be2318e6b67a1975e2db408 https://github.com/galaxyproject/galaxy/commit/e4ab9b08c885eb5c6be2318e6b67… Author: Cristian <cche(a)users.noreply.github.com> Date: 2017-06-30 (Fri, 30 Jun 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Correct indent and add a break Commit: 8a309ceca454f5b74566d33fbde28121d961eea0 https://github.com/galaxyproject/galaxy/commit/8a309ceca454f5b74566d33fbde2… Author: Cristian <> Date: 2017-06-30 (Fri, 30 Jun 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Moved the code up and added an explanatory comment. Also added spaces within the parens to match the existing style. Commit: 641a268d713767ac11dbddab1e9e7159b5b8d111 https://github.com/galaxyproject/galaxy/commit/641a268d713767ac11dbddab1e9e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #4268 from cche/cche-import-hist-withsubdir Importing old exported histories failing Compare: https://github.com/galaxyproject/galaxy/compare/db486b50ef45...641a268d7137

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[galaxyproject/galaxy] d10758: Merge pull request #3077 from galaxyproject/releas...
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d10758a4f22daa24bdf55863f360493a4a3902f7 https://github.com/galaxyproject/galaxy/commit/d10758a4f22daa24bdf55863f360… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/ui/ui-modal.js M config/galaxy.ini.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js M templates/user/index.mako M templates/webapps/galaxy/workflow/run.mako M test/shed_functional/functional/test_1400_review_migration_stages.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #3077 from galaxyproject/release_16.07 [master] bring master on par with release_16.07 Commit: 378ed53a33eee02c3620310c7245e7a85d279427 https://github.com/galaxyproject/galaxy/commit/378ed53a33eee02c3620310c7245… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M 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static/scripts/libs/raven.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js A static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js A 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static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M static/style/blue/bootstrap-tour.css M static/style/blue/jquery.rating.css R static/style/blue/tool_menu.css M static/welcome.html.sample R templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_toolsheds.mako M templates/admin/tool_shed_repository/common.mako R templates/admin/tool_shed_repository/preview_repository.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/show_params.mako M templates/user/change_password.mako M templates/user/info.mako M templates/user/register.mako M templates/user/username.mako M templates/webapps/galaxy/admin/index.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M 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test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_libraries.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py A test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/api.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py A test/casperjs/api-batch-tests.js M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/color_param.xml M test/functional/tools/column_multi_param.xml M test/functional/tools/column_param.xml M test/functional/tools/identifier_collection.xml M 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test/functional/tools/version_command_tool_dir.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/qunit/package.json M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/qunit/tests/history_contents_model_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_0310_hg_api_features.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M 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test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_mapping.py M test/unit/test_galaxy_transactions.py M test/unit/test_objectstore.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tools/data_source/data_source.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.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/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.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.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/secure_hash_message_digest.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/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py 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/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/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/phenotype_association/pagetag.py M tools/phenotype_association/senatag.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/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge branch 'release_16.10' Commit: 8b538f17feb17eba11b3025a2dfb3ba35414a78e https://github.com/galaxyproject/galaxy/commit/8b538f17feb17eba11b3025a2dfb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/plugins/tours/core.history.yaml M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/output_collect.py M static/maps/mvc/tool/tool-form-composite.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.map M static/scripts/mvc/tool/tool-form-composite.js M test/api/test_tools.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tox.ini Log Message: ----------- Merge branch 'release_16.10' Commit: 3a2ff46c28172ef78510f4bea2f4be75ce660667 https://github.com/galaxyproject/galaxy/commit/3a2ff46c28172ef78510f4bea2f4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt 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/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .ci/py3_sources.txt M Makefile 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-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.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/ui/ui-misc.js A client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/local_conda_mapping.