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

[galaxyproject/usegalaxy-playbook] 68e7fb: Update and fix Jupyter on Test
by GitHub 30 Nov '16

30 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 68e7fbd23245e21504db78c8c0ff65c2cd894669 https://github.com/galaxyproject/usegalaxy-playbook/commit/68e7fbd23245e215… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info M roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_apache.conf.j2 M roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_nginx.conf.j2 M stage/galaxy_version.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Update and fix Jupyter on Test Commit: db0307a737b35926bded36bd2c991c4b54d32f04 https://github.com/galaxyproject/usegalaxy-playbook/commit/db0307a737b35926… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M production/group_vars/galaxywebservers.yml Log Message: ----------- Limit docker memory Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/bd4f3a0eca9b...…

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[galaxyproject/galaxy] 4398ab: Check also for cgroup memory warnings if job was c...
by GitHub 30 Nov '16

30 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy 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: 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: 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/2d510fae981f...ead8e15f42a4

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[galaxyproject/galaxy] 74d8fa: Change 'History Actions' to 'Current History' in h...
by GitHub 30 Nov '16

30 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 74d8faac9f07407ac9df344a78c9ecb06c178f93 https://github.com/galaxyproject/galaxy/commit/74d8faac9f07407ac9df344a78c9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.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 M static/scripts/mvc/history/options-menu.js Log Message: ----------- Change 'History Actions' to 'Current History' in history options menu. as it was before 1cc57b1eb2c295dbd68837c864740b6ff079b83d. Commit: ec08ec60bb4dadaf6f8759f9dce79f764f26c909 https://github.com/galaxyproject/galaxy/commit/ec08ec60bb4dadaf6f8759f9dce7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-21 (Mon, 21 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.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 M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3205 from blankenberg/history-current-options-name_16.10 [16.10] Change 'History Actions' to 'Current History' in history options menu. Commit: a9dab631fb00252ac122ea297262e89f63887019 https://github.com/galaxyproject/galaxy/commit/a9dab631fb00252ac122ea297262… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-section.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 Log Message: ----------- Preserve custom event handler for form inputs Commit: 0b2d0c1746c9b7d7cc5781fedc5c6a02af3bdfdb https://github.com/galaxyproject/galaxy/commit/0b2d0c1746c9b7d7cc5781fedc5c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-section.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 Log Message: ----------- Merge pull request #3210 from guerler/fix_output_label_handler [16.10] Preserve custom event handler for form inputs Commit: 9a2bae7381b1ee8e2411681a76d75767b05ceffe https://github.com/galaxyproject/galaxy/commit/9a2bae7381b1ee8e2411681a76d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako Log Message: ----------- simplify the UI of deps installation by hiding the details under toggle button Commit: 068ee6bd0ceb942ec67e634a7e6e434314cbe7fe https://github.com/galaxyproject/galaxy/commit/068ee6bd0ceb942ec67e634a7e6e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py Log Message: ----------- fix install repo test Commit: 706bc3fbb118087cc057e6559e0262a6aca31127 https://github.com/galaxyproject/galaxy/commit/706bc3fbb118087cc057e6559e02… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py Log Message: ----------- fix test and hide shed_conf select udner details Commit: 73d010efa4236ed8ef0e46bb10d5e39233ae2d6b https://github.com/galaxyproject/galaxy/commit/73d010efa4236ed8ef0e46bb10d5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- fix another test Commit: 4b794729b0cfd347d189a9a1e62273ab1788bc3e https://github.com/galaxyproject/galaxy/commit/4b794729b0cfd347d189a9a1e622… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- fix a bug that renders conda dependency selection everytime Commit: 94edc94b73e047612ae51ca2e075f17ac8e238bb