September 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy]
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/blank_log_lines Home: https://github.com/galaxyproject/galaxy **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] 661ad9: Remove empty log messages
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 661ad9bd1ef5562b23f542eb40dc4f42b488f1bf https://github.com/galaxyproject/galaxy/commit/661ad9bd1ef5562b23f542eb40dc… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove empty log messages e.g. ``` galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,005 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,005 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,005 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,006 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,007 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,007 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,008 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,008 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,008 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,009 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_hcluster/mothur_hcluster/1.36.1.0, version: 1.36.1.0 into tool panel.... galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,009 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,010 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,010 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,011 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,011 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,011 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,012 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,013 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,013 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,013 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,014 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,014 ``` Commit: eaa1211e474943838988d6ceec3e38111cb59236 https://github.com/galaxyproject/galaxy/commit/eaa1211e474943838988d6ceec3e… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Cleaner check for log message Commit: 66c6c84c4d61a504d0aefe0cadceef0dffad2c74 https://github.com/galaxyproject/galaxy/commit/66c6c84c4d61a504d0aefe0cadce… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #6763 from galaxyproject/blank_log_lines Remove empty log messages Compare: https://github.com/galaxyproject/galaxy/compare/9062363c4320...66c6c84c4d61 **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] eaa121: Cleaner check for log message
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/blank_log_lines Home: https://github.com/galaxyproject/galaxy Commit: eaa1211e474943838988d6ceec3e38111cb59236 https://github.com/galaxyproject/galaxy/commit/eaa1211e474943838988d6ceec3e… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Cleaner check for log message **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] 661ad9: Remove empty log messages
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/blank_log_lines Home: https://github.com/galaxyproject/galaxy Commit: 661ad9bd1ef5562b23f542eb40dc4f42b488f1bf https://github.com/galaxyproject/galaxy/commit/661ad9bd1ef5562b23f542eb40dc… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove empty log messages e.g. ``` galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,005 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,005 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,005 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,006 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,007 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,007 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,008 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,008 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,008 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,009 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_hcluster/mothur_hcluster/1.36.1.0, version: 1.36.1.0 into tool panel.... galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,009 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,010 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,010 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,011 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,011 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,011 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,012 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,013 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,013 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,013 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,014 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,014 ``` **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] 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 client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/list/list-view.js A client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tag.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/tool/tools.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.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 A 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-tabs.js M client/galaxy/scripts/mvc/upload/collection/rules-input-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-ftp.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/form_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster.js R client/galaxy/style/less/autocomplete_tagging.less R client/galaxy/style/less/base.less R 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client/yarn.lock M config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/job_conf.xml.sample_basic M config/local_conda_mapping.yml.sample M config/plugins/tours/core.scratchbook.yaml A config/plugins/visualizations/hivtrace/config/hivtrace.xml A config/plugins/visualizations/hivtrace/static/448c34a56d699c29117adc64c43affeb.woff2 A config/plugins/visualizations/hivtrace/static/674f50d287a8c48dc19ba404d20fe713.eot A config/plugins/visualizations/hivtrace/static/89889688147bd7575d6327160d64e760.svg A config/plugins/visualizations/hivtrace/static/912ec66d7572ff821749319396470bde.svg A config/plugins/visualizations/hivtrace/static/af7ae505a9eed503f8b8e6982036873e.woff2 A config/plugins/visualizations/hivtrace/static/b06871f281fee6b241d60582ae9369b9.ttf A config/plugins/visualizations/hivtrace/static/e18bbf611f2a2e43afc071aa2f4e1512.ttf A 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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. 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lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/bunch.py M lib/galaxy/util/checkers.py M lib/galaxy/util/expressions.py M lib/galaxy/util/none_like.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/permutations.py M lib/galaxy/util/renamed_temporary_file.py M lib/galaxy/util/rules_dsl.py M lib/galaxy/util/template.py M lib/galaxy/util/ucsc.py M lib/galaxy/version.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/cloud.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/uwsgi_schema.yml M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.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 A pytest.ini M run_tests.sh M scripts/api/README M scripts/functional_tests.py M scripts/galaxy-main A scripts/pages_identifier_conversion.py M scripts/plugin_staging.py M scripts/secret_decoder_ring.py M scripts/slideshow/example.md M static/style/blue/base.css M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/display_common.mako M templates/legacy/grid_base.mako M templates/tagging_common.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/repository/tool_form.mako 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 A test/api/test_roles.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/api.py M test/base/data/rules_dsl_spec.yml M test/base/data/test_workflow_with_runtime_input.ga M test/base/driver_util.py M test/base/integration_util.py M test/base/populators.py M test/base/rules_test_data.py M test/base/workflow_fixtures.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/interface.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/conftest.py A test/functional/known_broken_tools.txt M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/test_toolbox_pytest.py 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/delay_job_conf.xml A test/integration/delay_rules/__init__.py A test/integration/delay_rules/rules.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 A test/integration/test_job_recovery.py M test/integration/test_job_resubmission.py M test/integration/test_mules_as_job_handlers.py A test/integration/test_objectstore_selection.py M test/integration/test_scripts.py M test/integration/tool_sheds_conf.xml M test/integration/uses_shed.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryContentsManager.py A test/unit/managers/test_TagManager.py M test/unit/tools/test_parsing.py M test/unit/tools/test_toolbox.py M test/unit/workflows/test_workflow_progress.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/ucsc_tablebrowser_test.xml M tools/filters/bed_to_bigbed.xml M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.xml M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extractor.xml M tools/filters/tailWrapper.xml M tools/filters/uniq.xml M tools/filters/wc_gnu.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_importer.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_split_by_species.xml M 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.

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