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/rstudio/config/rstudio.xml M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/charts/webpack.config.js M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js A display_applications/igv/genome_fasta.xml M doc/schema_template.md M doc/source/admin/dependency_resolvers.rst M doc/source/admin/interactive_environments.rst M doc/source/admin/interactive_environments.svg M doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M doc/source/dev/faq.rst M doc/source/dev/interactive_environments.rst R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst M doc/source/project/organization.rst A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M lib/galaxy/actions/admin.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M 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lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M 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test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_mapper.py M test/unit/test_sockets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_tool_deps.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/workflow_support.py M tools/data_source/fetch.py R tools/filters/gff/sort_gtf.py M tools/plotting/bar_chart.xml M tox.ini Log Message: ----------- Merge branch 'release_17.01' Commit: 52b5e62de498f08ccd55f792d555c884f8bd6e98 https://github.com/galaxyproject/galaxy/commit/52b5e62de498f08ccd55f792d555… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M display_applications/igv/bigwig.xml M doc/source/releases/17.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/runners/__init__.py M 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templates/webapps/galaxy/user/manage_info.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' Commit: dd439530509f12ede24f8e9763f2bdb5314e2c13 https://github.com/galaxyproject/galaxy/commit/dd439530509f12ede24f8e9763f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' Commit: 7e64fa395c6c56a0973f56ecc1aa615f15d9fe80 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static/scripts/mvc/workflow/workflow-view.js A static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/ui/autocom_tagging.js M static/scripts/viz/phyloviz.js M static/style/blue/base.css M templates/admin/reload_tool.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/grid_base.mako M templates/show_params.mako R templates/user/dbkeys.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/galaxy.masthead.mako R templates/webapps/galaxy/user/manage_info.mako M templates/webapps/galaxy/workflow/display.mako R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako M 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test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml M test/qunit/package.json M test/qunit/test-data/paired-collection-creator.data.js M test/qunit/tests/form_tests.js M test/qunit/tests/ui_tests.js M test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py A test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.xml M tools/filters/trimmer.py M tools/filters/trimmer.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge branch 'release_17.05' Commit: d1681153bece3ed294e5b305e18d822745638b5b https://github.com/galaxyproject/galaxy/commit/d1681153bece3ed294e5b305e18d… Author: Ashok Varadharajan <ashvark(a)users.noreply.github.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M CONTRIBUTING.md A SECURITY_POLICY.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.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/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/overrides.less M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/config/neo.xml M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M 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static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.library.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.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 R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.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 R templates/webapps/galaxy/visualization/list_published.mako R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/list_published.mako R templates/webapps/galaxy/workflow/run.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 A test-data/5_Ig-like.gff 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 M test/unit/unittest_utils/galaxy_mock.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/wc_gnu.xml Log Message: ----------- Merge pull request #1 from galaxyproject/dev Merging Commit: 320da989b19a281542d47fe5ef8064aac5db2576 https://github.com/galaxyproject/galaxy/commit/320da989b19a281542d47fe5ef80… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Log Message: ----------- Merge remote-tracking branch 'upstream/master' into dev Commit: ccf12bb26157353769b25566df31ff2189c9c686 https://github.com/galaxyproject/galaxy/commit/ccf12bb26157353769b25566df31… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/model/__init__.py Log Message: ----------- allowing 'real_system_username' to accept a common-system-user to run all the jobs Commit: db486b50ef459a99356ab67c7c69e25be2f165e9 https://github.com/galaxyproject/galaxy/commit/db486b50ef459a99356ab67c7c69… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #4294 from ashvark/real_system_username Submitting the galaxy jobs as a predefined system user: using 'real_system_username' Compare: https://github.com/galaxyproject/galaxy/compare/feefa03ba234...db486b50ef45

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[galaxyproject/galaxy] 6c4936: Localization support for Tool Help
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c493693c1f610653bcd3bbc0e75c4848fbc81a0 https://github.com/galaxyproject/galaxy/commit/6c493693c1f610653bcd3bbc0e75… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Localization support for Tool Help Commit: e5383b8fe42eab9cb22368a9eb8c5ebd082d1843 https://github.com/galaxyproject/galaxy/commit/e5383b8fe42eab9cb22368a9eb8c… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- forget l Commit: feefa03ba2347f57bc37838ba695e9c28a822191 https://github.com/galaxyproject/galaxy/commit/feefa03ba2347f57bc37838ba695… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Merge pull request #4306 from manabuishii/patch-6 Localization support for Tool Help Compare: https://github.com/galaxyproject/galaxy/compare/bf63ea2bdc48...feefa03ba234

