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

[galaxyproject/galaxy] 21b44b: Fix all E201 and E202 style errors
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 21b44bf348ae10d170ab96a3b6f30bf9dbbd5a4a https://github.com/galaxyproject/galaxy/commit/21b44bf348ae10d170ab96a3b6f3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/style/source_material/circle.py M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M lib/galaxy/__init__.py M lib/galaxy/actions/admin.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.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/subcollections.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M 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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/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/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.py M tools/visualization/LAJ_code.py Log Message: ----------- Fix all E201 and E202 style errors using the following command: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 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test/shed_functional/functional/test_1470_updating_installed_repositories.py M test/shed_functional/functional_tests.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_UserManager.py M tools/data_source/data_source.py M tools/data_source/upload.py M tools/filters/axt_to_lav.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/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Fix E127 errors introduced by previous commit using: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 . ``` Commit: a8d7b2df8bb0ccf49b2ca7247f2451b6123a5fd8 https://github.com/galaxyproject/galaxy/commit/a8d7b2df8bb0ccf49b2ca7247f24… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/folder_contents.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/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/controllers/user.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/microbes/BeautifulSoup.py M scripts/tool_shed/deprecate_repositories_without_metadata.py Log Message: ----------- Fix more indentation errors Commit: a85ee599ffc66ce3a5954ad819c864064bff838a https://github.com/galaxyproject/galaxy/commit/a85ee599ffc66ce3a5954ad819c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/style/source_material/circle.py M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M 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test/shed_functional/functional/test_0400_repository_component_reviews.py M test/shed_functional/functional/test_0410_repository_component_review_access_control.py M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py M test/shed_functional/functional/test_0430_browse_utilities.py M test/shed_functional/functional/test_0440_deleting_dependency_definitions.py M test/shed_functional/functional/test_0460_upload_to_repository.py M test/shed_functional/functional/test_0470_tool_dependency_repository_type.py M test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py M test/shed_functional/functional/test_0490_export_import_repositories.py M test/shed_functional/functional/test_0500_export_repository_simple_dependency.py M test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py M test/shed_functional/functional/test_0520_import_export_circular_dependencies.py M test/shed_functional/functional/test_0530_repository_admin_feature.py M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py M test/shed_functional/functional/test_1000_install_basic_repository.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py M test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py M test/shed_functional/functional/test_1070_invalid_tool.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py M test/shed_functional/functional/test_1110_install_tool_from_tool_search.py M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py M test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/shed_functional/functional/test_1160_tool_help_images.py M test/shed_functional/functional/test_1170_prior_installation_required.py M test/shed_functional/functional/test_1180_circular_prior_installation_required.py M test/shed_functional/functional/test_1190_complex_prior_installation_required.py M test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1400_review_migration_stages.py M test/shed_functional/functional/test_1410_update_manager.py M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py M test/shed_functional/functional/test_1430_repair_installed_repository.py M test/shed_functional/functional/test_1440_missing_env_sh_files.py M test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py M test/shed_functional/functional/test_1460_data_managers.py M test/shed_functional/functional/test_1470_updating_installed_repositories.py M test/shed_functional/functional_tests.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/datatypes/test_data.py M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_datasets.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_rules/10_site.py M test/unit/jobs/test_runner_local.py M test/unit/jobs/test_runner_params.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M 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_routes.py M test/unit/test_security_helper.py M test/unit/test_sqlite_utils.py M test/unit/test_topsort.py M test/unit/tools/filter_modules/filtermod.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_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_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_panel.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_extract_summary.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 M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py 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_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.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_feature_count.py 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/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/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/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/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.py M tools/visualization/LAJ_code.py Log Message: ----------- Merge pull request #4440 from nsoranzo/fix_E201_E202 Fix E201 and E202 style errors Compare: https://github.com/galaxyproject/galaxy/compare/008a1d849c4e...a85ee599ffc6