https://github.com/galaxyproject/galaxy/commit/94edc94b73e047612ae51ca2e075… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: 0a9b6d8755dee530232ab893a3bad199407aa0bc https://github.com/galaxyproject/galaxy/commit/0a9b6d8755dee530232ab893a3ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo) Commit: 2b1765751b29008aecbd782f28269ac4e63db239 https://github.com/galaxyproject/galaxy/commit/2b1765751b29008aecbd782f2826… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: f919a98601252ab8f87bffff6e449105e770aadf https://github.com/galaxyproject/galaxy/commit/f919a98601252ab8f87bffff6e44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: 82f30e7645156b5f35c2b4cd77314e6275663979 https://github.com/galaxyproject/galaxy/commit/82f30e7645156b5f35c2b4cd7731… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: 64bc9241ed785d4d552c5fac21cd412558c54567 https://github.com/galaxyproject/galaxy/commit/64bc9241ed785d4d552c5fac21cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix NameError Commit: cf769dd09deb73624b22628208fa103cc4f27150 https://github.com/galaxyproject/galaxy/commit/cf769dd09deb73624b22628208fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: cc7cd47ef54a09efbf8272d1e024f6f2ac92594b https://github.com/galaxyproject/galaxy/commit/cc7cd47ef54a09efbf8272d1e024… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Add integration test-case for install tool dependency API endpoint Commit: f10fd793a68ed9413bec708daa48cef65769d09f https://github.com/galaxyproject/galaxy/commit/f10fd793a68ed9413bec708daa48… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_2bit.xml Log Message: ----------- Install the correct converter dependency Commit: 045a2f0d471f7b4186aff625f3cea9abfa549fa2 https://github.com/galaxyproject/galaxy/commit/045a2f0d471f7b4186aff625f3ce… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: 16b49d9140edbf116f83b51b957cd61c4f2d91df https://github.com/galaxyproject/galaxy/commit/16b49d9140edbf116f83b51b957c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: 1efd4d4b3b99ec40071aa4d6fb7cf4030c51e2e0 https://github.com/galaxyproject/galaxy/commit/1efd4d4b3b99ec40071aa4d6fb7c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: 2a4ccac4039342c98d71bc72177aa951db6c4ba1 https://github.com/galaxyproject/galaxy/commit/2a4ccac4039342c98d71bc72177a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: e3f8b724648cee51636502959096adba88045e14 https://github.com/galaxyproject/galaxy/commit/e3f8b724648cee51636502959096… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py 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 pull request #3226 from martenson/16-10-install-ux [16.10] admin installation ux Commit: d6f0e6b37c318a0202e0e266828e6325100cab19 https://github.com/galaxyproject/galaxy/commit/d6f0e6b37c318a0202e0e266828e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py 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/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.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 lib/tool_shed/galaxy_install/install_manager.py M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3227 from mvdbeek/cached_deps_16.10 [16.10] Backport #3106 and #3222: Cached conda environments and API to manage them Commit: a26568bdfaefc5748ff3b2385fa9424ece6c652c https://github.com/galaxyproject/galaxy/commit/a26568bdfaefc5748ff3b2385fa9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and flake8-import-order Do not pin when forward-merging to dev branch! Commit: 888a8f91537e22dcbdea174a65eaecbced9ea8a8 https://github.com/galaxyproject/galaxy/commit/888a8f91537e22dcbdea174a65ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3232 from nsoranzo/release_16.10_pin_flake8 [16.10] Pin flake8 and flake8-import-order 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 Compare: https://github.com/galaxyproject/galaxy/compare/1bbab2d89d2c...2d510fae981f

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[galaxyproject/galaxy] b70557: Fix configuration API admin checking and tests.
by GitHub 30 Nov '16

30 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy 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: 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. Compare: https://github.com/galaxyproject/galaxy/compare/b165757288f0...1bbab2d89d2c

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[galaxyproject/galaxy] b8e283: Adding code for replacing mako for user preference...
by GitHub 30 Nov '16

