August 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 07a94a: Revise composite row views
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07a94a6e15157cafc6fde587624d8be486f249c9 https://github.com/galaxyproject/galaxy/commit/07a94a6e15157cafc6fde587624d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/style/blue/base.css Log Message: ----------- Revise composite row views Commit: 2122ba55065e89b7b4ffbc63c1647d0e8cfcf5ea https://github.com/galaxyproject/galaxy/commit/2122ba55065e89b7b4ffbc63c164… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Revise composite main view Commit: e3003a0abf845695406ea8f4d44a4accaefdd5a7 https://github.com/galaxyproject/galaxy/commit/e3003a0abf845695406ea8f4d44a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/style/blue/base.css Log Message: ----------- Fix progress bar Commit: 2a14fd8ce4d5e1932eb2dc2fcf21bbf1474ddc2a https://github.com/galaxyproject/galaxy/commit/2a14fd8ce4d5e1932eb2dc2fcf21… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Revise and properly indent upload-ftp code Commit: 80c414ab98b439b06c94c35a6369b878af0112b8 https://github.com/galaxyproject/galaxy/commit/80c414ab98b439b06c94c35a6369… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/upload-model.js M static/maps/mvc/upload/upload-model.js.map Log Message: ----------- Fix indent for upload-model Commit: 9c196a822f8510934c16fe1a3a73a1c138059139 https://github.com/galaxyproject/galaxy/commit/9c196a822f8510934c16fe1a3a73… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/upload-settings.js M static/maps/mvc/upload/upload-settings.js.map Log Message: ----------- Fix indent for upload-settings Commit: ed2722996f2c3c0b33ec9212da2c722cf86a8ef8 https://github.com/galaxyproject/galaxy/commit/ed2722996f2c3c0b33ec9212da2c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Revise default-row view Commit: 966e33e3ac6a10177670c0b4616fefecb8c83958 https://github.com/galaxyproject/galaxy/commit/966e33e3ac6a10177670c0b4616f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/style/blue/base.css Log Message: ----------- Revise uploader default view Commit: 60a496c6dacaeaff1f58f7ad06e8d67bf7410657 https://github.com/galaxyproject/galaxy/commit/60a496c6dacaeaff1f58f7ad06e8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Fix info text style and color Commit: ba10f032f1c9a1a392b4e826d01785f8c0428673 https://github.com/galaxyproject/galaxy/commit/ba10f032f1c9a1a392b4e826d017… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js Log Message: ----------- Fix no transitional progress bar reset for composite uploader rows Commit: af3e0e23628a3726c803883d58e9f39db0bc2410 https://github.com/galaxyproject/galaxy/commit/af3e0e23628a3726c803883d58e9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js A client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/style/less/base.less A client/galaxy/style/less/collection.less R client/galaxy/style/less/collections.less A client/galaxy/style/less/dataset.less A client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less A client/galaxy/style/less/ui/error-modal.less M client/galaxy/style/less/ui/search-input.less M client/galaxy/style/less/upload.less M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/layout/panel.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/base-mvc.js.map A static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map A static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/ui/search-input.js.map M static/maps/utils/ajax-queue.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/panel.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js A static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-model.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-model.js A 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/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/ui/search-input.js M static/scripts/utils/ajax-queue.js M static/style/blue/base.css M static/style/blue/bootstrap-tour.css M static/style/blue/jquery.rating.css M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M test/qunit/tests/history_contents_model_tests.js M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'dev' into refactor_uploader Commit: 4c6d04e3a773e25f3c8a709546c8eb65c939a1ab https://github.com/galaxyproject/galaxy/commit/4c6d04e3a773e25f3c8a709546c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/default/default-row.js M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Fix test cases Commit: e685211851c1ecfa3999df5df26c7509a1c2047a https://github.com/galaxyproject/galaxy/commit/e685211851c1ecfa3999df5df26c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix spacing, remove multi line comments Commit: ae9961eab3c98cf1fce768e55e853e10d5d456de https://github.com/galaxyproject/galaxy/commit/ae9961eab3c98cf1fce768e55e85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Use listenTo for collection events Commit: 370c00124157d5ffb01752d8c0dbb4c0283ac4c2 https://github.com/galaxyproject/galaxy/commit/370c00124157d5ffb01752d8c0db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: 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-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/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-ftp.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Merge pull request #2711 from guerler/refactor_uploader Refactor uploader dialog, use local css classes, avoid model listeners Compare: https://github.com/galaxyproject/galaxy/compare/710174cbf98d...370c00124157

1 0

[galaxyproject/galaxy] b2e734: Add samtools --version-only check
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b2e734e6b7b42039b017c45f134850824eb14649 https://github.com/galaxyproject/galaxy/commit/b2e734e6b7b42039b017c45f1348… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add samtools --version-only check In Bam class Commit: 710174cbf98d6ff60c3793f33431cdee471844dc https://github.com/galaxyproject/galaxy/commit/710174cbf98d6ff60c3793f33431… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #2705 from remimarenco/dev Add samtools --version-only check Compare: https://github.com/galaxyproject/galaxy/compare/2d15e50d0f5c...710174cbf98d

1 0

[galaxyproject/infrastructure-playbook] 0ee33a: Remove Jetstream @ IU instances for production pha...
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0ee33a1ca83af9e89d054f58cdee00fc8a41b00b https://github.com/galaxyproject/infrastructure-playbook/commit/0ee33a1ca83… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory Log Message: ----------- Remove Jetstream @ IU instances for production phase

