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

[galaxyproject/galaxy] 9791dd: Fix regressions in library API
by GitHub 24 Oct '17

24 Oct '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 9791dd22d4d9084989cafa3498ae313dd4cd13f0 https://github.com/galaxyproject/galaxy/commit/9791dd22d4d9084989cafa3498ae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Fix regressions in library API Introduced in commit 93a8bfc7cb5e9c3395c5057910ec39d68ad787b4 Commit: a4a8f155376119277df2cfebd13376e919873c4f https://github.com/galaxyproject/galaxy/commit/a4a8f155376119277df2cfebd133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M lib/galaxy/util/path/ntpath.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge pull request #4854 from nsoranzo/release_16.07_fix_test_regressions [16.07] Fix regressions in library API Compare: https://github.com/galaxyproject/galaxy/compare/0e698813a96f...a4a8f1553761

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[galaxyproject/galaxy] 72dd4a: add Analyze75 datatype
by GitHub 24 Oct '17

24 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72dd4a3a79e0b1ed0ba35b2a398a56c1265be02f https://github.com/galaxyproject/galaxy/commit/72dd4a3a79e0b1ed0ba35b2a398a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-10-21 (Sat, 21 Oct 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- add Analyze75 datatype Commit: 319d1cb79458c4a0cebeaee1262a85759cac25d0 https://github.com/galaxyproject/galaxy/commit/319d1cb79458c4a0cebeaee1262a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-10-21 (Sat, 21 Oct 2017) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- lint fixes Commit: 52b16ecd329d42cab76494c8d13bd3be9805b32c https://github.com/galaxyproject/galaxy/commit/52b16ecd329d42cab76494c8d13b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Merge pull request #4841 from bgruening/Analyze75 add Analyze75 datatype Compare: https://github.com/galaxyproject/galaxy/compare/62826a116054...52b16ecd329d

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[galaxyproject/infrastructure-playbook] 6a359a: Looking at cron mails once every few years is a go...
by GitHub 24 Oct '17

24 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6a359a07e10184dfb53f2c1da174466cd9507f88 https://github.com/galaxyproject/infrastructure-playbook/commit/6a359a07e10… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M roles/mailman/files/mm_discard_report.py Log Message: ----------- Looking at cron mails once every few years is a good idea Commit: 8242a889c64f795735ef475244541946d5e55f07 https://github.com/galaxyproject/infrastructure-playbook/commit/8242a889c64… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M galaxyenv/group_vars/jenkinsslaves.yml Log Message: ----------- Install pandoc on Jenkins workers Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/211366fb42…

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[galaxyproject/galaxy] f5981e: add tldr for security
by GitHub 24 Oct '17

24 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: f5981e6ef381d5c4be33e0725cdb697a5515ca7b https://github.com/galaxyproject/galaxy/commit/f5981e6ef381d5c4be33e0725cdb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- add tldr for security Commit: add3a97bb014392d773c7a5bb8243f7341c1219c https://github.com/galaxyproject/galaxy/commit/add3a97bb014392d773c7a5bb824… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- this is not markdown Commit: cfb61e069659fa43b4ad290b4cc4a93ebd71e3e0 https://github.com/galaxyproject/galaxy/commit/cfb61e069659fa43b4ad290b4cc4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Rework security wording a bit. I waffle on adding security notes for the 17.09-only issues... Commit: 01b244a810434a1184d3e72ff9476af2a1243dcc https://github.com/galaxyproject/galaxy/commit/01b244a810434a1184d3e72ff947… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Merge pull request #4853 from martenson/improve-RN [17.09] release notes - add tldr for security Compare: https://github.com/galaxyproject/galaxy/compare/73b31ce3199a...01b244a81043

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[galaxyproject/galaxy] 9b4de7: Fix all E722 errors and ignore E741
by GitHub 24 Oct '17