30 Nov '16

Branch: refs/heads/dev 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 https://github.com/galaxyproject/galaxy/commit/dc80c8962b31192929037448ffba… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/add-edit-address.js M client/galaxy/scripts/mvc/user/manage-user-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merging the api calls for user info into one api call Commit: 69800d41da8a131fcaee40ff1a6aa1194afe1427 https://github.com/galaxyproject/galaxy/commit/69800d41da8a131fcaee40ff1a6a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/user/manage-user-information.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding user type form and address filters Commit: 431fad09e06afe2a13ccd21e3ffff3ef826ee341 https://github.com/galaxyproject/galaxy/commit/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 paths: M client/galaxy/scripts/mvc/user/add-edit-address.js M client/galaxy/scripts/mvc/user/api-keys.js M client/galaxy/scripts/mvc/user/change-communication.js M client/galaxy/scripts/mvc/user/change-password.js M client/galaxy/scripts/mvc/user/change-permissions.js M client/galaxy/scripts/mvc/user/manage-user-information.js M client/galaxy/scripts/mvc/user/toolbox-filter.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fixing styling and removing commented out code Commit: 60d4570c54dcd58d69ff907c832881a2328b2545 https://github.com/galaxyproject/galaxy/commit/60d4570c54dcd58d69ff907c8328… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M .ci/first_startup.sh M .ci/flake8_blacklist.txt A .ci/flake8_lint_include_list.txt A .ci/flake8_wrapper_imports.sh M 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client/galaxy/scripts/mvc/user/change-password.js R client/galaxy/scripts/mvc/user/manage-user-information.js R client/galaxy/scripts/mvc/user/toolbox-filter.js M client/galaxy/scripts/mvc/user/user-preferences.js A static/maps/mvc/user/change-api-key.js.map A static/maps/mvc/user/change-communication.js.map A static/maps/mvc/user/change-password.js.map A static/maps/mvc/user/change-permissions.js.map A static/maps/mvc/user/change-toolbox-filter.js.map A static/maps/mvc/user/change-user-information.js.map A static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/user/change-api-key.js A static/scripts/mvc/user/change-communication.js A static/scripts/mvc/user/change-password.js A static/scripts/mvc/user/change-permissions.js A static/scripts/mvc/user/change-toolbox-filter.js A static/scripts/mvc/user/change-user-information.js A static/scripts/mvc/user/user-preferences.js Log Message: ----------- Add packed files, use consistent file naming Commit: 31867733173911de306ea45184ce62ba1eea63ea https://github.com/galaxyproject/galaxy/commit/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 https://github.com/galaxyproject/galaxy/commit/0c70b5bca27e51a84af1e9381f28… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-29 (Thu, 29 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js A client/galaxy/scripts/mvc/user/change-api-key.js A client/galaxy/scripts/mvc/user/change-toolbox-filter.js A client/galaxy/scripts/mvc/user/change-user-information.js M lib/galaxy/model/__init__.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py M static/maps/mvc/form/form-section.js.map M static/maps/mvc/user/change-permissions.js.map M static/maps/mvc/user/change-user-information.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/user/change-permissions.js M static/scripts/mvc/user/change-user-information.js Log Message: ----------- Build address field dict Commit: 60ed49a6acb48ed82fdbdca1d45c8184d25360d3 https://github.com/galaxyproject/galaxy/commit/60ed49a6acb48ed82fdbdca1d45c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Add user info form conditional builder Commit: ed104067aa6504890dedfd54dd89a56952cafc9b https://github.com/galaxyproject/galaxy/commit/ed104067aa6504890dedfd54dd89… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fix Commit: 8d9dc602d0d336872a08548fd1a27c59794477eb https://github.com/galaxyproject/galaxy/commit/8d9dc602d0d336872a08548fd1a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Add type form, untested Commit: baa4676282d0acd85e721e8819910f3553bff1c1 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https://github.com/galaxyproject/galaxy/commit/ee8a887dcdd228b2e3c9c8e2526d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Use single api endpoint to build user information form with addresses Commit: bf3d447f0d9c26405344dcfe43763d0515df2efb https://github.com/galaxyproject/galaxy/commit/bf3d447f0d9c26405344dcfe4376… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Remove user info handler Commit: 6b9ab97f4aeadca9c2a637c8f346642facfbbdc2 https://github.com/galaxyproject/galaxy/commit/6b9ab97f4aeadca9c2a637c8f346… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-30 (Fri, 30 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fix typo Commit: b737a2c6d791399bf59a8ef645851709ad5ad0ce 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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 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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 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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 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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 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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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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: ----------- Adding edit feature for email and username along with client side validations for the Manage User Info form Commit: f593ad6c70bc891f84cdee1d481c3ebd142da9b4 https://github.com/galaxyproject/galaxy/commit/f593ad6c70bc891f84cdee1d481c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-10-30 (Sun, 30 Oct 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Fixing bug with numbers in postal code and phone number Commit: c40be4f4c63ef99018ba899579e1776922f71662 https://github.com/galaxyproject/galaxy/commit/c40be4f4c63ef99018ba899579e1… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-10-30 (Sun, 30 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M Makefile M client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/webhooks/demo/history_test1/config/history_test1.yml A config/plugins/webhooks/demo/history_test2/config/history_test2.yml