1 0

[galaxyproject/galaxy] 0b8c98: Include database/jobs_directory in gitignore
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b8c984b76d696fcc36ee3bfc76ad8b91e3ea20c https://github.com/galaxyproject/galaxy/commit/0b8c984b76d696fcc36ee3bfc76a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M .gitignore Log Message: ----------- Include database/jobs_directory in gitignore Commit: c6d2c8bf50fdb4d0b0685fabe1be47693cc99fe0 https://github.com/galaxyproject/galaxy/commit/c6d2c8bf50fdb4d0b0685fabe1be… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Managers: implement a new view for history serialization to bypass state_counts, state, or state_ids; add create_time and update_time to both summaries of hdas and hdcas; serialize contents for histories using a contents serializer (avoiding hda and hdca serialization and just serializing the results of the union) Commit: 0a0edd9788357e3c9fd617f5f8ef64f589e0d9e1 https://github.com/galaxyproject/galaxy/commit/0a0edd9788357e3c9fd617f5f8ef… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- History: have controller 'current history' faux-api methods return the 'current' view from the serializer Commit: 8d1cd494ce025d5b20c6e3087e3f1f44610254a8 https://github.com/galaxyproject/galaxy/commit/8d1cd494ce025d5b20c6e3087e3f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: extract history preferences to it's own module Commit: f395793704015ed2dffafe2584259ef81aa20efd https://github.com/galaxyproject/galaxy/commit/f395793704015ed2dffafe258425… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: clean up history contents Commit: 0e4118cda67dc00ebb2fbc2ee6cd1fe674555210 https://github.com/galaxyproject/galaxy/commit/0e4118cda67dc00ebb2fbc2ee6cd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- UI, history: clean up history model Commit: c030af5643ff01aa0bad0b6c6fa7bc4b3b47f6c5 https://github.com/galaxyproject/galaxy/commit/c030af5643ff01aa0bad0b6c6fa7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: move to History.fetch for most ajax loading Commit: 9102096f4e80580239d46a726d3aa7066806564b https://github.com/galaxyproject/galaxy/commit/9102096f4e80580239d46a726d3a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: simplify set up of sessionStorage/HistoryPrefs Commit: 40a597dfda0474675f68ae391135ae059cc93082 https://github.com/galaxyproject/galaxy/commit/40a597dfda0474675f68ae391135… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js Log Message: ----------- UI, history: first pass at paginating history-contents Commit: 1465a02790bd41dba9c573d943b9c9c0cd47ada6 https://github.com/galaxyproject/galaxy/commit/1465a02790bd41dba9c573d943b9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: fix history-contents comparator Commit: 5ed4f74c8deb8a6879d329f7de0a9ab898f98839 https://github.com/galaxyproject/galaxy/commit/5ed4f74c8deb8a6879d329f7de0a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: rework fetch options building, have history-contents maintain includeHidden/Deleted Commit: 563096e302ded396766478152d71c2028a96cabe https://github.com/galaxyproject/galaxy/commit/563096e302ded396766478152d71… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js A client/galaxy/scripts/mvc/history/history-preferences.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map A static/maps/mvc/history/history-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js A static/scripts/mvc/history/history-preferences.js Log Message: ----------- UI, history: add missing history-preferences file, separate out controlled fetch collection Commit: 3102c4ca68aaacc646309517c2fd65cc14237d34 https://github.com/galaxyproject/galaxy/commit/3102c4ca68aaacc646309517c2fd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, history: move order into ControlledFetchCollection Commit: fc5debdd3be9a46071762c093afbd2b655ca6ef9 https://github.com/galaxyproject/galaxy/commit/fc5debdd3be9a46071762c093afb… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: fix first search loading indicator on history-view Commit: 670484cebcebb49eea8b6fab445cce42d5292002 https://github.com/galaxyproject/galaxy/commit/670484cebcebb49eea8b6fab445c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: fix current history panel loading indicator Commit: 61e4ed51eb275fa979a946d074bb71f51b1ac424 https://github.com/galaxyproject/galaxy/commit/61e4ed51eb275fa979a946d074bb… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-18 (Fri, 18 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/list/list-item.js M static/maps/mvc/list/list-item.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/list/list-item.js Log Message: ----------- UI, history, lists: fix rendered event trigger from list-items Commit: 09567db13130bdbd0d7617cd4ff136d29cab1b90 https://github.com/galaxyproject/galaxy/commit/09567db13130bdbd0d7617cd4ff1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base-mvc.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: minor cleanup Commit: 39f1d62cefede05be1518bd44488b41ee4f10b51 https://github.com/galaxyproject/galaxy/commit/39f1d62cefede05be1518bd44488… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js Log Message: ----------- UI, history: render counts from model data (instead of views), fix history-contents to filter properly Commit: ffbac21753dce1bec667539b3574dd4c3191b6d8 https://github.com/galaxyproject/galaxy/commit/ffbac21753dce1bec667539b3574… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: fix missing _attachView Commit: a0bbbaa918b51cf619303c33d2ad32e87fe3d784 https://github.com/galaxyproject/galaxy/commit/a0bbbaa918b51cf619303c33d2ad… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js A static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/history/hda-model.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-model.js M static/scripts/mvc/history/history-structure-view.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/list/list-view.js Log Message: ----------- UI, history: add missing file (controlled-fetch-collection), fix fetchUpdated filters to bypass visible default filter for proper updating during workflows, fetch deleted and hidden via ajax when clicked, cleanup Commit: 9af60047f27f2da7f024eeb0a745d6f2bc99a7bc https://github.com/galaxyproject/galaxy/commit/9af60047f27f2da7f024eeb0a745… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, histories: progressively load search details for history contents on first search Commit: daa7625542567caf23d4081b7e7c70d6958bed26 https://github.com/galaxyproject/galaxy/commit/daa7625542567caf23d4081b7e7c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: implement infinite scrolling in all histories Commit: d2d066243e02cc3c612069e6015467e462212881 https://github.com/galaxyproject/galaxy/commit/d2d066243e02cc3c612069e60154… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-28 (Mon, 28 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/list/list-view.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/list/list-view.js M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, history: fix history/view.mako and history/display.mako to order their collections, load contents via ajax, and paginate correctly; Routes: correct history/view to allow history/view to view current history and history/view/{id} for cleaner urls Commit: 2a6694dda56ea909a5b3a1fc856c202de46d1750 https://github.com/galaxyproject/galaxy/commit/2a6694dda56ea909a5b3a1fc856c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-view.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-view.js M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, multi-history: update history collection to use PaginatedCollection, extract HistoryInnerView; Routes: re-add /history route, correct /history/view route for optional id Commit: 040f82a615489aea00040a1e232de5194c6e85d7 https://github.com/galaxyproject/galaxy/commit/040f82a615489aea00040a1e232d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- Corrections to search and order change in history/view_multiple - Load initial histories using ajax instead of bootstrapping. - Fix rendering after order change. - Fix 'none found' message when searching datasets. - Correct fetch filters when including deleted histories. Commit: 5dab37c155650e77a04769c04258151fbd22e08e https://github.com/galaxyproject/galaxy/commit/5dab37c155650e77a04769c04258… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M .gitignore M Makefile 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/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.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-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/tool_data_table_conf.xml.sample M config/tool_shed.ini.sample A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M doc/source/releases/index.rst M lib/galaxy/config.py A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/display_applications/application.py A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/q.fps M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/model/util.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/util/__init__.py R lib/galaxy/util/dictobj.py M lib/galaxy/util/jstree.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.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/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/bootstrap_history.py M scripts/functional_tests.py M scripts/summarize_timings.py M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js R static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/utils/utils.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M static/style/blue/library.css A templates/admin/tool_shed_repository/browse_categories.mako A templates/admin/tool_shed_repository/browse_category.mako M templates/admin/tool_shed_repository/initiate_repository_installation.mako A templates/admin/tool_shed_repository/preview_repository.mako M templates/base/base_panels.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/toolsheds.mako M templates/webapps/galaxy/library/common/library_info.mako A test/base/driver_util.py M test/base/twilltestcase.py R test/functional/test_admin_features.py R test/functional/test_data_security.py R test/functional/test_dataset_features.py R test/functional/test_get_data.py R test/functional/test_library_features.py R test/functional/test_library_security.py R test/functional/test_metadata_editing.py R test/functional/test_sample_tracking.py R test/functional/test_tags.py M test/functional/test_toolbox.py R test/functional/test_ucsc_table_browser.py R test/functional/test_user_info.py M test/functional/tools/collection_creates_list.xml A test/functional/tools/for_workflows/create_input_collection.xml A test/functional/tools/for_workflows/split.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/upload_tool_conf.xml M test/functional/workflow.py R test/install_and_test_tool_shed_repositories/__init__.py R test/install_and_test_tool_shed_repositories/base/__init__.py R test/install_and_test_tool_shed_repositories/base/test_db_util.py R test/install_and_test_tool_shed_repositories/base/twilltestcase.py R test/install_and_test_tool_shed_repositories/base/util.py R test/install_and_test_tool_shed_repositories/functional/__init__.py R test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py R test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/__init__.py R test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py A test/manual/launch_and_run.sh A test/manual/workflow_job_conf.xml M test/manual/workflows_scaling.py M test/qunit/test-app.js A test/qunit/tests/form_tests.html A test/qunit/tests/form_tests.js A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.js M test/tool_shed/base/twilltestcase.py A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/test_lazy_process.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- (merge conflicted bundles) Commit: ea921d2d7a529242c25acbab787a9f6c0a280fbf https://github.com/galaxyproject/galaxy/commit/ea921d2d7a529242c25acbab787a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-contents.js M lib/galaxy/webapps/galaxy/api/history_contents.py M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- Add view/keys ability to history_contents.create This allows the client to fetch the create_time for proper ordering of history contents directly after a copy. Commit: c4f8a30bbddffbf8e514a8112f46ec8e340f62fe https://github.com/galaxyproject/galaxy/commit/c4f8a30bbddffbf8e514a8112f46… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/layout/panel.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/panel.js M static/scripts/mvc/annotation.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js Log Message: ----------- UI, history: correct current dataset, tags, annos Correct the 'currently used dataset' indicator (the left, blue border) making sure it clears when non-dataset related content loads in the center panel. Correct the toggling of tags and annotations in the current history view forcing the subviews to show/hide based on the history view and not by toggling them individually. Commit: 747d4755742d7e2e327f549b283e680068232dd9 https://github.com/galaxyproject/galaxy/commit/747d4755742d7e2e327f549b283e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/history-model.js Log Message: ----------- UI, history: fix visual update of setting_metadata When a dataset moved from setting_metadata to some ready state, no change (besides the state change) would be registered by the model when the fetch returned. This would prevent an automatic re-render of the view and the dataset would appear to be stuck in setting_ metadata. Commit: 5f88d5dac5cad5836e6ee8e5f0ef18cd31fb4ba9 https://github.com/galaxyproject/galaxy/commit/5f88d5dac5cad5836e6ee8e5f0ef… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, history: cleanup empty and loading messages - Refactors renderEmptyMessage into base history view - Fixes contents loading indicator selector - Styles contents loading indicator (still oogly tho) Commit: 53163c3c6021e8b3d961a04ae6d7512543309587 https://github.com/galaxyproject/galaxy/commit/53163c3c6021e8b3d961a04ae6d7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, history: revise options menu batch operations - Have both 'Unhide hidden' and 'Delete hidden' fetch hidden datasets (since we now can't rely on complete contents) - Move both from options and into history-view-edit-current - Some minor cleanup of options-menu Commit: b1d930494a8b7a4ccd181e61aa7038cdb4b49814 https://github.com/galaxyproject/galaxy/commit/b1d930494a8b7a4ccd181e61aa70… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/style/less/base.less A client/galaxy/style/less/ui/error-modal.less M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/ui-modal.js M static/style/blue/base.css Log Message: ----------- UI: extract error-modal from history Extract the error handler and display used in history-view to it's own module (mvc/ui/error-modal) and use it to remove alerts elsewhere. This may be a start at standardizing error handling in some of the mvc code. Commit: f9d61e4a4b8392554efcae89183b7fa2b75dfef9 https://github.com/galaxyproject/galaxy/commit/f9d61e4a4b8392554efcae89183b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M .gitignore M README.rst M client/galaxy/scripts/layout/menu.