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[galaxyproject/galaxy] 51df43: Support Localization Scratchbook
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51df43b98a9fc78a4ade71313eda571ab72f0af6 https://github.com/galaxyproject/galaxy/commit/51df43b98a9fc78a4ade71313eda… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Support Localization Scratchbook Commit: bf63ea2bdc480dcbe4a12b5dc1bbaf7475e99536 https://github.com/galaxyproject/galaxy/commit/bf63ea2bdc480dcbe4a12b5dc1bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Merge pull request #4307 from manabuishii/patch-7 Support Localization Scratchbook Compare: https://github.com/galaxyproject/galaxy/compare/030eaf83ac42...bf63ea2bdc48

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[galaxyproject/galaxy] 324d78: Turn all item selection grids from mako to diction...
by GitHub 12 Jul '17

12 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 324d78a5639b30a07c3afc3bed01508c4092a19f https://github.com/galaxyproject/galaxy/commit/324d78a5639b30a07c3afc3bed01… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M templates/webapps/galaxy/page/select_items_grid.mako Log Message: ----------- Turn all item selection grids from mako to dictionary response mode Commit: dfa4343e8fc717c4aa521ba8b55ce5cf306369d7 https://github.com/galaxyproject/galaxy/commit/dfa4343e8fc717c4aa521ba8b55c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: R templates/webapps/galaxy/page/select_items_grid.mako Log Message: ----------- Remove selection grid mako Commit: 7ae74c51d9eb9705f3171965a1f02e6c5ff69bf3 https://github.com/galaxyproject/galaxy/commit/7ae74c51d9eb9705f3171965a1f0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Remove unused, legacy link Commit: 8a7783809f40fad9556725f5cc59fa816f164175 https://github.com/galaxyproject/galaxy/commit/8a7783809f40fad9556725f5cc59… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/galaxy.pages.js.map M static/maps/mvc/grid/grid-view.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/galaxy.pages.js M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Use grid view to build embedded selection grids for pages Commit: 378319776bd1a7537053b1c2b3a9e65b58b63c8a https://github.com/galaxyproject/galaxy/commit/378319776bd1a7537053b1c2b3a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M client/galaxy/scripts/galaxy.pages.js M static/maps/galaxy.pages.js.map M static/scripts/galaxy.pages.js Log Message: ----------- Add insert and embed functions Commit: 3fcd73ee35fe4c9101bc04f36310153e72db9cfa https://github.com/galaxyproject/galaxy/commit/3fcd73ee35fe4c9101bc04f36310… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M client/galaxy/scripts/galaxy.pages.js M static/maps/galaxy.pages.js.map M static/scripts/galaxy.pages.js Log Message: ----------- Remove change to original handler function Commit: 030eaf83ac4226c052159357bd65ad9279cacf5d https://github.com/galaxyproject/galaxy/commit/030eaf83ac4226c052159357bd65… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/webapps/galaxy/controllers/page.py M static/maps/galaxy.pages.js.map M static/maps/mvc/grid/grid-view.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/galaxy.pages.js M static/scripts/mvc/grid/grid-view.js M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/select_items_grid.mako Log Message: ----------- Merge pull request #4293 from guerler/grid_pages_selection_grid Use dictionary endpoints for item selection grids in page editor Compare: https://github.com/galaxyproject/galaxy/compare/45288ccce067...030eaf83ac42

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[galaxyproject/galaxy] 0bc083: Initialize PithosObjectStore (Pithos backend)
by GitHub 11 Jul '17

