Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b8e2833b5bcb26242ef08967fe342a81c2811172 https://github.com/galaxyproject/galaxy/commit/b8e2833b5bcb26242ef08967fe342... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-07-30 (Sat, 30 Jul 2016) Changed paths: M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/user/manage-user-information.js A client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/base.less 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/layout/menu.js M static/style/blue/base.css Log Message: ----------- Adding code for replacing mako for user preferences with simple features Commit: 77f5655de1f606ae08f533ef27318d39097dbcd2 https://github.com/galaxyproject/galaxy/commit/77f5655de1f606ae08f533ef27318... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-07-30 (Sat, 30 Jul 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/manage-user-information.js M client/galaxy/scripts/mvc/user/user-preferences.js A lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Adding routes and api calls for user preferences Commit: a63f63440ebe66715608907c809abeab59279166 https://github.com/galaxyproject/galaxy/commit/a63f63440ebe66715608907c809ab... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-07-31 (Sun, 31 Jul 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/manage-user-information.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Adding login information section for manage user information feature Commit: aaedf684f0e9693fc98f5867cde62170bbf35879 https://github.com/galaxyproject/galaxy/commit/aaedf684f0e9693fc98f5867cde62... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/manage-user-information.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/style/blue/base.css Log Message: ----------- Adding code for validating and saving email and username Commit: 07409a89f86df86b86fc621fcc8b2f8533cf6116 https://github.com/galaxyproject/galaxy/commit/07409a89f86df86b86fc621fcc8b2... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-01 (Mon, 01 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/manage-user-information.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fixing a bug with multiple events firing Commit: cc168ce95423c096bbd5ef198cb24c0549ef4c0e https://github.com/galaxyproject/galaxy/commit/cc168ce95423c096bbd5ef198cb24... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/manage-user-information.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Adding all the features for manage user info Commit: 044eb9768362b7d341911a78446be6f3760746ac https://github.com/galaxyproject/galaxy/commit/044eb9768362b7d341911a78446be... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M static/scripts/bundled/libs.bundled.js Log Message: ----------- adding the bundled file Commit: 976e6e5ac6757db777db6d8248889f7053e2e776 https://github.com/galaxyproject/galaxy/commit/976e6e5ac6757db777db6d8248889... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: A client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/manage-user-information.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.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 M static/style/blue/base.css Log Message: ----------- Adding change password feature Commit: 0558225f5f98ececedbcef4f8232baec84620e70 https://github.com/galaxyproject/galaxy/commit/0558225f5f98ececedbcef4f8232b... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding missing files Commit: ce1a478d8d073fbb5fda88834e4f4132bb5acfb3 https://github.com/galaxyproject/galaxy/commit/ce1a478d8d073fbb5fda88834e4f4... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.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 M static/style/blue/base.css Log Message: ----------- Adding Change Permissions on history feature Commit: bbd020e8a7b84de184885428650bec488d102856 https://github.com/galaxyproject/galaxy/commit/bbd020e8a7b84de184885428650be... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: A client/galaxy/scripts/mvc/user/change-permissions.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- adding missing files Commit: 976729ad553ff34bff14f80eda94bfdbbf25491a https://github.com/galaxyproject/galaxy/commit/976729ad553ff34bff14f80eda94b... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: A client/galaxy/scripts/mvc/user/api-keys.js M client/galaxy/scripts/mvc/user/change-permissions.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.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/style/blue/base.css Log Message: ----------- Adding Generate API key feature Commit: 23744c36f28e1d3633363720236695a1f6113395 https://github.com/galaxyproject/galaxy/commit/23744c36f28e1d363336372023669... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-08 (Mon, 08 Aug 2016) Changed paths: M client/galaxy/style/less/base.less Log Message: ----------- adding missing file Commit: cb79eac22ede7d9facc07b170d6b2c64bb217142 https://github.com/galaxyproject/galaxy/commit/cb79eac22ede7d9facc07b170d6b2... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-14 (Sun, 14 Aug 2016) Changed paths: A client/galaxy/scripts/mvc/user/change-communication.js A client/galaxy/scripts/mvc/user/toolbox-filter.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.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/style/blue/base.css Log Message: ----------- Adding Manage toolbox filter and Change communication settings features Commit: d7c6ca2bbd875a910e759acca015be40e5562064 https://github.com/galaxyproject/galaxy/commit/d7c6ca2bbd875a910e759acca015b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/ui.less M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/form/form-parameters.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/form/form-parameters.js M static/style/blue/base.css Log Message: ----------- Use form view to build password change form Commit: f11a87628f0c9571dc953976119f1a80d290460a https://github.com/galaxyproject/galaxy/commit/f11a87628f0c9571dc953976119f1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/user-preferences.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Connect main preference page with password change view without using global variables Commit: 43054acb2e577f4928fb8a76931cb7825194888d https://github.com/galaxyproject/galaxy/commit/43054acb2e577f4928fb8a76931cb... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/ui.less M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/form/form-parameters.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/form/form-parameters.js M static/style/blue/base.css Log Message: ----------- Merge pull request #16 from guerler/remove_mako_user_pref_form_view Use form view to build change password form Commit: 4016b3e3037db64e04537b248f4d48f330b294db https://github.com/galaxyproject/galaxy/commit/4016b3e3037db64e04537b248f4d4... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.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 Log Message: ----------- Change communication setting feature with form view Commit: baae49f607480d98c2d63b6378f891c2eda4e154 https://github.com/galaxyproject/galaxy/commit/baae49f607480d98c2d63b6378f89... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-28 (Sun, 28 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/user/api-keys.js M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/user-preferences.js 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 Log Message: ----------- Updating API key feature for user preferences with form view Commit: 1adbcfc0ec1fcccd1987946f83118c496d9eb635 https://github.com/galaxyproject/galaxy/commit/1adbcfc0ec1fcccd1987946f83118... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/toolbox-filter.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.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: ----------- Adding toolbox permissions feature using form view Commit: e06d206eedf4ac36bfc03417d76fee6057fcae03 https://github.com/galaxyproject/galaxy/commit/e06d206eedf4ac36bfc03417d76fe... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-08-31 (Wed, 31 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/user/manage-user-information.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.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 Log Message: ----------- Adding user login information using form view Commit: 4addb9497299cd9c3ff0e65b0b30ecf7beb5aa41 https://github.com/galaxyproject/galaxy/commit/4addb9497299cd9c3ff0e65b0b30e... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/user/manage-user-information.js M client/galaxy/scripts/mvc/user/toolbox-filter.js M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/form/form-parameters.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js Log Message: ----------- Extending the form view to have labels and buttons Commit: 46cd30bb3523d182f319f9640d552a72dbae5ca5 https://github.com/galaxyproject/galaxy/commit/46cd30bb3523d182f319f9640d552... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-communication.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Updating the communication setting changes as reviewed/suggested by Aysam Guerler Commit: 994eddfd5a15e85f37cb3ff0af734d31d276eb8a https://github.com/galaxyproject/galaxy/commit/994eddfd5a15e85f37cb3ff0af734... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-communication.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unused field value update, and api request parameters Commit: 5d8bd3f72eb6f06c18bb5fc47a8fc2d269b1c1f7 https://github.com/galaxyproject/galaxy/commit/5d8bd3f72eb6f06c18bb5fc47a8fc... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-communication.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix spacing Commit: 399f4ae9c06abc9a06240be158905b62085abd16 https://github.com/galaxyproject/galaxy/commit/399f4ae9c06abc9a06240be158905... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Change comment Commit: 4b7324bab96cf5fea85b13216902589e6568b71c https://github.com/galaxyproject/galaxy/commit/4b7324bab96cf5fea85b132169025... Author: anup kumar <anup.rulez@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-communication.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #18 from guerler/fix_communication_settings Remove unused field value update, and api request parameters Commit: ebc1cc6ff3ac216ff54628e4ff5e66eca90d2f38 https://github.com/galaxyproject/galaxy/commit/ebc1cc6ff3ac216ff54628e4ff5e6... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/user/api-keys.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Revise api key generation form Commit: 6a17e10d751b427ede173f40907d5fb5032201cb https://github.com/galaxyproject/galaxy/commit/6a17e10d751b427ede173f40907d5... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/api-keys.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix info text Commit: 14d045c54e0e91181689a2281115d17aee39561f https://github.com/galaxyproject/galaxy/commit/14d045c54e0e91181689a2281115d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/api-keys.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unused variable Commit: e84251a7310005c7d16b6f87b423c178b0583065 https://github.com/galaxyproject/galaxy/commit/e84251a7310005c7d16b6f87b423c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/api-keys.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix request parameter Commit: d59fa629cf269e7d118b38a48dbe85a8634dac60 https://github.com/galaxyproject/galaxy/commit/d59fa629cf269e7d118b38a48dbe8... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/api-keys.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unused variable Commit: ab559072d22b8b98aa2fd001d79dd42f791ebb0a https://github.com/galaxyproject/galaxy/commit/ab559072d22b8b98aa2fd001d79dd... Author: anup kumar <anup.rulez@gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/user/api-keys.