A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml A config/plugins/webhooks/demo/phdcomics/helper/__init__.py A config/plugins/webhooks/demo/phdcomics/static/script.js A config/plugins/webhooks/demo/phdcomics/static/styles.css A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml A config/plugins/webhooks/demo/trans_object/helper/__init__.py A config/plugins/webhooks/demo/xkcd/config/xkcd.yml A config/plugins/webhooks/demo/xkcd/static/script.js A config/plugins/webhooks/demo/xkcd/static/styles.css M 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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 errors Commit: f04ea9f8db2dcfbe0f5c94fedcbc90b70aa237a4 https://github.com/galaxyproject/galaxy/commit/f04ea9f8db2dcfbe0f5c94fedcbc… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Changing the config variable name for toggling new user preferences Commit: a22cd27ced212ae8343f3c43c765f57c1cb2dfb3 https://github.com/galaxyproject/galaxy/commit/a22cd27ced212ae8343f3c43c765… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Commenting variables in config file Commit: 8f49202778c72389d567ef840df518e473b0e4f3 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doc/source/admin/interactive_environments_success.png M doc/source/admin/mulled_containers.rst M doc/source/conf.py M doc/source/dev/build_a_job_runner.rst M doc/source/dev/index.rst A doc/source/dev/inherit.png A doc/source/dev/interactive_environments_success.png A doc/source/dev/queue.png A doc/source/dev/queue_b.png A doc/source/dev/runner_diag.png M doc/source/index.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.linters.rst M doc/source/lib/galaxy.tools.parameters.rst R doc/source/lib/galaxy.util.backports.importlib.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.rst M doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst M doc/source/releases/16.07.rst M doc/source/releases/index.rst M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/metrics/instrumenters/__init__.py M lib/galaxy/managers/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/roles.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/simplegraph.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/bootstrap_history.py R scripts/bootstrap_history_announce_template.rst M scripts/galaxy-main M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/ui/ui-tabs.js.map A static/maps/mvc/ui/ui-thumbnails.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-tabs.js A static/scripts/mvc/ui/ui-thumbnails.js M static/style/blue/base.css M templates/user/index.mako M test/qunit/package.json M test/qunit/tests/ui_tests.js Log Message: ----------- Merge with dev Commit: 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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 lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Remove unused variables and libraries, fix lint Commit: 301c5ec637d8adb6cfa88bd9f728a623ccc06310 https://github.com/galaxyproject/galaxy/commit/301c5ec637d8adb6cfa88bd9f728… 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: ----------- Apply autopep8, fix lint Commit: d5804d6ba7c555ea9d984dea2fb5b87f62c02311 https://github.com/galaxyproject/galaxy/commit/d5804d6ba7c555ea9d984dea2fb5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-03 (Thu, 03 Nov 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/style/less/base.less M config/galaxy.ini.sample M lib/galaxy/model/__init__.py M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/galaxy/api/user_preferences.py M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Merge pull request #28 from guerler/remove_mako_user_pref_000 Restore changes Commit: eb178129c102b4645ba76071bd528a683a176242 https://github.com/galaxyproject/galaxy/commit/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, 04 Nov 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/user_preferences.py Log Message: ----------- Revise address handling, use regex, temporary disable validation and user info forms saving Commit: d7d6c743e8dc8199a9f481d0ba046afee18723b7 https://github.com/galaxyproject/galaxy/commit/d7d6c743e8dc8199a9f481d0ba04… 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: ----------- Ensure storing address attributes as text value Commit: be80dddf6cc680124cc964d981ebd27ffcca3540 https://github.com/galaxyproject/galaxy/commit/be80dddf6cc680124cc964d981eb… 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: ----------- Delete previous addresses for now Commit: 82703e35f6e936c977662483e122a613df8fd275 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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: 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: 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: 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 client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/source_material/circle.py M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/tool_data_table_conf.xml.sample M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M doc/Makefile M doc/parse_gx_xsd.py M doc/patch.py M doc/source/admin/interactive_environments.rst M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_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_2bit.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.py 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.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml M lib/galaxy/datatypes/converters/gff_to_bed_converter.py 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.py 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/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_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.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py 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.py M lib/galaxy/datatypes/converters/interval_to_coverage.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml M lib/galaxy/datatypes/converters/len_to_linecount.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/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/sam_to_bam.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml M 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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: 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: 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: 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: 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: 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/fd0a52a9a9ae...b165757288f0

