February 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 2805fe: Decrease limits for workshop
by GitHub 23 Feb '17

23 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2805fee3209d2e9452e4d0fb95fd39bd11b848da https://github.com/galaxyproject/usegalaxy-playbook/commit/2805fee3209d2e94… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Decrease limits for workshop

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[galaxyproject/galaxy] 2cfd83: Reduce indentation from 6 to 4 whitespaces
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2cfd833e457f513d5e83f9a7f8ca77f96741942e https://github.com/galaxyproject/galaxy/commit/2cfd833e457f513d5e83f9a7f8ca… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Reduce indentation from 6 to 4 whitespaces Fix a TODO Remove funny but unused sub-sub-items. Commit: 647fcad924a969ae35299b7ef6e60672ddb7a6a0 https://github.com/galaxyproject/galaxy/commit/647fcad924a969ae35299b7ef6e6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3653 from nsoranzo/fix_bootstrap_history Fix RELEASE_ISSUE_TEMPLATE in bootstrap_history.py Compare: https://github.com/galaxyproject/galaxy/compare/18e514d9b72b...647fcad924a9

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[galaxyproject/galaxy] 0da2ac: Rebuild client -- bad merge previously.
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0da2ac78e6ac5583271881dabd4b4d0a3bcf59cd https://github.com/galaxyproject/galaxy/commit/0da2ac78e6ac5583271881dabd4b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M static/maps/mvc/tool/tool-form-composite.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/tool/tool-form-composite.js Log Message: ----------- Rebuild client -- bad merge previously. Commit: 18e514d9b72b6efb57772009de1c0d65b791fa1b https://github.com/galaxyproject/galaxy/commit/18e514d9b72b6efb57772009de1c… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M static/maps/mvc/tool/tool-form-composite.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/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3652 from dannon/rebuild_client Rebuild client -- bad merge previously. Compare: https://github.com/galaxyproject/galaxy/compare/c52715fd69fb...18e514d9b72b

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[galaxyproject/usegalaxy-playbook] 44c246: Disable sentry logging on Test since sentry is dow...
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 44c2466d0b3fd324a79f5ec29826810aaf9b9cf7 https://github.com/galaxyproject/usegalaxy-playbook/commit/44c2466d0b3fd324… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- Disable sentry logging on Test since sentry is down indefinitely Commit: 365f0dab007dc9e014afd70ba3af03969b150b23 https://github.com/galaxyproject/usegalaxy-playbook/commit/365f0dab007dc9e0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Add a default for supervisord_host_configs in the stage environment. Not sure why this isn't done in the role? Maybe it should be? Commit: 6b9626f49cc8054e42b9952a4153603f51c42a69 https://github.com/galaxyproject/usegalaxy-playbook/commit/6b9626f49cc8054e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: A files/galaxy/common/dynamic_rules/nvc_dynamic_memory.py A files/galaxy/test.galaxyproject.org/dynamic_rules/bridges_select.py R files/galaxy/test.galaxyproject.org/dynamic_rules/greenfield_select.py A files/galaxy/test.galaxyproject.org/dynamic_rules/nvc_dynamic_memory.py R files/galaxy/test.galaxyproject.org/dynamic_rules/nvc_dynamic_memory.py A files/galaxy/usegalaxy.org/dynamic_rules/bridges_select.py A files/galaxy/usegalaxy.org/dynamic_rules/nvc_dynamic_memory.py M production/group_vars/galaxyservers.yml M roles/usegalaxy_privileged/tasks/main.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/supervisor/galaxy_handler.j2 Log Message: ----------- Move the dynamic rules back from CVMFS since updating them there is really tedious and disconnected from any sort of change management (and that was the original plan anyway). Done for Test, will do Main later (but Main is ready, just needs to have the galaxy_infrastructure playbook run to update supervisor). Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/16147fb88ec5...…

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[galaxyproject/galaxy] b8e283: Adding code for replacing mako for user preference...
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: b8e2833b5bcb26242ef08967fe342a81c2811172 https://github.com/galaxyproject/galaxy/commit/b8e2833b5bcb26242ef08967fe34… Author: anuprulez <anup.rulez(a)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/77f5655de1f606ae08f533ef2731… Author: anuprulez <anup.rulez(a)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/a63f63440ebe66715608907c809a… Author: anuprulez <anup.rulez(a)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/aaedf684f0e9693fc98f5867cde6… Author: anuprulez <anup.rulez(a)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/07409a89f86df86b86fc621fcc8b… Author: anuprulez <anup.rulez(a)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/cc168ce95423c096bbd5ef198cb2… Author: anuprulez <anup.rulez(a)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/044eb9768362b7d341911a78446b… Author: anuprulez <anup.rulez(a)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/976e6e5ac6757db777db6d824888… Author: anuprulez <anup.rulez(a)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/0558225f5f98ececedbcef4f8232… Author: anuprulez <anup.rulez(a)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/ce1a478d8d073fbb5fda88834e4f… Author: anuprulez <anup.rulez(a)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/bbd020e8a7b84de184885428650b… Author: anuprulez <anup.rulez(a)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/976729ad553ff34bff14f80eda94… Author: anuprulez <anup.rulez(a)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/23744c36f28e1d36333637202366… Author: anuprulez <anup.rulez(a)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/cb79eac22ede7d9facc07b170d6b… Author: anuprulez <anup.rulez(a)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/d7c6ca2bbd875a910e759acca015… Author: guerler <aysam.guerler(a)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/f11a87628f0c9571dc953976119f… Author: guerler <aysam.guerler(a)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/43054acb2e577f4928fb8a76931c… Author: Björn Grüning <bjoern(a)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/4016b3e3037db64e04537b248f4d… Author: anuprulez <anup.rulez(a)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/baae49f607480d98c2d63b6378f8… Author: anuprulez <anup.rulez(a)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/1adbcfc0ec1fcccd1987946f8311… Author: anuprulez <anup.rulez(a)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/e06d206eedf4ac36bfc03417d76f… Author: anuprulez <anup.rulez(a)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/4addb9497299cd9c3ff0e65b0b30… Author: anuprulez <anup.rulez(a)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/46cd30bb3523d182f319f9640d55… Author: anuprulez <anup.rulez(a)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/994eddfd5a15e85f37cb3ff0af73… Author: guerler <aysam.guerler(a)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/5d8bd3f72eb6f06c18bb5fc47a8f… Author: guerler <aysam.guerler(a)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/399f4ae9c06abc9a06240be15890… Author: guerler <aysam.guerler(a)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/4b7324bab96cf5fea85b13216902… Author: anup kumar <anup.rulez(a)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/ebc1cc6ff3ac216ff54628e4ff5e… Author: guerler <aysam.guerler(a)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/6a17e10d751b427ede173f40907d… Author: guerler <aysam.guerler(a)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/14d045c54e0e91181689a2281115… Author: guerler <aysam.guerler(a)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/e84251a7310005c7d16b6f87b423… Author: guerler <aysam.guerler(a)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/d59fa629cf269e7d118b38a48dbe… Author: guerler <aysam.guerler(a)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/ab559072d22b8b98aa2fd001d79d… Author: anup kumar <anup.rulez(a)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/8f1156295989b11c127bba1d5043… Author: anuprulez <anup.rulez(a)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/222d1f2cac83adb0ebea0c24701e… Author: anuprulez <anup.rulez(a)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/b4d0dfcc92ba9790f2975a557aaf… Author: anuprulez <anup.rulez(a)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/9915ef7837fc75758b2329681fce… Author: anuprulez <anup.rulez(a)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/961e01e700ecd775f4f7c2edd1aa… Author: anuprulez <anup.rulez(a)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/4bca99940f3f55425775b0f9cb4d… Author: anuprulez <anup.rulez(a)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/123aa562c0878406eb0eaa16eb85… Author: anuprulez <anup.rulez(a)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/3b5905985de402c92051d1da97df… Author: anuprulez <anup.rulez(a)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 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form and address filters Commit: 431fad09e06afe2a13ccd21e3ffff3ef826ee341 https://github.com/galaxyproject/galaxy/commit/431fad09e06afe2a13ccd21e3fff… Author: anuprulez <anup.rulez(a)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/c83fa12e56d221c162488225a6e6… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed 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test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/data_source/upload.xml M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tox.ini Log Message: ----------- Merging with dev Commit: 5e0c346adbdb7be67a9e6a0bed8b4a6b34744022 https://github.com/galaxyproject/galaxy/commit/5e0c346adbdb7be67a9e6a0bed8b… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- dict creation Commit: 2d6854cb5fe2153e9295e00807a9270f8456d357 https://github.com/galaxyproject/galaxy/commit/2d6854cb5fe2153e9295e00807a9… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- simplify code Commit: 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----------- Add packed files, use consistent file naming Commit: 31867733173911de306ea45184ce62ba1eea63ea https://github.com/galaxyproject/galaxy/commit/31867733173911de306ea45184ce… Author: guerler <aysam.guerler(a)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/faa7cb525b78ca53895ddf526c97… Author: guerler <aysam.guerler(a)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 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Author: guerler <aysam.guerler(a)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/ef362ef3c3c557d31aa62268cb51… Author: guerler <aysam.guerler(a)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/57a93e70135f6f788d3a29620068… Author: guerler <aysam.guerler(a)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/dc01a1a51a609bf1f66a046960f3… Author: guerler <aysam.guerler(a)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/b31ab08f092ac80a1df2e04d6319… Author: guerler <aysam.guerler(a)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/c5641cc87ac33b258849ead4b76a… Author: guerler <aysam.guerler(a)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 static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.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/base/interactor.py A test/functional/tools/metadata_column_names.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/tests/form_tests.js 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 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 Log Message: ----------- Merge branch 'dev' into remove_mako_preferences_revision Commit: eadc6f26d27eb87011813e0ab9575fb42950fd6c https://github.com/galaxyproject/galaxy/commit/eadc6f26d27eb87011813e0ab957… Author: guerler <aysam.guerler(a)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/98d31d0adcf8e4a6c083a2d5edb8… Author: guerler <aysam.guerler(a)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/30a8c0a2451b98289cb063861d45… Author: guerler <aysam.guerler(a)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/f353fe6e7ec3ad1390c6f9d42099… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-10-12 (Wed, 12 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/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-modal.js 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/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 lib/galaxy/config.py M lib/galaxy/datatypes/registry.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/__init__.py M 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/a06980c72fd5bf2ba2aa95ebd2dd… Author: Björn Grüning <bjoern(a)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 lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/metrics/collectl/__init__.py M 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/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/queue_worker.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/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 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/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/form/form-section.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-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js 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 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/42d4a677bfc5457219d47c3fc051… Author: guerler <aysam.guerler(a)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/7273f43c0d211a6e11d8c0370bcb… Author: guerler <aysam.guerler(a)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/6005ce9fd7bfa224f59b00f70501… Author: guerler <aysam.guerler(a)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/35bca940bd35d8303df55a7e11c2… Author: guerler <aysam.guerler(a)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/e5f729b40bfa7534e7b535d3c205… Author: guerler <aysam.guerler(a)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/f87047cc0c10e41c4ae7e892ecc4… Author: guerler <aysam.guerler(a)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/1eeb21f344020b52e44008364b83… Author: guerler <aysam.guerler(a)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/fdff89596eeae060b626e1f376ee… Author: guerler <aysam.guerler(a)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/e9a712c82d4ea007fea8ffbbbc99… Author: guerler <aysam.guerler(a)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/64b1bd1e613470117e6310ce4b8c… Author: guerler <aysam.guerler(a)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/5f20a2b1181c0bb0584979f212f6… Author: guerler <aysam.guerler(a)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/dd45dd6477963dd60067f31b2034… Author: guerler <aysam.guerler(a)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/27216933f036fb603e65c2c1bf4d… Author: guerler <aysam.guerler(a)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/783272416ed4416e57143843ad26… Author: Björn Grüning <bjoern(a)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/b248acd5c26e7cb7a69cad69a45a… Author: guerler <aysam.guerler(a)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/95e39bbc591a1d3d0e475b99add6… Author: guerler <aysam.guerler(a)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/a7df03710a8ee6254f7867b134f3… Author: guerler <aysam.guerler(a)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/ef6534285224e397772b91eb5aef… Author: guerler <aysam.guerler(a)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/b4b779dd04f1d7286a2014ce206a… Author: guerler <aysam.guerler(a)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/f6ecb45040c4e39c83ab4493a9c3… Author: guerler <aysam.guerler(a)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/d31998835ed543c4c528a11f8cde… Author: guerler <aysam.guerler(a)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/aa5ed9d2facc4a3549fd2eef55d1… Author: guerler <aysam.guerler(a)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/4fa9984eaa9b834fbf30209033e6… Author: guerler <aysam.guerler(a)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/1305b42b498e79940a81f0c33292… Author: Björn Grüning <bjoern(a)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/3050e3db2ad39db7b9060ee167eb… Author: guerler <aysam.guerler(a)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/f4e5819c68b6e6705fd64fa102a2… Author: guerler <aysam.guerler(a)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/36e8f967dfd1b970c3f3f303e438… Author: guerler <aysam.guerler(a)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/4dfb61033bad820a544500fc4ac6… Author: guerler <aysam.guerler(a)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/0d09e6e7bc73f0206401e77ca97d… Author: guerler <aysam.guerler(a)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/ee2b7c4159427f223fea0b9fd5b5… Author: guerler <aysam.guerler(a)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/c408090c392f6fe4765a7e037ef3… Author: guerler <aysam.guerler(a)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/fdd8099c342c9298a0669b18e763… Author: guerler <aysam.guerler(a)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/dd0951ecc39b577febaf75f3235a… Author: guerler <aysam.guerler(a)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/dfec446c4c6439bdd340ee38471e… Author: guerler <aysam.guerler(a)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/b6951841df274f455681cd4332f9… Author: guerler <aysam.guerler(a)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/3b164bd9f83c70ea798b1461ec03… Author: guerler <aysam.guerler(a)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/30c2dcce923da2825f307faee9cc… Author: guerler <aysam.guerler(a)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/d70f5a4ff46163330db07d3bebd7… Author: guerler <aysam.guerler(a)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/b792a6feb49c3f5071506b689d32… Author: guerler <aysam.guerler(a)gmail.com> Date: 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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/f88b72f3474b98877417a0af7c12… Author: guerler <aysam.guerler(a)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/88f6067364667c5a0ad7c3f1f9e2… Author: guerler <aysam.guerler(a)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/897137d94994121ea5f12d1b94a5… Author: guerler <aysam.guerler(a)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/fe1676af01b2a5317faa0e0e29e1… Author: guerler <aysam.guerler(a)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/02cf8326058ba920a676fb02b5d4… Author: guerler <aysam.guerler(a)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/76f2287dbcf1ab553397bf3bf217… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-22 (Sat, 22 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M Makefile M 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lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/checkers.py A lib/galaxy/util/image_util.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/web/framework/middleware/static.py M lib/galaxy/webapps/galaxy/api/tours.py M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/workflow_util.py A scripts/slideshow/__init__.py A scripts/slideshow/build_slideshow.py A scripts/slideshow/example.md A scripts/slideshow/slideshow_template.html A scripts/slideshow/style.sample.css M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-buttons.js.map 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 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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 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/4b14761f7ca94aba77495be79752… Author: guerler <aysam.guerler(a)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/7a0850116f6001f589e295b0279e… Author: guerler <aysam.guerler(a)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/97890f68e96d58698a4561ae8c67… Author: guerler <aysam.guerler(a)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/d8aea401bea1bfa8eced7b309a90… Author: guerler <aysam.guerler(a)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/8b66acaf9a405d83a557e1bf0a33… Author: guerler <aysam.guerler(a)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/2a16b25e83883ea7e4086994d02b… Author: Björn Grüning <bjoern(a)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/c89e415f2cfabd41743b460d0551… Author: anuprulez <anup.rulez(a)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/e0a38a5bed8555f6ea18a00c7d0d… Author: anuprulez <anup.rulez(a)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/6e09d71ab04f5181a7fd1a65b6ba… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: 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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/14612f8a92560796bbfdb7fb3560… Author: anuprulez <anup.rulez(a)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/fb75c23f0d8d5a97eb49f8701da3… Author: anuprulez <anup.rulez(a)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/8a8ca4e5918b9e7f4a7a92562d8e… Author: anuprulez <anup.rulez(a)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/fd6bf953278f67cfebda46ffd3e0… Author: anuprulez <anup.rulez(a)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/c828ec65f8a927875d7194a49ac2… Author: anuprulez <anup.rulez(a)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 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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: 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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/2ed916390162689900f79e8026cc… Author: guerler <aysam.guerler(a)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/eff7ba7b6d3c910faff79efe893b… Author: guerler <aysam.guerler(a)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 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a561368195e696de8239bcea4aba9472ef3965b2 https://github.com/galaxyproject/galaxy/commit/a561368195e696de8239bcea4aba… Author: guerler <aysam.guerler(a)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/55d1fae34362dac33d6d42b49f19… Author: guerler <aysam.guerler(a)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/d2bbed967b81ff663414b5053232… Author: guerler <aysam.guerler(a)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/bbc5c2afb501fec6bc43dfeca60a… Author: guerler <aysam.guerler(a)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/3a53ae41efdfa671689fe9071fda… Author: guerler <aysam.guerler(a)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/6e37b1f0fd84981555927bde0256… Author: guerler <aysam.guerler(a)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 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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/eb178129c102b4645ba76071bd52… Author: guerler <aysam.guerler(a)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/25a8edd66c6c999451c97535d250… Author: guerler <aysam.guerler(a)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/ec63866deeac2c4c5139078c2db6… Author: guerler <aysam.guerler(a)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/f00cd6af2e53cbf56cc08dee26df… Author: guerler <aysam.guerler(a)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 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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/a9a0d8fab0002050f7e7a505f614… Author: guerler <aysam.guerler(a)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/928611f4cf69c95c669e1aceaa0f… Author: guerler <aysam.guerler(a)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/6c8ff8ce30642dbc4015dc061e07… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-04 (Fri, 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https://github.com/galaxyproject/galaxy/commit/bbec45c70652bb58919b12ebce96… Author: guerler <aysam.guerler(a)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/eda1fe6fb73cc393fbf935306718… Author: guerler <aysam.guerler(a)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/0045e8cbc8fb2c488583a6fb27fb… Author: guerler <aysam.guerler(a)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/363e136e8c37bae91b4eaac65d3c… Author: guerler <aysam.guerler(a)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/f52f953b01925ffc91a96b97f9b2… Author: guerler <aysam.guerler(a)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/0e25f118dd69febb9dcc4a6b5c7b… Author: guerler <aysam.guerler(a)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/0d7e074bcf47cdf95b17588e30f5… Author: guerler <aysam.guerler(a)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/f17e335407599f40b40fce97be0a… Author: guerler <aysam.guerler(a)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/22763844a67f332ae739ae536b8f… Author: guerler <aysam.guerler(a)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/b1da023f3205f8228170e6972373… Author: guerler <aysam.guerler(a)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/021b4d6e7341e55d01a52da4d516… Author: guerler <aysam.guerler(a)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/e649bd01c94a10bedb2ea499e859… Author: guerler <aysam.guerler(a)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/29b5f33742c7ca0b09fe3690b824… Author: guerler <aysam.guerler(a)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/305f8d19639b6c344c01762dfe6c… Author: guerler <aysam.guerler(a)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/f58ff7b1c6e28e73d16180fc8050… Author: guerler <aysam.guerler(a)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/37fffc16674efa9c2ab123c6ebc6… Author: guerler <aysam.guerler(a)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/0810cd26de20ad4932332a767641… Author: guerler <aysam.guerler(a)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/5683edd76443987643dce013ce16… Author: guerler <aysam.guerler(a)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/0b2ba5017b8ab731170909e601b1… Author: guerler <aysam.guerler(a)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/dee59fc8b59ad75fccb874a7d36f… Author: guerler <aysam.guerler(a)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/433ac08dafe4de7ee60940477a72… Author: guerler <aysam.guerler(a)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/7a6cd700597c873a6cae59b1021b… Author: guerler <aysam.guerler(a)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/826f006b48aa07e4450779539ea5… Author: guerler <aysam.guerler(a)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/56844f52bb76d8be4825f4368fd5… Author: guerler <aysam.guerler(a)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/44cd6ef738703454755044cd68ab… Author: guerler <aysam.guerler(a)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/8004fea3fc7f5feb70d71431f43b… Author: guerler <aysam.guerler(a)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/e40c2554a5efcbe937f7e3b6d067… Author: guerler <aysam.guerler(a)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/2675bc17d266a57abd80fdf85db4… Author: guerler <aysam.guerler(a)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/00ae244b6ab2bcad1b71bd40f8e4… Author: guerler <aysam.guerler(a)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/5f6efbec861eb1b5ddf084d7a70b… Author: guerler <aysam.guerler(a)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/38d2ab3cd5806edc1e053bbcc6d3… Author: Björn Grüning <bjoern(a)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/e4a97c88d04894110d0388131657… Author: guerler <aysam.guerler(a)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/46acf5c7bd42d2d58d4494d8adcc… Author: guerler <aysam.guerler(a)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/3b6bf1ab6094a177eea917edb98b… Author: Björn Grüning <bjoern(a)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: 5ab4ae4f2f630ea12c8b4e82e90cd8dca2758a6f https://github.com/galaxyproject/galaxy/commit/5ab4ae4f2f630ea12c8b4e82e90c… Author: ashok <ashok(a)localhost.localdomain> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Changes for Fastq Compression. Commit: 7597da61e5de1796f0cf4ce2f6ea577cb390f311 https://github.com/galaxyproject/galaxy/commit/7597da61e5de1796f0cf4ce2f6ea… Author: ashok <ashok(a)localhost.localdomain> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- Updated sequence.py and datatypes_conf.xml Commit: aabfa4283d396ba01ea42b47ab0b8601122096bd https://github.com/galaxyproject/galaxy/commit/aabfa4283d396ba01ea42b47ab0b… Author: ashok <ashvark(a)gmail.com> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py M tools/data_source/upload.py Log Message: ----------- Changes to keep the compressed fastq file as it is with out decompressing. Commit: eed7f2ce086460cc29b0f89def0986d727eec15a https://github.com/galaxyproject/galaxy/commit/eed7f2ce086460cc29b0f89def09… Author: guerler <aysam.guerler(a)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: 7d4840ce6b46a2b51f0d5332d72e7b4d956ac808 https://github.com/galaxyproject/galaxy/commit/7d4840ce6b46a2b51f0d5332d72e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M tools/data_source/upload.py Log Message: ----------- For fastq.gz support inherit from Fastq and Binary and enhance FastQ format to be gzip aware. Commit: af2b31e1fbc7ea2383e9f1ad3ea9d44db48bc41c https://github.com/galaxyproject/galaxy/commit/af2b31e1fbc7ea2383e9f1ad3ea9… Author: Björn Grüning <bjoern(a)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: 10f1bb5459c4d27ca9142c0f4da1c8502ac9f1b2 https://github.com/galaxyproject/galaxy/commit/10f1bb5459c4d27ca9142c0f4da1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py A test-data/1.fastqsanger.gz A test/functional/tools/compressed_fastq_conversion.xml A test/functional/tools/compressed_fastq_no_conversion.xml Log Message: ----------- Create a BaseFastq class and add test tools Having a BaseFastq class allows Fastq and FastqGz classes to inherit from BaseFastq. FastqGz is therfor not a Fastq datatype and goes through the converter. Also add 2 tools to demonstrate that compressed fastq will be converted to uncompressed fastq if the tool specifies `format="fastq"`, while `format="fastq.gz"` leaves files compressed. The tool test can be run with: ``` planemo test --galaxy_root . test/functional/tools/compressed_fastq_no_conversion.xml planemo test --galaxy_root . test/functional/tools/compressed_fastq_conversion.xml ``` Note that fastq conversion appears to required a galaxy user session, and planemo testing fails. Interactive testing with `planemo serve` is not affected and works fine. Commit: b44a977e649e3c6ac7cfc0bc519c242139296789 https://github.com/galaxyproject/galaxy/commit/b44a977e649e3c6ac7cfc0bc519c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml M lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml Log Message: ----------- Quote paths in converters Commit: bcf08f630d40b45b852db56e4a59c362c3cfc2bf https://github.com/galaxyproject/galaxy/commit/bcf08f630d40b45b852db56e4a59… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Ensure closing of open files Commit: 304c05f3a3a99a9d450c06145bf3985f72f8b7db https://github.com/galaxyproject/galaxy/commit/304c05f3a3a99a9d450c06145bf3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml Log Message: ----------- Remove deprecated page attribute Commit: 4499d870d3b31c009d2e61c4c976d9016d1df36e https://github.com/galaxyproject/galaxy/commit/4499d870d3b31c009d2e61c4c976… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Update committers list Commit: e5b56f102ae003707ad97d9fbb75270543397921 https://github.com/galaxyproject/galaxy/commit/e5b56f102ae003707ad97d9fbb75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01.dev Commit: 3dd28291c339d4ca1f2b165ed6cb2c9d82a7cdd9 https://github.com/galaxyproject/galaxy/commit/3dd28291c339d4ca1f2b165ed6cb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Log Message: ----------- Merge branch 'version-16.10' into version-17.01.dev Commit: 50f5c15f63a388466f8e77437226a93405baa382 https://github.com/galaxyproject/galaxy/commit/50f5c15f63a388466f8e77437226… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3192 from dannon/version-17.01.dev Version 17.01.dev Commit: a209523639a822dc546b9d2d946e6199df172368 https://github.com/galaxyproject/galaxy/commit/a209523639a822dc546b9d2d946e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M test/base/twilltestcase.py M test/functional/test_library_templates.py Log Message: ----------- Large cleanup of unused methods from twilltestcase. In addition to deleting unused methods, this also moves ones only used by test_library_templates into that file. Commit: 2bf1cf50a37d5295425798374959fbda0257b609 https://github.com/galaxyproject/galaxy/commit/2bf1cf50a37d5295425798374959… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M test/base/twilltestcase.py M test/functional/test_library_templates.