24 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b4de72ca68afc2353beff333775422039baae25 https://github.com/galaxyproject/galaxy/commit/9b4de72ca68afc2353beff333775… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_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/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/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.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 M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/group_roles.py M lib/galaxy/webapps/galaxy/api/group_users.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/request_types.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy_ext/metadata/set_metadata.py M lib/psyco_full.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/drmaa_external_runner.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/rst2html.py M scripts/runtime_stats.py M scripts/tool_shed/migrate_tools_to_repositories.py M setup.cfg M test/base/testcase.py M test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_tool_deps.py M tools/data_source/data_source.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/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/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_feature_count.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.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_importer.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_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.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/solid2fastq.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_mapping/bfast_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 Log Message: ----------- Fix all E722 errors and ignore E741 Introduced in flake8 3.5.0 Fix import order. Commit: 62826a116054030ba50b801f3923a24768de197c https://github.com/galaxyproject/galaxy/commit/62826a116054030ba50b801f3923… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_gff_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/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/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.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 M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/generic_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handler_factory.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/cli/job/slurm.py M lib/galaxy/jobs/runners/util/cli/job/torque.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/sample_tracking/request_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/path/ntpath.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/group_roles.py M lib/galaxy/webapps/galaxy/api/group_users.py M lib/galaxy/webapps/galaxy/api/groups.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/request_types.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/samples.py M lib/galaxy/webapps/galaxy/api/tool_data.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy_ext/metadata/set_metadata.py M lib/psyco_full.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/admin_util.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/drmaa_external_runner.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/rst2html.py M scripts/runtime_stats.py M scripts/tool_shed/migrate_tools_to_repositories.py M setup.cfg M test/base/testcase.py M test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_tool_deps.py M tools/data_source/data_source.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/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/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_feature_count.py M tools/filters/gff_to_bed_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/sff_extract.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_importer.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_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/vcf_to_maf_customtrack.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/solid2fastq.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_mapping/bfast_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 Log Message: ----------- Merge pull request #4847 from nsoranzo/flake8_3.5.0 Fix all E722 errors and ignore E741 Compare: https://github.com/galaxyproject/galaxy/compare/fa295c0f6346...62826a116054

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[galaxyproject/galaxy] d97fcf: Prettier pre-bugfix.
by GitHub 24 Oct '17

24 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d97fcf3a8d3dac835010a1f5e5fdb55121459627 https://github.com/galaxyproject/galaxy/commit/d97fcf3a8d3dac835010a1f5e5fd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js.map Log Message: ----------- Prettier pre-bugfix. Commit: 546a8c6df9835482bc4c5f55d007c9a83b1f408d https://github.com/galaxyproject/galaxy/commit/546a8c6df9835482bc4c5f55d007… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Remove unnecessary (not sure what the intent was here) assignment in return. Commit: fa295c0f6346cb917a2e0843a292b5d82768720a https://github.com/galaxyproject/galaxy/commit/fa295c0f6346cb917a2e0843a292… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #4852 from dannon/fix_jsutils_time Fix jsutils time - fixes charts visualize Compare: https://github.com/galaxyproject/galaxy/compare/2db575b2418f...fa295c0f6346

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[galaxyproject/galaxy] f08700: rename wiki to hub
by GitHub 24 Oct '17

24 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f08700b208b7ca2cc74f6d4795257355bc449068 https://github.com/galaxyproject/galaxy/commit/f08700b208b7ca2cc74f6d479525… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- rename wiki to hub Commit: 2db575b2418f640be5eee85997a6f1920988c10b https://github.com/galaxyproject/galaxy/commit/2db575b2418f640be5eee85997a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #4850 from martenson/bootstrap minor changes to release checklist Compare: https://github.com/galaxyproject/galaxy/compare/2f2acb98e089...2db575b2418f

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[galaxyproject/galaxy] 4dcba2: initial release notes for 17.09
by GitHub 24 Oct '17