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[galaxyproject/galaxy] c72f43: Avoid adding `(imported from API)` to workflows
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c72f43dc5fb48e358d65caf6c59876ba0f15324e https://github.com/galaxyproject/galaxy/commit/c72f43dc5fb48e358d65caf6c598… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Avoid adding `(imported from API)` to workflows This should fail a few tests which I will fix with additional commits. Doing this from GitHub... Commit: 9ef13a1c724a2bb326bba3556019448ef69ae8fd https://github.com/galaxyproject/galaxy/commit/9ef13a1c724a2bb326bba3556019… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M test/api/test_search.py Log Message: ----------- Remove `(imported from API)` suffix from test Commit: 03a3d34f1e2326c99798299d53fc6b7026aadb09 https://github.com/galaxyproject/galaxy/commit/03a3d34f1e2326c99798299d53fc… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Remove `(imported from API)` suffix from test Commit: 008a1d849c4eb86ab52fd032ae611e4844c3cf09 https://github.com/galaxyproject/galaxy/commit/008a1d849c4eb86ab52fd032ae61… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_search.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #4434 from chambm/patch-1 Avoid adding `(imported from API)` to workflows Compare: https://github.com/galaxyproject/galaxy/compare/1b69b9a5fedb...008a1d849c4e

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[galaxyproject/galaxy] 25bd71: Remove print of non-existent attribute 'content'
by GitHub 17 Aug '17

17 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 25bd7178c157f24523333caaf7f5a0a54f264abe https://github.com/galaxyproject/galaxy/commit/25bd7178c157f24523333caaf7f5… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M scripts/api/upload_to_history.py Log Message: ----------- Remove print of non-existent attribute 'content' Commit: 1b69b9a5fedbd232e76ef684734170e7b06fe3e9 https://github.com/galaxyproject/galaxy/commit/1b69b9a5fedbd232e76ef6847341… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M scripts/api/upload_to_history.py Log Message: ----------- Merge pull request #4439 from chambm/patch-2 Remove print of non-existent attribute 'content' Compare: https://github.com/galaxyproject/galaxy/compare/04583346a197...1b69b9a5fedb

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[galaxyproject/galaxy] 613f4f: Use dict format for admin tool versions grid
by GitHub 16 Aug '17