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge pull request #19 from guerler/fix_communication_settings Revise api key generation form Commit: 8f1156295989b11c127bba1d50438b516d7d80a8 https://github.com/galaxyproject/galaxy/commit/8f1156295989b11c127bba1d50438... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-10 (Sat, 10 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/toolbox-filter.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Updating toolbox filters Commit: 222d1f2cac83adb0ebea0c24701ef2d01fcf6eb5 https://github.com/galaxyproject/galaxy/commit/222d1f2cac83adb0ebea0c24701ef... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-10 (Sat, 10 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/toolbox-filter.js Log Message: ----------- Removing extra spaces Commit: b4d0dfcc92ba9790f2975a557aaf0ecc6cb52af7 https://github.com/galaxyproject/galaxy/commit/b4d0dfcc92ba9790f2975a557aaf0... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-11 (Sun, 11 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/user/manage-user-information.js M static/maps/mvc/form/form-parameters.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js Log Message: ----------- Adding user address filter feature using radiobuttons in manange user information Commit: 9915ef7837fc75758b2329681fce96bf94c3be01 https://github.com/galaxyproject/galaxy/commit/9915ef7837fc75758b2329681fce9... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: A client/galaxy/scripts/mvc/user/add-edit-address.js M client/galaxy/scripts/mvc/user/manage-user-information.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.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: ----------- Adding add, edit, delete and undelete features for manage user information page Commit: 961e01e700ecd775f4f7c2edd1aa4ac2a4efdc22 https://github.com/galaxyproject/galaxy/commit/961e01e700ecd775f4f7c2edd1aa4... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/manage-user-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Replacing input building logic to server side for login form Commit: 4bca99940f3f55425775b0f9cb4d9fcdfba8f08e https://github.com/galaxyproject/galaxy/commit/4bca99940f3f55425775b0f9cb4d9... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-17 (Sat, 17 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/manage-user-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Updating the display of user addresses Commit: 123aa562c0878406eb0eaa16eb857661da63996c https://github.com/galaxyproject/galaxy/commit/123aa562c0878406eb0eaa16eb857... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-17 (Sat, 17 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/user/manage-user-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-options.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-options.js Log Message: ----------- Adding edit, delete and undelete using radio button views and inputs built at server Commit: 3b5905985de402c92051d1da97dfc26c43a94e41 https://github.com/galaxyproject/galaxy/commit/3b5905985de402c92051d1da97dfc... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-options.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-options.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-options.js Log Message: ----------- Removing the unchecked attribute from select Commit: dc80c8962b31192929037448ffba1423819712f7 https://github.com/galaxyproject/galaxy/commit/dc80c8962b31192929037448ffba1... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/add-edit-address.js M client/galaxy/scripts/mvc/user/manage-user-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merging the api calls for user info into one api call Commit: 69800d41da8a131fcaee40ff1a6aa1194afe1427 https://github.com/galaxyproject/galaxy/commit/69800d41da8a131fcaee40ff1a6aa... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/manage-user-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding user type form and address filters Commit: 431fad09e06afe2a13ccd21e3ffff3ef826ee341 https://github.com/galaxyproject/galaxy/commit/431fad09e06afe2a13ccd21e3ffff... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/user/change-permissions.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/form/form-parameters.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-parameters.js Log Message: ----------- Adding Change permissions view Commit: c83fa12e56d221c162488225a6e61d632b46d7e0 https://github.com/galaxyproject/galaxy/commit/c83fa12e56d221c162488225a6e61... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/add-edit-address.js M client/galaxy/scripts/mvc/user/api-keys.js M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/change-permissions.js M client/galaxy/scripts/mvc/user/manage-user-information.js M client/galaxy/scripts/mvc/user/toolbox-filter.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fixing styling and removing commented out code Commit: 60d4570c54dcd58d69ff907c832881a2328b2545 https://github.com/galaxyproject/galaxy/commit/60d4570c54dcd58d69ff907c83288... 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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/data.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/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-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/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M 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Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- some more fixes Commit: 7e1a4a393d0b10e167341f8476a6bca069e6693f https://github.com/galaxyproject/galaxy/commit/7e1a4a393d0b10e167341f8476a6b... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- whitespace fixes Commit: a34bdc4647ed58a4ce4d4c33ecd6f42811e1568f https://github.com/galaxyproject/galaxy/commit/a34bdc4647ed58a4ce4d4c33ecd6f... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- use enumerate Commit: 30afad5cc5cb2514a9dcf6e8a354c1254274b3ed https://github.com/galaxyproject/galaxy/commit/30afad5cc5cb2514a9dcf6e8a354c... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- use enumerate Commit: fb4a6d1c1ce69bb425226b7097cf79e3f7357ba3 https://github.com/galaxyproject/galaxy/commit/fb4a6d1c1ce69bb425226b7097cf7... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- style Commit: 55d94e9a2317de2a6fdd5626475e023d2a432e6e https://github.com/galaxyproject/galaxy/commit/55d94e9a2317de2a6fdd5626475e0... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #20 from bgruening/small_fixes Small fixes Commit: df38ca9fe809b9a1888386502643d85c5fbc1b9d https://github.com/galaxyproject/galaxy/commit/df38ca9fe809b9a1888386502643d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Minor style fix Commit: 597214a65f4681b8fa81e4b80f990d6da5849f76 https://github.com/galaxyproject/galaxy/commit/597214a65f4681b8fa81e4b80f990... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: R client/galaxy/scripts/mvc/user/api-keys.js M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/change-password.js R client/galaxy/scripts/mvc/user/manage-user-information.js R client/galaxy/scripts/mvc/user/toolbox-filter.js M client/galaxy/scripts/mvc/user/user-preferences.js A static/maps/mvc/user/change-api-key.js.map A static/maps/mvc/user/change-communication.js.map A static/maps/mvc/user/change-password.js.map A static/maps/mvc/user/change-permissions.js.map A static/maps/mvc/user/change-toolbox-filter.js.map A static/maps/mvc/user/change-user-information.js.map A static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/user/change-api-key.js A static/scripts/mvc/user/change-communication.js A static/scripts/mvc/user/change-password.js A static/scripts/mvc/user/change-permissions.js A static/scripts/mvc/user/change-toolbox-filter.js A static/scripts/mvc/user/change-user-information.js A static/scripts/mvc/user/user-preferences.js Log Message: ----------- Add packed files, use consistent file naming Commit: 31867733173911de306ea45184ce62ba1eea63ea https://github.com/galaxyproject/galaxy/commit/31867733173911de306ea45184ce6... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/user/change-user-information.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unused options for api index endpoint Commit: faa7cb525b78ca53895ddf526c972eb4ef390c2d https://github.com/galaxyproject/galaxy/commit/faa7cb525b78ca53895ddf526c972... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-28 (Wed, 28 Sep 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Add to_dict functions to form_builder Commit: 0c70b5bca27e51a84af1e9381f28ce3cd33e55b0 https://github.com/galaxyproject/galaxy/commit/0c70b5bca27e51a84af1e9381f28c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js A client/galaxy/scripts/mvc/user/change-api-key.js A client/galaxy/scripts/mvc/user/change-toolbox-filter.js A client/galaxy/scripts/mvc/user/change-user-information.js M lib/galaxy/model/__init__.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/form/form-section.js.map M static/maps/mvc/user/change-permissions.js.map M static/maps/mvc/user/change-user-information.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/user/change-permissions.js M static/scripts/mvc/user/change-user-information.js Log Message: ----------- Build address field dict Commit: 60ed49a6acb48ed82fdbdca1d45c8184d25360d3 https://github.com/galaxyproject/galaxy/commit/60ed49a6acb48ed82fdbdca1d45c8... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Add user info form conditional builder Commit: ed104067aa6504890dedfd54dd89a56952cafc9b https://github.com/galaxyproject/galaxy/commit/ed104067aa6504890dedfd54dd89a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fix Commit: 8d9dc602d0d336872a08548fd1a27c59794477eb https://github.com/galaxyproject/galaxy/commit/8d9dc602d0d336872a08548fd1a27... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Add type form, untested Commit: baa4676282d0acd85e721e8819910f3553bff1c1 https://github.com/galaxyproject/galaxy/commit/baa4676282d0acd85e721e8819910... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Remove unused parsing Commit: c7f21301ddc3b5d95e3085bffd3e39f0b14924f0 https://github.com/galaxyproject/galaxy/commit/c7f21301ddc3b5d95e3085bffd3e3... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fix tabs Commit: 15081cf00c5ff36d4e001c544ee2a523156be5be https://github.com/galaxyproject/galaxy/commit/15081cf00c5ff36d4e001c544ee2a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Validate custom fields Commit: ee8a887dcdd228b2e3c9c8e2526d42ce69a8f777 https://github.com/galaxyproject/galaxy/commit/ee8a887dcdd228b2e3c9c8e2526d4... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Use single api endpoint to build user information form with addresses Commit: bf3d447f0d9c26405344dcfe43763d0515df2efb https://github.com/galaxyproject/galaxy/commit/bf3d447f0d9c26405344dcfe43763... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Remove user info handler Commit: 6b9ab97f4aeadca9c2a637c8f346642facfbbdc2 https://github.com/galaxyproject/galaxy/commit/6b9ab97f4aeadca9c2a637c8f3466... Author: guerler <aysam.guerler@gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fix typo Commit: b737a2c6d791399bf59a8ef645851709ad5ad0ce https://github.com/galaxyproject/galaxy/commit/b737a2c6d791399bf59a8ef645851... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Fix password field type Commit: eb5eb99b8415d00eac466b53550563dcbb241aa8 https://github.com/galaxyproject/galaxy/commit/eb5eb99b8415d00eac466b5355056... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Add dictionary representation for checkboxes Commit: da95fb95479d9e69efe95198b271e5d9eb232ff2 https://github.com/galaxyproject/galaxy/commit/da95fb95479d9e69efe95198b271e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove commas Commit: ebaead0a890cfdcf3b17dc9be1f152045c16e74f https://github.com/galaxyproject/galaxy/commit/ebaead0a890cfdcf3b17dc9be1f15... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Add basic select field support for form builder Commit: ef362ef3c3c557d31aa62268cb5135da1f1e6b33 https://github.com/galaxyproject/galaxy/commit/ef362ef3c3c557d31aa62268cb513... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove space Commit: 57a93e70135f6f788d3a29620068a8b46ab10777 https://github.com/galaxyproject/galaxy/commit/57a93e70135f6f788d3a29620068a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove more spaces in widget handling Commit: dc01a1a51a609bf1f66a046960f324c8e98713c2 https://github.com/galaxyproject/galaxy/commit/dc01a1a51a609bf1f66a046960f32... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Fix field building style Commit: b31ab08f092ac80a1df2e04d63194eca139c0e58 https://github.com/galaxyproject/galaxy/commit/b31ab08f092ac80a1df2e04d63194... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused ftp field from basic form builder Commit: c5641cc87ac33b258849ead4b76a533947ad528e https://github.com/galaxyproject/galaxy/commit/c5641cc87ac33b258849ead4b76a5... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt 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-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M doc/schema_template.md M doc/source/project/issues.rst M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/data.py 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/managers/workflows.py M lib/galaxy/model/mapping.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M scripts/bootstrap_history.py 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-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-portlet.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/mvc/tool/tool-form-base.js M 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tools/extract/extract_genomic_dna.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/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/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py Log Message: ----------- Merge branch 'dev' into remove_mako_preferences_revision Commit: eadc6f26d27eb87011813e0ab9575fb42950fd6c https://github.com/galaxyproject/galaxy/commit/eadc6f26d27eb87011813e0ab9575... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused drilldown element from basic form builder Commit: 98d31d0adcf8e4a6c083a2d5edb8c5a7b756246e https://github.com/galaxyproject/galaxy/commit/98d31d0adcf8e4a6c083a2d5edb8c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused library parameter from basic form builder Commit: 30a8c0a2451b98289cb063861d455387df2a0c5a https://github.com/galaxyproject/galaxy/commit/30a8c0a2451b98289cb063861d455... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-user-information.js M static/maps/mvc/user/change-user-information.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-user-information.js Log Message: ----------- Remove form customization patches Commit: f353fe6e7ec3ad1390c6f9d42099733ad3b3ff84 https://github.com/galaxyproject/galaxy/commit/f353fe6e7ec3ad1390c6f9d420997... 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lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/runners/__init__.py A lib/galaxy/jobs/runners/godocker.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py 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/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/genomes.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/library_common.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M scripts/bootstrap_history.py M setup.cfg 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-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/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-modal.js M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py A test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/color_param.xml A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/workflows/test_run_parameters.py M tox.ini Log Message: ----------- Merge branch 'dev' into remove_mako_preferences_revision Commit: a06980c72fd5bf2ba2aa95ebd2dd81a56c361d9c https://github.com/galaxyproject/galaxy/commit/a06980c72fd5bf2ba2aa95ebd2dd8... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .ci/py3_sources.txt M .travis.yml M client/galaxy/scripts/mvc/form/form-section.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-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js R client/galaxy/scripts/mvc/user/api-keys.js A client/galaxy/scripts/mvc/user/change-api-key.js M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/change-password.js A client/galaxy/scripts/mvc/user/change-toolbox-filter.js A client/galaxy/scripts/mvc/user/change-user-information.js R client/galaxy/scripts/mvc/user/manage-user-information.js R client/galaxy/scripts/mvc/user/toolbox-filter.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M doc/parse_gx_xsd.py M doc/schema_template.md M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst A doc/source/admin/mulled_containers.rst M doc/source/api/guidelines.rst M doc/source/project/issues.rst M lib/galaxy/config.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M 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lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/genomes.py M lib/galaxy/webapps/galaxy/api/user_preferences.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/library_common.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M scripts/bootstrap_history.py M setup.cfg M static/maps/mvc/form/form-section.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-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-portlet.js.map A 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static/scripts/mvc/user/change-password.js A static/scripts/mvc/user/change-permissions.js A static/scripts/mvc/user/change-toolbox-filter.js A static/scripts/mvc/user/change-user-information.js A static/scripts/mvc/user/user-preferences.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/library/common/common.mako M templates/webapps/galaxy/workflow/run.mako R templates/webapps/galaxy/workflow/run_complete.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py A test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/tools/color_param.xml A test/functional/tools/metadata_column_names.xml A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/qunit/tests/form_tests.js M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_parameter_parsing.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_run_parameters.py M tools/data_source/data_source.py M tools/data_source/hbvar_filter.py M tools/data_source/microbial_import_code.py M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/secure_hash_message_digest.py M tools/filters/sff_extract.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/vcf_to_maf_customtrack.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/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/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge pull request #22 from guerler/remove_mako_preferences_revision Remove mako preferences revision Commit: 42d4a677bfc5457219d47c3fc051b01e14a4b0c3 https://github.com/galaxyproject/galaxy/commit/42d4a677bfc5457219d47c3fc051b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-api-key.js M client/galaxy/scripts/mvc/user/change-user-information.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/change-api-key.js.map M static/maps/mvc/user/change-user-information.js.map M static/maps/mvc/user/user-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/mvc/user/change-api-key.js M static/scripts/mvc/user/change-user-information.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Fix inconsistent naming Commit: 7273f43c0d211a6e11d8c0370bcb604b006e1026 https://github.com/galaxyproject/galaxy/commit/7273f43c0d211a6e11d8c0370bcb6... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-toolbox-filter.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/change-toolbox-filter.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/mvc/user/change-toolbox-filter.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Rename more endpoints and functions for consistency Commit: 6005ce9fd7bfa224f59b00f705018c93c1bd2601 https://github.com/galaxyproject/galaxy/commit/6005ce9fd7bfa224f59b00f705018... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix naming Commit: 35bca940bd35d8303df55a7e11c22107f95eb0a5 https://github.com/galaxyproject/galaxy/commit/35bca940bd35d8303df55a7e11c22... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-user-information.js M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/user/change-user-information.js.map M static/scripts/mvc/user/change-user-information.js Log Message: ----------- Ensure proper names for address fields Commit: e5f729b40bfa7534e7b535d3c205fff56693fc8b https://github.com/galaxyproject/galaxy/commit/e5f729b40bfa7534e7b535d3c205f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-user-information.js M static/maps/mvc/user/change-user-information.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-user-information.js Log Message: ----------- Add save icon Commit: f87047cc0c10e41c4ae7e892ecc4fa930f1f4d35 https://github.com/galaxyproject/galaxy/commit/f87047cc0c10e41c4ae7e892ecc4f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: R client/galaxy/scripts/mvc/user/add-edit-address.js M client/galaxy/scripts/mvc/user/change-api-key.js M static/maps/mvc/user/change-api-key.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unecessary view Commit: 1eeb21f344020b52e44008364b83e4f46d0cdcd0 https://github.com/galaxyproject/galaxy/commit/1eeb21f344020b52e44008364b83e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-api-key.js M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/change-permissions.js M client/galaxy/scripts/mvc/user/change-toolbox-filter.js M client/galaxy/scripts/mvc/user/change-user-information.js M static/maps/mvc/user/change-api-key.js.map M static/maps/mvc/user/change-communication.js.map M static/maps/mvc/user/change-password.js.map M static/maps/mvc/user/change-permissions.js.map M static/maps/mvc/user/change-toolbox-filter.js.map M static/maps/mvc/user/change-user-information.js.map M static/scripts/mvc/user/change-api-key.js M static/scripts/mvc/user/change-communication.js M static/scripts/mvc/user/change-password.js M static/scripts/mvc/user/change-permissions.js M static/scripts/mvc/user/change-toolbox-filter.js M static/scripts/mvc/user/change-user-information.js Log Message: ----------- Remove inconsistent function names Commit: fdff89596eeae060b626e1f376eead7e79437180 https://github.com/galaxyproject/galaxy/commit/fdff89596eeae060b626e1f376eea... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Revise main view handling Commit: e9a712c82d4ea007fea8ffbbbc9910a02e3c1714 https://github.com/galaxyproject/galaxy/commit/e9a712c82d4ea007fea8ffbbbc991... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Fix Commit: 64b1bd1e613470117e6310ce4b8cd9710f4dbb1b https://github.com/galaxyproject/galaxy/commit/64b1bd1e613470117e6310ce4b8cd... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-api-key.js M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/change-toolbox-filter.js M client/galaxy/scripts/mvc/user/change-user-information.js M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/change-api-key.js.map M static/maps/mvc/user/change-communication.js.map M static/maps/mvc/user/change-password.js.map M static/maps/mvc/user/change-toolbox-filter.js.map M static/maps/mvc/user/change-user-information.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-api-key.js M static/scripts/mvc/user/change-communication.js M static/scripts/mvc/user/change-password.js M static/scripts/mvc/user/change-toolbox-filter.js M static/scripts/mvc/user/change-user-information.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Remove redundant page loaders Commit: 5f20a2b1181c0bb0584979f212f6866cc8aaf87b https://github.com/galaxyproject/galaxy/commit/5f20a2b1181c0bb0584979f212f68... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Add missing options Commit: dd45dd6477963dd60067f31b20349885361c429b https://github.com/galaxyproject/galaxy/commit/dd45dd6477963dd60067f31b20349... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Add footer, directly call template helper for links Commit: 27216933f036fb603e65c2c1bf4dad0e30696836 https://github.com/galaxyproject/galaxy/commit/27216933f036fb603e65c2c1bf4da... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Use void href Commit: 783272416ed4416e57143843ad26eabf14c0cd35 https://github.com/galaxyproject/galaxy/commit/783272416ed4416e57143843ad26e... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: R client/galaxy/scripts/mvc/user/add-edit-address.js M client/galaxy/scripts/mvc/user/change-api-key.js M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/change-permissions.js M client/galaxy/scripts/mvc/user/change-toolbox-filter.js M client/galaxy/scripts/mvc/user/change-user-information.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/change-api-key.js.map M static/maps/mvc/user/change-communication.js.map M static/maps/mvc/user/change-password.js.map M static/maps/mvc/user/change-permissions.js.map M static/maps/mvc/user/change-toolbox-filter.js.map M static/maps/mvc/user/change-user-information.js.map M static/maps/mvc/user/user-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/mvc/user/change-api-key.js M static/scripts/mvc/user/change-communication.js M static/scripts/mvc/user/change-password.js M static/scripts/mvc/user/change-permissions.js M static/scripts/mvc/user/change-toolbox-filter.js M static/scripts/mvc/user/change-user-information.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Merge pull request #23 from guerler/remove_mako_preferences_revision More unifications and adjustments Commit: b248acd5c26e7cb7a69cad69a45a87743021da40 https://github.com/galaxyproject/galaxy/commit/b248acd5c26e7cb7a69cad69a45a8... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/change-communication.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-communication.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Iterate communications endpoint Commit: 95e39bbc591a1d3d0e475b99add64953c3f2a920 https://github.com/galaxyproject/galaxy/commit/95e39bbc591a1d3d0e475b99add64... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-api-key.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/change-api-key.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-api-key.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Fix api_key endpoint Commit: a7df03710a8ee6254f7867b134f39984746c4ab2 https://github.com/galaxyproject/galaxy/commit/a7df03710a8ee6254f7867b134f39... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-18 (Tue, 18 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/auth/__init__.py M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/change-password.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-password.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Align password endpoint Commit: ef6534285224e397772b91eb5aef9a0e70f2b387 https://github.com/galaxyproject/galaxy/commit/ef6534285224e397772b91eb5aef9... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-api-key.js M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/user/change-api-key.js.map M static/maps/mvc/user/change-communication.js.map M static/maps/mvc/user/change-password.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-api-key.js M static/scripts/mvc/user/change-communication.js M static/scripts/mvc/user/change-password.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Raise and display errors Commit: b4b779dd04f1d7286a2014ce206a27abe832c55f https://github.com/galaxyproject/galaxy/commit/b4b779dd04f1d7286a2014ce206a2... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-api-key.js A client/galaxy/scripts/mvc/user/change-information.js R client/galaxy/scripts/mvc/user/change-user-information.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/change-api-key.js.map A static/maps/mvc/user/change-information.js.map R static/maps/mvc/user/change-user-information.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-api-key.js A static/scripts/mvc/user/change-information.js R static/scripts/mvc/user/change-user-information.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Add packed files, fix general user information endpoints Commit: f6ecb45040c4e39c83ab4493a9c392b26b825adb https://github.com/galaxyproject/galaxy/commit/f6ecb45040c4e39c83ab4493a9c39... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Prepare permissions and filter endpoints Commit: d31998835ed543c4c528a11f8cdebebc3a67b098 https://github.com/galaxyproject/galaxy/commit/d31998835ed543c4c528a11f8cdeb... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-toolbox-filter.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/change-toolbox-filter.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-toolbox-filter.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Revise toolbox filter ui and api endpoint Commit: aa5ed9d2facc4a3549fd2eef55d19f0705b953cf https://github.com/galaxyproject/galaxy/commit/aa5ed9d2facc4a3549fd2eef55d19... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fix filter handling if current label is missing? Commit: 4fa9984eaa9b834fbf30209033e619dd28cddaf0 https://github.com/galaxyproject/galaxy/commit/4fa9984eaa9b834fbf30209033e61... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-api-key.js M client/galaxy/scripts/mvc/user/change-toolbox-filter.js M static/maps/mvc/user/change-api-key.js.map M static/maps/mvc/user/change-toolbox-filter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-api-key.js M static/scripts/mvc/user/change-toolbox-filter.js Log Message: ----------- Add icons for filter and api key forms Commit: 1305b42b498e79940a81f0c3329238723369516b https://github.com/galaxyproject/galaxy/commit/1305b42b498e79940a81f0c332923... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-10-19 (Wed, 19 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-api-key.js M client/galaxy/scripts/mvc/user/change-communication.js A client/galaxy/scripts/mvc/user/change-information.js M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/change-toolbox-filter.js R client/galaxy/scripts/mvc/user/change-user-information.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/auth/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/change-api-key.js.map M static/maps/mvc/user/change-communication.js.map A static/maps/mvc/user/change-information.js.map M static/maps/mvc/user/change-password.js.map M static/maps/mvc/user/change-toolbox-filter.js.map R static/maps/mvc/user/change-user-information.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-api-key.js M static/scripts/mvc/user/change-communication.js A static/scripts/mvc/user/change-information.js M static/scripts/mvc/user/change-password.js M static/scripts/mvc/user/change-toolbox-filter.js R static/scripts/mvc/user/change-user-information.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Merge pull request #24 from guerler/remove_mako_preferences_revision Remove mako preferences revision Commit: 3050e3db2ad39db7b9060ee167eb86775f66db64 https://github.com/galaxyproject/galaxy/commit/3050e3db2ad39db7b9060ee167eb8... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-permissions.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/user/change-permissions.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-permissions.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Permissions ui/endpoint revision Commit: f4e5819c68b6e6705fd64fa102a2ef2ec7fbe16d https://github.com/galaxyproject/galaxy/commit/f4e5819c68b6e6705fd64fa102a2e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-permissions.js M static/maps/mvc/user/change-permissions.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-permissions.js Log Message: ----------- Align permissions ui wrapper Commit: 36e8f967dfd1b970c3f3f303e4387c0d7ca29ed7 https://github.com/galaxyproject/galaxy/commit/36e8f967dfd1b970c3f3f303e4387... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/change-information.js M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/change-permissions.js M client/galaxy/scripts/mvc/user/change-toolbox-filter.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/user/change-communication.js.map M static/maps/mvc/user/change-permissions.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-communication.js M static/scripts/mvc/user/change-information.js M static/scripts/mvc/user/change-password.js M static/scripts/mvc/user/change-permissions.js M static/scripts/mvc/user/change-toolbox-filter.js Log Message: ----------- Use select2 fields for permission assignment Commit: 4dfb61033bad820a544500fc4ac6d9db7f2c5de9 https://github.com/galaxyproject/galaxy/commit/4dfb61033bad820a544500fc4ac6d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/change-permissions.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/user/change-communication.js.map M static/maps/mvc/user/change-password.js.map M static/maps/mvc/user/change-permissions.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-communication.js M static/scripts/mvc/user/change-password.js M static/scripts/mvc/user/change-permissions.js Log Message: ----------- Remove more unused code Commit: 0d09e6e7bc73f0206401e77ca97d65602423a300 https://github.com/galaxyproject/galaxy/commit/0d09e6e7bc73f0206401e77ca97d6... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-password.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/user/change-password.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-password.js Log Message: ----------- Align password form, build input dictionaries in the backend Commit: ee2b7c4159427f223fea0b9fd5b552bed5ce53ed https://github.com/galaxyproject/galaxy/commit/ee2b7c4159427f223fea0b9fd5b55... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/change-api-key.js M client/galaxy/scripts/mvc/user/change-communication.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/user/change-api-key.js.map M static/maps/mvc/user/change-communication.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/change-api-key.js M static/scripts/mvc/user/change-communication.js Log Message: ----------- Build all input elements used for user preferences in backend Commit: c408090c392f6fe4765a7e037ef3fe8cb1d58d08 https://github.com/galaxyproject/galaxy/commit/c408090c392f6fe4765a7e037ef3f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: R client/galaxy/scripts/mvc/user/change-api-key.js R client/galaxy/scripts/mvc/user/change-communication.js R client/galaxy/scripts/mvc/user/change-information.js R client/galaxy/scripts/mvc/user/change-password.js R client/galaxy/scripts/mvc/user/change-permissions.js R client/galaxy/scripts/mvc/user/change-toolbox-filter.js M client/galaxy/scripts/mvc/user/user-preferences.js R static/maps/mvc/user/change-api-key.js.map R static/maps/mvc/user/change-communication.js.map R static/maps/mvc/user/change-information.js.map R static/maps/mvc/user/change-password.js.map R static/maps/mvc/user/change-permissions.js.map R static/maps/mvc/user/change-toolbox-filter.js.map M static/maps/mvc/user/user-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 R static/scripts/mvc/user/change-api-key.js R static/scripts/mvc/user/change-communication.js R static/scripts/mvc/user/change-information.js R static/scripts/mvc/user/change-password.js R static/scripts/mvc/user/change-permissions.js R static/scripts/mvc/user/change-toolbox-filter.