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/templates/jupyter.mako A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/tool_data_table_conf.xml.sample A contrib/galaxy_supervisor.conf A display_applications/biom/biom_simple.xml M doc/source/lib/modules.rst R doc/source/lib/pulsar.client.rst R doc/source/lib/pulsar.client.staging.rst R doc/source/lib/pulsar.client.transport.rst R doc/source/lib/pulsar.rst M lib/galaxy/config.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/issue1818.tabular M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/base.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py R lib/pulsar/__init__.py R lib/pulsar/client/__init__.py R lib/pulsar/client/action_mapper.py R lib/pulsar/client/amqp_exchange.py R lib/pulsar/client/amqp_exchange_factory.py R lib/pulsar/client/client.py R lib/pulsar/client/config_util.py R lib/pulsar/client/decorators.py R lib/pulsar/client/destination.py R lib/pulsar/client/interface.py R lib/pulsar/client/job_directory.py R lib/pulsar/client/manager.py R lib/pulsar/client/object_client.py R lib/pulsar/client/path_mapper.py R lib/pulsar/client/setup_handler.py R lib/pulsar/client/staging/__init__.py R lib/pulsar/client/staging/down.py R lib/pulsar/client/staging/up.py R lib/pulsar/client/transport/__init__.py R lib/pulsar/client/transport/curl.py R lib/pulsar/client/transport/poster.py R lib/pulsar/client/transport/requests.py R lib/pulsar/client/transport/ssh.py R lib/pulsar/client/transport/standard.py R lib/pulsar/client/util.py M run_tests.sh M scripts/common_startup.sh M scripts/functional_tests.py M static/maps/layout/menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M templates/admin/tool_shed_repository/preview_repository.mako M templates/sharing_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/visualization/gie.mako R templates/webapps/galaxy/workflow/export.mako M templates/webapps/galaxy/workflow/list.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako M test/base/driver_util.py A test/base/integration_util.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/upload_tool_conf.xml A test/integration/__init__.py A test/integration/embedded_pulsar_job_conf.xml A test/integration/test_pulsar_embedded.py A test/shed_functional/__init__.py A test/shed_functional/base/__init__.py A test/shed_functional/base/common.py A test/shed_functional/base/test_db_util.py A test/shed_functional/base/twilltestcase.py A test/shed_functional/functional/__init__.py A test/shed_functional/functional/test_0000_basic_repository_features.py A test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py A test/shed_functional/functional/test_0020_basic_repository_dependencies.py A test/shed_functional/functional/test_0030_repository_dependency_revisions.py A test/shed_functional/functional/test_0040_repository_circular_dependencies.py A test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py A test/shed_functional/functional/test_0060_workflows.py A test/shed_functional/functional/test_0070_invalid_tool.py A test/shed_functional/functional/test_0080_advanced_circular_dependencies.py A test/shed_functional/functional/test_0090_tool_search.py A test/shed_functional/functional/test_0100_complex_repository_dependencies.py A test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py A test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_0130_datatype_converters.py A test/shed_functional/functional/test_0140_tool_help_images.py A test/shed_functional/functional/test_0150_prior_installation_required.py A test/shed_functional/functional/test_0160_circular_prior_installation_required.py A test/shed_functional/functional/test_0170_complex_prior_installation_required.py A test/shed_functional/functional/test_0300_reset_all_metadata.py A test/shed_functional/functional/test_0310_hg_api_features.py A test/shed_functional/functional/test_0400_repository_component_reviews.py A test/shed_functional/functional/test_0410_repository_component_review_access_control.py A test/shed_functional/functional/test_0420_citable_urls_for_repositories.py A test/shed_functional/functional/test_0430_browse_utilities.py A test/shed_functional/functional/test_0440_deleting_dependency_definitions.py A test/shed_functional/functional/test_0450_skip_tool_tests.py A test/shed_functional/functional/test_0460_upload_to_repository.py A test/shed_functional/functional/test_0470_tool_dependency_repository_type.py A test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py A test/shed_functional/functional/test_0490_export_import_repositories.py A test/shed_functional/functional/test_0500_export_repository_simple_dependency.py A test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py A test/shed_functional/functional/test_0520_import_export_circular_dependencies.py A test/shed_functional/functional/test_0530_repository_admin_feature.py A test/shed_functional/functional/test_0540_get_all_metadata_from_api.py A test/shed_functional/functional/test_1000_install_basic_repository.py A test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py A test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py A test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py A test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py A test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py A test/shed_functional/functional/test_1060_install_repository_with_workflow.py A test/shed_functional/functional/test_1070_invalid_tool.py A test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py A test/shed_functional/functional/test_1090_repository_dependency_handling.py A test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py A test/shed_functional/functional/test_1110_install_tool_from_tool_search.py A test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py A test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_1150_datatype_converters.py A test/shed_functional/functional/test_1160_tool_help_images.py A test/shed_functional/functional/test_1170_prior_installation_required.py A test/shed_functional/functional/test_1180_circular_prior_installation_required.py A test/shed_functional/functional/test_1190_complex_prior_installation_required.py A test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py A test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py A test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py A test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py A test/shed_functional/functional/test_1300_reset_all_metadata.py A test/shed_functional/functional/test_1400_review_migration_stages.py A test/shed_functional/functional/test_1410_update_manager.py A test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py A test/shed_functional/functional/test_1430_repair_installed_repository.py A test/shed_functional/functional/test_1440_missing_env_sh_files.py A test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py A test/shed_functional/functional/test_1460_data_managers.py A test/shed_functional/functional/test_1470_updating_installed_repositories.py A test/shed_functional/functional_tests.py A test/shed_functional/test_data/0460_files/repository_dependencies.xml A test/shed_functional/test_data/0460_files/repository_dependencies_in_root.tar A test/shed_functional/test_data/0460_files/repository_dependencies_in_subfolder.tar A test/shed_functional/test_data/0460_files/tool_dependencies.xml A test/shed_functional/test_data/0460_files/tool_dependencies_in_root.tar A test/shed_functional/test_data/0460_files/tool_dependencies_in_subfolder.tar A test/shed_functional/test_data/0480_files/tool_dependencies.xml A test/shed_functional/test_data/0540_files/column_maker/column_maker.tar A test/shed_functional/test_data/0540_files/column_maker/repository_dependencies.xml A test/shed_functional/test_data/0540_files/convert_chars/convert_chars.tar A test/shed_functional/test_data/0540_files/convert_chars/tool_dependencies.xml A test/shed_functional/test_data/0540_files/package_bwa/tool_dependencies.xml A test/shed_functional/test_data/1420_files/binary_tarballs/atlas.tar A test/shed_functional/test_data/1420_files/binary_tarballs/boost.tar A test/shed_functional/test_data/1420_files/binary_tarballs/bzlib.tar A test/shed_functional/test_data/1420_files/binary_tarballs/lapack.tar A test/shed_functional/test_data/1420_files/binary_tarballs/numpy.tar A test/shed_functional/test_data/1420_files/binary_tarballs/rdkit.tar A test/shed_functional/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml A test/shed_functional/test_data/1440_files/complex_dependency/tool_dependencies.xml A test/shed_functional/test_data/1440_files/dependency_definition/tool_dependencies.xml A test/shed_functional/test_data/1460_files/data_manager_files/test_data_manager.tar A test/shed_functional/test_data/bed_to_gff_converter/bed_to_gff_converter.tar A test/shed_functional/test_data/bismark/bismark.tar A test/shed_functional/test_data/bismark/bismark_methylation_extractor.xml A test/shed_functional/test_data/blast/blast_datatypes.tar A test/shed_functional/test_data/blast/blastxml_to_top_descr.tar A test/shed_functional/test_data/bwa/bwa_base.tar A test/shed_functional/test_data/bwa/bwa_color.tar A test/shed_functional/test_data/bwa/complex/bwa_base.tar A test/shed_functional/test_data/bwa/complex/readme/tool_dependencies.xml A test/shed_functional/test_data/bwa/complex/tool_dependencies.xml A test/shed_functional/test_data/column_maker/column_maker.tar A test/shed_functional/test_data/convert_chars/convert_chars.tar A test/shed_functional/test_data/emboss/0470_files/emboss_complex_dependency.tar A test/shed_functional/test_data/emboss/0470_files/tool_dependencies.xml A test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/shed_functional/test_data/emboss/emboss.tar A test/shed_functional/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/filtering/README A test/shed_functional/test_data/filtering/filtering_0000.txt A test/shed_functional/test_data/filtering/filtering_1.1.0.tar A test/shed_functional/test_data/filtering/filtering_2.2.0.tar A test/shed_functional/test_data/filtering/filtering_test_data.tar A test/shed_functional/test_data/filtering/readme.txt A test/shed_functional/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga A test/shed_functional/test_data/freebayes/freebayes.tar A test/shed_functional/test_data/freebayes/freebayes.xml A test/shed_functional/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml A test/shed_functional/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml A test/shed_functional/test_data/freebayes/sam_fa_indices.loc.sample A test/shed_functional/test_data/freebayes/tool_data_table_conf.xml.sample A test/shed_functional/test_data/freebayes/tool_dependencies.xml A test/shed_functional/test_data/htseq_count/htseq_count.tar A test/shed_functional/test_data/package_matplotlib/package_matplotlib_1_2.tar A test/shed_functional/test_data/package_matplotlib/tool_dependencies.xml A test/shed_functional/test_data/package_numpy/package_numpy_1_7.tar A test/shed_functional/test_data/proteomics_datatypes/proteomics_datatypes.tar A test/shed_functional/test_data/readme.txt A test/shed_functional/test_data/repository_capsules/0490_filtering.tar.gz A test/shed_functional/test_data/repository_capsules/0500_emboss_5.tar.gz A test/shed_functional/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz A test/shed_functional/test_data/repository_capsules/0520_filtering.tar.gz R test/tool_shed/__init__.py R test/tool_shed/base/__init__.py R test/tool_shed/base/common.py R test/tool_shed/base/test_db_util.py R test/tool_shed/base/twilltestcase.py R test/tool_shed/functional/__init__.py R test/tool_shed/functional/test_0000_basic_repository_features.py R test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py R test/tool_shed/functional/test_0020_basic_repository_dependencies.py R test/tool_shed/functional/test_0030_repository_dependency_revisions.py R test/tool_shed/functional/test_0040_repository_circular_dependencies.py R test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py R test/tool_shed/functional/test_0060_workflows.py R test/tool_shed/functional/test_0070_invalid_tool.py R test/tool_shed/functional/test_0080_advanced_circular_dependencies.py R test/tool_shed/functional/test_0090_tool_search.py R test/tool_shed/functional/test_0100_complex_repository_dependencies.py R test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py R test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_0130_datatype_converters.py R test/tool_shed/functional/test_0140_tool_help_images.py R test/tool_shed/functional/test_0150_prior_installation_required.py R test/tool_shed/functional/test_0160_circular_prior_installation_required.py R test/tool_shed/functional/test_0170_complex_prior_installation_required.py R test/tool_shed/functional/test_0300_reset_all_metadata.py R test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0400_repository_component_reviews.py R test/tool_shed/functional/test_0410_repository_component_review_access_control.py R test/tool_shed/functional/test_0420_citable_urls_for_repositories.py R test/tool_shed/functional/test_0430_browse_utilities.py R test/tool_shed/functional/test_0440_deleting_dependency_definitions.py R test/tool_shed/functional/test_0450_skip_tool_tests.py R test/tool_shed/functional/test_0460_upload_to_repository.py R test/tool_shed/functional/test_0470_tool_dependency_repository_type.py R test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py R test/tool_shed/functional/test_0490_export_import_repositories.py R test/tool_shed/functional/test_0500_export_repository_simple_dependency.py R test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py R test/tool_shed/functional/test_0520_import_export_circular_dependencies.py R test/tool_shed/functional/test_0530_repository_admin_feature.py R test/tool_shed/functional/test_0540_get_all_metadata_from_api.py R test/tool_shed/functional/test_1000_install_basic_repository.py R test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py R test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py R test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py R test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py R test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py R test/tool_shed/functional/test_1060_install_repository_with_workflow.py R test/tool_shed/functional/test_1070_invalid_tool.py