- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] a3f699: Upgraded multiple repositories using ephemeris.
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a3f69979a7b6bac56c60c4a086bc1fbaa1d07cab https://github.com/galaxyproject/usegalaxy-playbook/commit/a3f69979a7b6bac5… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Upgraded multiple repositories using ephemeris. - picard v2.18.2 - fasta_nucleotide_changer v1.0.2 - ncbi_blast_plus v0.3.0 - bam_to_scidx v1.0.1 - fastq_to_fasta v1.0.2 - ggplot2_heatmap2 v2.2.1+galaxy1 - vsearch v2.8.3 - vegan_rarefaction v2.4-3 - vegan_fisher_alpha v2.4-3 - vegan_diversity 2.4-3 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 3f4024: Disable text field after upload
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f4024d47bddcb920ee00c99dbf5f14e2465f7e2 https://github.com/galaxyproject/galaxy/commit/3f4024d47bddcb920ee00c99dbf5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Disable text field after upload Commit: 9062363c4320dba06090292d18bf131cc3ec23aa https://github.com/galaxyproject/galaxy/commit/9062363c4320dba06090292d18bf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6762 from guerler/disable_text_field Disable file name text field after upload Compare: https://github.com/galaxyproject/galaxy/compare/5355fe9877ea...9062363c4320 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 6ac596: Add removal of upgrade logic specific to datatypes...
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 6ac5966c5e1a95e93c5923a4eddf5fa971518bd6 https://github.com/galaxyproject/galaxy/commit/6ac5966c5e1a95e93c5923a4eddf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add removal of upgrade logic specific to datatypes from 17.05 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 611764: Remove cruft releated to upgrading from 17.05 Gala...
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 611764b81a761c034bfd040b76818187a555807e https://github.com/galaxyproject/galaxy/commit/611764b81a761c034bfd040b7681… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Remove cruft releated to upgrading from 17.05 Galaxies. These interact poorly with recent changes in 18.09 and in nearly all cases should no longer be needed at this point. Commit: ea7359b08b21a9e0febe6cd98a9fd4488c133546 https://github.com/galaxyproject/galaxy/commit/ea7359b08b21a9e0febe6cd98a9f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Merge pull request #6761 from jmchilton/remove_upgrade_cruft [18.09] Remove upgrade cruft related to datatypes. Compare: https://github.com/galaxyproject/galaxy/compare/ac65832cb5e4...ea7359b08b21 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] e3b63e: Add migration script for cloudauthz table.
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e3b63e16d08fe08556bc690eaf5eec3e00b8aaae https://github.com/galaxyproject/galaxy/commit/e3b63e16d08fe08556bc690eaf5e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: A lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py Log Message: ----------- Add migration script for cloudauthz table. Commit: c25e69253f105b9f20ed1b114e5bfdeecad60310 https://github.com/galaxyproject/galaxy/commit/c25e69253f105b9f20ed1b114e5b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Add CloudAuthz class to model. Commit: dd9e8a5e6258ab14c7481691c3b5e6ef54c00836 https://github.com/galaxyproject/galaxy/commit/dd9e8a5e6258ab14c7481691c3b5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Add CloudAuthz to mapping. Commit: 14288a2b150d49e46577c2e8238e93d927548202 https://github.com/galaxyproject/galaxy/commit/14288a2b150d49e46577c2e8238e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py Log Message: ----------- Add authn_id and user_id to cloudauthz. Commit: 7f5a59d1347af33285b7e6df5955cedf9d456221 https://github.com/galaxyproject/galaxy/commit/7f5a59d1347af33285b7e6df5955… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: A lib/galaxy/managers/cloudauthzs.py A lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add cloudauthz api and manger, and define a route for API calls. Commit: c6af14ba28e1f36fef4008b57595e90e1282e5cd https://github.com/galaxyproject/galaxy/commit/c6af14ba28e1f36fef4008b57595… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Add CloudAuthz summary view serializer. Commit: ee255be84748748bfd01e6862fed0c2970f55ac2 https://github.com/galaxyproject/galaxy/commit/ee255be84748748bfd01e6862fed… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Fix a bug in CloudAuthz summary view serializer. Commit: 5bf003011a5efc8eb9d02d61170e23bbd1481c81 https://github.com/galaxyproject/galaxy/commit/5bf003011a5efc8eb9d02d61170e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Update CloudAuthz index; return all the cloudauthz records for a user. Commit: 6f043824978bccdc208929c84ac7ca83f00ca9f5 https://github.com/galaxyproject/galaxy/commit/6f043824978bccdc208929c84ac7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Change router for cloudauthz index. Commit: 8a980b1f7f7e2aa3b16ce66e1852be14e2d784c1 https://github.com/galaxyproject/galaxy/commit/8a980b1f7f7e2aa3b16ce66e1852… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Refactoring *thzs -> *thz; remove (s). Commit: 7760c98953524e6e5355f7ca678759dd7f2977d9 https://github.com/galaxyproject/galaxy/commit/7760c98953524e6e5355f7ca6787… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Assess cloudauthz config type in API before passing it to its manager. Commit: 193b73f26ecb661a4fb180a64806a0c7f0c6a2ba https://github.com/galaxyproject/galaxy/commit/193b73f26ecb661a4fb180a64806… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py Log Message: ----------- Fix a wrong order of imports. Commit: 0585f73384221cc024a62ecb1857f53670ced091 https://github.com/galaxyproject/galaxy/commit/0585f73384221cc024a62ecb1857… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Update cloudauthz API documentation. Commit: afa31d8b0978010e91724e86e2b08e9ffe698796 https://github.com/galaxyproject/galaxy/commit/afa31d8b0978010e91724e86e2b0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Update exception handling in cloudauthz to leverage Galaxy.exceptions. Commit: bff2f9f9f72988ffec9b9f92b935f48e39b79423 https://github.com/galaxyproject/galaxy/commit/bff2f9f9f72988ffec9b9f92b935… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Decode and assert `authn_id` in cloudauthz API. Commit: 70a90c47a65660f5fabb233cb3859755d097edab https://github.com/galaxyproject/galaxy/commit/70a90c47a65660f5fabb233cb385… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M .gitignore M Makefile M client/GruntFile.js M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue A client/galaxy/scripts/components/WorkflowImport.vue A client/galaxy/scripts/layout/communication-server-view.js R client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/bootstrap-tour.js R client/galaxy/scripts/libs/bootstrap.js A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M 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doc/source/admin/special_topics/bug_reports.rst M extract_dataset_parts.sh M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml R lib/galaxy/datatypes/converters/fastagz_to_fasta.xml R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R 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lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/util/hg_util.py M manage_db.sh M run_tests.sh M scripts/bootstrap_history.py M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh A scripts/docker_swarm_manager.py M scripts/get_uwsgi_args.py A static/images/fonts/FontAwesome.otf M static/images/fonts/fontawesome-webfont.eot A static/images/fonts/fontawesome-webfont.svg M static/images/fonts/fontawesome-webfont.ttf M static/images/fonts/fontawesome-webfont.woff A static/images/fonts/fontawesome-webfont.woff2 M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css M static/welcome.html.sample M templates/base/base_panels.mako M templates/sharing_base.