16 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 613f4fb1ced3c9a7e0d1417b8c9c14b681479bdd https://github.com/galaxyproject/galaxy/commit/613f4fb1ced3c9a7e0d1417b8c9c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use dict format for admin tool versions grid Commit: 381bf173d095ce51ba66d9cf19f5827c75c36dc8 https://github.com/galaxyproject/galaxy/commit/381bf173d095ce51ba66d9cf19f5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove message from tool versions Commit: cdfaebdaa4722226cf121454aa02b455d324d265 https://github.com/galaxyproject/galaxy/commit/cdfaebdaa4722226cf121454aa02… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Switch quotas grid to dict format Commit: 0e1b80b28f7558104c9a36bd1d224c60d91c2c70 https://github.com/galaxyproject/galaxy/commit/0e1b80b28f7558104c9a36bd1d22… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add async quota grid operations Commit: ad60f5a8ea4eaf574b4ffa1e51baa5bbe8282d47 https://github.com/galaxyproject/galaxy/commit/ad60f5a8ea4eaf574b4ffa1e51ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/actions/admin.py Log Message: ----------- Allow empty params Commit: 83a48f8f336a4c73dd1faabe3c84ce8801fb181d https://github.com/galaxyproject/galaxy/commit/83a48f8f336a4c73dd1faabe3c84… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Build quota renaming form in admin panel using client side form builder Commit: 9dcc181f72d5f31b3d5feb45f673996714aca913 https://github.com/galaxyproject/galaxy/commit/9dcc181f72d5f31b3d5feb45f673… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix error message handling for quota operations, set default value for payloads to none Commit: 643f262ea913e8cc0f3bb5e39acf2af80194c71f https://github.com/galaxyproject/galaxy/commit/643f262ea913e8cc0f3bb5e39acf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use client form builder to render edit quota amount form Commit: ad2dc168307037070205db27d7bdb09fb82d549f https://github.com/galaxyproject/galaxy/commit/ad2dc168307037070205db27d7bd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix link to edit quota Commit: ae181d776fb9a565d7b51c18aa8edcae09018bc3 https://github.com/galaxyproject/galaxy/commit/ae181d776fb9a565d7b51c18aa8e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Provide async support for unsetting default quotas Commit: bd542000fa9ec420ba0f2e17d2b8f8047eb72f8c https://github.com/galaxyproject/galaxy/commit/bd542000fa9ec420ba0f2e17d2b8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py 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 Log Message: ----------- Build set default quota forms using client form builder Commit: 17cd7d16c2db988581e26ad59a88a57302a202c9 https://github.com/galaxyproject/galaxy/commit/17cd7d16c2db988581e26ad59a88… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py 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 Log Message: ----------- Add manage role support for quotas Commit: 9f580d0630026157f2727651cce2e8f444f78cdc https://github.com/galaxyproject/galaxy/commit/9f580d0630026157f2727651cce2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Use consistent naming for group and role parameters Commit: 0f84d8bd91722c4bd36d5a736d6ca02a57460cfc https://github.com/galaxyproject/galaxy/commit/0f84d8bd91722c4bd36d5a736d6c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add client side form to create new quota Commit: 5647dfe5dbb22b7d09b1b760e41a2e0cd96cd8c8 https://github.com/galaxyproject/galaxy/commit/5647dfe5dbb22b7d09b1b760e41a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: R templates/admin/quota/quota.mako R templates/admin/quota/quota_create.mako R templates/admin/quota/quota_edit.mako R templates/admin/quota/quota_rename.mako R templates/admin/quota/quota_set_default.mako Log Message: ----------- Remove unused quota makos Commit: 33acc1f8a337977eb85e9ba570f3404476411edc https://github.com/galaxyproject/galaxy/commit/33acc1f8a337977eb85e9ba570f3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/tool_conf.xml.sample A config/user_preferences_extra_conf.yml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.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/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.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 A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako M templates/webapps/tool_shed/repository/common.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml M test/unit/tools/test_parsing.py Log Message: ----------- Merge branch 'admin_grid_groups' into admin_grid_toolversion Commit: ef2c32ae84706897e70fa41808f46d95f1132ec9 https://github.com/galaxyproject/galaxy/commit/ef2c32ae84706897e70fa41808f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix lint Commit: b726c33c80b33ece878343b6208e65f3d983008f 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lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml A lib/galaxy/webapps/uwsgi_schema.yml M lib/galaxy/workflow/modules.py M openid/yahoo.xml M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh A scripts/config_sample_to_kwalify.py M scripts/manage_tools.