R test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py R test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_tool_from_tool_search.py R test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py R test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_prior_installation_required.py R test/tool_shed/functional/test_1180_circular_prior_installation_required.py R test/tool_shed/functional/test_1190_complex_prior_installation_required.py R test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py R test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py R test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py R test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py R test/tool_shed/functional/test_1300_reset_all_metadata.py R test/tool_shed/functional/test_1400_review_migration_stages.py R test/tool_shed/functional/test_1410_update_manager.py R test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py R test/tool_shed/functional/test_1430_repair_installed_repository.py R test/tool_shed/functional/test_1440_missing_env_sh_files.py R test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py R test/tool_shed/functional/test_1460_data_managers.py R test/tool_shed/functional/test_1470_updating_installed_repositories.py R test/tool_shed/functional_tests.py R test/tool_shed/test_data/0460_files/repository_dependencies.xml R test/tool_shed/test_data/0460_files/repository_dependencies_in_root.tar R test/tool_shed/test_data/0460_files/repository_dependencies_in_subfolder.tar R test/tool_shed/test_data/0460_files/tool_dependencies.xml R test/tool_shed/test_data/0460_files/tool_dependencies_in_root.tar R test/tool_shed/test_data/0460_files/tool_dependencies_in_subfolder.tar R test/tool_shed/test_data/0480_files/tool_dependencies.xml R test/tool_shed/test_data/0540_files/column_maker/column_maker.tar R test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml R test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar R test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml R test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml R test/tool_shed/test_data/1420_files/binary_tarballs/atlas.tar R test/tool_shed/test_data/1420_files/binary_tarballs/boost.tar R test/tool_shed/test_data/1420_files/binary_tarballs/bzlib.tar R test/tool_shed/test_data/1420_files/binary_tarballs/lapack.tar R test/tool_shed/test_data/1420_files/binary_tarballs/numpy.tar R test/tool_shed/test_data/1420_files/binary_tarballs/rdkit.tar R test/tool_shed/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml R test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml R test/tool_shed/test_data/1440_files/dependency_definition/tool_dependencies.xml R test/tool_shed/test_data/1460_files/data_manager_files/test_data_manager.tar R test/tool_shed/test_data/bed_to_gff_converter/bed_to_gff_converter.tar R test/tool_shed/test_data/bismark/bismark.tar R test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml R test/tool_shed/test_data/blast/blast_datatypes.tar R test/tool_shed/test_data/blast/blastxml_to_top_descr.tar R test/tool_shed/test_data/bwa/bwa_base.tar R test/tool_shed/test_data/bwa/bwa_color.tar R test/tool_shed/test_data/bwa/complex/bwa_base.tar R test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml R test/tool_shed/test_data/bwa/complex/tool_dependencies.xml R test/tool_shed/test_data/column_maker/column_maker.tar R test/tool_shed/test_data/convert_chars/convert_chars.tar R test/tool_shed/test_data/emboss/0470_files/emboss_complex_dependency.tar R test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml R test/tool_shed/test_data/emboss/datatypes/datatypes_conf.xml R test/tool_shed/test_data/emboss/emboss.tar R test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/filtering/README R test/tool_shed/test_data/filtering/filtering_0000.txt R test/tool_shed/test_data/filtering/filtering_1.1.0.tar R test/tool_shed/test_data/filtering/filtering_2.2.0.tar R test/tool_shed/test_data/filtering/filtering_test_data.tar R test/tool_shed/test_data/filtering/readme.txt R test/tool_shed/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga R test/tool_shed/test_data/freebayes/freebayes.tar R test/tool_shed/test_data/freebayes/freebayes.xml R test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml R test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml R test/tool_shed/test_data/freebayes/sam_fa_indices.loc.sample R test/tool_shed/test_data/freebayes/tool_data_table_conf.xml.sample R test/tool_shed/test_data/freebayes/tool_dependencies.xml R test/tool_shed/test_data/htseq_count/htseq_count.tar R test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar R test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml R test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar R test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar R test/tool_shed/test_data/readme.txt R test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz R test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz R test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz R test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz M test/unit/managers/test_HistoryContentsManager.py A test/unit/shed_unit/__init__.py A test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_td_common_util.py A test/unit/shed_unit/test_tool_panel_manager.py R test/unit/tool_shed_unit_tests/__init__.py R test/unit/tool_shed_unit_tests/test_fabric_util.py R test/unit/tool_shed_unit_tests/test_td_common_util.py R test/unit/tool_shed_unit_tests/test_tool_panel_manager.py M test/unit/tools/test_conda_resolution.py A tool-data/biom_simple_display.loc.sample Log Message: ----------- (manual merge with dev) Commit: 434845fe464ba3f955b3dba349d65c35d19bdf6b https://github.com/galaxyproject/galaxy/commit/434845fe464ba3f955b3dba349d6… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M test/unit/managers/test_HistoryManager.py Log Message: ----------- Tests: remove peek from history.contents serilaization Commit: 1fedef02fb634025fcf8d303cb4842b119cfbe1c https://github.com/galaxyproject/galaxy/commit/1fedef02fb634025fcf8d303cb48… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: doc and TODO cleanup Commit: 958a5e8d424a837a7e740dc9526455d2856608d4 https://github.com/galaxyproject/galaxy/commit/958a5e8d424a837a7e740dc95264… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/style/blue/base.css Log Message: ----------- UI, history: fix subtitle counts and cleanup - Move comma-sep into css - Correct count calc in handlers - Console stmts, templating, and method order Commit: 8a6f96f73400ef8d5749a51841cd073a273fe8b0 https://github.com/galaxyproject/galaxy/commit/8a6f96f73400ef8d5749a51841cd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: simplify createHDCA and ajaxQueue - use collection.create in createHDCA - use ajax-queue module in history-contents.ajaxQueue - Small fixes to DC.hasDetails, and item view rendering Commit: 81d36f903bc0e037cc6da67e101512aca542bad1 https://github.com/galaxyproject/galaxy/commit/81d36f903bc0e037cc6da67e1015… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-item.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, histories: fix pagination for published - Ensure all web controller history json is using view='current' - Fix rendering of already fetched contents when searching and/or progressively fetching details - minor doc cleanup Commit: ee240f46673e962a1c1df8ef20910b197b09df38 https://github.com/galaxyproject/galaxy/commit/ee240f46673e962a1c1df8ef2091… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- (bundle scripts) Commit: c8512faf447c34dba6127e856e1dabb98248815e https://github.com/galaxyproject/galaxy/commit/c8512faf447c34dba6127e856e1d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M .ci/py3_sources.txt M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M contrib/galaxy.debian-init M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py R lib/tool_shed/scripts/api/add_repository_registry_entry.py R lib/tool_shed/scripts/api/common.py R lib/tool_shed/scripts/api/create_categories.py R lib/tool_shed/scripts/api/create_users.py R lib/tool_shed/scripts/api/export.py R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py R lib/tool_shed/scripts/api/import_capsule.py R lib/tool_shed/scripts/api/remove_repository_registry_entry.py R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py R lib/tool_shed/scripts/check_repositories_for_functional_tests.py R lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py R lib/tool_shed/scripts/deprecate_repositories_without_metadata.py R lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/util/shed_util_common.py A scripts/tool_shed/api/add_repository_registry_entry.py A scripts/tool_shed/api/common.py A scripts/tool_shed/api/create_categories.py A scripts/tool_shed/api/create_users.py A scripts/tool_shed/api/export.py A scripts/tool_shed/api/get_filtered_repository_revisions.py A scripts/tool_shed/api/import_capsule.py A scripts/tool_shed/api/remove_repository_registry_entry.py A scripts/tool_shed/api/reset_metadata_on_repositories.py A scripts/tool_shed/api/tool_shed_repository_revision_update.py A scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh A scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py A scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py A scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh A scripts/tool_shed/bootstrap_tool_shed/user_info.xml.sample A scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/check_repositories_for_functional_tests.py A scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/check_tool_dependency_definition_repositories.py A scripts/tool_shed/clean_up_tool_dependency_directory.py A scripts/tool_shed/deprecate_repositories_without_metadata.py A scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: f3b8d5b0e308c5e9ef9b0a97d311d19f3f998794 https://github.com/galaxyproject/galaxy/commit/f3b8d5b0e308c5e9ef9b0a97d311… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M Makefile M lib/galaxy/version.py M run_tool_shed.sh M scripts/bootstrap_history.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: 7cb32818062b7f30647ec66608902029575a5454 https://github.com/galaxyproject/galaxy/commit/7cb32818062b7f30647ec6660890… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M .gitignore M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- Remove console and .gitignore duplication Commit: da5443161639217da86b5f54bf277c3021e67667 https://github.com/galaxyproject/galaxy/commit/da5443161639217da86b5f54bf27… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: remove scoping overrides Commit: 0a1d7982aa4b16b6111f92ccfc5814f49306b80a https://github.com/galaxyproject/galaxy/commit/0a1d7982aa4b16b6111f92ccfc58… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- API, history: contents_shown to contents_active Renames serialization attribute contents_shown to contents_active to better match original terminology. Adds both state_counts and active_counts to HistoryContentsManager and then has serialize_contents_states and serialize_contents_active call them from the HistorySerializer. Commit: fd3abf4104a58b7add3be22d89286356dbb4caee https://github.com/galaxyproject/galaxy/commit/fd3abf4104a58b7add3be22d8928… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- API, history: rename current view 'dev-detailed' Because current was a horrible and confusing name and dev-detailed may highlight the volitility of the view more. Commit: 0484017e6832f418cd0f20b074d27a329cd0fc22 https://github.com/galaxyproject/galaxy/commit/0484017e6832f418cd0f20b074d2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/style/less/base.less A client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M static/maps/mvc/history/history-view-edit-current.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-view-edit-current.js M static/style/blue/base.css Log Message: ----------- UI, history: move history panel to flexbox This allows us to avoid using absolutely positioned elements and simplifies style rules a bit. Commit: 7722bf23ad4ccd60c114a3de1ceaa422924cfc7c https://github.com/galaxyproject/galaxy/commit/7722bf23ad4ccd60c114a3de1cea… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/bower.json M client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/libs/underscore.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/libs/underscore.js M static/scripts/mvc/list/list-view.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI: update underscorejs and fix findIndex IE 11 does not have [].findIndex and the new scrolling causes an error there. Underscore 1.8 has a cross-browser version and this commit updates underscore and replaces the use of the native call. Commit: 1600d6c6e6f641c203d3f45787f19bda68d88d97 https://github.com/galaxyproject/galaxy/commit/1600d6c6e6f641c203d3f45787f1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-view-edit.js Log Message: ----------- UI, history: shorten deleted/hidden load indicator Commit: 94f6f1e0049c962941b51d28ee0f0351423fbc52 https://github.com/galaxyproject/galaxy/commit/94f6f1e0049c962941b51d28ee0f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/style/less/base.less M client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M static/maps/mvc/history/history-view-edit-current.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit-current.js M static/style/blue/base.css Log Message: ----------- UI, history: move towards a fixed header Commit: b5580c23f63f214fb465892b430c0d62d75fc3f9 https://github.com/galaxyproject/galaxy/commit/b5580c23f63f214fb465892b430c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: R buildbot_setup.sh M config/job_conf.xml.sample_advanced R install_and_test_tool_shed_repositories.sh M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/configuration.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_repositories_for_functional_tests.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M test/casperjs/casperjs_runner.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: 89cb03a037d770c4c895d4e8f872de04d385ada9 https://github.com/galaxyproject/galaxy/commit/89cb03a037d770c4c895d4e8f872… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/history_contents.py Log Message: ----------- History contents manager: improve contents query Serializers in the index_v2 of history_contents were re- querying the database for mapped model attributes. - eagerload collection on hdcas - undefer _metadata on hdas - eaglerload tags and annotations for both - rework annotatable manager mixin to cycle through annotations bypassing the get_item_annotation_str call (which would bypass item.annotations even if already loaded) Anecdotally provides significant speed up. Commit: 32520078af5bf062344f9355894c3d83ebaf638d https://github.com/galaxyproject/galaxy/commit/32520078af5bf062344f9355894c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: raise pagination limits - fetch more when scroll bar is at 512, not 128 px from bottom - fetch 200 at first then 100 each fetch (from 100, 50) - fetch 500 per fetch when searching (progressivelyFetchDetails) Commit: 4c7f367680898b16c395748c501bbca0c56e02ce https://github.com/galaxyproject/galaxy/commit/4c7f367680898b16c395748c501b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/less/base.less M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/managers/context.