11 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0bc0833bd14992cc8db9329ec1fcfa8d312869c1 https://github.com/galaxyproject/galaxy/commit/0bc0833bd14992cc8db9329ec1fc… Author: Stavros Sachtouris <saxtouri(a)admin.grnet.gr> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/pithos.py Log Message: ----------- Initialize PithosObjectStore (Pithos backend) Introduce galay.objectstore.pithos module Create the PithosObjectStore class Create auxiliary methods to: - define/parse configuration for Pithos+ - authenticate with Synnefo - initialize a Pithos+ client Commit: fe6a983a881507c157cdb614a414e3d38fb3c622 https://github.com/galaxyproject/galaxy/commit/fe6a983a881507c157cdb614a414… Author: Stavros Sachtouris <saxtouri(a)admin.grnet.gr> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M lib/galaxy/objectstore/pithos.py Log Message: ----------- Implement "exists" and "_construct_path" methods The "_construct_path" constructs a path from an object and will also be used in methods to follow. Commit: 8049c0f76d25f9efb96cc6bb5ebbcee9ebc93489 https://github.com/galaxyproject/galaxy/commit/8049c0f76d25f9efb96cc6bb5ebb… Author: Stavros Sachtouris <saxtouri(a)admin.grnet.gr> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M lib/galaxy/objectstore/pithos.py Log Message: ----------- Implement some cache-based methods + basic cache Methods: exists, create, size, delete, get_data, get_filename Also, implemented basic cache functionality: _get_cache_path, _in_cache, _fix_permissions, _pull_into_cache Did not implement a "_pull_from_cache" method, since kamaki offers simple commands for this. Commit: f0626839114e96a7427d9b114a1d91efa6c9eafe https://github.com/galaxyproject/galaxy/commit/f0626839114e96a7427d9b114a1d… Author: Stavros Sachtouris <saxtouri(a)admin.grnet.gr> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M lib/galaxy/objectstore/pithos.py Log Message: ----------- Implement methods for sync, share and quotas Namely: update_from_file, get_object_url, get_store_usage_percent Commit: c9966dfc465d4026b8dd3a423f3d482a6a82ee5d https://github.com/galaxyproject/galaxy/commit/c9966dfc465d4026b8dd3a423f3d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M lib/galaxy/objectstore/pithos.py Log Message: ----------- Add catch import errors for conditional request Commit: 45288ccce067c138045de62a378df855d3fe1913 https://github.com/galaxyproject/galaxy/commit/45288ccce067c138045de62a378d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/pithos.py Log Message: ----------- Merge pull request #3611 from saxtouri/feature-pithos Synnefo/Pithos+ object store backend Compare: https://github.com/galaxyproject/galaxy/compare/3d98ce7d8601...45288ccce067

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[galaxyproject/galaxy] 4761e2: Redirect masthead link to client endpoint
by GitHub 10 Jul '17

10 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4761e2ccdddd9d14b49acd8952fee2a817aa8c1d https://github.com/galaxyproject/galaxy/commit/4761e2ccdddd9d14b49acd8952fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/layout/menu.js Log Message: ----------- Redirect masthead link to client endpoint Commit: a8a9ac3abe68968e4f801a2e0af76b282eb31648 https://github.com/galaxyproject/galaxy/commit/a8a9ac3abe68968e4f801a2e0af7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: R templates/webapps/galaxy/history/list_published.mako Log Message: ----------- Remove published histories mako Commit: 60ae053671ee8e9a1c50c6660ae80090c4d24172 https://github.com/galaxyproject/galaxy/commit/60ae053671ee8e9a1c50c6660ae8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Modify controller endpoint to return dict instead of filled mako template Commit: fbabc0e8e4202006005ad325430d84f90ebf570e https://github.com/galaxyproject/galaxy/commit/fbabc0e8e4202006005ad325430d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Register endpoint as client side endpoint Commit: 411268c013cc669341146f420097d8f1f7dfdf11 https://github.com/galaxyproject/galaxy/commit/411268c013cc669341146f420097… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: 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: ----------- Apply webpack Commit: 3d98ce7d8601761fe73753ade116cdd4a11126c4 https://github.com/galaxyproject/galaxy/commit/3d98ce7d8601761fe73753ade116… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/layout/menu.js.map 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 M static/scripts/layout/menu.js R templates/webapps/galaxy/history/list_published.mako Log Message: ----------- Merge pull request #4291 from guerler/grid_published_histories Grid published histories Compare: https://github.com/galaxyproject/galaxy/compare/0d9b60fd749f...3d98ce7d8601

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[galaxyproject/galaxy] f439fd: conditional postclick execution onNext
by GitHub 10 Jul '17