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako A test-data/filter1_in6.bed A test-data/filter1_test6.bed M test-data/rules/uniprot.json A test-data/sort_out1.bed A test-data/sort_out2.bed A test-data/sort_out3.tab A test-data/sort_out4.sam M test/api/test_tools.py M test/api/test_workflows.py A test/base/data/rules_dsl_spec.yml M test/base/populators.py A test/base/rules_test_data.py A test/base/workflow_fixtures.py M test/base/workflows_format_2/main.py M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_scripts.py R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py A test/unit/test_rule_utils.py M test/unit/tools/test_parsing.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/sorter.py M tools/filters/sorter.xml M tools/filters/wig_to_bigwig.xml M tools/stats/filtering.py M tools/stats/filtering.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into cloudauthz Commit: 4a944cebe9bf94579cd06eb3a4f5d4a46004f2ab https://github.com/galaxyproject/galaxy/commit/4a944cebe9bf94579cd06eb3a4f5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Check if an `authn_id` exist & if user it belongs to the logged-in user. Commit: 900f88e87784a7a80901af1fa2d72b16f0a4e394 https://github.com/galaxyproject/galaxy/commit/900f88e87784a7a80901af1fa2d7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py Log Message: ----------- Fix a typo: "og" -> "log" Commit: fd269464a154aa03b70dc55cb1bd996c81218052 https://github.com/galaxyproject/galaxy/commit/fd269464a154aa03b70dc55cb1bd… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Add a method to authnz manager to request CloudAuthz cloud access token. Commit: 3933b44627258cb68f4c16c2499f84f3f2c8837d https://github.com/galaxyproject/galaxy/commit/3933b44627258cb68f4c16c2499f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M .ci/flake8_blacklist.txt M .ci/jenkins/selenium/run_tests.sh M .travis.yml A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md R client/galaxy/docs/galaxy-styles.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue A 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test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml M tools/data_source/upload.py M tools/filters/cutWrapper.pl M tools/filters/random_lines_two_pass.py M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/sr_mapping/bfast_wrapper.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into cloudauthz Commit: 3c9b852faf3150692b954c5e3d52911346d4aa10 https://github.com/galaxyproject/galaxy/commit/3c9b852faf3150692b954c5e3d52… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: R lib/galaxy/model/migrate/versions/0142_add_cloudauthz_tables.py A lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py Log Message: ----------- Update the migration script number. Commit: e0e02c2e1d75790874c423d48fc4edfb325c20b3 https://github.com/galaxyproject/galaxy/commit/e0e02c2e1d75790874c423d48fc4… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Add a method to authnz manager to get cloud access credentials. Commit: e510f07528221ddf325dcced890db2432a4cb7db https://github.com/galaxyproject/galaxy/commit/e510f07528221ddf325dcced890d… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-12 (Sun, 12 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Replace credentials with authz_id in the upload API of cloud storage. Commit: 841f04400003ddc44465e5c2c1c0ef1a86cf6e18 https://github.com/galaxyproject/galaxy/commit/841f04400003ddc44465e5c2c1c0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-12 (Sun, 12 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update cloud upload manager to use authz id instead of credentials. Commit: e1da0471604498ee207e7cae4f563f063d81b34b https://github.com/galaxyproject/galaxy/commit/e1da0471604498ee207e7cae4f56… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Configure AWS using temporary credentials generated by CloudAuthz. Commit: 64f3b3db526105e023c990a6a1ebf074e4df92c8 https://github.com/galaxyproject/galaxy/commit/64f3b3db526105e023c990a6a1eb… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug calling different function from authnz manager. Commit: 123785ef2510e1ed185a28b4c6423de2cd018e0d https://github.com/galaxyproject/galaxy/commit/123785ef2510e1ed185a28b4c642… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update the upload manager to adhere with latest CB interface changes. Commit: e292b2b38a7f448de3a060a3ec4ac1ae5803cbc3 https://github.com/galaxyproject/galaxy/commit/e292b2b38a7f448de3a060a3ec4a… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- In cloud API: accept encoded authz id, and decode it. Commit: e6b93a090be676501ab418eb7e59da201fcbc307 https://github.com/galaxyproject/galaxy/commit/e6b93a090be676501ab418eb7e59… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Assert if user can assume a specific authz. Commit: 8d9f86b7fb285c7543cf30021a81be62e10e3644 https://github.com/galaxyproject/galaxy/commit/8d9f86b7fb285c7543cf30021a81… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Handle item cloudauthn accessibility in its manager rather than API. Commit: be882841e15545923f1af63338951ff2ff572823 https://github.com/galaxyproject/galaxy/commit/be882841e15545923f1af6333895… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Check for accessibility and availability of authz config. Commit: f36d5b549cb41547e816c7c7a37014cd5ae830f4 https://github.com/galaxyproject/galaxy/commit/f36d5b549cb41547e816c7c7a370… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py Log Message: ----------- Make a func in cloudauthz manager static. Commit: a77971bce9694ba307197cbbc51b40bd1cb4d49e https://github.com/galaxyproject/galaxy/commit/a77971bce9694ba307197cbbc51b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/managers/cloudauthzs.py Log Message: ----------- Update exception messages to avoid exposing decoded IDs in Authz manager Commit: cba657b7f6ddd8cca5ba8f31b016ee55281cfd58 https://github.com/galaxyproject/galaxy/commit/cba657b7f6ddd8cca5ba8f31b016… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M templates/webapps/galaxy/workflow/editor.mako M tools/stats/filtering.xml Log Message: ----------- Merge remote-tracking branch 'origin/refresh_token' into cloudauthz Commit: 3f2f8fd3e04530d5ed76ae5122a0eb32550605e5 https://github.com/galaxyproject/galaxy/commit/3f2f8fd3e04530d5ed76ae5122a0… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Move the on_the_fly_config func to module level. Commit: 12ef351cd2821291a4d90ff7a882dde40e6140b4 https://github.com/galaxyproject/galaxy/commit/12ef351cd2821291a4d90ff7a882… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Pass strategy requesting ID token in get_cloud_access_credentials. Commit: 34484e9e1eb92b8955943e95d8a36b63f983a7ea https://github.com/galaxyproject/galaxy/commit/34484e9e1eb92b8955943e95d8a3… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- pass trans when asking for cloud access credentials. Commit: e4ea4af05676d6c28e639d9404dc29e6a523ef90 https://github.com/galaxyproject/galaxy/commit/e4ea4af05676d6c28e639d9404dc… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Define a mapping connecting a user instance with its cloud authzs. Commit: c97313e0eb951ed56de39b534ac4669dfc33d03f https://github.com/galaxyproject/galaxy/commit/c97313e0eb951ed56de39b534ac4… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Implement equals, eq & ne for CloudAuthz type. Commit: d2fbff164b56a6249916d9ab36ae595c269982c1 https://github.com/galaxyproject/galaxy/commit/d2fbff164b56a6249916d9ab36ae… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Avoid two cloud authz configuration with exact same config. Commit: 50876622fb7dc2503183dd8062846e8669fd4228 https://github.com/galaxyproject/galaxy/commit/50876622fb7dc2503183dd806284… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloudauthzs.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Move a function from cloudauthzs to authnz manager. Commit: 7e68a992d3772ccd8ebbfb6a52f19fea6efbd78b https://github.com/galaxyproject/galaxy/commit/7e68a992d3772ccd8ebbfb6a52f1… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py Log Message: ----------- Move the logic of getting authnz config from manager to authnz/managers. Commit: e1d014939fe752cfcf99debc60e5756efe211fbf https://github.com/galaxyproject/galaxy/commit/e1d014939fe752cfcf99debc60e5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-16 (Thu, 16 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Change a deepcopy of cloudauthz config, instead of the reference. Commit: 764ba3cdcedde28c0d96bfdb15e6321e096ea3cd https://github.com/galaxyproject/galaxy/commit/764ba3cdcedde28c0d96bfdb15e6… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Encapsulate getting cloud authz credentials in a try-catch block. Commit: 2915a2989a79742beb7e9a8bb31fcb422c3759f1 https://github.com/galaxyproject/galaxy/commit/2915a2989a79742beb7e9a8bb31f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Use _future_expose_api in cloudauthz APIs for better exception handling. Commit: c8e5427e5d48c98a2075648c7ff97040e0e8300f https://github.com/galaxyproject/galaxy/commit/c8e5427e5d48c98a2075648c7ff9… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Encapsulate can_user_assume_authn in a try-catch block. Commit: d223baa37ce4d61dd54e3b0dc29bf279d637fde9 https://github.com/galaxyproject/galaxy/commit/d223baa37ce4d61dd54e3b0dc29b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py Log Message: ----------- Move getting cloudauthz by id from cloud API to authnz manager. Commit: 656fe5512765a636375380ef78dedc53cd73ad0f https://github.com/galaxyproject/galaxy/commit/656fe5512765a636375380ef78de… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Update the get_cloud_access_credentials doc-string. Commit: 49976cb900c669a43b51d485475642e6b067d058 https://github.com/galaxyproject/galaxy/commit/49976cb900c669a43b51d4854756… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Update the try_get_authz_config doc-string. Commit: c934165b1df40f0487cf0e7a58c5f812dfa13856 https://github.com/galaxyproject/galaxy/commit/c934165b1df40f0487cf0e7a58c5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Extend cloudauthz as per provider requirements. Commit: e448a4e167957004611cd0f770dc233c0352ee99 https://github.com/galaxyproject/galaxy/commit/e448a4e167957004611cd0f770dc… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Refactor a method name, and fix a bug in authnz manager. Commit: 9c8e1c41ddc25a60d80b87cfe10ff6cb4ec9a595 https://github.com/galaxyproject/galaxy/commit/9c8e1c41ddc25a60d80b87cfe10f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-17 (Fri, 17 Aug 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update doc string of upload manager. Commit: e91c9b4588ef7671ed9562a94ac98f32c5c62d0a https://github.com/galaxyproject/galaxy/commit/e91c9b4588ef7671ed9562a94ac9… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: A .ci/jenkins/api-py3/run_tests.sh A .ci/jenkins/framework-py3/run_tests.sh A .ci/jenkins/integration-py3/run_tests.sh A .ci/jenkins/main-tools-py3/run_tests.sh A .ci/jenkins/main-tools/run_tests.sh A .ci/jenkins/selenium-py3/run_tests.sh M .coveragerc M .gitignore M .travis.yml M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M 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tools/maf/maf_to_bed.py M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/maf_to_interval.xml M tools/next_gen_conversion/solid2fastq.xml M tools/phenotype_association/ldtools.xml M tools/phenotype_association/ldtools_wrapper.sh M tools/phenotype_association/linkToGProfile.pl M tools/phenotype_association/linkToGProfile.xml M tools/phenotype_association/senatag.py M tools/plotting/boxplot.xml M tools/solid_tools/solid_qual_stats.py M tools/solid_tools/solid_qual_stats.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/grouping.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into cloudauthz # Conflicts: # lib/galaxy/managers/cloud.py Commit: f399d2981565d7395a02a80574a2d9c0dc12d950 https://github.com/galaxyproject/galaxy/commit/f399d2981565d7395a02a80574a2… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Add cloudauthz to the requirements, and update-dependencies. Commit: b679bc038d1f9faf88590e1fdd0789142efbaa00 https://github.com/galaxyproject/galaxy/commit/b679bc038d1f9faf88590e1fdd07… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Update requirements with patch in #6694 and manually revert dropping pyinotify. Commit: 13cf6615c6e1c5b4a105b45a2e1619dc4e95c6ec https://github.com/galaxyproject/galaxy/commit/13cf6615c6e1c5b4a105b45a2e16… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Fix lint issues in cloudauthz api. Commit: afed829a73131e158e3c4c08e19f8aedc2867631 https://github.com/galaxyproject/galaxy/commit/afed829a73131e158e3c4c08e19f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-11 (Tue, 11 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Fix lint issues with authnz/managers.py Commit: ba566a30563855f05f2fb667c3966afb4cd70334 https://github.com/galaxyproject/galaxy/commit/ba566a30563855f05f2fb667c396… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Upgrade to Cloudauthz v0.2.0. Commit: c0a36ca20d0f95b56898ba06a6dd705b3c1afaea https://github.com/galaxyproject/galaxy/commit/c0a36ca20d0f95b56898ba06a6dd… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Raise an exception if cannot get/refresh an ID token in cloudauthz. Commit: cc2fa14932ae1b3029865dcd8200bbb9fe72660c https://github.com/galaxyproject/galaxy/commit/cc2fa14932ae1b3029865dcd8200… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Do not surround getting cloud access credentials in a try-catch block. Commit: 915fc9ef024980917af1198f691ecdc4602e6baa https://github.com/galaxyproject/galaxy/commit/915fc9ef024980917af1198f691e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Catch CloudAuthz exceptions. Commit: d7c26f33527b9ce2adfe5ef79432608dfcd8d4cb https://github.com/galaxyproject/galaxy/commit/d7c26f33527b9ce2adfe5ef79432… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove an extra `objects` in getting objects from a bucket. Commit: 4ceab06486d6eb3adeedc86da64c260ff4adcd7e https://github.com/galaxyproject/galaxy/commit/4ceab06486d6eb3adeedc86da64c… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-14 (Fri, 14 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Fix lint issues. Commit: 60f08316ec9b66a6ebbd8a224b09cb0fb89825ae https://github.com/galaxyproject/galaxy/commit/60f08316ec9b66a6ebbd8a224b09… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-15 (Sat, 15 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Do not assert credentials using cloudbridge. Commit: af6ded604dfe5fa2898e616820edf7948eca1261 https://github.com/galaxyproject/galaxy/commit/af6ded604dfe5fa2898e616820ed… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-15 (Sat, 15 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Update exception message (and log it) in a cloud object is not found. Commit: e792480c74faf0500b2d1328a99c788482baa7ec https://github.com/galaxyproject/galaxy/commit/e792480c74faf0500b2d1328a99c… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-15 (Sat, 15 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Surround downloading datasets to cloud in a try-catch to capture issues such as invalid credentials. Commit: e4184188323996513fba84794e80bfb86f4d122d https://github.com/galaxyproject/galaxy/commit/e4184188323996513fba84794e80… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-15 (Sat, 15 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Report both successfully and unsuccessfully downloaded datasets to cloud Commit: cfb77903293ded0e829064da2786058463a3bfce https://github.com/galaxyproject/galaxy/commit/cfb77903293ded0e829064da2786… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-15 (Sat, 15 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- log unsuccessful cloud downloads as `debug` not `exception`. Commit: aecf9929027df8d6d3d348815acfc698c9661e7c https://github.com/galaxyproject/galaxy/commit/aecf9929027df8d6d3d348815acf… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-16 (Sun, 16 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix lint issues in cloud manager. Commit: 386eee076268964fe89299b82d5551ab0d08f75d https://github.com/galaxyproject/galaxy/commit/386eee076268964fe89299b82d55… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove a confusing debug log message. Commit: 00d883f2913767298c7616c4357048f6a8ae5d22 https://github.com/galaxyproject/galaxy/commit/00d883f2913767298c7616c43570… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Remove an unused `user` argument from cloud connection config method. Commit: 9bba80a322b85f12a9950f583eab39a4aa830215 https://github.com/galaxyproject/galaxy/commit/9bba80a322b85f12a9950f583eab… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Add more logging to cloudauthz api. Commit: 64d7418aae31cfee91f22112ac17d4f76f0f1276 https://github.com/galaxyproject/galaxy/commit/64d7418aae31cfee91f22112ac17… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Import Params in cloud manager. Commit: 0eb7892130b4b2099c2800919ad9cfb5c09a2cf7 https://github.com/galaxyproject/galaxy/commit/0eb7892130b4b2099c2800919ad9… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py Log Message: ----------- Add a description field to cloudauthz. Commit: f97c2550ec10d99a91cfe28dd3be96d1214d4499 https://github.com/galaxyproject/galaxy/commit/f97c2550ec10d99a91cfe28dd3be… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- Read cloudauthz description from api payload. Commit: 46183c91ec3d43927b4c9c83e297c7b3f2482635 https://github.com/galaxyproject/galaxy/commit/46183c91ec3d43927b4c9c83e297… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloud.py Log Message: ----------- Remove provider from cloud upload api, leverage authnz.provider instead. Commit: 5e8cf269163773acf5674e8565615b9bd2b66b8d https://github.com/galaxyproject/galaxy/commit/5e8cf269163773acf5674e856561… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/managers/cloud.py Log Message: ----------- Reuse a retrieved cloudauthz. Commit: 8f9a2c7c073b8d265f33b851467a6a4e906d86a4 https://github.com/galaxyproject/galaxy/commit/8f9a2c7c073b8d265f33b851467a… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Refactor authz -> cloudauthz. Commit: 6d4163ae966a5d27753f2cd22cd43e341713aec4 https://github.com/galaxyproject/galaxy/commit/6d4163ae966a5d27753f2cd22cd4… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- Fix a bug using undefined variable in cloud manager. Commit: cd571144b3ef74230bb68a19debe419cf8622249 https://github.com/galaxyproject/galaxy/commit/cd571144b3ef74230bb68a19debe… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Update a function doc-string in authnz manager. Commit: 5355fe9877eadd1c26fe120169c5fe3dc0611332 https://github.com/galaxyproject/galaxy/commit/5355fe9877eadd1c26fe120169c5… Author: Enis Afgan <afgane(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/managers/cloud.py A lib/galaxy/managers/cloudauthzs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0143_add_cloudauthz_tables.py M lib/galaxy/webapps/galaxy/api/cloud.py A lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #5903 from VJalili/cloudauthz Tested this by creating an authorization and, after creating an appropriate role in the AWS IAM dashboard, uploading some data from a private S3 bucket - works as expected. Some useful requests are available in the (newly created) Postman team for the Galaxy project (ping me for an invite): https://galaxyproject.postman.co/ Compare: https://github.com/galaxyproject/galaxy/compare/1549aaa169a7...5355fe9877ea **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 63c5e9: Upgrade several installed repositories on main
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 63c5e9391d2dc52d071694cb243f9d8febc903f6 https://github.com/galaxyproject/usegalaxy-playbook/commit/63c5e9391d2dc52d… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Upgrade several installed repositories on main - bedtools - deeptools_bam_compare - deeptools_bam_coverage - deeptools_bam_pe_fragmentsize - deeptools_bigwig_compare - deeptools_compute_gc_bias - deeptools_compute_matrix - deeptools_correct_gc_bias - deeptools_multi_bam_summary - deeptools_multi_bigwig_summary - deeptools_plot_correlation - deeptools_plot_coverage - deeptools_plot_enrichment - deeptools_plot_fingerprint - deeptools_plot_heatmap - deeptools_plot_pca - deeptools_plot_profile - collection_column_join - bam_to_scidx - vcf2tsv **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 80e6bc: Fix default upload row template indention
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80e6bc846644dbbeab7e479581f3aa5504a70c16 https://github.com/galaxyproject/galaxy/commit/80e6bc846644dbbeab7e479581f3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-22 (Sat, 22 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js Log Message: ----------- Fix default upload row template indention Commit: 41891f91e0255405232fdaf4e960c76edbf18a16 https://github.com/galaxyproject/galaxy/commit/41891f91e0255405232fdaf4e960… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-22 (Sat, 22 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js Log Message: ----------- Fix upload title input style Commit: 0b22e0c9950674924298c995dca56afcf8181f87 https://github.com/galaxyproject/galaxy/commit/0b22e0c9950674924298c995dca5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-22 (Sat, 22 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js Log Message: ----------- Remove static styling from default upload row template Commit: dce1b8fdab8c47031ca6b5329e6a37841744621b https://github.com/galaxyproject/galaxy/commit/dce1b8fdab8c47031ca6b5329e6a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-22 (Sat, 22 Sep 2018) Changed paths: M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Fix mode icon cursor Commit: 4f03a00d9cd7c34b6e81b88a9c3b7b9d7452fcd1 https://github.com/galaxyproject/galaxy/commit/4f03a00d9cd7c34b6e81b88a9c3b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-22 (Sat, 22 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Fix icon indention in buttons Commit: 1549aaa169a730dcdc0c819628572e5e622c4fad https://github.com/galaxyproject/galaxy/commit/1549aaa169a730dcdc0c81962857… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6758 from guerler/upload_row_template Fixes for the upload row template Compare: https://github.com/galaxyproject/galaxy/compare/a70e9ad2ce56...1549aaa169a7 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 8c05e2: Add grapdot datatype.
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 8c05e2f5f1677950a3279ffa30ccbf8949aa35e4 https://github.com/galaxyproject/galaxy/commit/8c05e2f5f1677950a3279ffa30cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add grapdot datatype. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 1a1904: add graph DOT datatype
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 1a19043789498f1d45725840b0761939d5dad2a5 https://github.com/galaxyproject/galaxy/commit/1a19043789498f1d45725840b076… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-09-23 (Sun, 23 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add graph DOT datatype Commit: 8d025aa4ed75f63924d9e11f9d0c65ca3aca7be0 https://github.com/galaxyproject/galaxy/commit/8d025aa4ed75f63924d9e11f9d0c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-09-23 (Sun, 23 Sep 2018) Changed paths: M config/plugins/visualizations/graphviz/config/graphviz.xml Log Message: ----------- add graph_dot datatype to graphvis Commit: ac65832cb5e4fa7a3e57af3722a09c7dfa4ac2ea https://github.com/galaxyproject/galaxy/commit/ac65832cb5e4fa7a3e57af3722a0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/visualizations/graphviz/config/graphviz.xml Log Message: ----------- Merge pull request #6760 from bgruening/graph_dot [18.09] Add graph dot datatype and enable it in visualisations Compare: https://github.com/galaxyproject/galaxy/compare/8a4fe72f6710...ac65832cb5e4 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 25fc16: Update RN with new merges.