24 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 4dcba21d838bd2bad806687d7c212d7da0b8e85e https://github.com/galaxyproject/galaxy/commit/4dcba21d838bd2bad806687d7c21… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: A doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst A doc/source/releases/18.01_announce.rst Log Message: ----------- initial release notes for 17.09 Commit: 272ed6217d4662f7bdc6b385206a7f301295a033 https://github.com/galaxyproject/galaxy/commit/272ed6217d4662f7bdc6b385206a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- add deprecations Commit: 06d3f4051543e7c319e775884ea3aab8abef9a2c https://github.com/galaxyproject/galaxy/commit/06d3f4051543e7c319e775884ea3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- amend add missing line Commit: eab76b9ae014c4fa2dd3a1ba09199f3351536924 https://github.com/galaxyproject/galaxy/commit/eab76b9ae014c4fa2dd3a1ba0919… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- add listing of 17.09 release to index Commit: 812b04d14eb1c3d3ec016efb6aa8f1024811c560 https://github.com/galaxyproject/galaxy/commit/812b04d14eb1c3d3ec016efb6aa8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst Log Message: ----------- more work on RN Commit: 5bde1d1c3a0239ef37369f59e90ceca863d6821f https://github.com/galaxyproject/galaxy/commit/5bde1d1c3a0239ef37369f59e90c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst Log Message: ----------- Small progress on 17.09 release notes. Commit: ee27188b59d174f4db16d2ce4b7cd2181ea93517 https://github.com/galaxyproject/galaxy/commit/ee27188b59d174f4db16d2ce4b7c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: A client/galaxy/scripts/libs/jquery/jquery.complexify.js A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/releases/17.09_announce.rst Log Message: ----------- add security release notes Commit: 180472a3d8ceb40f6d015c0bfe5ef1dd08da5513 https://github.com/galaxyproject/galaxy/commit/180472a3d8ceb40f6d015c0bfe5e… Author: Dave Clements <clements(a)galaxyproject.org> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Small edits to 17.09 release notes. Commit: c8efbb3327cb4e2805c0099975c5a2be70b95a21 https://github.com/galaxyproject/galaxy/commit/c8efbb3327cb4e2805c0099975c5… Author: Dave Clements <clements(a)galaxyproject.org> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Fixed indenting in release notes. Commit: 4252f4f813c3d5a390ead3d86c4eec78273163cb https://github.com/galaxyproject/galaxy/commit/4252f4f813c3d5a390ead3d86c4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- Small 17.09 release note improvements. Commit: 199ec6dd4c70c733edd200e61d6470dedcf0da85 https://github.com/galaxyproject/galaxy/commit/199ec6dd4c70c733edd200e61d64… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- Condense several 17.09 release notes items. Commit: 3e8bf27fca44f5b70ac9e7e1f66acbdb11c98162 https://github.com/galaxyproject/galaxy/commit/3e8bf27fca44f5b70ac9e7e1f66a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- More release notes improvements. Move a couple things higher, merge a couple more things, improved language (toward sentences). Commit: 1b5421c1df5392ce83a66de22dceb6ef404134bf https://github.com/galaxyproject/galaxy/commit/1b5421c1df5392ce83a66de22dce… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- Merge pull request #24 from tnabtaf/17.09_release_notes 17.09 release notes edits Commit: 00bc7a51f9c780e15041b465e0245848f7b26244 https://github.com/galaxyproject/galaxy/commit/00bc7a51f9c780e15041b465e024… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- More 17.09 release note fixes. Merge more items, fix more sentences, etc... Commit: d1190bb067146d76bc16ec403562d4ba2d905710 https://github.com/galaxyproject/galaxy/commit/d1190bb067146d76bc16ec403562… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09_announce.rst Log Message: ----------- deprecate undocumented refresh_on_change functionality Commit: fe440d27367ef00b663057bf8ebe30b7b9ab0344 https://github.com/galaxyproject/galaxy/commit/fe440d27367ef00b663057bf8ebe… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: M doc/source/releases/17.09.rst Log Message: ----------- Merge branch '17.09_release_notes' of github.com:martenson/galaxy into 17.09_release_notes Commit: 6bbf345c282782efac6a026d36f60296571deabe https://github.com/galaxyproject/galaxy/commit/6bbf345c282782efac6a026d36f6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: R client/galaxy/scripts/libs/jquery/jquery.complexify.js R doc/source/api/api.rst R doc/source/api/ts_api.rst Log Message: ----------- remove wrongly added files Commit: 73b31ce3199ac73a0208dd784420800064278454 https://github.com/galaxyproject/galaxy/commit/73b31ce3199ac73a0208dd784420… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-24 (Tue, 24 Oct 2017) Changed paths: A doc/source/releases/17.09.rst M doc/source/releases/17.09_announce.rst A doc/source/releases/18.01_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #4772 from martenson/17.09_release_notes [17.09] release notes Compare: https://github.com/galaxyproject/galaxy/compare/cfe3dfc6eb93...73b31ce3199a