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-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/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/interactor.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'admin_grid_groups' into admin_grid_toolversion Commit: 9dfee375e9782f421832ecc44981a2cbdfc4f183 https://github.com/galaxyproject/galaxy/commit/9dfee375e9782f421832ecc44981… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Optionally allow to show or hide select all Commit: a1897bd32a112e68ce09b71fd6ad98e6b97f267b https://github.com/galaxyproject/galaxy/commit/a1897bd32a112e68ce09b71fd6ad… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Hide select all for role and group selectors Commit: d6f6a78ab8464bf1a10cbca74632873993744933 https://github.com/galaxyproject/galaxy/commit/d6f6a78ab8464bf1a10cbca74632… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js M static/maps/mvc/form/form-wrapper.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.map M static/scripts/mvc/form/form-wrapper.js Log Message: ----------- Use 'Save' as default title for configuration forms Commit: 4688eef2a41e79b44e8cb19ad87d5f2fc9a3aaf1 https://github.com/galaxyproject/galaxy/commit/4688eef2a41e79b44e8cb19ad87d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix user id decoding, fix optional array handling Commit: 96cad03980b314a7a89a01a5e1d442b2855a22e8 https://github.com/galaxyproject/galaxy/commit/96cad03980b314a7a89a01a5e1d4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix label for default quotas Commit: 246489a7aa2b950d7a12bf2610faaaed26d90a55 https://github.com/galaxyproject/galaxy/commit/246489a7aa2b950d7a12bf2610fa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/actions/admin.py Log Message: ----------- Fix messages Commit: f9e889215021f7a99a4ccfe4612431caa963f63c https://github.com/galaxyproject/galaxy/commit/f9e889215021f7a99a4ccfe46124… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Catch user input error for auto created roles and groups Commit: bebc5ff56ae41a2660f884a2b04604b2a473dd11 https://github.com/galaxyproject/galaxy/commit/bebc5ff56ae41a2660f884a2b046… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Move decode id to correct location Commit: f1e13cef05759bc7782248c08d595043d03161fe https://github.com/galaxyproject/galaxy/commit/f1e13cef05759bc7782248c08d59… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/actions/admin.py Log Message: ----------- More messages to validate inputs Commit: 86cdaaf610011b2b0c43f1bd93d36d87907b30e7 https://github.com/galaxyproject/galaxy/commit/86cdaaf610011b2b0c43f1bd93d3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add validation messages if resource ids are not correct Commit: 2073151bf2f6b2c2427c10934b1feea967d010ff https://github.com/galaxyproject/galaxy/commit/2073151bf2f6b2c2427c10934b1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Log Message: ----------- Merge branch 'dev' into admin_grid_toolversion Commit: fdcd46918d52c4ee8ab7c2c421fd3e559c9a1fdc https://github.com/galaxyproject/galaxy/commit/fdcd46918d52c4ee8ab7c2c421fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unfilterable columns from group and quota search grids Commit: 2c4cf686f8fffd17bb7a248571fa7d502f52a046 https://github.com/galaxyproject/galaxy/commit/2c4cf686f8fffd17bb7a248571fa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M 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static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.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.map M static/scripts/galaxy.pages.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/scroll-panel.js M static/scripts/utils/graph.js M static/scripts/utils/uploadbox.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge branch 'dev' into admin_grid_toolversion and repack Commit: 04583346a1970f9bab4f0cd3b9e8693de4fedbf9 https://github.com/galaxyproject/galaxy/commit/04583346a1970f9bab4f0cd3b9e8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js R templates/admin/quota/quota.mako R templates/admin/quota/quota_create.mako R templates/admin/quota/quota_edit.mako R templates/admin/quota/quota_rename.mako R templates/admin/quota/quota_set_default.mako Log Message: ----------- Merge pull request #4411 from guerler/admin_grid_toolversion replace mako templates for tool lineage and quotas grids Compare: https://github.com/galaxyproject/galaxy/compare/1b7f25eeaec9...04583346a197