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 25fc1617030d392f85abb65ccd95f913561919e2 https://github.com/galaxyproject/galaxy/commit/25fc1617030d392f85abb65ccd95… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Update RN with new merges. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] ac82e7: Add backrefs to mapped objects pointing at Dataset
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac82e7561c70b7492b03150da849058af1131837 https://github.com/galaxyproject/galaxy/commit/ac82e7561c70b7492b03150da849… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Add backrefs to mapped objects pointing at Dataset Commit: a70e9ad2ce5691fa6dcda7b4871645c2d4607616 https://github.com/galaxyproject/galaxy/commit/a70e9ad2ce5691fa6dcda7b48716… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #6754 from natefoo/dataset-backrefs Add backrefs to mapped objects pointing at Dataset Compare: https://github.com/galaxyproject/galaxy/compare/f6d3059f7e1b...a70e9ad2ce56 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 827e08: Initial work on updating styles
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 827e082bc521cfb287fc5572cdf386c6dc415d7e https://github.com/galaxyproject/galaxy/commit/827e082bc521cfb287fc5572cdf3… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/theme/blue.scss A client/galaxy/style/source_material/error_icon.svg M client/galaxy/style/source_material/galaxy_icons.svg A client/galaxy/style/source_material/info_icon.svg A client/galaxy/style/source_material/ok_icon.svg A client/galaxy/style/source_material/wait_icon.svg A client/galaxy/style/source_material/warn_icon.svg M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Initial work on updating styles Commit: 546eb18ca1e1a3f22fd162b5bcf674705c173601 https://github.com/galaxyproject/galaxy/commit/546eb18ca1e1a3f22fd162b5bcf6… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Improving spacing and forms. Commit: 7ddac47efaa9fa8435e4cb4c207bf557429dcd2d https://github.com/galaxyproject/galaxy/commit/7ddac47efaa9fa8435e4cb4c207b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove custom margin classes Commit: b5c8adb713806d2ad9a48a6f202ed57d584099cc https://github.com/galaxyproject/galaxy/commit/b5c8adb713806d2ad9a48a6f202e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove custom form error highlighting Commit: c25fcbdff9bbf05c102efea6fcc8e3144c5ad002 https://github.com/galaxyproject/galaxy/commit/c25fcbdff9bbf05c102efea6fcc8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove unused no-padding style Commit: 487c1199c9cdc603c7874750784c8f2323d3f8e6 https://github.com/galaxyproject/galaxy/commit/487c1199c9cdc603c7874750784c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove custom label wrapper Commit: 52b1e03419102821d6bfe7eb8bc77585d0162943 https://github.com/galaxyproject/galaxy/commit/52b1e03419102821d6bfe7eb8bc7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Remove unused generic icon size handler, move to upload styles Commit: 36aa8594e2126ea1b30c62f1e0511a5558708a4e https://github.com/galaxyproject/galaxy/commit/36aa8594e2126ea1b30c62f1e051… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Add comments for style helpers, remove unused styles Commit: f8d974d92d98edc43a35b0cc060b1ac249ee7a0c https://github.com/galaxyproject/galaxy/commit/f8d974d92d98edc43a35b0cc060b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove custom styles for admin side panel Commit: 40277c46aef2f7507026acd8c8f2c1d711800fad https://github.com/galaxyproject/galaxy/commit/40277c46aef2f7507026acd8c8f2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Properly extend tab styles, remove unused specifications Commit: a5f22f60156be5e6228da32b5e48dbf00dc75408 https://github.com/galaxyproject/galaxy/commit/a5f22f60156be5e6228da32b5e48… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Build user preferences without custom styles Commit: a5d4eba337632740dd640e5389d3683429b06557 https://github.com/galaxyproject/galaxy/commit/a5d4eba337632740dd640e5389d3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Revise list selectors, remove custom styles Commit: 1de8006e788fb74a9336231025c3adb1fa6ac6eb https://github.com/galaxyproject/galaxy/commit/1de8006e788fb74a9336231025c3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-11 (Wed, 11 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Use es6 string for library selection template Commit: fc4254bc1b0e75e52156c4b9a5453b73d7dd8e35 https://github.com/galaxyproject/galaxy/commit/fc4254bc1b0e75e52156c4b9a545… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-12 (Thu, 12 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove custom styles for ui-slider, fix code convention for if-statements Remove label test Commit: 5311c6d78260188e95d3a84f23d9521a0e075088 https://github.com/galaxyproject/galaxy/commit/5311c6d78260188e95d3a84f23d9… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #7 from guerler/styles-refresh-2018-adds Styles refresh 2018 additions and custom style removals Commit: de45a0037918ad9ba69b58d39ea8eac75b19fa3c https://github.com/galaxyproject/galaxy/commit/de45a0037918ad9ba69b58d39ea8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Reduce portlet style customization, fix appearance Commit: 87bc585302a13e2a40227a0fce0667d572685625 https://github.com/galaxyproject/galaxy/commit/87bc585302a13e2a40227a0fce06… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Consolidate portlet sub section styles Commit: 0e5bff875ad423d49f443be8f5b1f2f58c044b74 https://github.com/galaxyproject/galaxy/commit/0e5bff875ad423d49f443be8f5b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove narrow portlet, reuse section portlet instead Commit: 3210ec0d0dec1aa64ffef813ee4483ee258f10ed https://github.com/galaxyproject/galaxy/commit/3210ec0d0dec1aa64ffef813ee44… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix collapsible handling, improve contrast Commit: 413272237ef9c1e0558c0319b0855e782af88194 https://github.com/galaxyproject/galaxy/commit/413272237ef9c1e0558c0319b085… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix portlet margins Commit: 6af59d2e2c50a843f6fb83266c6372408d15afea https://github.com/galaxyproject/galaxy/commit/6af59d2e2c50a843f6fb83266c63… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #8 from guerler/styles-refresh-2018-adds-2 Consolidate portlet classes, fix tool form views Commit: ff633a0ab3c26cc2fb285bdb3ae98f8d849d94dc https://github.com/galaxyproject/galaxy/commit/ff633a0ab3c26cc2fb285bdb3ae9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove ui-form-section style Commit: ccb5962750a5cdefb23a961a7953e693c8c93fe8 https://github.com/galaxyproject/galaxy/commit/ccb5962750a5cdefb23a961a7953… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove portlet plain class Commit: dcab17c08a8a236531c17d7316bcb821b1b0543f 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lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/authnz.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/steps.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/web_util.py R openid/aol.xml A pytest.ini M run_tests.sh M scripts/common_startup_functions.sh M scripts/functional_tests.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M 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tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge branch 'dev' into styles-refresh-2018-3 Commit: 2e77d5f7fb80b11cdba33ae130195e29fe83e830 https://github.com/galaxyproject/galaxy/commit/2e77d5f7fb80b11cdba33ae13019… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Remove message size customization Commit: 5d33cf16326723e54e64b44f6eacd2f8f348cc79 https://github.com/galaxyproject/galaxy/commit/5d33cf16326723e54e64b44f6eac… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Reduce and move table 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lib/tool_shed/util/web_util.py R openid/aol.xml A pytest.ini M run_tests.sh M scripts/common_startup_functions.sh M scripts/functional_tests.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/plugin_staging.py M scripts/secret_decoder_ring.py M static/style/blue/base.css M templates/base/base_panels.mako M templates/display_common.mako M templates/legacy/grid_base.mako M templates/show_params.mako M templates/tagging_common.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/base_panels.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/11.tabular A test-data/configfile.json M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py A test/api/test_roles.