10 Jul '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: f439fd30eb1f803daf8e1898bc1648c8cee131f8 https://github.com/galaxyproject/galaxy/commit/f439fd30eb1f803daf8e1898bc16… Author: Andrea Bagnacani <andrea.bagnacani(a)uni-rostock.de> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tours.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 M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tours.js Log Message: ----------- conditional postclick execution onNext Commit: e58b24db6133720edf442ca85702e4bba050e9c9 https://github.com/galaxyproject/galaxy/commit/e58b24db6133720edf442ca85702… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tours.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 M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tours.js Log Message: ----------- Merge pull request #4228 from bagnacan/release_17.05_backport_4062 [17.05] conditional postclick execution onNext Compare: https://github.com/galaxyproject/galaxy/compare/fc613d2d60c1...e58b24db6133

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[galaxyproject/galaxy] 390afd: Updating the node tooltip to add confidence level ...
by GitHub 08 Jul '17

08 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 390afd6e83c2d8d4a885a28e91664045d6102b1c https://github.com/galaxyproject/galaxy/commit/390afd6e83c2d8d4a885a28e9166… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M client/galaxy/scripts/viz/phyloviz.js M static/maps/viz/phyloviz.js.map M static/scripts/viz/phyloviz.js Log Message: ----------- Updating the node tooltip to add confidence level information Commit: ee948063e1795342404187b59faed172e4cfa16d https://github.com/galaxyproject/galaxy/commit/ee948063e1795342404187b59fae… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M client/galaxy/scripts/viz/phyloviz.js M static/maps/viz/phyloviz.js.map M static/scripts/viz/phyloviz.js Log Message: ----------- Show the confidence value as text on phylogenetic tree branches Commit: 23f3a31d277586a107dc1ecead5191e335b901dc https://github.com/galaxyproject/galaxy/commit/23f3a31d277586a107dc1ecead51… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M client/galaxy/scripts/viz/phyloviz.js M static/maps/viz/phyloviz.js.map M static/scripts/viz/phyloviz.js Log Message: ----------- Round off the confidence values Commit: c26d06839190e8d75d744bc4884cb670e44a77ee https://github.com/galaxyproject/galaxy/commit/c26d06839190e8d75d744bc4884c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M client/galaxy/scripts/viz/phyloviz.js M static/maps/viz/phyloviz.js.map M static/scripts/viz/phyloviz.js Log Message: ----------- Update logic to show node name and bootstrap Commit: 574b470eb29d7e0ee7b5d70a75ab031286ca673c https://github.com/galaxyproject/galaxy/commit/574b470eb29d7e0ee7b5d70a75ab… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/overrides.less M lib/galaxy/datatypes/tabular.py M lib/galaxy/tools/__init__.py M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into enhancement_phylocanvas Commit: 0d9b60fd749fe5affab68618984d8d1272ca0a76 https://github.com/galaxyproject/galaxy/commit/0d9b60fd749fe5affab68618984d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-07-08 (Sat, 08 Jul 2017) Changed paths: M client/galaxy/scripts/viz/phyloviz.js M static/maps/viz/phyloviz.js.map M static/scripts/viz/phyloviz.js Log Message: ----------- Merge pull request #4292 from bgruening/enhancement_phylocanvas Enhancement for Phyloviz viz plugin Compare: https://github.com/galaxyproject/galaxy/compare/c169c3a0908a...0d9b60fd749f

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[galaxyproject/galaxy] ac44db: Update tool_conf.xml.main to reflect main's curren...
by GitHub 07 Jul '17

07 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac44dbb533284bb47e4190b16821311984129d8a https://github.com/galaxyproject/galaxy/commit/ac44dbb533284bb47e4190b16821… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Update tool_conf.xml.main to reflect main's current state. Commit: c169c3a0908addeff88bae6a86f2e5ef199aeb3c https://github.com/galaxyproject/galaxy/commit/c169c3a0908addeff88bae6a86f2… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Merge pull request #4295 from davebx/update_main_tool_conf Update tool_conf.xml.main to reflect main's current state. Compare: https://github.com/galaxyproject/galaxy/compare/ba5549b47193...c169c3a0908a

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[galaxyproject/galaxy] 26d48c: Fix empty tabular output error when using discover...
by GitHub 06 Jul '17