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[galaxyproject/galaxy] 7ef9b4: Remove spurious null check.
by GitHub 16 Aug '17

16 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ef9b4cdafd0e2c6e68cba3729d9bd99645ef15f https://github.com/galaxyproject/galaxy/commit/7ef9b4cdafd0e2c6e68cba3729d9… Author: Max Schaefer <max(a)semmle.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/job/job-params.js Log Message: ----------- Remove spurious null check. Commit: 43ddd4732034ca2ee658ccd4ab0ae17d4a1bbe40 https://github.com/galaxyproject/galaxy/commit/43ddd4732034ca2ee658ccd4ab0a… Author: Max Schaefer <max(a)semmle.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/toolshed/scripts/mvc/groups/group-list-view.js M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/web/proxy/js/lib/proxy.js M scripts/communication/template/communication.js Log Message: ----------- Add missing `var` declarations. In all these cases, a variable was not declared to be a local using `var` (and hence was implicitly interpreted as a global variable), but all uses of that variable were preceded by a definition within the same function, suggesting that the variable was, in fact, meant to be local, not global. Commit: 48b835c35cd746c23c185ae69577ab6ae9fc4ee8 https://github.com/galaxyproject/galaxy/commit/48b835c35cd746c23c185ae69577… Author: Max Schaefer <max(a)semmle.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/viz/circster.js Log Message: ----------- Remove an unused variable. The result of the `_.map` call was never used, so I replaced it with `_.each`. Commit: 8950d4423ff7d02bcf95b417676b2ef1c311333a https://github.com/galaxyproject/galaxy/commit/8950d4423ff7d02bcf95b417676b… Author: Max Schaefer <max(a)semmle.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Move two variable definitions to combine them with their declarations. Commit: 57c6284269c3256529f9c55953279eccb07dfabf https://github.com/galaxyproject/galaxy/commit/57c6284269c3256529f9c5595327… Author: Max Schaefer <max(a)semmle.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M static/maps/galaxy.pages.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/toolshed/categories-view.js.map M static/maps/mvc/toolshed/repo-status-view.js.map M static/maps/mvc/toolshed/repositories-view.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/scroll-panel.js.map M static/maps/utils/graph.js.map M static/maps/utils/uploadbox.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.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.map M static/scripts/galaxy.pages.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/scroll-panel.js M static/scripts/utils/graph.js M static/scripts/utils/uploadbox.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Run `make client`. Commit: 1b7f25eeaec96ae8b6a5336090dca675076b07bd https://github.com/galaxyproject/galaxy/commit/1b7f25eeaec96ae8b6a5336090dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/toolshed/scripts/mvc/groups/group-list-view.js M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/web/proxy/js/lib/proxy.js M scripts/communication/template/communication.js M static/maps/galaxy.pages.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/toolshed/categories-view.js.map M static/maps/mvc/toolshed/repo-status-view.js.map M static/maps/mvc/toolshed/repositories-view.js.map M static/maps/mvc/toolshed/repository-queue-view.js.map M static/maps/mvc/toolshed/repository-view.js.map M static/maps/mvc/toolshed/util.js.map M static/maps/mvc/toolshed/workflows-view.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/scroll-panel.js.map M static/maps/utils/graph.js.map M static/maps/utils/uploadbox.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.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.map M static/scripts/galaxy.pages.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/scroll-panel.js M static/scripts/utils/graph.js M static/scripts/utils/uploadbox.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #4421 from xiemaisi/fix-lgtm-alerts Fix lgtm alerts Compare: https://github.com/galaxyproject/galaxy/compare/c5a91491c646...1b7f25eeaec9

1 0

[galaxyproject/galaxy] 522ca9: Fix private role validation
by GitHub 16 Aug '17

16 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 522ca9e5c2ebbf274af26b466c1bab5fb5bc5625 https://github.com/galaxyproject/galaxy/commit/522ca9e5c2ebbf274af26b466c1b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Fix private role validation Commit: c5a91491c64610ede9421af8b89ddf8389238be3 https://github.com/galaxyproject/galaxy/commit/c5a91491c64610ede9421af8b89d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #4432 from guerler/fix_role_association_check Fix private role validation Compare: https://github.com/galaxyproject/galaxy/compare/b6f0600e98b7...c5a91491c646

1 0

[galaxyproject/galaxy] 210d3e: Refactor to clean up args in one method of galaxy....
by GitHub 16 Aug '17