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[galaxyproject/galaxy] a26568: Pin flake8 and flake8-import-order
by GitHub 30 Nov '16

30 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: a26568bdfaefc5748ff3b2385fa9424ece6c652c https://github.com/galaxyproject/galaxy/commit/a26568bdfaefc5748ff3b2385fa9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M tox.ini Log Message: ----------- Pin flake8 and flake8-import-order Do not pin when forward-merging to dev branch! Commit: 888a8f91537e22dcbdea174a65eaecbced9ea8a8 https://github.com/galaxyproject/galaxy/commit/888a8f91537e22dcbdea174a65ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-30 (Wed, 30 Nov 2016) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3232 from nsoranzo/release_16.10_pin_flake8 [16.10] Pin flake8 and flake8-import-order Compare: https://github.com/galaxyproject/galaxy/compare/d6f0e6b37c31...888a8f91537e

1 0

[galaxyproject/galaxy] 94edc9: Add cached dependency manager
by GitHub 29 Nov '16

29 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 94edc94b73e047612ae51ca2e075f17ac8e238bb https://github.com/galaxyproject/galaxy/commit/94edc94b73e047612ae51ca2e075… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: 0a9b6d8755dee530232ab893a3bad199407aa0bc https://github.com/galaxyproject/galaxy/commit/0a9b6d8755dee530232ab893a3ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo) Commit: 2b1765751b29008aecbd782f28269ac4e63db239 https://github.com/galaxyproject/galaxy/commit/2b1765751b29008aecbd782f2826… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: f919a98601252ab8f87bffff6e449105e770aadf https://github.com/galaxyproject/galaxy/commit/f919a98601252ab8f87bffff6e44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: 82f30e7645156b5f35c2b4cd77314e6275663979 https://github.com/galaxyproject/galaxy/commit/82f30e7645156b5f35c2b4cd7731… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: 64bc9241ed785d4d552c5fac21cd412558c54567 https://github.com/galaxyproject/galaxy/commit/64bc9241ed785d4d552c5fac21cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix NameError Commit: cf769dd09deb73624b22628208fa103cc4f27150 https://github.com/galaxyproject/galaxy/commit/cf769dd09deb73624b22628208fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: cc7cd47ef54a09efbf8272d1e024f6f2ac92594b https://github.com/galaxyproject/galaxy/commit/cc7cd47ef54a09efbf8272d1e024… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Add integration test-case for install tool dependency API endpoint Commit: f10fd793a68ed9413bec708daa48cef65769d09f https://github.com/galaxyproject/galaxy/commit/f10fd793a68ed9413bec708daa48… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_2bit.xml Log Message: ----------- Install the correct converter dependency Commit: 045a2f0d471f7b4186aff625f3cea9abfa549fa2 https://github.com/galaxyproject/galaxy/commit/045a2f0d471f7b4186aff625f3ce… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: 16b49d9140edbf116f83b51b957cd61c4f2d91df https://github.com/galaxyproject/galaxy/commit/16b49d9140edbf116f83b51b957c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: 1efd4d4b3b99ec40071aa4d6fb7cf4030c51e2e0 https://github.com/galaxyproject/galaxy/commit/1efd4d4b3b99ec40071aa4d6fb7c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: 2a4ccac4039342c98d71bc72177aa951db6c4ba1 https://github.com/galaxyproject/galaxy/commit/2a4ccac4039342c98d71bc72177a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-29 (Tue, 29 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: d6f0e6b37c318a0202e0e266828e6325100cab19 https://github.com/galaxyproject/galaxy/commit/d6f0e6b37c318a0202e0e266828e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py 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/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.