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M static/maps/layout/page.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/workflow/workflow-terminals.js M static/style/blue/base.css M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/tool_shed/repository/view_changeset.mako M test/base/interactor.py M test/shed_functional/base/twilltestcase.py M tools/data_source/upload.py M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- (merge conflicts with dev) Commit: d9591127d89c61f5f172bc33d7532917facb3689 https://github.com/galaxyproject/galaxy/commit/d9591127d89c61f5f172bc33d753… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-22 (Fri, 22 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-item.js M static/style/blue/base.css Log Message: ----------- UI, histories: move to a section based pagination Breaks history contents into 500 element sections rendering each in a accordian-style menu. Elements are sectioned according to their hids and no more than 500 are rendered at any time. Commit: 9956eecb6ab25d71153ed2c877d7d4a9b4db5f07 https://github.com/galaxyproject/galaxy/commit/9956eecb6ab25d71153ed2c877d7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-25 (Mon, 25 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, history: paginate by hid and show sections - Order by hid or hid-asc (this loses the ability use others) - Paginate by 'sections' of 500 hids showing only one expanded section at a time -- pro: this prevents large numbers of contents in the dom at once -- con: the visible contents can be very sparse (e.g. 2 of 500) - Pagination only begins if more than 500 contents - HistoryContents now has a parent reference (.history) Commit: 994300d3f65904b0532d383e5d6778520ea183ba https://github.com/galaxyproject/galaxy/commit/994300d3f65904b0532d383e5d67… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-29 (Fri, 29 Apr 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: polish sectioning enough to show (This is an extremely rough commit meant to have a working prototype for others to test the UX abstraction of sectioning the histories) - Reworks contents so that they're nested inside sections - Fixes all a handful of the errors the previous change causes Commit: cf27a6ae28f6b2f02cee80ee4695275a0dd413c9 https://github.com/galaxyproject/galaxy/commit/cf27a6ae28f6b2f02cee80ee4695… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-29 (Fri, 29 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: fetchHiddenInSection, clickSection - add fetchHiddenInSection to load hidden contents in a particular section - extract event handler from clickSection link to allow getting data-section from different part of the DOM in annotated history Commit: 3686ed55c39430d911e17a9e3821090c5de76a1f https://github.com/galaxyproject/galaxy/commit/3686ed55c39430d911e17a9e3821… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/utils/ajax-queue.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/utils/ajax-queue.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/utils/ajax-queue.js Log Message: ----------- UI, history: use arrays when filtering contents - Moves all history filtering to returning arrays and not new HistoryContents (subset collections) - Reworks contents.ajaxQueue - Moves filterAndUpdate to contents from HistoryView Commit: a7c7af94af6564ab2bd7660b26f8bf81fc00ca4c https://github.com/galaxyproject/galaxy/commit/a7c7af94af6564ab2bd7660b26f8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: fix create HDCA and return promise Commit: 7a6794e104fc978b279c61d15812791302d6fef2 https://github.com/galaxyproject/galaxy/commit/7a6794e104fc978b279c61d15812… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.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/multi-panel.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: move show deleted/hidden into content - Move d/h (deleted/hidden) control into history contents - normalize names (show_deleted, showDeleted --> includeDeleted) - add History.contentsShown that checks d/h flags to return num. shown - move HistoryPreferences into HistoryContents.storage Misc. fixes: - fix collection.off to stopListening - provide interface to HistoryPreferences so that consumers don't need the model keys (easier to change them later on) - (some) cleanup Commit: 2d9ec54fe2126ab21249c0f8918a27802b7b85bb https://github.com/galaxyproject/galaxy/commit/2d9ec54fe2126ab21249c0f8918a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-06 (Fri, 06 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: auto-expand sections - track scrolling and auto expand sections when scroll 'cursor' is over them for more than a certain time - improve rendering speed by using previously existing renders Commit: f8e89ff3fc36eced72f568b8fa6cf6632b22ff06 https://github.com/galaxyproject/galaxy/commit/f8e89ff3fc36eced72f568b8fa6c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-12 (Thu, 12 May 2016) Changed paths: M CONTRIBUTORS.md M Makefile M client/README.md M client/bower.json M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/citation/citation-model.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/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.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/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-drilldown.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-select-default.js M client/galaxy/scripts/ui/hoverhighlight.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.scratchbook.yaml M config/plugins/visualizations/charts/static/views/group.js R config/plugins/visualizations/graphview/config/graphview.xml R config/plugins/visualizations/graphview/static/graphview.css R config/plugins/visualizations/graphview/static/graphview.js R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js R config/plugins/visualizations/graphview/templates/graphview.mako M config/reports.ini.sample M config/tool_shed.ini.sample M lib/galaxy/config.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/context.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/__init__.py M lib/galaxy/tools/linters/citations.py M lib/galaxy/tools/linters/command.py A lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py R lib/galaxy/tools/linters/top_level.py M lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/workflow/run.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M static/maps/layout/page.js.map M static/maps/libs/backbone.js.map M static/maps/libs/bootstrap-tour.js.map M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js M static/scripts/libs/backbone.js M static/scripts/libs/bootstrap-tour.js M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/mvc/citation/citation-model.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/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.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/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/base/base_panels.mako M templates/display_base.mako M templates/sharing_base.mako M templates/show_params.mako A templates/slug_editing_js.mako M templates/webapps/galaxy/data_manager/view_job.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M test/api/test_tools.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py A test/functional/tools/multi_data_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_pulsar_embedded.py M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.14.0.css R test/qunit/test-libs/qunit-1.14.0.js A test/qunit/test-libs/qunit-1.23.1.css A test/qunit/test-libs/qunit-1.23.1.js A test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-1.9.1.js M test/qunit/tests/form_tests.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js A test/qunit/tests/utils_test.html A test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js R test/shed_functional/functional/test_0450_skip_tool_tests.py M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py A test/shed_functional/test_data/0550_files/filtering_1.0.tgz A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml M test/unit/test_objectstore.py M tools/data_source/biomart.xml M tools/filters/trimmer.xml Log Message: ----------- (merge conflicts) Commit: 4423a381afa68e4ce3e47f44ed8c7973dee62a3e https://github.com/galaxyproject/galaxy/commit/4423a381afa68e4ce3e47f44ed8c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: merge sectioned history layout This merges with history-contents.pagination, adding sections of history contents by hids but reverts the auto-expansion of those sections when the scroll bar is moved 'over' them. Commit: 16830e8eb250f1ebd3db4afaee7dbddf03ebd60d https://github.com/galaxyproject/galaxy/commit/16830e8eb250f1ebd3db4afaee7d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M CONTRIBUTORS.md M Makefile M client/README.md M client/bower.json M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/libs/backbone.js M client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/jquery/jquery.migrate.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/libs/underscore.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li.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/dataset/dataset-model.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-section.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.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-library-view.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/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-drilldown.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-select-default.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/ui/hoverhighlight.js M client/galaxy/scripts/ui/loading-indicator.js M client/galaxy/scripts/ui/mode-button.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.scratchbook.yaml M config/plugins/visualizations/charts/static/views/group.js R config/plugins/visualizations/graphview/config/graphview.xml R config/plugins/visualizations/graphview/static/graphview.css R config/plugins/visualizations/graphview/static/graphview.js R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js R config/plugins/visualizations/graphview/templates/graphview.mako M config/reports.ini.sample M config/tool_shed.ini.sample R install_and_test_tool_shed_repositories.sh M lib/galaxy/config.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/context.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/sharable.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/__init__.py M lib/galaxy/tools/linters/citations.py M lib/galaxy/tools/linters/command.py A lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py R lib/galaxy/tools/linters/top_level.py M lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py A scripts/api/filter_failed_datasets_from_collection.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_repositories_for_functional_tests.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py R scripts/tool_shed/check_tool_dependency_definition_repositories.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M static/maps/layout/page.js.map M static/maps/libs/backbone.js.map M static/maps/libs/bootstrap-tour.js.map M static/maps/libs/d3.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/jquery/jquery.migrate.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/libs/underscore.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/ui/hoverhighlight.js.map M static/maps/ui/loading-indicator.js.map M static/maps/ui/mode-button.js.map M static/maps/ui/pagination.js.map M static/maps/ui/peek-column-selector.js.map M static/maps/utils/localization.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/page.js M static/scripts/libs/backbone.js M static/scripts/libs/bootstrap-tour.js M static/scripts/libs/d3.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/jquery/jquery.migrate.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/libs/underscore.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-li.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/dataset/dataset-model.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.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.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/workflow/workflow-terminals.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/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/base/base_panels.mako M templates/display_base.mako M templates/sharing_base.mako M templates/show_params.mako A templates/slug_editing_js.mako M templates/webapps/galaxy/data_manager/view_job.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_changeset.mako A test-data/composite_output_expected_log M test/api/test_tools.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/base/interactor.py M test/functional/tools/composite_output.xml A test/functional/tools/multi_data_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_pulsar_embedded.py M test/qunit/test-common.js R test/qunit/test-libs/qunit-1.14.0.css R test/qunit/test-libs/qunit-1.14.0.js A test/qunit/test-libs/qunit-1.23.1.css A test/qunit/test-libs/qunit-1.23.1.js A test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-1.9.1.js M test/qunit/tests/form_tests.js M test/qunit/tests/list-of-pairs-collection-creator.js M test/qunit/tests/metrics-logger.js M test/qunit/tests/page_tests.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js A test/qunit/tests/utils_test.html A test/qunit/tests/utils_test.js M test/qunit/tests/workflow_editor_tests.js M test/shed_functional/base/twilltestcase.py R test/shed_functional/functional/test_0450_skip_tool_tests.py M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py A test/shed_functional/test_data/0550_files/filtering_1.0.tgz A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml M test/unit/jobs/test_command_factory.