- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 982e87: Allow supplying name of pasted data, issue #4162
by GitHub 27 Aug '18

27 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 982e878f8e5903b42df291015522c6b3334f6035 https://github.com/galaxyproject/galaxy/commit/982e878f8e5903b42df291015522… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Allow supplying name of pasted data, issue #4162 Commit: 163018c35177a9356a7e6f789ee719f3be5d861e https://github.com/galaxyproject/galaxy/commit/163018c35177a9356a7e6f789ee7… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2018-07-18 (Wed, 18 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- keep default Galaxy dataset name of pasted content to Pasted Entry Commit: 7fa539162791e5e1eca836616b31381f2ad62b05 https://github.com/galaxyproject/galaxy/commit/7fa539162791e5e1eca836616b31… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js Log Message: ----------- Merge pull request #6415 from FredericBGA/supplying_name_pasted_data Allow supplying name of pasted data Compare: https://github.com/galaxyproject/galaxy/compare/660a51495b52...7fa539162791 **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] 51c6e2: Add a step in PSA pipeline to determine if ID toke...
by GitHub 27 Aug '18

27 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51c6e2f6ba6b654b7f234c0440cfaa95ac2735b4 https://github.com/galaxyproject/galaxy/commit/51c6e2f6ba6b654b7f234c0440cf… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add a step in PSA pipeline to determine if ID token exists. Commit: 405a08522e8f54341478dde5c88868e33ed55ec7 https://github.com/galaxyproject/galaxy/commit/405a08522e8f54341478dde5c888… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- check for missing ID and refresh tokens. Commit: 0ed0bdf203c6d088487c24e42fd50951039f7e74 https://github.com/galaxyproject/galaxy/commit/0ed0bdf203c6d088487c24e42fd5… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add some comments explaining when some OIDC-related errors can happen. Commit: 3e6fa40ec84206558aa11679170fd747ff2f20b3 https://github.com/galaxyproject/galaxy/commit/3e6fa40ec84206558aa11679170f… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Fix some lint issues in psa_authnz.py. Commit: b29311fdab1a08a70eee7fad69f77bc72d8e88bc https://github.com/galaxyproject/galaxy/commit/b29311fdab1a08a70eee7fad69f7… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Get ID token, if expired, refresh it. Commit: 27db877816bdba5f91ada327c63b7a7717341e18 https://github.com/galaxyproject/galaxy/commit/27db877816bdba5f91ada327c63b… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove the `get_access_token` as it hides a base method. Commit: f0a8c541d8c83e6e6bbd7731ba4197cae549b47a https://github.com/galaxyproject/galaxy/commit/f0a8c541d8c83e6e6bbd7731ba41… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add a comment explaining a PSA pipeline step. Commit: 9d7f50c6c074a9d3e39763180d6e270f7290164f https://github.com/galaxyproject/galaxy/commit/9d7f50c6c074a9d3e39763180d6e… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-08-15 (Wed, 15 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py Log Message: ----------- Add doc string for `contains_required_data` function. Commit: 660a51495b52cf886db31dbcc807e54c5b787469 https://github.com/galaxyproject/galaxy/commit/660a51495b52cf886db31dbcc807… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M lib/galaxy/authnz/psa_authnz.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6606 from VJalili/refresh_token Refresh an expired OIDC ID token Compare: https://github.com/galaxyproject/galaxy/compare/af99f49d82d9...660a51495b52 **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] 296105: row ids that are all numeric become ints...
by GitHub 27 Aug '18