16 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 210d3e31ab8bd71569ed6399cfc1894223e4ec36 https://github.com/galaxyproject/galaxy/commit/210d3e31ab8bd71569ed6399cfc1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Refactor to clean up args in one method of galaxy.tools. Commit: 997e7114be722e56e5633cd10b554d6d1428dfc8 https://github.com/galaxyproject/galaxy/commit/997e7114be722e56e5633cd10b55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M test/unit/tools_support.py Log Message: ----------- More correct tool creation in tools_support. Now supports creating tool subclasses based on tool source. Commit: db91b29df96d354c8972f63513ed755b5dd4418d https://github.com/galaxyproject/galaxy/commit/db91b29df96d354c8972f63513ed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Have more tests use mock_galaxy's MockApp. Commit: a462afa0b7094a5fa439b0aa3b751e26cc18bd98 https://github.com/galaxyproject/galaxy/commit/a462afa0b7094a5fa439b0aa3b75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Eliminate second unit test variant of MockApp. As well as my failed experiment in mocking out sqlalchemy - I think the in-memory database is more useful than mocking out sqlalchemy in retrospect. Commit: 7de7f3f63a438a9d2b2b452d61e3118a710826c7 https://github.com/galaxyproject/galaxy/commit/7de7f3f63a438a9d2b2b452d61e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M test/unit/tools_support.py Log Message: ----------- "Fix" import order of tools_support for Travis. Commit: b6f0600e98b74a301c2eb787263cd89e5ca487ca https://github.com/galaxyproject/galaxy/commit/b6f0600e98b74a301c2eb787263c… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #4387 from jmchilton/tool_unit_test_cleanup Cleanup of Unit Test Code for Loading Tools Compare: https://github.com/galaxyproject/galaxy/compare/8eb487e7c138...b6f0600e98b7

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[galaxyproject/galaxy] 09c4b1: Break connection in workflow editor if necessary
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 09c4b1037b0034093488ed679628b9f614849a5e https://github.com/galaxyproject/galaxy/commit/09c4b1037b0034093488ed679628… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.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/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Break connection in workflow editor if necessary When switching tool versions in the workflow editor connections are maintained by default. If a tool changes the datatype one may end up with a connection between incompatible input/outputs. Therefore we update the datatypes and explicitly destroy invalid connections. Commit: 8eb487e7c1383cedd971de8128bb9ba143abaa41 https://github.com/galaxyproject/galaxy/commit/8eb487e7c1383cedd971de8128bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.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/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #4431 from mvdbeek/break_connections Break connection in workflow editor if necessary Compare: https://github.com/galaxyproject/galaxy/compare/4bddd617fe5d...8eb487e7c138