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 lib/tool_shed/galaxy_install/install_manager.py M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3227 from mvdbeek/cached_deps_16.10 [16.10] Backport #3106 and #3222: Cached conda environments and API to manage them Compare: https://github.com/galaxyproject/galaxy/compare/e3f8b724648c...d6f0e6b37c31

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[galaxyproject/galaxy] 9a2bae: simplify the UI of deps installation
by GitHub 29 Nov '16

29 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 9a2bae7381b1ee8e2411681a76d75767b05ceffe https://github.com/galaxyproject/galaxy/commit/9a2bae7381b1ee8e2411681a76d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M templates/admin/tool_shed_repository/common.mako Log Message: ----------- simplify the UI of deps installation by hiding the details under toggle button Commit: 068ee6bd0ceb942ec67e634a7e6e434314cbe7fe https://github.com/galaxyproject/galaxy/commit/068ee6bd0ceb942ec67e634a7e6e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py Log Message: ----------- fix install repo test Commit: 706bc3fbb118087cc057e6559e0262a6aca31127 https://github.com/galaxyproject/galaxy/commit/706bc3fbb118087cc057e6559e02… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py Log Message: ----------- fix test and hide shed_conf select udner details Commit: 73d010efa4236ed8ef0e46bb10d5e39233ae2d6b https://github.com/galaxyproject/galaxy/commit/73d010efa4236ed8ef0e46bb10d5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- fix another test Commit: 4b794729b0cfd347d189a9a1e62273ab1788bc3e https://github.com/galaxyproject/galaxy/commit/4b794729b0cfd347d189a9a1e622… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-28 (Mon, 28 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- fix a bug that renders conda dependency selection everytime Commit: e3f8b724648cee51636502959096adba88045e14 https://github.com/galaxyproject/galaxy/commit/e3f8b724648cee51636502959096… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-29 (Tue, 29 Nov 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py 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 pull request #3226 from martenson/16-10-install-ux [16.10] admin installation ux Compare: https://github.com/galaxyproject/galaxy/compare/0b2d0c1746c9...e3f8b724648c

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[galaxyproject/galaxy] 40a95a: Add API to install resolver tool dependencies
by GitHub 28 Nov '16

28 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/c8ea393ccb13...fd0a52a9a9ae

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[galaxyproject/galaxy] 8109a7: Add EDAM topic(s) and operation(s) elements to XSD...
by GitHub 28 Nov '16

28 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy 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: 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. Compare: https://github.com/galaxyproject/galaxy/compare/5b4a0689d56e...c8ea393ccb13

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