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/api.py M test/base/data/test_workflow_topoambigouity.ga M test/base/data/test_workflow_topoambigouity_auto_laidout.ga M test/base/data/test_workflow_with_runtime_input.ga M test/base/driver_util.py M test/base/populators.py M test/base/rules_test_data.py M test/base/workflows_format_2/converter.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/conftest.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/test_toolbox_pytest.py A test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml A test/functional/tools/column_param_configfile.xml A test/functional/tools/inputs_as_json_with_paths.xml M test/functional/tools/metadata_biom1.xml M test/functional/tools/parallelism.xml M test/functional/tools/parallelism_optional.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/unicode_stream.xml R test/functional/twilltestcase.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/objectstore_selection_job_conf.xml A test/integration/objectstore_selection_job_resource_parameters_conf.xml A test/integration/objectstore_selection_rules/__init__.py A test/integration/objectstore_selection_rules/rules.py M test/integration/test_data_manager_table_reload.py M test/integration/test_mules_as_job_handlers.py A test/integration/test_objectstore_jobs.py A test/integration/test_objectstore_selection.py M test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py M test/integration/tool_sheds_conf.xml M test/integration/uses_shed.py M test/selenium_tests/framework.py M test/selenium_tests/test_admin_app.py M test/selenium_tests/test_history_panel_collections.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_params.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryManager.py M test/unit/test_galaxy_mapping.py A test/unit/test_model_copy.py M test/unit/test_objectstore.py M test/unit/test_remote_shell.py M test/unit/test_rule_utils.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py A tool-data/intermine_simple_display.loc.sample M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample A tools/data_source/intermine.xml M tools/data_source/ucsc_tablebrowser_test.xml M tools/data_source/upload.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge branch 'styles-refresh-2018-3' into styles-refresh-2018 Commit: a5311b490356bb1b4d7543a4ddd2007bc3bc14a7 https://github.com/galaxyproject/galaxy/commit/a5311b490356bb1b4d7543a4ddd2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Use default alert style, remove ui-message customizations Commit: 889d5154931b64d04c9439646749ad05b5c650e7 https://github.com/galaxyproject/galaxy/commit/889d5154931b64d04c9439646749… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove use form text styles Commit: 4fd94ceb5feb1a2c46e7647887aa3c27fb6f9fa1 https://github.com/galaxyproject/galaxy/commit/4fd94ceb5feb1a2c46e7647887aa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M 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styles Commit: 570bc975f0bf40ec32fd24862b4bddac65e76159 https://github.com/galaxyproject/galaxy/commit/570bc975f0bf40ec32fd24862b4b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Consolidate backbone wrapper for default buttons Commit: 069b97d8ddea1305a316ae073b09f8457574767d 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client/galaxy/style/scss/theme/blue.scss R client/galaxy/style/scss/theme/plain.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Remove outdated plain theme, consolidate blue theme Commit: 787b19a481bb90bc40197e485b17ba641d39ffea https://github.com/galaxyproject/galaxy/commit/787b19a481bb90bc40197e485b17… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Restore default gray-600 color used for text-muted Commit: 47429b486d53717caae84f8704898e584a66ea37 https://github.com/galaxyproject/galaxy/commit/47429b486d53717caae84f870489… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/frame.scss M 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----------- Fix tour tests. Commit: 3eb266a5dceaa873602a792ceefe45a412daa866 https://github.com/galaxyproject/galaxy/commit/3eb266a5dceaa873602a792ceefe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Remove unused variable, revisit issue in later Commit: f6d3059f7e1b08141f99b36aa555c10df3886305 https://github.com/galaxyproject/galaxy/commit/f6d3059f7e1b08141f99b36aa555… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/views/description.js M client/galaxy/scripts/mvc/visualization/chart/views/editor.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/settings.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js R client/galaxy/scripts/qunit/tests/popover_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/frame.scss R client/galaxy/style/scss/galaxy_bootstrap/overrides.scss R client/galaxy/style/scss/galaxy_bootstrap/variables.scss R client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/list-item.scss A client/galaxy/style/scss/overrides.scss M client/galaxy/style/scss/theme/blue.scss R client/galaxy/style/scss/theme/plain.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss A client/galaxy/style/source_material/error_icon.svg M client/galaxy/style/source_material/galaxy_icons.svg A client/galaxy/style/source_material/info_icon.svg A client/galaxy/style/source_material/ok_icon.svg A client/galaxy/style/source_material/wait_icon.svg A client/galaxy/style/source_material/warn_icon.svg M config/plugins/tours/core.galaxy_ui.yaml M static/style/blue/base.css M static/style/blue/library.css M templates/display_base.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/display.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_stock_tours.py Log Message: ----------- Merge pull request #6422 from jxtx/styles-refresh-2018 Initial work on updating styles Compare: https://github.com/galaxyproject/galaxy/compare/7481d97a33ba...f6d3059f7e1b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 5f32ac: Automatically determine the correct Jetstream imag...
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5f32ac85ecb6b8cef89ffb68f7221d96f2c8857d https://github.com/galaxyproject/infrastructure-playbook/commit/5f32ac85ecb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M roles/slurmscale/files/group_vars/all/spawn.yml M roles/slurmscale/files/resume.yml M roles/slurmscale/tasks/main.yml Log Message: ----------- Automatically determine the correct Jetstream image since it changes. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] e0b35d: Disable new objectstore feature temporarily due to...
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e0b35d32e8cda56e28a1993d991e72a2242e457d https://github.com/galaxyproject/usegalaxy-playbook/commit/e0b35d32e8cda56e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Disable new objectstore feature temporarily due to bugs **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f65e61: Use mapped-over collectionType when inferring coll...
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: f65e616c1afe6d9ec0bb9680fa90ee8e9d311900 https://github.com/galaxyproject/galaxy/commit/f65e616c1afe6d9ec0bb9680fa90… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Use mapped-over collectionType when inferring collectionType through format_source Commit: 3ffbf5b4b6138177ed7581d7845432bec138ee23 https://github.com/galaxyproject/galaxy/commit/3ffbf5b4b6138177ed7581d78454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Append mapped-over collection type to output collection type So if for instance the connected input is a regular input with a list:list input and the output is a paired collection we set the output collection type to list:list:paired. Commit: eb37ad3752f5dbe4806e74f85b4fcee63ab407fa https://github.com/galaxyproject/galaxy/commit/eb37ad3752f5dbe4806e74f85b4f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Only reset the right hand side of a connection on disconnect Commit: e10180dea108785a017b7be37b7ff5d85a2eebf1 https://github.com/galaxyproject/galaxy/commit/e10180dea108785a017b7be37b7f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- (minor) client-format Commit: 8a4fe72f6710270ca453b75d61e8dbc96feadcc5 https://github.com/galaxyproject/galaxy/commit/8a4fe72f6710270ca453b75d61e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge branch 'collection_type_source_followup' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/0fb115e046b3...8a4fe72f6710 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 7eac08: Undo auto-propagation of group tags.