27 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 296105ee395194c48d962671a8c367469ea74907 https://github.com/galaxyproject/galaxy/commit/296105ee395194c48d962671a8c3… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- row ids that are all numeric become ints... Since the "F" prefix is checked with substring, row_id must always be a string Commit: 55d350d015f20afc1c350130caaa0aa9858b7aa0 https://github.com/galaxyproject/galaxy/commit/55d350d015f20afc1c350130caaa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M static/scripts/admin.toolshed.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/chart.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.interactive_environments.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/i18n.js M static/scripts/layout/communication-server-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js M static/scripts/legacy/grid/grid-model.js M static/scripts/legacy/grid/grid-template.js M static/scripts/legacy/grid/grid-view.js M static/scripts/mocha/test.js M static/scripts/mocha/tests/rules_tests.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M 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static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/job-states-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/job/job-params.js M static/scripts/mvc/lazy/lazy-limited.js M 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static/scripts/mvc/visualization/chart/views/settings.js M static/scripts/mvc/visualization/chart/views/viewer.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports/run_stats.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Add static for 2a148ff1ec37c68e280c431fceee88ee0510e017 Commit: 03c485ee45e96784b269896a23223d233c566b89 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static/scripts/layout/scratchbook.js M static/scripts/legacy/grid/grid-model.js M static/scripts/legacy/grid/grid-template.js M static/scripts/legacy/grid/grid-view.js M static/scripts/mocha/test.js M static/scripts/mocha/tests/rules_tests.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-choice.js M 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static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-queue-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/toolshed-model.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/icon-button.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-rules-edit.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/ui/ui-thumbnails.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/collection/rules-input-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-extension.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-utils.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/visualization/chart/chart-client.js M static/scripts/mvc/visualization/chart/components/model.js M static/scripts/mvc/visualization/chart/components/screenshot.js M static/scripts/mvc/visualization/chart/utilities/datasets.js M static/scripts/mvc/visualization/chart/utilities/jobs.js M static/scripts/mvc/visualization/chart/utilities/series.js M static/scripts/mvc/visualization/chart/views/description.js M static/scripts/mvc/visualization/chart/views/editor.js M static/scripts/mvc/visualization/chart/views/groups.js M static/scripts/mvc/visualization/chart/views/menu.js M static/scripts/mvc/visualization/chart/views/settings.js M static/scripts/mvc/visualization/chart/views/viewer.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/de/locale.js M static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/scripts/onload.js M static/scripts/polyfills.js M static/scripts/reports/run_stats.js M static/scripts/toolshed/groups/group-detail-view.js M static/scripts/toolshed/groups/group-list-view.js M static/scripts/toolshed/groups/group-listrow-view.js M static/scripts/toolshed/groups/group-model.js M static/scripts/toolshed/toolshed.groups.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js Log Message: ----------- Merge pull request #6639 from bwlang/patch-2 [18.05] row ids that are all numeric become ints... Compare: https://github.com/galaxyproject/galaxy/compare/709e49f104e2...03c485ee45e9 **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] 49eae7: Fix for workflow extraction cleanup routine.
by GitHub 27 Aug '18

27 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 49eae728916af02a6fbd3ce9d69599c08d4e58b9 https://github.com/galaxyproject/galaxy/commit/49eae728916af02a6fbd3ce9d695… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Fix for workflow extraction cleanup routine. Workflow extraction would be incorrect if you had parameters ordered and named as e.g. "somename" and "somename_2" in the input root. When these parameters are both dataset inputs, this would cause a server error. Commit: af99f49d82d917b681157ec8f5a4506c6a37cab6 https://github.com/galaxyproject/galaxy/commit/af99f49d82d917b681157ec8f5a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-27 (Mon, 27 Aug 2018) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Merge pull request #6636 from blankenberg/11yowffix Fix for workflow extraction cleanup routine. Compare: https://github.com/galaxyproject/galaxy/compare/0e69ca8bfbc3...af99f49d82d9 **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] 6e8a7f: Fix empty handling rule.
by GitHub 26 Aug '18

26 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e8a7fddb1727a7b6f4c3ae4817d38fe73f2079b https://github.com/galaxyproject/galaxy/commit/6e8a7fddb1727a7b6f4c3ae4817d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Fix empty handling rule. Commit: 42ddfbde4c429b6bd3a19f901f0f3bf7db1d85ba https://github.com/galaxyproject/galaxy/commit/42ddfbde4c429b6bd3a19f901f0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js M test/base/data/rules_dsl_spec.yml Log Message: ----------- Fill out, polish the rule spec a little more. Drop use of startsWith in favor of indexOf for PhantomJS testing. Commit: 6cd8650b5a5530835e6d396e81d6f481ca6b141a https://github.com/galaxyproject/galaxy/commit/6cd8650b5a5530835e6d396e81d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove stray debug statement left in 18.05. Commit: 4d83746cc2f83c1208abcefbce3e66a00f01076a https://github.com/galaxyproject/galaxy/commit/4d83746cc2f83c1208abcefbce3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Allow loading tag metadata from existing objects in rule builder. This should allow nesting and filtering from tags - including group tags. Commit: 58072302539dd7c5283ee11c13512a19a9bf99fb https://github.com/galaxyproject/galaxy/commit/58072302539dd7c5283ee11c1351… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-27 (Fri, 27 Jul 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/util/rules_dsl.py M test/api/test_tools.py M test/base/data/rules_dsl_spec.yml M test/base/populators.py M test/base/rules_test_data.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Implement rule builder rule to quickly grab group tag value. Should make it a lot easier to nested and filter on group tag values. Commit: 0e69ca8bfbc3c93bd18a22a32cd77494d55e915e https://github.com/galaxyproject/galaxy/commit/0e69ca8bfbc3c93bd18a22a32cd7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/rules_dsl.py M test/api/test_tools.py M test/base/data/rules_dsl_spec.yml M test/base/populators.py M test/base/rules_test_data.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #6545 from jmchilton/rule_builder_use_group_tags Allow Consuming Tags in the Apply Rules Tool Compare: https://github.com/galaxyproject/galaxy/compare/a3fc0b9f324f...0e69ca8bfbc3 **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] 84597a: Lists-as-tuples collection operations.
by GitHub 26 Aug '18