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[galaxyproject/galaxy] 71db6b: Fix lint
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71db6b461da3d3b2e3c6880c9d2bf90bcd44098e https://github.com/galaxyproject/galaxy/commit/71db6b461da3d3b2e3c6880c9d2b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix lint Fix Commit: c72aca479729ddee6a8bf8e19431b41e98d39d89 https://github.com/galaxyproject/galaxy/commit/c72aca479729ddee6a8bf8e19431… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Revise admin groups endpoint Commit: 097cae67956b972cd609f1155890d122c5bb3742 https://github.com/galaxyproject/galaxy/commit/097cae67956b972cd609f1155890… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups Commit: 9822dede69c95796c24e87a1c60cd845788095d1 https://github.com/galaxyproject/galaxy/commit/9822dede69c95796c24e87a1c60c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add client route Commit: 1bf2d1782fca4c79708261ca98cabe92822e86cb https://github.com/galaxyproject/galaxy/commit/1bf2d1782fca4c79708261ca98ca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use client side formbuilder for rename group form Commit: 7a58fd113d32659c9ea6e0c4fdb830d5c1ca7a72 https://github.com/galaxyproject/galaxy/commit/7a58fd113d32659c9ea6e0c4fdb8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove self directed operation Commit: b2d54b377c6c78f016ccb730178afd3f7a70c0b3 https://github.com/galaxyproject/galaxy/commit/b2d54b377c6c78f016ccb730178a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add async support for group deleting Commit: afdfbf69ff8d1636c661c5758f52c636f9160220 https://github.com/galaxyproject/galaxy/commit/afdfbf69ff8d1636c661c5758f52… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add async support for undeleting groups Commit: 96557cd136730033c3a4b84e506b3cc5831d06af https://github.com/galaxyproject/galaxy/commit/96557cd136730033c3a4b84e506b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Add async support for purging groups Commit: 037b7fa75754ae90917d0ee25b1565c9ab29cd03 https://github.com/galaxyproject/galaxy/commit/037b7fa75754ae90917d0ee25b15… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove exposure of async operation handlers, align naming Commit: 3840c6d61735fa674239be19a10af04d0d3647f9 https://github.com/galaxyproject/galaxy/commit/3840c6d61735fa674239be19a10a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix purge handler for groups Commit: 1e83a48c4635ba05576cdb8e42bbdf8f971b825a https://github.com/galaxyproject/galaxy/commit/1e83a48c4635ba05576cdb8e42bb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove exposure of user related operations Commit: 1795247bd849e3d7d1c034416d27d5c1672039e8 https://github.com/galaxyproject/galaxy/commit/1795247bd849e3d7d1c034416d27… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove new line Commit: e805db6896352042aa5eb8482febbd75af46b008 https://github.com/galaxyproject/galaxy/commit/e805db6896352042aa5eb8482feb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use client to build create groups form Commit: 5605f390fe36c8ab562d049b105db7164b8097c1 https://github.com/galaxyproject/galaxy/commit/5605f390fe36c8ab562d049b105d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Build manage users and roles for groups with client form builder Commit: c827bb0a867e2fcdf89417bb7ea912641e49cf8a https://github.com/galaxyproject/galaxy/commit/c827bb0a867e2fcdf89417bb7ea9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/tool_shed/util/admin_util.py R templates/admin/dataset_security/group/group.mako R templates/admin/dataset_security/group/group_create.mako R templates/admin/dataset_security/group/group_rename.mako A templates/webapps/tool_shed/admin/dataset_security/group/group.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako Log Message: ----------- Move unused mako templates to toolshed, adjust paths Commit: dbad2556d05dead2ac0991a7897d95f1eda16087 https://github.com/galaxyproject/galaxy/commit/dbad2556d05dead2ac0991a7897d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups Commit: c57c36b51465b1bfaefcf486b9814c32f7f92840 https://github.com/galaxyproject/galaxy/commit/c57c36b51465b1bfaefcf486b981… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove over indent Commit: 4a77956dc8756300825c3744ccfa3a4646be5775 https://github.com/galaxyproject/galaxy/commit/4a77956dc8756300825c3744ccfa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-09 (Wed, 09 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups Commit: b38ccbc10547ded7e3afec262a5819bd3d44613f https://github.com/galaxyproject/galaxy/commit/b38ccbc10547ded7e3afec262a58… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js A client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/galaxy_bootstrap/overrides.less M config/datatypes_conf.xml.sample A config/error_report.yml.sample M config/tool_conf.xml.sample A config/user_preferences_extra_conf.yml.sample A doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0135_add_library_tags.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/error_reports/__init__.py A lib/galaxy/tools/error_reports/plugins/__init__.py A lib/galaxy/tools/error_reports/plugins/biostars.py A lib/galaxy/tools/error_reports/plugins/email.py A lib/galaxy/tools/error_reports/plugins/json.py A lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_objects.py A lib/galaxy/tools/sort_collection_list.xml M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/biostar.py M lib/galaxy/util/plugin_config.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.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/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/extract.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/grt/export.py M scripts/grt/upload.py A static/maps/mvc/dataset/dataset-error.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.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 A static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M templates/show_params.mako R templates/webapps/galaxy/dataset/errors.mako M templates/webapps/tool_shed/repository/common.mako A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml M test/unit/tools/test_parsing.py Log Message: ----------- Merge branch 'admin_grid_roles' into admin_grid_groups Commit: ad2f39c1e6475c65fcb1e300201c035701640f10 https://github.com/galaxyproject/galaxy/commit/ad2f39c1e6475c65fcb1e300201c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix lint Commit: eccdc8c248fabef6bc5a988cdb1889c1aa32ca7a https://github.com/galaxyproject/galaxy/commit/eccdc8c248fabef6bc5a988cdb18… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Removed unreached message line Commit: fd5f42dc17009cfdfbfc08583549ba608efb166a https://github.com/galaxyproject/galaxy/commit/fd5f42dc17009cfdfbfc08583549… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M Makefile M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample R config/reports.ini.sample A config/reports.yml.sample R config/tool_shed.ini.sample A config/tool_shed.yml.sample A doc/source/admin/reports.rst A doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.xls M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py M lib/galaxy/util/properties.py M lib/galaxy/web/framework/webapp.py A lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/reports/buildapp.py A lib/galaxy/webapps/reports/config_schema.yml A lib/galaxy/webapps/reports/uwsgi_schema.yml M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/tool_shed/config_schema.yml A lib/galaxy/webapps/tool_shed/uwsgi_schema.yml A lib/galaxy/webapps/uwsgi_schema.yml M openid/yahoo.xml M run.sh M run_reports.sh M run_tool_shed.sh A scripts/common_startup_functions.sh A scripts/config_sample_to_kwalify.py M scripts/manage_tools.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/interactor.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py A test/unit/config/1607_root_filters/config/galaxy.ini A test/unit/config/1607_root_filters/config/tool_shed.ini A test/unit/config/1607_root_samples/config/galaxy.ini A test/unit/config/1607_root_samples/config/reports.ini A test/unit/config/1607_root_samples/config/tool_shed.ini A test/unit/config/test_config_manage.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into admin_grid_groups Commit: e72948cb743e50b50a21bf7f778792ba36ec38bd https://github.com/galaxyproject/galaxy/commit/e72948cb743e50b50a21bf7f7787… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-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/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge branch 'dev' into admin_grid_groups Commit: 4bddd617fe5df41efcebacdda7a6bb1d280ac2ce https://github.com/galaxyproject/galaxy/commit/4bddd617fe5df41efcebacdda7a6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/util/admin_util.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R templates/admin/dataset_security/group/group.mako R templates/admin/dataset_security/group/group_create.mako R templates/admin/dataset_security/group/group_rename.mako A templates/webapps/tool_shed/admin/dataset_security/group/group.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako Log Message: ----------- Merge pull request #4405 from guerler/admin_grid_groups Admin grid groups revision Compare: https://github.com/galaxyproject/galaxy/compare/462b7def5d9b...4bddd617fe5d