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Reduce requirements for using get_filename in TwillTestCase. Do not use a self.tool_shed_test_file and make self.shed_tools_dict optional. Commit: b83cfe434ad875744d11d7516dc9cc11dfdec419 https://github.com/galaxyproject/galaxy/commit/b83cfe434ad875744d11d7516dc9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M test/base/api.py M test/base/interactor.py M test/base/twilltestcase.py Log Message: ----------- Refactor generic FunctionalTestCase from TwillTestCase. ApiTestCase uses this newer, smaller base class since these tests do not depend on Twill. Commit: 33894ca744be3fa2eebab6942832f2931d5f0bec https://github.com/galaxyproject/galaxy/commit/33894ca744be3fa2eebab6942832… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M test/base/api.py M test/base/interactor.py M test/base/twilltestcase.py M test/functional/test_library_templates.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #3190 from jmchilton/test_cleanup Various Test Cleanups and Refactorings Commit: 9914130fb4d5bc33b70d9e241c08421dc0acc5c0 https://github.com/galaxyproject/galaxy/commit/9914130fb4d5bc33b70d9e241c08… Author: guerler <aysam.guerler(a)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/d52f4fd52374def376367c3141f9… Author: guerler <aysam.guerler(a)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/364f57d06d0910d593a96d1748a2… Author: guerler <aysam.guerler(a)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 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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/51972a9916e8b113399bbcbb0748… Author: guerler <aysam.guerler(a)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/eabc648b9cda89df5d5207162361… Author: guerler <aysam.guerler(a)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/1f3f4be1caa56a2782a18c397c7c… Author: guerler <aysam.guerler(a)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/9653d148a22f5bd537d7339ab100… Author: guerler <aysam.guerler(a)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/b02eb9e7e0c2d5dfa35a72ee13e5… Author: guerler <aysam.guerler(a)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/998fd3036d9887ece8aaa651c272… Author: guerler <aysam.guerler(a)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/2cf91d4b1554b2fc22866e887cd6… Author: guerler <aysam.guerler(a)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: 99000fbed3b6c13274a3ddf9eb58310cb40653f7 https://github.com/galaxyproject/galaxy/commit/99000fbed3b6c13274a3ddf9eb58… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- update rename dataset action to accept . in repeat input parameters, also when not using additional operations like '|basename'. e.g. for filter bam 0.0.1: #{input_bams_0.input_bam} and #{input_bams_0.input_bam|basename} work. And for filter bam 0.0.2: #{input_bams1} and #{input_bams2|basename} work. Commit: 3ea730f734c71e5e3aa182c96f7be81850ee8527 https://github.com/galaxyproject/galaxy/commit/3ea730f734c71e5e3aa182c96f7b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-11-18 (Fri, 18 Nov 2016) Changed paths: M templates/webapps/galaxy/user/list_users.mako Log Message: ----------- Fix table Commit: 52c8e495dc1746e4280c7d6837dd590f9b98566e https://github.com/galaxyproject/galaxy/commit/52c8e495dc1746e4280c7d6837dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-19 (Sat, 19 Nov 2016) Changed paths: M templates/webapps/galaxy/user/list_users.mako Log Message: ----------- Merge pull request #3200 from erasche/user-info-page Fix table Commit: c0a7fabc354598b1a40ea87291c28f70127db357 https://github.com/galaxyproject/galaxy/commit/c0a7fabc354598b1a40ea87291c2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Don't load tools from paths that start with `.` or `_` Commit: 78b533d1b5445c843090ec42c134d2fa335134a3 https://github.com/galaxyproject/galaxy/commit/78b533d1b5445c843090ec42c134… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3201 from mvdbeek/do_not_load_tools_from_hidden_paths Don't load tools from paths that start with `.` or `_` Commit: d2c95b43fa33f9f4b14d274ffa60beb03a80fbb6 https://github.com/galaxyproject/galaxy/commit/d2c95b43fa33f9f4b14d274ffa60… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 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 lib/galaxy/webapps/galaxy/controllers/root.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/bundled/login.bundled.js.map M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tools.js Log Message: ----------- Merge pull request #3204 from galaxyproject/release_16.10 Merge release_16.10 into dev Commit: c122e74240fb35222d5d2d0f0b08e783dc0d561a https://github.com/galaxyproject/galaxy/commit/c122e74240fb35222d5d2d0f0b08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Fixes for core.galaxy_ui.yaml. Neither of these prevent the tour from working but I think they are bugs. The extra click isn't an elemment that is clickable at that point in the tour and the referenced id isn't available so nothing in particular is tagged in the UI at that point. Commit: 097300ea6219e14b66b23a0e05f2808b16f10015 https://github.com/galaxyproject/galaxy/commit/097300ea6219e14b66b23a0e05f2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Merge pull request #3206 from jmchilton/tour_fixes Fixes for core.galaxy_ui.yaml. Commit: 6fd77db920d088ba6ebc64a4ac8ab7524d5ce654 https://github.com/galaxyproject/galaxy/commit/6fd77db920d088ba6ebc64a4ac8a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Preliminary fix for mapping tools with paired collection input over list:paired collections. Commit: 1aba7549debca136048d2850dae28b1185e30469 https://github.com/galaxyproject/galaxy/commit/1aba7549debca136048d2850dae2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M test/functional/tools/paired_collection_map_over_structured_like.xml Log Message: ----------- Add inherit_format tag to paired_collection_map_over_structured_like tool Commit: 55eac47d0fe9083c84afc613f451bfa68649b4d8 https://github.com/galaxyproject/galaxy/commit/55eac47d0fe9083c84afc613f451… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M test/functional/tools/paired_collection_map_over_structured_like.xml Log Message: ----------- Fix test tool -- functional test framework appears to not support mapping over test-data Commit: a39941a3c57f0cf1d0db848debfed4d54c321627 https://github.com/galaxyproject/galaxy/commit/a39941a3c57f0cf1d0db848debfe… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M test/api/test_tools.py Log Message: ----------- Add failing test for structured_like paired input Commit: daa19009296db8fba3337df76d6e2fba59b4ba06 https://github.com/galaxyproject/galaxy/commit/daa19009296db8fba3337df76d6e… Author: guerler <aysam.guerler(a)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/564a7236cacf06841a02d7ffdf60… Author: guerler <aysam.guerler(a)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/a4ae3c953bf8b0778f32fe9b3cd3… Author: guerler <aysam.guerler(a)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/cfe0305f39d183952206b2f76da9… Author: guerler <aysam.guerler(a)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/15668f2ff37d1f25d665c60f01b1… Author: guerler <aysam.guerler(a)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/5fe064d4c88d6657f65fc10feb06… Author: guerler <aysam.guerler(a)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/2366eda8f3bebe9e0f71e5deea0e… Author: guerler <aysam.guerler(a)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/2108043ded3e631b929d2be58534… Author: guerler <aysam.guerler(a)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/f960be7b43e1b00b95f92218a7af… Author: guerler <aysam.guerler(a)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/bb33e8959fca912912f7b7b988c9… Author: guerler <aysam.guerler(a)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/d4760ed2105d0f3743569458416c… Author: guerler <aysam.guerler(a)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: bbc403b2e1411f2a54fe3c28283dbd26dddbc780 https://github.com/galaxyproject/galaxy/commit/bbc403b2e1411f2a54fe3c28283d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Add cached dependency manager Similar to https://github.com/galaxyproject/galaxy/pull/2986, implement a mechanism that allows tool dependencies to be cached. If the `use_cached_dependency_manager` option is set to True in galaxy.ini, we build a hash of the combination of a tools' requirements, and store the resulting environment in a directory specified by the `tool_dependency_cache_dir` option in galaxy.ini. Commit: 185856f6afd36d627cd722402e687188b400333b https://github.com/galaxyproject/galaxy/commit/185856f6afd36d627cd722402e68… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo) Commit: 5606d84f22e2bb21966c65ff37fd8c47013961c9 https://github.com/galaxyproject/galaxy/commit/5606d84f22e2bb21966c65ff37fd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Rework cached dependencies to be more robust to updates or changes in depedencies, folder structure and resolver configuration. Instead of hashing name, type and version of a dependency, hash the json representation of the dependencies returned by the dependency resolver, which include the path to the environment and the depedency type. This is only applied to resolvers whose cacheable attribute is set to True (conda-only, currently). Commit: 66af4295cbb669389a68dcc19403798b84d0f2bc https://github.com/galaxyproject/galaxy/commit/66af4295cbb669389a68dcc19403… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Build dependency cache at install time and only activate cached environments if they exist. Commit: df93db40b118777cad6887386d7fc03df3acbf92 https://github.com/galaxyproject/galaxy/commit/df93db40b118777cad6887386d7f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Only attempt to build cache once per install and override __eq__ for ToolRequirement, to simplify checking if ToolRequirements are already installed/cached. Commit: 21b859e555e6e199eece79cb1d718e7b17d827a1 https://github.com/galaxyproject/galaxy/commit/21b859e555e6e199eece79cb1d71… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix NameError Commit: db93fd32859b9b1f326877833cb843edffd48d66 https://github.com/galaxyproject/galaxy/commit/db93fd32859b9b1f326877833cb8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M config/galaxy.ini.sample 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/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #3106 from mvdbeek/cached_dep_manager Add cached dependency manager Commit: 6aab802e5ad8e1f4e088e95f0e1483a60e6e4b7e https://github.com/galaxyproject/galaxy/commit/6aab802e5ad8e1f4e088e95f0e14… Author: Dannon Baker <dannon.baker(a)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: ----------- Tour routing tweaks, allows us to drop the model out of menu Commit: a40d5ebe69cbe79c8486a26e9a1ef99291f83b59 https://github.com/galaxyproject/galaxy/commit/a40d5ebe69cbe79c8486a26e9a1e… Author: guerler <aysam.guerler(a)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/14e635aaee2699cb395443d802de… Author: guerler <aysam.guerler(a)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/6cb1a2c39e40a752e756e355beb1… Author: guerler <aysam.guerler(a)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/98c5a59a182a2f64f6bb24086374… Author: guerler <aysam.guerler(a)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/12623ac1a4a746d204320a649f2b… Author: guerler <aysam.guerler(a)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: fef5523ed443c45b6d93dfd3ec72ae09f358019c https://github.com/galaxyproject/galaxy/commit/fef5523ed443c45b6d93dfd3ec72… Author: Aysam Guerler <aysam.guerler(a)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 pull request #3214 from dannon/tour_routing Tour routing tweaks, allows us to drop the model out of menu Commit: b38c6afefebd6d0a9bb99005efb1a78a5083a585 https://github.com/galaxyproject/galaxy/commit/b38c6afefebd6d0a9bb99005efb1… Author: guerler <aysam.guerler(a)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: 3d57c22b6324dda9e3ab6c92a2592dd20374abc6 https://github.com/galaxyproject/galaxy/commit/3d57c22b6324dda9e3ab6c92a259… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/actions/admin.py M lib/galaxy/datatypes/images.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/jobs/splitters/basic.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/quota/__init__.py M lib/galaxy/tools/actions/data_manager.py M lib/galaxy/tools/actions/data_source.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/dbkeys.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/search.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/steps.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/repository_types/unrestricted.py M lib/tool_shed/util/web_util.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/drmaa_external_runner.py M test/api/test_datasets.py M test/api/test_history_contents_provenance.py M test/unit/test_sockets.py M tools/data_source/fetch.py Log Message: ----------- Fix I201 errors from flake8-import-order Also fix Python3 compatibility. Remove unused method galaxy.tools.parameters.sanitize.ToolParameterSanitizer.restore_param() . Commit: 20d45ee62c73d25b1757e9ab7a6cba5f122cfd88 https://github.com/galaxyproject/galaxy/commit/20d45ee62c73d25b1757e9ab7a6c… Author: guerler <aysam.guerler(a)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/16a60538d978ae196121f6fe474a… Author: guerler <aysam.guerler(a)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/416b94f1953f04147033bdd470b2… Author: guerler <aysam.guerler(a)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/6e1b26115ed6879294f011a12435… Author: guerler <aysam.guerler(a)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/7afc7ac6eb1eddd0a381042633ff… Author: guerler <aysam.guerler(a)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/0f6013c7286ff73761577944e96a… Author: guerler <aysam.guerler(a)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: 7d945f762e2ed61ebd88f613337b04c7e4c53e8a https://github.com/galaxyproject/galaxy/commit/7d945f762e2ed61ebd88f613337b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fix https://github.com/galaxyproject/galaxy/issues/3213 discovered by @nsoranzo. Commit: ad0e6a437ed8be4fdb5513574cac2c5f8570122a https://github.com/galaxyproject/galaxy/commit/ad0e6a437ed8be4fdb5513574cac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/actions/admin.py M lib/galaxy/datatypes/images.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/jobs/splitters/basic.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/quota/__init__.py M lib/galaxy/tools/actions/data_manager.py M lib/galaxy/tools/actions/data_source.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/dbkeys.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/search.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/steps.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/repository_types/unrestricted.py M lib/tool_shed/util/web_util.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/drmaa_external_runner.py M test/api/test_datasets.py M test/api/test_history_contents_provenance.py M test/unit/test_sockets.py M tools/data_source/fetch.py Log Message: ----------- Merge pull request #3215 from nsoranzo/flake8-import-order Fix I201 errors from flake8-import-order Commit: 1ad89511540e6800cd2d0da5d878c1c77d8ccfe9 https://github.com/galaxyproject/galaxy/commit/1ad89511540e6800cd2d0da5d878… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-23 (Wed, 23 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3216 from jmchilton/when_datatype_isinstance Fix conditional when datatype in XML schema. Commit: b4252724e5e5dc0088828778d36ae767f3608f23 https://github.com/galaxyproject/galaxy/commit/b4252724e5e5dc0088828778d36a… Author: Maximilian Friedersdorff <max(a)friedersdorff.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Estimate the walltime usage over the last 30 days. Log at debug level if usage is over 20 seconds. Commit: a680d90d54c39236bedd0e8fe4fe20568aa81372 https://github.com/galaxyproject/galaxy/commit/a680d90d54c39236bedd0e8fe4fe… Author: Maximilian Friedersdorff <max(a)friedersdorff.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M config/galaxy.ini.sample M lib/galaxy/actions/admin.py M lib/galaxy/config.py M lib/galaxy/datatypes/images.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/jobs/splitters/basic.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/quota/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/data_manager.py M lib/galaxy/tools/actions/data_source.py M lib/galaxy/tools/actions/history_imp_exp.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.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/lint.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/dbkeys.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/search.py M lib/galaxy/webapps/tool_shed/controllers/groups.py M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py M lib/galaxy/webapps/tool_shed/util/ratings_util.py M lib/galaxy/workflow/steps.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/repository_types/unrestricted.py M lib/tool_shed/util/web_util.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/drmaa_external_runner.py M static/maps/layout/menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M test/api/test_datasets.py M test/api/test_history_contents_provenance.py M test/unit/test_sockets.py M tools/data_source/fetch.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 99a037d5b92828cbef097ae8434e1d172df3c888 https://github.com/galaxyproject/galaxy/commit/99a037d5b92828cbef097ae8434e… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml M lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A test-data/1.fastqsanger.bz2 A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml R test/functional/tools/compressed_fastq_conversion.xml R test/functional/tools/compressed_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml Log Message: ----------- add fastq(*).bz2 datatypes and converters Commit: 833f2c3dbef2469fe7437e8939e329ddff8d2793 https://github.com/galaxyproject/galaxy/commit/833f2c3dbef2469fe7437e8939e3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml M lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A test-data/1.fastqsanger.bz2 A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml R test/functional/tools/compressed_fastq_conversion.xml R test/functional/tools/compressed_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml Log Message: ----------- Merge pull request #1 from abretaud/bz2 Add fastq(*).bz2 datatypes and converters Commit: 500ed949e66cb0ddec757022cae8be230722d755 https://github.com/galaxyproject/galaxy/commit/500ed949e66cb0ddec757022cae8… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Fix indentation and import (#2) * fix indentation and import * import fix * refix indentation * better looking imports Commit: b327523c3011c81e164f12833ff010eb411d963e https://github.com/galaxyproject/galaxy/commit/b327523c3011c81e164f12833ff0… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- wrong import name (#3) Commit: 7d8bbd599a2528a3e0e9264d64d0da3e494b5016 https://github.com/galaxyproject/galaxy/commit/7d8bbd599a2528a3e0e9264d64d0… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- python lint Commit: 43abc55284fd4a1d7ea62535797d29f9977ef0af https://github.com/galaxyproject/galaxy/commit/43abc55284fd4a1d7ea62535797d… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- python lint Commit: 2408502c2d316869df0f84b65e50db3114f9529a https://github.com/galaxyproject/galaxy/commit/2408502c2d316869df0f84b65e50… Author: Maximilian Friedersdorff <max(a)friedersdorff.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Add total_walltime limit type Add to sample config, config reader and unittest Commit: 8e4072179789517427727339e3e9a2e911fae6a6 https://github.com/galaxyproject/galaxy/commit/8e4072179789517427727339e3e9… Author: Maximilian Friedersdorff <max(a)friedersdorff.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Use conf for walltime limit and window. Pause job if necessary Commit: 3d4de14840847636ad81c36bd64449fb959220b9 https://github.com/galaxyproject/galaxy/commit/3d4de14840847636ad81c36bd644… Author: Maximilian Friedersdorff <max(a)friedersdorff.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py Log Message: ----------- Comply with galaxy style guide regarding whitespace. Commit: 296889d0dfa767c3649c6331a911ba0fd904f9fd https://github.com/galaxyproject/galaxy/commit/296889d0dfa767c3649c6331a911… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-25 (Fri, 25 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- lint fix Commit: 4398abd1d370a20bf420772d2eda5b9b7e89a26d https://github.com/galaxyproject/galaxy/commit/4398abd1d370a20bf420772d2eda… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-11-25 (Fri, 25 Nov 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Check also for cgroup memory warnings if job was cancelled Commit: db1b51a0802e392787c3a71e7a8bd202b568bf3a https://github.com/galaxyproject/galaxy/commit/db1b51a0802e392787c3a71e7a8b… Author: Maximilian Friedersdorff <max(a)friedersdorff.com> Date: 2016-11-25 (Fri, 25 Nov 2016) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Fix errors in documentation for total_walltime limit Commit: 91e65aa42c8e2439883da1d690e770a5a9df1a79 https://github.com/galaxyproject/galaxy/commit/91e65aa42c8e2439883da1d690e7… Author: Maximilian Friedersdorff <max(a)friedersdorff.com> Date: 2016-11-25 (Fri, 25 Nov 2016) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Move datetime import to the top of the file. Commit: e1276175b16d7a60e4eefab659a1173383a47d06 https://github.com/galaxyproject/galaxy/commit/e1276175b16d7a60e4eefab659a1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-11-25 (Fri, 25 Nov 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Handle also COMPLETED state in _complete_terminal_job Commit: af58f82083b1c9e38453364b58ae6e21c92502f8 https://github.com/galaxyproject/galaxy/commit/af58f82083b1c9e38453364b58ae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-11-25 (Fri, 25 Nov 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix _get_slurm_state_with_sacct() for not completed jobs Commit: 8109a711cf192dbefc4e5757fc10413008235123 https://github.com/galaxyproject/galaxy/commit/8109a711cf192dbefc4e5757fc10… Author: Hervé MENAGER <herve.menager(a)pasteur.fr> Date: 2016-11-25 (Fri, 25 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add EDAM topic(s) and operation(s) elements to XSD file. Commit: 40a95a300326bddeb0e78add288a47f4f23c087c https://github.com/galaxyproject/galaxy/commit/40a95a300326bddeb0e78add288a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-27 (Sun, 27 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add API to install resolver tool dependencies and to build a tool dependency cache (if activated in galaxy.ini). An example to install dependencies for the twobit converter: ``` import bioblend.galaxy url = 'http://localhost:8080/' api_key = 'admin_api_key' tool_id = 'CONVERTER_fasta_to_2bit' endpoint = "api/tools/%s/install_dependencies" % tool_id gi = bioblend.galaxy.GalaxyInstance(url, api_key) gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id}) ``` If `use_cached_dependency_manager` is activated in the galaxy.ini, a cached environment can be built like this: ``` endpoint = "api/tools/%s/build_dependency_cache" % tool_id gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id}) ``` Commit: e905b8baeb9081400ad775bcc20c2956808a11fd https://github.com/galaxyproject/galaxy/commit/e905b8baeb9081400ad775bcc20c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-27 (Sun, 27 Nov 2016) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Add integration test-case for install tool dependency API endpoint Commit: 3e48f3792bc10c081a8079cfa3d773531d6dad15 https://github.com/galaxyproject/galaxy/commit/3e48f3792bc10c081a8079cfa3d7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-27 (Sun, 27 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_2bit.xml Log Message: ----------- Install the correct converter dependency Commit: 8ff7ffa063c491b886bbeed1e1eb2e69fb6f3e68 https://github.com/galaxyproject/galaxy/commit/8ff7ffa063c491b886bbeed1e1eb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-27 (Sun, 27 Nov 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Add `force_rebuild` param to build_dependency_cache This will remove a pre-existing cached dependency directory. Commit: 3ebbb37c4dc09648ee08877eeb87a1db90a75d35 https://github.com/galaxyproject/galaxy/commit/3ebbb37c4dc09648ee08877eeb87… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-27 (Sun, 27 Nov 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py Log Message: ----------- Add dependency_resolvers/clean endpoint Commit: 23c6b1c6ff6b810fed69c05eec74166cd2d8fc5f https://github.com/galaxyproject/galaxy/commit/23c6b1c6ff6b810fed69c05eec74… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-11-27 (Sun, 27 Nov 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- add a conda clean function to remove downloaded tarballs after installation Commit: 00ca0a600a083bf05e2c8f90610851972e7e94ea https://github.com/galaxyproject/galaxy/commit/00ca0a600a083bf05e2c8f906108… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py Log Message: ----------- Connect `clean` endpoint properly and add `-y` to exec_clean Commit: f467bcb70697bdaac0f94f187970b98f9b58bfe9 https://github.com/galaxyproject/galaxy/commit/f467bcb70697bdaac0f94f187970… Author: Maximilian Friedersdorff <max(a)friedersdorff.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Add total_walltime to legacy job conf Commit: 70bd8c9c45b263894ba96879bedce1af66adc283 https://github.com/galaxyproject/galaxy/commit/70bd8c9c45b263894ba96879bedc… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Small fixes to bootstrap_history.py Commit: a4b70aaf92dfa560cd41aca876c95959763472f9 https://github.com/galaxyproject/galaxy/commit/a4b70aaf92dfa560cd41aca876c9… Author: guerler <aysam.guerler(a)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: 7c4fac6f1c3b1ef25809d7b343dd2fa1eff4973b https://github.com/galaxyproject/galaxy/commit/7c4fac6f1c3b1ef25809d7b343dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3223 from nsoranzo/bootstrap_history_fixes Small fixes to bootstrap_history.py Commit: 5b4a0689d56eea376df0aa7488e5d913d314dbf3 https://github.com/galaxyproject/galaxy/commit/5b4a0689d56eea376df0aa7488e5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #3189 from carlfeberhard/committers [PROCEDURES] Update committers list Commit: c8ea393ccb13216c0d1045adb836c7e20f072c6f https://github.com/galaxyproject/galaxy/commit/c8ea393ccb13216c0d1045adb836… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3221 from hmenager/xsd_add_edam_elements Add EDAM topic(s) and operation(s) elements to XSD file. Commit: fd0a52a9a9aeba2e9ac5b555992c481a562b9162 https://github.com/galaxyproject/galaxy/commit/fd0a52a9a9aeba2e9ac5b555992c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3222 from mvdbeek/api_cache_env Add API to install resolver tool dependencies Commit: b7055791257e51cf22a5d2dc9c0cf2af529a3a5e https://github.com/galaxyproject/galaxy/commit/b7055791257e51cf22a5d2dc9c0c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py A test/api/test_configuration.py R test/casperjs/api-configuration-tests.js Log Message: ----------- Fix configuration API admin checking and tests. - Move CasperJS tests for configuration API into API test framework. - Fix bug where configuration API wouldn't treat master API key as coming from an admin user. Commit: 72960de216cac3d37de168f4eb8bcc760dd68632 https://github.com/galaxyproject/galaxy/commit/72960de216cac3d37de168f4eb8b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: ----------- adjust menu tooltips to be oneliners Commit: e4222b9ae6676c80d22551dc61c3ba14ce2cb315 https://github.com/galaxyproject/galaxy/commit/e4222b9ae6676c80d22551dc61c3… Author: guerler <aysam.guerler(a)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/57fb15984c9038427abd05d801d5… Author: guerler <aysam.guerler(a)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/f1e20b64f5c223e90a164cb0f4d0… Author: guerler <aysam.guerler(a)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/7f3c7b0e2342719526ca9fd4e4cb… Author: guerler <aysam.guerler(a)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/e0a4171113c983fd9d6238a2d492… Author: guerler <aysam.guerler(a)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/e6c1e8e4e830f48203e0d26ed848… Author: guerler <aysam.guerler(a)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/b165757288f0d8d277f8e246601e… Author: Martin Cech <cech.marten(a)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 Commit: 1bbab2d89d2c7af7b6d3d0ffd0b3ece2d153705f https://github.com/galaxyproject/galaxy/commit/1bbab2d89d2c7af7b6d3d0ffd0b3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py A test/api/test_configuration.py R test/casperjs/api-configuration-tests.js Log Message: ----------- Merge pull request #3228 from jmchilton/configuration_test Fix configuration API admin checking and tests. Commit: 2d510fae981f0255f04b21272f99e995f0a16f0b https://github.com/galaxyproject/galaxy/commit/2d510fae981f0255f04b21272f99… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M static/maps/mvc/form/form-section.js.map 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-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: static/maps/mvc/form/form-section.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/bundled/login.bundled.js.map static/scripts/mvc/form/form-section.js Commit: 710c2639f94faac0ef2f999456e183330e4efa54 https://github.com/galaxyproject/galaxy/commit/710c2639f94faac0ef2f999456e1… Author: Martin Cech <cech.marten(a)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/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.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/configuration.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.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/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/history/options-menu.js M static/scripts/mvc/ui/ui-misc.js A static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako 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 A test/api/test_configuration.py M test/api/test_users.py R test/casperjs/api-configuration-tests.js M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- Merge branch 'dev' into adjust-menu-tooltips Conflicts: static/maps/layout/menu.