26 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84597a12356aaa5b5d59ba95c30691739fed2300 https://github.com/galaxyproject/galaxy/commit/84597a12356aaa5b5d59ba95c306… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/build_list.xml A lib/galaxy/tools/extract_dataset.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_parsing.py Log Message: ----------- Lists-as-tuples collection operations. Commit: a3fc0b9f324f3aa2a4824b260f3057a36471857a https://github.com/galaxyproject/galaxy/commit/a3fc0b9f324f3aa2a4824b260f30… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/build_list.xml A lib/galaxy/tools/extract_dataset.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #6312 from jmchilton/tuple_operations Lists-as-tuples collection operations Compare: https://github.com/galaxyproject/galaxy/compare/2560919bd04d...a3fc0b9f324f **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] 626195: Integration test for job recovery (before and afte...
by GitHub 25 Aug '18

25 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 626195335ee70dbc2d0568603e0627744d07d529 https://github.com/galaxyproject/galaxy/commit/626195335ee70dbc2d0568603e06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-21 (Tue, 21 Aug 2018) Changed paths: M test/base/driver_util.py M test/base/integration_util.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/test_job_recovery.py M test/integration/test_job_resubmission.py Log Message: ----------- Integration test for job recovery (before and after handler has picked it up). Commit: ded2311799a772914ddb9c732d59ba2f4de572b4 https://github.com/galaxyproject/galaxy/commit/ded2311799a772914ddb9c732d59… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Handle job_wrapper.working_directory correctly during job recovery. Commit: 2560919bd04d6f27e14fcf9f580aea66244afa30 https://github.com/galaxyproject/galaxy/commit/2560919bd04d6f27e14fcf9f580a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-08-25 (Sat, 25 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py M test/base/driver_util.py M test/base/integration_util.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/test_job_recovery.py M test/integration/test_job_resubmission.py Log Message: ----------- Merge pull request #6620 from jmchilton/job_recovery_test Integration test for job recovery. Compare: https://github.com/galaxyproject/galaxy/compare/107c89a0a994...2560919bd04d **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] ead33c: Installed PlantTribes tools.
by GitHub 24 Aug '18

24 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ead33c95c90d7b1ae0490616fac0ac2c7be81aa1 https://github.com/galaxyproject/usegalaxy-playbook/commit/ead33c95c90d7b1a… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-08-24 (Fri, 24 Aug 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: ----------- Installed PlantTribes tools. **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] 2d4b71: Test case to clarify workflow API a bit in simple ...
by GitHub 24 Aug '18

24 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2d4b717aaff3fc8a76852af8a16744f1085fa8cc https://github.com/galaxyproject/galaxy/commit/2d4b717aaff3fc8a76852af8a167… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case to clarify workflow API a bit in simple cases. Commit: c593bd1772dc6d8780153115641d556bea347bc9 https://github.com/galaxyproject/galaxy/commit/c593bd1772dc6d8780153115641d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow uniform access to job state for WorkflowInvocationSteps. Use the concept of job_source_type and job_source_id used by IDs to summarize the state and list out individual jobs in the response as a shortcut. This information used to be readily accessible before 18.01. Commit: 35ebdc5b1029bbe782c2852b5f6b094d97dbd7ea https://github.com/galaxyproject/galaxy/commit/35ebdc5b1029bbe782c2852b5f6b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Add a legacy_job_state mode to restore 17.09 workflow invocation behavior. Commit: 3879a019490a05f9e26e3651e6de52d0586d5963 https://github.com/galaxyproject/galaxy/commit/3879a019490a05f9e26e3651e6de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_workflows.py Log Message: ----------- Add API endpoint to index all invocations for a user or history. Refactor toward managers to allow unified serialization of invocations and such. Add test case. Commit: 107c89a0a994a50fd37589fbd2b4d104064c7336 https://github.com/galaxyproject/galaxy/commit/107c89a0a994a50fd37589fbd2b4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6580 from jmchilton/wf_invocation_update Add API endpoint to fetch a history's workflow invocations. Compare: https://github.com/galaxyproject/galaxy/compare/dfdf3dd5eac4...107c89a0a994 **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] ac29ab: Fix metadata elements reset when creating Metadata...
by GitHub 24 Aug '18

24 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac29abb6266fb9b83c985b27804db607c503ef51 https://github.com/galaxyproject/galaxy/commit/ac29abb6266fb9b83c985b27804d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-23 (Thu, 23 Aug 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Fix metadata elements reset when creating Metadata files This is a fallout out from 9780d069c8646fb4f02de848d62159680d95ae79 Commit: dfdf3dd5eac4f6ae182ddf3d50490dc73a4dd614 https://github.com/galaxyproject/galaxy/commit/dfdf3dd5eac4f6ae182ddf3d5049… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-24 (Fri, 24 Aug 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Merge pull request #6631 from mvdbeek/fix_metadata_element_rest Fix metadata elements reset when creating Metadata files Compare: https://github.com/galaxyproject/galaxy/compare/6220a557f766...dfdf3dd5eac4 **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