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 7eac08979b1f474254e9a6a0b2005d365e09c143 https://github.com/galaxyproject/galaxy/commit/7eac08979b1f474254e9a6a0b200… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Undo auto-propagation of group tags. @mvdbeek and I discussed this in the Galaxy project gitter a few weeks ago and decided the propagation is too aggressive and should likely be done manually at the end of a workflow for now - using for instance the set tags collection operation tool. Commit: 0fb115e046b3a492db6b592d8b38459104d696bf https://github.com/galaxyproject/galaxy/commit/0fb115e046b3a492db6b592d8b38… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6750 from jmchilton/1809_tags_walkback [18.09] Undo auto-propagation of group tags. Compare: https://github.com/galaxyproject/galaxy/compare/9b5045a05c88...0fb115e046b3 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/ansible-galaxy] 3e60d5: init travis script and test playbook
by GitHub 21 Sep '18

21 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 3e60d5801b0577e0e3574a514838ce13e65a3d4c https://github.com/galaxyproject/ansible-galaxy/commit/3e60d5801b0577e0e357… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: A .travis.yml A tests/test_playbook.yml Log Message: ----------- init travis script and test playbook Commit: 2f9de4a553d3561743b47cff34b579f2fce03c3e https://github.com/galaxyproject/ansible-galaxy/commit/2f9de4a553d3561743b4… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M defaults/main.yml Log Message: ----------- Added variables for folder ownership and permissions Commit: 85b579c12319ec4d9d14a81992157aa2875e2213 https://github.com/galaxyproject/ansible-galaxy/commit/85b579c12319ec4d9d14… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/database.yml Log Message: ----------- Added become statements and setting database dir ownership & permissions Commit: 5febd3ca7e3a879ec20eb7b0bded8d5077e2e7b9 https://github.com/galaxyproject/ansible-galaxy/commit/5febd3ca7e3a879ec20e… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/dependencies.yml Log Message: ----------- Added become statements Commit: 26871a0cc59083a21fe9c098c9ac73fed3d00ef4 https://github.com/galaxyproject/ansible-galaxy/commit/26871a0cc59083a21fe9… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/mutable_setup.yml Log Message: ----------- Added become statements and setting config & shed tools dir ownership & permissions Commit: e01155439ed882666d7d663e39b537aa2f076582 https://github.com/galaxyproject/ansible-galaxy/commit/e01155439ed882666d7d… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/static_setup.yml M tasks/virtualenv.yml Log Message: ----------- Added become statements Commit: 0745f52b597067844c27afac52277e020226764d https://github.com/galaxyproject/ansible-galaxy/commit/0745f52b597067844c27… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M tasks/clone.yml Log Message: ----------- Added become statements and setting galaxy dir ownership & permissions Commit: cac16f1209e2e02b4a8167801c7cc41610585703 https://github.com/galaxyproject/ansible-galaxy/commit/cac16f1209e2e02b4a81… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- removed unnecessary docker lines Commit: dafe6ad12abf0f471d2954d2ed0be8d193bcac10 https://github.com/galaxyproject/ansible-galaxy/commit/dafe6ad12abf0f471d29… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M tasks/clone.yml M tasks/database.yml M tasks/dependencies.yml Log Message: ----------- added become statements which apply outside of travis Commit: 78d9bd9754c57258c5a13af1c873ef4509de0d16 https://github.com/galaxyproject/ansible-galaxy/commit/78d9bd9754c57258c5a1… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- Update .travis.yml Commit: 1b54661490b9660f554b2a681fdb040aa9ba816f https://github.com/galaxyproject/ansible-galaxy/commit/1b54661490b9660f554b… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- pinning Ansible version to 2.4 https://github.com/galaxyproject/ansible-galaxy/pull/38/files/dafe6ad12abf0… Commit: 838cd85876d7bd6e3d3e10dde6b377ac6a3ab02b https://github.com/galaxyproject/ansible-galaxy/commit/838cd85876d7bd6e3d3e… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- Install an upgraded pip and virtualenv Commit: fccea6b2cde19e3c961e2c7d2d9672d5d12f57ae https://github.com/galaxyproject/ansible-galaxy/commit/fccea6b2cde19e3c961e… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M .travis.yml Log Message: ----------- Install git Commit: a74e098c29917cf7c5120e5bec6f788238a4d7a5 https://github.com/galaxyproject/ansible-galaxy/commit/a74e098c29917cf7c512… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M tasks/clone.yml M tasks/database.yml M tasks/dependencies.yml M tasks/mutable_setup.yml M tasks/static_setup.yml M tasks/virtualenv.yml Log Message: ----------- Drop unnecessary become Commit: bdafc7e265a16fec35e74a30a47e557e46b38e06 https://github.com/galaxyproject/ansible-galaxy/commit/bdafc7e265a16fec35e7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M tests/test_playbook.yml Log Message: ----------- Add become on play level Commit: cbd0201114858f0af391c03ddd9f3f54a8e70fa0 https://github.com/galaxyproject/ansible-galaxy/commit/cbd0201114858f0af391… Author: Mark Esler <eslerm(a)umn.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M tasks/clone.yml M tasks/database.yml M tasks/dependencies.yml M tasks/mutable_setup.yml M tasks/static_setup.yml M tasks/virtualenv.yml M tests/test_playbook.yml Log Message: ----------- Merge pull request #5 from mvdbeek/drop_become Thank you! Commit: f606476bbaa96fbfc472a973dadd023fbebaad0c https://github.com/galaxyproject/ansible-galaxy/commit/f606476bbaa96fbfc472… Author: eslerm <eslerm(a)umn.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M defaults/main.yml M tasks/clone.yml M tasks/database.yml M tasks/mutable_setup.yml M tasks/static_setup.yml Log Message: ----------- drop unnecessary file and variable Commit: 9ee412e2d63d706437134f3a307774af7eeb8fd8 https://github.com/galaxyproject/ansible-galaxy/commit/9ee412e2d63d70643713… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: A .travis.yml M tasks/clone.yml M tasks/static_setup.yml A tests/test_playbook.yml Log Message: ----------- Merge pull request #38 from eslerm/travis Travis-CI Compare: https://github.com/galaxyproject/ansible-galaxy/compare/fa0df02a3eaf...9ee4… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] eae35f: Deduplicate pgcleanup.py
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eae35fab3304224ab6d55ffeae40d6b6611a99cb https://github.com/galaxyproject/galaxy/commit/eae35fab3304224ab6d55ffeae40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Deduplicate pgcleanup.py Commit: 7b8af87091eb5686ad390073f678d9088f6af10b https://github.com/galaxyproject/galaxy/commit/7b8af87091eb5686ad390073f678… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-18 (Tue, 18 Sep 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Add a pgcleanup function for purging error HDAs Commit: 7481d97a33ba7fb2a003ae2ad51414c04ae826b0 https://github.com/galaxyproject/galaxy/commit/7481d97a33ba7fb2a003ae2ad514… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M scripts/cleanup_datasets/pgcleanup.py Log Message: ----------- Merge pull request #6736 from natefoo/pgcleanup pgcleanup.py enhancements Compare: https://github.com/galaxyproject/galaxy/compare/bae08f3ca226...7481d97a33ba **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 649390: Increase Toolshed uWSGI proxy timeout
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6493903ab85efa59019c9b9e056e2ae97319d300 https://github.com/galaxyproject/usegalaxy-playbook/commit/6493903ab85efa59… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M env/common/group_vars/toolshedwebservers.yml Log Message: ----------- Increase Toolshed uWSGI proxy timeout **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] b5e221: Fix page editor height for flex panels.