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/layout/menu.js Commit: cc9b741a1dffaa20121f24fcb05cdd63fbb2b8b2 https://github.com/galaxyproject/galaxy/commit/cc9b741a1dffaa20121f24fcb05c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Log when slurm_state is 'COMPLETED' Commit: bf8cffa2b32fd2af33be60a802c2fc49c3d406f9 https://github.com/galaxyproject/galaxy/commit/bf8cffa2b32fd2af33be60a802c2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: 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: ----------- repack client Commit: ead8e15f42a4d74cbbd23dd50380a2facb285714 https://github.com/galaxyproject/galaxy/commit/ead8e15f42a4d74cbbd23dd50380… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #3218 from nsoranzo/slurm_fixes 3 enhancements for the SLURM job runner Commit: 16b027e12509356a53a4fd1268855d913e5438f3 https://github.com/galaxyproject/galaxy/commit/16b027e12509356a53a4fd126885… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M test/base/driver_util.py M test/base/twilltestcase.py Log Message: ----------- Configure a test Galaxy as needed for functional test cases. ./run_tests.sh is still good for launching one Galaxy for a bunch of different test cases - but now you can do really simple things like: ``` $ nosetests test/api/test_tours.py ``` In this scenario, the test case class will check if run_tests.sh has created a test driver to use and if it hasn't - one will be made just for the test case (like the new integration tests). Commit: b6ee471f35fc3d821d07fe406aa759731704eda4 https://github.com/galaxyproject/galaxy/commit/b6ee471f35fc3d821d07fe406aa7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M test/base/driver_util.py Log Message: ----------- Allow test data resolver to work with GALAXY_TEST_EXTERNAL. Commit: 82728df1555141be4fa3e7be16e151124b1dfc89 https://github.com/galaxyproject/galaxy/commit/82728df1555141be4fa3e7be16e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M lib/galaxy/dependencies/dev-requirements.txt M run_tests.sh A scripts/dump_tour.py M scripts/functional_tests.py M templates/webapps/galaxy/workflow/list.mako M test/base/driver_util.py R test/casperjs/anon-history-tests.js R test/casperjs/hda-state-tests.js R test/casperjs/history-options-tests.js R test/casperjs/history-panel-tests.js R test/casperjs/history-share-tests.js R test/casperjs/login-tests.js R test/casperjs/registration-tests.js R test/casperjs/upload-tests.js A test/functional/tools/for_tours/filtering.py A test/functional/tools/for_tours/filtering.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/galaxy_selenium/__init__.py A test/galaxy_selenium/cli.py A test/galaxy_selenium/data.py A test/galaxy_selenium/driver_factory.py A test/galaxy_selenium/has_driver.py A test/galaxy_selenium/navigates_galaxy.py A test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/sizzle.py A test/selenium_tests/__init__.py A test/selenium_tests/framework.py A test/selenium_tests/test_anon_history.py A test/selenium_tests/test_history_dataset_state.py A test/selenium_tests/test_history_options.py A test/selenium_tests/test_history_panel.py A test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_login.py A test/selenium_tests/test_registration.py A test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_uploads.py A test/selenium_tests/test_workflow_editor.py Log Message: ----------- Replace CasperJS browser tests with Selenium tests. See documentation added to run_tests.sh. This can be configured to target local web browsers or Selenium remote services as detailed in that script. Individual tests can be executed with nosetests directly or groups of tests can share a common test Galaxy spin up when using ./run_tests.sh. If GALAXY_TEST_EXTERNAL=<url> is set - it will be respected and Galaxy will not be spun up (remember the URL needs to be reachable from the Selenium server inside the Docker container). Every test failure writes a current screenshot of Galaxy to database/test_errors. I will be honest that the desire to move toward selenium is based solely on failing to get the Casper tests to pass consistently due to bugs causing segfaults in the underlying tools (probably casperjs or phantomjs?). Over the past year I have tried multiple versions of dependencies, etc... and it never works out for me. Likewise Martin has never been able to get the tests to run consistently under Jenkins. I don't think Python or JavaScript is inherently better, this wasn't based on a personal preference about what kind of test I want to write. Despite this being the primary reason, there are clear benefits to Selenium. It tests the actual web browsers we support, generates screenshots, has better documented and more robust tooling, can scale across clusters. Less clear, but certainly still a benefit of being Python based is that it fits with the rest of the test framework more cleanly than CasperJS. Finally Carl's last words on CasperJS were "Ditch it". The following specific tests were added or replaced: - Implemented tour testing via Selenium (walk the two working stock tours and verify elements avaiable and clicks are valid). This is how I discovered #3206. - Added completely new workflow GUI test (basic creation from URL and in editor). - Replaced broken CasperJS registeration tests (text and expectations now wrong) with a Selenium variant that works against dev. - Replaced broken anonymous history CasperJS tests with working Selenium tests. - Replaced broken upload CasperJS tests with working Selenium tests. - Replaced history options CasperJS tests with Selenium tests. - Replaced login CasperJS tests with Selenium tests. - Replaced history-share-tests.js with test_history_options.py - Replaced history-panel-tests.js with test_history_panel.py - Replaced a big part of hda-state-tests.js with test_history_dataset_state.py I'm confident these utilities represent a sharable and higher-level abstraction around functional testing of Galaxy that can be used outside of Galaxy's testing framework. So a subset of the functional test stuff is in a separate module with minimal dependencies that I intend to make stand alone and pip installable like galaxy-lib. This module consists of: - Sizzle stuff in its own package. This code allows Selenium to reason with jQuery selectors instead of vanilla CSS selectors. - Functionality for creating a Selenium driver and virtual display. - The ``HasDriver`` mixin - this provides higher level navigation utilities not specifically tied to Galaxy. - A package with abstractions for navigating Galaxy. This provides a higher-level interfactor for things such as logging in and out, registering a user, navigating menus, fetching Galaxy style tooltips and error messages, and walking Galaxy tours. In order to demonstrate this new module is useful outside of Galaxy tests - I've included a CLI package to ease building argparse utilities around these abstractions and implemented a simple demonstration script that walks a Galaxy tour and dumps screenshots of Galaxy at each step to a folder. This is more of a demonstration of the utilities than an actual polished end user tool - though it might be helpful in linting and debugging tours. In the future I hope to extend this scripting to implement - Periodic deployment testing to ensure things like Jupyter work in production. - A best practice recipe for Galaxy QA testing by deployers. - An utility to generate dozens of screenshots of various aspects of Galaxy so we can quickly visually inspect ever part of the GUI before big releases. xref https://github.com/galaxyproject/starforge/pull/115 xref #1419 Commit: 9b0390defb6832cb6ce56899b6962cd92dac9aee https://github.com/galaxyproject/galaxy/commit/9b0390defb6832cb6ce56899b696… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M test/api/test_api_batch.py R test/casperjs/api-batch-tests.js Log Message: ----------- Remove CasperJS api-batch-tests.js - already available in API test framework. Commit: 5cd2c551043d383aa93452c8bd68bf1ded0def1e https://github.com/galaxyproject/galaxy/commit/5cd2c551043d383aa93452c8bd68… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: R test/casperjs/api-tool-tests.js R test/casperjs/api-user-tests.js Log Message: ----------- Remove CasperJS API user and history tests... ... more complete testing for both is available in API tests. Commit: bf896d621d860f3c93d2276bc02350a2b92b6052 https://github.com/galaxyproject/galaxy/commit/bf896d621d860f3c93d2276bc023… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M test/api/test_histories.py R test/casperjs/api-history-tests.js Log Message: ----------- Move CasperJS history API tests in api/test_histories.py. Commit: 74c4ac3662257776a08bc724a2919547856da819 https://github.com/galaxyproject/galaxy/commit/74c4ac3662257776a08bc724a291… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M run_tests.sh Log Message: ----------- Create simple scripts for all Jenkins tests. Makes it easier to run exact tests (or subset of tests) from Jenkins locally. Selenium script is particularily interesting because it represents a very simple entry point into selenium testing. Commit: 8519e12a474ec5337036136e19c66ed9352ac91a https://github.com/galaxyproject/galaxy/commit/8519e12a474ec5337036136e19c6… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- change conda channel order Commit: 1f221aab22f4840d18847859f5099d4dc721b864 https://github.com/galaxyproject/galaxy/commit/1f221aab22f4840d18847859f509… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- change channel order Commit: 0c91f65a99c43608faaa9f7b504646a326d6adaa https://github.com/galaxyproject/galaxy/commit/0c91f65a99c43608faaa9f7b5046… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Change channel order in documentation Commit: 3b84136d4f0ad15d4965b1ca6baa19e6d51e22d4 https://github.com/galaxyproject/galaxy/commit/3b84136d4f0ad15d4965b1ca6baa… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-01 (Thu, 01 Dec 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 #3230 from martenson/adjust-menu-tooltips adjust menu tooltips to be oneliners Commit: dabc54e40e17e7bcee323c583c77612603670da8 https://github.com/galaxyproject/galaxy/commit/dabc54e40e17e7bcee323c583c77… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Clearly state which are the 'Procedure Documents' Commit: 16167bd01cf8fd0128dd7e7abf25a4fbfd9468ed https://github.com/galaxyproject/galaxy/commit/16167bd01cf8fd0128dd7e7abf25… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Move 'Direct Commit Access' subsection to 'Committers' section Commit: 8de85e4b470c65ddcfe7a39911a92b1fa01e1449 https://github.com/galaxyproject/galaxy/commit/8de85e4b470c65ddcfe7a39911a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Clarify that only PRs modifying tagged release branches require 2 +1 votes Commit: 53b6413df9194da6845b8f4eece2464ef2b1100c https://github.com/galaxyproject/galaxy/commit/53b6413df9194da6845b8f4eece2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Attempt fix of logic for GALAXY_TEST_SELENIUM_HEADLESS == "auto". Pointed out by @dannon. Commit: fa3d2063c4df595e5d0bfd47d7bf30b8b3a567eb https://github.com/galaxyproject/galaxy/commit/fa3d2063c4df595e5d0bfd47d7bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Update selenium test's use of docker-compose to prevent interference across builds. Commit: e731b6f5983a16fdfb1d6418ac5c89a61da77714 https://github.com/galaxyproject/galaxy/commit/e731b6f5983a16fdfb1d6418ac5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Fix and enhance Jenkins test for Selenium. - If condition on fa3d2063c4df595e5d0bfd47d7bf30b8b3a567eb was exactly wrong. - Check for docker-compose services up before and during polling to wait for Galaxy - if Galaxy isn't going to work just die. - Improved logging. Commit: 495ab5992701a64e5cef9997180b75123cd74fd8 https://github.com/galaxyproject/galaxy/commit/495ab5992701a64e5cef9997180b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Another fix for Selenium Jenkins. docker-compose strips out dashes and underscores in the project name when creating containers. Commit: 45edf1bb41fd29abb7b4258942e77a4503c49d6f https://github.com/galaxyproject/galaxy/commit/45edf1bb41fd29abb7b4258942e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Add bed datatype to framework tests because Filter1 now a framework test tool. Commit: 80e64b8cc0dd8f469a6807368339b9a245515006 https://github.com/galaxyproject/galaxy/commit/80e64b8cc0dd8f469a6807368339… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M scripts/dump_tour.py Log Message: ----------- PEP-8 fix as pointed out by @nsoranzo. Commit: 6435db510594a48394896a8e5d8d2a7d129b629d https://github.com/galaxyproject/galaxy/commit/6435db510594a48394896a8e5d8d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- change nitesh's handle to reflect reality Commit: d0c39d6e96bd182852e461761a99e0029c282205 https://github.com/galaxyproject/galaxy/commit/d0c39d6e96bd182852e461761a99… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-02 (Fri, 02 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Sort environment variables in job info page Commit: 86447eced8eb1d0966253a15e3f889bfc97dad17 https://github.com/galaxyproject/galaxy/commit/86447eced8eb1d0966253a15e3f8… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2016-12-02 (Fri, 02 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/test/1.smat M lib/galaxy/datatypes/text.py Log Message: ----------- Add support for ESTScan scores matrices (smat) data type Commit: f52f44230d859e7f3b576710b7c0120e86b66934 https://github.com/galaxyproject/galaxy/commit/f52f44230d859e7f3b576710b7c0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-02 (Fri, 02 Dec 2016) Changed paths: A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M lib/galaxy/dependencies/dev-requirements.txt M run_tests.sh A scripts/dump_tour.py M scripts/functional_tests.py M templates/webapps/galaxy/workflow/list.mako M test/api/test_api_batch.py M test/api/test_histories.py M test/base/driver_util.py M test/base/twilltestcase.py R test/casperjs/anon-history-tests.js R test/casperjs/api-batch-tests.js R test/casperjs/api-history-tests.js R test/casperjs/api-tool-tests.js R test/casperjs/api-user-tests.js R test/casperjs/hda-state-tests.js R test/casperjs/history-options-tests.js R test/casperjs/history-panel-tests.js R test/casperjs/history-share-tests.js R test/casperjs/login-tests.js R test/casperjs/registration-tests.js R test/casperjs/upload-tests.js A test/functional/tools/for_tours/filtering.py A test/functional/tools/for_tours/filtering.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/galaxy_selenium/__init__.py A test/galaxy_selenium/cli.py A test/galaxy_selenium/data.py A test/galaxy_selenium/driver_factory.py A test/galaxy_selenium/has_driver.py A test/galaxy_selenium/navigates_galaxy.py A test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/sizzle.py A test/selenium_tests/__init__.py A test/selenium_tests/framework.py A test/selenium_tests/test_anon_history.py A test/selenium_tests/test_history_dataset_state.py A test/selenium_tests/test_history_options.py A test/selenium_tests/test_history_panel.py A test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_login.py A test/selenium_tests/test_registration.py A test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_uploads.py A test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #3239 from jmchilton/more_selenium Replace CasperJS browser tests with Selenium tests. Commit: 2f9862f3c33c01af244b20173b1106a2ec26d3db https://github.com/galaxyproject/galaxy/commit/2f9862f3c33c01af244b20173b11… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-02 (Fri, 02 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #3256 from erasche/sort-env-vars Sort environment variables in job info page Commit: 982a35df087a2cd51eef97bef978144ee5bdb863 https://github.com/galaxyproject/galaxy/commit/982a35df087a2cd51eef97bef978… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-03 (Sat, 03 Dec 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Merge pull request #3217 from interactomix/dev Per user total walltime limit. Commit: d79d6b96816759bde4234523bbd7a2384474f420 https://github.com/galaxyproject/galaxy/commit/d79d6b96816759bde4234523bbd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-04 (Sun, 04 Dec 2016) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Improved logging for selenium docker-compose problems. If containers fail to start, (as the Galaxy container for the selenium test appears to fail currently) print docker logs for that container. Commit: 5fb334aaee5bff40b51bdca955bb06e21e2a07d8 https://github.com/galaxyproject/galaxy/commit/5fb334aaee5bff40b51bdca955bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-04 (Sun, 04 Dec 2016) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash Log Message: ----------- Increase timeout based on logging on docker.galaxyproject.org. Commit: 851f66f3e8996c34ed306c09de7f1e8b661e25ea https://github.com/galaxyproject/galaxy/commit/851f66f3e8996c34ed306c09de7f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Actually dump all logs on failure... Commit: 5b1b191f2ee555be0247310e1a6c303d783d9ffa https://github.com/galaxyproject/galaxy/commit/5b1b191f2ee555be0247310e1a6c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge branch 'release_16.10' into dev Commit: d7c6f39a9eb8b117c1fe8f98af1aa3bb527be953 https://github.com/galaxyproject/galaxy/commit/d7c6f39a9eb8b117c1fe8f98af1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Increase release delta to 4 months ahead of 17.05. Commit: 45afe7aa61478d88b7b99c08429f4012328247d1 https://github.com/galaxyproject/galaxy/commit/45afe7aa61478d88b7b99c08429f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- fix typo Commit: ab52cc46ed9365eab85881abfcb196b1e2fca63d https://github.com/galaxyproject/galaxy/commit/ab52cc46ed9365eab85881abfcb1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge branch 'release_16.10' into dev Commit: 142ba89a990328548ecbafb5af06ba6799950cd8 https://github.com/galaxyproject/galaxy/commit/142ba89a990328548ecbafb5af06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- Fix tour URLs in welcome Commit: 328f9d1ba0bf60ca8e6be706327a3ad3b0c6e656 https://github.com/galaxyproject/galaxy/commit/328f9d1ba0bf60ca8e6be706327a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M static/welcome.html.sample Log Message: ----------- Merge pull request #3274 from dannon/fix_tour_welcome Fix tour URLs in welcome Commit: cd1ae6b9d26ac3bbb83adcfc0c058221df43ac5a https://github.com/galaxyproject/galaxy/commit/cd1ae6b9d26ac3bbb83adcfc0c05… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3271 from jmchilton/increase_release_timing Increase release delta to 4 months ahead of 17.05. Commit: 33dec01ba2183d2f980947cc467dfab7f9bf4ddb https://github.com/galaxyproject/galaxy/commit/33dec01ba2183d2f980947cc467d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-07 (Wed, 07 Dec 2016) Log Message: ----------- Merge branch 'release_16.10' into dev Commit: cbd527b9a4671c7abe9a22cf69e869b5d2de858a https://github.com/galaxyproject/galaxy/commit/cbd527b9a4671c7abe9a22cf69e8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js A doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst A doc/source/releases/17.01_announce.rst M lib/tool_shed/util/tool_util.py M scripts/bootstrap_history.py M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: b31c3b24ac82a52d095a6e808c3e489dc308c045 https://github.com/galaxyproject/galaxy/commit/b31c3b24ac82a52d095a6e808c3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Fix logo image when serving Galaxy from a subdirectory. Commit: 7da5b17cac75ad7d60454e4ef5bac6d36550bf86 https://github.com/galaxyproject/galaxy/commit/7da5b17cac75ad7d60454e4ef5ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Add a useful logging statement in run_tests.sh. Commit: 0ee095024005862aa2aed585569af1086bbb557e https://github.com/galaxyproject/galaxy/commit/0ee095024005862aa2aed585569a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Fix for new run_tests.sh option to clean PYC files. Commit: eefd716f1f86e8c964f54d133b91db2a0a575b44 https://github.com/galaxyproject/galaxy/commit/eefd716f1f86e8c964f54d133b91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M test/api/test_datasets.py M test/api/test_history_contents.py A test/api/test_visualizations.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js Log Message: ----------- Migrate more CasperJS API tests to the API test framework. - Replace visualization tests (api-visualizations-tests.js -> test_visualizations.py). - Replace dataset API tests (api-dataset-tests.js -> test_datasets.py). - Start work on migrating history dataset API tests (api-hda-tests.js -> test_history_contents.py). Commit: e3d1bd6e0d82eaaea4efa638fa32bd8648f9cddb https://github.com/galaxyproject/galaxy/commit/e3d1bd6e0d82eaaea4efa638fa32… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Merge pull request #3264 from jmchilton/improved_selenium_logging Improved logging for selenium docker-compose problems. Commit: 6f5d8fb6ac2bbe68bc178346c102f5d6df756770 https://github.com/galaxyproject/galaxy/commit/6f5d8fb6ac2bbe68bc178346c102… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3285 from jmchilton/run_tests_touchups Small touchups to run_tests.sh. Commit: d478cc41a6734a537bb12a44eeebe7907f71c19b https://github.com/galaxyproject/galaxy/commit/d478cc41a6734a537bb12a44eeeb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #3240 from nsoranzo/procedures_clarifications [PROCEDURES] Procedures clarifications Commit: d61356dfeaaa4e2e7f0b0a58875a90da67aa210c https://github.com/galaxyproject/galaxy/commit/d61356dfeaaa4e2e7f0b0a58875a… Author: Anne Fouilloux <annefou(a)uio.no> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/datatypes/text.py Log Message: ----------- changed ipython to jupyter When converting jupyter notebook to html, ipython command is used instead of jupyter (ipython is becoming obsolete). Commit: 95305a3ee2bfbe4f9a54d7918f37d12735851b9d https://github.com/galaxyproject/galaxy/commit/95305a3ee2bfbe4f9a54d7918f37… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M doc/Makefile A doc/fix_schema_rst.sh M doc/source/admin/index.rst M doc/source/admin/webhooks.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst Log Message: ----------- Merge branch 'release_16.10' into dev Commit: 06de9d0ae060318244c0c9b653e31058ddd826a7 https://github.com/galaxyproject/galaxy/commit/06de9d0ae060318244c0c9b653e3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Commit: ef7adcec5300819d411b1fb148baf999f2d54422 https://github.com/galaxyproject/galaxy/commit/ef7adcec5300819d411b1fb148ba… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- lexists vs. exists Commit: 767c0400ae92bc541c146ce4ead351b6eacb1fb7 https://github.com/galaxyproject/galaxy/commit/767c0400ae92bc541c146ce4ead3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/jobs/command_factory.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Fix SLURM job re-submission. Approach from @Takadonet - fixes #3289. Commit: e6374bfc211f4192113eea28bbe588a33a197e9a https://github.com/galaxyproject/galaxy/commit/e6374bfc211f4192113eea28bbe5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #3253 from martenson/procedure-nitesh [PROCEDURES] change Nitesh's handle to reflect reality Commit: 96bd4552e1b1a7b18d57f8e0d0f1a5da22b085a1 https://github.com/galaxyproject/galaxy/commit/96bd4552e1b1a7b18d57f8e0d0f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Further tighten up GG format. I encountered similar input problems to #864 - this helps a little. - Ensure first column is a valid marker as outlined on https://genome.ucsc.edu/goldenpath/help/hgGenomeHelp.html. - Avoid readlines() since it may allocate huge amounts on memory on certain inputs. - Eliminate bare exception. Rebased with bug fixes in original commit and better testing and tighter exception handling as suggested by @nsoranzo. Commit: 176d4d5cf49a5859357ba88f38ef6a2136fb8570 https://github.com/galaxyproject/galaxy/commit/176d4d5cf49a5859357ba88f38ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #3233 from jmchilton/gg_datatype Further tighten up GG format. Commit: 8b9337ffd3f3911ed229dcdce1086f682302a4ae https://github.com/galaxyproject/galaxy/commit/8b9337ffd3f3911ed229dcdce108… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge pull request #3301 from bgruening/lexists lexists vs. exists Commit: 93da60c48e9947b2ae5f7ff080db20fbcd59c51f https://github.com/galaxyproject/galaxy/commit/93da60c48e9947b2ae5f7ff080db… Author: Anne Fouilloux <annefou(a)uio.no> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M doc/source/admin/interactive_environments.svg M doc/source/dev/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/datatypes/text.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/proxy/js/Dockerfile M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Changed ipython with jupyter not only for converting jupyter notebook to HTML (with nbconvert) but also where ipython/IPython was referenced. Some files still contain ipython but this is mostly related to documentation or to the IE docker container itself. Commit: 7468ea3d34312b1562454d43a2eaf0158ac5478e https://github.com/galaxyproject/galaxy/commit/7468ea3d34312b1562454d43a2ea… Author: Anne Fouilloux <annefou(a)uio.no> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M doc/Makefile A doc/fix_schema_rst.sh M doc/source/admin/index.rst M doc/source/admin/webhooks.rst M doc/source/project/organization.rst M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/deps/installable.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev to take into account the latest changes done on the galaxyproject Commit: 32898fb6bfada2b0a57ac45813f2751cc77dd7c5 https://github.com/galaxyproject/galaxy/commit/32898fb6bfada2b0a57ac45813f2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/tools/deps/mulled/invfile.lua Log Message: ----------- Bring in galaxyproject/galaxy-lib#36 from @bgruening. Commit: f6a573a4191cf9c90fb4aac78d20064e11cb1c7b https://github.com/galaxyproject/galaxy/commit/f6a573a4191cf9c90fb4aac78d20… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/tools/deps/mulled/invfile.lua Log Message: ----------- Merge pull request #3304 from jmchilton/galaxy-lib-update-4 Bring in galaxyproject/galaxy-lib#36 from @bgruening. Commit: 28c2acf17dfc2b73276de0ba7cb73c93d730dde5 https://github.com/galaxyproject/galaxy/commit/28c2acf17dfc2b73276de0ba7cb7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M Makefile Log Message: ----------- Adds a 'make charts' makefile target to make it more obvious how to build these. Not invoked automatically though, since these should very rarely conflict and we don't want to have version build difference conflicts (harmless) all the time. Commit: 8eba2f2f1bbc32a97eb51b97712fb67691723282 https://github.com/galaxyproject/galaxy/commit/8eba2f2f1bbc32a97eb51b97712f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M config/plugins/visualizations/charts/webpack.config.js Log Message: ----------- Remove unnecessary require -- webpack is expected as the executor here Commit: a0ae63d8c2983f17aa75b161bd25fa505af20a6c https://github.com/galaxyproject/galaxy/commit/a0ae63d8c2983f17aa75b161bd25… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M Makefile Log Message: ----------- Set NODE_MODULES var for 'grunt charts', required due to the execution model here. Commit: 49cdd7082d86c07ab07bb1bee8e4b26baf6b4eb8 https://github.com/galaxyproject/galaxy/commit/49cdd7082d86c07ab07bb1bee8e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M Makefile Log Message: ----------- Shot in the dark at @nsoranzo's build woes. Commit: fc5ac197914bd1a957fd074424adee115f7a2d96 https://github.com/galaxyproject/galaxy/commit/fc5ac197914bd1a957fd074424ad… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/jobs/command_factory.