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[galaxyproject/galaxy] 504e2a: Add client route for toolshed browsing grid
by GitHub 23 Oct '17

23 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 504e2aa96a7ed63e9574bc0e8fa27c39c379a903 https://github.com/galaxyproject/galaxy/commit/504e2aa96a7ed63e9574bc0e8fa2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add client route for toolshed browsing grid Commit: 98fa946e21d98647d6b742d89934ed7a83d65650 https://github.com/galaxyproject/galaxy/commit/98fa946e21d98647d6b742d89934… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/__init__.py M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/postgresql_fake.tar.bz2 M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py R lib/galaxy/util/backports/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/image_util.py R lib/galaxy/util/log/__init__.py R lib/galaxy/util/log/fluent_log.py A lib/galaxy/util/logging/__init__.py A lib/galaxy/util/logging/fluent_log.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/webapps/tool_shed/model/__init__.py M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.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/history/history-view.js M static/scripts/mvc/history/options-menu.js A test-data/selenium-test-notebook.ipynb M test/api/test_tools.py A test/api/test_tools_upload.py M test/base/api.py M test/base/api_util.py A test/base/constants.py M test/base/populators.py M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/navigation.yml M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py A test/selenium_tests/test_jupyter.py A test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_landing.py A test/selenium_tests/test_navigates_galaxy.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into remove_toolshed_grids Commit: b93eb72858ed1866380acf35cfd2bfd4edd9e183 https://github.com/galaxyproject/galaxy/commit/b93eb72858ed1866380acf35cfd2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 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_toolshed.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: ----------- Load manage repo grid without mako Commit: e19006d0f803e77372b1f9a858e0197240a1bd2f https://github.com/galaxyproject/galaxy/commit/e19006d0f803e77372b1f9a858e0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix check_for_updates operation without self redirect Commit: 0b2ae99693edfccca2c5fca0ec727fcd14b07e24 https://github.com/galaxyproject/galaxy/commit/0b2ae99693edfccca2c5fca0ec72… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Revise operation handling for repository management grid Commit: 1115547d6b48746199f168ce5359dff15469a795 https://github.com/galaxyproject/galaxy/commit/1115547d6b48746199f168ce5359… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Change redirects to client side route for repositories Commit: d46d45aa26bbe4a3b4bf84a6d9a2e8b8e60a1ce4 https://github.com/galaxyproject/galaxy/commit/d46d45aa26bbe4a3b4bf84a6d9a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M templates/admin/tool_shed_repository/repository_actions_menu.mako Log Message: ----------- Fix redirect in pull down menu for repository manager Commit: 791c45f05ea28e34340e26399f4256de746a7554 https://github.com/galaxyproject/galaxy/commit/791c45f05ea28e34340e26399f42… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Add support for multirow operation Commit: fa6133eed4c518c7b26220ef6063a630ef05cc74 https://github.com/galaxyproject/galaxy/commit/fa6133eed4c518c7b26220ef6063… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix error handling status for repositories endpoint Commit: e31b37eab116fbe0b185843c4a9b2c6b047ab1de https://github.com/galaxyproject/galaxy/commit/e31b37eab116fbe0b185843c4a9b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/onload.js M config/galaxy.ini.sample M lib/galaxy/dependencies/conditional-requirements.txt M 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guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix global update call operation Commit: 323bc3d1dc374c6978121d92eac1b3734b1a15b4 https://github.com/galaxyproject/galaxy/commit/323bc3d1dc374c6978121d92eac1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 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: ----------- Re-add forms route Commit: 84218e38c0fe8c8b9c606598ccf9c2ac1a26148d https://github.com/galaxyproject/galaxy/commit/84218e38c0fe8c8b9c606598ccf9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix url for global operation Commit: 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lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M static/maps/mvc/grid/grid-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.