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b5e221929687809adfb30cad8280767f3a8412c5 https://github.com/galaxyproject/galaxy/commit/b5e221929687809adfb30cad8280… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Fix page editor height for flex panels. Commit: 9b5045a05c882c652935d9daaf589a10d776190c https://github.com/galaxyproject/galaxy/commit/9b5045a05c882c652935d9daaf58… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge pull request #6747 from dannon/fix_page_editor_height [18.09] Fix page editor height for flex panels. Compare: https://github.com/galaxyproject/galaxy/compare/287648f5d9f9...9b5045a05c88 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 2209c3: Minor cleanup.
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 2209c3171de52dbe83683d2644b0ec6befbaa763 https://github.com/galaxyproject/galaxy/commit/2209c3171de52dbe83683d2644b0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Minor cleanup. Commit: 037ddfeab5decd47d4d2bd8771e975dc1857703a https://github.com/galaxyproject/galaxy/commit/037ddfeab5decd47d4d2bd8771e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Fix active content setting for views with explicitly defined models Commit: 96593cb444063d6cc6819dd77d7b2fb89c250054 https://github.com/galaxyproject/galaxy/commit/96593cb444063d6cc6819dd77d7b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Import cleanup and documentation for dataset-li-edit. Commit: 11b5157825ee318b763f6c48b674b968f114aebb https://github.com/galaxyproject/galaxy/commit/11b5157825ee318b763f6c48b674… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Use standard faIconButton for visualize. Commit: 4aa2b8f919f28b798ba9a2401c602990287338b6 https://github.com/galaxyproject/galaxy/commit/4aa2b8f919f28b798ba9a2401c60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Disentangle this/self/frames in scratchbook's events. Commit: 077f3088ece5c8617b044d53764aebff1768b34f https://github.com/galaxyproject/galaxy/commit/077f3088ece5c8617b044d53764a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Correct visualization link to use router or scratchbook as appropriate. Commit: 3f29d32898efd121f315b2147e917584e9dec28f https://github.com/galaxyproject/galaxy/commit/3f29d32898efd121f315b2147e91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Strip unused function, cleanup. Commit: 0018ab989b117c953dd2b02e1e06cc80af1ddff2 https://github.com/galaxyproject/galaxy/commit/0018ab989b117c953dd2b02e1e06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Add event hook for non-bb-view center panel id setting, use it for dataset visualization. Commit: d17ea03442448472f1e5e5d4e12e73459f1736e7 https://github.com/galaxyproject/galaxy/commit/d17ea03442448472f1e5e5d4e12e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Minor formatting tweaks. Commit: 87ecf1428e841bced376e504d1d468319a7853c9 https://github.com/galaxyproject/galaxy/commit/87ecf1428e841bced376e504d1d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Use pre-fetched dataset id Commit: 287648f5d9f95ccd1b625037e30de0ab3e62e7f5 https://github.com/galaxyproject/galaxy/commit/287648f5d9f95ccd1b625037e30d… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Merge pull request #6725 from dannon/fix_active_highlight [18.09] Fix active highlight Compare: https://github.com/galaxyproject/galaxy/compare/30728899054d...287648f5d9f9 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] ff7351: Decrease stratum1 squid memory to hopefully preven...
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ff7351e512d9471167b39de5438a331aae05981e https://github.com/galaxyproject/infrastructure-playbook/commit/ff7351e512d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M env/galaxy/group_vars/cvmfsstratum1servers/vars.yml Log Message: ----------- Decrease stratum1 squid memory to hopefully prevent squid from dying on cvmfs1-iu0 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 75ae1d: Attempted slurmscale fix
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 75ae1d079a7ed28e9d5172f82b786d9c145f7aee https://github.com/galaxyproject/infrastructure-playbook/commit/75ae1d079a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M roles/slurmscale/files/resume.yml Log Message: ----------- Attempted slurmscale fix **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 806bea: Test that newest version will be returned if tool ...
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 806beaca9b4b51322214e68619407e8a0545a19d https://github.com/galaxyproject/galaxy/commit/806beaca9b4b51322214e6861940… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Test that newest version will be returned if tool id or version don't match Commit: c8552970dd7c2eeb9d765911843ed3e866b84ce3 https://github.com/galaxyproject/galaxy/commit/c8552970dd7c2eeb9d765911843e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort by tool version when picking a tool with an unavailable version Commit: 94082a878dca784eb57c6be1fd552a63f85bcfad https://github.com/galaxyproject/galaxy/commit/94082a878dca784eb57c6be1fd55… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Unit test that fails if we don't return the latest version upon version mismatch Commit: 3ea9d086bfe295a210d6f249ef2c39d8a65ef042 https://github.com/galaxyproject/galaxy/commit/3ea9d086bfe295a210d6f249ef2c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort rval so that newest tool appears last in rval Commit: f6f526a0a50a98143d4845f8907067b6f42e1dea https://github.com/galaxyproject/galaxy/commit/f6f526a0a50a98143d4845f89070… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Use tool_version instead of version parameter To be consistent with other routes that accept this parameter. Commit: 3017568e77cf950b8b611a16ea7ce9fcc2159e81 https://github.com/galaxyproject/galaxy/commit/3017568e77cf950b8b611a16ea7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Drop unnecessary history in test_show_with_wrong_tool_version_in_tool_id test Commit: 02c177152bd7dbef02d4ea5d40449745e913b38b https://github.com/galaxyproject/galaxy/commit/02c177152bd7dbef02d4ea5d4044… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6740 from mvdbeek/backport_tool_version_select_fixes [18.05] Backport tool version select fixes Commit: 30728899054dde65ddd9fe99dc8424166ee0c5ad https://github.com/galaxyproject/galaxy/commit/30728899054dde65ddd9fe99dc84… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/d312c48ea768...30728899054d **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 806bea: Test that newest version will be returned if tool ...
by GitHub 20 Sep '18

20 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 806beaca9b4b51322214e68619407e8a0545a19d https://github.com/galaxyproject/galaxy/commit/806beaca9b4b51322214e6861940… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Test that newest version will be returned if tool id or version don't match Commit: c8552970dd7c2eeb9d765911843ed3e866b84ce3 https://github.com/galaxyproject/galaxy/commit/c8552970dd7c2eeb9d765911843e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort by tool version when picking a tool with an unavailable version Commit: 94082a878dca784eb57c6be1fd552a63f85bcfad https://github.com/galaxyproject/galaxy/commit/94082a878dca784eb57c6be1fd55… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Unit test that fails if we don't return the latest version upon version mismatch Commit: 3ea9d086bfe295a210d6f249ef2c39d8a65ef042 https://github.com/galaxyproject/galaxy/commit/3ea9d086bfe295a210d6f249ef2c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort rval so that newest tool appears last in rval Commit: f6f526a0a50a98143d4845f8907067b6f42e1dea https://github.com/galaxyproject/galaxy/commit/f6f526a0a50a98143d4845f89070… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Use tool_version instead of version parameter To be consistent with other routes that accept this parameter. Commit: 3017568e77cf950b8b611a16ea7ce9fcc2159e81 https://github.com/galaxyproject/galaxy/commit/3017568e77cf950b8b611a16ea7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Drop unnecessary history in test_show_with_wrong_tool_version_in_tool_id test Commit: 02c177152bd7dbef02d4ea5d40449745e913b38b https://github.com/galaxyproject/galaxy/commit/02c177152bd7dbef02d4ea5d4044… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6740 from mvdbeek/backport_tool_version_select_fixes [18.05] Backport tool version select fixes Compare: https://github.com/galaxyproject/galaxy/compare/d014469f070e...02c177152bd7 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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