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #3290 from jmchilton/clean_working_directory Fix SLURM job re-submission. Commit: 015c32854f2d9ff9402b73f9fe8b291cd2346df5 https://github.com/galaxyproject/galaxy/commit/015c32854f2d9ff9402b73f9fe8b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M Makefile Log Message: ----------- Override possible env var use which can break this -- we always want to use Galaxy's modules here anyway Commit: c7568a1d871b8c4c3816130c33a24e1e21e12f29 https://github.com/galaxyproject/galaxy/commit/c7568a1d871b8c4c3816130c33a2… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M Makefile M config/plugins/visualizations/charts/webpack.config.js Log Message: ----------- Merge pull request #3306 from dannon/charts_makefile_target Adds a 'make charts' makefile target to make it more obvious how to build these. Commit: 584114a4698076b79d77124b27867d6ea2386188 https://github.com/galaxyproject/galaxy/commit/584114a4698076b79d77124b2786… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/tool_shed/galaxy_install/install_manager.py M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: config/plugins/visualizations/charts/static/repository/build/registry.js config/plugins/visualizations/charts/static/repository/build/registry.js.map Commit: 8a80b2dc712bd16465197799a4ef3cc8dab01bc9 https://github.com/galaxyproject/galaxy/commit/8a80b2dc712bd16465197799a4ef… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- change order in galaxy.ini Commit: 3d492657028b3a29c9e3707cb609db87f4a783f6 https://github.com/galaxyproject/galaxy/commit/3d492657028b3a29c9e3707cb609… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- change oder in docs Commit: f693643ea87dc807277cb6c2e8c3a2f9946fe5d4 https://github.com/galaxyproject/galaxy/commit/f693643ea87dc807277cb6c2e8c3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- change channel order in conda.py Commit: ad8d48c0a39de2afb360f58aee40f60f10dd25da https://github.com/galaxyproject/galaxy/commit/ad8d48c0a39de2afb360f58aee40… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-12 (Mon, 12 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3237 from galaxyproject/conda_channel change conda channel order Commit: e08e7827e5df961554e05a0c87eaa7359659c2c3 https://github.com/galaxyproject/galaxy/commit/e08e7827e5df961554e05a0c87ea… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Eliminate unnecessary file close Commit: 81a0cbf4721d7279e3a5b901e1646380d797635b https://github.com/galaxyproject/galaxy/commit/81a0cbf4721d7279e3a5b901e164… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml 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/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.xml M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml Log Message: ----------- Update datatype converter tools - dos2unix - Fix indentation - Add missing tool version - Remove deprecated <page> elements - Remove deprecated 'interpreter' attribute of <command> - Quote some data parameters in <command> - Remove some duplicated requirement Commit: ac8450f013284bc5b8502cfec0d64e809390ce02 https://github.com/galaxyproject/galaxy/commit/ac8450f013284bc5b8502cfec0d6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml Log Message: ----------- Add CDATA. Use && to concatenate commands. Quote $chromInfo Commit: cf7119c474e294eae79320fa5a51e5cdb5fa5835 https://github.com/galaxyproject/galaxy/commit/cf7119c474e294eae79320fa5a51… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-12-13 (Tue, 13 Dec 2016) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml 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/encodepeak_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml M lib/galaxy/datatypes/converters/fasta_to_len.xml M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.xml M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.xml M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml Log Message: ----------- Merge pull request #3305 from nsoranzo/converter_tools Update datatype converter tools Commit: bb4e7c1a64df3b3c7c5c5c6391310883726a0af4 https://github.com/galaxyproject/galaxy/commit/bb4e7c1a64df3b3c7c5c5c639131… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Add change_password functionality back to the user controller. This was removed a bit too soon in https://github.com/galaxyproject/galaxy/commit/14e635aaee2699cb395443d802de…, without a replacement available. There's significant work involved in a replacement, so @guerler and I agreed to simply add the endpoint back for now. Commit: e627f55be69aead2c8aec7dfe7f230c125cf2f7d https://github.com/galaxyproject/galaxy/commit/e627f55be69aead2c8aec7dfe7f2… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Merge pull request #3283 from jmchilton/logo_source Fix logo image when serving Galaxy from a subdirectory. Commit: ac581a5453e6f43a4900d55d67a3c1bd75081f47 https://github.com/galaxyproject/galaxy/commit/ac581a5453e6f43a4900d55d67a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M run_tests.sh M test/base/api.py M test/base/integration_util.py M test/integration/test_resolvers.py Log Message: ----------- Improved documentation and design of integration tests. - Allow running through ``run_tests.sh``. - Enable more verbose test errors for Conda tests. - Refactor how integration tests depend on API testing (use a Mixin instead of subclassing conceptually conflicting TestCase classes). Commit: 00c6ee17b7f742efdd895fae44771edacba77c4b https://github.com/galaxyproject/galaxy/commit/00c6ee17b7f742efdd895fae4477… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M .ci/jenkins/integration/run_tests.sh Log Message: ----------- Fix Jenkins script test for integration tests. Commit: b78287f1508db2c06f0c309ed8d3747adb4d17fa https://github.com/galaxyproject/galaxy/commit/b78287f1508db2c06f0c309ed8d3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M test/base/driver_util.py M test/base/interactor.py M test/functional/test_toolbox.py A test/integration/retry_jobs_job_conf.xml A test/integration/retry_jobs_job_resource_parameters_conf.xml A test/integration/retry_runner.py A test/integration/test_retry_jobs.py M test/unit/jobs/test_mapper.py Log Message: ----------- Integration test for advanced job runner stuff. Set of test cases that cover job resource handlers and resubmit job destinations. Commit: 0559cff6e94b250ddd98275b119ab51b36491e34 https://github.com/galaxyproject/galaxy/commit/0559cff6e94b250ddd98275b119a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py A test/integration/resubmission_job_conf.xml A test/integration/resubmission_job_resource_parameters_conf.xml A test/integration/resubmission_rules/__init__.py A test/integration/resubmission_rules/rules.py A test/integration/resubmission_runners.py R test/integration/retry_jobs_job_conf.xml R test/integration/retry_jobs_job_resource_parameters_conf.xml R test/integration/retry_runner.py A test/integration/test_job_resubmission.py R test/integration/test_retry_jobs.py Log Message: ----------- Implement resubmit on unknown failures. Commit: 7d52b28ab2ab0314cd4fa31108a6750cb9750ef3 https://github.com/galaxyproject/galaxy/commit/7d52b28ab2ab0314cd4fa31108a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M test/integration/resubmission_job_conf.xml M test/integration/test_job_resubmission.py Log Message: ----------- Allow expressions in job_conf resubmission conditions. Since we allow dynamic job runners clearly job_conf.xml must be considered a trusted document. Still I know that some are uneasy with eval generally so I only allow a very safe subset of Python expressions in this job_conf document. Commit: 949d1224892861bd27207dd0799e2b356576c2cb https://github.com/galaxyproject/galaxy/commit/949d1224892861bd27207dd0799e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Fix preservation of resubmits for resubmitted jobs. Create an abstraction for the explicit handling of resubmits that is done during job recovery at startup. xref https://github.com/galaxyproject/galaxy/commit/5539a083e21b601bfd2f87fa3417… Commit: 7e338d790964f594ae67b33e6a72e1777e774b8c https://github.com/galaxyproject/galaxy/commit/7e338d790964f594ae67b33e6a72… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/__init__.py M test/integration/resubmission_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py Log Message: ----------- Add attempt to resubmission expression language. Commit: 325b0354754815d32ed458d212d8c1c192630b0b https://github.com/galaxyproject/galaxy/commit/325b0354754815d32ed458d212d8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M test/integration/resubmission_job_conf.xml Log Message: ----------- Add a self re-submission test. Commit: 18eb1c8d0e4c3f7616d44fd177c90943695b7053 https://github.com/galaxyproject/galaxy/commit/18eb1c8d0e4c3f7616d44fd177c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/__init__.py M test/integration/resubmission_job_conf.xml M test/integration/resubmission_job_resource_parameters_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py Log Message: ----------- Add seconds_running and seconds_since_queued to condition expression langauge. Commit: 334dfe1b116775466ef772a9d7a98d6247959ed0 https://github.com/galaxyproject/galaxy/commit/334dfe1b116775466ef772a9d7a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/__init__.py M test/integration/resubmission_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py Log Message: ----------- Allow (and test) using expressions in job re-submission delays. So you can backoff re-submission with ``delay="attempt * 30"`` for instance - which will cause a re-submission delay to increase by 30 seconds for each resubmission of a job. Commit: c4069da7429242bdbf7fb02da9716e4e8413512c https://github.com/galaxyproject/galaxy/commit/c4069da7429242bdbf7fb02da971… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #3313 from dannon/password_reset_fixes Add change_password functionality back to the user controller. Commit: 521a585a23459714e9723903363ffa495918cc60 https://github.com/galaxyproject/galaxy/commit/521a585a23459714e9723903363f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/jobs/runners/local.py M test/integration/resubmission_runners.py Log Message: ----------- Two lint fixes for #3291. Commit: da784093b3683b3586075aed3c70e38c3adc7c22 https://github.com/galaxyproject/galaxy/commit/da784093b3683b3586075aed3c70… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- Merge branch 'release_16.10' into dev Commit: ed4e87ecad31f48ecefa11b7c9a7aae4c71939aa https://github.com/galaxyproject/galaxy/commit/ed4e87ecad31f48ecefa11b7c9a7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/style/less/dataset.less M static/maps/mvc/dataset/dataset-li-edit.js.map A static/maps/mvc/user/change-password.js.map A static/maps/mvc/user/extra-information.js.map A static/maps/mvc/user/manage-user-information.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 A static/scripts/mvc/user/change-password.js A static/scripts/mvc/user/extra-information.js A static/scripts/mvc/user/manage-user-information.js M static/style/blue/base.css Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/bundled/login.bundled.js.map static/style/blue/base.css Commit: 498dddb03fe33df71ec887a9c53311ce53069e31 https://github.com/galaxyproject/galaxy/commit/498dddb03fe33df71ec887a9c533… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M .ci/jenkins/integration/run_tests.sh M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/model/__init__.py M run_tests.sh M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/functional/test_toolbox.py A test/integration/resubmission_job_conf.xml A test/integration/resubmission_job_resource_parameters_conf.xml A test/integration/resubmission_rules/__init__.py A test/integration/resubmission_rules/rules.py A test/integration/resubmission_runners.py A test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M test/unit/jobs/test_mapper.py Log Message: ----------- Merge pull request #3291 from jmchilton/integration_tests_0 Ready Integration Testing for Prime Time Commit: 74923463cf4139ef084b155467975c7040ba5561 https://github.com/galaxyproject/galaxy/commit/74923463cf4139ef084b15546797… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'release_16.10' into dev Commit: ad738447e7003429dfe43198a339a8bf78231287 https://github.com/galaxyproject/galaxy/commit/ad738447e7003429dfe43198a339… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M doc/source/releases/16.10.rst M doc/source/releases/16.10_announce.rst Log Message: ----------- Merge branch 'release_16.10' into dev Commit: 36895d1dce26efc5db8f172b5b329b5dcbc54202 https://github.com/galaxyproject/galaxy/commit/36895d1dce26efc5db8f172b5b32… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-15 (Thu, 15 Dec 2016) Log Message: ----------- Merge branch 'release_16.10' into dev Commit: b4c4d9836cbfc77230dd156e4ff701040b8c08f7 https://github.com/galaxyproject/galaxy/commit/b4c4d9836cbfc77230dd156e4ff7… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- fixed a typo Commit: 330cb432e819ebb2e8f28bf99a6aad3d5b70c863 https://github.com/galaxyproject/galaxy/commit/330cb432e819ebb2e8f28bf99a6a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-15 (Thu, 15 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3322 from anatskiy/hotfix/run_tests_typo run_tests.sh: a small typo Commit: a473c0787a42618d26269e79732f6e997016c9d2 https://github.com/galaxyproject/galaxy/commit/a473c0787a42618d26269e79732f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Provide a fallback to old IPython named config option... ... as suggested by @bgruening in https://github.com/galaxyproject/galaxy/pull/3294#pullrequestreview-12532937. Commit: 553f781d39218d9b717e5a09ebfcf5214e680e16 https://github.com/galaxyproject/galaxy/commit/553f781d39218d9b717e5a09ebfc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M doc/source/admin/interactive_environments.svg M doc/source/dev/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/datatypes/text.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/proxy/js/Dockerfile M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge pull request #3294 from annefou/dev changed ipython to jupyter Commit: 147de088177c262c9ad3fd13ac4929217bee6618 https://github.com/galaxyproject/galaxy/commit/147de088177c262c9ad3fd13ac49… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/test/1.smat M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #3258 from gregvonkuster/smat2 Add support for ESTScan scores matrices (smat) data type Commit: cbd9f68f760178b113b624078372f955b486d32e https://github.com/galaxyproject/galaxy/commit/cbd9f68f760178b113b624078372… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M test/api/test_tools.py Log Message: ----------- Fixup test case for #3209. Commit: 58a3a5b71b00c974b19eae514b09abfc04b74170 https://github.com/galaxyproject/galaxy/commit/58a3a5b71b00c974b19eae514b09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of gff_filter_by_attribute. Broken during security patching - Travis tests are failing now against dev. Commit: f4282c8672df5fb1f4d1f401c0209e1c6f253ca5 https://github.com/galaxyproject/galaxy/commit/f4282c8672df5fb1f4d1f401c020… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py A test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3209 from mvdbeek/fix_paired_list Fix for mapping tools with paired collection input and a structured_like tag over list:paired collections Commit: 2845bfaf9609e55e785a71606ec535a225e7529d https://github.com/galaxyproject/galaxy/commit/2845bfaf9609e55e785a71606ec5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Merge pull request #3324 from jmchilton/fix_lint_security Fix linting of gff_filter_by_attribute. Commit: 27673f5e08b67d432a0bd369aea6eac248ba8f93 https://github.com/galaxyproject/galaxy/commit/27673f5e08b67d432a0bd369aea6… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample A display_applications/igv/genome_fasta.xml A lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- Addition of Genome fasta file loading in local IGV instance, and addition of fai format and fasta to fai converter Commit: 8cc2efb74f6679aee72cfdbc35a592d7abd2f4dc https://github.com/galaxyproject/galaxy/commit/8cc2efb74f6679aee72cfdbc35a5… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- removal of old commented line Commit: 1d0f15d1750e88dc1bf6ba835be2561771f99ce6 https://github.com/galaxyproject/galaxy/commit/1d0f15d1750e88dc1bf6ba835be2… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M display_applications/igv/genome_fasta.xml Log Message: ----------- Edit of Authors Commit: f4070ba9815ffacd28523f6e87398dea42271e8f https://github.com/galaxyproject/galaxy/commit/f4070ba9815ffacd28523f6e8739… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Syntax cleaning Commit: a504e8ea7be42940800dcb67d2c00d478868fb2c https://github.com/galaxyproject/galaxy/commit/a504e8ea7be42940800dcb67d2c0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample A display_applications/igv/genome_fasta.xml A lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- Merge pull request #3327 from Delphine-L/IGV_display_fasta Addition of IGV display for genome fasta file Commit: 02501b938724ce7a788c6e6d91b7b506e0e5f25b https://github.com/galaxyproject/galaxy/commit/02501b938724ce7a788c6e6d91b7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #3325 from jmchilton/juypter_fixes Provide a fallback to old IPython named config option... Commit: 48bc9ba31d43af09823b66726af86c7cfb0b8bba https://github.com/galaxyproject/galaxy/commit/48bc9ba31d43af09823b66726af8… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- add an option to specify the port, which is used to connect the UIs Commit: f83a1bacf6531a3efe404e93faca924d5a01bd3f https://github.com/galaxyproject/galaxy/commit/f83a1bacf6531a3efe404e93faca… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3328 from bgruening/ie_port_overwrite IE enhancement Commit: 96678f57ccef01f322a6c6525defaa73333e56d0 https://github.com/galaxyproject/galaxy/commit/96678f57ccef01f322a6c6525def… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M doc/source/dev/faq.rst Log Message: ----------- More IPython to Jupyter changes Follow-up on #3294. Commit: 433b993ecae7d306d4222ca5d91a4a31cd907e52 https://github.com/galaxyproject/galaxy/commit/433b993ecae7d306d4222ca5d91a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh Log Message: ----------- Slim down testing ``Dockerfile``. - Remove broken CasperJS from testing Dockerfile. - Remove multi-process mode. Multi-process mode was difficult to maintain and the last time I did testing at scale I found docker-galaxy-stable to be much more useful and easy to use. The test framework now supports GALAXY_TEST_EXTERNAL again so it should be easy enough to rig something up with docker-compose that actually uses a best practice container for scaling tests such as those in ``test/manual``. Commit: 415ddbb3bf8d44acdcabc29478544420a45fc7e4 https://github.com/galaxyproject/galaxy/commit/415ddbb3bf8d44acdcabc2947854… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge branch 'release_16.10' into dev Commit: 9bb570f62f8e6f135f2776808a6a92e91ec8b7cb https://github.com/galaxyproject/galaxy/commit/9bb570f62f8e6f135f2776808a6a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Allow admins to see API keys under REMOTE_USER Commit: c36fbebb443ae5b5263ba6cad6ad36113bb52f44 https://github.com/galaxyproject/galaxy/commit/c36fbebb443ae5b5263ba6cad6ad… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- genbank datatype Commit: c61be93b70fd65b4bccf5f8416b58086ae98a085 https://github.com/galaxyproject/galaxy/commit/c61be93b70fd65b4bccf5f8416b5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Prettier Job information page Commit: 5e2249c1b4698db4880fb74e422a903585bc3054 https://github.com/galaxyproject/galaxy/commit/5e2249c1b4698db4880fb74e422a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Address review concerns Commit: 43075015dd7bd81bef0394259f0a60721f4163df https://github.com/galaxyproject/galaxy/commit/43075015dd7bd81bef0394259f0a… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3339 from erasche/genbank Genbank datatype Commit: e1b54f60f20e13353d9742fb15ec4cfd2c48fd2e https://github.com/galaxyproject/galaxy/commit/e1b54f60f20e13353d9742fb15ec… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-12-20 (Tue, 20 Dec 2016) Log Message: ----------- Merge branch 'release_16.10' into dev Commit: a7818e306598e5aa800123578cdad7936c88f34f https://github.com/galaxyproject/galaxy/commit/a7818e306598e5aa800123578cda… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py R test/functional/workflow.py Log Message: ----------- Remove workflow testing stuff in test/functional and references. There are more fully developed approaches including Planemo and wft4galaxy (https://github.com/phnmnl/wft4galaxy) Commit: 318e5a23ad0ef2d50debfe72a0366ec5fd8513c3 https://github.com/galaxyproject/galaxy/commit/318e5a23ad0ef2d50debfe72a036… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Update UCSC_SERVERS list to include new SOE prefix. Commit: fe2ec33d0bb67b0cbf0ef9297b737592f4f938bb https://github.com/galaxyproject/galaxy/commit/fe2ec33d0bb67b0cbf0ef9297b73… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Remove empty header from non-admin view Commit: dd062b5ca8de36a43b133a58b09d374ce07d63bd https://github.com/galaxyproject/galaxy/commit/dd062b5ca8de36a43b133a58b09d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/env.py M templates/show_params.mako Log Message: ----------- Remove replace, just don't add in first place Commit: 1c7055fe3b974d06c8e166e39ac1a53d2f078642 https://github.com/galaxyproject/galaxy/commit/1c7055fe3b974d06c8e166e39ac1… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Split metric table into sections Commit: 4756cab4cbcca729e3db66f33a8d031b796eb8d2 https://github.com/galaxyproject/galaxy/commit/4756cab4cbcca729e3db66f33a8d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Remove visual noise Commit: e407b4b2c7226fc00d5cf2c42126ab83409bca7a https://github.com/galaxyproject/galaxy/commit/e407b4b2c7226fc00d5cf2c42126… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3338 from erasche/admin_see_apikeys Allow admins to see API keys under REMOTE_USER Commit: 64b0d0326097f96c7637bd6355ca790c4ef8d4be https://github.com/galaxyproject/galaxy/commit/64b0d0326097f96c7637bd6355ca… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- cleanup css a bit Commit: cc32dcae4be031a95c393fd4efee459d398ae9c7 https://github.com/galaxyproject/galaxy/commit/cc32dcae4be031a95c393fd4efee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_tool_form.py Log Message: ----------- Initial tool form and dataset detail selenium testing. - Test parameters and tables appear on dataset details page after running a tool. - Test a simple tool execution with an integer field. - Test re-run a tool. - Test a tool with a data drop down. - Improved select2 abstractions. Commit: 097cf7f0fbcce7bc82539e17c12f7355deeaa558 https://github.com/galaxyproject/galaxy/commit/097cf7f0fbcce7bc82539e17c12f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Job metrics: Sort metrics on displayed title not key used for database. Commit: ef1fd488241a18952df146d30852054ab27a4a63 https://github.com/galaxyproject/galaxy/commit/ef1fd488241a18952df146d30852… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M templates/show_params.mako Log Message: ----------- Fix bad merge in cc32dcae4be031a95c393fd4efee459d398ae9c7. Spotted by @erasche. Commit: a5af4d155f6e4ab549c50e51703de49ee3052d16 https://github.com/galaxyproject/galaxy/commit/a5af4d155f6e4ab549c50e51703d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M test/selenium_tests/test_tool_form.py Log Message: ----------- Fix Python 3 linting error for #3340. Commit: af90b42a68d119118d3fd2845738ef4835799af1 https://github.com/galaxyproject/galaxy/commit/af90b42a68d119118d3fd2845738… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/env.py M templates/show_params.mako M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #3340 from erasche/nicer_info_page Prettier Job Information Page Commit: 83d9ddd0b3e090829e70b95ac6bd26b63179e40f https://github.com/galaxyproject/galaxy/commit/83d9ddd0b3e090829e70b95ac6bd… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M templates/show_params.mako Log Message: ----------- Expose job metrics Commit: 538447be76da011508eb4a8784eefe2b9e45b270 https://github.com/galaxyproject/galaxy/commit/538447be76da011508eb4a8784ee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/interactive_environments.rst M doc/source/dev/faq.rst Log Message: ----------- Merge pull request #3333 from nsoranzo/followup_on_3294 More IPython to Jupyter changes Commit: 306c64d1bc3cec871f38b522ad3f7bf8e0ca3a66 https://github.com/galaxyproject/galaxy/commit/306c64d1bc3cec871f38b522ad3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #3197 from scholtalbers/workflows-rename-output-minor-update update rename dataset action to accept . in repeat input parameters Commit: 38d3163b2c7d0e9c4e428f4884cbed971a2f5bae https://github.com/galaxyproject/galaxy/commit/38d3163b2c7d0e9c4e428f4884cb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Fix history list selector Commit: 10720fa4f9e26b3feec1a90468f4ecc726a99c05 https://github.com/galaxyproject/galaxy/commit/10720fa4f9e26b3feec1a90468f4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml M test/selenium_tests/test_stock_tours.py Log Message: ----------- Fixup and test core.history.yaml tour. Commit: ae87eb94131e2a0da8ebae4ca6137ba111072852 https://github.com/galaxyproject/galaxy/commit/ae87eb94131e2a0da8ebae4ca613… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M templates/show_params.mako Log Message: ----------- Address the review comments Commit: 74dfcd32891b5a24b9c255097f780143cc28a104 https://github.com/galaxyproject/galaxy/commit/74dfcd32891b5a24b9c255097f78… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- cache deps on the fly when first used Commit: 9dbe766e42d3c22d09c5809823b8fec144ac5966 https://github.com/galaxyproject/galaxy/commit/9dbe766e42d3c22d09c5809823b8… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- add build_cache_on_first_run option Commit: 26ba67083ca8bbf33134a6caa032792a1d27f907 https://github.com/galaxyproject/galaxy/commit/26ba67083ca8bbf33134a6caa032… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- make travis happy Commit: 132e284d371992995c14eefbc299110533ec48b4 https://github.com/galaxyproject/galaxy/commit/132e284d371992995c14eefbc299… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 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: ----------- Bug fix for masthead webhook if Galaxy.page is undefined for workflow, data libraries etc pages Commit: ef82eec6109721c4a5c2f4ab2e760f73bf46c7ce 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lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/1.smat M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/proxy/js/Dockerfile M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/galaxy_install/install_manager.py M run_tests.sh M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/user/change-password.js.map A static/maps/mvc/user/extra-information.js.map A static/maps/mvc/user/manage-user-information.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/user/change-password.js A static/scripts/mvc/user/extra-information.js A static/scripts/mvc/user/manage-user-information.js M static/style/blue/base.css M templates/show_params.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/workflow/editor.mako M test/api/test_tools.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/functional/test_toolbox.py A test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py A test/integration/resubmission_job_conf.xml A test/integration/resubmission_job_resource_parameters_conf.xml A test/integration/resubmission_rules/__init__.py A test/integration/resubmission_rules/rules.py A test/integration/resubmission_runners.py A test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_tool_form.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_mapper.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merging with dev Commit: 7ae30948be60e34bc7b54cbf74f23da45414bad1 https://github.com/galaxyproject/galaxy/commit/7ae30948be60e34bc7b54cbf74f2… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #3345 from dannon/ucsc_redirect_fix Update UCSC_SERVERS list to include new(ish?) soe subdomain Commit: 20632b2757f789bc751faa280fa34eebe78e41db https://github.com/galaxyproject/galaxy/commit/20632b2757f789bc751faa280fa3… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/search/__init__.py M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding fuzzy search to tool search Commit: c000e68baae47dc7624465dacc3c6aa0217ece0a https://github.com/galaxyproject/galaxy/commit/c000e68baae47dc7624465dacc3c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml M test/selenium_tests/test_stock_tours.py Log Message: ----------- Merge pull request #3185 from dannon/tour_history_fixes History Introduction tour fixes for structural changes Commit: 1a0dde830c3e9f33a02564d824fe0c468b5724cf https://github.com/galaxyproject/galaxy/commit/1a0dde830c3e9f33a02564d824fe… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- change option name and default value Commit: cac828ee8e91a8e0f4671042702e6898157bfd4e https://github.com/galaxyproject/galaxy/commit/cac828ee8e91a8e0f4671042702e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M templates/show_params.mako Log Message: ----------- Merge pull request #3344 from erasche/expose-metrics Expose metrics to non-admins Commit: 2783212c754ee9449688ce89893ada18afc0b8af https://github.com/galaxyproject/galaxy/commit/2783212c754ee9449688ce89893a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge branch 'release_16.10' into dev Commit: 8463c8a2024eef59d4faded15fd40f7850d7de7e https://github.com/galaxyproject/galaxy/commit/8463c8a2024eef59d4faded15fd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-22 (Thu, 22 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3358 from jmchilton/dev_merge Merge latest release 16.10 into dev. Commit: 52e4b6e89e862ce2a9e3897782a0836272be6581 https://github.com/galaxyproject/galaxy/commit/52e4b6e89e862ce2a9e3897782a0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: R tools/filters/gff/sort_gtf.py Log Message: ----------- Remove seemingly unused file sort_gtf.py. Added in df28aec040f05f2d97856f5d8c4f07ba2a7e1966 - not used in that commit. Commit: 58c1828c4c268aa80f1fe62888227d64d63b65d2 https://github.com/galaxyproject/galaxy/commit/58c1828c4c268aa80f1fe6288822… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M run_tests.sh M scripts/functional_tests.py R test/functional/workflow.py Log Message: ----------- Merge pull request #3342 from jmchilton/remove_workflow_testing Remove workflow testing stuff in test/functional and references. Commit: f34bb5e1f66e47ae13396f8ab8d8336aa635a255 https://github.com/galaxyproject/galaxy/commit/f34bb5e1f66e47ae13396f8ab8d8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-24 (Sat, 24 Dec 2016) Changed paths: M lib/galaxy/config.py M test/base/driver_util.py Log Message: ----------- Don't override Global tempfile.tmpdir for tests. Tests may bring up multiple Galaxy instances - for integration tests this leads to a longer temp path with each new Galaxy instance brought up. This in turn breaks Conda for tests on Jenkins. Commit: a0aa70baa0573ff891f51f3ffbc29e07dcf970a5 https://github.com/galaxyproject/galaxy/commit/a0aa70baa0573ff891f51f3ffbc2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-24 (Sat, 24 Dec 2016) Changed paths: M test/integration/test_job_resubmission.py Log Message: ----------- Fix broken integration test. It was simply checking the wrong condition. Commit: 261524e57fd353267016cfce3a7ca8de2b27d89c https://github.com/galaxyproject/galaxy/commit/261524e57fd353267016cfce3a7c… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: M lib/galaxy/config.py M test/base/driver_util.py M test/integration/test_job_resubmission.py Log Message: ----------- Merge pull request #3365 from jmchilton/integration_tests_1 Attempt to fix broken integration tests on Jenkins. Commit: 0383f5abc199fef22541adda9020fa84b8e98239 https://github.com/galaxyproject/galaxy/commit/0383f5abc199fef22541adda9020… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: R scripts/run_selenium_tests.sh Log Message: ----------- Remove defunct script run_selenium_tests.sh. Commit: 3ec3653adb4e796eb97625c339d03cba78ace726 https://github.com/galaxyproject/galaxy/commit/3ec3653adb4e796eb97625c339d0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Fix auto creation of XUnit reports for Jenkins. This is why Jenkins isn't picking up reports for integration and Selenium tests automatically. Commit: dfcd8e4bf69cccd50a5482b5440937e11e569b84 https://github.com/galaxyproject/galaxy/commit/dfcd8e4bf69cccd50a5482b54409… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py Log Message: ----------- Rework display of inputs for workflow form. - If steps have labels, use them. - Use workflow icon from workflow editor in step bar. - Eliminate "Step Index" from display of workflow steps. Commit: cd0387f7ba0da51806cea4224da20f908faadc97 https://github.com/galaxyproject/galaxy/commit/cd0387f7ba0da51806cea4224da2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-icons.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.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Repack client scripts. Commit: d4f70648898a58b50613224cda82ea88f1b12934 https://github.com/galaxyproject/galaxy/commit/d4f70648898a58b50613224cda82… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: R scripts/run_selenium_tests.sh Log Message: ----------- Merge pull request #3367 from jmchilton/remove_script Remove defunct script run_selenium_tests.sh. Commit: 4c22cefadd877a4ea5a78a24cda56c62504dfe96 https://github.com/galaxyproject/galaxy/commit/4c22cefadd877a4ea5a78a24cda5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3368 from jmchilton/fix_jenkins_xunit_reports Fix auto creation of XUnit reports for Jenkins. Commit: 487506cc79d105f318f6a03e7a6f397ae765b9e8 https://github.com/galaxyproject/galaxy/commit/487506cc79d105f318f6a03e7a6f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: M run_tests.sh Log Message: ----------- Fix automatic handling of Jenkins BUILD_NUMBER in Dockerized tests. Follow up #3368, this fix is also needed. I think we are getting closer... xref #3199 xref #3360 Commit: c8ef41f1f1212457c2040ba4f14d7403c3f2aeb9 https://github.com/galaxyproject/galaxy/commit/c8ef41f1f1212457c2040ba4f14d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.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 M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Undo changes label handling adjustments to form-input and form-section modules Commit: 69e6ff724fd69fe6fec976667b22b0a717328379 https://github.com/galaxyproject/galaxy/commit/69e6ff724fd69fe6fec976667b22… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.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 M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Merge pull request #51 from guerler/workflow_inputs_display_000 Undo changes label handling adjustments to form-input and form-section modules Commit: ccdf09b099c1201aa1e4b5d0537547cf162998cf https://github.com/galaxyproject/galaxy/commit/ccdf09b099c1201aa1e4b5d05375… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unused local variable Commit: e846b517c16014d5b32ffef4d23998d5cd2170d2 https://github.com/galaxyproject/galaxy/commit/e846b517c16014d5b32ffef4d239… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Rely on backend to specify label Commit: e260c8eb05b7e7ca9d39d136041d84314f13d1d8 https://github.com/galaxyproject/galaxy/commit/e260c8eb05b7e7ca9d39d136041d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Fix UX problem when sharing objects with users. The problem is that by default Galaxy doesn't expose usernames and user e-mails via this form but a select2 + search is used anyway making it appear that any selection matches an actual user. It is confusing. Fixes #3250 reported by @peterjc. xref #1111 Commit: 71b64472c645cacbba3674f5a0f48c675b29437d https://github.com/galaxyproject/galaxy/commit/71b64472c645cacbba3674f5a0f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Repack scripts Commit: d84221ea47719049c5415f7edc88736d22955f44 https://github.com/galaxyproject/galaxy/commit/d84221ea47719049c5415f7edc88… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.