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Revise inbound/center handling Commit: 6a52dcc4e50774667417af379699b474cef9f04e https://github.com/galaxyproject/galaxy/commit/6a52dcc4e50774667417af379699… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove inbound handler Commit: f1d53ef2a60b6b664d38d7dbfa13419022b6ff71 https://github.com/galaxyproject/galaxy/commit/f1d53ef2a60b6b664d38d7dbfa13… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Remove unused inbound pseudo class Commit: 31fd8a30805c5bb9cc788624a0890c78a7bdcc15 https://github.com/galaxyproject/galaxy/commit/31fd8a30805c5bb9cc788624a089… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-06 (Fri, 06 Oct 2017) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Add center redirect support for operations Redirect updates request to center panel Remove center redirect Commit: 857af99c610ca37afea38711560b52c36b2391ff https://github.com/galaxyproject/galaxy/commit/857af99c610ca37afea38711560b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-13 (Fri, 13 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/Dockerfile M .ci/jenkins/selenium/docker-compose.yml 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test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/filters/bed_to_gff_converter.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_exon_bed.xml M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/metag_tools/shrimp_wrapper.py M tools/sr_assembly/velvetg_wrapper.py M tox.ini Log Message: ----------- Merge branch 'dev' into remove_toolshed_grids Commit: 6c7efc284201aed56c1d8383cb596e8ab0001b83 https://github.com/galaxyproject/galaxy/commit/6c7efc284201aed56c1d8383cb59… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Display uninstall form in center panel, remove redirect Commit: 8f2db7f3177cd5d499473b3228085f41f136d52b https://github.com/galaxyproject/galaxy/commit/8f2db7f3177cd5d499473b322808… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Redirect operations to manage repository instead of grid Commit: 3f5b3f1f734dd83e09aff23ce5170ac358444ed9 https://github.com/galaxyproject/galaxy/commit/3f5b3f1f734dd83e09aff23ce517… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Remove redirects for repository revision installation Commit: 3811278d97c3d9469824e2f7e250a10fda5a8082 https://github.com/galaxyproject/galaxy/commit/3811278d97c3d9469824e2f7e250… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Show activation mako in center panel Commit: 145a7bd75782d117b1577dc5b9530fae4ae7cc49 https://github.com/galaxyproject/galaxy/commit/145a7bd75782d117b1577dc5b953… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Replace remaining redirects from makos in iframes with error messages Commit: 50322cedb9ea51a7d5765278b37db778a6287847 https://github.com/galaxyproject/galaxy/commit/50322cedb9ea51a7d5765278b37d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Fix a redirect to success message Commit: 5c8ca35ba6d874bae565aeb42edc124469d25d2d https://github.com/galaxyproject/galaxy/commit/5c8ca35ba6d874bae565aeb42edc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Show error message when installing latest revision fails Commit: 368a86b50303044ab999320d56934870f0df45ba https://github.com/galaxyproject/galaxy/commit/368a86b50303044ab999320d5693… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/repair_repository.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako Log Message: ----------- Remove deprecated repair repository feature Commit: c161d51423154a23058f60ef9436cfef20120bd5 https://github.com/galaxyproject/galaxy/commit/c161d51423154a23058f60ef9436… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove unused status parameter Commit: 34b07b807b1ff8464a314ed6ed3e52cd0aa1e1d0 https://github.com/galaxyproject/galaxy/commit/34b07b807b1ff8464a314ed6ed3e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Remove unused message parameter Commit: 3c5fc3fc424cd2470ebe435b216d2090b3196305 https://github.com/galaxyproject/galaxy/commit/3c5fc3fc424cd2470ebe435b216d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Use message mako to display purging success message Commit: f191a1ef44b06140f7c0d106669e77749b069fe1 https://github.com/galaxyproject/galaxy/commit/f191a1ef44b06140f7c0d106669e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Remove debug statement Commit: eec678ca7c1bf9c4c7515c7ef9f0453cffec2230 https://github.com/galaxyproject/galaxy/commit/eec678ca7c1bf9c4c7515c7ef9f0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-16 (Mon, 16 Oct 2017) Changed paths: M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1430_repair_installed_repository.py Log Message: ----------- Remove repair tests Commit: 098059c619909b049f9571d38afe582dbb602f7f https://github.com/galaxyproject/galaxy/commit/098059c619909b049f9571d38afe… Author: guerler 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static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/job-dag.