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[galaxyproject/galaxy] d0b06a: Don't cast tool_version to string if tool_version ...
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d0b06a3b1da09ff3394e9ea036d788676817b58f https://github.com/galaxyproject/galaxy/commit/d0b06a3b1da09ff3394e9ea036d7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Don't cast tool_version to string if tool_version is None-type If a version is not specifically requested a wrong version (`None` cast to `'None'`) of a tool will be loaded in the workflow editor instead of the latest version. That should address @martenson's remark in https://github.com/galaxyproject/galaxy/pull/4373#issuecomment-321896674 (and maybe also https://github.com/galaxyproject/galaxy/issues/557#issuecomment-213498153) Commit: 6ad6fd9252bf5ec44beb00cb434876e170dc9548 https://github.com/galaxyproject/galaxy/commit/6ad6fd9252bf5ec44beb00cb4348… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Rebuild tool_version_cache on DetachedInstanceError Commit: 7f78ee7b18b83961b305cac19aa8949a4452710d https://github.com/galaxyproject/galaxy/commit/7f78ee7b18b83961b305cac19aa8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4420 from mvdbeek/fix_wrong_tool_version_cast [17.05] Don't cast tool_version to string if tool_version is None-type Commit: 07a30499994b33e27c0b1765df9f32c9bfcea0b2 https://github.com/galaxyproject/galaxy/commit/07a30499994b33e27c0b1765df9f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into dev Conflicts: lib/galaxy/model/tool_shed_install/__init__.py Commit: 462b7def5d9b9298d50cea2e62cfbf89bd463d25 https://github.com/galaxyproject/galaxy/commit/462b7def5d9b9298d50cea2e62cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4427 from nsoranzo/merge_release_17.05 Merge release_17.05 into dev Compare: https://github.com/galaxyproject/galaxy/compare/27be24963837...462b7def5d9b

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