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/test_objectstore.py M test/unit/unittest_utils/galaxy_mock.py M tools/data_source/biomart.xml M tools/data_source/upload.py M tools/filters/trimmer.xml M tools/stats/grouping.py M tools/stats/grouping.xml Log Message: ----------- (merge conflicts) Commit: 4db7940a5cad685b9a81bf0f2ccc9ecac7f6aa7a https://github.com/galaxyproject/galaxy/commit/4db7940a5cad685b9a81bf0f2ccc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/history-panel.js M client/galaxy/style/less/base.less A client/galaxy/style/less/dataset.less M client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/style/blue/base.css Log Message: ----------- History: move to a flex based layout Change right-hand side of Analysis page and the history-panel within it to use flexbox for layout. Allow scrolling withiin list-items not the entire view itself. Provides a fixed header containing the history controls. Commit: ca842c264664c6ba364e3645027858f6c1a88a8d https://github.com/galaxyproject/galaxy/commit/ca842c264664c6ba364e36450278… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less A client/galaxy/style/less/dataset.less A client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M lib/galaxy/datatypes/registry.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/sharable.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/cwl.py A scripts/api/filter_failed_datasets_from_collection.py M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/tool/tool-form.js M static/style/blue/base.css A test-data/composite_output_expected_log M test/functional/tools/composite_output.xml M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge branch 'history.fixed-header' ...into history-contents.limiting Commit: 6e866335d207848e566926f13d255ba53b3cae3c https://github.com/galaxyproject/galaxy/commit/6e866335d207848e566926f13d25… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view.js M static/style/blue/base.css Log Message: ----------- UI, history: paginate w/ horizontal scrolling - Render sections side by side and allow scrolling between sections - Also: improve accesibility query by eagerloading dataset.actions and using cache for user roles Commit: c6f8a9f00cc7722c2aa28a087227c6822b6dd667 https://github.com/galaxyproject/galaxy/commit/c6f8a9f00cc7722c2aa28a087227… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-23 (Mon, 23 May 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js A client/galaxy/scripts/ui/scrollable-pages.js M static/maps/mvc/history/history-view.js.map A static/maps/ui/scrollable-pages.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-view.js A static/scripts/ui/scrollable-pages.js Log Message: ----------- (add missing files) Commit: 9a3fb8ab37237d9b7ad5c3aa0fd3b62a0468ebc4 https://github.com/galaxyproject/galaxy/commit/9a3fb8ab37237d9b7ad5c3aa0fd3… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js R client/galaxy/scripts/ui/scrollable-pages.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map R static/maps/ui/scrollable-pages.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js R static/scripts/ui/scrollable-pages.js M static/style/blue/base.css M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, history: rollback other pagination prototypes Attempts to remove most of the sectioning/infinite scrolling prototypes but leave the cleanup/refactoring in place for another attempt. Commit: 5ff73677bbd06d6fb33e0ceb29e7af29a28adce5 https://github.com/galaxyproject/galaxy/commit/5ff73677bbd06d6fb33e0ceb29e7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M Makefile M README.rst M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/form/form-data.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-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/tool/tool-form-base.js R client/galaxy/scripts/mvc/tool/tool-template.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-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/frame.less M client/galaxy/style/less/ui.less M config/job_conf.xml.sample_advanced M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/splitters/multi.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/roles.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/openid/providers.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/util/maf_utilities.py A lib/galaxy/tools/verify/__init__.py A lib/galaxy/tools/verify/asserts/__init__.py A lib/galaxy/tools/verify/asserts/tabular.py A lib/galaxy/tools/verify/asserts/text.py A lib/galaxy/tools/verify/asserts/xml.py A lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/__init__.py R lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/directory_hash.py M lib/galaxy/util/inflection.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/group_roles.py M lib/galaxy/webapps/galaxy/api/group_users.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/search.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/galaxy_install/utility_containers/__init__.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/repository_registry.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/xml_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/api/data_manager_example_execute.py M scripts/api/search.py M scripts/api/upload_to_history.py M scripts/bootstrap_history.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py M scripts/extract_dataset_part.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/runtime_stats.py M scripts/tool_shed/api/common.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M static/maps/layout/scratchbook.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/scratchbook.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/show_params.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M test/api/test_datasets.py M test/api/test_tools.py M test/api/test_workflows.py R test/base/asserts/__init__.py R test/base/asserts/tabular.py R test/base/asserts/text.py R test/base/asserts/xml.py M test/base/driver_util.py R test/base/test_data.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/casperjs/server_env.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py A test/functional/tools/composite_output_tests.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/qunit/test-app.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js M test/qunit/tests/modal_tests.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0060_workflows.py M test/shed_functional/functional/test_0100_complex_repository_dependencies.py M test/shed_functional/functional/test_0170_complex_prior_installation_required.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_0310_hg_api_features.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py M test/shed_functional/functional/test_1190_complex_prior_installation_required.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py M test/shed_functional/functional_tests.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.xml M tools/filters/axt_to_fasta.xml M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav.xml M tools/filters/bed2gff.xml M tools/filters/bed_to_bigbed.xml M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff2bed.xml M tools/filters/gff_to_bed_converter.py M tools/filters/gtf2bedgraph.xml M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/mergeCols.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_split_by_species.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml Log Message: ----------- (merge conflicts) Commit: 769a2e583bdbe1939d26c5e4e1e549b36b690d59 https://github.com/galaxyproject/galaxy/commit/769a2e583bdbe1939d26c5e4e1e5… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/style/less/history.less M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-item.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako Log Message: ----------- UI, history: re-implement pagination Hopefully in a simpler way. This version does not account for hid sections, but uses limit offset - which leaves other (non-hid) sort orders as an option. This commit also fixes: * issues with the fixed header in the published section * ajax loading for histories embedded in pages Commit: 495c352cd90e603364f6737569f83a557d878423 https://github.com/galaxyproject/galaxy/commit/495c352cd90e603364f6737569f8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: add pagination load indicator And fixes some styling issues. Commit: 2a38b11e87bf58872850c23af0185c98cab491e4 https://github.com/galaxyproject/galaxy/commit/2a38b11e87bf58872850c23af018… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M lib/galaxy/managers/base.py M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, history: fixes - re-delegates events for collection views - extends clicking for contents-container in annotated history view - loads first 10 histories *and* current history for initial set in multi-history page Commit: 8b2b289973f0ee87b14bb9688306a8dc23ac7e2f https://github.com/galaxyproject/galaxy/commit/8b2b289973f0ee87b14bb9688306… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M client/galaxy/style/less/base.less A client/galaxy/style/less/collection.less R client/galaxy/style/less/collections.less M static/style/blue/bootstrap-tour.css M static/style/blue/jquery.rating.css Log Message: ----------- Styles: minor fixes - corrects plurality of collection.less - chmod on bootstrap-tour.css and jquery.rating.css Commit: 1297ce261a43228cb3ed11f26fccd88aebcb93df https://github.com/galaxyproject/galaxy/commit/1297ce261a43228cb3ed11f26fcc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/collection.less M client/galaxy/style/less/history.less M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: fix flex for collection view Commit: 01a25ff64f82075f0de07700a2772e3f5ff40337 https://github.com/galaxyproject/galaxy/commit/01a25ff64f82075f0de07700a277… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: rendering fixes - Tries to strike a balance between subview reuse using detach to preserve event hash and subview re-creation when fully re-rendering a history by removing views from the viewMap. - Makes actions section a full height to make empty, anon histories looking normal. - Makes dataset models wait until the change is returned from the server before triggering change on the model. Commit: d89843ead7176b90aef13b7b26cc3f73fedc4c3b https://github.com/galaxyproject/galaxy/commit/d89843ead7176b90aef13b7b26cc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/list/list-view.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/list/list-view.js M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, history: fix to delete_current most_recent Fixes delete_current's call to most_recent, filtering out the deleted and purged histories. Now, on delete_current the most recently *non- deleted* history will be switched to. Commit: 86acee5a743e7afca530f9a194f82c0ed83c4b1a https://github.com/galaxyproject/galaxy/commit/86acee5a743e7afca530f9a194f8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css M templates/webapps/galaxy/history/embed.mako Log Message: ----------- UI, history: fix search and misc. - corrects search to work for individual history views - refactors handleItem{Deletion,Visible}Change in history view edit - reverts the experiment in the branch that recycled subviews between renders - this simplifies many things - corrects the rendering, signals, and timing of loading indicators - small fixes, refactorings, and simplifications Commit: a41ff4265b4f54b832e40c0dc71707db5eb307e6 https://github.com/galaxyproject/galaxy/commit/a41ff4265b4f54b832e40c0dc717… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M lib/galaxy/managers/base.py M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: more minor fixes Commit: ae6cb1bf88ba4293c6be4c5df3a717bccaca73fd https://github.com/galaxyproject/galaxy/commit/ae6cb1bf88ba4293c6be4c5df3a7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-annotated.js M static/style/blue/base.css M templates/webapps/galaxy/history/display.mako Log Message: ----------- UI, history: fix annotations in published history Commit: f072ee7807591902b8ae605474aa089a33ead93d https://github.com/galaxyproject/galaxy/commit/f072ee7807591902b8ae605474aa… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-14 (Tue, 14 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/dataset.less M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako Log Message: ----------- UI, history: change to front page when adding - Causes the contents to load the 'front' page before adding new datasets. This allows them to be added in the proper place. - Fixes annotation display on datasets. - Adds annotation loading to histories embedded in Pages. Commit: 1b2c5dea990ed91325eb6a85b16184a1647d2e20 https://github.com/galaxyproject/galaxy/commit/1b2c5dea990ed91325eb6a85b161… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/style/blue/base.css M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, history: show search progress in subtitle Commit: 233d6d8d32e94671ce387efdb39f35bd3454eb8d https://github.com/galaxyproject/galaxy/commit/233d6d8d32e94671ce387efdb39f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-view.js M static/style/blue/base.css Log Message: ----------- UI, history: minor style/pagination fixes Commit: 6eb1cefe88b50eea7beb982bbfaf5674f13e7313 https://github.com/galaxyproject/galaxy/commit/6eb1cefe88b50eea7beb982bbfaf… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: get element count for all histories - Moves the ajax call for hdca element counts to a listener of the loading-done event. This allows (almost) all history views to be decorated with hdca counts. Commit: fd78f99d61bcb141475875b85d3beb2945bc3a8e https://github.com/galaxyproject/galaxy/commit/fd78f99d61bcb141475875b85d3b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M .ci/py3_sources.txt M client/bower.json R client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/library.less M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/tool_conf.xml.sample M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/source/dev/faq.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/NuBBE_1_obabel_3D.pdbqt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py A lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/s3.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py A lib/galaxy/tools/filter_failed_collection.xml A lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py A lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/verify/__init__.py A lib/galaxy/tools/zip_collection.xml M lib/galaxy/util/__init__.py R lib/galaxy/util/directory_hash.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy_utils/sequence/fastq.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/attribute_handlers.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/container_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/utility_container_manager.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py R static/maps/libs/tracekit.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/libs/tracekit.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/repair_repository.mako M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako M templates/show_params.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/repository/common.mako A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 M test/api/helpers.py M test/api/test_tools.