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Remove redundancies Commit: fdd8099c342c9298a0669b18e763b0ab8abd63b5 https://github.com/galaxyproject/galaxy/commit/fdd8099c342c9298a0669b18e763b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Use generic form to view all preference forms Commit: dd0951ecc39b577febaf75f3235af2b25fff53a7 https://github.com/galaxyproject/galaxy/commit/dd0951ecc39b577febaf75f3235af... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Use traditional ajax submission for arrays Commit: dfec446c4c6439bdd340ee38471e37a778503acf https://github.com/galaxyproject/galaxy/commit/dfec446c4c6439bdd340ee38471e3... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Add auto save feature for communication settings Commit: b6951841df274f455681cd4332f9bd64218fb9e6 https://github.com/galaxyproject/galaxy/commit/b6951841df274f455681cd4332f9b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Fix messages Commit: 3b164bd9f83c70ea798b1461ec0326f1149f6fa4 https://github.com/galaxyproject/galaxy/commit/3b164bd9f83c70ea798b1461ec032... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-20 (Thu, 20 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fix password message Commit: 30c2dcce923da2825f307faee9ccaecbbff16f71 https://github.com/galaxyproject/galaxy/commit/30c2dcce923da2825f307faee9cca... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fix permission api endpoint Commit: d70f5a4ff46163330db07d3bebd75952b522b604 https://github.com/galaxyproject/galaxy/commit/d70f5a4ff46163330db07d3bebd75... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Remove unnecessary line Commit: b792a6feb49c3f5071506b689d32c96b64328473 https://github.com/galaxyproject/galaxy/commit/b792a6feb49c3f5071506b689d32c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M Makefile M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/utils/utils.js M config/galaxy.ini.sample R config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/config/charts.xml M config/plugins/visualizations/charts/package.json R config/plugins/visualizations/charts/sample.txt R config/plugins/visualizations/charts/static/app.css R config/plugins/visualizations/charts/static/app.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js R 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static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/utils/utils.js M test/api/test_histories.py M test/api/test_libraries.py M test/api/test_workflow_extraction.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/driver_util.py A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/version_command.py A test/functional/tools/version_command_interpreter.xml A test/functional/tools/version_command_plain.xml A test/functional/tools/version_command_tool_dir.xml M test/unit/jobs/test_job_wrapper.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools_support.py M test/unit/unittest_utils/utility.py M tools/data_source/upload.py M tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py Log Message: ----------- Merge branch 'dev' into remove_mako_preferences_revision Commit: f88b72f3474b98877417a0af7c128bdc8b18c8c6 https://github.com/galaxyproject/galaxy/commit/f88b72f3474b98877417a0af7c128... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Show icons in selection list Commit: 88f6067364667c5a0ad7c3f1f9e20014be00d66c https://github.com/galaxyproject/galaxy/commit/88f6067364667c5a0ad7c3f1f9e20... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Prepare minor touch up of preference list rendering Commit: 897137d94994121ea5f12d1b94a5346e8293eb09 https://github.com/galaxyproject/galaxy/commit/897137d94994121ea5f12d1b94a53... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Change messages Commit: fe1676af01b2a5317faa0e0e29e16c8b0cb3a85a https://github.com/galaxyproject/galaxy/commit/fe1676af01b2a5317faa0e0e29e16... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-21 (Fri, 21 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Improve preference ui Commit: 02cf8326058ba920a676fb02b5d44fd35d5b4a69 https://github.com/galaxyproject/galaxy/commit/02cf8326058ba920a676fb02b5d44... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-22 (Sat, 22 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Prepare logout and openid handling Commit: 76f2287dbcf1ab553397bf3bf2170cc37c16b5ab https://github.com/galaxyproject/galaxy/commit/76f2287dbcf1ab553397bf3bf2170... 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tools/filters/gff/gff_filter_by_attribute.py M tools/stats/filtering.py Log Message: ----------- Merge pull request #25 from guerler/remove_mako_preferences_revision Remove unused code blocks, unify form handling, fix permissions endpoint Commit: 4b14761f7ca94aba77495be7975267a066cf472a https://github.com/galaxyproject/galaxy/commit/4b14761f7ca94aba77495be797526... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-22 (Sat, 22 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Add session logout feature Commit: 7a0850116f6001f589e295b0279ef37d95a196eb https://github.com/galaxyproject/galaxy/commit/7a0850116f6001f589e295b0279ef... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-22 (Sat, 22 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css Log Message: ----------- Move fixed css to styles, move footer to template Commit: 97890f68e96d58698a4561ae8c678202ac7ffc5a https://github.com/galaxyproject/galaxy/commit/97890f68e96d58698a4561ae8c678... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-22 (Sat, 22 Oct 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Use margins instead of fixed width for icons Commit: d8aea401bea1bfa8eced7b309a90647195aad296 https://github.com/galaxyproject/galaxy/commit/d8aea401bea1bfa8eced7b309a906... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-22 (Sat, 22 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Fix footer template Commit: 8b66acaf9a405d83a557e1bf0a33a326d017868d https://github.com/galaxyproject/galaxy/commit/8b66acaf9a405d83a557e1bf0a33a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Display mako based openid manager until grids have been revisited Commit: 2a16b25e83883ea7e4086994d02bf0cdc238f8f0 https://github.com/galaxyproject/galaxy/commit/2a16b25e83883ea7e4086994d02bf... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-10-25 (Tue, 25 Oct 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css Log Message: ----------- Merge pull request #26 from guerler/remove_mako_preferences_revision Add basic logout feature, link former openid manager page, remove inline styles Commit: c89e415f2cfabd41743b460d0551423f2c547fe5 https://github.com/galaxyproject/galaxy/commit/c89e415f2cfabd41743b460d05514... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-10-27 (Thu, 27 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.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.map Log Message: ----------- Adding insert address features to one point save user information api call Commit: e0a38a5bed8555f6ea18a00c7d0d7d15619fb90a https://github.com/galaxyproject/galaxy/commit/e0a38a5bed8555f6ea18a00c7d0d7... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Updating add address feature for client side validations and adding delete address feature Commit: 6e09d71ab04f5181a7fd1a65b6ba9303944611bf https://github.com/galaxyproject/galaxy/commit/6e09d71ab04f5181a7fd1a65b6ba9... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Adding edit feature for email and username along with client side validations for the Manage User Info form Commit: f593ad6c70bc891f84cdee1d481c3ebd142da9b4 https://github.com/galaxyproject/galaxy/commit/f593ad6c70bc891f84cdee1d481c3... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-10-30 (Sun, 30 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fixing bug with numbers in postal code and phone number Commit: c40be4f4c63ef99018ba899579e1776922f71662 https://github.com/galaxyproject/galaxy/commit/c40be4f4c63ef99018ba899579e17... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-10-30 (Sun, 30 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M Makefile M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.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 A client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css M config/tool_data_table_conf.xml.sample A doc/source/admin/images_webhooks/history-menu.png A doc/source/admin/images_webhooks/masthead.png A doc/source/admin/images_webhooks/masthead_trans_object.png A doc/source/admin/images_webhooks/tool.png A doc/source/admin/images_webhooks/workflow.png A doc/source/admin/webhooks.rst M doc/source/slideshow/architecture/images/galaxy_schema.png M lib/galaxy/app.py M lib/galaxy/auth/providers/alwaysreject.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/localdb.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/test.CEL M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/metrics/collectl/cli.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/collectl/subsystems.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/metrics/instrumenters/core.py M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/metrics/instrumenters/uname.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/godocker.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/runners/util/drmaa/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/properties.py M lib/galaxy/util/topsort.py M lib/galaxy/web/__init__.py M lib/galaxy/web/buildapp.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/middleware/error.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/webapps/galaxy/api/tours.py A lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/__init__.py M lib/galaxy/webapps/tool_shed/__init__.py M lib/galaxy/webapps/tool_shed/controllers/user.py A lib/galaxy/webhooks/__init__.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py M scripts/db_shell.py M static/maps/layout/menu.js.map M static/maps/mvc/history/options-menu.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 A static/maps/mvc/tool/tool-webhooks.js.map A static/maps/mvc/webhooks.js.map M static/maps/mvc/workflow/workflow-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/layout/menu.js M static/scripts/mvc/history/options-menu.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 A static/scripts/mvc/tool/tool-webhooks.js A static/scripts/mvc/webhooks.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/galaxy/workflow/index.mako R templates/webapps/galaxy/workflow/missing_tools.mako R templates/webapps/galaxy/workflow/myexp_export_content.mako R templates/webapps/galaxy/workflow/rename.mako M test/api/test_histories.py M test/api/test_libraries.py M test/unit/tools/test_tool_dependency_description.py Log Message: ----------- Merge with dev Commit: 14612f8a92560796bbfdb7fb35609169a00472b5 https://github.com/galaxyproject/galaxy/commit/14612f8a92560796bbfdb7fb35609... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-10-30 (Sun, 30 Oct 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Updating conditions for communication settings for new user preferences Commit: fb75c23f0d8d5a97eb49f8701da333d14a75ea36 https://github.com/galaxyproject/galaxy/commit/fb75c23f0d8d5a97eb49f8701da33... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-10-31 (Mon, 31 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Adding more client side validations for Change password feature and code comments and a bit of code cleanup Commit: 8a8ca4e5918b9e7f4a7a92562d8e6157013e760a https://github.com/galaxyproject/galaxy/commit/8a8ca4e5918b9e7f4a7a92562d8e6... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Updating the User information add and edit feature for Form Definitions Commit: fd6bf953278f67cfebda46ffd3e04ad8b6026ecc https://github.com/galaxyproject/galaxy/commit/fd6bf953278f67cfebda46ffd3e04... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-11-01 (Tue, 01 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/user/user-preferences.