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-section.js M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Add label hiding option without need to overwrite actual label Commit: 06cc5f58288fbd6e3762a91fdd8e76b715f7c4e6 https://github.com/galaxyproject/galaxy/commit/06cc5f58288fbd6e3762a91fdd8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Fix implicit conversion for sessionless tool API calls. Also fixes it for backgrounded workflow invocations (fixes #3268 reported by @guerler). Includes a new test tool w/test definition that exercises this functionality. This tool fails without these changes. Commit: b6e9f4a6eefb53d2f3b8b415b80e1a674bd7cc8d https://github.com/galaxyproject/galaxy/commit/b6e9f4a6eefb53d2f3b8b415b80e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix workflow extraction of dataset/collections name. It works fine if multiple names are chosen, but if only one input is selected and named it doesn't work. This is a temporary workaround until that page is replaced by API calls with superior typing. Fixes #3247 reported by @peterjc. Commit: bcd660c9f0d27e7da87f8c124d09526882382f13 https://github.com/galaxyproject/galaxy/commit/bcd660c9f0d27e7da87f8c124d09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-28 (Wed, 28 Dec 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Refine workflow step title display in run form. - Go back to prefixing with the step number as discussed on #3369. - Use the label regardless of step type - don't ignore tool labels. Commit: bb80c842777efd0ffd980060410cb72b253f9f45 https://github.com/galaxyproject/galaxy/commit/bb80c842777efd0ffd980060410c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-28 (Wed, 28 Dec 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 #3349 from bgruening/mastheadwebhookextend Masthead Webhook bug fix Commit: 91c5b76667f28523bddde96171cd38af5f1ca2ba https://github.com/galaxyproject/galaxy/commit/91c5b76667f28523bddde96171cd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-31 (Sat, 31 Dec 2016) Changed paths: M lib/galaxy/tools/parameters/grouping.py M test/api/test_tools.py Log Message: ----------- Fix upload to respect explicit name override on pasted uploads. Commit: e350c8b0517410e65f82e0c1276ef727ac6ae0ec https://github.com/galaxyproject/galaxy/commit/e350c8b0517410e65f82e0c1276e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-01 (Sun, 01 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Use a newer conda version by default Commit: 5f0a4131dfdba219a0298f1ad3f8e7270b499a17 https://github.com/galaxyproject/galaxy/commit/5f0a4131dfdba219a0298f1ad3f8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-01 (Sun, 01 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add diamond database Commit: 9654618a0afdaa1e5c6fd63a627800a6025a7bfa https://github.com/galaxyproject/galaxy/commit/9654618a0afdaa1e5c6fd63a6278… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-01 (Sun, 01 Jan 2017) Changed paths: R tools/filters/gff/sort_gtf.py Log Message: ----------- Merge pull request #3362 from jmchilton/remove_sort Remove seemingly unused file sort_gtf.py. Commit: 408254f935288e8a1be007de3b633285e5ac61a7 https://github.com/galaxyproject/galaxy/commit/408254f935288e8a1be007de3b63… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-01 (Sun, 01 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3348 from abretaud/fill_cache Cache depencencies on the fly when first used Commit: 29e5bd4915f8ff7128e1740723c4c9bb66c665d0 https://github.com/galaxyproject/galaxy/commit/29e5bd4915f8ff7128e1740723c4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-01 (Sun, 01 Jan 2017) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3370 from jmchilton/integration_tests_2 Fix automatic handling of Jenkins BUILD_NUMBER in Dockerized tests. Commit: 968b97a0ac81cd65397c6e2c0de538b2be16c6a7 https://github.com/galaxyproject/galaxy/commit/968b97a0ac81cd65397c6e2c0de5… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- harmonised the use of capital and small letters Commit: 7588e9df3d7b0d1cc3da0090aa062cea91dce8ea https://github.com/galaxyproject/galaxy/commit/7588e9df3d7b0d1cc3da0090aa06… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- added image datatypes Commit: 88e838c587e4425f940dc19cd9848e8f12f42b35 https://github.com/galaxyproject/galaxy/commit/88e838c587e4425f940dc19cd984… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- added tiff subtypes Commit: f4eadd71fd1da0a18863cd7e1718369cdf9af03d https://github.com/galaxyproject/galaxy/commit/f4eadd71fd1da0a18863cd7e1718… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- harmonised the use of capital and small letters Commit: 47e0d5d8103c22741555faab1063d1ad5b698e03 https://github.com/galaxyproject/galaxy/commit/47e0d5d8103c22741555faab1063… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- added hamatsu sub datatypes Commit: 7a370a4ff6bb5aa24ca9758cb9bbfadbe808e3b0 https://github.com/galaxyproject/galaxy/commit/7a370a4ff6bb5aa24ca9758cb9bb… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Escapes some variables Commit: 85333d4be47478d6e6107316a15776488f987e46 https://github.com/galaxyproject/galaxy/commit/85333d4be47478d6e6107316a157… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3378 from galaxyproject/upgrade_conda Use a newer conda version by default Commit: f46d8ad739aed601f02c07b60c69c29f12c3b189 https://github.com/galaxyproject/galaxy/commit/f46d8ad739aed601f02c07b60c69… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- harmonised the use of capital and small letters Commit: 8d4f9955a66c94604634d436a4262cfef395b3e5 https://github.com/galaxyproject/galaxy/commit/8d4f9955a66c94604634d436a426… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/__init__.py A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_command_factory.py M test/unit/tools_support.py Log Message: ----------- Limit adjusting Galaxy's Python environment to legacy tools. Don't expose Galaxy's environment to tools unless there is evidence we need to. This should restrict future bugs by limitting what tools are exposed to Galaxy's internals and will fix bugs related to Conda dependencies masking Galaxy - such as #2994. Should fix #2994. Rebased with language and tool best practice fixes thanks to @mvdbeek. Commit: 7bac8bbc786ba9697cf1e0a0e8597c8d06aa1721 https://github.com/galaxyproject/galaxy/commit/7bac8bbc786ba9697cf1e0a0e859… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/__init__.py A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_command_factory.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #3364 from jmchilton/clean_python Limit adjusting Galaxy's Python environment to legacy tools. Commit: 560813d908461cbeeeadf04c0fce487ac4ff9b35 https://github.com/galaxyproject/galaxy/commit/560813d908461cbeeeadf04c0fce… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- Merge pull request #3380 from ThomasWollmann/image_datatypes Added image datatypes Commit: 50257aac80c7aedf41ad436d475640d586ca732c https://github.com/galaxyproject/galaxy/commit/50257aac80c7aedf41ad436d4756… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Add re-submission info to job_conf.xml.sample_advanced. Commit: 34f0b0fe8911c01562c7dfc0e83e0d56df50f66c https://github.com/galaxyproject/galaxy/commit/34f0b0fe8911c01562c7dfc0e83e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Implement a Galaxy config option for default job re-submission conditions. Commit: a870ac887cf43881906badecb2db7413b25cb96c https://github.com/galaxyproject/galaxy/commit/a870ac887cf43881906badecb2db… Author: ThomasWollmann <ThomasWollmann(a)users.noreply.github.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.xml M config/plugins/interactive_environments/rstudio/config/rstudio.xml M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- added STL datatype (#2679) * added STL datatype * added image support to rstudio IE * added image support to jupyter IE * changed boolean to lower case * lint * lint * revert file extension refactoring * upgraded numpy-stl * Update constructive_solid_geometry.py added additional check to refine stl sniffer * Update constructive_solid_geometry.py * removed stl sniffer * cleanup of dependencies * revert file extension refactoring * upgraded numpy-stl * Update constructive_solid_geometry.py added additional check to refine stl sniffer * Update constructive_solid_geometry.py * removed stl sniffer * cleanup of dependencies * lint Commit: c7c6c565da4d1ab32db3ce14b91eeb057c49da3b https://github.com/galaxyproject/galaxy/commit/c7c6c565da4d1ab32db3ce14b91e… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/verify/asserts/text.py Log Message: ----------- Fix typo ouptup instead of output in assertion message Commit: 1ef96f031b81c7f35ce57c1a376875be75d766e3 https://github.com/galaxyproject/galaxy/commit/1ef96f031b81c7f35ce57c1a3768… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/verify/asserts/text.py Log Message: ----------- Merge pull request #3384 from pvanheus/patch-1 Fix typo Commit: e0e2d6da7e3184282b64784ca2c0c424a2a28b03 https://github.com/galaxyproject/galaxy/commit/e0e2d6da7e3184282b64784ca2c0… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- added nrrd datatype Commit: 325b06928552604ad90c0c2183a724c04eb5e9b9 https://github.com/galaxyproject/galaxy/commit/325b06928552604ad90c0c2183a7… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/images.py Log Message: ----------- fixed default extension of nrrd Commit: b28051a8867d1e0be50869eee3ab416d7f2819c3 https://github.com/galaxyproject/galaxy/commit/b28051a8867d1e0be50869eee3ab… Author: Thomas Wollmann <thomas.s.wollmann(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- fixed typo Commit: f854a8b01cef74369bd3049dfb5d981a5310d21a https://github.com/galaxyproject/galaxy/commit/f854a8b01cef74369bd3049dfb5d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py M test/api/test_tools.py Log Message: ----------- Fix upload to respect explicit name override on pasted uploads. Commit: d9ffbc433ef417c08d5d040b27a6d3d626d54872 https://github.com/galaxyproject/galaxy/commit/d9ffbc433ef417c08d5d040b27a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M test/api/test_workflows.py A test/functional/tools/for_workflows/mapper2.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test cases for renaming datasets based on tool input datasets. Includes test cases for #3197 and #662. Commit: a18b24e0679016da159703a4e6b873f0ae95cf4e https://github.com/galaxyproject/galaxy/commit/a18b24e0679016da159703a4e6b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M test/api/helpers.py M test/api/test_workflows.py M test/functional/tools/for_workflows/mapper2.xml Log Message: ----------- Allow rename PJA to target input collections. Implements #2346 w/test case. Commit: eb544104787835c63282e1b1342818bf1be6228e https://github.com/galaxyproject/galaxy/commit/eb544104787835c63282e1b13428… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/images.py Log Message: ----------- lint fixes Commit: c9a876e659b30e69bd17586e9c9f213c9a81dc1b https://github.com/galaxyproject/galaxy/commit/c9a876e659b30e69bd17586e9c9f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/images.py Log Message: ----------- Merge pull request #3385 from ThomasWollmann/image_datatypes added nrrd image datatype Commit: 0518cbf02e5541514dbbca6178213dcc046b7bc4 https://github.com/galaxyproject/galaxy/commit/0518cbf02e5541514dbbca617821… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add sniffer for dmnd extension Commit: 87000dca9ef49d7d6e068cf50313dec43dd10a3c https://github.com/galaxyproject/galaxy/commit/87000dca9ef49d7d6e068cf50313… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add dmnd class Commit: 8cfbfcdaff4cfdeefe4e11733ac1530eebb80da2 https://github.com/galaxyproject/galaxy/commit/8cfbfcdaff4cfdeefe4e11733ac1… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Add test to dmnd Commit: 275f2fb84beffb89c7a8a22d14a176455d9bf328 https://github.com/galaxyproject/galaxy/commit/275f2fb84beffb89c7a8a22d14a1… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/diamond_db.dmnd Log Message: ----------- Add test data for diamond datatype Commit: 34471bbc47b5bd428099c8f5518c0329b3c86582 https://github.com/galaxyproject/galaxy/commit/34471bbc47b5bd428099c8f5518c… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Correct the header Commit: a78ae1bb7149199122f7dd2f8fd6b09599eb3ca4 https://github.com/galaxyproject/galaxy/commit/a78ae1bb7149199122f7dd2f8fd6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Fix tool shed pre-population against current dev. I don't know how this ever worked to be honest - but these changes make a lot of sense. I think there was another bug somewhere that prevented this bug from exhibiting itself. Commit: b75ee68d9f6305646a55d816fb1173210e36eab9 https://github.com/galaxyproject/galaxy/commit/b75ee68d9f6305646a55d816fb11… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M run_tests.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Run Galaxy tests in --dockerize mode as UID of tester. Fixes #1541 and should really help Jenkins clean up after itself. Commit: 387c08b39b63b9e3abf738b67267b04baf949a67 https://github.com/galaxyproject/galaxy/commit/387c08b39b63b9e3abf738b67267… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M tox.ini Log Message: ----------- Merge branch 'release_16.10' into dev Commit: 5a1caa5912a515b35257a2e8b911293c2eb7aad1 https://github.com/galaxyproject/galaxy/commit/5a1caa5912a515b35257a2e8b911… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M run_tests.sh M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #3387 from jmchilton/docker_fix Docker Testing Fixes (for Jenkins for instance) Commit: 9843e404b70b58616e55cf26e8a514a8df628771 https://github.com/galaxyproject/galaxy/commit/9843e404b70b58616e55cf26e8a5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py M test/api/test_tools.py Log Message: ----------- Merge pull request #3377 from jmchilton/upload_fix Fix upload to respect explicit name override on pasted uploads. Commit: 41f5ff48ed848f4fe111f78c8f364e32abdfe405 https://github.com/galaxyproject/galaxy/commit/41f5ff48ed848f4fe111f78c8f36… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3375 from jmchilton/fix_3268 [16.10] Fix implicit conversion for sessionless tool API calls. Commit: bb5d450b32afca22b666095e9ea4482f08647e3d https://github.com/galaxyproject/galaxy/commit/bb5d450b32afca22b666095e9ea4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Merge pull request #3319 from jmchilton/job_resubmission_refinement_0 Make it easier to use job re-submission conditions. Commit: 690b512dbded1989fa3c98af3b7733d258ec3f97 https://github.com/galaxyproject/galaxy/commit/690b512dbded1989fa3c98af3b77… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M test/api/test_datasets.py M test/api/test_history_contents.py A test/api/test_visualizations.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js Log Message: ----------- Merge pull request #3288 from jmchilton/casper2api_0 Migrate more CasperJS API tests to the API test framework. Commit: dad4c60d852d3c2cd06d4327c20f2b2ee516c9cf https://github.com/galaxyproject/galaxy/commit/dad4c60d852d3c2cd06d4327c20f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M test/api/helpers.py M test/api/test_workflows.py A test/functional/tools/for_workflows/mapper2.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3381 from jmchilton/rename_improvements Test cases & small enhancement to workflow renaming PJAs. Commit: de35c85b655e7de0e5f349a2d61e4f11d73ef23e https://github.com/galaxyproject/galaxy/commit/de35c85b655e7de0e5f349a2d61e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt R test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_history_contents_provenance.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_search.py M test/api/test_tools.py R test/api/test_workflow_1.ga R test/api/test_workflow_2.ga R test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py R test/api/test_workflow_map_reduce_pause.ga R test/api/test_workflow_matching_lists.ga R test/api/test_workflow_missing_tool.ga R test/api/test_workflow_pause.ga R test/api/test_workflow_topoambigouity.ga R test/api/test_workflow_topoambigouity_auto_laidout.ga R test/api/test_workflow_validation_1.ga R test/api/test_workflow_with_runtime_input.ga M test/api/test_workflows.py R test/api/workflows_format_2/README.txt R test/api/workflows_format_2/__init__.py R test/api/workflows_format_2/converter.py R test/api/workflows_format_2/interface.py R test/api/workflows_format_2/main.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga A test/base/populators.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py M test/manual/workflows_scaling.py Log Message: ----------- Refactor API helpers for re-use in rest of test framework. - Move api.helpers to base.populators. - Refactor helper subclasses adapted to use bioblend instead of test framework stuff into base.populators for greater visibility. - Refactor workflow format 2 testing stuff for reuse by Selenium. Commit: a0177fe2f4cfa0f02e835788c3f036a17786da37 https://github.com/galaxyproject/galaxy/commit/a0177fe2f4cfa0f02e835788c3f0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/base/workflows_format_2/main.py M test/unit/workflows/workflow_support.py Log Message: ----------- Add ability to import workflows without Galaxy modifying tool version. Needed to test workflow tool upgrades when loading workflows, but I think it is good to have a way to preserve the original tool state as well for the sake of absolute reproducibility/tracibility. Commit: 76b8a69c37093e1b222b4f264370934ee8c04bb7 https://github.com/galaxyproject/galaxy/commit/76b8a69c37093e1b222b4f264370… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Capture page source and DOM of top-level frame on Selenium errors. Dump to the same directory as the last screenshot related to the error. Commit: 78b099f3a78520412a63a0c6353fe4ef09c9f4e3 https://github.com/galaxyproject/galaxy/commit/78b099f3a78520412a63a0c6353f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py Log Message: ----------- Expand selenium test coverage for workflows. Expand and then break out workflow management tests into its own file since these aren't related to the workflow editor per se. Includes new tests of workflow "viewing" and "renaming". Add a new file for testing workflow execution. This currently contains tests for simple execution with a single input and a test for running workflows with tool version upgrades. This includes a refactoring of some existing tests related to checking various things in the history panel - as part of building up good history panel abstractions. The previous constructs were ported fairly literally from older CasperJS tests. These abstractions therefore referred to everything has "hda"s instead of history items. The newer abstractions therefore allow for collections and are built around HIDs (a visual thing exposed to the user) instead of HDA IDs. I think this is higher-level and more appropriate for a web functional test. Rebase into workflow GUI tests. Commit: caf9bf21de894312a3a3d164ae4ac3be37e487e1 https://github.com/galaxyproject/galaxy/commit/caf9bf21de894312a3a3d164ae4a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Refactor DependencyManager to walk dependencies resolvers first, then requirements. Invert previous loop to give resolvers a chance to resolve everything at once in subsequent commits. Commit: 0a280e7d48c64d0a9daed6514eafe0314a6aa940 https://github.com/galaxyproject/galaxy/commit/0a280e7d48c64d0a9daed6514eaf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Give dependency resolvers a shot at resolving all dependencies at once. Commit: c2ac19275064b4c5b07685133f28bb509fd6be7d https://github.com/galaxyproject/galaxy/commit/c2ac19275064b4c5b07685133f28… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py A test/functional/tools/mulled_example_conflict.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement resolve_all on Conda dependency resolver. This is a somewhat substantial reversal in the typical way that the Conda resolver works. Everything related to caching, copying, linking, and building environments on the fly should now only apply if both of the following conditions are met (1) there is more than one requirement tag in a tool and (2) not all of them are resolvable exactly by the Conda resolver. For recipes that don't meet both of these two criteria - the normal case I would suspect going forward - Galaxy will just look for a hashed environment for these requirements built for all the requirements at once whenever the requirements are installed. The new 90% case, such environments should be much less buggy for two primary reasons. - #3299 is solved - in other words Conda is deferred to and if packages have potential conflicts - Conda can choose the right combination of build specifiers to resolve things correctly. - Environments are no longer built on a per-job basis - this means file system problems related to linking and copying aren't really an issue and complexity related to caching can be safely ignored. My guess is we should re-write all the Conda docs to make the other use case seem like a corner case - because hopefully it is now. This commit includes a test tool that wouldn't work without the rewrite I believe. Commit: a24ce4c61f6899d13bd2197144fa0a3ea379af5a https://github.com/galaxyproject/galaxy/commit/a24ce4c61f6899d13bd2197144fa… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-icons.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.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge branch 'workflow_inputs_display' of https://github.com/jmchilton/galaxy into jmchilton-workflow_inputs_display Commit: 5bfffac06965136c970f3ddfd20ff770dc092324 https://github.com/galaxyproject/galaxy/commit/5bfffac06965136c970f3ddfd20f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- repack Commit: 627fafafdfb1fea1cc5c456f11752c090129336f https://github.com/galaxyproject/galaxy/commit/627fafafdfb1fea1cc5c456f1175… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-icons.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.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-icons.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge branch 'jmchilton-workflow_inputs_display' into dev Commit: dcf3b21752070c8a2b2747cc921db91fdd3ab42d https://github.com/galaxyproject/galaxy/commit/dcf3b21752070c8a2b2747cc921d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py R test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_history_contents_provenance.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_search.py M test/api/test_tools.py R test/api/test_workflow_1.ga R test/api/test_workflow_2.ga R test/api/test_workflow_batch.ga M test/api/test_workflow_extraction.py R test/api/test_workflow_map_reduce_pause.ga R test/api/test_workflow_matching_lists.ga R test/api/test_workflow_missing_tool.ga R test/api/test_workflow_pause.ga R test/api/test_workflow_topoambigouity.ga R test/api/test_workflow_topoambigouity_auto_laidout.ga R test/api/test_workflow_validation_1.ga R test/api/test_workflow_with_runtime_input.ga M test/api/test_workflows.py R test/api/workflows_format_2/README.txt R test/api/workflows_format_2/__init__.py R test/api/workflows_format_2/converter.py R test/api/workflows_format_2/interface.py R test/api/workflows_format_2/main.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga A test/base/populators.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/manual/workflows_scaling.py A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #3371 from jmchilton/selenium_workflow Expand selenium test coverage for workflows. Commit: e1fbdc6808d3cf5b20870c07b39326bb13836ef1 https://github.com/galaxyproject/galaxy/commit/e1fbdc6808d3cf5b20870c07b393… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Merge pull request #3373 from jmchilton/remove_unused_select2 Fix UX problem when sharing objects with users. Commit: 64faeece93c1ecb59ff4d10b7664660e7886d419 https://github.com/galaxyproject/galaxy/commit/64faeece93c1ecb59ff4d10b7664… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #3286 from jmchilton/slim_test_dockerfile Slim down testing ``Dockerfile``. Commit: 0e509a98ed79daf250fdd486f827d14335e88486 https://github.com/galaxyproject/galaxy/commit/0e509a98ed79daf250fdd486f827… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Create merged environments at install time Currently tested with UI only Commit: d3291c15f96c05d17900606ca670acc4f9c90391 https://github.com/galaxyproject/galaxy/commit/d3291c15f96c05d17900606ca670… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js Log Message: ----------- fix PHD Comics plugin Commit: ad92bbf9bebafed22395e0199efd35a838ac1f4a https://github.com/galaxyproject/galaxy/commit/ad92bbf9bebafed22395e0199efd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Restore the cached environments for now ... better to completely eliminate them later Commit: dd9aa82db69167e26b31d4f12da851c95ff2ee64 https://github.com/galaxyproject/galaxy/commit/dd9aa82db69167e26b31d4f12da8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js Log Message: ----------- Merge pull request #3392 from anatskiy/phdcomics_fix Fix PHD Comics plugin Commit: fd8243b3d3a6ac0fcaea5f7ccfd7d5ec472b083b https://github.com/galaxyproject/galaxy/commit/fd8243b3d3a6ac0fcaea5f7ccfd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #52 from mvdbeek/install_time_improvements Create merged environments at install time Commit: 48a22d6e53c08de37a8a39cc5bb0228789a19033 https://github.com/galaxyproject/galaxy/commit/48a22d6e53c08de37a8a39cc5bb0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Revert "Restore the cached environments for now ... better to completely eliminate them later" This reverts commit ad92bbf9bebafed22395e0199efd35a838ac1f4a. Commit: 50bee381d35b97c951982ddbed442f8068574a46 https://github.com/galaxyproject/galaxy/commit/50bee381d35b97c951982ddbed44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Revert "Create merged environments at install time" This reverts commit 0e509a98ed79daf250fdd486f827d14335e88486. Commit: eea89de19adffe3a18f562cac7c97087e8a2e604 https://github.com/galaxyproject/galaxy/commit/eea89de19adffe3a18f562cac7c9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Use resolver to explicitly install dependencies This avoids replicating the resolver logic when installing dependencies and should be better than https://github.com/jmchilton/galaxy/pull/52 Commit: 63e70f4f2f47f5b952bb7817e93b0e61c8614dd7 https://github.com/galaxyproject/galaxy/commit/63e70f4f2f47f5b952bb7817e93b… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #3376 from jmchilton/fix_3247 [16.10] Fix workflow extraction of dataset/collections name. Commit: 5dcb2f317bc3a3f07e30e1fce070ed012f0e7379 https://github.com/galaxyproject/galaxy/commit/5dcb2f317bc3a3f07e30e1fce070… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Change the header to find for dmnd Commit: 50f9f74884068690f7c5e125b4aae10fd48bf41e https://github.com/galaxyproject/galaxy/commit/50f9f74884068690f7c5e125b4aa… Author: Bérénice Batut <bebatut(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Add extra line to fix flake8 Commit: f50272be0dee7d63ba452bc033ce6b5970a27e4a https://github.com/galaxyproject/galaxy/commit/f50272be0dee7d63ba452bc033ce… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/diamond_db.dmnd Log Message: ----------- Merge pull request #33 from ASaiM/dmnddb Add sniffer for dmnd files Commit: f358d14670cc0e4974bfdda1db96d5c63e553ee0 https://github.com/galaxyproject/galaxy/commit/f358d14670cc0e4974bfdda1db96… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/diamond_db.dmnd Log Message: ----------- Merge pull request #3379 from bgruening/dmnddb Add diamond database as datatype Commit: d1cf0def31b9060f5fe4b4f116ae8a8f47d0633e https://github.com/galaxyproject/galaxy/commit/d1cf0def31b9060f5fe4b4f116ae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Do not allow recursive replacements in PJA. May result in infinite loops in workflow scheduling threads. Commit: d1eeafcc8f647fda2362b20c8625224b49520493 https://github.com/galaxyproject/galaxy/commit/d1eeafcc8f647fda2362b20c8625… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case d1cf0def31b9060f5fe4b4f116ae8a8f47d0633e. Commit: 5c325236189ce17344ffedc1d821e94c6fb33483 https://github.com/galaxyproject/galaxy/commit/5c325236189ce17344ffedc1d821… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #53 from mvdbeek/install_time_2 Install time 2 Commit: 1082385b0b8b343482d7c06056473cf80b568779 https://github.com/galaxyproject/galaxy/commit/1082385b0b8b343482d7c0605647… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3395 from jmchilton/pja_infinite_loop Do not allow recursive replacements in PJA renames. Commit: 79752b5b4a0e80a6cd4b02aed8cfd93d8d61208a https://github.com/galaxyproject/galaxy/commit/79752b5b4a0e80a6cd4b02aed8cf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Do not allow recursive replacements in PJA. May result in infinite loops in workflow scheduling threads. Commit: 542dc4077f35d3760d3a8b51716acffce2574bef https://github.com/galaxyproject/galaxy/commit/542dc4077f35d3760d3a8b51716a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/tool_shed/galaxy_install/install_manager.py A test/functional/tools/mulled_example_conflict.