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/interactor.py M test/base/twilltestcase.py A test/functional/tools/checksum.xml A test/functional/tools/exit_code_from_file.xml A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_0000_basic_repository_features.py M test/shed_functional/functional/test_1000_install_basic_repository.py M test/unit/tools/test_actions.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/workflows/test_run_parameters.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/filters/axt_to_lav.py Log Message: ----------- (merge conflicts) Commit: 48f48e9bd29430f58363eb47d95154ff4854ebe7 https://github.com/galaxyproject/galaxy/commit/48f48e9bd29430f58363eb47d951… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js M static/style/blue/base.css M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, history: style cleanup, small tweaks - Corrects history control sizing on Safari - Corrects ul, li rendering of history in Chrome - Lengthens fadeout of loading indicator to better transition when rendering large numbers of contents - Corrects page controls in history/view Commit: 6c6bfe5614f6fed3c88b19789369ee3f5aabc86b https://github.com/galaxyproject/galaxy/commit/6c6bfe5614f6fed3c88b19789369… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/library/common/import_datasets_to_histories.mako M tools/filters/sff_extract.py Log Message: ----------- (merge conflicts) Commit: cc8d421c570df3b3b8c53ba49ad1247729102ad1 https://github.com/galaxyproject/galaxy/commit/cc8d421c570df3b3b8c53ba49ad1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/style/less/ui/search-input.less M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/maps/ui/search-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js M static/scripts/ui/search-input.js M static/style/blue/base.css Log Message: ----------- UI, history: search and ui/search-input - clarifies search progress in subtitle of edit/current histories - corrects found display in subtitle when no results are found - does not cause a search and render when entering the same terms - does not clear search on full backspace or cut of input text - does not cause clear and render if no previous terms existed - removes onchange from search input (not needed yet) Commit: b1d652e59d6ccde1e73c90ffd483bbd600d110ff https://github.com/galaxyproject/galaxy/commit/b1d652e59d6ccde1e73c90ffd483… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M .ci/py3_sources.txt M Makefile M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/jupyter/config/jupyter.xml A display_applications/igv/bigwig.xml M lib/galaxy/config.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/managers/base.py M lib/galaxy/managers/context.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/config.py M run_tests.sh M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_runner.py M scripts/fetch_eggs.py M scripts/set_dataset_sizes.py M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M templates/user/change_password.mako M test/api/helpers.py M test/api/test_datasets.py M test/api/test_tool_data.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional_tests.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_toolbox.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: dd37dedc2a1e570053b8be9b0f8896cca8bc4cd0 https://github.com/galaxyproject/galaxy/commit/dd37dedc2a1e570053b8be9b0f88… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: scroll to new items, clean up Commit: 8a159ade93040ea1cb6a0657c7089eebc5a92366 https://github.com/galaxyproject/galaxy/commit/8a159ade93040ea1cb6a0657c708… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/style/less/history.less M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-view.js M static/style/blue/base.css Log Message: ----------- UI, history: clean up Commit: aee39774121ef2610387431b6024ddd12c997834 https://github.com/galaxyproject/galaxy/commit/aee39774121ef2610387431b6024… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-11 (Mon, 11 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, history: switch to front when dropping content When a history with a drop target accepts data to be copied, this has the view's current page switch to the top/front before the copy happens. Commit: e842e0b2ba5c77674e11f8a1a0eceb4765db2621 https://github.com/galaxyproject/galaxy/commit/e842e0b2ba5c77674e11f8a1a0ec… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-11 (Mon, 11 Jul 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M test/qunit/tests/history_contents_model_tests.js Log Message: ----------- Tests, history: hda delete happens after return - Change qunit test history_contents_model_tests to account for the use of the '{ wait: true }' backbone flag being used when 'save'd. This causes the attribute to be set when the ajax call returns successfully. Commit: a33203b3b5d5ad9b74ff00a693dcb85efff746e3 https://github.com/galaxyproject/galaxy/commit/a33203b3b5d5ad9b74ff00a693dc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: increase page select affordance Commit: 817c63eeea3d13604f7e9faa817d973f18ab52c6 https://github.com/galaxyproject/galaxy/commit/817c63eeea3d13604f7e9faa817d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/workflow/modules.py M scripts/common_startup.sh M setup.cfg M static/maps/mvc/dataset/data.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-template.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/data.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-template.js M test/api/test_tools.py A test/functional/tools/identifier_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: 709ae896ea40a60127d814087c6f56327f79bf3e https://github.com/galaxyproject/galaxy/commit/709ae896ea40a60127d814087c6f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M lib/galaxy/managers/history_contents.py Log Message: ----------- Serializer: better name & doc Commit: 87fbdc4ad6345ebe56d652358e34e9de57981535 https://github.com/galaxyproject/galaxy/commit/87fbdc4ad6345ebe56d652358e34… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-12 (Tue, 12 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- UI, history: create tooltip on each render Commit: 53f34b8c9e2105972e82f22a5f802399b6656f0a https://github.com/galaxyproject/galaxy/commit/53f34b8c9e2105972e82f22a5f80… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- UI, history: rerender contents on unhiding hidden - Waits till all hidden datasets are saved as unhidden and then, if the history is not showing hidden datasets, rerenders the entire contents Commit: 97b171632d9b16e54fad4b46b0f419bf31866882 https://github.com/galaxyproject/galaxy/commit/97b171632d9b16e54fad4b46b0f4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/history/history-view.js.map M static/maps/mvc/list/list-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/mvc/history/history-view.js M static/scripts/mvc/list/list-view.js Log Message: ----------- UI, history: render on deleted/hidden toggle - Fixes lack of render when only one hidden/deleted dataset is shown by sending a `renderAll` flag then caught by the update listener Commit: 62de9bf76a6e5a6d7857ad031f8499d7453e12ea https://github.com/galaxyproject/galaxy/commit/62de9bf76a6e5a6d7857ad031f84… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_lint_include_list.txt A .ci/flake8_wrapper_imports.sh M .ci/py3_sources.txt M .gitignore M .travis.yml A client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.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/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.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/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.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/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/library/jobs.js M config/plugins/visualizations/charts/static/library/storage.js R config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/models/chart.js M config/plugins/visualizations/charts/static/models/config.js R config/plugins/visualizations/charts/static/models/group.js R config/plugins/visualizations/charts/static/models/groups.js M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css M config/plugins/visualizations/charts/static/views/editor.js R config/plugins/visualizations/charts/static/views/group.js A config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewer.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/graphviz/static/js/graphVis.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/tool_data_table_conf.xml.sample A config/tool_destinations.yml.sample A display_applications/ucsc/trackhub.xml A doc/source/admin/grt.rst M doc/source/admin/index.rst M doc/source/admin/interactive_environments.rst M doc/source/dev/index.rst A doc/source/dev/interactive_environments.rst M doc/source/lib/galaxy.objectstore.rst M lib/galaxy/config.py M lib/galaxy/datatypes/data.py A lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/tracks.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/actions/post.py A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/azure_blob.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py A lib/galaxy/tools/toolbox/requirements.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A lib/galaxy/webapps/reports/controllers/history.py A lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/shed_util_common.py A scripts/communication/communication_server.py A scripts/communication/template/communication.css A scripts/communication/template/communication.html A scripts/communication/template/communication.js A scripts/grt.py A scripts/grt.yml.sample M setup.cfg A static/maps/layout/generic-nav-view.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/layout/generic-nav-view.js M static/scripts/layout/menu.js M static/scripts/layout/page.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/form/form-data.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-misc.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-tabs.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js A static/style/base.css M static/style/blue/base.css M templates/admin/impersonate.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/preview_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/ind_share_base.mako M templates/js-app.mako A templates/user/communication_settings.mako M templates/user/index.mako M templates/webapps/galaxy/history/grid.mako A templates/webapps/reports/history_and_dataset_per_user.mako A templates/webapps/reports/history_and_dataset_type.mako A templates/webapps/reports/history_per_user.mako M templates/webapps/reports/index.mako A templates/webapps/reports/tool_error_messages.mako A templates/webapps/reports/tool_execution_time.mako A templates/webapps/reports/tool_execution_time_per_month.mako A templates/webapps/reports/tools_and_job_state.mako A templates/webapps/reports/tools_and_job_state_per_month.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/export_repository.mako A test-data/neostore.zip M test/api/test_users.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/twilltestcase.py A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml A test/integration/test_resolvers.py M test/qunit/tests/ui_tests.js M test/qunit/tests/upload_dialog_tests.js M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py A test/unit/datatypes/test_data.py A test/unit/jobs/dynamic_tool_destination/__init__.py A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml A test/unit/jobs/dynamic_tool_destination/data/test.empty A test/unit/jobs/dynamic_tool_destination/data/test.fasta A test/unit/jobs/dynamic_tool_destination/data/test1.full A test/unit/jobs/dynamic_tool_destination/data/test3.full A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_conda_resolution.py M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: 21b93be1104ac2175ba128ee604425ee44ea17cf https://github.com/galaxyproject/galaxy/commit/21b93be1104ac2175ba128ee6044… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M Makefile M client/bower.json A client/galaxy/scripts/libs/jquery.complexify.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/style/less/base.less M client/grunt-tasks/install-libs.js M client/webpack.config.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/version.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M run_tests.sh M scripts/bootstrap_history.py M scripts/nosetests.py A static/maps/libs/jquery.complexify.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/raven.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/scripts/mvc/history/options-menu.js M static/style/blue/base.css M templates/user/change_password.mako M templates/user/register.mako M test/unit/tools/test_tool_deps.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history-contents.limiting Commit: 2d15e50d0f5c65d0dc9d896d1e47ba546d5a7e42 https://github.com/galaxyproject/galaxy/commit/2d15e50d0f5c65d0dc9d896d1e47… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js A client/galaxy/scripts/mvc/history/history-preferences.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/ui/search-input.js M client/galaxy/scripts/utils/ajax-queue.js M client/galaxy/style/less/base.less A client/galaxy/style/less/collection.less R client/galaxy/style/less/collections.less A client/galaxy/style/less/dataset.less A client/galaxy/style/less/flex.less M client/galaxy/style/less/history.less M client/galaxy/style/less/list-item.less A client/galaxy/style/less/ui/error-modal.less M client/galaxy/style/less/ui/search-input.less M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/layout/panel.js.map M static/maps/mvc/annotation.js.map M static/maps/mvc/base-mvc.js.map A static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map A static/maps/mvc/history/history-preferences.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/ui/error-modal.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/ui/search-input.js.map M static/maps/utils/ajax-queue.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/panel.js M static/scripts/mvc/annotation.js M static/scripts/mvc/base-mvc.js A static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-model.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-model.js A 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/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/ui/error-modal.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/ui/search-input.js M static/scripts/utils/ajax-queue.js M static/style/blue/base.css M static/style/blue/bootstrap-tour.css M static/style/blue/jquery.rating.css M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M test/qunit/tests/history_contents_model_tests.js M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge branch 'history-contents.limiting' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7389b93bd613...2d15e50d0f5c