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/page.js Log Message: ----------- Adding config for enabling the new user preferences UI Commit: c828ec65f8a927875d7194a49ac26b4d5348e69c https://github.com/galaxyproject/galaxy/commit/c828ec65f8a927875d7194a49ac26... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fixing styling errors Commit: f04ea9f8db2dcfbe0f5c94fedcbc90b70aa237a4 https://github.com/galaxyproject/galaxy/commit/f04ea9f8db2dcfbe0f5c94fedcbc9... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Changing the config variable name for toggling new user preferences Commit: a22cd27ced212ae8343f3c43c765f57c1cb2dfb3 https://github.com/galaxyproject/galaxy/commit/a22cd27ced212ae8343f3c43c765f... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Commenting variables in config file Commit: 8f49202778c72389d567ef840df518e473b0e4f3 https://github.com/galaxyproject/galaxy/commit/8f49202778c72389d567ef840df51... Author: anuprulez <anup.rulez@gmail.com> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M Makefile M client/galaxy/scripts/mvc/library/library-dataset-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/ui/ui-tabs.js A client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/client/app.css M config/plugins/visualizations/charts/static/client/views/editor.js R config/plugins/visualizations/charts/static/client/views/types.js M doc/Makefile M doc/parse_gx_xsd.py M doc/patch.py M doc/schema_template.md M doc/source/admin/conda_faq.rst M doc/source/admin/interactive_environments.rst R doc/source/admin/interactive_environments_success.png M doc/source/admin/mulled_containers.rst M doc/source/conf.py M doc/source/dev/build_a_job_runner.rst M doc/source/dev/index.rst A doc/source/dev/inherit.png A doc/source/dev/interactive_environments_success.png A doc/source/dev/queue.png A doc/source/dev/queue_b.png A doc/source/dev/runner_diag.png M doc/source/index.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.linters.rst M doc/source/lib/galaxy.tools.parameters.rst R doc/source/lib/galaxy.util.backports.importlib.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/managers/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/simplegraph.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/bootstrap_history.py R scripts/bootstrap_history_announce_template.rst M scripts/galaxy-main M static/maps/mvc/library/library-dataset-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/ui/ui-tabs.js.map A static/maps/mvc/ui/ui-thumbnails.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/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-tabs.js A static/scripts/mvc/ui/ui-thumbnails.js M static/style/blue/base.css M templates/user/index.mako M test/qunit/package.json M test/qunit/tests/ui_tests.js Log Message: ----------- Merge with dev Commit: aece1f4870ea3468cf3d78a8234d8cb8c96b4f4a https://github.com/galaxyproject/galaxy/commit/aece1f4870ea3468cf3d78a8234d8... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unused submit field special case handling Commit: caf8eb5d4c98333f6b1ef73586d2ae17b6fda5f0 https://github.com/galaxyproject/galaxy/commit/caf8eb5d4c98333f6b1ef73586d2a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix spaces layout menu Commit: 962e4f3130cd883af928bb168e7c11cacbfaaa24 https://github.com/galaxyproject/galaxy/commit/962e4f3130cd883af928bb168e7c1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use list to detect acceptable values for communication settings Commit: 2ed916390162689900f79e8026ccca82c9a283d9 https://github.com/galaxyproject/galaxy/commit/2ed916390162689900f79e8026ccc... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Undo new line in form input wrapper Commit: eff7ba7b6d3c910faff79efe893b1d1fd0acae81 https://github.com/galaxyproject/galaxy/commit/eff7ba7b6d3c910faff79efe893b1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js Log Message: ----------- Undo new line in form parameter factory Commit: 849d54f20e541e5bfdc8e9157204634ef7df6a56 https://github.com/galaxyproject/galaxy/commit/849d54f20e541e5bfdc8e91572046... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove new line form section wrapper, repack scripts Commit: 5c83dbebc46a5726214e730014ba2b5e24ce48d5 https://github.com/galaxyproject/galaxy/commit/5c83dbebc46a5726214e730014ba2... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- These styles are not used Commit: 6a4e175c03960393712167a6887c4e8f21d650a4 https://github.com/galaxyproject/galaxy/commit/6a4e175c03960393712167a6887c4... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Restore galaxy.ini.sample Commit: a561368195e696de8239bcea4aba9472ef3965b2 https://github.com/galaxyproject/galaxy/commit/a561368195e696de8239bcea4aba9... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add new user preference activation flag to galaxy.ini.sample Commit: 55d1fae34362dac33d6d42b49f192ca7b32cb2ff https://github.com/galaxyproject/galaxy/commit/55d1fae34362dac33d6d42b49f192... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove unused backend routes Commit: d2bbed967b81ff663414b505323222db673882eb https://github.com/galaxyproject/galaxy/commit/d2bbed967b81ff663414b50532322... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fix underscores for private functions in user_preferences api endpoints Commit: bbc5c2afb501fec6bc43dfeca60a21ce8a1826e7 https://github.com/galaxyproject/galaxy/commit/bbc5c2afb501fec6bc43dfeca60a2... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Restore user preference api Commit: 3a53ae41efdfa671689fe9071fda68084e67ee1a https://github.com/galaxyproject/galaxy/commit/3a53ae41efdfa671689fe9071fda6... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Move new private functions below parent caller, fix indent, remove spaces Commit: 6e37b1f0fd84981555927bde0256a9e7c326d7d7 https://github.com/galaxyproject/galaxy/commit/6e37b1f0fd84981555927bde0256a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Remove unused variables and libraries, fix lint Commit: 301c5ec637d8adb6cfa88bd9f728a623ccc06310 https://github.com/galaxyproject/galaxy/commit/301c5ec637d8adb6cfa88bd9f728a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Apply autopep8, fix lint Commit: d5804d6ba7c555ea9d984dea2fb5b87f62c02311 https://github.com/galaxyproject/galaxy/commit/d5804d6ba7c555ea9d984dea2fb5b... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: 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 M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/style/less/base.less M config/galaxy.ini.sample M lib/galaxy/model/__init__.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py 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 #28 from guerler/remove_mako_user_pref_000 Restore changes Commit: eb178129c102b4645ba76071bd528a683a176242 https://github.com/galaxyproject/galaxy/commit/eb178129c102b4645ba76071bd528... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fix add address caller name Commit: 25a8edd66c6c999451c97535d2508b405764f7bb https://github.com/galaxyproject/galaxy/commit/25a8edd66c6c999451c97535d2508... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Revise communication preference check Commit: ec63866deeac2c4c5139078c2db6d8dca5312649 https://github.com/galaxyproject/galaxy/commit/ec63866deeac2c4c5139078c2db6d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M run_tool_shed.sh Log Message: ----------- Merge branch 'dev' into remove_mako_user_pref_000 Commit: f00cd6af2e53cbf56cc08dee26df72f40023338b https://github.com/galaxyproject/galaxy/commit/f00cd6af2e53cbf56cc08dee26df7... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Reinsert space to sample config Commit: b37ac03cec65f479fd2d74678dacad0c92b914cc https://github.com/galaxyproject/galaxy/commit/b37ac03cec65f479fd2d74678daca... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M static/maps/layout/menu.js.map M static/maps/mvc/form/form-parameters.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/form/form-parameters.js Log Message: ----------- Fix parameter factory Commit: 6b7936cbf4744c97034ecd5f96e082d6935e6c49 https://github.com/galaxyproject/galaxy/commit/6b7936cbf4744c97034ecd5f96e08... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Get user in set information through same function like all other endpoints Commit: 6f6cc9041143b96249df7d0a71e826ccdcfd0980 https://github.com/galaxyproject/galaxy/commit/6f6cc9041143b96249df7d0a71e82... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Directly import MessageException into user preferences api Commit: 17ae8cdcc0e9b7f7283fbbd7f5316259400a71ee https://github.com/galaxyproject/galaxy/commit/17ae8cdcc0e9b7f7283fbbd7f5316... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Add encoded user form id to dict, add to form select, resolve initial value Commit: 2e97c7919d045717a922b6e97d68b24e1e3bb3c5 https://github.com/galaxyproject/galaxy/commit/2e97c7919d045717a922b6e97d68b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fix user info form generation and stored value parsing Commit: a9a0d8fab0002050f7e7a505f614f81eae5ae74b https://github.com/galaxyproject/galaxy/commit/a9a0d8fab0002050f7e7a505f614f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Parse field label if available Commit: 928611f4cf69c95c669e1aceaa0f4b9f114dd21d https://github.com/galaxyproject/galaxy/commit/928611f4cf69c95c669e1aceaa0f4... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Validate and update username and email first, revise error handling Commit: 6c8ff8ce30642dbc4015dc061e078441baa38d61 https://github.com/galaxyproject/galaxy/commit/6c8ff8ce30642dbc4015dc061e078... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Revise address handling, use regex, temporary disable validation and user info forms saving Commit: d7d6c743e8dc8199a9f481d0ba046afee18723b7 https://github.com/galaxyproject/galaxy/commit/d7d6c743e8dc8199a9f481d0ba046... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Ensure storing address attributes as text value Commit: be80dddf6cc680124cc964d981ebd27ffcca3540 https://github.com/galaxyproject/galaxy/commit/be80dddf6cc680124cc964d981ebd... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Delete previous addresses for now Commit: 82703e35f6e936c977662483e122a613df8fd275 https://github.com/galaxyproject/galaxy/commit/82703e35f6e936c977662483e122a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Remove duplicate flush Commit: 62d1fe750987f9044565e73b23e90713582b080e https://github.com/galaxyproject/galaxy/commit/62d1fe750987f9044565e73b23e90... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Revise user info form saving Commit: ee54415e72ae74692cb1a07e1cd6fee7dd15cd05 https://github.com/galaxyproject/galaxy/commit/ee54415e72ae74692cb1a07e1cd6f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Move prefix constant out of loop Commit: bbec45c70652bb58919b12ebce96bbf7d54e645e https://github.com/galaxyproject/galaxy/commit/bbec45c70652bb58919b12ebce96b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Properly update user information forms Commit: eda1fe6fb73cc393fbf9353067181ec539e44222 https://github.com/galaxyproject/galaxy/commit/eda1fe6fb73cc393fbf9353067181... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Fix boolean value handling in form builder Commit: 0045e8cbc8fb2c488583a6fb27fba3a6186484c1 https://github.com/galaxyproject/galaxy/commit/0045e8cbc8fb2c488583a6fb27fba... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Add whitespaces, fix imports Commit: 363e136e8c37bae91b4eaac65d3c032360def7c9 https://github.com/galaxyproject/galaxy/commit/363e136e8c37bae91b4eaac65d3c0... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Update existing user addresses instead of recreating them Commit: f52f953b01925ffc91a96b97f9b24b0428bfc371 https://github.com/galaxyproject/galaxy/commit/f52f953b01925ffc91a96b97f9b24... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Rename short_desc to desc to align with stored address attribute Commit: 0e25f118dd69febb9dcc4a6b5c7b91e7085d0284 https://github.com/galaxyproject/galaxy/commit/0e25f118dd69febb9dcc4a6b5c7b9... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Show preference return and save buttons as portlet operations Commit: 0d7e074bcf47cdf95b17588e30f5fe7e556983ac https://github.com/galaxyproject/galaxy/commit/0d7e074bcf47cdf95b17588e30f5f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Unify value handling for form parameters in form builder Commit: f17e335407599f40b40fce97be0a9fcc57e91b65 https://github.com/galaxyproject/galaxy/commit/f17e335407599f40b40fce97be0a9... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Parse optional security encoder to field level Commit: 22763844a67f332ae739ae536b8fe301ffb80b56 https://github.com/galaxyproject/galaxy/commit/22763844a67f332ae739ae536b8fe... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Handle help text and optional flags specified through form builder ui Commit: b1da023f3205f8228170e6972373e657a6dda0c6 https://github.com/galaxyproject/galaxy/commit/b1da023f3205f8228170e6972373e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Add default value handling for form field values not stored in user values Commit: 021b4d6e7341e55d01a52da4d516d4e4d598422f https://github.com/galaxyproject/galaxy/commit/021b4d6e7341e55d01a52da4d516d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Allow to distinguish between request methods within small api functions Commit: e649bd01c94a10bedb2ea499e859f20b1f66231d https://github.com/galaxyproject/galaxy/commit/e649bd01c94a10bedb2ea499e859f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fix lint, rename info form Commit: 29b5f33742c7ca0b09fe3690b8242217a257a525 https://github.com/galaxyproject/galaxy/commit/29b5f33742c7ca0b09fe3690b8242... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Insert basic address validation, reduce validation rules Commit: 305f8d19639b6c344c01762dfe6c6a681e4c7d14 https://github.com/galaxyproject/galaxy/commit/305f8d19639b6c344c01762dfe6c6... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Use payload instead of kwd Commit: f58ff7b1c6e28e73d16180fc80508f3f28e06c1f https://github.com/galaxyproject/galaxy/commit/f58ff7b1c6e28e73d16180fc80508... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Specify json as request content type Commit: 37fffc16674efa9c2ab123c6ebc6054d5b09b001 https://github.com/galaxyproject/galaxy/commit/37fffc16674efa9c2ab123c6ebc60... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Remove debug statement Commit: 0810cd26de20ad4932332a7676414db5531ffe12 https://github.com/galaxyproject/galaxy/commit/0810cd26de20ad4932332a7676414... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Remove unused traditional flag from ajax put request Commit: 5683edd76443987643dce013ce16c333548c7cf0 https://github.com/galaxyproject/galaxy/commit/5683edd76443987643dce013ce16c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Loop once through custom forms Commit: 0b2ba5017b8ab731170909e601b17d8910030350 https://github.com/galaxyproject/galaxy/commit/0b2ba5017b8ab731170909e601b17... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Remove unused custom address validation routine, validate through fields() instead Commit: dee59fc8b59ad75fccb874a7d36f171f9ec4dd93 https://github.com/galaxyproject/galaxy/commit/dee59fc8b59ad75fccb874a7d36f1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Remove unused import Commit: 433ac08dafe4de7ee60940477a72f983be3158e7 https://github.com/galaxyproject/galaxy/commit/433ac08dafe4de7ee60940477a72f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/form_builder.py Log Message: ----------- Fix workflow and history selection fields Commit: 7a6cd700597c873a6cae59b1021b0c85ae9acc8f https://github.com/galaxyproject/galaxy/commit/7a6cd700597c873a6cae59b1021b0... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove redundant optional handling for history fields Commit: 826f006b48aa07e4450779539ea5b042a3c837b4 https://github.com/galaxyproject/galaxy/commit/826f006b48aa07e4450779539ea5b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/web/form_builder.py Log Message: ----------- Remove unused get_display_text caller Commit: 56844f52bb76d8be4825f4368fd5e2bc66475745 https://github.com/galaxyproject/galaxy/commit/56844f52bb76d8be4825f4368fd5e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Catch resource request errors when accessing form data Commit: 44cd6ef738703454755044cd68abb2ac2a492023 https://github.com/galaxyproject/galaxy/commit/44cd6ef738703454755044cd68abb... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Show new preference form instead of old one if clicked on and active Commit: 8004fea3fc7f5feb70d71431f43babfc7dae6cc8 https://github.com/galaxyproject/galaxy/commit/8004fea3fc7f5feb70d71431f43ba... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Add dots to complete notification sentences for email and public name validation Commit: e40c2554a5efcbe937f7e3b6d06733a002c4b32f https://github.com/galaxyproject/galaxy/commit/e40c2554a5efcbe937f7e3b6d0673... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js R lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Move preference handlers to users endpoint Commit: 2675bc17d266a57abd80fdf85db4f0a2a36165a5 https://github.com/galaxyproject/galaxy/commit/2675bc17d266a57abd80fdf85db4f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Adjust endpoint headers, merge api_key handler Commit: 00ae244b6ab2bcad1b71bd40f8e43da750a6ba8a https://github.com/galaxyproject/galaxy/commit/00ae244b6ab2bcad1b71bd40f8e43... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/users.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Use regular show endpoint to access quota details Commit: 5f6efbec861eb1b5ddf084d7a70b182148fbe042 https://github.com/galaxyproject/galaxy/commit/5f6efbec861eb1b5ddf084d7a70b1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Fix quota helper Commit: 38d2ab3cd5806edc1e053bbcc6d36e501bf74dd8 https://github.com/galaxyproject/galaxy/commit/38d2ab3cd5806edc1e053bbcc6d36... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/user/user-preferences.js M config/galaxy.ini.sample M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/webapp.py R lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M run_tool_shed.sh M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Merge pull request #29 from guerler/remove_mako_user_pref_000 Fixes add address caller, parameter factory and revises preferences check Commit: e4a97c88d04894110d03881316573367b183cba6 https://github.com/galaxyproject/galaxy/commit/e4a97c88d04894110d03881316573... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Remove unused dict values from get_information endpoint Commit: 46acf5c7bd42d2d58d4494d8adcc0325e4e9e9d0 https://github.com/galaxyproject/galaxy/commit/46acf5c7bd42d2d58d4494d8adcc0... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-08 (Tue, 08 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Add missing sql component Commit: 3b6bf1ab6094a177eea917edb98b53b6d64a060d https://github.com/galaxyproject/galaxy/commit/3b6bf1ab6094a177eea917edb98b5... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #30 from guerler/remove_mako_user_pref_000 Remove unused library, add missing sql component Commit: eed7f2ce086460cc29b0f89def0986d727eec15a https://github.com/galaxyproject/galaxy/commit/eed7f2ce086460cc29b0f89def098... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Rename to Preferences Commit: af2b31e1fbc7ea2383e9f1ad3ea9d44db48bc41c https://github.com/galaxyproject/galaxy/commit/af2b31e1fbc7ea2383e9f1ad3ea9d... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #31 from guerler/remove_mako_user_pref_000 Restore menu item label Commit: 9914130fb4d5bc33b70d9e241c08421dc0acc5c0 https://github.com/galaxyproject/galaxy/commit/9914130fb4d5bc33b70d9e241c084... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Remove logout endpoint from api, redirect to controller endpoint instead Commit: d52f4fd52374def376367c3141f912a3e0303d94 https://github.com/galaxyproject/galaxy/commit/d52f4fd52374def376367c3141f91... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use separate endpoints instead of identifying the request type Commit: 364f57d06d0910d593a96d1748a26cc507d88e4b https://github.com/galaxyproject/galaxy/commit/364f57d06d0910d593a96d1748a26... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M CONTRIBUTORS.md M Makefile M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/tool_data_table_conf.xml.sample M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/Makefile M doc/parse_gx_xsd.py M doc/patch.py M doc/source/admin/interactive_environments.rst M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M 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scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/filter_failed_datasets_from_collection.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/auth/pam_auth_helper.py M scripts/build_toolbox.py M scripts/build_universe_config.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.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/communication/communication_server.py M scripts/create_db.py 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/external_chown_script.py M scripts/extract_dataset_part.py M scripts/extract_toolbox_sections.py M scripts/functional_tests.py M scripts/grt.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/slideshow/build_slideshow.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/add_repository_registry_entry.py M scripts/tool_shed/api/create_categories.py M scripts/tool_shed/api/create_users.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/api/import_capsule.py M scripts/tool_shed/api/remove_repository_registry_entry.py M scripts/tool_shed/api/reset_metadata_on_repositories.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py M scripts/tool_shed/clean_up_tool_dependency_directory.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tool/tool-form-workflow.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/dataset/dataset-li-edit.js M static/scripts/mvc/tool/tool-form-workflow.js M static/style/blue/base.css M static/welcome.html.sample M templates/webapps/galaxy/workflow/editor.mako A test-data/bam_from_sam.bam A test-data/sam_with_header.sam M test/api/test_workflows.py M test/api/workflows_format_2/main.py M test/base/api.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/interactor.py M test/base/twilltestcase.py M test/functional/test_library_templates.py A test/functional/tools/sam_to_bam.xml M test/manual/workflows_scaling.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.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/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.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 test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample M tools/data_source/data_source.py M tools/data_source/genbank.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_fasta.py M tools/filters/bed_to_gff_converter.py M tools/filters/catWrapper.py M tools/filters/convert_characters.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py 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/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.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/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' into remove_mako_user_pref Commit: 51972a9916e8b113399bbcbb074802de8023d59f https://github.com/galaxyproject/galaxy/commit/51972a9916e8b113399bbcbb07480... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Use inputs tag to indicate that the response is consistently for input handling Commit: eabc648b9cda89df5d52071623613857b2d40f04 https://github.com/galaxyproject/galaxy/commit/eabc648b9cda89df5d52071623613... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix api_key and toolbox filter endpoints Commit: 1f3f4be1caa56a2782a18c397c7cdb961065bd91 https://github.com/galaxyproject/galaxy/commit/1f3f4be1caa56a2782a18c397c7cd... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Fix lint Commit: 9653d148a22f5bd537d7339ab1006afd99243765 https://github.com/galaxyproject/galaxy/commit/9653d148a22f5bd537d7339ab1006... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix routing declaration style Commit: b02eb9e7e0c2d5dfa35a72ee13e598dba74297fe https://github.com/galaxyproject/galaxy/commit/b02eb9e7e0c2d5dfa35a72ee13e59... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M test/api/test_users.py Log Message: ----------- Add basic information test case, fix validation Commit: 998fd3036d9887ece8aaa651c272d2360f5f9f85 https://github.com/galaxyproject/galaxy/commit/998fd3036d9887ece8aaa651c272d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M test/api/test_users.py Log Message: ----------- Add test case to add address to user information Commit: 2cf91d4b1554b2fc22866e887cd6f3106d0e7230 https://github.com/galaxyproject/galaxy/commit/2cf91d4b1554b2fc22866e887cd6f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M test/api/test_users.py Log Message: ----------- Add test case for communication server settings Commit: daa19009296db8fba3337df76d6e2fba59b4ba06 https://github.com/galaxyproject/galaxy/commit/daa19009296db8fba3337df76d6e2... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Fix link to user preferences when library view is shown Commit: 564a7236cacf06841a02d7ffdf607392ac52925c https://github.com/galaxyproject/galaxy/commit/564a7236cacf06841a02d7ffdf607... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Remove api keys from user dropdown Commit: a4ae3c953bf8b0778f32fe9b3cd36ead7db7a03d https://github.com/galaxyproject/galaxy/commit/a4ae3c953bf8b0778f32fe9b3cd36... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Only show communication settings if communication host has been specified Commit: cfe0305f39d183952206b2f76da9ded322d946aa https://github.com/galaxyproject/galaxy/commit/cfe0305f39d183952206b2f76da9d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Fix missing user tool filter handling Commit: 15668f2ff37d1f25d665c60f01b18d39273d90d1 https://github.com/galaxyproject/galaxy/commit/15668f2ff37d1f25d665c60f01b18... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M lib/galaxy/managers/configuration.py Log Message: ----------- Fix tabs in configuration handler Commit: 5fe064d4c88d6657f65fc10feb06cf05f8515c3b https://github.com/galaxyproject/galaxy/commit/5fe064d4c88d6657f65fc10feb06c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Mention history in permissions link Commit: 2366eda8f3bebe9e0f71e5deea0e1f034e054796 https://github.com/galaxyproject/galaxy/commit/2366eda8f3bebe9e0f71e5deea0e1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Use person icon for user information and chat bubbles for communication settings Commit: 2108043ded3e631b929d2be585344062bbdbdd2f https://github.com/galaxyproject/galaxy/commit/2108043ded3e631b929d2be585344... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Use current user icon for now, new user icon will be available in fa 4.7 Commit: f960be7b43e1b00b95f92218a7afc54e0ae48e68 https://github.com/galaxyproject/galaxy/commit/f960be7b43e1b00b95f92218a7afc... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/layout/menu.js.map M static/maps/mvc/user/user-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/layout/menu.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Route user preferences analogous to tours Commit: bb33e8959fca912912f7b7b988c949c3d83e2be1 https://github.com/galaxyproject/galaxy/commit/bb33e8959fca912912f7b7b988c94... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Align spacing, code style alignment Commit: d4760ed2105d0f3743569458416cfd5e3ab41da3 https://github.com/galaxyproject/galaxy/commit/d4760ed2105d0f3743569458416cf... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M static/maps/layout/menu.js.map M static/scripts/layout/menu.js Log Message: ----------- Enable new user preference ui by default Commit: a40d5ebe69cbe79c8486a26e9a1ef99291f83b59 https://github.com/galaxyproject/galaxy/commit/a40d5ebe69cbe79c8486a26e9a1ef... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py R templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Remove manage info endpoint from controller Commit: 14e635aaee2699cb395443d802dede15d6f25240 https://github.com/galaxyproject/galaxy/commit/14e635aaee2699cb395443d802ded... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py R templates/user/change_password.mako R templates/user/communication_settings.mako R templates/user/edit_address.mako R templates/user/new_address.mako R templates/user/permissions.mako R templates/user/toolbox_filters.mako R templates/user/username.mako A templates/webapps/tool_shed/user/change_password.mako A templates/webapps/tool_shed/user/username.mako Log Message: ----------- Remove unused controller endpoints, move makos used by toolshed Commit: 6cb1a2c39e40a752e756e355beb102bc398d692e https://github.com/galaxyproject/galaxy/commit/6cb1a2c39e40a752e756e355beb10... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py R templates/webapps/galaxy/user/api_keys.mako A templates/webapps/tool_shed/user/api_keys.mako Log Message: ----------- Move api_keys mako and endpoint to toolshed Commit: 98c5a59a182a2f64f6bb240863748144ad3e77bc https://github.com/galaxyproject/galaxy/commit/98c5a59a182a2f64f6bb240863748... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tools.js M config/galaxy.ini.sample M config/plugins/tours/core.galaxy_ui.yaml M lib/galaxy/config.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/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/tool_shed/galaxy_install/install_manager.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tools.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 M static/scripts/mvc/tool/tools.js M templates/webapps/galaxy/user/list_users.mako Log Message: ----------- Merge branch 'dev' into remove_mako_user_pref Commit: 12623ac1a4a746d204320a649f2b5ebe673507f1 https://github.com/galaxyproject/galaxy/commit/12623ac1a4a746d204320a649f2b5... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py Log Message: ----------- Fix lint Commit: b38c6afefebd6d0a9bb99005efb1a78a5083a585 https://github.com/galaxyproject/galaxy/commit/b38c6afefebd6d0a9bb99005efb1a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js 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 Log Message: ----------- Merge branch 'dev' into remove_mako_user_pref Commit: 20d45ee62c73d25b1757e9ab7a6cba5f122cfd88 https://github.com/galaxyproject/galaxy/commit/20d45ee62c73d25b1757e9ab7a6cb... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Temporary routing, not best practice Commit: 16a60538d978ae196121f6fe474a97ae10520309 https://github.com/galaxyproject/galaxy/commit/16a60538d978ae196121f6fe474a9... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/layout/menu.js.map M static/maps/mvc/user/user-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/layout/menu.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Fix history back, and forward Commit: 416b94f1953f04147033bdd470b201c9e08114f8 https://github.com/galaxyproject/galaxy/commit/416b94f1953f04147033bdd470b20... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Avoid using navigate, reload page until routing has been established Commit: 6e1b26115ed6879294f011a12435a977d66e3e44 https://github.com/galaxyproject/galaxy/commit/6e1b26115ed6879294f011a12435a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/managers/configuration.py M static/maps/mvc/user/user-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.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Hide communication server form if disabled Commit: 7afc7ac6eb1eddd0a381042633ff848f43e2abdb https://github.com/galaxyproject/galaxy/commit/7afc7ac6eb1eddd0a381042633ff8... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M templates/user/register.mako Log Message: ----------- Do not edit custom widgets when registering new user Commit: 0f6013c7286ff73761577944e96a8d555e94962b https://github.com/galaxyproject/galaxy/commit/0f6013c7286ff73761577944e96a8... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Advanced user preferences based on custom settings can be set after registration, using the new form Commit: a4b70aaf92dfa560cd41aca876c95959763472f9 https://github.com/galaxyproject/galaxy/commit/a4b70aaf92dfa560cd41aca876c95... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py Log Message: ----------- Fix lint Commit: e4222b9ae6676c80d22551dc61c3ba14ce2cb315 https://github.com/galaxyproject/galaxy/commit/e4222b9ae6676c80d22551dc61c3b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-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.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Drop default tooltip Commit: 57fb15984c9038427abd05d801d59e21e296dd6d https://github.com/galaxyproject/galaxy/commit/57fb15984c9038427abd05d801d59... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Emphasize that users need certain permissions to access the history Commit: f1e20b64f5c223e90a164cb0f4d07667f7aec340 https://github.com/galaxyproject/galaxy/commit/f1e20b64f5c223e90a164cb0f4d07... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py A templates/webapps/tool_shed/user/index.mako Log Message: ----------- Move old user preference template to toolshed directory Commit: 7f3c7b0e2342719526ca9fd4e4cb2d7b2889735f https://github.com/galaxyproject/galaxy/commit/7f3c7b0e2342719526ca9fd4e4cb2... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Undo history permission hint Commit: e0a4171113c983fd9d6238a2d4922f69dd4cd8b8 https://github.com/galaxyproject/galaxy/commit/e0a4171113c983fd9d6238a2d4922... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/user/user-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.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Attempt to rephrase user preference description for history permissions Commit: e6c1e8e4e830f48203e0d26ed848a0d27860a7c9 https://github.com/galaxyproject/galaxy/commit/e6c1e8e4e830f48203e0d26ed848a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-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.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Rename label for history permissions Commit: b165757288f0d8d277f8e246601eb83aea3c1c8a https://github.com/galaxyproject/galaxy/commit/b165757288f0d8d277f8e246601eb... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-misc.js A client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/controllers/user.py M static/maps/layout/menu.js.map M static/maps/layout/page.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/ui/ui-misc.js.map A static/maps/mvc/user/user-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/layout/menu.js M static/scripts/layout/page.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/ui/ui-misc.js A static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css R templates/user/change_password.mako R templates/user/communication_settings.mako R templates/user/edit_address.mako R templates/user/new_address.mako R templates/user/permissions.mako M templates/user/register.mako R templates/user/toolbox_filters.mako R templates/user/username.mako R templates/webapps/galaxy/user/api_keys.mako R templates/webapps/galaxy/user/manage_info.mako A templates/webapps/tool_shed/user/api_keys.mako A templates/webapps/tool_shed/user/change_password.mako A templates/webapps/tool_shed/user/index.mako A templates/webapps/tool_shed/user/username.mako M test/api/test_users.py Log Message: ----------- Merge pull request #3118 from bgruening/remove_mako_user_pref New User Preferences User Interface Compare: https://github.com/galaxyproject/galaxy/compare/fd0a52a9a9ae...b165757288f0