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3391 from jmchilton/resolve_all_at_once Resolve Conda Dependencies All at Once Commit: 24b250ab3369489b91361c22bdf51b1729861e85 https://github.com/galaxyproject/galaxy/commit/24b250ab3369489b91361c22bdf5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #3397 from jmchilton/backport_3395 [16.10] Backport #3395 Commit: ca40f984b0dfda58af1aa55d167edf615582192a https://github.com/galaxyproject/galaxy/commit/ca40f984b0dfda58af1aa55d167e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/bower.json A client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py A static/maps/libs/showdown.js.map A static/scripts/libs/showdown.js A templates/webapps/galaxy/dataset/markdown.mako A test/functional/tools/creates_html.xml A test/functional/tools/creates_html_index.html A test/functional/tools/creates_markdown.xml A test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Markdown datatype support. With test tools demonstrating HTML and Markdown outputs from tools. Implements #3396 as part of the Qiime hackathon. Commit: 09f0272ede3a17a5445956179acded53e213a1c4 https://github.com/galaxyproject/galaxy/commit/09f0272ede3a17a5445956179acd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M test/docker/README.md Log Message: ----------- Document how to create Docker testing images. With fix noted by @martenson. Commit: aba7618a3a110c3c4893d23ddb2a9d3a446c14a0 https://github.com/galaxyproject/galaxy/commit/aba7618a3a110c3c4893d23ddb2a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M run_tests.sh Log Message: ----------- Update the testing image used with ``--dockerize``ed tests. Should prevent Jenkins from writing files as root. Commit: 6c4dff3f4604857f5c067c87a7a568a2e3acf0a5 https://github.com/galaxyproject/galaxy/commit/6c4dff3f4604857f5c067c87a7a5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M test/docker/README.md Log Message: ----------- Merge pull request #3400 from jmchilton/document_docker_testing_image Document how to create Docker testing images. Commit: 3c494c42e2b42da7e934b38954df910d20bf286d https://github.com/galaxyproject/galaxy/commit/3c494c42e2b42da7e934b38954df… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/bower.json A client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py A static/maps/libs/showdown.js.map A static/scripts/libs/showdown.js A templates/webapps/galaxy/dataset/markdown.mako A test/functional/tools/creates_html.xml A test/functional/tools/creates_html_index.html A test/functional/tools/creates_markdown.xml A test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3399 from jmchilton/markdown Markdown datatype support. Commit: 8368b1784356112682b4eb93692d57582f009b34 https://github.com/galaxyproject/galaxy/commit/8368b1784356112682b4eb93692d… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M doc/source/api/guidelines.rst Log Message: ----------- fix typo Commit: 778bcd00451aa863899d520aaac38fad7b9cae35 https://github.com/galaxyproject/galaxy/commit/778bcd00451aa863899d520aaac3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M doc/source/api/guidelines.rst Log Message: ----------- Merge pull request #3402 from manabuishii/patch-3 fix typo Commit: 1d52e9a32ceca303b12a1de84604e68069ed0e85 https://github.com/galaxyproject/galaxy/commit/1d52e9a32ceca303b12a1de84604… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Merge pull request #3403 from yhoogstrate/visualizations_escape Escapes some variables Commit: 2d991bba073a9e1f40b18f6c927e4adf6ca1ddb9 https://github.com/galaxyproject/galaxy/commit/2d991bba073a9e1f40b18f6c927e… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Escapes some variables Commit: 535dd7a5f54617b12684eaa179066b4877965dd2 https://github.com/galaxyproject/galaxy/commit/535dd7a5f54617b12684eaa17906… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Merge pull request #3404 from dannon/backport_viz_escape [16.10] Backport of visualization hda.name escapes Commit: 8041525223b2deeffb4b588afe6e480b62fa6c07 https://github.com/galaxyproject/galaxy/commit/8041525223b2deeffb4b588afe6e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3401 from jmchilton/testing_image_update Update the testing image used with ``--dockerize``ed tests. Commit: d49e014a63641db37814ab0b31b7aa4d1eded786 https://github.com/galaxyproject/galaxy/commit/d49e014a63641db37814ab0b31b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- The /user/logout endpoint is now used for both remote and internal users to handle logout logic, and should be accessible here. Commit: b0ac7daecdda4001f6bcd7d70a15bb30375216e5 https://github.com/galaxyproject/galaxy/commit/b0ac7daecdda4001f6bcd7d70a15… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3405 from dannon/remoteuser_logout_fix [16.10] Remoteuser Logout Fix. Commit: be530a849428393ec2b16f5b0786cbe4fba148cd https://github.com/galaxyproject/galaxy/commit/be530a849428393ec2b16f5b0786… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into dev Commit: 34458725b826fb9cd8da2d245c094abd5041345c https://github.com/galaxyproject/galaxy/commit/34458725b826fb9cd8da2d245c09… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3406 from dannon/dev Merges 16.10 into dev Commit: a87feb11ff61dc0a8ea2657c8afe99cd115d1eda https://github.com/galaxyproject/galaxy/commit/a87feb11ff61dc0a8ea2657c8afe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml Log Message: ----------- Merge pull request #3145 from mvdbeek/fastqgz Support for gzipped fastq formats Commit: e74ca27dbfc8c9f6244ba7f786a9460bdf0af753 https://github.com/galaxyproject/galaxy/commit/e74ca27dbfc8c9f6244ba7f786a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py R static/maps/libs/showdown.js.map R static/scripts/libs/showdown.js R templates/webapps/galaxy/dataset/markdown.mako R test/functional/tools/creates_html.xml R test/functional/tools/creates_html_index.html R test/functional/tools/creates_markdown.xml R test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revert "Markdown datatype support." Commit: a60b7da85e2b9ef83aa86a0593dd5b810802ddf3 https://github.com/galaxyproject/galaxy/commit/a60b7da85e2b9ef83aa86a0593dd… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- fix typo Commit: 7bb8376490a251573252177ab4112caba64b4684 https://github.com/galaxyproject/galaxy/commit/7bb8376490a251573252177ab411… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Merge pull request #3409 from manabuishii/patch-4 fix typo Commit: e0990e2ab58895e9667438aa3207f1a15e9ec3bf https://github.com/galaxyproject/galaxy/commit/e0990e2ab58895e9667438aa3207… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- extend API version information extend API version information #1907 https://github.com/galaxyproject/galaxy/issues/1907 output json file contents with version_major ``` {"extra": {"user_tag": "_fix_job_runner_issue", "commit-id": "abcde123"}, "version_major": "16.10"} ``` First check environment value GALAXY_VERSION_JSON_FILE. if it's not set, try "galaxy root direcotory"/version.json. if json file is not find, extra set empty. Commit: 4946313fc9dc27d2bc2e3d0464682d8308b8702c https://github.com/galaxyproject/galaxy/commit/4946313fc9dc27d2bc2e3d046468… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py R static/maps/libs/showdown.js.map R static/scripts/libs/showdown.js R templates/webapps/galaxy/dataset/markdown.mako R test/functional/tools/creates_html.xml R test/functional/tools/creates_html_index.html R test/functional/tools/creates_markdown.xml R test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3408 from galaxyproject/revert-3399-markdown Revert "Markdown datatype support." Commit: a5c445966ef3ea8385493ffd2ca6bf6dce8611aa https://github.com/galaxyproject/galaxy/commit/a5c445966ef3ea8385493ffd2ca6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js A static/maps/libs/showdown.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/showdown.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Swap the client's ui-misc.Message to escape by default. Commit: e1083132b89f854e2ec824f97f187e925ba0abe6 https://github.com/galaxyproject/galaxy/commit/e1083132b89f854e2ec824f97f18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Add UnescapedMessage, for when we actually need to display a message with html contents. Any users of this must escape contents on their own. Commit: cc4cd55c1df0fd3ae78bdbff99ad70c2ed723def https://github.com/galaxyproject/galaxy/commit/cc4cd55c1df0fd3ae78bdbff99ad… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Fix RStudio login Thanks @shiltemann for reporting this Commit: 3060da4ee53e44c0814eebe2c468f2d3dc352233 https://github.com/galaxyproject/galaxy/commit/3060da4ee53e44c0814eebe2c468… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Export UnescapedMessage from ui-misc. Commit: 45a9d586b6e1db89bf0813aa93af5b3bbaf72efc https://github.com/galaxyproject/galaxy/commit/45a9d586b6e1db89bf0813aa93af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Formatting cleanup. Commit: 890107334d25b80ee1fc02d00df011f2e7e9d88a https://github.com/galaxyproject/galaxy/commit/890107334d25b80ee1fc02d00df0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Reversion of ui-misc messagebox changes. Commit: 2d69909218b287f8085a599e0a2a1214480330c9 https://github.com/galaxyproject/galaxy/commit/2d69909218b287f8085a599e0a2a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Merge pull request #3415 from dannon/revert_uimisc [16.10]Reversion of ui-misc messagebox changes. Commit: 68f5bc7a1ae092da266dae78adba5de8ebfd6eb2 https://github.com/galaxyproject/galaxy/commit/68f5bc7a1ae092da266dae78adba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js Log Message: ----------- Reapply ui-misc.Message changes post-reversion. Following up with fixes to other uses of this component. Commit: f9b9ebdd38cf2ee1634bf7daab171a25a8cec953 https://github.com/galaxyproject/galaxy/commit/f9b9ebdd38cf2ee1634bf7daab17… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Expose anyway if the user is an admin user Commit: 7c02ed7a9d1ab2c5101fbc4753ae7ee35d770c14 https://github.com/galaxyproject/galaxy/commit/7c02ed7a9d1ab2c5101fbc4753ae… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Mirror change in #3250 Fixes #3372 Commit: b798895af0c815783f741aa8c6278ed71ee6f0f2 https://github.com/galaxyproject/galaxy/commit/b798895af0c815783f741aa8c627… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Swap form-view to use the new UnescapedMessage Commit: 6fc538837bc541ea9ad46fefc3e54ca676526bc9 https://github.com/galaxyproject/galaxy/commit/6fc538837bc541ea9ad46fefc3e5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Remove extraneous tag Commit: c2d1a2a1897ba05e5067433fcecdfcd60c761009 https://github.com/galaxyproject/galaxy/commit/c2d1a2a1897ba05e5067433fcecd… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- fix lint Commit: 0c0e58d5fb6c48418c36e547e976dde1dfd79942 https://github.com/galaxyproject/galaxy/commit/0c0e58d5fb6c48418c36e547e976… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- fix lint Commit: ec425007b11fd871b473a488e5321bb4450bccbf https://github.com/galaxyproject/galaxy/commit/ec425007b11fd871b473a488e532… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako Log Message: ----------- Merge pull request #3417 from erasche/fix-3372 Fix accidental email exposure Commit: c94ccb3f28cdf3acbfe863b386c5dcb58752fe50 https://github.com/galaxyproject/galaxy/commit/c94ccb3f28cdf3acbfe863b386c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Merge pull request #3414 from erasche/fix-rstudio-login [16.10] Fix RStudio login Commit: 422cf1917e97b612e972b3824fcf831c510dc535 https://github.com/galaxyproject/galaxy/commit/422cf1917e97b612e972b3824fcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Switch to Miniconda3. It is the platformed used by bioconda for testing and will be supported longer than the older Python 2 variant. This shouldn't require Python 3 be installed on the host running Galaxy. Commit: d66d3a1a308a94dd548f29448b479c9d9b66a239 https://github.com/galaxyproject/galaxy/commit/d66d3a1a308a94dd548f29448b47… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Add a log message to explain long pause during startup. When conda_auto_init is used. Commit: 07806e628adf164e95543393a9f37a187acb9a0e https://github.com/galaxyproject/galaxy/commit/07806e628adf164e95543393a9f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash Log Message: ----------- Another fix for Selenium testing on Jenkins. Turns out that random sleep for 30 seconds was every bit as brittle as it seemed. This is a bit better. Commit: e573826e02e822abd63fe452b065efd690e277da https://github.com/galaxyproject/galaxy/commit/e573826e02e822abd63fe452b065… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash Log Message: ----------- Merge pull request #3422 from jmchilton/selenium_fixes_0 Another fix for Selenium testing on Jenkins. Commit: 1f9812b5d522118f79a304e3c4f5f69e28661b05 https://github.com/galaxyproject/galaxy/commit/1f9812b5d522118f79a304e3c4f5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3419 from jmchilton/conda_tweaks Target Miniconda3 when installing Conda. Commit: cdaa20858a4b20f0080a851c6380c41e610f1346 https://github.com/galaxyproject/galaxy/commit/cdaa20858a4b20f0080a851c6380… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add whoami API Commit: b242dc3ab18c003bd3c8219305730be22d0729e9 https://github.com/galaxyproject/galaxy/commit/b242dc3ab18c003bd3c821930573… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Fix docs concerns Commit: 537d6e645ae142962cdf59e6365299b8c99706bf https://github.com/galaxyproject/galaxy/commit/537d6e645ae142962cdf59e63652… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix "exact" property for merged conda dependencies. This was broken with there initial commit as part of #3391. Commit: 8c46cd5afcb63ece8d37b5051be723a359c1cc71 https://github.com/galaxyproject/galaxy/commit/8c46cd5afcb63ece8d37b5051be7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Correct API path Commit: b2cf773befd655ccae204c358703c9061916a32f https://github.com/galaxyproject/galaxy/commit/b2cf773befd655ccae204c358703… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A static/maps/libs/showdown.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.map A static/scripts/libs/showdown.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into dev Commit: 08454cfa2a0ff2d02b3ec2a61740dd429c8a67f8 https://github.com/galaxyproject/galaxy/commit/08454cfa2a0ff2d02b3ec2a61740… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Name function appropriately for Javascript instead of being stuck in Python. Commit: 2ed131d206dbf73a141b7baf76c5ffcce6fef206 https://github.com/galaxyproject/galaxy/commit/2ed131d206dbf73a141b7baf76c5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-14 (Sat, 14 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix display of repository dependency status that broke with the introduction of the all-at-once dependency resolution in #3391 and addresses in part #3398. I have only restored the (collapsed) display of dependencies for all requirements in a repository, so breaking the information out on a per tool basis remains on the TODO list. Commit: ebf18440ac09c364fa1fb6b1cdd1640808ffd593 https://github.com/galaxyproject/galaxy/commit/ebf18440ac09c364fa1fb6b1cdd1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #3427 from mvdbeek/fix_dependency_display_and_api Fix dependency display and api Commit: 02a8a7da0a0f2e3ff9c6d3cb7c5f2e1d56621a24 https://github.com/galaxyproject/galaxy/commit/02a8a7da0a0f2e3ff9c6d3cb7c5f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Merge pull request #3416 from dannon/ui_misc_message_fixes [16.10] Sanitize ui-misc.Message, implement UnescapedMessage for uses where we need html Commit: 8c34293602ec99b7deb128f60e2086f89f25e64a https://github.com/galaxyproject/galaxy/commit/8c34293602ec99b7deb128f60e20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- More idiomatic Python for extended version information. - Eliminate the use of a bare except. - Use a ``with`` to ensure file handling is cleaned up. Commit: ce0780abef5fd1e832175975b6243525a6e4cbad https://github.com/galaxyproject/galaxy/commit/ce0780abef5fd1e832175975b624… Author: yhoogstrate <y.hoogstrate(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Custom dbkey builds: additional variable escaping Commit: 8cb61626811d51afef0f7e27e9713fa98e6b664a https://github.com/galaxyproject/galaxy/commit/8cb61626811d51afef0f7e27e971… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Merge branch 'release_16.10' into dev Conflicts: static/maps/mvc/ui/ui-misc.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/ui/ui-misc.js Commit: 10d27609af607208e182b7ce18b0447281de942c https://github.com/galaxyproject/galaxy/commit/10d27609af607208e182b7ce18b0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Do not wrap __class__ attribute of SafeStringWrapper Fix #3353 by not recursing on the parent classes, which may lead to an abstract class. Also fix a method name of "object" class. 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test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/manual/workflows_scaling.py A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/tools_support.py M test/unit/workflows/workflow_support.py R tools/filters/gff/sort_gtf.py M tox.ini Log Message: ----------- Merging with dev Commit: ea0d50648c2c64abb7093fba47acec020919163f https://github.com/galaxyproject/galaxy/commit/ea0d50648c2c64abb7093fba47ac… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M 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test/functional/tools/compressed_gz_fastq_no_conversion.xml A test/functional/tools/implicit_conversion.xml A test/functional/tools/mulled_example_conflict.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merging with dev Commit: a4dec71b7ac0fedcd5f14179b7ace172d1466308 https://github.com/galaxyproject/galaxy/commit/a4dec71b7ac0fedcd5f14179b7ac… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Adding Whoosh NgramFilter and making it configurable through config Commit: 28133bead15e955e70fcbec8e09d1de06598b345 https://github.com/galaxyproject/galaxy/commit/28133bead15e955e70fcbec8e09d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Adding and removing blank lines Commit: bf3a487f2017d248317e9ea70e567f57a70d9cc9 https://github.com/galaxyproject/galaxy/commit/bf3a487f2017d248317e9ea70e56… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Fix import order and Python3 compatibility for lib/galaxy/tools/ xref. #1715 Commit: dd2ab483c095848a372a57de3ce4f08677c402fb https://github.com/galaxyproject/galaxy/commit/dd2ab483c095848a372a57de3ce4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-16 (Mon, 16 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3423 from erasche/whoami Add whoami API Commit: 9f4add70d0967ccb6ddf1bd2d1393685ef639e97 https://github.com/galaxyproject/galaxy/commit/9f4add70d0967ccb6ddf1bd2d139… Author: Abdulrahman Azab <eng.azab(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Bug fix in mulled.py This bug was causing running docker with sudo while it should not Commit: 910bbdfc54fe4a84e16ebe9ed9bc7fe0eed28dc6 https://github.com/galaxyproject/galaxy/commit/910bbdfc54fe4a84e16ebe9ed9bc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/mulled.py Log Message: ----------- Merge pull request #3434 from abdulrahmanazab/patch-4 Bug fix in mulled.py Commit: d2e019844471ee29f9b2433e0f90f53ea54a7b7f https://github.com/galaxyproject/galaxy/commit/d2e019844471ee29f9b2433e0f90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #3431 from nsoranzo/python3 Fix import order and Python3 compatibility for lib/galaxy/tools/ Commit: 9373b69f8b6dd93f747d5b12bea7e4f75aef3add https://github.com/galaxyproject/galaxy/commit/9373b69f8b6dd93f747d5b12bea7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix bug with job re-submission introduced in 34f0b0fe8911c01562c7dfc0e83e0d56df50f66c. Commit: 7f62eb0c83c18949fdf945c4c194b89d74e66cae https://github.com/galaxyproject/galaxy/commit/7f62eb0c83c18949fdf945c4c194… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M test/selenium_tests/test_history_sharing.py Log Message: ----------- Fix history sharing test broken with #3417. Commit: 6fdd0014d38ac8455f26e12b9f44b55d46bc9ee6 https://github.com/galaxyproject/galaxy/commit/6fdd0014d38ac8455f26e12b9f44… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Remove debugging "assert False" in workflow editor test. Commit: e1612d24eaf67f7dd517caa210131a54f141d2cd https://github.com/galaxyproject/galaxy/commit/e1612d24eaf67f7dd517caa21013… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M test/selenium_tests/test_workflow_management.py Log Message: ----------- Update URL used by Selenium tests that changed with a recent commit. Commit: 5c48402b0202e438d663c4dc151d835c7725a4f6 https://github.com/galaxyproject/galaxy/commit/5c48402b0202e438d663c4dc151d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Various fixes for test image Docker user switching. - Fix if testing as user with GID 109 (fixes #3425). - Fix if testing as a user with any UID or GID that already exists in the container. - More logging to indicate the "problems" being printed to standard output in these cases are not problems. - Fix sqlite being readonly in the container for the test user. Commit: 29cdd6007fa333e8e9caa85a1fc58ae389405cf2 https://github.com/galaxyproject/galaxy/commit/29cdd6007fa333e8e9caa85a1fc5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #3439 from jmchilton/fix_resubmissions Fix bug with job re-submission introduced in 34f0b0fe8911c01562c7dfc0e83e0d56df50f66c Commit: 4a3c6c871d75a2e457b5ceb6cd081df827d60425 https://github.com/galaxyproject/galaxy/commit/4a3c6c871d75a2e457b5ceb6cd08… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Add nice css to error email Apparently you have to inline it for certain web email clients to show it.. Commit: 9646d264a1a9d9d9107c2311deb4e6f319bb417d https://github.com/galaxyproject/galaxy/commit/9646d264a1a9d9d9107c2311deb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py Log Message: ----------- Merge pull request #3411 from manabuishii/extend_api_version extend API version information Commit: 94150df087b29810111952853a03fdb6ddd34631 https://github.com/galaxyproject/galaxy/commit/94150df087b29810111952853a03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #3445 from erasche/email-template-css Inline CSS in error report email Commit: b00887b9d7e471c65155740db548effd75dc4703 https://github.com/galaxyproject/galaxy/commit/b00887b9d7e471c65155740db548… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-18 (Wed, 18 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fixup circular dependency in #3427. Unfortunately the "root" of the problem is that galaxy.tools.deps.requirements.ToolRequirement should be importable without importing galaxy.tools - but it cannot be currently just because of the way things are structured. Commit: c4f5a2cfb8b7a34faf05367a5f4d8073ab229b98 https://github.com/galaxyproject/galaxy/commit/c4f5a2cfb8b7a34faf05367a5f4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #3447 from jmchilton/ts_import_cycle Fixup circular dependency in #3427. Commit: 54b527b1fc35d6ea66215df04144491f42e558e4 https://github.com/galaxyproject/galaxy/commit/54b527b1fc35d6ea66215df04144… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merging with dev Commit: 2573699c0ac1a12f808acb4006bc9e5f05f822a9 https://github.com/galaxyproject/galaxy/commit/2573699c0ac1a12f808acb4006bc… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Adding line breaks for import section Commit: 4071b3eb79e49806a6cd8df141be452366ba1942 https://github.com/galaxyproject/galaxy/commit/4071b3eb79e49806a6cd8df141be… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #3440 from jmchilton/selenium_fixes_1 Fix most broken Selenium tests. Commit: b4475ba9df9b9425b5791e15c8c070b638768286 https://github.com/galaxyproject/galaxy/commit/b4475ba9df9b9425b5791e15c8c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge pull request #3429 from nsoranzo/release_16.10_fix_3353 [16.10] Do not wrap __class__ attribute of SafeStringWrapper Commit: f5082604f7282587bb8385dbdb3bb91905bee87b https://github.com/galaxyproject/galaxy/commit/f5082604f7282587bb8385dbdb3b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Do not wrap __class__ attribute of SafeStringWrapper Fix #3353 by not recursing on the parent classes, which may lead to an abstract class. Also fix a method name of "object" class. Commit: 1af1583caa1b5c62c92573fe42693338ba457fcf https://github.com/galaxyproject/galaxy/commit/1af1583caa1b5c62c92573fe4269… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Fix various transiently failing Selenium tests. I'm pretty sure the problem is that I was waiting on conditions (e.g. datasets to become "ok") using the API and then assuming the state of the GUI elements was the same. Obviously though the GUI is polling the API and there is some lag there. This commit changes things to specifically wait on history panel GUI changes - obviously the better thing to wait on in a GUI test. Commit: c9fdb6e3efd2721dc193ea5f1d5cfe6c014ad94e https://github.com/galaxyproject/galaxy/commit/c9fdb6e3efd2721dc193ea5f1d5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M lib/galaxy/util/object_wrapper.py Log Message: ----------- Merge pull request #3449 from dannon/backport_mistargeted_3429 [16.10] Backport of 3429, safestringwrapper Commit: 60b57397e7f8227f0a5017141c81fdcc81d59ede https://github.com/galaxyproject/galaxy/commit/60b57397e7f8227f0a5017141c81… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-19 (Thu, 19 Jan 2017) Log Message: ----------- Merge branch 'release_16.10' into dev Commit: d8f23b393527e2ea5b495cc850eeec25fdc64a8b https://github.com/galaxyproject/galaxy/commit/d8f23b393527e2ea5b495cc850ee… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #3450 from jmchilton/selenium_fixes_2 Fix various transiently failing Selenium tests. Commit: 45bf7ad8c4437edc95847de47e2f46a393fc1726 https://github.com/galaxyproject/galaxy/commit/45bf7ad8c4437edc95847de47e2f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-19 (Thu, 19 Jan 2017) Changed paths: M tools/plotting/bar_chart.xml Log Message: ----------- Make requirement tags in bar_chart.xml functional with default dependency resolver. I'm not sure if we need to update the version since previously these tags were purely for documentation and had no functional purpose. xref this comment https://github.com/galaxyproject/galaxy/pull/3444#issuecomment-273909855 from @bgruening Commit: f8552c19dc55ddeeeb7441190891f52cdd9d9ef3 https://github.com/galaxyproject/galaxy/commit/f8552c19dc55ddeeeb7441190891… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Document shared_inputs for parallelism tag in tool XSD. Commit: 22f4696f7d54a90a31f253d05a7ed1314db4b943 https://github.com/galaxyproject/galaxy/commit/22f4696f7d54a90a31f253d05a7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: A test/functional/tools/explicit_conversion.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement tool testing and documenting explicit conversion tags. Commit: 074e10ac00a7dde7c2fc5e76928392e073791b30 https://github.com/galaxyproject/galaxy/commit/074e10ac00a7dde7c2fc5e769283… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml Log Message: ----------- Fix tool XSD to document <conversion> tag for data parameters. Rebased with English fixes and small tool cleanups thanks to @nsoranzo. Commit: dba4d95961a3ccadd4a0822f13f0f02730889a8a https://github.com/galaxyproject/galaxy/commit/dba4d95961a3ccadd4a0822f13f0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: M test/functional/tools/column_param.xml M test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml Log Message: ----------- Reduced usage of from_work_dir in test tools. Per recommendation of @bgruening. Commit: 3945f3b885a291c9b1a1ebf85a56137e2d1b22e2 https://github.com/galaxyproject/galaxy/commit/3945f3b885a291c9b1a1ebf85a56… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-20 (Fri, 20 Jan 2017) Changed paths: M doc/schema_template.md M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/column_param.xml A test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3457 from jmchilton/xsd_fixes_2 Tool Documentation and Testing Improvements Commit: 596d12da44908e158905d7c1bce30d9e3557b258 https://github.com/galaxyproject/galaxy/commit/596d12da44908e158905d7c1bce3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/views.py A lib/galaxy/util/oset.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Implement ToolRequirements class This class holds indiviual ToolRequirement objects as an ordered set. This makes it easier to compare, intersect, and get unions of multiple ToolRequirements and to filter for resolvable or package type dependencies. This will be useful when installing tool dependencies in batch. Commit: 5ee7e2e3e26bdbdecec0b74ed4154734d9b56ae4 https://github.com/galaxyproject/galaxy/commit/5ee7e2e3e26bdbdecec0b74ed415… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Log failed dep resolution just once Commit: 9c9b405b6f969421c2073a53dad117ffefed17c6 https://github.com/galaxyproject/galaxy/commit/9c9b405b6f969421c2073a53dad1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Add test for set on list of ToolRequirements Commit: d9f9a31c32b9d1a2121d5db6e2b8f81dbf12d7c8 https://github.com/galaxyproject/galaxy/commit/d9f9a31c32b9d1a2121d5db6e2b8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #3443 from jmchilton/test_docker_fix Various fixes for test image Docker user switching. Commit: 7700c3cf7f0789a4a921f32ff9b1e8037634d63e https://github.com/galaxyproject/galaxy/commit/7700c3cf7f0789a4a921f32ff9b1… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M tools/plotting/bar_chart.xml Log Message: ----------- Merge pull request #3454 from jmchilton/gnuplot_deps Make requirement tags in bar_chart.xml functional with default dependency resolvers. Commit: e5de94ceb9b6a8876a646d4cfc281d5c12f1125a https://github.com/galaxyproject/galaxy/commit/e5de94ceb9b6a8876a646d4cfc28… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-22 (Sun, 22 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- fix condor containers Commit: 00d1e15f74bec373934bceeb0d7ca73d8a93da78 https://github.com/galaxyproject/galaxy/commit/00d1e15f74bec373934bceeb0d7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #3462 from bgruening/fix_condor_containers fix condor containers Commit: 4eade311dbebdf90168821fafe3e4d09f4423565 https://github.com/galaxyproject/galaxy/commit/4eade311dbebdf90168821fafe3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/views.py A lib/galaxy/util/oset.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #3461 from mvdbeek/ToolRequirements Implement ToolRequirements class Commit: 3f93b19ff34bf51d81b353eb5e11e1748fa35df4 https://github.com/galaxyproject/galaxy/commit/3f93b19ff34bf51d81b353eb5e11… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- fix condor containers Commit: cd2cf494fe1ede4ae5b43417f0da21b2ca6473a0 https://github.com/galaxyproject/galaxy/commit/cd2cf494fe1ede4ae5b43417f0da… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.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/xsd/galaxy.xsd A test/functional/tools/requirement_specification_1.xml A test/functional/tools/requirement_specification_2.xml Log Message: ----------- Allow finer grain specification of requirements. This adapts CWL-style ``SoftwareRequirement`` ``specs`` to solve #1927. Here I'm trying to implement the CWL specification in a way that helps enable the feasibility of Conda packaging in Galaxy. It is a delicate balancing act aimed to upset as many interested parties as I can. To understand the problem - consider the ``blast+`` requirement found in the Galaxy wrappers. It looks something like this: ``` <requirement type="package" version="2.2.31" name="blast+"> ``` Great, that works for Galaxy and Tool Shed packages. It doesn't work for bioconda at all. I think this problem is fairly uncommon - most packages have simple names shared across Debian, Brew, Conda, etc... - but it does happen in some cases that there are inconsistencies. Some people have taken to duplicating the requirement - this is bad and should not be done since they are mutually exclusive and Galaxy will attempt to resolve both. This introduces the following syntax for tools with profile >= 16.10: ``` <requirement type="package" version="2.2.31" name="blast+"> <specification uri="https://anaconda.org/bioconda/blast" /> <specification uri="https://packages.debian.org/sid/ncbi-blast+" version="2.2.31-3" /> </requirement> ``` This allows finer grain resolution of the requirement without sacrificing the abstract name at the top. It allows the name and the version to be adapted by resolvers as needed (hopefully rarely so). This syntax is the future facing one, but obviously this tool would not work on older Galaxy versions. To remedy this - an alternative syntax can be used for tools targetting Galaxy verions pre-16.10: ``` <requirement type="package" version="2.2" specification_uris="https://anaconda.org/bioconda/blast@2.2.31,https://packages.debian.org/jess…">blast+</requirement> ``` This syntax sucks - but it does give newer Galaxies the ability to resolve the specifications without breaking the more simple functionality for older Galaxies. For more information on the CWL side of this - checkout the discussion on https://github.com/common-workflow-language/cwltool/pull/214. The CWL specification information is defined at http://www.commonwl.org/v1.0/CommandLineTool.html#SoftwarePackage. Conflicts: lib/galaxy/tools/deps/__init__.py test/functional/tools/samples_tool_conf.xml Commit: 330d71d37ce7eaa60b5c8c20ae83aeb36fec4a6c https://github.com/galaxyproject/galaxy/commit/330d71d37ce7eaa60b5c8c20ae83… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/xsd/galaxy.xsd R test/functional/tools/requirement_specification_1.xml R test/functional/tools/requirement_specification_2.xml Log Message: ----------- Remove tool XML modifications for requirement specifications. Per discussion on #3117 - some people were in favor of the idea but some were opposed. I think it is still important to implement this for CWL tools and useful from a library perspective. This just removes changes to Galaxy tool XML. Commit: baf9b82847fc526af56ed8efa7aba4d31d62f400 https://github.com/galaxyproject/galaxy/commit/baf9b82847fc526af56ed8efa7ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- More modular config option handling for dependency resolvers. The handling of global configuration options for Conda specific options was hacky and a poor design. This is much more modular and allows the elegant cascading option sources for all resolvers. Commit: 49a11073a49242fbd86e3ec05fb5029194ec23fd https://github.com/galaxyproject/galaxy/commit/49a11073a49242fbd86e3ec05fb5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Give resolver's with a resolve_all method an interface. This follows the existing pattern within the module. Commit: 8e20e71556cfc90da548243d390deb52d4e9110d https://github.com/galaxyproject/galaxy/commit/8e20e71556cfc90da548243d390d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Change interface of depependency resolver's resolve for consistency. If resolve_all takes in requirements, then so should resolve. Commit: 35b2b735ff7495576de88b7469c7118f65cb2838 https://github.com/galaxyproject/galaxy/commit/35b2b735ff7495576de88b7469c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Modify specification interface with better name. Commit: 2fad74ddcf63c03fc2d7fd77fa3838de637a1bf4 https://github.com/galaxyproject/galaxy/commit/2fad74ddcf63c03fc2d7fd77fa38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Implement dependency mapping for environment modules, galaxy packages, and Conda. Commit: 3d9cdeb70c0170b7795c35e458c878ebe19caf1a https://github.com/galaxyproject/galaxy/commit/3d9cdeb70c0170b7795c35e458c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/properties.py M run.sh A scripts/manage_tool_dependencies.py Log Message: ----------- Outline infrastructure for managing Conda installations outside of Galaxy. - Construct a DependencyManager according to Galaxy's configuration before Galaxy starts to allow auto installation of Conda. - Add script for managing tool dependencies outside of a Galaxy environment. - Refactor to allow this to be done without duplicating logic related to defaults, configuration handling, etc.... Implements #3426. Commit: 312f941e46fdbbe6198b6b0e6a3f00867946a6bd https://github.com/galaxyproject/galaxy/commit/312f941e46fdbbe6198b6b0e6a3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Swap default for Conda "auto_init" to True. Everyone gets a Conda when Galaxy starts up. Commit: 0b7c6761c8dbb2baf7391dc4a08c4dbed2ccc7f2 https://github.com/galaxyproject/galaxy/commit/0b7c6761c8dbb2baf7391dc4a08c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M scripts/manage_tool_dependencies.py Log Message: ----------- Rework #3433 for changes in #3444. Commit: 9baf6d6d8d8d089a8d2c2687ef498a396006b920 https://github.com/galaxyproject/galaxy/commit/9baf6d6d8d8d089a8d2c2687ef49… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: A config/local_conda_mapping.yml.sample M lib/galaxy/config.