1 0

[galaxyproject/galaxy] 7bf0cc: Remove the old HubAssembly class
by GitHub 03 Aug '16

03 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 7bf0cc72418308e54b6ec180a8913623004c8288 https://github.com/galaxyproject/galaxy/commit/7bf0cc72418308e54b6ec180a891… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M lib/galaxy/datatypes/tracks.py Log Message: ----------- Remove the old HubAssembly class Commit: 3206199652330659aa9f1cebe75c6940787f85d4 https://github.com/galaxyproject/galaxy/commit/3206199652330659aa9f1cebe75c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-03 (Wed, 03 Aug 2016) Changed paths: M lib/galaxy/datatypes/tracks.py Log Message: ----------- Merge pull request #2701 from remimarenco/release_16.07 [16.07] Fix: Remove the old HubAssembly class Compare: https://github.com/galaxyproject/galaxy/compare/ed7c357668df...320619965233

1 0

[galaxyproject/galaxy] 2b7fc3: Fixing button width on Composite upload dialog
by GitHub 02 Aug '16

02 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b7fc3d3778adfae0b4ddc9967ea6183ca3c6cc9 https://github.com/galaxyproject/galaxy/commit/2b7fc3d3778adfae0b4ddc9967ea… Author: galaxy <galaxy(a)galaxy.development> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/style/less/upload.less M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Fixing button width on Composite upload dialog Commit: 7389b93bd61396f86b85cbc0b4fa818221563204 https://github.com/galaxyproject/galaxy/commit/7389b93bd61396f86b85cbc0b4fa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/style/less/upload.less M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Merge pull request #2703 from sszakony/dev Fixing button width on Composite upload dialog #2591 Compare: https://github.com/galaxyproject/galaxy/compare/d8c22b70e897...7389b93bd613

1 0

[galaxyproject/infrastructure-playbook] 966138: Decrease Jetstream @ TACC usage for production pha...
by GitHub 02 Aug '16

02 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 966138c57e8b91355d1235586df5b3d5d7221841 https://github.com/galaxyproject/infrastructure-playbook/commit/966138c57e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- Decrease Jetstream @ TACC usage for production phase

1 0

[galaxyproject/galaxy] bb209c: Add a password strength evaluation bar
by GitHub 01 Aug '16

01 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb209c6e59e240bb1dc73d88a1fddd34fcc0f9e9 https://github.com/galaxyproject/galaxy/commit/bb209c6e59e240bb1dc73d88a1fd… Author: Ben Fulton <befulton(a)iu.edu> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M client/bower.json A client/galaxy/scripts/libs/jquery.complexify.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/style/less/base.less M client/grunt-tasks/install-libs.js M client/webpack.config.js A static/maps/libs/jquery.complexify.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/raven.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/style/blue/base.css M templates/user/change_password.mako M templates/user/register.mako Log Message: ----------- Add a password strength evaluation bar Modify the register and change_password pages to show a bar evaluating the strength of the password. Bar displays in red for passwords < 6 chars or below a certain minimum complexity; green otherwise. Adds a dependency on Complexify, a password evaluator written by Dan Palmer. Commit: d8c22b70e897afa2f988751c30294e90f1df8985 https://github.com/galaxyproject/galaxy/commit/d8c22b70e897afa2f988751c3029… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M client/bower.json A client/galaxy/scripts/libs/jquery.complexify.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/style/less/base.less M client/grunt-tasks/install-libs.js M client/webpack.config.js A static/maps/libs/jquery.complexify.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/raven.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/style/blue/base.css M templates/user/change_password.mako M templates/user/register.mako Log Message: ----------- Merge branch 'PasswordStrengthBar' into dev Compare: https://github.com/galaxyproject/galaxy/compare/dd4eabb48426...d8c22b70e897

1 0

[galaxyproject/galaxy] 2b4a85: History, UI: use id of displayed history in delete
by GitHub 01 Aug '16

01 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b4a8557f1f0057447c729717f22452d14ac11ef https://github.com/galaxyproject/galaxy/commit/2b4a8557f1f0057447c729717f22… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- History, UI: use id of displayed history in delete - Refactor `delete current` to `delete` and require an id arg. - Update history options menu to pass the id of the displayed/ current history to the above delete controller endpoint. This means that the current history panel will delete the history that's displayed (instead of potentially a different history that's been set to the current history on the server side). Note: this isn't an ideal refactoring but should solve the below issue temporarily until we move more of the session state out of API. Closes #894 Commit: 877655c1f06e5076512e2f0e16cc7d1458471643 https://github.com/galaxyproject/galaxy/commit/877655c1f06e5076512e2f0e16cc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-view.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/style/less/ui.less M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-buttons.js M static/style/blue/base.css M templates/base.mako M templates/base/base_panels.mako M templates/js-app.mako Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history.delete_current-id Commit: cdab64820c554120545d7207d3861612d2a99ea9 https://github.com/galaxyproject/galaxy/commit/cdab64820c554120545d7207d386… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-29 (Fri, 29 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_lint_include_list.txt A .ci/flake8_wrapper_imports.sh M .travis.yml M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/object_store_conf.xml.sample A config/plugins/interactive_environments/neo/config/allowed_images.yml.sample A config/plugins/interactive_environments/neo/config/neo.ini.sample A config/plugins/interactive_environments/neo/config/neo.xml A config/plugins/interactive_environments/neo/static/js/neo.js A config/plugins/interactive_environments/neo/templates/neo.mako M doc/source/lib/galaxy.objectstore.rst M lib/galaxy/config.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/model/mapping.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/azure_blob.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/parameters/basic.py A lib/galaxy/tools/toolbox/requirements.py M lib/galaxy/version.py M lib/galaxy/web/__init__.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py A lib/galaxy/webapps/reports/controllers/history.py A lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/shed_util_common.py M setup.cfg M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/preview_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base/base_panels.mako A templates/webapps/reports/history_and_dataset_per_user.mako A templates/webapps/reports/history_and_dataset_type.mako A templates/webapps/reports/history_per_user.mako M templates/webapps/reports/index.mako A templates/webapps/reports/tool_error_messages.mako A templates/webapps/reports/tool_execution_time.mako A templates/webapps/reports/tool_execution_time_per_month.mako A templates/webapps/reports/tools_and_job_state.mako A templates/webapps/reports/tools_and_job_state_per_month.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/export_repository.mako M test/base/driver_util.py M test/base/twilltestcase.py A test/integration/test_resolvers.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into history.delete_current-id Commit: dd4eabb48426a24ca6c960469b3fbb39edff821f https://github.com/galaxyproject/galaxy/commit/dd4eabb48426a24ca6c960469b3f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #2654 from carlfeberhard/history.delete_current-id History, UI: use id of displayed history in delete Compare: https://github.com/galaxyproject/galaxy/compare/6db43585c16c...dd4eabb48426

1 0

[galaxyproject/galaxy] 2c7555: Fix sed usage in Makefile to be compatible with bo...
by GitHub 01 Aug '16

01 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2c75551a026ee02efd8127084f6f21e2327886a9 https://github.com/galaxyproject/galaxy/commit/2c75551a026ee02efd8127084f6f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M Makefile Log Message: ----------- Fix sed usage in Makefile to be compatible with both gnu and bsd sed. -i's argument is not optional for bsd, but an empty string (no backup extension) works fine and has the same behavior as gnu sed. Commit: 00e41385d75f83bbb35abc5830e3859715a2039e https://github.com/galaxyproject/galaxy/commit/00e41385d75f83bbb35abc5830e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M Makefile Log Message: ----------- The previous approach to sed worked great on bsd sed, but gnu sed doesn't understand an empty '' in-place extension the same way. So, fixed one, broke the other. This approach with the -e argument feels like a total hack since it explits the fact that bsd sed consumes the -e as the argument to -i, but it still has the command interpreted correctly. Commit: ef0d27d677b482d81b89d843cc06d46048a08d03 https://github.com/galaxyproject/galaxy/commit/ef0d27d677b482d81b89d843cc06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M Makefile Log Message: ----------- Change extension of the file that gets immediately deleted to address nsoranzo's concern about bsd utilities. Commit: 6db43585c16c22bb28f5e19c4e1db49444c7971d https://github.com/galaxyproject/galaxy/commit/6db43585c16c22bb28f5e19c4e1d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #2695 from dannon/sed_compat sed bsd compatibility for release versioning in Makefile Compare: https://github.com/galaxyproject/galaxy/compare/3fd0e405fd6c...6db43585c16c

1 0