06 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 26d48c876cd2bd39bd8c0e404d54e6de520ce1df https://github.com/galaxyproject/galaxy/commit/26d48c876cd2bd39bd8c0e404d54… Author: Pierrick Roger Mele <pierrick.rogermele(a)icloud.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/tabular.py A tools/mtbls-dwnld Log Message: ----------- Fix empty tabular output error when using discover_datasets. Commit: 4b9b3724e87e7ea0c6b81da36df5f6b00124c6c6 https://github.com/galaxyproject/galaxy/commit/4b9b3724e87e7ea0c6b81da36df5… Author: Pierrick Roger Mele <pierrick.rogermele(a)icloud.com> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: R tools/mtbls-dwnld Log Message: ----------- Remove tool symbolic link added by accident. Commit: edbe273a95d727278b37c4457912e27355ec2cf3 https://github.com/galaxyproject/galaxy/commit/edbe273a95d727278b37c4457912… Author: Pierrick Roger Mele <pierrick.rogermele(a)icloud.com> Date: 2017-06-28 (Wed, 28 Jun 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/apps/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/grid/grid-view.js A client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit-current.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/user/user-preferences.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/config/neo.xml M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/search/static/script.js M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M cron/updateucsc.sh.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M scripts/api/library_upload_dir.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/onload.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/layout/panel.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/js-app.mako R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako R templates/webapps/galaxy/visualization/list_published.mako R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/list_published.mako R templates/webapps/galaxy/workflow/run.mako M test/functional/tools/sample_datatypes_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py M tools/filters/wc_gnu.xml Log Message: ----------- Merge branch 'dev' into issue-4231-fix-empty-tabular-output Commit: 8b0187317564d70b3a5bc5f67ee78461879fd43e https://github.com/galaxyproject/galaxy/commit/8b0187317564d70b3a5bc5f67ee7… Author: Pierrick Roger Mele <pierrick.rogermele(a)icloud.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Implement Nicola Sorenzo's proposal for set_meta() method. Commit: 2a737d0b794d03d16774bcd6250561eda92d9abc https://github.com/galaxyproject/galaxy/commit/2a737d0b794d03d16774bcd62505… Author: Pierrick Roger Mele <pierrick.rogermele(a)icloud.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Set two blank lines before class definition, in order for travis linting to pass. Commit: ba5549b47193f1ac87a2fa8d145e3d4d1541c554 https://github.com/galaxyproject/galaxy/commit/ba5549b47193f1ac87a2fa8d145e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #4240 from pierrickrogermele/issue-4231-fix-empty-tabular-output Fix empty tabular output error when using discover_datasets. Compare: https://github.com/galaxyproject/galaxy/compare/e7731684518e...ba5549b47193

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[galaxyproject/galaxy] 3c488b: Return empty tool_version when tool is not loaded ...
by GitHub 06 Jul '17

06 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c488b24d0c5dd2460a7f82346c5dde5bb8bae78 https://github.com/galaxyproject/galaxy/commit/3c488b24d0c5dd2460a7f82346c5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Return empty tool_version when tool is not loaded into tool panel Commit: e7731684518eec8336234994f32dda7246a5f5e0 https://github.com/galaxyproject/galaxy/commit/e7731684518eec8336234994f32d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #4285 from mvdbeek/fix_wf_editor_crash_uninstalled_tool Return empty tool_version when tool is not loaded into tool panel Compare: https://github.com/galaxyproject/galaxy/compare/8b3c10553b26...e7731684518e

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[galaxyproject/galaxy] eb5843: Remove p style under blockquote
by GitHub 06 Jul '17

06 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eb5843643298e0c8ac5f2a568ffed1cba47adb21 https://github.com/galaxyproject/galaxy/commit/eb5843643298e0c8ac5f2a568ffe… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-04 (Tue, 04 Jul 2017) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/overrides.less 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 M static/style/blue/base.css Log Message: ----------- Remove p style under blockquote Commit: 8b3c10553b26fed01c6825c47df397bacdf5d5a2 https://github.com/galaxyproject/galaxy/commit/8b3c10553b26fed01c6825c47df3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/overrides.less M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'erasche/blockquotep' into dev (rebuilt client as well) Compare: https://github.com/galaxyproject/galaxy/compare/1ecaa0698732...8b3c10553b26

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

05 Jul '17

Branch: refs/heads/release_17.01 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 Compare: https://github.com/galaxyproject/galaxy/compare/96e1cf58f480...bfb3ce6e7907

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