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml A test/functional/tools/legacy_r.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_resolvers.py Log Message: ----------- Samples and defaults for Conda mapping. - Map R to r-base and blast+ to blast for conda dependencies. - Add sample environment modules file showing off the new mapping feature. - Add integration test case to verify the default conda mapping (R -> r-base in particular). Commit: 3e3d41fb94c00a9c6b068626b6f541e714b2500e https://github.com/galaxyproject/galaxy/commit/3e3d41fb94c00a9c6b068626b6f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Fix unit test test_tool_deps to not auto-install Conda. This became the default behavior with conda_auto_init defaulting to True. Commit: 915b653b91af25bf126125be875bd6ab2d9f320c https://github.com/galaxyproject/galaxy/commit/915b653b91af25bf126125be875b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #3463 from jmchilton/16.07_container_fix [16.07] fix condor containers Commit: 56ed9db21d16e5c42e0d05c7102b681089ba2354 https://github.com/galaxyproject/galaxy/commit/56ed9db21d16e5c42e0d05c7102b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/linters/inputs.py Log Message: ----------- Fix linting of <conditional>s If the first param is boolean with truevalue="True" or falsavalue="False", or a select with an option having value "True" or "False", the linter was wrongly complaining with both: No <when /> block found for select option 'True' and: No <option /> block found for when block 'true' Commit: 5bd8a0fa0232f5fa56cc4ace557d3b8f0d5cbdf0 https://github.com/galaxyproject/galaxy/commit/5bd8a0fa0232f5fa56cc4ace557d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #3356 from bgruening/fuzzysearch Fuzzy search for tools search Commit: 98ee91f467039f27f4e10d730f78057d1421e833 https://github.com/galaxyproject/galaxy/commit/98ee91f467039f27f4e10d730f78… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/util/properties.py M run.sh A scripts/manage_tool_dependencies.py A test/functional/tools/legacy_r.xml M test/functional/tools/samples_tool_conf.xml M test/integration/test_resolvers.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #3444 from jmchilton/deps_framework_overhaul Implement Dependency Resolver Mapping Commit: 8daa58adcc6c28004a2697407bce8f28d8bb5411 https://github.com/galaxyproject/galaxy/commit/8daa58adcc6c28004a2697407bce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/linters/inputs.py Log Message: ----------- Merge pull request #3464 from nsoranzo/conditional_linting Fix linting of <conditional>s Commit: 1b589f252ed12eefc48c37f018e04faf142e5898 https://github.com/galaxyproject/galaxy/commit/1b589f252ed12eefc48c37f018e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M doc/schema_template.md M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/object_wrapper.py A lib/galaxy/util/oset.py M lib/galaxy/util/properties.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M run.sh A scripts/manage_tool_dependencies.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.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.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M test/docker/base/run_test_wrapper.sh M test/functional/tools/column_param.xml A test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml A test/functional/tools/legacy_r.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_resolvers.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/unit/tools/test_tool_deps.py M tools/plotting/bar_chart.xml Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into escape_vis Conflicts: static/scripts/bundled/libs.bundled.js.map Commit: d19f22e3fabfd7f22b6970fe857ed636462ca8e5 https://github.com/galaxyproject/galaxy/commit/d19f22e3fabfd7f22b6970fe857e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/viz/trackster/tracks.js Log Message: ----------- Merge pull request #3448 from yhoogstrate/escape_vis Custom dbkey builds: additional variable escaping Commit: ab87216d59178dee482adf4d065cc507d590f1f8 https://github.com/galaxyproject/galaxy/commit/ab87216d59178dee482adf4d065c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01.rc1 Commit: 1c0c378debdee4aeb9699f11ad2b3314323888b6 https://github.com/galaxyproject/galaxy/commit/1c0c378debdee4aeb9699f11ad2b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: ffa4af0a8e79acb673e90e543d67b7be0be3b631 https://github.com/galaxyproject/galaxy/commit/ffa4af0a8e79acb673e90e543d67… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3466 from jmchilton/version-17.01 [17.01] Update version to 17.01.rc1 Commit: c85b28c6d2c3e39801ea9138d84bfa2a0ded536c https://github.com/galaxyproject/galaxy/commit/c85b28c6d2c3e39801ea9138d84b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: df8be3add7fc87fc5ad6e4e38217332a57d3915a https://github.com/galaxyproject/galaxy/commit/df8be3add7fc87fc5ad6e4e38217… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M test/integration/test_resolvers.py Log Message: ----------- Fix cached dependency manager. Broken with baf9b82847fc526af56ed8efa7aba4d31d62f400. Also fix test case that made me think it was okay in the first place. Commit: 28b7b1faff9420c0010c117b573917741b1974ef https://github.com/galaxyproject/galaxy/commit/28b7b1faff9420c0010c117b5739… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Upgrade six to 1.10.0. This is required by the setuptools release released today. So if anything uses setuptools (e.g. it seems we get twill from PyPI instead of wheels.galaxyproject.org) it will fail because we have downgraded six it seems. Commit: 0bf7efb89a189e14e3b9d85ef2355a3821a498ce https://github.com/galaxyproject/galaxy/commit/0bf7efb89a189e14e3b9d85ef235… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #3471 from jmchilton/17_01_six_upgrade [17.01] Upgrade six to 1.10.0. Commit: dc49b1c220bb96b1675ab50bdbccf7eca8d739bc https://github.com/galaxyproject/galaxy/commit/dc49b1c220bb96b1675ab50bdbcc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3470 from jmchilton/cached_dependency_manager_fixes [17.01] Fix cached dependency manager. Commit: 7f232a25b5a9c91131b64d8c72744a9f34d30045 https://github.com/galaxyproject/galaxy/commit/7f232a25b5a9c91131b64d8c7274… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix path to Smat datatype Commit: f882cb9b2ef45fd3b1dfb36d7bf1edb64b540e01 https://github.com/galaxyproject/galaxy/commit/f882cb9b2ef45fd3b1dfb36d7bf1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and plugins in tox.ini For all tox environments used in .travis.yml except the ones allowed to fail. Commit: 191813ab80a237476012333a1cb96834ce933124 https://github.com/galaxyproject/galaxy/commit/191813ab80a237476012333a1cb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3476 from nsoranzo/release_17.01_pin_flake8 [17.01] Pin flake8 and plugins in tox.ini Commit: a396b280dc6a26581bb3e5059e6aebcc4790b6cb https://github.com/galaxyproject/galaxy/commit/a396b280dc6a26581bb3e5059e6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3475 from nsoranzo/release_17.01_fix_smat_datatype [17.01] Fix path to Smat datatype Commit: dd77cdb62576a62ea7e8ce8e31d2d7d78aef7823 https://github.com/galaxyproject/galaxy/commit/dd77cdb62576a62ea7e8ce8e31d2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Add API test for converters after toolbox reload Commit: 78b4f8f7627a63be7ba593109c1ffd36891168ba https://github.com/galaxyproject/galaxy/commit/78b4f8f7627a63be7ba593109c1f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py Log Message: ----------- Reload converter tools after toolbox reload Commit: 36ecf28adaa3328cac3248dc7e8c3ef79211c204 https://github.com/galaxyproject/galaxy/commit/36ecf28adaa3328cac3248dc7e8c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M test/api/test_datatypes.py Log Message: ----------- Use CONVERTER_fasta_to_tabular as example converter (thx @jmchilton) Commit: 496fa5144dc373952c0d815b844b17fef394f632 https://github.com/galaxyproject/galaxy/commit/496fa5144dc373952c0d815b844b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-25 (Wed, 25 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Improve dataset state information in selection fields Commit: ccacbb7c3b7dc453b687fb7ec332f4d6793d689d https://github.com/galaxyproject/galaxy/commit/ccacbb7c3b7dc453b687fb7ec332… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use dataset matcher for unhidden datasets only Commit: 78a37b2a191403a87ea05fc88f890504fad400c4 https://github.com/galaxyproject/galaxy/commit/78a37b2a191403a87ea05fc88f89… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Fix test case Commit: c3650d9fb6b2c422d62db1c10c4bfffe425e5f36 https://github.com/galaxyproject/galaxy/commit/c3650d9fb6b2c422d62db1c10c4b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-26 (Thu, 26 Jan 2017) Changed paths: A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst Log Message: ----------- add initial release notes Commit: fe87cd889f2bdab122fccd0db99aa31af864d1db https://github.com/galaxyproject/galaxy/commit/fe87cd889f2bdab122fccd0db99a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Allow mapping requirements with version None to a specific version (so that all-in-one dependency resolution is applied) but do not match a specific requirement (i.e samtools 0.1.19) when mapping ``` - from: name: samtools version: None to: name: samtools version: 1.3.1 ``` This will only map samtools requirements that do not specify a version. If you want to override a specifically requested version, you need to include that version, i.e ``` - from: name: samtools version: None to: name: samtools version: 1.3.1 - from: name: samtools version: 0.1.19 to: name: samtools version: 1.2 ``` Commit: d3093013f95a4a0d324213f6ab4461f6d196d1fd https://github.com/galaxyproject/galaxy/commit/d3093013f95a4a0d324213f6ab44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M config/local_conda_mapping.yml.sample Log Message: ----------- Extend default mapping Commit: 3dcdad9eba31bf1b689f9bfb2e95908f8c4c2c55 https://github.com/galaxyproject/galaxy/commit/3dcdad9eba31bf1b689f9bfb2e95… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add sam_to_bam to list of tools requiring Galaxy's environment. Only a very old version of sam_to_bam required this - but I guess it is actively used on usegalaxy.org since there was a bug report from @jennaj. Commit: 44a90033dbe1c635e37952711e28de1016ee1090 https://github.com/galaxyproject/galaxy/commit/44a90033dbe1c635e37952711e28… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M config/local_conda_mapping.yml.sample Log Message: ----------- Use Null instead of None to get the non-string None value. str(from_raw.get(version)) will turn it into 'None' anyway. Commit: f51355a183852565a857f825776bd38321cf2ff8 https://github.com/galaxyproject/galaxy/commit/f51355a183852565a857f825776b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3506 from martenson/release_17.01 [17.01] Add sam_to_bam to list of tools requiring Galaxy's environment. Commit: b92e9b509354a570424da4b1ff86a5f75bba585a https://github.com/galaxyproject/galaxy/commit/b92e9b509354a570424da4b1ff86… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-27 (Fri, 27 Jan 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Add unit tests that asserts new dependency mapping rules Commit: a30d6dfa2090096975ca614a85cde53ae9c948bb https://github.com/galaxyproject/galaxy/commit/a30d6dfa2090096975ca614a85cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M config/local_conda_mapping.yml.sample Log Message: ----------- Drop openbabel mapping from 2.32 to 2.4.1 (thx @bgruening) Commit: 14529b9dd56b45afe6d06babf88eb6a164c517e5 https://github.com/galaxyproject/galaxy/commit/14529b9dd56b45afe6d06babf88e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Collapse list of tool requirements after mapping With this change, the merged environment name for requirements that have been specified using multiple names (e.g. sickle (for TS) and sickle-trim (conda/docker)) will be sickle-trim if mapping sickle to sickle-trim (instead of mulled-v1-<hash>). Commit: 54036e9f7d41606f40d87859c45dbc35f794b2b3 https://github.com/galaxyproject/galaxy/commit/54036e9f7d41606f40d87859c45d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M test/unit/tools/test_data_parameters.py Log Message: ----------- Fix test case for deleted mock hdas Commit: 1c979769dc73e4e8824213161caa82837f340802 https://github.com/galaxyproject/galaxy/commit/1c979769dc73e4e8824213161caa… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- explicit sniffing of FastqGz/FastqBz2 types Commit: b3c9f82b1a6fa743e927e545704e868a0f100e25 https://github.com/galaxyproject/galaxy/commit/b3c9f82b1a6fa743e927e545704e… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-01-29 (Sun, 29 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqdsrc_to_fastq.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py Log Message: ----------- Added fastq.dsrc datatype Commit: dccf20ab7968e2d67afa32470b74776fbfef3a84 https://github.com/galaxyproject/galaxy/commit/dccf20ab7968e2d67afa32470b74… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/converters/fastqdsrc_to_fastq.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py Log Message: ----------- Revert "Added fastq.dsrc datatype" This reverts commit b3c9f82b1a6fa743e927e545704e868a0f100e25. Inadvertent commit to PR branch Commit: 1f818ad1d6b22f42f4c3b5599812852730e01de8 https://github.com/galaxyproject/galaxy/commit/1f818ad1d6b22f42f4c3b5599812… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- added newline to make lint happy Commit: 02dd2e4708e7167248c48b2452621cf31a6bdba6 https://github.com/galaxyproject/galaxy/commit/02dd2e4708e7167248c48b245262… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge pull request #3495 from guerler/fix_dataset_label [17.01] Properly label hidden datasets in dataset selectors Commit: 6ba0291eea85723514a7a983f009e4033f660ea0 https://github.com/galaxyproject/galaxy/commit/6ba0291eea85723514a7a983f009… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M config/local_conda_mapping.yml.sample M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M test/unit/tools/test_tool_deps.py Log Message: ----------- Modify representation of mapping to None. (#4) I feel that mapping from ``` - from: blast+ to: blast ``` should be the same as ``` - from: name: blast+ version: Null to: blast ``` since it should just be syntatic sugar. And I think that second version reads like it should by default apply to all versions. I feel therefore it is probably better to explicitly require stating that a mapping only applies to unversioned requirements. This commit does that by introducing the syntax: ``` - from: name: blast+ unversioned: true to: name: blast version: 1.3.4 ``` It feels better to have strongly typed entities like this than to introduce magic constants such as: ``` - from: name: blast+ version: __unversioned__ to: name: blast version: 1.3.4 ``` which is another route this could have gone I guess. Commit: ea7e1cc945cb529293a93b14612bb03f5096902a https://github.com/galaxyproject/galaxy/commit/ea7e1cc945cb529293a93b14612b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Use ToolRequirements (uses OrderedSet internally) to collapse redundant requirements instead of set to maintain the order of specified requirements. Commit: aba3d8844b7a56e47ebbed42ec3de46debb82d75 https://github.com/galaxyproject/galaxy/commit/aba3d8844b7a56e47ebbed42ec3d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3514 from jvolkening/release_17.01 [17.01] explicit sniffing of FastqGz/FastqBz2 types Commit: cbba01c8dc9f5303712a5c46fcee475be5e03bd8 https://github.com/galaxyproject/galaxy/commit/cbba01c8dc9f5303712a5c46fcee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Disable sniffing of fastq files by default. Start Galaxy with GALAXY_ENABLE_BETA_COMPRESSED_FASTQ_SNIFFING=1 to re-enable this. Commit: a43d7ab8f43b891b30ded632da728e9076ae03f6 https://github.com/galaxyproject/galaxy/commit/a43d7ab8f43b891b30ded632da72… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Add missing compressed attribute thanks to @nsoranzo. Commit: 8b08384be3bc84f5474617e4c4dc9466ff036a67 https://github.com/galaxyproject/galaxy/commit/8b08384be3bc84f5474617e4c4dc… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3510 from jmchilton/1701_disable_compressed_fastq_sniffing [17.01] Disable compressed fastq sniffing by default. Commit: e4999510ee2bc44802b4891a1a09b00489b01a9c https://github.com/galaxyproject/galaxy/commit/e4999510ee2bc44802b4891a1a09… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Merge pull request #3486 from mvdbeek/converter_reload [16.10] BUG: Reload converter tools after toolbox reload Commit: 5ad185590148390ec27750567273f59546eec219 https://github.com/galaxyproject/galaxy/commit/5ad185590148390ec27750567273… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Disable conda_auto_init by default for most tests. Executing framework, API, and/or selenium tests was causing Conda to be installed. This isn't needed - the only tests that test Conda dependencies are unit tests and integration tests that explicitly configure this Conda installation. Commit: a8e59b7b238d123d2407021bd7d62465fbb7d43d https://github.com/galaxyproject/galaxy/commit/a8e59b7b238d123d2407021bd7d6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-30 (Mon, 30 Jan 2017) Changed paths: M test/base/driver_util.py Log Message: ----------- Merge pull request #3517 from jmchilton/disable_testing_conda [17.01] Disable conda_auto_init by default for most tests. Commit: 1fe0f2f76b67bbb034af48e0ee963da4dd176284 https://github.com/galaxyproject/galaxy/commit/1fe0f2f76b67bbb034af48e0ee96… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01.rst Log Message: ----------- bring in @nsoranzo's comments Commit: 47863ff13444b1596e12fb4903229717593bdea4 https://github.com/galaxyproject/galaxy/commit/47863ff13444b1596e12fb490322… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst M doc/source/releases/_thanks.rst Log Message: ----------- more work towards reasonable release notes Commit: cc40b9d45514e1388e2d98e676fe5b75b28d6a3e https://github.com/galaxyproject/galaxy/commit/cc40b9d45514e1388e2d98e676fe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M lib/galaxy/model/mapping.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- This enforces serial workflow scheduling within the context of a particular history. Commit: 749a503534033d3260681b75ad829a640d1c4a3b https://github.com/galaxyproject/galaxy/commit/749a503534033d3260681b75ad82… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Minor typo in sample. Commit: 8be1429dda7e158601371331494501fd6043a5e0 https://github.com/galaxyproject/galaxy/commit/8be1429dda7e1586013713314945… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Add configuration for history_local_serial_workflow_scheduling Commit: 2b55fc75ebad92183e78a80b3240f7b978bd448d https://github.com/galaxyproject/galaxy/commit/2b55fc75ebad92183e78a80b3240… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Might be more palatable if this is defaulted to false. Commit: 2209b899b7075a5cf0f076d31248cc3ec244688e https://github.com/galaxyproject/galaxy/commit/2209b899b7075a5cf0f076d31248… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Fix bug in sample description from #3364. Commit: 82ec7828af24f51815dd502fab25c02dbe79e95b https://github.com/galaxyproject/galaxy/commit/82ec7828af24f51815dd502fab25… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3521 from jmchilton/fix_sample_desc_3364 [17.01] Fix sample description bug from #3364. Commit: 21525ee25ef2b7b49733d845affe6fd9ede5b7b2 https://github.com/galaxyproject/galaxy/commit/21525ee25ef2b7b49733d845affe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- clarify fastq compression handling Commit: e0d2f6dbc8b8bc5d96855cc74bf62fa56c731fd6 https://github.com/galaxyproject/galaxy/commit/e0d2f6dbc8b8bc5d96855cc74bf6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- clarify how to prevent unpacking of archives Commit: 2d2e7ddc958f9908fa72caca540c333929e8b517 https://github.com/galaxyproject/galaxy/commit/2d2e7ddc958f9908fa72caca540c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Don't encourage uploads of fastq in release notes. My understanding is nearly all data now produced is fastqsanger. Commit: 39c03fc6a0be3b56b1972411c281b06391ac65c1 https://github.com/galaxyproject/galaxy/commit/39c03fc6a0be3b56b1972411c281… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #3509 from mvdbeek/allow_mapping_from_none [17.01] Add `unversioned` keyword to limit mappings to requirements without version Commit: 32e624195b827b1e3ba607337c1b87067651b0c2 https://github.com/galaxyproject/galaxy/commit/32e624195b827b1e3ba607337c1b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst Log Message: ----------- Add all PRs and authors for compressed fastq support Commit: 76076dfeff8de4eb9509e60563a6cc905d2b5b22 https://github.com/galaxyproject/galaxy/commit/76076dfeff8de4eb9509e60563a6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- remove jmchilton from credits the Galaxy-lab members are explicitly omitted from RN mentions Commit: 9217889d2e23d339665a95a06d97112a28e91b2b https://github.com/galaxyproject/galaxy/commit/9217889d2e23d339665a95a06d97… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Add ashvark to author list Commit: 2f0a635e9f270007ec1da64b7ed054ff47cbb35e https://github.com/galaxyproject/galaxy/commit/2f0a635e9f270007ec1da64b7ed0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01.rst Log Message: ----------- Various improvements to the release notes. - Rewording things to focus on reader concerns. - Grouping things into single bullets (like testing stuff) and close to similar topics (like Conda stuff). - Eliminated some things which should have been marked #minor Commit: 9a7066c4b4c9f3824257cc00695b87ef9a065c0f https://github.com/galaxyproject/galaxy/commit/9a7066c4b4c9f3824257cc00695b… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/verify/asserts/xml.py Log Message: ----------- fix <is_valid_xml> output test assert check Commit: e3f50e90f8ab9e8313d077da2961a81bafb7c90a https://github.com/galaxyproject/galaxy/commit/e3f50e90f8ab9e8313d077da2961… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst Log Message: ----------- More work on 17.01 release notes. Commit: f985b613ea1002a6595e073dfb459880ad7fdfdf https://github.com/galaxyproject/galaxy/commit/f985b613ea1002a6595e073dfb45… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Fix new history naming for batchmode workflow runs Commit: 58241e8dcb71500d399dbe2089f5b20f1eb89b53 https://github.com/galaxyproject/galaxy/commit/58241e8dcb71500d399dbe2089f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Rebuild client for 17.01 with latest node. Commit: 9dc1bbd3bc4697f5fbf1e183883aba9277058706 https://github.com/galaxyproject/galaxy/commit/9dc1bbd3bc4697f5fbf1e183883a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Merge pull request #3535 from dannon/minor_fix [17.01] Rebuild client for 17.01 with latest node. Commit: 31725972ef9342145effa6ad24d912022afb278c https://github.com/galaxyproject/galaxy/commit/31725972ef9342145effa6ad24d9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix conda resolver when conda_auto_init = True and install = False Conda dependencies were being prematurely installed during installation of repositories from the ToolShed (at the point where we are just trying to list already installed dependencies). Commit: a121b889ef584086c96c6b9230198b3e2a04d6f6 https://github.com/galaxyproject/galaxy/commit/a121b889ef584086c96c6b923019… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Only read 6 bytes. Fixes #3529 Commit: c602336cc82fe60c54d10834c26fb8b0eafe81b0 https://github.com/galaxyproject/galaxy/commit/c602336cc82fe60c54d10834c26f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix for rerunning a job when the tool does not exist. Commit: 3858528d90c1380ae33c7e6087ee3ee1a9bb85f9 https://github.com/galaxyproject/galaxy/commit/3858528d90c1380ae33c7e6087ee… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3537 from jmchilton/backport_genbank_fix [17.01] Backport of fix unbounded readline in genbank datatype Commit: da7fed47445d8d1483eb456f32af19a0b0ff5412 https://github.com/galaxyproject/galaxy/commit/da7fed47445d8d1483eb456f32af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix wiggle to wiggle2simple1 for Python path changes in #3364. Fixes #3539. #minor Commit: 840c3b0fd846ea5fb58fb34378717aeadea7e81a https://github.com/galaxyproject/galaxy/commit/840c3b0fd846ea5fb58fb3437871… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Fix integration test for default Conda mapping. It worked locally simply because I had R already installed on my system globally. Commit: a7cc18d616a2fe020d1946eac91ab248f9a1c995 https://github.com/galaxyproject/galaxy/commit/a7cc18d616a2fe020d1946eac91a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix tools that use Galaxy sequence utilities for #3364. Thanks to @peterjc for reporting and @martenson for grepping. xref #minor #3364 Commit: bb15a431f006dfbe0d9777529300b8e1981fc988 https://github.com/galaxyproject/galaxy/commit/bb15a431f006dfbe0d9777529300… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3540 from jmchilton/wiggle_fix_1701 [17.01] Fix wiggle to wiggle2simple1 for Python path changes in #3364. Commit: da0affd45d4fb5479d0e0adcc4efa147bee41e63 https://github.com/galaxyproject/galaxy/commit/da0affd45d4fb5479d0e0adcc4ef… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3542 from jmchilton/more_python_preservation [17.01] Fix tools that use Galaxy sequence utilities for #3364. Commit: 639e2e5b2c4631901450a58710acbee373b498d8 https://github.com/galaxyproject/galaxy/commit/639e2e5b2c4631901450a58710ac… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- minor tweaks of RN Commit: 105557ba35317120af7f241aebec99f43c4c8553 https://github.com/galaxyproject/galaxy/commit/105557ba35317120af7f241aebec… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: A test-data/simple.xml A test/functional/tools/is_valid_xml.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- added functional test for <is_valid_xml> Commit: 2322bc1ff59e85fb4f9db281d04b96e124dd73aa https://github.com/galaxyproject/galaxy/commit/2322bc1ff59e85fb4f9db281d04b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3541 from jmchilton/backport_3508 [17.01] Fix integration test for default Conda mapping. Commit: f1062afa55c486a0b35418bf7e7e988136c78cb6 https://github.com/galaxyproject/galaxy/commit/f1062afa55c486a0b35418bf7e7e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #3538 from blankenberg/fix-rerun-no-tool [17.01] Fix for rerunning a job when the tool does not exist. Commit: 0ce7f6897fe7a037ae9ff9a79c082c56fec0e929 https://github.com/galaxyproject/galaxy/commit/0ce7f6897fe7a037ae9ff9a79c08… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- add comments from @mvdbeek Commit: 715e73adc97ea2c88639a50d1aaf88b9a1f3bcdc https://github.com/galaxyproject/galaxy/commit/715e73adc97ea2c88639a50d1aaf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M doc/source/releases/17.01.rst Log Message: ----------- minor changes thanks to @nsoranzo Commit: 961efb4d9af9ea17fbd0f80b7f07158f2cb971ad https://github.com/galaxyproject/galaxy/commit/961efb4d9af9ea17fbd0f80b7f07… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3536 from blankenberg/17.01-conda-fix [17.01] Fix conda resolver when conda_auto_install = True and install = False Commit: f6919651f8225c2d48c7b2ecb667e365d7be7bf7 https://github.com/galaxyproject/galaxy/commit/f6919651f8225c2d48c7b2ecb667… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/verify/asserts/xml.py A test-data/simple.xml A test/functional/tools/is_valid_xml.