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-li.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/job/job-params.js.map M static/maps/mvc/lazy/lazy-limited.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-librarylist-view.js.map 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static/maps/mvc/tours.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/icon-button.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-select-ftp.js.map M static/maps/mvc/ui/ui-select-genomespace.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/mvc/ui/ui-thumbnails.js.map M static/maps/mvc/upload/collection/collection-row.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-extension.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-connector.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-icons.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/de/locale.js.map M static/maps/nls/es/locale.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/maps/onload.js.map M static/maps/polyfills.js.map M static/maps/reports_webapp/run_stats.js.map M static/maps/ui/autocom_tagging.js.map M static/maps/ui/editable-text.js.map M static/maps/ui/fa-icon-button.js.map M static/maps/ui/filter-control.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/ui/popupmenu.js.map M static/maps/ui/scroll-panel.js.map M static/maps/ui/search-input.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/ajax-queue.js.map M static/maps/utils/async-save-text.js.map M static/maps/utils/config.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/levenshtein.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/natural-sort.js.map M static/maps/utils/query-string-parsing.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/maps/viz/bbi-data-manager.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/sweepster.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/slotting.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/trackster/util.js.map M static/maps/viz/visualization.js.map M static/maps/viz/viz_views.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.map M static/scripts/bundled/login.bundled.js.map M test/functional/tools/collection_split_on_column.xml Log Message: ----------- Merge branch 'dev' into remove_toolshed_grids Commit: 7f5048bc98dd3080db22f80e75b1dd688f981a0b https://github.com/galaxyproject/galaxy/commit/7f5048bc98dd3080db22f80e75b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-parameters.js M config/datatypes_conf.xml.sample M config/plugins/webhooks/demo/tour_generator/static/script.js M doc/source/slideshow/architecture/galaxy_architecture.md A lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/jobs/handler.py M lib/galaxy_ext/metadata/set_metadata.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-parameters.js.map 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/dataset/dataset-li-edit.js Log Message: ----------- Merge branch 'dev' into remove_toolshed_grids Commit: 2f2acb98e08934c5dae508c27490b42cf9b28313 https://github.com/galaxyproject/galaxy/commit/2f2acb98e08934c5dae508c27490… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-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 M static/scripts/layout/page.js M static/scripts/mvc/grid/grid-view.js R templates/admin/tool_shed_repository/repair_repository.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py M test/shed_functional/functional/test_1430_repair_installed_repository.py Log Message: ----------- Merge remote-tracking branch 'guerler/remove_toolshed_grids' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b8dfceb72aa4...2f2acb98e089

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[galaxyproject/usegalaxy-playbook] 753093: Update SSL certs
by GitHub 23 Oct '17

23 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 753093371c088b3bab13db053174dd43abd48cb6 https://github.com/galaxyproject/usegalaxy-playbook/commit/753093371c088b3b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-23 (Mon, 23 Oct 2017) Changed paths: M env/common/files/ssl/radegast.galaxyproject.org_cert.pem M env/common/files/ssl/wildcard_cert.pem M env/common/group_vars/sslservers/vault.yml Log Message: ----------- Update SSL certs

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