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3530 from jvolkening/release_17.01 fix <is_valid_xml> output test assert check Commit: b6cd80a5b35938847d4b306501a4e1fc7030c441 https://github.com/galaxyproject/galaxy/commit/b6cd80a5b35938847d4b306501a4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/api/configuration.py M test/api/test_datatypes.py Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 62e6639d4716462dc4c6d5292c362a4ce0ba8a31 https://github.com/galaxyproject/galaxy/commit/62e6639d4716462dc4c6d5292c36… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M test/api/test_datatypes.py Log Message: ----------- Fix import order Broken in commit dd77cdb62576a62ea7e8ce8e31d2d7d78aef7823 . Need to remove the file from .ci/flake8_lint_include_list.txt because 'base' is not in application-import-names Commit: 409ca0a3c7eec50aaaec15215d380ec098ce4ec1 https://github.com/galaxyproject/galaxy/commit/409ca0a3c7eec50aaaec15215d38… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #3520 from dannon/history_serial_workflow_scheduling [17.01] History-local serial workflow scheduling. Commit: 49970e786fcf2d885b6a81aa61786cba7912f3fe https://github.com/galaxyproject/galaxy/commit/49970e786fcf2d885b6a81aa6178… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M test/api/test_datatypes.py Log Message: ----------- Merge pull request #3549 from nsoranzo/release_17.01_fix_import_order [17.01] Fix import order Commit: 4df803a930c1546d41e4adeef9a0cc286cf6ada0 https://github.com/galaxyproject/galaxy/commit/4df803a930c1546d41e4adeef9a0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Merge pull request #3532 from guerler/fix_new_history_naming [16.10] Fix new history naming for batchmode workflow runs Commit: f9edf39f58b9942b461e5238c9df60ab5765faea https://github.com/galaxyproject/galaxy/commit/f9edf39f58b9942b461e5238c9df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Migrate galaxy_utils to a wheel. Alternative approach to #3542 which was not future proof with Conda dependencies. I think this should be now. xref #3364 #2994 http://dev.list.galaxyproject.org/Tools-using-Galaxy-s-Python-library-td467… Rebased with fixes from @nsoranzo and @mvdbeek. Commit: 934bf6b056bc2475b217d62524e95de564c7a7a8 https://github.com/galaxyproject/galaxy/commit/934bf6b056bc2475b217d62524e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Ensure toolbox conf watcher updates cached hash when config change is detected Commit: b41b8e305bac3425b9bd20cda43936b23bd02abd https://github.com/galaxyproject/galaxy/commit/b41b8e305bac3425b9bd20cda439… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #3558 from natefoo/toolconf-watch-hash [16.10] Ensure toolbox conf watcher updates cached hash when config change is detected Commit: 43873b8a6de5a6f1669f8364fff54c206b5f2f84 https://github.com/galaxyproject/galaxy/commit/43873b8a6de5a6f1669f8364fff5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #3560 from galaxyproject/release_16.10 [17.01] Merge 16.10 into 17.01 Commit: 16a97e47c70f544d7acd30aac107a6687f01b736 https://github.com/galaxyproject/galaxy/commit/16a97e47c70f544d7acd30aac107… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-05 (Sun, 05 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt R doc/source/lib/galaxy_utils.rst R doc/source/lib/galaxy_utils.sequence.rst M doc/source/lib/modules.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Merge pull request #3551 from jmchilton/galaxy_utils_external [17.01] Migrate galaxy_utils to a wheel. Commit: 9feb8b3f02038c5cadad858d4b4675467ec90616 https://github.com/galaxyproject/galaxy/commit/9feb8b3f02038c5cadad858d4b46… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: A doc/source/releases/17.01.rst M doc/source/releases/17.01_announce.rst A doc/source/releases/17.05_announce.rst M doc/source/releases/_thanks.rst Log Message: ----------- Merge pull request #3497 from martenson/17.01_release_notes [17.01] add release notes Commit: 012e261692a2ed8eb3e3c6ca4496b0bd48c99a84 https://github.com/galaxyproject/galaxy/commit/012e261692a2ed8eb3e3c6ca4496… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Remove debugging warn statement. I don't think it was meant to be here. Commit: f2e15588bfad5ad04e4f6530b9b7966e65d138ad https://github.com/galaxyproject/galaxy/commit/f2e15588bfad5ad04e4f6530b9b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #3566 from jmchilton/1701_user_warn [17.01] Remove debugging warn statement. Commit: 10b743d1d99b0a544002adf57c61a0168ca24e2a https://github.com/galaxyproject/galaxy/commit/10b743d1d99b0a544002adf57c61… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix default for Pulsar option "dependency_resolution" to match documentation. Commit: 6eb735be8265e0e10d2a5bb7c3845c27dcbff6fb https://github.com/galaxyproject/galaxy/commit/6eb735be8265e0e10d2a5bb7c384… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #3575 from jmchilton/pulsar_default_fix [17.01] Fix default for Pulsar option "dependency_resolution" to match documentation. Commit: 561606621cd207c05ec4da33cb7f8c3b9f6f5bfa https://github.com/galaxyproject/galaxy/commit/561606621cd207c05ec4da33cb7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Update index.rst Commit: 884cff33fa04915f426f8c24bb53494ff43f0a36 https://github.com/galaxyproject/galaxy/commit/884cff33fa04915f426f8c24bb53… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #3577 from martenson/release-docs-menu [17.01] list new release docs Commit: a7d05a47da592e76fd88ed699f034e13e2dba08e https://github.com/galaxyproject/galaxy/commit/a7d05a47da592e76fd88ed699f03… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Prevent make_html_table() datatype methods from raising Exceptions This was preventing the browse of a data library which contained a purged dataset of gg datatype. Also fix import order and Python3 compatibility. Commit: f8dcae95364b79a1612c7a0d04b489d874512aa7 https://github.com/galaxyproject/galaxy/commit/f8dcae95364b79a1612c7a0d04b4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Remove edam_format for Genbank from config/datatypes_conf.xml.sample This was preventing the loading of the datatype: WARNING 2017-02-10 11:07:05,162 Cannot specify edam_format without setting subclass to True, skipping datatype. Bug introduced in commit c36fbebb443ae5b5263ba6cad6ad36113bb52f44 . Also backport commit 5657a8b809e5938d3d996a77c826811e1176c108 from dev. Commit: 087c75e76ff44cf49eb0b458520d2df4db31e32e https://github.com/galaxyproject/galaxy/commit/087c75e76ff44cf49eb0b458520d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #3585 from nsoranzo/release_17.01_datatypes_fixes [17.01] Two datatypes fixes Commit: 69552ba63b90604a0d0f0315cad5f42e3344eac5 https://github.com/galaxyproject/galaxy/commit/69552ba63b90604a0d0f0315cad5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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/tool/tool-form-base.js Log Message: ----------- Fix root location for tool reloader Commit: 4a22bb902b121f91c370b30c64590dd46997a412 https://github.com/galaxyproject/galaxy/commit/4a22bb902b121f91c370b30c6459… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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/tool/tool-form-base.js Log Message: ----------- Merge pull request #3595 from guerler/fix_tool_reload_002 [17.01] Fix root location for tool reloader Commit: 4483f014107d92340573c7113745821e4863c148 https://github.com/galaxyproject/galaxy/commit/4483f014107d92340573c7113745… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Fix ScIdx datatype sniffer Check for EOF before line stripping, otherwise empty or whitespace lines will be considered EOF. Found when uploading a GFF file which was erroneously sniffed as scidx. Commit: 5db0b7681bb60e0671c0d80d06e3d980ef3aab6e https://github.com/galaxyproject/galaxy/commit/5db0b7681bb60e0671c0d80d06e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #3602 from nsoranzo/release_17.01_fix_scidx_sniffer Fix ScIdx datatype sniffer Commit: 255aa0470f44ea90d2b4d738e07b8f6d08874c3b https://github.com/galaxyproject/galaxy/commit/255aa0470f44ea90d2b4d738e07b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Fix workflow save-as url not using galaxy's prefix. Commit: c86d2ee8bcbdde82ac5e6f450241ef7fed076665 https://github.com/galaxyproject/galaxy/commit/c86d2ee8bcbdde82ac5e6f450241… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #3610 from dannon/fix-editor-save-as-url [17.01] Fix workflow save-as url not using galaxy's prefix. Commit: 4689cf16bf77b0e7b0d22d193b695d7d5df24d6c https://github.com/galaxyproject/galaxy/commit/4689cf16bf77b0e7b0d22d193b69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Recalculate user disk usage on logout. Not as ideal as just having it be accurate all the time, but it 1) avoids adding yet another control people need to dig for when they need to recalculate, and 2) makes things right when following 'turn it off and on again' Commit: 43d80a0b6052b59f8be768ad810fee952a436ce3 https://github.com/galaxyproject/galaxy/commit/43d80a0b6052b59f8be768ad810f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Tooltips to suggest relog for quota correction. Commit: 966d578b47f4999ba0f8db874bf927e5f4246d7f https://github.com/galaxyproject/galaxy/commit/966d578b47f4999ba0f8db874bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Slightly more defensive programming -- we don't expose this in the UI unless there *is* a trans.user, but we might as well be careful here. Commit: 0e9eb78636da19c68ff3c981ff8090b63a7d11ae https://github.com/galaxyproject/galaxy/commit/0e9eb78636da19c68ff3c981ff80… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- deprecate repair repository feature Commit: 944feb2411d1381b1743f3365b6380e883c9cccb https://github.com/galaxyproject/galaxy/commit/944feb2411d1381b1743f3365b63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Minor tooltip tweaks. Commit: c82530fd2384f5df2457e8f5dd33368cc13abc48 https://github.com/galaxyproject/galaxy/commit/c82530fd2384f5df2457e8f5dd33… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge pull request #3614 from dannon/logout-recalc-backport [17.01] Logout recalc backport and additional logic Commit: 29d229cedd697ff79595b223d651dd0d97ded457 https://github.com/galaxyproject/galaxy/commit/29d229cedd697ff79595b223d651… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Merge pull request #3615 from martenson/release_17.01 [17.01] deprecate repair repository feature Commit: ab6ae42c7a7d76b3fbf024edbbdec407b7b1f490 https://github.com/galaxyproject/galaxy/commit/ab6ae42c7a7d76b3fbf024edbbde… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- Cancel existing delayed updates when changing pages in the history. Commit: ac191f5f2a10c003788a291501331b68fb521bc7 https://github.com/galaxyproject/galaxy/commit/ac191f5f2a10c003788a29150133… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- [17.01] Make active_datasets_children_and_roles just active_datasets_and_roles. I guess somewhere in the tool building process we eliminated children from appearing the form. Remove unused code that used the children selector in the tool form. Commit: eb42d130d34c9393f3386ba115de6fe561e9ef18 https://github.com/galaxyproject/galaxy/commit/eb42d130d34c9393f3386ba115de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Fix unit tests for that last commit. Commit: 792bd4f8835e9aef355a904b773f208a022e5e95 https://github.com/galaxyproject/galaxy/commit/792bd4f8835e9aef355a904b773f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Implementation of slow query logging. Disabled by default. Commit: 9135226ae40dd2222172fd6883511f682c72f7a4 https://github.com/galaxyproject/galaxy/commit/9135226ae40dd2222172fd688351… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Aarrghs spacing. Commit: 42d2a1a4e33b28c98faef4f003edebb600710562 https://github.com/galaxyproject/galaxy/commit/42d2a1a4e33b28c98faef4f003ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add forgotten sample change. Commit: 28fe37c977b18d83d91e7a1d604112f62857073f https://github.com/galaxyproject/galaxy/commit/28fe37c977b18d83d91e7a1d6041… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Style tweaks. My flake8-in-editor had silently died and was not warning me anymore, super. Commit: b14dccab631b2a68ca0131ceca27426668d9b2e2 https://github.com/galaxyproject/galaxy/commit/b14dccab631b2a68ca0131ceca27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Import formatting... Commit: d2ec75084b2eeae30ce61168462fec03f1211b6e https://github.com/galaxyproject/galaxy/commit/d2ec75084b2eeae30ce61168462f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #3624 from jmchilton/active_children_drop [17.01] Drop children from query that prefetches data for dataset matching. Commit: 56f7af455c5638aef16d2fd7ac07cd0644f7009a https://github.com/galaxyproject/galaxy/commit/56f7af455c5638aef16d2fd7ac07… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Merge pull request #3625 from dannon/backport_query_logging [17.01] Usable slow query logging Commit: f155a9420a23241c6dc7e404ce487c803a911726 https://github.com/galaxyproject/galaxy/commit/f155a9420a23241c6dc7e404ce48… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M tools/filters/random_lines_two_pass.py Log Message: ----------- temp Commit: 62ee8e8404fb86155d9893a8eeab1cf58473d795 https://github.com/galaxyproject/galaxy/commit/62ee8e8404fb86155d9893a8eeab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix Python environment hack to allow "fixing" tool ids at some version. This is a less broken alternative to #3620 and something I intended to ultimately do anyway. sam-to-bam used to be broken but now it isn't, we need to express that. Ideally we would move most of the things from the unversioned list to the versioned list as they are fixed. xref https://github.com/galaxyproject/galaxy/pull/3620#issuecomment-280674067 xref https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813… xref #3351 xref galaxyproject/tools-iuc#1148 Commit: 409f50e282885a686b2cdbe75bfe5a5f0e8dde38 https://github.com/galaxyproject/galaxy/commit/409f50e282885a686b2cdbe75bfe… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Add default docker_connect_port to interactive environments config dictionary. Commit: eb6c0e410e600171fa3ce4fffb78bc205aad5292 https://github.com/galaxyproject/galaxy/commit/eb6c0e410e600171fa3ce4fffb78… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Rework preserve python environment expression according to :eagle::eyes: suggestion. https://github.com/galaxyproject/galaxy/pull/3630#discussion_r101798306 Commit: 851f08cb00eac7582a90bafe660b561ebea4c50b https://github.com/galaxyproject/galaxy/commit/851f08cb00eac7582a90bafe660b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3631 from blankenberg/gie-jupyter-fix-17.01 [17.01] Add default docker_connect_port to interactive environments config dictionary. Commit: f53b6474828d1f8ab1170630ce5851bb913ebec7 https://github.com/galaxyproject/galaxy/commit/f53b6474828d1f8ab1170630ce58… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- WIP: Fix for conda=4.3 Commit: d37ed7e7dadcf568b22836f477ce5afd2a377af7 https://github.com/galaxyproject/galaxy/commit/d37ed7e7dadcf568b22836f477ce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Adjust offline fix to work for a broader range of potential target Condas. This logic could in theory be backported all the way to 16.01 I suppose now. Commit: 1e3c9ab945c4616510b5b4ff2726aab89585bef4 https://github.com/galaxyproject/galaxy/commit/1e3c9ab945c4616510b5b4ff2726… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- More revisions to fixing --offline mode to Conda. Incorporate package extraction fixes thanks to @nsoranzo, the fix for version 4.1 and 4.0 thanks to @mvdbeek, a comment for @bgruening and a new test tool that makes it a bit easier to test this. Commit: 0024aa458216589589d35b9366c6347c0c280860 https://github.com/galaxyproject/galaxy/commit/0024aa458216589589d35b9366c6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M test/functional/tools/mulled_example_multi_incomplete.xml Log Message: ----------- Add a clarification to new test tool. Commit: f6cc1dcf077f9d98c38afdd93d47e60c42ac06e5 https://github.com/galaxyproject/galaxy/commit/f6cc1dcf077f9d98c38afdd93d47… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3632 from jmchilton/conda_43_fix [17.01] Fix Conda --offline logic for bug in 4.0,4.1,4.3. Commit: f1f6bf6c3a765e05f8a2dc2b127ee480a485b42e https://github.com/galaxyproject/galaxy/commit/f1f6bf6c3a765e05f8a2dc2b127e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix annotation display for data inputs Commit: ce264f9542df6d4ba779309fb8e7822c6f351f2e https://github.com/galaxyproject/galaxy/commit/ce264f9542df6d4ba779309fb8e7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Reimplement *old* method for unhide/delete-all-hidden using a temporary web controller endpoint. Commit: a3a7e1001cc0ffa985fd7e987c7190f2d74492ff https://github.com/galaxyproject/galaxy/commit/a3a7e1001cc0ffa985fd7e987c71… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M tools/filters/random_lines_two_pass.py Log Message: ----------- Strip stashed-yet-merged debug detritus from history UI fixes. Commit: bf602a8add58289900fa64cc5c1163c0721f1d10 https://github.com/galaxyproject/galaxy/commit/bf602a8add58289900fa64cc5c11… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Yet more debugging cruft. This is why we have reviews. Commit: 493cf2816134562188ba009e8bf04ffbcc18a2ac https://github.com/galaxyproject/galaxy/commit/493cf2816134562188ba009e8bf0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3621 from dannon/fix-paginated-history-updates [17.01] History Fixes Commit: 0278753d0e2db921cd7d3f55cef483defff5cdb9 https://github.com/galaxyproject/galaxy/commit/0278753d0e2db921cd7d3f55cef4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Increase patience of Galaxy tests throughout. This should help reduce various API and Selenium transient failures. Commit: 09c08d1f61f93ec7973cab1d2cd24532d20e3bb7 https://github.com/galaxyproject/galaxy/commit/09c08d1f61f93ec7973cab1d2cd2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3636 from guerler/fix_annotation [17.01] Fix annotation display for data inputs Commit: caf57c6f3e21eb38e3331d1a1dd44f2cd5b68dc2 https://github.com/galaxyproject/galaxy/commit/caf57c6f3e21eb38e3331d1a1dd4… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #3637 from jmchilton/backport_3589 [17.01] Backport #3589 Commit: f7a14e1c90270f557d52fda196400653b0b9d09f https://github.com/galaxyproject/galaxy/commit/f7a14e1c90270f557d52fda19640… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Use `command -v` rather than `which` when determining Galaxy Python for external set metadata. Commit: 305f461d45ab010c10fa6061cd7d248e354a9967 https://github.com/galaxyproject/galaxy/commit/305f461d45ab010c10fa6061cd7d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fix inability to access API key for users Commit: 62475c50a03927aa2461543c227c60909adff332 https://github.com/galaxyproject/galaxy/commit/62475c50a03927aa2461543c227c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3640 from erasche/fix-api-access-external [17.01] Fix inability to access API key for users Commit: 29f8b54c9a8a975473ecbee96992ec400fd138b5 https://github.com/galaxyproject/galaxy/commit/29f8b54c9a8a975473ecbee96992… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Merge pull request #3638 from natefoo/use-version-not-which [17.01] Use `command -v` rather than `which` when determining Galaxy Python for external set metadata Commit: 6733c36318bacce0bbf33a8d266f6a08de3ba019 https://github.com/galaxyproject/galaxy/commit/6733c36318bacce0bbf33a8d266f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- [17.01] Restore logging statement missing when resolve_all is used. Broken in #3391. Commit: 49ef352235f7c998e79ca5423fab9725ea28d8be https://github.com/galaxyproject/galaxy/commit/49ef352235f7c998e79ca5423fab… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3646 from jmchilton/resolve_all_logging [17.01] Restore logging statement missing when resolve_all is used. Commit: 9ebe2d2dd6efde7a66c52681aa57c52342ad992d https://github.com/galaxyproject/galaxy/commit/9ebe2d2dd6efde7a66c52681aa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3630 from jmchilton/python_hack_scalpel [17.01] Fix Python environment hack to allow "fixing" tool ids at some version. Commit: 90de3f2588a61382e70b6209ea39293c6a3987f1 https://github.com/galaxyproject/galaxy/commit/90de3f2588a61382e70b6209ea39… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01 Commit: 3a2ff46c28172ef78510f4bea2f4be75ce660667 https://github.com/galaxyproject/galaxy/commit/3a2ff46c28172ef78510f4bea2f4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .ci/py3_sources.txt M Makefile 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/form/form-view.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/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/ui/ui-misc.js A client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/user/user-quotameter.js A client/galaxy/scripts/mvc/workflow/workflow-icons.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/local_conda_mapping.yml.sample M 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test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_mapper.py M test/unit/test_sockets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_tool_deps.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/workflow_support.py M tools/data_source/fetch.py R tools/filters/gff/sort_gtf.py M tools/plotting/bar_chart.xml M tox.ini Log Message: ----------- Merge branch 'release_17.01' Compare: https://github.com/galaxyproject/galaxy/compare/8b538f17feb1...3a2ff46c2817

1 0

[galaxyproject/galaxy]
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/tags/v17.01 Home: https://github.com/galaxyproject/galaxy

1 0

[galaxyproject/galaxy] 62ee8e: Fix Python environment hack to allow "fixing" tool...
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 62ee8e8404fb86155d9893a8eeab1cf58473d795 https://github.com/galaxyproject/galaxy/commit/62ee8e8404fb86155d9893a8eeab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix Python environment hack to allow "fixing" tool ids at some version. This is a less broken alternative to #3620 and something I intended to ultimately do anyway. sam-to-bam used to be broken but now it isn't, we need to express that. Ideally we would move most of the things from the unversioned list to the versioned list as they are fixed. xref https://github.com/galaxyproject/galaxy/pull/3620#issuecomment-280674067 xref https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813… xref #3351 xref galaxyproject/tools-iuc#1148 Commit: eb6c0e410e600171fa3ce4fffb78bc205aad5292 https://github.com/galaxyproject/galaxy/commit/eb6c0e410e600171fa3ce4fffb78… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Rework preserve python environment expression according to :eagle::eyes: suggestion. https://github.com/galaxyproject/galaxy/pull/3630#discussion_r101798306 Commit: 6733c36318bacce0bbf33a8d266f6a08de3ba019 https://github.com/galaxyproject/galaxy/commit/6733c36318bacce0bbf33a8d266f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- [17.01] Restore logging statement missing when resolve_all is used. Broken in #3391. Commit: 49ef352235f7c998e79ca5423fab9725ea28d8be https://github.com/galaxyproject/galaxy/commit/49ef352235f7c998e79ca5423fab… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3646 from jmchilton/resolve_all_logging [17.01] Restore logging statement missing when resolve_all is used. Commit: 9ebe2d2dd6efde7a66c52681aa57c52342ad992d https://github.com/galaxyproject/galaxy/commit/9ebe2d2dd6efde7a66c52681aa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3630 from jmchilton/python_hack_scalpel [17.01] Fix Python environment hack to allow "fixing" tool ids at some version. Commit: 387805fc1365dbf976e6d3e10ae4a11817e501da https://github.com/galaxyproject/galaxy/commit/387805fc1365dbf976e6d3e10ae4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/jobs/command_factory.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/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: client/galaxy/scripts/mvc/tool/tool-form-composite.js preserved the dev version static/maps/mvc/tool/tool-form-composite.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/tool/tool-form-composite.js Commit: d1c9ffb94c06a7a39cff37a38e78f43fd4e0ca10 https://github.com/galaxyproject/galaxy/commit/d1c9ffb94c06a7a39cff37a38e78… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.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/tool/tool-form-composite.js Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Conflicts: client/galaxy/scripts/mvc/tool/tool-form-composite.js preserved dev version static/maps/mvc/tool/tool-form-composite.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/tool/tool-form-composite.js Commit: 90de3f2588a61382e70b6209ea39293c6a3987f1 https://github.com/galaxyproject/galaxy/commit/90de3f2588a61382e70b6209ea39… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01 Commit: c52715fd69fba88746181601e8210eb3cbc8b145 https://github.com/galaxyproject/galaxy/commit/c52715fd69fba88746181601e821… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9563a691b05f...c52715fd69fb

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[galaxyproject/galaxy] 90de3f: Update version to 17.01
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 90de3f2588a61382e70b6209ea39293c6a3987f1 https://github.com/galaxyproject/galaxy/commit/90de3f2588a61382e70b6209ea39… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01

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[galaxyproject/galaxy] ab6ae4: Cancel existing delayed updates when changing page...
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab6ae42c7a7d76b3fbf024edbbdec407b7b1f490 https://github.com/galaxyproject/galaxy/commit/ab6ae42c7a7d76b3fbf024edbbde… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js Log Message: ----------- Cancel existing delayed updates when changing pages in the history. Commit: f155a9420a23241c6dc7e404ce487c803a911726 https://github.com/galaxyproject/galaxy/commit/f155a9420a23241c6dc7e404ce48… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M tools/filters/random_lines_two_pass.py Log Message: ----------- temp Commit: f53b6474828d1f8ab1170630ce5851bb913ebec7 https://github.com/galaxyproject/galaxy/commit/f53b6474828d1f8ab1170630ce58… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- WIP: Fix for conda=4.3 Commit: d37ed7e7dadcf568b22836f477ce5afd2a377af7 https://github.com/galaxyproject/galaxy/commit/d37ed7e7dadcf568b22836f477ce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Adjust offline fix to work for a broader range of potential target Condas. This logic could in theory be backported all the way to 16.01 I suppose now. Commit: 1e3c9ab945c4616510b5b4ff2726aab89585bef4 https://github.com/galaxyproject/galaxy/commit/1e3c9ab945c4616510b5b4ff2726… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- More revisions to fixing --offline mode to Conda. Incorporate package extraction fixes thanks to @nsoranzo, the fix for version 4.1 and 4.0 thanks to @mvdbeek, a comment for @bgruening and a new test tool that makes it a bit easier to test this. Commit: 0024aa458216589589d35b9366c6347c0c280860 https://github.com/galaxyproject/galaxy/commit/0024aa458216589589d35b9366c6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M test/functional/tools/mulled_example_multi_incomplete.xml Log Message: ----------- Add a clarification to new test tool. Commit: f6cc1dcf077f9d98c38afdd93d47e60c42ac06e5 https://github.com/galaxyproject/galaxy/commit/f6cc1dcf077f9d98c38afdd93d47… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3632 from jmchilton/conda_43_fix [17.01] Fix Conda --offline logic for bug in 4.0,4.1,4.3. Commit: f1f6bf6c3a765e05f8a2dc2b127ee480a485b42e https://github.com/galaxyproject/galaxy/commit/f1f6bf6c3a765e05f8a2dc2b127e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix annotation display for data inputs Commit: ce264f9542df6d4ba779309fb8e7822c6f351f2e https://github.com/galaxyproject/galaxy/commit/ce264f9542df6d4ba779309fb8e7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Reimplement *old* method for unhide/delete-all-hidden using a temporary web controller endpoint. Commit: a3a7e1001cc0ffa985fd7e987c7190f2d74492ff https://github.com/galaxyproject/galaxy/commit/a3a7e1001cc0ffa985fd7e987c71… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M tools/filters/random_lines_two_pass.py Log Message: ----------- Strip stashed-yet-merged debug detritus from history UI fixes. Commit: bf602a8add58289900fa64cc5c1163c0721f1d10 https://github.com/galaxyproject/galaxy/commit/bf602a8add58289900fa64cc5c11… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Yet more debugging cruft. This is why we have reviews. Commit: 493cf2816134562188ba009e8bf04ffbcc18a2ac https://github.com/galaxyproject/galaxy/commit/493cf2816134562188ba009e8bf0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3621 from dannon/fix-paginated-history-updates [17.01] History Fixes Commit: 0278753d0e2db921cd7d3f55cef483defff5cdb9 https://github.com/galaxyproject/galaxy/commit/0278753d0e2db921cd7d3f55cef4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Increase patience of Galaxy tests throughout. This should help reduce various API and Selenium transient failures. Commit: 09c08d1f61f93ec7973cab1d2cd24532d20e3bb7 https://github.com/galaxyproject/galaxy/commit/09c08d1f61f93ec7973cab1d2cd2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3636 from guerler/fix_annotation [17.01] Fix annotation display for data inputs Commit: caf57c6f3e21eb38e3331d1a1dd44f2cd5b68dc2 https://github.com/galaxyproject/galaxy/commit/caf57c6f3e21eb38e3331d1a1dd4… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #3637 from jmchilton/backport_3589 [17.01] Backport #3589 Commit: f7a14e1c90270f557d52fda196400653b0b9d09f https://github.com/galaxyproject/galaxy/commit/f7a14e1c90270f557d52fda19640… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Use `command -v` rather than `which` when determining Galaxy Python for external set metadata. Commit: 305f461d45ab010c10fa6061cd7d248e354a9967 https://github.com/galaxyproject/galaxy/commit/305f461d45ab010c10fa6061cd7d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fix inability to access API key for users Commit: 62475c50a03927aa2461543c227c60909adff332 https://github.com/galaxyproject/galaxy/commit/62475c50a03927aa2461543c227c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3640 from erasche/fix-api-access-external [17.01] Fix inability to access API key for users Commit: 29f8b54c9a8a975473ecbee96992ec400fd138b5 https://github.com/galaxyproject/galaxy/commit/29f8b54c9a8a975473ecbee96992… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Merge pull request #3638 from natefoo/use-version-not-which [17.01] Use `command -v` rather than `which` when determining Galaxy Python for external set metadata Commit: 24eba8c58ee9d7f8907c83f5d72ea01997d56ab4 https://github.com/galaxyproject/galaxy/commit/24eba8c58ee9d7f8907c83f5d72e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: client/galaxy/scripts/mvc/tool/tool-form-composite.js static/maps/mvc/tool/tool-form-composite.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/tool/tool-form-composite.js Commit: 9563a691b05f65ec3bdcd9135f75878b2ec666e3 https://github.com/galaxyproject/galaxy/commit/9563a691b05f65ec3bdcd9135f75… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3641 from nsoranzo/merge_17.01 Merge 17.01 into dev Compare: https://github.com/galaxyproject/galaxy/compare/badf49daa54a...9563a691b05f

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[galaxyproject/galaxy] 62ee8e: Fix Python environment hack to allow "fixing" tool...
by GitHub 22 Feb '17

22 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 62ee8e8404fb86155d9893a8eeab1cf58473d795 https://github.com/galaxyproject/galaxy/commit/62ee8e8404fb86155d9893a8eeab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix Python environment hack to allow "fixing" tool ids at some version. This is a less broken alternative to #3620 and something I intended to ultimately do anyway. sam-to-bam used to be broken but now it isn't, we need to express that. Ideally we would move most of the things from the unversioned list to the versioned list as they are fixed. xref https://github.com/galaxyproject/galaxy/pull/3620#issuecomment-280674067 xref https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813… xref #3351 xref galaxyproject/tools-iuc#1148 Commit: eb6c0e410e600171fa3ce4fffb78bc205aad5292 https://github.com/galaxyproject/galaxy/commit/eb6c0e410e600171fa3ce4fffb78… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Rework preserve python environment expression according to :eagle::eyes: suggestion. https://github.com/galaxyproject/galaxy/pull/3630#discussion_r101798306 Commit: 9ebe2d2dd6efde7a66c52681aa57c52342ad992d https://github.com/galaxyproject/galaxy/commit/9ebe2d2dd6efde7a66c52681aa57… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3630 from jmchilton/python_hack_scalpel [17.01] Fix Python environment hack to allow "fixing" tool ids at some version. Compare: https://github.com/galaxyproject/galaxy/compare/49ef352235f7...9ebe2d2dd6ef

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