Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 139bacb7d3e507ea56b8c8997e47408db87b5fa3 https://github.com/galaxyproject/galaxy/commit/139bacb7d3e507ea56b8c8997e474... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Remove broken tour step. This causes the Selenium tests to fail under various conditions - but legimately so. The referenced target link disappears pretty quickly after the step in the previous click. When I run them in the web browser and this step is "disconnected" and in the center of the screen and as a result it isn't clear what links are being referred to. Commit: ca847e2d588db417bb66664a76ecfdb2105ccc41 https://github.com/galaxyproject/galaxy/commit/ca847e2d588db417bb66664a76ecf... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py Log Message: ----------- Merge pull request #3568 from natefoo/nagios Update Nagios check Commit: be09b7c2ccf2ef861927795c16fb1306ef37ff1a https://github.com/galaxyproject/galaxy/commit/be09b7c2ccf2ef861927795c16fb1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #3582 from jmchilton/selenium_fixes Remove broken tour step. Commit: 07a92fd3ef084a6d7cbe27199d281e534e35cec1 https://github.com/galaxyproject/galaxy/commit/07a92fd3ef084a6d7cbe27199d281... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Remove tool_model usage from client Commit: f7092bd959cfae7f6ee0262a993a2dc5867416e4 https://github.com/galaxyproject/galaxy/commit/f7092bd959cfae7f6ee0262a993a2... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Clean up Selenium resources better. Commit: 171655930aa44227d6b88709aac638dea77a6cd0 https://github.com/galaxyproject/galaxy/commit/171655930aa44227d6b88709aac63... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Move populate state to parameter handling module Commit: 3e3eb4d1397effc8b46c913bb80f3c02773ac506 https://github.com/galaxyproject/galaxy/commit/3e3eb4d1397effc8b46c913bb80f3... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Unify build_module handler Commit: 62d42f711e26e0ab176041ce9a552d1af1290f1a https://github.com/galaxyproject/galaxy/commit/62d42f711e26e0ab176041ce9a552... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Parse payload directly to from_dict handler, handle tool specific attributes in corresponding module wrapper Commit: 7d35a029174da0e3c8f481c0662139b9a59b3051 https://github.com/galaxyproject/galaxy/commit/7d35a029174da0e3c8f481c066213... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Merge pull request #3583 from jmchilton/selenium_fixes Clean up docker-compose resources better for Selenium tests. Commit: f3309822c856e50c61d94c2e021859342d40c5fb https://github.com/galaxyproject/galaxy/commit/f3309822c856e50c61d94c2e02185... Author: jvolkening <jdv@base2bio.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- add option to send API key in header Commit: 812ad3af18b087372b31188ac173b7e9238d712b https://github.com/galaxyproject/galaxy/commit/812ad3af18b087372b31188ac173b... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M test/selenium_tests/test_uploads.py Log Message: ----------- Fix transiently failing Selenium upload test. Commit: 6f5743d052fb4c2ee227d71bf6106f2be9f4428a https://github.com/galaxyproject/galaxy/commit/6f5743d052fb4c2ee227d71bf6106... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #3584 from jvolkening/http_header_api_key add option to send API key in header Commit: d27e0570cb0b372288114498fa1ad26a1f5df188 https://github.com/galaxyproject/galaxy/commit/d27e0570cb0b372288114498fa1ad... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Remove name handling field from workflow module forms Commit: ed52230952a1411a39cff3bde7a7ed66e1344f6f https://github.com/galaxyproject/galaxy/commit/ed52230952a1411a39cff3bde7a7e... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: config/datatypes_conf.xml.sample Commit: 1922d50f903f0c6ad1440d9128a1a23d37cc529c https://github.com/galaxyproject/galaxy/commit/1922d50f903f0c6ad1440d9128a1a... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Increase patience of Galaxy tests throughout. This should help reduce various API and Selenium transient failures. Commit: 1858e43d46355be344c0fab9e61a2e5a57dc8947 https://github.com/galaxyproject/galaxy/commit/1858e43d46355be344c0fab9e61a2... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Unify handling/parsing of label and fixed module name to build title in workflow run form Commit: d484355832a1c6518d38326ef4fbb526423c0e34 https://github.com/galaxyproject/galaxy/commit/d484355832a1c6518d38326ef4fbb... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Provide attributes to front-end, build title on client side Commit: dc0e9fd79eaff575a731409ed7f1771c6cd82b93 https://github.com/galaxyproject/galaxy/commit/dc0e9fd79eaff575a731409ed7f17... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Avoid step duplication when ordering steps on the fly Commit: 2ad612349683dd4ab3bde476f9153e90415f0b53 https://github.com/galaxyproject/galaxy/commit/2ad612349683dd4ab3bde476f9153... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #3589 from jmchilton/test_timeout_increases Increase patience of Galaxy tests throughout. Commit: 66a24c8830f5a87579f5e6e4f55c8efbf9073b0f https://github.com/galaxyproject/galaxy/commit/66a24c8830f5a87579f5e6e4f55c8... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #3587 from jmchilton/selenium_fixes Fix transiently failing Selenium upload test. Commit: b9f1e29eaf32cda146fea2b102157489a639ea51 https://github.com/galaxyproject/galaxy/commit/b9f1e29eaf32cda146fea2b102157... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove redundant label handling from subworkflows Commit: 7ac954f757d2485ae7543db15f400dca0b94fdf3 https://github.com/galaxyproject/galaxy/commit/7ac954f757d2485ae7543db15f400... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Strip name handler Commit: 11f9e1863f9616d58fc00a22526f71b2bca7b880 https://github.com/galaxyproject/galaxy/commit/11f9e1863f9616d58fc00a22526f7... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix label and annotation handling for subworkflows Commit: c6c210a4fa47d0fc47306d30b9dbf40589f68cd8 https://github.com/galaxyproject/galaxy/commit/c6c210a4fa47d0fc47306d30b9dbf... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Remove uncommented code block from request builder Commit: eb95131ab3a03a3675c3e6d6db23caca524b3da6 https://github.com/galaxyproject/galaxy/commit/eb95131ab3a03a3675c3e6d6db23c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Export label instead of name for description export Commit: a79ae2a8c297c1c0f6c0e61271a2ca05ae0aa0f0 https://github.com/galaxyproject/galaxy/commit/a79ae2a8c297c1c0f6c0e61271a2c... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M CONTRIBUTING.md M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M scripts/slideshow/slideshow_template.html Log Message: ----------- Align architecture slides with training-material remarkjs template. - Copy over the training material style CSS template and add to it only what is needed. - Cleanup style and layout handling in architecture slides markdown. - Update generated images for white background. - Small updates in content to architecture for recent changes (and CONTRIBUTING.md linked to from slides). Commit: d9b36176a8181168f5c4553ead4f9e6545d7e856 https://github.com/galaxyproject/galaxy/commit/d9b36176a8181168f5c4553ead4f9... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3580 from jj-umn/patch-5 Add d3_hierarchy subclass Commit: 93453e490f2490899d818473d79eeddf9f6d0808 https://github.com/galaxyproject/galaxy/commit/93453e490f2490899d818473d79ee... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M templates/admin/reload_tool.mako Log Message: ----------- Avoid html response when reloading tool through the api Commit: b466ff6cd8dc86c03f0d6322e26b94605087bb39 https://github.com/galaxyproject/galaxy/commit/b466ff6cd8dc86c03f0d6322e26b9... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Fix root location for tool reloader Commit: 1aa459f19d45221957ff0be6a5f708bf6bd41a41 https://github.com/galaxyproject/galaxy/commit/1aa459f19d45221957ff0be6a5f70... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Use shared modal viewer Commit: cd52f20961fcdee3453b5c5ce28b84f25b50f3f3 https://github.com/galaxyproject/galaxy/commit/cd52f20961fcdee3453b5c5ce28b8... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Align code style to existing code in tool form base Commit: 727bfbd258c548917d2025708368f73b57199648 https://github.com/galaxyproject/galaxy/commit/727bfbd258c548917d2025708368f... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Fix error message style, raise message exception if tool has not been found Commit: 8e59ec1e2be863dc00cb86d1689e7169cd43b6e5 https://github.com/galaxyproject/galaxy/commit/8e59ec1e2be863dc00cb86d1689e7... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Remove unused tooltips for submenu options, fix response Commit: 10943712b829ac48760fc5ecd25405d768cc9dd4 https://github.com/galaxyproject/galaxy/commit/10943712b829ac48760fc5ecd2540... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Revise dropdown item label Commit: 9590d4551439c7b9ae13f704508bfef376ff1fc4 https://github.com/galaxyproject/galaxy/commit/9590d4551439c7b9ae13f704508bf... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Improve success message upon tool xml reloading Commit: 73b8fc45aa088b17970c5309108442d968c70a7b https://github.com/galaxyproject/galaxy/commit/73b8fc45aa088b17970c530910844... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Check once for admin operations when building dropdown list in tool form Commit: d298c1c0da5871105898166ca72dd224f7897fc6 https://github.com/galaxyproject/galaxy/commit/d298c1c0da5871105898166ca72dd... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix lint issues Commit: 047c833db79fef8daa25ddf022f85d2ef9386d63 https://github.com/galaxyproject/galaxy/commit/047c833db79fef8daa25ddf022f85... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Align subworkflow handling, fix run request through input name Commit: 823ac3cc6172db54c35fdae43553af304a6a162b https://github.com/galaxyproject/galaxy/commit/823ac3cc6172db54c35fdae43553a... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- add new Search plugin styles Commit: 2e787394cc0b9ea1a73ba87235faa4f38c1e495e https://github.com/galaxyproject/galaxy/commit/2e787394cc0b9ea1a73ba87235faa... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: M test/selenium_tests/test_stock_tours.py Log Message: ----------- Disable transiently failing tour test. See code comment for more information - I am tracking the issue here https://github.com/galaxyproject/galaxy/issues/3598. I think it is important to resolve that test and fix the usability problems with current tours but I'd like to get the Selenium tests stable and testing against new PRs first. Commit: 9ceaa0d41583b66efb1c228755ca4368c0bdb6af https://github.com/galaxyproject/galaxy/commit/9ceaa0d41583b66efb1c228755ca4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: M test/selenium_tests/test_stock_tours.py Log Message: ----------- Merge pull request #3599 from jmchilton/disable_galaxy_ui_test Disable transiently failing tour test. Commit: 9bb9feb0a8aeec36ded548aa8d28927e2b26d678 https://github.com/galaxyproject/galaxy/commit/9bb9feb0a8aeec36ded548aa8d289... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Recalculate user disk usage on logout. Not as ideal as just having it be accurate all the time, but it 1) avoids adding yet another control people need to dig for when they need to recalculate, and 2) makes things right when following 'turn it off and on again' Commit: fcbb7c3de17841027da5c2ec16cf11f78e709872 https://github.com/galaxyproject/galaxy/commit/fcbb7c3de17841027da5c2ec16cf1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Tooltips to suggest relog for quota correction. Commit: 412d8e1bb6c82a9aa8a86971e64e4242a5341419 https://github.com/galaxyproject/galaxy/commit/412d8e1bb6c82a9aa8a86971e64e4... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Adding NGL viewer for molecule representation Commit: d066ae2223ef006a7621ddaa30ecd24ffa2942dd https://github.com/galaxyproject/galaxy/commit/d066ae2223ef006a7621ddaa30ecd... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M doc/source/slideshow/architecture/galaxy_architecture.md Log Message: ----------- Link fixes thanks to @nsoranzo. Commit: d382537008da588b68a86925a42f0828a9e376d8 https://github.com/galaxyproject/galaxy/commit/d382537008da588b68a86925a42f0... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Merge pull request #3590 from guerler/fix_order_steps Avoid step duplication when ordering steps on the fly Commit: 75a17bc311662fae24b679a7b41146552f796992 https://github.com/galaxyproject/galaxy/commit/75a17bc311662fae24b679a7b4114... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M CONTRIBUTING.md M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M scripts/slideshow/slideshow_template.html Log Message: ----------- Merge pull request #3594 from jmchilton/architecture_touchup Align architecture slides with training-material remarkjs template. Commit: e06f56a61521563f1bd17c5ad09df94264d45772 https://github.com/galaxyproject/galaxy/commit/e06f56a61521563f1bd17c5ad09df... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: static/maps/mvc/tool/tool-form-base.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/tool/tool-form-base.js Commit: b4b75b276c9d41181e89322754c64abba57cd753 https://github.com/galaxyproject/galaxy/commit/b4b75b276c9d41181e89322754c64... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3579 from jmchilton/deprecated_change_format_when Update tool XSD for (hopefully deprecated) change_format syntax. Commit: 9f9d0cb4082b66e385bd43e31995cbaa5a2a0e09 https://github.com/galaxyproject/galaxy/commit/9f9d0cb4082b66e385bd43e31995c... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge branch 'release_17.01' into dev Commit: 4fc0b84910adef446daa20a68cd69b0721a4d362 https://github.com/galaxyproject/galaxy/commit/4fc0b84910adef446daa20a68cd69... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M templates/admin/reload_tool.mako Log Message: ----------- Merge remote-tracking branch 'guerler/fix_tool_reload_003' into dev Commit: ac46305686c81a94b60a76dd6904a772a784ff24 https://github.com/galaxyproject/galaxy/commit/ac46305686c81a94b60a76dd6904a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Minor fix of core.galaxy-ui tour in more robustly selecting first reload icon in the active history. Commit: 9597b9b62b66d933ae5d891ff45550d23a86b6f2 https://github.com/galaxyproject/galaxy/commit/9597b9b62b66d933ae5d891ff4555... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Merge pull request #3608 from dannon/minor-tour-fix Minor fix of core.galaxy-ui tour in more robustly selecting first rel… Commit: dfa1ddacb93acf341b71148114450c993379adc1 https://github.com/galaxyproject/galaxy/commit/dfa1ddacb93acf341b71148114450... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Restore legacy name handling for backward compatibility Commit: 93f190dd0518005f195960333895b645556860cd https://github.com/galaxyproject/galaxy/commit/93f190dd0518005f195960333895b... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Restore previous export behavior Commit: c4491b2d834cdbb61cf009d57c1d3f1086bcfbdb https://github.com/galaxyproject/galaxy/commit/c4491b2d834cdbb61cf009d57c1d3... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix quotes Commit: 79c24066b444b7bd7a85f0ec2ccdd4b131c4da9e https://github.com/galaxyproject/galaxy/commit/79c24066b444b7bd7a85f0ec2ccdd... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/datatypes_conf.xml.sample M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/steps.py M scripts/slideshow/slideshow_template.html M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M templates/admin/reload_tool.mako M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml M test/selenium_tests/framework.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge branch 'dev' into unify_name_label Commit: 3f07555173f89f39b4823767daaa25bd92ec7d68 https://github.com/galaxyproject/galaxy/commit/3f07555173f89f39b4823767daaa2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M CONTRIBUTING.md M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/plugins/tours/core.galaxy_ui.yaml M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M lib/galaxy/datatypes/interval.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/steps.py M scripts/slideshow/slideshow_template.html M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M templates/admin/reload_tool.mako A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' into recalc-on-logout Commit: df22e40522d7777cc3c82a4e32b64fe2d95d9273 https://github.com/galaxyproject/galaxy/commit/df22e40522d7777cc3c82a4e32b64... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge pull request #3600 from dannon/recalc-on-logout Recalculate user disk usage on logout. Commit: 1cb8a5da38006cace8c48966a5326b2d3747c574 https://github.com/galaxyproject/galaxy/commit/1cb8a5da38006cace8c48966a5326... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix import order Commit: 6330f6051790b7d86bdd5674697163efc3c2a0f0 https://github.com/galaxyproject/galaxy/commit/6330f6051790b7d86bdd567469716... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge branch 'dev' into unify_name_label Commit: 6864bc30b4a02495220d1552026c0cacb5d41af7 https://github.com/galaxyproject/galaxy/commit/6864bc30b4a02495220d1552026c0... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Replacing url by download_url to fetch files Commit: 8ce1291359c88148023e5bb3f44a9eb38c78a864 https://github.com/galaxyproject/galaxy/commit/8ce1291359c88148023e5bb3f44a9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'release_17.01' into dev Commit: dcda376c9ca68742eb58efe6f3438d4d6c5f834f https://github.com/galaxyproject/galaxy/commit/dcda376c9ca68742eb58efe6f3438... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Restore subworkflow behavior, no need for modifications anymore Commit: 48639028df5b59e7547a2e716b9c7e34e9743a41 https://github.com/galaxyproject/galaxy/commit/48639028df5b59e7547a2e716b9c7... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Removing utils.get to fetch pdb files Commit: 452ab0d509171033e901bf65cf2556ef411e5161 https://github.com/galaxyproject/galaxy/commit/452ab0d509171033e901bf65cf255... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Implementation of slow query logging. Disabled by default. Commit: 78282a288bd1528dfd5222f47baaaeaaf1480f17 https://github.com/galaxyproject/galaxy/commit/78282a288bd1528dfd5222f47baaa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Aarrghs spacing. Commit: 19e18dd5719abe08e361bf4b50a7bf4bbbd554e1 https://github.com/galaxyproject/galaxy/commit/19e18dd5719abe08e361bf4b50a7b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add forgotten sample change. Commit: c390da3cbd933c27ad0c731bc3b557ad916a72cd https://github.com/galaxyproject/galaxy/commit/c390da3cbd933c27ad0c731bc3b55... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Change default settings, avoid flickering on startup Commit: 7810f5a8648c913045ae042a7c991642dbc045c8 https://github.com/galaxyproject/galaxy/commit/7810f5a8648c913045ae042a7c991... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Style tweaks. My flake8-in-editor had silently died and was not warning me anymore, super. Commit: eb5ded2a439d1c9491700650842f9ece04cfad33 https://github.com/galaxyproject/galaxy/commit/eb5ded2a439d1c9491700650842f9... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Remove likely un-needed check. Commit: da24f4c8ad03a34da9323041e634d4bbe55617b4 https://github.com/galaxyproject/galaxy/commit/da24f4c8ad03a34da9323041e634d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Import formatting... Commit: 149dfa007f70fe6794b8c1f37708ac8fbb7cccef https://github.com/galaxyproject/galaxy/commit/149dfa007f70fe6794b8c1f37708a... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Merge pull request #3616 from dannon/slow_query_logging Slow query logging Commit: a7572145e9c0d4872cde027d547ef4c31c87af10 https://github.com/galaxyproject/galaxy/commit/a7572145e9c0d4872cde027d547ef... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Merge pull request #3618 from jmchilton/remove_unneeded_15 Remove un-needed check in histories manager code Commit: 5cd05161413b73c5eb6ea7393b78cafd213409b9 https://github.com/galaxyproject/galaxy/commit/5cd05161413b73c5eb6ea7393b78c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'dev' into unify_name_label Commit: 7472568fe5102a77ff69c47db0f19d7fd0a8487a https://github.com/galaxyproject/galaxy/commit/7472568fe5102a77ff69c47db0f19... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js M config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Remove unused name from stage parameter Commit: 43f2a648230b5b0ee46c124cc3df95b758e50fb2 https://github.com/galaxyproject/galaxy/commit/43f2a648230b5b0ee46c124cc3df9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js Log Message: ----------- Merge pull request #3601 from bgruening/ngl_viewer NGL Viewer for molecule representation Commit: be5eaf4881b9624c67a7e3125dbb080032502477 https://github.com/galaxyproject/galaxy/commit/be5eaf4881b9624c67a7e3125dbb0... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: A scripts/cookie.py Log Message: ----------- Util to encode or decode values Commit: 6849752fb68b018aaf30f61d9d3c564894ed9e2b https://github.com/galaxyproject/galaxy/commit/6849752fb68b018aaf30f61d9d3c5... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: R scripts/cookie.py A scripts/secret_decoder_ring.py Log Message: ----------- Rename, Strip F for Folder Commit: fb2450ff33ebdbdeb3f1205bdc58c38519921e7a https://github.com/galaxyproject/galaxy/commit/fb2450ff33ebdbdeb3f1205bdc58c... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M scripts/secret_decoder_ring.py Log Message: ----------- document scriptg Commit: 89e32ee526e7f2ebc64be8bd46337a6edef78cab https://github.com/galaxyproject/galaxy/commit/89e32ee526e7f2ebc64be8bd46337... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: A scripts/secret_decoder_ring.py Log Message: ----------- Merge pull request #3622 from erasche/encode-decode-util Util to encode or decode values Commit: 678a8627984852ea4282f6a25bf8c5176783c7c3 https://github.com/galaxyproject/galaxy/commit/678a8627984852ea4282f6a25bf8c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Fix Commit: 7ad46c22694ac7b58acdaefca59ca82cca328f25 https://github.com/galaxyproject/galaxy/commit/7ad46c22694ac7b58acdaefca59ca... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix subworkflow caller Commit: c75671484058bc5c0cec8f07dda081cff7c0eb57 https://github.com/galaxyproject/galaxy/commit/c75671484058bc5c0cec8f07dda08... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Properly initialize subworkflow parameter Commit: 841cbfd9c7bf1efe2c10bbbff59da22ce67e800c https://github.com/galaxyproject/galaxy/commit/841cbfd9c7bf1efe2c10bbbff59da... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix content id parsing, through error if subworkflow could not be found Commit: 4610da47863c9ca9c5eb092bfd031f32c6984b96 https://github.com/galaxyproject/galaxy/commit/4610da47863c9ca9c5eb092bfd031... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix style Commit: f548af88076b11d33e3a24b50102108a076df1b4 https://github.com/galaxyproject/galaxy/commit/f548af88076b11d33e3a24b501021... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Add test case for state populating Commit: f6649f890499a2e4569057e4b1921f0c95426e11 https://github.com/galaxyproject/galaxy/commit/f6649f890499a2e4569057e4b1921... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py Log Message: ----------- Merge branch 'release_17.01' into dev Commit: 2ff6f910373a2eaf547472f8b4be7f92cda495bb https://github.com/galaxyproject/galaxy/commit/2ff6f910373a2eaf547472f8b4be7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Log Message: ----------- Merge branch 'release_17.01' into dev Commit: e5da52e388af093e432efeae9f395a7f92ce97da https://github.com/galaxyproject/galaxy/commit/e5da52e388af093e432efeae9f395... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Fix kombu documentation link, add a tiny bit more description to handle the old TODO. Commit: 28089a3ae1ea4eb8be62364aaaef65ae019dc127 https://github.com/galaxyproject/galaxy/commit/28089a3ae1ea4eb8be62364aaaef6... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3629 from dannon/kombu_url_fix Fix kombu documentation link in galaxy.ini.sample Commit: 430ac221baea4c18af247eee8e9106869a570390 https://github.com/galaxyproject/galaxy/commit/430ac221baea4c18af247eee8e910... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge branch 'release_17.01' into dev Commit: 8557c32034c9723dc110719b26082312dde1a998 https://github.com/galaxyproject/galaxy/commit/8557c32034c9723dc110719b26082... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix sanitization Commit: cdb15f63925e9879744ae38e5e140e5eb9cc6c19 https://github.com/galaxyproject/galaxy/commit/cdb15f63925e9879744ae38e5e140... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: 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/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/workflow_util.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/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/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/workflow/workflow-view.js Log Message: ----------- Merge pull request #3593 from guerler/unify_name_label Introduce label and annotation attributes to subworkflows, fix annotation display, unify module form update handler Commit: 24eba8c58ee9d7f8907c83f5d72ea01997d56ab4 https://github.com/galaxyproject/galaxy/commit/24eba8c58ee9d7f8907c83f5d72ea... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: client/galaxy/scripts/mvc/tool/tool-form-composite.js static/maps/mvc/tool/tool-form-composite.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/tool/tool-form-composite.js Commit: 9abe8a7b91d969a5b3af2bc026911dcde8656e24 https://github.com/galaxyproject/galaxy/commit/9abe8a7b91d969a5b3af2bc026911... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/__init__.py Log Message: ----------- Allow composite datatypes of type auto_primary_file to automatically generate primary datatype for standard (non-upload) jobs when the tool does not already create the file. Commit: fd082663866c06afb35a179327b1df6efd9c77c7 https://github.com/galaxyproject/galaxy/commit/fd082663866c06afb35a179327b1d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Parse name to label on module initialization Commit: 8a4c0eb7e3ea096ed56471a010003e6717f31957 https://github.com/galaxyproject/galaxy/commit/8a4c0eb7e3ea096ed56471a010003... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use shared initialization procedure for subworkflows Commit: fc1e0702542af846c28e2910d77cbd07f0913769 https://github.com/galaxyproject/galaxy/commit/fc1e0702542af846c28e2910d77cb... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Hide name input fields for data input modules Commit: b91680a5b2dfc83b8ee974fdc9ed6f2ab405829c https://github.com/galaxyproject/galaxy/commit/b91680a5b2dfc83b8ee974fdc9ed6... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Use shared label/annotation input parameter building process Commit: e13958ffcd14f2eb62b29f446a535487dd344904 https://github.com/galaxyproject/galaxy/commit/e13958ffcd14f2eb62b29f446a535... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Remove tool module related annotation input parameter Commit: 92bd559c11e62ef1ab704b967621966a31f71e39 https://github.com/galaxyproject/galaxy/commit/92bd559c11e62ef1ab704b9676219... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Move label/annotation input parameters at top for all modules Commit: 0f742a6d8380af15ac87a9e654e1119a177bd426 https://github.com/galaxyproject/galaxy/commit/0f742a6d8380af15ac87a9e654e11... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: R client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-view-form.js M client/galaxy/scripts/mvc/workflow/workflow-view.js R static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/workflow/workflow-view-form.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/workflow/workflow-view-form.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Move workflow related tool form to workflow directory Commit: 3a7e6b0b744b9331ec175d8104a17519687fa464 https://github.com/galaxyproject/galaxy/commit/3a7e6b0b744b9331ec175d8104a17... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: A client/galaxy/scripts/mvc/workflow/workflow-forms.js R client/galaxy/scripts/mvc/workflow/workflow-view-form.js M client/galaxy/scripts/mvc/workflow/workflow-view.js R static/maps/mvc/workflow/workflow-view-form.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/scripts/mvc/workflow/workflow-view-form.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Enable labels for all modules, used shared building process Commit: ff7ab0853d6ea901253ba6175aa343fd9ef3a108 https://github.com/galaxyproject/galaxy/commit/ff7ab0853d6ea901253ba6175aa34... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix comments, show default wrapper first in code file Commit: b03904b52c6064e77a378347d9213ec0b270ebb9 https://github.com/galaxyproject/galaxy/commit/b03904b52c6064e77a378347d9213... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Allow input specific error handling, fix input parameter configuration Commit: c9b765794bb14adbaee13a44290e9df242778ffe https://github.com/galaxyproject/galaxy/commit/c9b765794bb14adbaee13a44290e9... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix form handler Commit: a967c088f78e39819d4cc0bd349166501e00d74e https://github.com/galaxyproject/galaxy/commit/a967c088f78e39819d4cc0bd34916... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Avoid parsing default names of inputs to labels Commit: f652e9c778af3835de929cfa7823cf1f0a0aed8a https://github.com/galaxyproject/galaxy/commit/f652e9c778af3835de929cfa7823c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove hidden input parameters, attempt to identify label directly from previous state Commit: a3de5b042e8edae2f7beee6554ae78e18f5f115b https://github.com/galaxyproject/galaxy/commit/a3de5b042e8edae2f7beee6554ae7... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Move backward compatibility handling of former names out of modules to the workflow manager Commit: 81f799c01f38bab0c584e9b39872d2a1dd7f0348 https://github.com/galaxyproject/galaxy/commit/81f799c01f38bab0c584e9b39872d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Revise comment Commit: afe2a6116a450fa69ae87705c14a4e43a7ef5830 https://github.com/galaxyproject/galaxy/commit/afe2a6116a450fa69ae87705c14a4... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use label to connect workflow steps Commit: badf49daa54a660a032ac22b2e4b7c84c92284e1 https://github.com/galaxyproject/galaxy/commit/badf49daa54a660a032ac22b2e4b7... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #3643 from blankenberg/composite-datatype-auto-gen Allow composite datatypes of type auto_primary_file to automatically generate dataset Commit: 9563a691b05f65ec3bdcd9135f75878b2ec666e3 https://github.com/galaxyproject/galaxy/commit/9563a691b05f65ec3bdcd9135f758... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3641 from nsoranzo/merge_17.01 Merge 17.01 into dev Commit: 387805fc1365dbf976e6d3e10ae4a11817e501da https://github.com/galaxyproject/galaxy/commit/387805fc1365dbf976e6d3e10ae4a... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: client/galaxy/scripts/mvc/tool/tool-form-composite.js preserved the dev version static/maps/mvc/tool/tool-form-composite.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/tool/tool-form-composite.js Commit: d1c9ffb94c06a7a39cff37a38e78f43fd4e0ca10 https://github.com/galaxyproject/galaxy/commit/d1c9ffb94c06a7a39cff37a38e78f... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Conflicts: client/galaxy/scripts/mvc/tool/tool-form-composite.js preserved dev version static/maps/mvc/tool/tool-form-composite.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/tool/tool-form-composite.js Commit: c52715fd69fba88746181601e8210eb3cbc8b145 https://github.com/galaxyproject/galaxy/commit/c52715fd69fba88746181601e8210... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Log Message: ----------- Merge branch 'release_17.01' into dev Commit: ae751adac8ae46d7f0eb2831666258143724bc0f https://github.com/galaxyproject/galaxy/commit/ae751adac8ae46d7f0eb283166625... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py Log Message: ----------- Adjust unit test to use labels instead of name through state Commit: 488c42aa4c3e3e903e0234804d3cd90277d9a930 https://github.com/galaxyproject/galaxy/commit/488c42aa4c3e3e903e0234804d3cd... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Use constants to filter default naming of input modules Commit: dde9ba83acfbedd50a59ccb211cf9d352c86de97 https://github.com/galaxyproject/galaxy/commit/dde9ba83acfbedd50a59ccb211cf9... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' into unify_label_name_000 Commit: 528b00667d4a053b3b8db4790323b0f655b18f9b https://github.com/galaxyproject/galaxy/commit/528b00667d4a053b3b8db4790323b... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix comment Commit: 619bfeffd503681ab7d6072426f621fde7485fd5 https://github.com/galaxyproject/galaxy/commit/619bfeffd503681ab7d6072426f62... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to use fixed default name for unlabeled subworkflow inputs Commit: 007b6599c21a4927d58629210f103829e947011f https://github.com/galaxyproject/galaxy/commit/007b6599c21a4927d58629210f103... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix name handling in build module Commit: 198d36f77bb444572f03a34aec7c695d0adc52e1 https://github.com/galaxyproject/galaxy/commit/198d36f77bb444572f03a34aec7c6... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix step title in composite tool form Commit: 05687b8a19785c89772db499d6ede5a097ba47ce https://github.com/galaxyproject/galaxy/commit/05687b8a19785c89772db499d6ede... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Strip debug output Commit: 102fffd172963c0e97a7b469c394c3d239935e9c https://github.com/galaxyproject/galaxy/commit/102fffd172963c0e97a7b469c394c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- When using the new slow query logger, include parameters. Originally left these out, but 1) logs are assumed to be secure, and 2) it's super useful Commit: 2cfd833e457f513d5e83f9a7f8ca77f96741942e https://github.com/galaxyproject/galaxy/commit/2cfd833e457f513d5e83f9a7f8ca7... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Reduce indentation from 6 to 4 whitespaces Fix a TODO Remove funny but unused sub-sub-items. Commit: 0da2ac78e6ac5583271881dabd4b4d0a3bcf59cd https://github.com/galaxyproject/galaxy/commit/0da2ac78e6ac5583271881dabd4b4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Rebuild client -- bad merge previously. Commit: 8130d8b4c88343cdd44243fe700eae3fb863cc1a https://github.com/galaxyproject/galaxy/commit/8130d8b4c88343cdd44243fe700ea... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Update against the latest changes in galaxy-dev. Commit: 18e514d9b72b6efb57772009de1c0d65b791fa1b https://github.com/galaxyproject/galaxy/commit/18e514d9b72b6efb57772009de1c0... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3652 from dannon/rebuild_client Rebuild client -- bad merge previously. Commit: 647fcad924a969ae35299b7ef6e60672ddb7a6a0 https://github.com/galaxyproject/galaxy/commit/647fcad924a969ae35299b7ef6e60... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3653 from nsoranzo/fix_bootstrap_history Fix RELEASE_ISSUE_TEMPLATE in bootstrap_history.py Commit: d9d3b22efdf5d7e0f4c9b371b0ea74a64ab53f46 https://github.com/galaxyproject/galaxy/commit/d9d3b22efdf5d7e0f4c9b371b0ea7... Author: Gildas Le Corguillé <lecorguille@users.noreply.github.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Update dynamic_tool_destination.py Commit: d19a158e10ada652fb1bf1549dac4f1f3446aa5a https://github.com/galaxyproject/galaxy/commit/d19a158e10ada652fb1bf1549dac4... Author: lecorguille <lecorguille@users.noreply.github.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Allow nest param in the dynamic_tool rule -> argument Commit: 99fdc37b815ab9c26f15250d722f2d30ab9691b2 https://github.com/galaxyproject/galaxy/commit/99fdc37b815ab9c26f15250d722f2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/exceptions/error_codes.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3654 from jmchilton/galaxy-lib-update Update against the latest changes in galaxy-lib Commit: 73c444eaf4074c98262b9de0011e686170b1b125 https://github.com/galaxyproject/galaxy/commit/73c444eaf4074c98262b9de0011e6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Merge pull request #3655 from lecorguille/patch-3 Update dynamic_tool_destination.py Commit: b18736d82447637d7257f3fd406e1c40a02afed0 https://github.com/galaxyproject/galaxy/commit/b18736d82447637d7257f3fd406e1... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js M config/plugins/visualizations/charts/static/repository/registry.json R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Updating Cytoscape viewer in Viz/Charts, replacing the previous 'basic' folder name to 'viewer' and updating the wrapper.js file Commit: 2c49779d81b8eb2eae1e9f4dd74de7e01647f675 https://github.com/galaxyproject/galaxy/commit/2c49779d81b8eb2eae1e9f4dd74de... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js 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/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: ----------- Separate condensed user preference form into three components, improve route handling Commit: 84f9d3c5c9dc27af1d121e9b84504109d9291ff0 https://github.com/galaxyproject/galaxy/commit/84f9d3c5c9dc27af1d121e9b84504... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) 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: ----------- Fix basic routing between main preference panel and individual user forms Commit: 3c31cbd21ed222060c31400eb0e0d0ea90b33ec0 https://github.com/galaxyproject/galaxy/commit/3c31cbd21ed222060c31400eb0e0d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) 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: ----------- Fix error message Commit: 88b4b7a7182fb48904d587b7a049e099169c7ccf https://github.com/galaxyproject/galaxy/commit/88b4b7a7182fb48904d587b7a049e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) 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: ----------- Properly handle openid redirect and sign out feature Commit: ceb11577bde43e6ee61ee1c89e6c002037039510 https://github.com/galaxyproject/galaxy/commit/ceb11577bde43e6ee61ee1c89e6c0... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) 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: ----------- Place row template into separate function Commit: 365c56f77f6b57c8930641864924ec9a67fdf174 https://github.com/galaxyproject/galaxy/commit/365c56f77f6b57c8930641864924e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/web/base/controllers/admin.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: ----------- Redirect admin user manager route to js-based preference forms Commit: 99397fad74d3e47c27073f44e36300d43f48a181 https://github.com/galaxyproject/galaxy/commit/99397fad74d3e47c27073f44e3630... Author: lecorguille <lecorguille@users.noreply.github.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- add the mzData datatype Commit: 036df2ac2003ab378f6a0227e4642d980639a5ab https://github.com/galaxyproject/galaxy/commit/036df2ac2003ab378f6a0227e4642... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Fix linting Commit: d5e4dc4753b8e6ab4a079b5fedb0ad1834bda157 https://github.com/galaxyproject/galaxy/commit/d5e4dc4753b8e6ab4a079b5fedb0a... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Merge pull request #3661 from lecorguille/datatype_mzdata add the mzData datatype Commit: 585c1070f29260895497c01bc7723317e3751934 https://github.com/galaxyproject/galaxy/commit/585c1070f29260895497c01bc7723... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Display an error message when IE loading raises an exception Commit: cbc1faf3a45d58353a9d352047fbbedb970e3215 https://github.com/galaxyproject/galaxy/commit/cbc1faf3a45d58353a9d352047fbb... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Set LDAP options only once. Always check option value is not empty in _get_subs() Better log message for malformed <ldap_options> Commit: 820c46cf63602b788ed282f4277a19129d4b3dd8 https://github.com/galaxyproject/galaxy/commit/820c46cf63602b788ed282f4277a1... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Repack scripts Commit: 2f53b1d6d12457e0eaba5ca5da8b95321c69ff54 https://github.com/galaxyproject/galaxy/commit/2f53b1d6d12457e0eaba5ca5da8b9... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/toolbox/base.py M scripts/bootstrap_history.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge branch 'dev' into unify_label_name_000 Commit: b9ba754ce6eb2d4b23c54aa557cb6c0a512c4082 https://github.com/galaxyproject/galaxy/commit/b9ba754ce6eb2d4b23c54aa557cb6... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-forms.js.map R static/maps/mvc/workflow/workflow.js.map M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix repacked files Commit: b4ba2768a246c3788bc9f4adc5f2741dd7ab4956 https://github.com/galaxyproject/galaxy/commit/b4ba2768a246c3788bc9f4adc5f27... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Ignore Node modules installed for the IE proxy when linting Commit: 10d0f627dcdfac2bd24085a599a7087809cec1bf https://github.com/galaxyproject/galaxy/commit/10d0f627dcdfac2bd24085a599a70... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Bump Jupyter container version to 16.01.1 Commit: 77a47d2f6f947a1ec7d24d068538bbabdf5e88dd https://github.com/galaxyproject/galaxy/commit/77a47d2f6f947a1ec7d24d068538b... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Merge pull request #3665 from natefoo/jupyter-16.01.1 Bump Jupyter container version to 16.01.1 Commit: 0baae35c56cfa26908ebff9a3124640489459c31 https://github.com/galaxyproject/galaxy/commit/0baae35c56cfa26908ebff9a31246... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Merge pull request #3664 from natefoo/lint-ignore-js-proxy Ignore Node modules installed for the IE proxy when linting Commit: efa856dbb91766dbf80c447c241dd37e1a5401ca https://github.com/galaxyproject/galaxy/commit/efa856dbb91766dbf80c447c241dd... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M templates/grid_base.mako Log Message: ----------- Attempt to fix grid routing options Commit: 075d53af92ea2640ba3005f36354712b966ea98e https://github.com/galaxyproject/galaxy/commit/075d53af92ea2640ba3005f363547... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix for transiently failing workflow test. The history can be complete before a workflow has fully scheduled if the workflow still has more jobs to schedule but all the current ones are complete. Commit: a5ea10622bf2616278827221d43a4ab635932edd https://github.com/galaxyproject/galaxy/commit/a5ea10622bf2616278827221d43a4... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Merge pull request #3662 from natefoo/ie-error-message Display an error message when IE loading raises an exception Commit: 8a8603be7f697c065382d61fb0539552d15d1f3f https://github.com/galaxyproject/galaxy/commit/8a8603be7f697c065382d61fb0539... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako Log Message: ----------- Enhance grid target handling for links Commit: d3f2df57699bf6b85fdb16f85d023d562342f778 https://github.com/galaxyproject/galaxy/commit/d3f2df57699bf6b85fdb16f85d023... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-25 (Sat, 25 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- improve wording of getgalaxy in bootstrapping script for RN Commit: c8dd5f9b25ac222ff37fe06bed5d1834f292e485 https://github.com/galaxyproject/galaxy/commit/c8dd5f9b25ac222ff37fe06bed5d1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-02-26 (Sun, 26 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3671 from martenson/improve-bootstrapping improve wording of getgalaxy in bootstrapping script for RN Commit: f645259dd0633cfdac2768c7de2d1de918bc1bbe https://github.com/galaxyproject/galaxy/commit/f645259dd0633cfdac2768c7de2d1... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Only keep the last path element when naming files uploaded via the URL paste method Commit: fb17e55a1daf90220e19980fd8fd56dd70b2cde2 https://github.com/galaxyproject/galaxy/commit/fb17e55a1daf90220e19980fd8fd5... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Use former version of autocomplete module for grids Commit: 3efe748279711e89852bf7bf173612ff9cbe45de https://github.com/galaxyproject/galaxy/commit/3efe748279711e89852bf7bf17361... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako Log Message: ----------- Strip partially removed autocomplete feature for history names, removed in #1303 Commit: 69b9b575172086376657433ff0a066bf732d4e4d https://github.com/galaxyproject/galaxy/commit/69b9b575172086376657433ff0a06... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding basic options like layout name and curve style for cytoscape graphs Commit: 73921a21e9164bad342269ed3fe3c347d42a5c8d https://github.com/galaxyproject/galaxy/commit/73921a21e9164bad342269ed3fe3c... Author: lecorguille <lecorguille@users.noreply.github.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- change the tool_destinations.yml the argument rules syntax Commit: 705eb17b02b748ce76b5644386c793a610d9ab90 https://github.com/galaxyproject/galaxy/commit/705eb17b02b748ce76b5644386c79... Author: lecorguille <lecorguille@users.noreply.github.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- fix python syntax Commit: d624b04f25510475bd1cb48fbcbdca471bc1a5d7 https://github.com/galaxyproject/galaxy/commit/d624b04f25510475bd1cb48fbcbdc... Author: lecorguille <lecorguille@users.noreply.github.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M config/tool_destinations.yml.sample Log Message: ----------- update the documentation Commit: 194fb1eb07b627682b258d5c302aeb75b266cf89 https://github.com/galaxyproject/galaxy/commit/194fb1eb07b627682b258d5c302ae... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako Log Message: ----------- Merge pull request #3676 from guerler/fix_jquery_autocomplete Strip broken autocomplete feature, webbrowsers console error is an artifact Commit: 33c528ee13e6c4317ac4acc9b48ba157c5976b6c https://github.com/galaxyproject/galaxy/commit/33c528ee13e6c4317ac4acc9b48ba... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Generate primary composite file after extra files collection. Commit: 1bac3b3be81821a4cbe687165985cfafd7989b46 https://github.com/galaxyproject/galaxy/commit/1bac3b3be81821a4cbe687165985c... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #3674 from natefoo/upload-drop-url-name Only keep the last path element when naming files uploaded via the URL paste method Commit: a505fa79ac26e2f30a4404f9a11f3b029abb5436 https://github.com/galaxyproject/galaxy/commit/a505fa79ac26e2f30a4404f9a11f3... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/auth/providers/ldap_ad.py Log Message: ----------- Merge pull request #3663 from nsoranzo/ldap_auth Set LDAP options only once. Commit: c80380dc57305be36e615ec13d1d17aecd285114 https://github.com/galaxyproject/galaxy/commit/c80380dc57305be36e615ec13d1d1... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/grid/grid-view.js M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/bootstrap_history.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into unify_label_name_000 Commit: 5efbab864cab6693d4bde2159661a6ff6c7caafd https://github.com/galaxyproject/galaxy/commit/5efbab864cab6693d4bde2159661a... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #3678 from blankenberg/composite-auto-after Generate primary composite file after extra files collection. Commit: f0a26f309dd330e49e8e7ad227db5e40507f60cc https://github.com/galaxyproject/galaxy/commit/f0a26f309dd330e49e8e7ad227db5... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/model/orm/engine_factory.py Log Message: ----------- Merge pull request #3649 from dannon/slowquery_tweak When using the new slow query logger, include parameters. Commit: 504f4ac670b3135b9df885d9d884d176dc494768 https://github.com/galaxyproject/galaxy/commit/504f4ac670b3135b9df885d9d884d... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding min and max zoom settings for graphs Commit: 0b4e52c8e93aa5693f97ff1fc5d0a4c272f58b18 https://github.com/galaxyproject/galaxy/commit/0b4e52c8e93aa5693f97ff1fc5d0a... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M doc/source/releases/17.01_announce.rst M lib/galaxy/queue_worker.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: lib/galaxy/managers/workflows.py Discarded all changes made to lib/galaxy/managers/workflows.py in https://github.com/galaxyproject/galaxy/pull/3681 Commit: cc6fa6a4c8607c0c2f33b2271a963da54756334f https://github.com/galaxyproject/galaxy/commit/cc6fa6a4c8607c0c2f33b2271a963... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/grid/grid-view.js M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M doc/source/releases/17.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M scripts/bootstrap_history.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako A templates/webapps/galaxy/user/manage_info.mako M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into ui_pref_routing Commit: d3840c5c4140807297b22ad1e9b7da97eb1a6570 https://github.com/galaxyproject/galaxy/commit/d3840c5c4140807297b22ad1e9b7d... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #3644 from guerler/unify_label_name_000 Introduce labels for all modules, remove name handling field for data inputs Commit: f0b03a59b51bd02a07b591900147d0e9a79053f7 https://github.com/galaxyproject/galaxy/commit/f0b03a59b51bd02a07b591900147d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py R templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Strip old user manager mako Commit: c281dd87ed83934ffe2654130d8c709892796142 https://github.com/galaxyproject/galaxy/commit/c281dd87ed83934ffe2654130d8c7... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'dev' into ui_pref_routing Commit: 7cc25c9082de5df6ff4ed89365f34f39dbbec545 https://github.com/galaxyproject/galaxy/commit/7cc25c9082de5df6ff4ed89365f34... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Parse tags with datatoolparameter options Commit: a02c1cfda10e2b600e5209db7f7be8dfb0069467 https://github.com/galaxyproject/galaxy/commit/a02c1cfda10e2b600e5209db7f7be... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add tags to name Commit: 4d5a03ba55eeb1a1f3884999f3399fb47503cbcc https://github.com/galaxyproject/galaxy/commit/4d5a03ba55eeb1a1f3884999f3399... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove brackets Commit: 9f4764f22cc63f7a734b9ea98707bfcb842aed14 https://github.com/galaxyproject/galaxy/commit/9f4764f22cc63f7a734b9ea98707b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Preserve tags (ignoring collection handling for now) when running tools. Commit: fa1f81cbcf5ac4c026bb624ee003f56405ef358e https://github.com/galaxyproject/galaxy/commit/fa1f81cbcf5ac4c026bb624ee003f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js 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/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: ----------- Users -> user in menu/interface usage. Commit: 42c090cb20e82bee50b8931aeeedca4e735f766b https://github.com/galaxyproject/galaxy/commit/42c090cb20e82bee50b8931aeeedc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) 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: ----------- Update users->user in the menu as well Commit: ca238c4323a9d8efd8bb6fca06da5dd87d86032f https://github.com/galaxyproject/galaxy/commit/ca238c4323a9d8efd8bb6fca06da5... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py Log Message: ----------- Add tags to mock hda Commit: 2135e63f8e144e21c926c8ea593acb5ce9615069 https://github.com/galaxyproject/galaxy/commit/2135e63f8e144e21c926c8ea593ac... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Filter tags regardless of given select field label Commit: a7ec0c8579267adf6355e6f678b734e3f1b63cc9 https://github.com/galaxyproject/galaxy/commit/a7ec0c8579267adf6355e6f678b73... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/text.py Log Message: ----------- Add datatypes for soon coming PlantTribes Galaxy tools. Commit: 7e19245c8af5b203c0a76f2ab5eee5a1856fdded https://github.com/galaxyproject/galaxy/commit/7e19245c8af5b203c0a76f2ab5eee... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M test/unit/tools/test_evaluation.py Log Message: ----------- Fix spacing Commit: ed95412b36a0f349951e088ad5707f5c62e5851f https://github.com/galaxyproject/galaxy/commit/ed95412b36a0f349951e088ad5707... Author: Saskia Hiltemann <zazkia@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako Log Message: ----------- add ethercalc interactive environment Commit: d47f582d152d095044ddb6454e880b8dedc7cab6 https://github.com/galaxyproject/galaxy/commit/d47f582d152d095044ddb6454e880... Author: Saskia Hiltemann <zazkia@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako Log Message: ----------- remove commented section Commit: a93c29fa4a438b93016cb5e31d0e4ef88ca88029 https://github.com/galaxyproject/galaxy/commit/a93c29fa4a438b93016cb5e31d0e4... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add tag filtering for collections Commit: 82137b433cf00f2b83a00e08b71bdea2bfebf9bd https://github.com/galaxyproject/galaxy/commit/82137b433cf00f2b83a00e08b71bd... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix append calling for collections Commit: 31d222c91031775629896feb027e00ea535ef7d9 https://github.com/galaxyproject/galaxy/commit/31d222c91031775629896feb027e0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/style/less/history.less M static/maps/mvc/history/hda-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hda-li.js M static/style/blue/base.css Log Message: ----------- 'name' tag rendering, very basic, needs styling and loading fixes Commit: 4fa76caf67e33ce38f2e45325d504e2f1ff824a7 https://github.com/galaxyproject/galaxy/commit/4fa76caf67e33ce38f2e45325d504... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Set $HOME to a temp directory rather than conda_prefix because conda_prefix may not be writable either. Commit: f6353c28f6f3a7012daf1eb95a7f7bcfd1d58d7c https://github.com/galaxyproject/galaxy/commit/f6353c28f6f3a7012daf1eb95a7f7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/style/less/history.less M static/style/blue/base.css Log Message: ----------- Fix underlines in nametags Commit: 9e5008984fc3ce1fd8359acfe502b3010ca76c1f https://github.com/galaxyproject/galaxy/commit/9e5008984fc3ce1fd8359acfe502b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M static/maps/mvc/history/hda-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hda-li.js Log Message: ----------- nametags first, then hid+title Commit: ef1344f03f291468b87c89d90b3a0f06ec9b0a79 https://github.com/galaxyproject/galaxy/commit/ef1344f03f291468b87c89d90b3a0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/style/less/history.less M static/style/blue/base.css Log Message: ----------- Adjust margins on labels Commit: a144ce58939b122cc1bfb0575081a2082942e773 https://github.com/galaxyproject/galaxy/commit/a144ce58939b122cc1bfb0575081a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/managers/hdas.py Log Message: ----------- Swap tags to default view for hdas -- may need to revisit this if it proves too expensive. Commit: 4b7fea8d3fe0afa062213f81a75003cac593ad74 https://github.com/galaxyproject/galaxy/commit/4b7fea8d3fe0afa062213f81a7500... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M static/maps/mvc/history/hda-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hda-li.js Log Message: ----------- Adjust positioning again for nametags, below the standard title but still visible above the fold. Commit: 845e43c1e537f66c8208165a82583b4ca814b1f0 https://github.com/galaxyproject/galaxy/commit/845e43c1e537f66c8208165a82583... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/json.py Log Message: ----------- Avoid autoconversion of boolean values when calling json loads Remove unused import Fix Commit: cb27f921c7e82f09c675e1e472417ad47d65bfab https://github.com/galaxyproject/galaxy/commit/cb27f921c7e82f09c675e1e472417... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/util/json.py Log Message: ----------- Fix comment Commit: bb604e65ee0f34ccce664f5798c55adbcedc9e5e https://github.com/galaxyproject/galaxy/commit/bb604e65ee0f34ccce664f5798c55... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3701 from natefoo/conda_home_temp Set $HOME to a temp directory rather than conda_prefix because conda_prefix may not be writable either. Commit: 0914c05f8823759af21b37ff0ea8a7e757c4ba3a https://github.com/galaxyproject/galaxy/commit/0914c05f8823759af21b37ff0ea8a... Author: shiltemann <zazkia@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- fix metadata failure for large count tables Commit: a3ab46ef26031ba4c1fb22ebd0232bdb930651e5 https://github.com/galaxyproject/galaxy/commit/a3ab46ef26031ba4c1fb22ebd0232... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M lib/galaxy/managers/hdas.py M static/maps/mvc/history/hda-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hda-li.js Log Message: ----------- Swap to a 'nametags' field in the high level view instead of returning all tags. TODO: Optimize this Commit: 293726c57933cb2465a650d005332241eac0f912 https://github.com/galaxyproject/galaxy/commit/293726c57933cb2465a650d005332... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Support Docker Engine swarm mode Commit: 2ee81a3faaef38547295f9a47f9f063423b40394 https://github.com/galaxyproject/galaxy/commit/2ee81a3faaef38547295f9a47f9f0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Client route priority is *last* Commit: b00dfc8a7b7bc739a84c5a229c161a917601d68a https://github.com/galaxyproject/galaxy/commit/b00dfc8a7b7bc739a84c5a229c161... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove extra empty line. Commit: 0fb9fbc3885eb11b7e49f97f6a129f9c0343e780 https://github.com/galaxyproject/galaxy/commit/0fb9fbc3885eb11b7e49f97f6a129... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) 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: ----------- Merge pull request #18 from dannon/ui_pref_routing User->Users Commit: 5818bbcbaaeca54a85bef9acaadd41d12386a6ad https://github.com/galaxyproject/galaxy/commit/5818bbcbaaeca54a85bef9acaadd4... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Prefer versioned Conda dependencies to unversioned Galaxy ones. Commit: 4aec70cae28f336212a6bc8f5d24a325cb851bab https://github.com/galaxyproject/galaxy/commit/4aec70cae28f336212a6bc8f5d24a... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3666 from natefoo/docker-swarm-mode Support Docker Engine swarm mode for Interactive Environments Commit: fe41ec185f85cdca4e0eb4a5705b511d20f699aa https://github.com/galaxyproject/galaxy/commit/fe41ec185f85cdca4e0eb4a5705b5... Author: Saskia Hiltemann <shiltemann@users.noreply.github.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- fix typos Commit: 735f56ec95dba7d58d8d1dad922a01c3074af1ce https://github.com/galaxyproject/galaxy/commit/735f56ec95dba7d58d8d1dad922a0... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Concat all tags to improve front-end performance Commit: 83df8d5c9653c8e213eed63aecb9377503eb42f2 https://github.com/galaxyproject/galaxy/commit/83df8d5c9653c8e213eed63aecb93... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Attempt to prefetch tags when building active datasets list Commit: 6b2f9be75ab16e69a8fb1c72d10d169d20ab7854 https://github.com/galaxyproject/galaxy/commit/6b2f9be75ab16e69a8fb1c72d10d1... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Use space instead of comma when concatenating tags Commit: 861368ae1c7fa21f4ee7b55fbb682f78e07ece9d https://github.com/galaxyproject/galaxy/commit/861368ae1c7fa21f4ee7b55fbb682... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/managers/hdas.py Log Message: ----------- Remove dead code from prior work in nametag collection, change to user_tname usage. Commit: 4120781713cc65d3c05064bee981cf826d5c4be8 https://github.com/galaxyproject/galaxy/commit/4120781713cc65d3c05064bee981c... Author: Evgeny Anatskiy <evgeny.anatskiy@gmail.com> Date: 2017-03-05 (Sun, 05 Mar 2017) Changed paths: M config/galaxy.ini.sample M config/plugins/webhooks/demo/search/static/styles.css Log Message: ----------- increase contrast and improve readability Commit: b769da1b3d67195d3a2cd908321f0f200dc2a8b0 https://github.com/galaxyproject/galaxy/commit/b769da1b3d67195d3a2cd908321f0... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Merge pull request #3706 from shiltemann/mothur-dataype-fix Mothur datatypes: fix metadata failure for large count tables Commit: 6e3a9661d45cb239e116660888834ea8037b726b https://github.com/galaxyproject/galaxy/commit/6e3a9661d45cb239e116660888834... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #3668 from jmchilton/workflow_transient_failing_test Fix for transiently failing workflow test. Commit: ad3025f46a00190674bbc4dbc3bfab16983f9cb4 https://github.com/galaxyproject/galaxy/commit/ad3025f46a00190674bbc4dbc3bfa... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M run_tests.sh M test/TESTING.md Log Message: ----------- Touch up Galaxy testing documentation. Commit: 5704013301f8b185fbc55324a79ab58937a48230 https://github.com/galaxyproject/galaxy/commit/5704013301f8b185fbc55324a79ab... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/selenium_tests/test_collection_builders.py Log Message: ----------- Implement initial collection builder UX test cases. Exercise list and paired builder's most basic functionality. Commit: 97d6e1b6c1ca56575c1297649fd0484c85e15a7a https://github.com/galaxyproject/galaxy/commit/97d6e1b6c1ca56575c1297649fd04... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge branch 'filter_dataset_tags' into dev Commit: 8800376eb41d262b41862b3a1ad160218b47d45d https://github.com/galaxyproject/galaxy/commit/8800376eb41d262b41862b3a1ad16... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Improved Selenium exception messages. For many common waiting operations used throughout many tests: ``` TimeoutException: Message: ``` Will become something like ``` TimeoutException: Message: Timeout waiting on CSS selector [#dataset-adb5f5c93f827949.state-failed] to become visible. ``` For HID waiting I've added the state and HID as well - so something like this: ``` TimeoutException: Message: Failed waiting on history item 1 state to change to [ok] current state [failed]. Timeout waiting on CSS selector [#dataset-adb5f5c93f827949.state-failed] to become visible. ``` Commit: 179e58c8b3a7d10fa15e238ec7d2f982aa3fed00 https://github.com/galaxyproject/galaxy/commit/179e58c8b3a7d10fa15e238ec7d2f... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M run_tests.sh M test/TESTING.md Log Message: ----------- Merge pull request #3715 from jmchilton/test_docs_0 Touch up Galaxy testing documentation. Commit: 5055283f49d73b7eb3b420875dfe8ccc1adb85de https://github.com/galaxyproject/galaxy/commit/5055283f49d73b7eb3b420875dfe8... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/style/less/history.less M lib/galaxy/managers/hdas.py M lib/galaxy/tools/actions/__init__.py A static/maps/analysis.js.map A static/maps/app.js.map A static/maps/app/analysis.js.map M static/maps/mvc/history/hda-li.js.map A static/scripts/analysis.js A static/scripts/app.js A static/scripts/app/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hda-li.js M static/style/blue/base.css Log Message: ----------- Merge branch 'tags_in_history' into dev Commit: ecaf1be02f2364a2494e7adabd3b8733e194baf7 https://github.com/galaxyproject/galaxy/commit/ecaf1be02f2364a2494e7adabd3b8... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Show tags in select search field Commit: e606dbdacbbad0b604f5395c1140571d9a219984 https://github.com/galaxyproject/galaxy/commit/e606dbdacbbad0b604f5395c11405... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix style Commit: 4c4f78857b7141227e6ac320c36aad7c3429b7b5 https://github.com/galaxyproject/galaxy/commit/4c4f78857b7141227e6ac320c36aa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M lib/galaxy/managers/hdas.py Log Message: ----------- Swap to using tag values to store name instead of child values. Commit: 0d95bf43ad84f014b404624a8e41f69f55b2a132 https://github.com/galaxyproject/galaxy/commit/0d95bf43ad84f014b404624a8e41f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Merge pull request #3718 from guerler/add_tags_to_label_000 Show tags in select search field Commit: 496f476b300733d818062fcace7e8d1a61517abc https://github.com/galaxyproject/galaxy/commit/496f476b300733d818062fcace7e8... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Fix tag escaping Commit: 2e5e6bb028165a735908543a063396f03bed375e https://github.com/galaxyproject/galaxy/commit/2e5e6bb028165a735908543a06339... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into nametags_to_value Commit: a52695dee6b179ed6cb24eaeb7146c946b28ccc9 https://github.com/galaxyproject/galaxy/commit/a52695dee6b179ed6cb24eaeb7146... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Escape title for select labels Commit: d20e19e85a11ab8cf7eaff4fd0b3ee3dee337ff2 https://github.com/galaxyproject/galaxy/commit/d20e19e85a11ab8cf7eaff4fd0b3e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Include values in tags and tag selection lgoic Commit: 942f0d98d912196e95cfbb6f390c321676c28bce https://github.com/galaxyproject/galaxy/commit/942f0d98d912196e95cfbb6f390c3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Only compose tag:value one time on the client. Commit: e54792f4263ed5ddacc1044fe0b2182735732fdb https://github.com/galaxyproject/galaxy/commit/e54792f4263ed5ddacc1044fe0b21... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #3720 from guerler/escape_tags Fix tag escaping Commit: 278da1b35653aa1ad5835b74206bb46bb4d6373a https://github.com/galaxyproject/galaxy/commit/278da1b35653aa1ad5835b74206bb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into nametags_to_value Commit: f8e6b84998ab13cc99037c5eda3425f81329cbe5 https://github.com/galaxyproject/galaxy/commit/f8e6b84998ab13cc99037c5eda342... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Compose tag:value serverside -- we don't benefit from having them split when shipped (yet) Commit: 477626385c14e3df00aa654194dd8502c064c5d7 https://github.com/galaxyproject/galaxy/commit/477626385c14e3df00aa654194dd8... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Filter tags by query term Commit: 192d75a4654411ad242819536a7968703697f524 https://github.com/galaxyproject/galaxy/commit/192d75a4654411ad242819536a796... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Strip hanging extra comma. Commit: b8b7739292676ba928664417be771bd6e3f8f087 https://github.com/galaxyproject/galaxy/commit/b8b7739292676ba928664417be771... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/managers/hdas.py M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #3719 from dannon/nametags_to_value Use values for 'name'tags instead of child tags. Commit: 006801ba1aace0a58f0ae90ba6a6777dfb834b58 https://github.com/galaxyproject/galaxy/commit/006801ba1aace0a58f0ae90ba6a67... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Escape FTP filename. Thanks @yhoogstrate Commit: 656a0f396ed6d64a8010d9a6a32f138539f0b296 https://github.com/galaxyproject/galaxy/commit/656a0f396ed6d64a8010d9a6a32f1... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Merge pull request #3722 from dannon/escape_ftp_filename Filename handling for FTP upload Commit: 79945f37c31d4d42be86bee352370af11b063271 https://github.com/galaxyproject/galaxy/commit/79945f37c31d4d42be86bee352370... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Do not require stored workflow id for subworkflows Commit: 9ccb0953ad63aa46464a0ef8ec3bb6d5d1944539 https://github.com/galaxyproject/galaxy/commit/9ccb0953ad63aa46464a0ef8ec3bb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/selenium_tests/test_collection_builders.py Log Message: ----------- Merge pull request #3716 from jmchilton/selenium_uploads_0 Selenium Testing Improvements Commit: 1b12259739e28bc69e68576a76aefcd61ee99358 https://github.com/galaxyproject/galaxy/commit/1b12259739e28bc69e68576a76aef... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #3698 from gregvonkuster/ptformats Add datatypes for soon coming PlantTribes Galaxy tools. Commit: 9aa911d509ac50f44ba4e6c5dca2cb9dba61ebbb https://github.com/galaxyproject/galaxy/commit/9aa911d509ac50f44ba4e6c5dca2c... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3723 from guerler/fix_subworkflow_id Do not require stored workflow id for subworkflows Commit: 0bfe9fa7ca1489d744351eecc4312838a20008eb https://github.com/galaxyproject/galaxy/commit/0bfe9fa7ca1489d744351eecc4312... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M README.rst M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R 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-misc.js M 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lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A 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lib/galaxy/util/compression_utils.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py A lib/galaxy/util/oset.py M lib/galaxy/util/properties.py M lib/galaxy/version.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/schedulers/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/galaxy/workflow/steps.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M run.sh M run_tests.sh M scripts/bootstrap_history.py M scripts/common_startup.sh A scripts/manage_tool_dependencies.py A scripts/secret_decoder_ring.py M scripts/slideshow/slideshow_template.html A static/maps/analysis.js.map A static/maps/app.js.map A 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static/scripts/mvc/history/history-view.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 R static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-canvas.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/ui/autocom_tagging.js M static/scripts/viz/trackster/tracks.js M static/style/blue/base.css M templates/admin/reload_tool.mako M templates/grid_base.mako A templates/webapps/galaxy/user/manage_info.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/tool_shed/repository/tool_form.mako A test-data/simple.xml M test/TESTING.md M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_tools.py A test/api/test_webhooks.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/driver_util.py M test/base/populators.py M test/docker/base/run_test_wrapper.sh M test/functional/tools/checksum.xml A test/functional/tools/is_valid_xml.xml A test/functional/tools/legacy_r.xml M test/functional/tools/md5sum.xml A test/functional/tools/mulled_example_multi_incomplete.xml A test/functional/tools/output_format_deprecated_when.xml A test/functional/tools/param_text_option.xml M test/functional/tools/samples_tool_conf.xml A test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/config/phdcomics.yaml A test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/static/script.js A test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/trans_object/config/trans_object.yaml A test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/static/script.js A test/functional/webhooks/xkcd/static/styles.css M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/galaxy_selenium/sizzle.py M test/integration/test_resolvers.py M test/qunit/tests/form_tests.js M test/qunit/tests/workflow_editor_tests.js M test/selenium_tests/framework.py A test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_tool_deps.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/upload.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merging with dev Commit: b9c1abd43a69241accd54d3531442b56508efc0f https://github.com/galaxyproject/galaxy/commit/b9c1abd43a69241accd54d3531442... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-03-07 (Tue, 07 Mar 2017) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Merge pull request #3374 from jmchilton/singleton_workflow_cycles Fix cycle detection for single node workflows. Commit: aa0af352cdd034872d24b3a5f497a04204c9c017 https://github.com/galaxyproject/galaxy/commit/aa0af352cdd034872d24b3a5f497a... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Add a simple UI to manage tool dependencies This page simply lists all loaded tools and their dependency status. On the left are checkboxes to select multiple tools, and at the bottom is a button to install the selected tool dependencies. Commit: 818c10832a1429b79e65906d106b6fda0ed28a35 https://github.com/galaxyproject/galaxy/commit/818c10832a1429b79e65906d106b6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Build the dependency status more efficiently: Pass a dictionary with ToolRequirements object as key and requirements status as value Commit: f882a14886de65b0079d5eea72a7bea044ab4a02 https://github.com/galaxyproject/galaxy/commit/f882a14886de65b0079d5eea72a7b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Add new view that primarily manages dependencies Commit: f1bb5a6a7114f1aa4dc331622183432604e9dbc7 https://github.com/galaxyproject/galaxy/commit/f1bb5a6a7114f1aa4dc3316221834... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- close opened div Commit: 96ae2893b3610e28101445f58966cffd61f873eb https://github.com/galaxyproject/galaxy/commit/96ae2893b3610e28101445f58966c... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- improve the markup and UX a bit Commit: 5dc73b7966d3c9e90e0a58823e34bc26663d5d71 https://github.com/galaxyproject/galaxy/commit/5dc73b7966d3c9e90e0a58823e34b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Add title and explanation for Manage Tool Dependencies page. Commit: 07490e428dc0a3596d7623a7a787443494626c63 https://github.com/galaxyproject/galaxy/commit/07490e428dc0a3596d7623a7a7874... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M client/galaxy/scripts/onload.js M config/galaxy.ini.sample A config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/static/script.js A config/plugins/webhooks/demo/search/static/styles.css M static/maps/onload.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/onload.js Log Message: ----------- Merge pull request #3460 from bgruening/search_overlay Overlay search for tools, wf, libraries and histories Commit: 0118c57af3ea2bae8b5c8c72fa45f431afb4aa8f https://github.com/galaxyproject/galaxy/commit/0118c57af3ea2bae8b5c8c72fa45f... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge pull request #3479 from mvdbeek/manage_tool_dependencies Add a simple UI to manage tool dependencies Commit: 704e6a6676c2aa6aafe4a283f50dcfd8a646682e https://github.com/galaxyproject/galaxy/commit/704e6a6676c2aa6aafe4a283f50dc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/json.py Log Message: ----------- Merge pull request #3702 from guerler/fix_boolean_handling Properly handle boolean values when parsed to a string-based/default tool parameter Commit: 90108e450fd2d13d3010e05a2fcb1224a2549a2a https://github.com/galaxyproject/galaxy/commit/90108e450fd2d13d3010e05a2fcb1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.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/onload.js Log Message: ----------- tool-form needs to not be required at the top level of the Galaxy webapp Commit: 2134d6c3856edf8358c185178f9efe35a232c03b https://github.com/galaxyproject/galaxy/commit/2134d6c3856edf8358c185178f9ef... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Use a redirect (which will get routed, soon) instead of instantiating a toolform within the overlay -- this is much lighter weight Commit: da9ee941afa604586cfc6dfdacb2594284b3e6f0 https://github.com/galaxyproject/galaxy/commit/da9ee941afa604586cfc6dfdacb25... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Standardize tabs/spaces in webhook overlay search Commit: 3d33586d4a5758e566dc5d1eceda91e97cd3d73a https://github.com/galaxyproject/galaxy/commit/3d33586d4a5758e566dc5d1eceda9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-08 (Wed, 08 Mar 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Cleanup pass on formatting/unused vars in webhooks Commit: 7bf6a581249ec409d33ccc060816b9f505185165 https://github.com/galaxyproject/galaxy/commit/7bf6a581249ec409d33ccc060816b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Remove outdated items from tool cache Commit: 9928a74c6c1cb57edbfba4068616bd5b15f51093 https://github.com/galaxyproject/galaxy/commit/9928a74c6c1cb57edbfba4068616b... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge ConfiguresGalaxyMixin.reload_toolbox() in _configure_toolbox() It's called only once from there when app is initialised, real toolbox reloads are performed by executing reload_toolbox() from lib/galaxy/queue_worker.py . Commit: a89954c8928f0997aa9a5781a39d18339914b387 https://github.com/galaxyproject/galaxy/commit/a89954c8928f0997aa9a5781a39d1... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Fix 2 typos Commit: 0d80b8807a70ff94a6f8dbee6279207c53869755 https://github.com/galaxyproject/galaxy/commit/0d80b8807a70ff94a6f8dbee62792... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Remove hash when expiring tool from tool cache and rename `clean_paths` to `paths_to_cleanup` (thx @nsoranzo). Commit: bcc4e025c36c3ee394c73cee06a8031cec6e9354 https://github.com/galaxyproject/galaxy/commit/bcc4e025c36c3ee394c73cee06a80... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py Log Message: ----------- Merge pull request #3732 from nsoranzo/reload_toolbox_merge Merge ConfiguresGalaxyMixin.reload_toolbox() in _configure_toolbox() Commit: 7b375664634075c1ad261eff42a2355637cfc363 https://github.com/galaxyproject/galaxy/commit/7b375664634075c1ad261eff42a23... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Use config_filename throughout ToolCache Commit: 33ababaeb48e8ecfad487a54e96550ce7e43bc78 https://github.com/galaxyproject/galaxy/commit/33ababaeb48e8ecfad487a54e9655... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py Log Message: ----------- Move the user calculate_and_set_disk_usage functionality to the model instead of the queue worker. Commit: c928f15b4d00bb798453d42a6f6a79042692edfc https://github.com/galaxyproject/galaxy/commit/c928f15b4d00bb798453d42a6f6a7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Robustify calculate_and_set_disk_usage for handling changes during the long calc Commit: cd6e7f73d8a54698aa63d670e8aba6e45f8eef1b https://github.com/galaxyproject/galaxy/commit/cd6e7f73d8a54698aa63d670e8aba... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Swap admin recalculate to use model-based recalc-and-set Commit: 751182640d1a76962cbac872ae31c0ce471872dd https://github.com/galaxyproject/galaxy/commit/751182640d1a76962cbac872ae31c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove now-unused import of pgcalc Commit: 8002ef31ea6f4cb52d6e907dcdf1d002ced45eb6 https://github.com/galaxyproject/galaxy/commit/8002ef31ea6f4cb52d6e907dcdf1d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Ensure there's a user before calling calculate_and_set_disk_usage Commit: e088a48323a06e80d55e85944a4c09cf368b8391 https://github.com/galaxyproject/galaxy/commit/e088a48323a06e80d55e85944a4c0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Add error logging to recalculate task. Commit: 2d964eb50c9f2f2246044a1d7b83e0f920046510 https://github.com/galaxyproject/galaxy/commit/2d964eb50c9f2f2246044a1d7b83e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- I have no idea what I would be doing without Nicola. Commit: 8911e491a56cdc3b8fb327bc702b4843d7d22a4d https://github.com/galaxyproject/galaxy/commit/8911e491a56cdc3b8fb327bc702b4... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #3734 from dannon/queue_worker_trim Quota recalculation logic consolidation Commit: 6e32b0f7c119ca6c3d54a761e64f49fe6a7f8280 https://github.com/galaxyproject/galaxy/commit/6e32b0f7c119ca6c3d54a761e64f4... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tool/tools.js M static/maps/mvc/dataset/dataset-li-edit.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.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/tool/tools.js Log Message: ----------- Use routing helper to navigate to tool form Commit: 5df0187d42d19c5a930bf067a52a2ef4cf9d3ec8 https://github.com/galaxyproject/galaxy/commit/5df0187d42d19c5a930bf067a52a2... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/history.less M client/galaxy/style/less/ui.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/static/script.js A config/plugins/webhooks/demo/search/static/styles.css A cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/text.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/json.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/workflow/steps.py M run_tests.sh A static/maps/analysis.js.map A static/maps/app.js.map A static/maps/app/analysis.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/onload.js.map A static/scripts/analysis.js A static/scripts/app.js A static/scripts/app/analysis.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 M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/onload.js M static/style/blue/base.css M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/tool_shed/repository/common.mako M test/TESTING.md M test/api/test_workflows.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/selenium_tests/test_collection_builders.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge branch 'dev' into ui_pref_routing Commit: 9f498f9c4be7d1ba6cfba38a2cc8993f732c013b https://github.com/galaxyproject/galaxy/commit/9f498f9c4be7d1ba6cfba38a2cc89... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Avoid reusing 'map' builtin Commit: 3ef22d2e6728bf890f14ef6465e88f757bd88b94 https://github.com/galaxyproject/galaxy/commit/3ef22d2e6728bf890f14ef6465e88... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Slightly more accurate check to verify we have a controller match Commit: 675c375cad69affacda74521d7e88f5227160cb6 https://github.com/galaxyproject/galaxy/commit/675c375cad69affacda74521d7e88... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- A try at two layer routing with failthrough to clientside routes. Commit: 036d35ac643ace26f1bad289d1989d3db8971ff2 https://github.com/galaxyproject/galaxy/commit/036d35ac643ace26f1bad289d1989... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Slight refactoring to reduce duplication in map matching Commit: 66e6be890bedbf59f98b1d10a54146175524df8a https://github.com/galaxyproject/galaxy/commit/66e6be890bedbf59f98b1d10a5414... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- No need to check API routes against clientside mapper, catch specific exception Commit: 5a7eab0f06b4eb9f877c8e582bb6e078622be1ad https://github.com/galaxyproject/galaxy/commit/5a7eab0f06b4eb9f877c8e582bb6e... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-03-09 (Thu, 09 Mar 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/search/static/script.js M static/maps/onload.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/onload.js Log Message: ----------- Merge pull request #3731 from dannon/fix_webhook_search_overlay Fix webhook search overlay interfering with masthead load Commit: 01e1bc6f3007aff1234e518977115c97bd20e1eb https://github.com/galaxyproject/galaxy/commit/01e1bc6f3007aff1234e518977115... Author: Jorrit Boekel <jorrit.boekel@scilifelab.se> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Added percolator proteomics datatypes for input and output Commit: b437be2c566c431267d814b7718380969b8bd3b7 https://github.com/galaxyproject/galaxy/commit/b437be2c566c431267d814b771838... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding SIF to JSON converter for Cytoscape viewer Commit: bf88e891977da140d36ba9a627ffebf19178b290 https://github.com/galaxyproject/galaxy/commit/bf88e891977da140d36ba9a627ffe... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge pull request #20 from dannon/ui_pref_routing Ui pref routing Commit: df73622becc820017a1873db00f64fdcbb6de27a https://github.com/galaxyproject/galaxy/commit/df73622becc820017a1873db00f64... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Fix route used in admin controller Commit: 05a689e2adf455f461556fa1aa9229cf4f0454ff https://github.com/galaxyproject/galaxy/commit/05a689e2adf455f461556fa1aa922... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/onload.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/onload.js Log Message: ----------- Merge branch 'dev' into ui_pref_routing Commit: 20916c16a9861cf1f491173cbded2bac0b61f378 https://github.com/galaxyproject/galaxy/commit/20916c16a9861cf1f491173cbded2... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) 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: ----------- Remove back button to simplify routing, avoid failing returns Commit: 66a02b6af192c78f53ad2901f55515cd9f712ab7 https://github.com/galaxyproject/galaxy/commit/66a02b6af192c78f53ad2901f5551... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M doc/source/admin/index.rst A doc/source/admin/tool_panel.rst M doc/source/conf.py M doc/source/dev/index.rst M doc/source/dev/interactive_environments.rst M doc/source/index.rst M doc/source/project/issues.rst Log Message: ----------- modify our docs in preparation for restructuring start moving admin content from old wiki Commit: 7523ff6983bd6511725509ae4f4d744b36223b97 https://github.com/galaxyproject/galaxy/commit/7523ff6983bd6511725509ae4f4d7... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add random identifier to request url in order to allow proper reload upon multiple navigation requests Commit: 2275d098eeeaeb115fa69b0d1fa7856f7bfa4d18 https://github.com/galaxyproject/galaxy/commit/2275d098eeeaeb115fa69b0d1fa78... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding graph resize property for window resize Commit: f94174912a09a56eebe2e14e63238c3f3f172327 https://github.com/galaxyproject/galaxy/commit/f94174912a09a56eebe2e14e63238... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- update xsd codefile doc with info from moin Commit: 817a9db1f7bca855fe8f35c4b188c10a5c3a6653 https://github.com/galaxyproject/galaxy/commit/817a9db1f7bca855fe8f35c4b188c... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: R doc/source/admin/chat-0.png R doc/source/admin/chat-1.png R doc/source/admin/chat-2.png R doc/source/admin/chat-3.png R doc/source/admin/chat-4.png R doc/source/admin/chat.rst R doc/source/admin/communication_server.png R doc/source/admin/communication_server_rooms.png R doc/source/admin/grt.rst M doc/source/admin/index.rst R doc/source/admin/interactive_environments.png R doc/source/admin/interactive_environments.rst R doc/source/admin/interactive_environments.svg R doc/source/admin/mulled_containers.rst A doc/source/admin/special_topics/chat-0.png A doc/source/admin/special_topics/chat-1.png A doc/source/admin/special_topics/chat-2.png A doc/source/admin/special_topics/chat-3.png A doc/source/admin/special_topics/chat-4.png A doc/source/admin/special_topics/chat.rst A doc/source/admin/special_topics/communication_server.png A doc/source/admin/special_topics/communication_server_rooms.png A doc/source/admin/special_topics/grt.rst A doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/interactive_environments.png A doc/source/admin/special_topics/interactive_environments.rst A doc/source/admin/special_topics/interactive_environments.svg A doc/source/admin/special_topics/mulled_containers.rst A doc/source/admin/special_topics/webhooks.rst R doc/source/admin/webhooks.rst M doc/source/index.rst Log Message: ----------- move some admin docs to separate special topics section Commit: 45971b29bd8b93825fe48134750bd866c82f7a9f https://github.com/galaxyproject/galaxy/commit/45971b29bd8b93825fe48134750bd... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Update dependency resolver docs for new default order Commit: 33ff2754cc75981796176b7e7ae75ce362db62a0 https://github.com/galaxyproject/galaxy/commit/33ff2754cc75981796176b7e7ae75... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3708 from natefoo/dep-resolve-order Prefer versioned Conda dependencies to unversioned Galaxy ones Commit: 46e452bfe820ddbb329e694d0eb2b7b755594910 https://github.com/galaxyproject/galaxy/commit/46e452bfe820ddbb329e694d0eb2b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix typo in install_dependencies docstring Commit: 8b5d408e438c346f04088374d70eaca65e06c292 https://github.com/galaxyproject/galaxy/commit/8b5d408e438c346f04088374d70ea... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.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/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py Log Message: ----------- Add API to remove requirements installed by Conda This is currently limited to the Conda dependency resolver, but other resolver would only need to implement the resolver.uninstall method and set can_uninstall_dependencies to True. To use this endpoint, POST to <galaxy_url>/tools/<tool_id>/uninstall_dependencies'. Commit: 3b067ef62a4dfa8af54bc4c75c6260f98d660aeb https://github.com/galaxyproject/galaxy/commit/3b067ef62a4dfa8af54bc4c75c626... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Return last non-zero returncode Commit: d5b5d29137ee1e5577530ed2c56579b9394520b3 https://github.com/galaxyproject/galaxy/commit/d5b5d29137ee1e5577530ed2c5657... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/integration/test_resolvers.py Log Message: ----------- Change endpoint to `api/tools/<tool_id>/dependencies` A POST will trigger installation and DELETE will trigger uninstalling the dependencies (Thx for the suggestion @jmchilton). Commit: 6902e62d38e3c5741a238736f640b5b847c5e8c2 https://github.com/galaxyproject/galaxy/commit/6902e62d38e3c5741a238736f640b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix uninstall when not all dependencies are resolved by all-in-one resolver Commit: 95106ea3c9ad875ce35b16c6b9bb8556f3d82076 https://github.com/galaxyproject/galaxy/commit/95106ea3c9ad875ce35b16c6b9bb8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-12 (Sun, 12 Mar 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Add UI for Conda dependency uninstall Commit: fc1df7bad17e53c54bd57602b82bbec22cc0e074 https://github.com/galaxyproject/galaxy/commit/fc1df7bad17e53c54bd57602b82bb... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.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/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/webapps/galaxy/admin/manage_dependencies.mako M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3725 from mvdbeek/remove_env_conda Add API and UI to remove requirements installed by Conda Commit: 38336e7e94b15b1580e32e4d0b4321836791db9b https://github.com/galaxyproject/galaxy/commit/38336e7e94b15b1580e32e4d0b432... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample M doc/source/admin/dependency_resolvers.rst 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 M lib/galaxy/tools/deps/views.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M templates/webapps/galaxy/admin/manage_dependencies.mako M test/integration/test_resolvers.py Log Message: ----------- Merge branch 'dev' into ui_pref_routing Commit: 7e1c04cc6df810ca3a4e726a85cc9566d9d1ff61 https://github.com/galaxyproject/galaxy/commit/7e1c04cc6df810ca3a4e726a85cc9... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3739 from martenson/update-codefile-schema update xsd codefile doc with info from moin Commit: 90b300cbd731df2e6005ca1dcd2f5c1c59a34e0e https://github.com/galaxyproject/galaxy/commit/90b300cbd731df2e6005ca1dcd2f5... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Return empty list if resolve_all() has failed This should solve the problems pointed out by :eyes: @nsoranzo introduced in https://github.com/galaxyproject/galaxy/pull/3725. This commit also clarifies this behaviour in the docstrings. Commit: 8192d3562937d07410aa5d7dd73727efc5832634 https://github.com/galaxyproject/galaxy/commit/8192d3562937d07410aa5d7dd7372... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Add `:returns: list of resolved dependencies` to docstring of `resolve_all` method Commit: 7d08f8f2fecf08743a58f71c431e1d71f84f0d76 https://github.com/galaxyproject/galaxy/commit/7d08f8f2fecf08743a58f71c431e1... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3746 from mvdbeek/resolve_all_fix_3725 BUG: Return empty list if resolve_all() has failed Commit: 08f66a924b8a46d673fc6237dec3a4e8fcb34f21 https://github.com/galaxyproject/galaxy/commit/08f66a924b8a46d673fc6237dec3a... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-03-13 (Mon, 13 Mar 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A config/swarm_manager_conf.yml.sample R cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M lib/galaxy/config.py A lib/galaxy/container/__init__.py A lib/galaxy/container/docker_swarm.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/mapper.js A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M static/maps/galaxy.interactive_environments.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- GIE container waiting and swarm management. 1. Create a new API endpoint and client spin to wait for GIE containers to become ready. IEs are not required to use it, but usage does require a slight change to their `load_notebook()` functions. 2. Add a Docker swarm manager daemon that runs automatically to add nodes when services are waiting, clean up exited services, and remove idle nodes. Shuts down automatically when there's nothing to do. The format of the GIE proxy session database has changed, if GIEs are running when you restart Galaxy, they will be interrupted. If you run the GIE proxy separate from Galaxy, you should restart it after upgrading. Commit: f21f963a23427e2b5aa1f58a7d9b0fb85aed7607 https://github.com/galaxyproject/galaxy/commit/f21f963a23427e2b5aa1f58a7d9b0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py Log Message: ----------- Change API path in docstrings to correct /api/dependency_resolvers/* Commit: e9c98e46ed580463a4f7a4ed989d11f7714ac13f https://github.com/galaxyproject/galaxy/commit/e9c98e46ed580463a4f7a4ed989d1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Don't have the clientside mapper register itself Commit: 65e7ee0c78e5c61a6ef9d9eaa8ccd6d8666014ad https://github.com/galaxyproject/galaxy/commit/65e7ee0c78e5c61a6ef9d9eaa8ccd... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py Log Message: ----------- Merge pull request #3749 from mvdbeek/docstring_fix_api Change API path in docstrings to correct /api/dependency_resolvers/* Commit: 3b0be252e3485b413d7978a91b14242b589702c5 https://github.com/galaxyproject/galaxy/commit/3b0be252e3485b413d7978a91b142... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Remove old deprecated option (explicit is defined at mapper instantiation, and we wat the default Commit: 6f8deb6f4a07bd57493d24cd90a9862dbf7e6d0c https://github.com/galaxyproject/galaxy/commit/6f8deb6f4a07bd57493d24cd90a98... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: R doc/source/admin/images_webhooks/history-menu.png R doc/source/admin/images_webhooks/masthead.png R doc/source/admin/images_webhooks/masthead_trans_object.png R doc/source/admin/images_webhooks/tool.png R doc/source/admin/images_webhooks/workflow.png A doc/source/admin/special_topics/images_webhooks/history-menu.png A doc/source/admin/special_topics/images_webhooks/masthead.png A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png A doc/source/admin/special_topics/images_webhooks/tool.png A doc/source/admin/special_topics/images_webhooks/workflow.png Log Message: ----------- move webhooks images where they belong Commit: 4b6373f042ad98f4f3ac664911ab35611280f204 https://github.com/galaxyproject/galaxy/commit/4b6373f042ad98f4f3ac664911ab3... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M doc/source/admin/index.rst Log Message: ----------- fix outdated links Commit: 93c2286442bbb27e9dd3db708064e6f3deb45287 https://github.com/galaxyproject/galaxy/commit/93c2286442bbb27e9dd3db708064e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Initialize clientside_routes regexes. Commit: 061b7d78f26d4aa1298a3a072fcc420d214d4f7b https://github.com/galaxyproject/galaxy/commit/061b7d78f26d4aa1298a3a072fcc4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Refactor failthrough mapping logic Commit: 5e11b54da59e09f9e31b71c00f3ecaf99842a0c5 https://github.com/galaxyproject/galaxy/commit/5e11b54da59e09f9e31b71c00f3ec... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Add the possibility to uninstall conda environments that are not in use by Galaxy Commit: 550bc423af0cb036d1a870c0c419533f25517bbf https://github.com/galaxyproject/galaxy/commit/550bc423af0cb036d1a870c0c4195... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Rename parameter, make it a bit more clear what this failthrough logic is doing. Commit: 88fb8650b9699a50348ddece8d336797aacd03c5 https://github.com/galaxyproject/galaxy/commit/88fb8650b9699a50348ddece8d336... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Bump routes to 2.4.1, fix (newly?) broken archive route. Commit: 44fd8aa9bbc77680083eb71d30840a41ce1f79ee https://github.com/galaxyproject/galaxy/commit/44fd8aa9bbc77680083eb71d30840... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge pull request #21 from dannon/ui_pref_routing Don't have the clientside mapper register itself Commit: 6700c08a96467d322e917347a63f1ec8c932700e https://github.com/galaxyproject/galaxy/commit/6700c08a96467d322e917347a63f1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt Log Message: ----------- Update Routes 2.4.1 hash Commit: 1578ffe1ca5bf28a34f91a892eed286ab69a14ba https://github.com/galaxyproject/galaxy/commit/1578ffe1ca5bf28a34f91a892eed2... Author: Clemens BlanK <blankclemens@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Add tool_list webhook plugin to create the tool list yaml file for this instance. Commit: 90ae42c3f1d0efc4f8b461e43a158eb5b7b95d4f https://github.com/galaxyproject/galaxy/commit/90ae42c3f1d0efc4f8b461e43a158... Author: Clemens BlanK <blankclemens@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Reduced API calls to speed it up. Commit: 417d1d251e7e7c735a8d4aefd53edcec941db1f4 https://github.com/galaxyproject/galaxy/commit/417d1d251e7e7c735a8d4aefd53ed... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M CITATION M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js Log Message: ----------- Initial commit to get this rolling, library-security does not exist and needs to be created, among others. Commit: bc870cdf66ecaaf218cd20debdbcc68b20e7f959 https://github.com/galaxyproject/galaxy/commit/bc870cdf66ecaaf218cd20debdbcc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Update galaxy.ini.sample and config. Commit: 11829c4f9df12cf8e8e3e7a14dc11e9a02afe6a4 https://github.com/galaxyproject/galaxy/commit/11829c4f9df12cf8e8e3e7a14dc11... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/managers/configuration.py M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- More defaults, these should be consolidated. Commit: d505fcf26027fd908b0a0fa1a6e1cb814c56b6ce https://github.com/galaxyproject/galaxy/commit/d505fcf26027fd908b0a0fa1a6e1c... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: A doc/source/admin/authentication.md M doc/source/admin/index.rst Log Message: ----------- New Authentication section of the docs. I pulled in this doc https://galaxyproject.org/develop/authentication/ which was very dated and somewhat incorrect and I filled it out with more details, updated configuration information, and a whole new section on the authentication framework. I also pulled in this doc https://galaxyproject.org/admin/user-accounts/ which was pretty good and I left it largely unchanged. Rebased to fix index inclusion and with edits suggested by :eagle::eyes:. Commit: e12c07cacd12fbf4a2fb148242be5bea7c13221e https://github.com/galaxyproject/galaxy/commit/e12c07cacd12fbf4a2fb148242be5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako Log Message: ----------- Use config.py for defaults used in managers/configuration. Commit: ed1d19a967989416caebd3588fe6b8b6460764e2 https://github.com/galaxyproject/galaxy/commit/ed1d19a967989416caebd3588fe6b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Update reports and toolshed app configs as well. Commit: 77b29880c8e9eddaf282e8738542aa57a189f6d2 https://github.com/galaxyproject/galaxy/commit/77b29880c8e9eddaf282e8738542a... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M run_tests.sh Log Message: ----------- Fix run_tests.sh --dockerize for Mac OS X usage. Without this I get the error message below and the tests do not execute. ``` ./run_tests.sh: line 279: UID: readonly variable ``` This was likely broken with b75ee68d9f6305646a55d816fb1173210e36eab9. Commit: d1eab2685f652f0b6f8c8119c51acf080c54556e https://github.com/galaxyproject/galaxy/commit/d1eab2685f652f0b6f8c8119c51ac... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Provide a fallback for GALAXY_TEST_UID if manually running Docker tests. Commit: d6654838f361a1e3064619cb059f9137579dc376 https://github.com/galaxyproject/galaxy/commit/d6654838f361a1e3064619cb059f9... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Fix pip install cache inside Galaxy testing container. It is causing Jenkins to fail throughout on https://github.com/galaxyproject/galaxy/pull/3179. Commit: b1429d4340f11591768bb853fd646508e32e0501 https://github.com/galaxyproject/galaxy/commit/b1429d4340f11591768bb853fd646... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Mirror latest galaxy-lib changes for Conda and CWL improvements. - I added more flexibility to mulled operations to work around bugs on OS X (galaxyproject/galaxy-lib#50). - I added the ability to use local packages with the Conda resolver (galaxyproject/galaxy-lib#47) - this allows Galaxy when used with Planemo to use locally built packages. Including Nicola's suggested changes here (https://github.com/galaxyproject/galaxy-lib/commit/6d53fc7dec6c48ea8fb00fa37...). - I switched the default Conda prefix to miniconda3 so the name matches what Galaxy is actually installing. galaxyproject/galaxy-lib#48. This would never actually be used with Galaxy since we decided it should maintain its own prefix rather than using the default - it is important for Planemo though. - I synced the galaxy.tools.cwl package with my latest downstream work that provides updates for latest developments in cwltool. https://github.com/galaxyproject/galaxy-lib/pull/53 - I added the ability to load tools via URI-like strings in addition to simple paths - this allows referencing URLs and Dockstore/GA4GH tools directly from the command-line with Planemo. https://github.com/galaxyproject/galaxy-lib/pull/52 There are some other bug fixes outside of these three main PRs related to the second point - minor refinements to get conda-build dependencies working and working automatically. - galaxyproject/galaxy-lib@bdacc4d - galaxyproject/galaxy-lib@1b7bca6 - galaxyproject/galaxy-lib@36b2e65 Commit: 6ece9acfde69fadd4e8b105c9c14ce572ddbfbcd https://github.com/galaxyproject/galaxy/commit/6ece9acfde69fadd4e8b105c9c14c... Author: Clemens BlanK <blankclemens@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Fix linting. Commit: d7cf8a4b33991c3117f725a1d418706b758703b5 https://github.com/galaxyproject/galaxy/commit/d7cf8a4b33991c3117f725a1d4187... Author: Clemens BlanK <blankclemens@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Fix Python 2.7 linting. Commit: bc203d022f92fd596514d935c0e569163e2cf4d1 https://github.com/galaxyproject/galaxy/commit/bc203d022f92fd596514d935c0e56... Author: Clemens BlanK <blankclemens@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Speed up list creation. Commit: 4f27240ef760446743b7b774404f159b713ae3ce https://github.com/galaxyproject/galaxy/commit/4f27240ef760446743b7b774404f1... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3737 from glormph/percolator_datatypes Percolator out datatypes Commit: aaa28071b3acaad514157dae856cb2f5a4895eef https://github.com/galaxyproject/galaxy/commit/aaa28071b3acaad514157dae856cb... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3752 from dannon/routes-bump Bump routes to 2.4.1 Commit: 149bbf87e3d57ffe22c51c283a94fbec33542f05 https://github.com/galaxyproject/galaxy/commit/149bbf87e3d57ffe22c51c283a94f... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A config/swarm_manager_conf.yml.sample R cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M lib/galaxy/config.py A lib/galaxy/container/__init__.py A lib/galaxy/container/docker_swarm.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/mapper.js A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M static/maps/galaxy.interactive_environments.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Merge pull request #3740 from natefoo/docker-swarm-mode-wait Interactive Environment container waiting and swarm management Commit: 0498c7f833fad513e2ca878843938e378475202b https://github.com/galaxyproject/galaxy/commit/0498c7f833fad513e2ca878843938... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/tool/tools.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/dataset/dataset-li-edit.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/user/user-preferences.js M templates/grid_base.mako R templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Merge pull request #3446 from guerler/ui_pref_routing Improve routing for user preference views Commit: d32317438c407799c2b33364af6e553fa03fbdfa https://github.com/galaxyproject/galaxy/commit/d32317438c407799c2b33364af6e5... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add build endpoints to user api Commit: 814d58f9810283c1e851b6c6ec062ab3cb0784bf https://github.com/galaxyproject/galaxy/commit/814d58f9810283c1e851b6c6ec062... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Remove empty lines, reduce comments Commit: c12c2d1dff45afe1a62321f45a26e2de2d696a99 https://github.com/galaxyproject/galaxy/commit/c12c2d1dff45afe1a62321f45a26e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Add potential len files to response for now, might move to client-side further down the road Commit: 72fb0d6f043e5085323059f80a39a9c2fab43b88 https://github.com/galaxyproject/galaxy/commit/72fb0d6f043e5085323059f80a39a... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Fix error handling for build deletion Commit: 32a8633f4e0b4fc06ba3b61027ae3127cd0c7ece https://github.com/galaxyproject/galaxy/commit/32a8633f4e0b4fc06ba3b61027ae3... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) 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/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: ----------- Add link to user preference page, return exception if chrom count failed Commit: 2153ef5b76a1958c0067abb6c5492d1df6767c3c https://github.com/galaxyproject/galaxy/commit/2153ef5b76a1958c0067abb6c5492... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js 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 Log Message: ----------- Add route for custom builds Commit: 56338972b9767b9e0be474d99b8f4ea915e6dd96 https://github.com/galaxyproject/galaxy/commit/56338972b9767b9e0be474d99b8f4... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js Log Message: ----------- Extending the sif to json converter to allow single nodes to be plotted Commit: 3d092d683efef26bde2d2d453c07caa8a8c4322e https://github.com/galaxyproject/galaxy/commit/3d092d683efef26bde2d2d453c07c... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/user/user-preferences.js M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/static/script.js A config/plugins/webhooks/demo/search/static/styles.css A config/swarm_manager_conf.yml.sample R cron/clean_docker_swarm_mode_services.sh M doc/source/admin/dependency_resolvers.rst M doc/source/admin/special_topics/interactive_environments.rst M lib/galaxy/config.py A lib/galaxy/container/__init__.py A lib/galaxy/container/docker_swarm.py M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/json.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/mapper.js 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/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/workflow/steps.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M static/maps/galaxy.interactive_environments.js.map M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/tool/tools.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/galaxy.interactive_environments.js M static/scripts/layout/menu.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/user/user-preferences.js M templates/grid_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako R templates/webapps/galaxy/user/manage_info.mako M templates/webapps/tool_shed/repository/common.mako M test/integration/test_resolvers.py Log Message: ----------- Merge branch 'dev' into admin-docs-from-hub Commit: c6bd499d001b667f20bd4caf99612a3d56b200c1 https://github.com/galaxyproject/galaxy/commit/c6bd499d001b667f20bd4caf99612... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding node text and colors for graphs Commit: 27cb4fbedca6ab44ecc5a154e3102462bd0a09af https://github.com/galaxyproject/galaxy/commit/27cb4fbedca6ab44ecc5a154e3102... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: R doc/source/admin/chat-0.png R doc/source/admin/chat-1.png R doc/source/admin/chat-2.png R doc/source/admin/chat-3.png R doc/source/admin/chat-4.png R doc/source/admin/chat.rst R doc/source/admin/communication_server.png R doc/source/admin/communication_server_rooms.png R doc/source/admin/grt.rst R doc/source/admin/images_webhooks/history-menu.png R doc/source/admin/images_webhooks/masthead.png R doc/source/admin/images_webhooks/masthead_trans_object.png R doc/source/admin/images_webhooks/tool.png R doc/source/admin/images_webhooks/workflow.png M doc/source/admin/index.rst R doc/source/admin/interactive_environments.png R doc/source/admin/interactive_environments.rst R doc/source/admin/interactive_environments.svg R doc/source/admin/mulled_containers.rst A doc/source/admin/special_topics/chat-0.png A doc/source/admin/special_topics/chat-1.png A doc/source/admin/special_topics/chat-2.png A doc/source/admin/special_topics/chat-3.png A doc/source/admin/special_topics/chat-4.png A doc/source/admin/special_topics/chat.rst A doc/source/admin/special_topics/communication_server.png A doc/source/admin/special_topics/communication_server_rooms.png A doc/source/admin/special_topics/grt.rst A doc/source/admin/special_topics/images_webhooks/history-menu.png A doc/source/admin/special_topics/images_webhooks/masthead.png A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png A doc/source/admin/special_topics/images_webhooks/tool.png A doc/source/admin/special_topics/images_webhooks/workflow.png A doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/interactive_environments.png A doc/source/admin/special_topics/interactive_environments.rst A doc/source/admin/special_topics/interactive_environments.svg A doc/source/admin/special_topics/mulled_containers.rst A doc/source/admin/special_topics/webhooks.rst A doc/source/admin/tool_panel.rst R doc/source/admin/webhooks.rst M doc/source/conf.py M doc/source/dev/index.rst M doc/source/dev/interactive_environments.rst M doc/source/index.rst M doc/source/project/issues.rst Log Message: ----------- Merge pull request #3738 from martenson/admin-docs-from-hub modify our docs in preparation for restructuring Commit: 460d876fc4814ab10badb859b64a05225b04e952 https://github.com/galaxyproject/galaxy/commit/460d876fc4814ab10badb859b64a0... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: A doc/source/admin/authentication.md M doc/source/admin/index.rst Log Message: ----------- Merge pull request #3751 from jmchilton/auth_docs New Authentication section of the docs. Commit: d42848ec9b73a89e1cbe20a3250481bd1b41a93a https://github.com/galaxyproject/galaxy/commit/d42848ec9b73a89e1cbe20a325048... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: A client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Add client view for custom builds, add api endpoint for builds metadata Commit: 0b26d561aabdb5af6e21e8d845f15325e18d8751 https://github.com/galaxyproject/galaxy/commit/0b26d561aabdb5af6e21e8d845f15... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-table.js Log Message: ----------- Align style of table view component to other ui views Commit: 88d4bf204c554c95ca40aa88504198f6705aa9a1 https://github.com/galaxyproject/galaxy/commit/88d4bf204c554c95ca40aa8850419... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M .ci/py3_sources.txt M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py Log Message: ----------- Fix KeyError when getting request and response content-type headers Fix https://github.com/galaxyproject/galaxy/issues/2551 Also fix Python3 compatibility, xref: #1715 Commit: 2a6391550b2256c18f2671b2260f58746b507db7 https://github.com/galaxyproject/galaxy/commit/2a6391550b2256c18f2671b2260f5... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding directed/undirected attribute for graphs Commit: 131aeb66b4884200c6c9433aef9a80aabf98d132 https://github.com/galaxyproject/galaxy/commit/131aeb66b4884200c6c9433aef9a8... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/watcher.py R lib/galaxy/util/postfork.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Abstract uWSGI handling into new galaxy.web.stack package. Commit: 718df44921db25eedf21f5fefb2b4a6ac7bc7792 https://github.com/galaxyproject/galaxy/commit/718df44921db25eedf21f5fefb2b4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: R lib/galaxy/tags/tag_handler.py Log Message: ----------- Prune empty tag handler Commit: 1b5d95a5800aeed632888a42473a7ce24b9623c5 https://github.com/galaxyproject/galaxy/commit/1b5d95a5800aeed632888a42473a7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: R lib/galaxy/tags/__init__.py Log Message: ----------- Remove unused (and empty) tags module. Commit: 0e7a71596d859728600bbf4569cae3bfd85574c9 https://github.com/galaxyproject/galaxy/commit/0e7a71596d859728600bbf4569cae... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M .ci/py3_sources.txt M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py Log Message: ----------- Merge pull request #3757 from nsoranzo/fix_for_2551 Fix KeyError when getting request and response content-type headers Commit: 689560d7db23240df193fc913d8165643eea8cac https://github.com/galaxyproject/galaxy/commit/689560d7db23240df193fc913d816... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Implement and connect client add request with endpoint Commit: 06f61927b5f9f6d35c7c0bdebdd330bae56f6710 https://github.com/galaxyproject/galaxy/commit/06f61927b5f9f6d35c7c0bdebdd33... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Fix delete request, fix error triggered by attempting invalid conversions Commit: 8b5e27aaeae1ac9b35b0959f2cccaa6988d69163 https://github.com/galaxyproject/galaxy/commit/8b5e27aaeae1ac9b35b0959f2ccca... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Add name validator Commit: d2692dc77bdd4db48cbcc77d9cd776e0cd7e8bab https://github.com/galaxyproject/galaxy/commit/d2692dc77bdd4db48cbcc77d9cd77... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-table.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/ui/ui-table.js.map M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-table.js M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Sort custom builds in table Commit: b1b87358e7fdb991cf1ef1b90aabfc8d182304b1 https://github.com/galaxyproject/galaxy/commit/b1b87358e7fdb991cf1ef1b90aabf... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Reset form after submission, highlight missing/failed chrom count Commit: 72b3b8596253500cbbf54bfe7a5415b08f46b14d https://github.com/galaxyproject/galaxy/commit/72b3b8596253500cbbf54bfe7a541... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M lib/galaxy/managers/tags.py M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Fix bug(?) that prevented associating multiple values to a tag. Commit: 200b3837c7956e4ee5b19b01eb67e62375e58e97 https://github.com/galaxyproject/galaxy/commit/200b3837c7956e4ee5b19b01eb67e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) 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: ----------- Remove debug statements for user preferences Commit: 977b1acc48e878fb90a7b52e973ae497052b8583 https://github.com/galaxyproject/galaxy/commit/977b1acc48e878fb90a7b52e973ae... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js Log Message: ----------- Remove duplicate keys from nls locales. Commit: d0eaeff9c4b47b922ae5c764fbe3722603ac1148 https://github.com/galaxyproject/galaxy/commit/d0eaeff9c4b47b922ae5c764fbe37... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/locale.js M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/locale.js Log Message: ----------- Add FR localization template. Needs translation next. Commit: 02327e7085559bd776bfda8743dc99edd2c3f14f https://github.com/galaxyproject/galaxy/commit/02327e7085559bd776bfda8743dc9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: A client/galaxy/scripts/nls/fr/locale.js A static/maps/nls/fr/locale.js.map A static/scripts/nls/fr/locale.js Log Message: ----------- Add FR localization template (the actual files). Needs translation next. Commit: e7b1d45a3990ce6db9fcdaa92dac6a18cb605345 https://github.com/galaxyproject/galaxy/commit/e7b1d45a3990ce6db9fcdaa92dac6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Add some basic (likely awful) FR translations just to check the machinery here. Commit: d7e4e8e162bbeb071e83d08bd22f17b8bc59602f https://github.com/galaxyproject/galaxy/commit/d7e4e8e162bbeb071e83d08bd22f1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Readability formatting for existing locales to set a standard moving forward. Commit: d4462cb3213e81c2d25b7575ca3865c7720437fd https://github.com/galaxyproject/galaxy/commit/d4462cb3213e81c2d25b7575ca386... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) 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: ----------- Localization support for menu. Commit: 4f82467117d12fe6bab70fb96e769d3c89d9c212 https://github.com/galaxyproject/galaxy/commit/4f82467117d12fe6bab70fb96e769... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- FR locale masthead support. Commit: 2ebf46effae518fc9d0dc1c574d2d5a30407b3ce https://github.com/galaxyproject/galaxy/commit/2ebf46effae518fc9d0dc1c574d2d... Author: Bérénice Batut <berenice.batut@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Correct some translation errors Commit: f7cb5b70fc6ba0142b88a467f8a06889a0c7911a https://github.com/galaxyproject/galaxy/commit/f7cb5b70fc6ba0142b88a467f8a06... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #10 from dannon/bebatut-patch-1 Correct some translation errors Commit: f174358b9542610ffa4c00588096a4e80583ae0a https://github.com/galaxyproject/galaxy/commit/f174358b9542610ffa4c00588096a... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M doc/source/releases/_header.rst Log Message: ----------- fix link to galaxy logo Commit: 85093dc13ad06eb8d4896f01d934846cd57c1473 https://github.com/galaxyproject/galaxy/commit/85093dc13ad06eb8d4896f01d9348... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M doc/source/admin/useful_scripts.rst Log Message: ----------- reword topic Commit: e02e2cb09e245ab5cbbe48d532e4f3ffe9a1612a https://github.com/galaxyproject/galaxy/commit/e02e2cb09e245ab5cbbe48d532e4f... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M doc/source/index.rst Log Message: ----------- improve doc-build-urself docs Commit: 9f42821f57c3126826ebc773407ac02084a965ea https://github.com/galaxyproject/galaxy/commit/9f42821f57c3126826ebc773407ac... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding Breadth First Search for cytoscape graphs. Tapping any node plays BFS Commit: 15273ad1489c9cdc216126ff36c2ec2d912e4165 https://github.com/galaxyproject/galaxy/commit/15273ad1489c9cdc216126ff36c2e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) 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/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Add uploader element Commit: bb5b8cf525562e1a930ad03a4071dffd341865e5 https://github.com/galaxyproject/galaxy/commit/bb5b8cf525562e1a930ad03a4071d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Declare submit caller for upload element Commit: 474b0c1d2ceade095fd995d19ba30334be612458 https://github.com/galaxyproject/galaxy/commit/474b0c1d2ceade095fd995d19ba30... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Sort models in table, fix message parameter, properly return models with count attribute Commit: 39c9f79970579556eac63c12d40174ee95e2c337 https://github.com/galaxyproject/galaxy/commit/39c9f79970579556eac63c12d4017... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Improve error handling, add success and warning messages Commit: 4180d2e08841628753a65966143c58d6c5630d90 https://github.com/galaxyproject/galaxy/commit/4180d2e08841628753a65966143c5... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Fix success message Commit: 542a84afd5552b94bfdaff4ca8a6c0c368f1489a https://github.com/galaxyproject/galaxy/commit/542a84afd5552b94bfdaff4ca8a6c... Author: lecorguille <lecorguille@users.noreply.github.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- first pass Commit: c4f906cb729e08412924186726dfaba12bf2f2d8 https://github.com/galaxyproject/galaxy/commit/c4f906cb729e08412924186726dfa... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #11 from lecorguille/i18n first pass Commit: 59526d82e8c1ce8e796b461d3e69eb8c03cc3030 https://github.com/galaxyproject/galaxy/commit/59526d82e8c1ce8e796b461d3e69e... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M README.rst Log Message: ----------- update logo URL Commit: caf0675176ae9b8a0b578fb8de3cba97695e9ad4 https://github.com/galaxyproject/galaxy/commit/caf0675176ae9b8a0b578fb8de3cb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M README.rst Log Message: ----------- Merge pull request #3768 from martenson/logo-url-update update logo URL Commit: 986134d766e69344c511e2627739a51f9d8cf044 https://github.com/galaxyproject/galaxy/commit/986134d766e69344c511e2627739a... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M scripts/secret_decoder_ring.py Log Message: ----------- Should exit immediately to avoid index error Commit: 90de3671f132848a9eaae9048bf091f1969d0caf https://github.com/galaxyproject/galaxy/commit/90de3671f132848a9eaae9048bf09... Author: Yvan Le Bras <yvan.le_bras@irisa.fr> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- pass 2 Commit: face53037d476bbc59e4674f861e903c23d52109 https://github.com/galaxyproject/galaxy/commit/face53037d476bbc59e4674f861e9... Author: Yvan Le Bras <yvan.le_bras@irisa.fr> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- pass 2 from Gildas Commit: 6b38ccada116ce2445a9bfc6fb513b54feacb65b https://github.com/galaxyproject/galaxy/commit/6b38ccada116ce2445a9bfc6fb513... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Uncomment and format FR localization. Commit: 9704b73500db07fde28c778a9977c6aa22aa237a https://github.com/galaxyproject/galaxy/commit/9704b73500db07fde28c778a9977c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Build client. Commit: 78074243d734c81891795d3ad25dffbe70130a29 https://github.com/galaxyproject/galaxy/commit/78074243d734c81891795d3ad25df... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) 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: ----------- Forgot localization for 'Login' Commit: eaf631efbfe7dc7b0624ded57adb4410dab93f30 https://github.com/galaxyproject/galaxy/commit/eaf631efbfe7dc7b0624ded57adb4... Author: lecorguille <lecorguille@users.noreply.github.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- second pass Commit: 4f749098d56b282125bf5644620f0bf5a273e5a3 https://github.com/galaxyproject/galaxy/commit/4f749098d56b282125bf5644620f0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M scripts/secret_decoder_ring.py Log Message: ----------- Merge pull request #3770 from erasche/index-error Should exit immediately to avoid index error Commit: 6d803463318a721bab91d4458fc8b1da540cc091 https://github.com/galaxyproject/galaxy/commit/6d803463318a721bab91d4458fc8b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #14 from lecorguille/i18npass2 second pass Commit: 0221bdf9c71b5567af8928a121d62970850fa8c2 https://github.com/galaxyproject/galaxy/commit/0221bdf9c71b5567af8928a121d62... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- One last rebuild w/ final changes. Commit: 11ee6ea6384e3fde47fb0eb10d466461ffc050ee https://github.com/galaxyproject/galaxy/commit/11ee6ea6384e3fde47fb0eb10d466... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) 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 'logged in as' localization usage. Commit: fe35ed009e72a65b0e120d4d29c8614652560db1 https://github.com/galaxyproject/galaxy/commit/fe35ed009e72a65b0e120d4d29c86... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Fix localization of Preferences Commit: 576ad4f95aa50fa80aa1de993bcbf03da5d2da98 https://github.com/galaxyproject/galaxy/commit/576ad4f95aa50fa80aa1de993bcbf... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- Add preferences to core translations, update search datasets Commit: af849e506257419f73dbac58d7618bc00104b60c https://github.com/galaxyproject/galaxy/commit/af849e506257419f73dbac58d7618... Author: lecorguille <lecorguille@users.noreply.github.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- fix Yvan integration :P Commit: dc201094aa3cf07967f1c16ae6bef88718476e37 https://github.com/galaxyproject/galaxy/commit/dc201094aa3cf07967f1c16ae6bef... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Duplicated word in localization Commit: 8aaee3d33b378a8fd9d29b90f9003b0217c7ad43 https://github.com/galaxyproject/galaxy/commit/8aaee3d33b378a8fd9d29b90f9003... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #15 from lecorguille/i18npass3 Fix Yvan integration :P Commit: cc37049af8c08e50e6ca81ce83f93f35a0711c6e https://github.com/galaxyproject/galaxy/commit/cc37049af8c08e50e6ca81ce83f93... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge branch 'i18n' of github.com:dannon/galaxy into i18n Commit: ae049fe54068408866265ad2f040ee5b0aa8a763 https://github.com/galaxyproject/galaxy/commit/ae049fe54068408866265ad2f040e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Merge more fixes, rebuild. Commit: f5844252ae9feee554342e69562c3ae65985bb82 https://github.com/galaxyproject/galaxy/commit/f5844252ae9feee554342e69562c3... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Attempt to determine line count upon file upload to allow early validation Commit: aea96855bb5da18623c51ab6e6885f5c9acaf19e https://github.com/galaxyproject/galaxy/commit/aea96855bb5da18623c51ab6e6885... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) 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/user-custom-builds.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Merge branch 'add_uploader' into remove_custom_builds_mako Commit: a2affcc618ae5ec8d0f36e55a0f7ef15de53ef68 https://github.com/galaxyproject/galaxy/commit/a2affcc618ae5ec8d0f36e55a0f7e... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding Depth First Search for cytoscape graphs Commit: e78e1607db1eacc175c8f731cdb879fe3e293476 https://github.com/galaxyproject/galaxy/commit/e78e1607db1eacc175c8f731cdb87... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Upload and preview file using HTML5, client-side file reader Commit: b557e31a4c29fcab875837c1ccc3c9cd9f37f6ba https://github.com/galaxyproject/galaxy/commit/b557e31a4c29fcab875837c1ccc3c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Fix form reset, remove debug statements Commit: abe156783a7305a8341e217ece31500c36631232 https://github.com/galaxyproject/galaxy/commit/abe156783a7305a8341e217ece315... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.js.map M static/scripts/mvc/user/user-custom-builds.js Log Message: ----------- Set default to fasta selection Commit: d50ca25a822a48e58b08c404fca1c25dfdc2bbd3 https://github.com/galaxyproject/galaxy/commit/d50ca25a822a48e58b08c404fca1c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Merge pull request #3729 from mvdbeek/cleanup_tool_cache Remove outdated items from tool cache when reloading the toolbox Commit: 95b6f033a447d25b5826a4e368caf2fc15201d10 https://github.com/galaxyproject/galaxy/commit/95b6f033a447d25b5826a4e368caf... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Display installed builds as searchable list Commit: 6b2a4ebd3653f25ef01e109ac7bdad601d6959a5 https://github.com/galaxyproject/galaxy/commit/6b2a4ebd3653f25ef01e109ac7bda... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Len-file hdas not needed in metadata Commit: 72cd0ba00ad05793751105dccf434c9868791b2a https://github.com/galaxyproject/galaxy/commit/72cd0ba00ad05793751105dccf434... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Adjust link to the new Galaxy HUB site Commit: b4fda2ccd49fd7b406a5521bce3243ff6ffb7950 https://github.com/galaxyproject/galaxy/commit/b4fda2ccd49fd7b406a5521bce324... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Merge pull request #16 from bgruening/wf_link /learn/advanced-workflow/variables-edit Commit: 39c1b1b24998d9ce77d660ad5dee525f71156720 https://github.com/galaxyproject/galaxy/commit/39c1b1b24998d9ce77d660ad5dee5... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Render len type help section Commit: 031ce2307367f021646c2a1640112599320076fc https://github.com/galaxyproject/galaxy/commit/031ce2307367f021646c2a1640112... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Merge pull request #3742 from jmchilton/galaxy-lib-20170311 Mirror latest galaxy-lib changes for Conda and CWL improvements. Commit: 76bcf23b434984cd45002192a72bb90d3c06ade5 https://github.com/galaxyproject/galaxy/commit/76bcf23b434984cd45002192a72bb... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Add help section content Commit: ad73c7d39d93683aba1b065b6660c4b5a98554bf https://github.com/galaxyproject/galaxy/commit/ad73c7d39d93683aba1b065b6660c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: R templates/user/dbkeys.mako Log Message: ----------- Remove mako Commit: 5ee585c681326072c489f26d2d2b084a6995a349 https://github.com/galaxyproject/galaxy/commit/5ee585c681326072c489f26d2d2b0... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Remove controller endpoint Commit: ff5166c2930f54a05601ab9a934319689df9c3f8 https://github.com/galaxyproject/galaxy/commit/ff5166c2930f54a05601ab9a93431... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M lib/galaxy/webapps/galaxy/controllers/user.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: ----------- Redirect masthead link to new custom builds ui Commit: a89a4f726ba60110810c99b372a53b48e9152c4e https://github.com/galaxyproject/galaxy/commit/a89a4f726ba60110810c99b372a53... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Revise style Commit: 72c96bd5c6c6c3c1dea3a662dd2fa2d802822401 https://github.com/galaxyproject/galaxy/commit/72c96bd5c6c6c3c1dea3a662dd2fa... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-18 (Sat, 18 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-custom-builds.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/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Hide select field if local fields are unavailable Commit: c658ef3c7efd56986c096dc71a73c06260351ccc https://github.com/galaxyproject/galaxy/commit/c658ef3c7efd56986c096dc71a73c... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-19 (Sun, 19 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/utils.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding Kruskal algorithm for graphs and color choosing scheme for highlighted edges Commit: 8e77fe93b8e0b1eae57d454adc13a86a376bae35 https://github.com/galaxyproject/galaxy/commit/8e77fe93b8e0b1eae57d454adc13a... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/managers/tags.py R lib/galaxy/tags/__init__.py R lib/galaxy/tags/tag_handler.py M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #3760 from dannon/nametag_fixes Tagging tweaks Commit: b1f12d41f66c2b07929c037363fc6d94b890b283 https://github.com/galaxyproject/galaxy/commit/b1f12d41f66c2b07929c037363fc6... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Simplify run_test_wrapper.sh per @natefoo comments. https://github.com/galaxyproject/galaxy/pull/3755/files#r106182107 Commit: 024e296ea8fa6dc7c3b3da3e74ac9e520e8daf73 https://github.com/galaxyproject/galaxy/commit/024e296ea8fa6dc7c3b3da3e74ac9... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/managers/datasets.py Log Message: ----------- Re-use job.finish abstraction in dataset manager stop_creating_job. It is used in purge a bit above and it is the better abstraction. Commit: f153400e95ff3888fab1b6c0fb7be5686a882532 https://github.com/galaxyproject/galaxy/commit/f153400e95ff3888fab1b6c0fb7be... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Rework jobs API to not use deprecated TestsDatasets mixin. Commit: cd36aa0878aed1a604a256098241068df169e4a3 https://github.com/galaxyproject/galaxy/commit/cd36aa0878aed1a604a2560982410... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M run_tests.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #3755 from jmchilton/docker_test_fixes Assorted Fixes for Dockerized Test Setup Commit: d18b4d13cbc25c85005e4b19a02abedbed7aba46 https://github.com/galaxyproject/galaxy/commit/d18b4d13cbc25c85005e4b19a02ab... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py Log Message: ----------- Add an exception for unsupported middleware wrapping for better failure handling. Commit: 0602712a35015bba52f3bc756b0ce0fa1c20728e https://github.com/galaxyproject/galaxy/commit/0602712a35015bba52f3bc756b0ce... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M scripts/api/README Log Message: ----------- deduplicate obsolete API readme Commit: 009e2cbf5e9592fd8af782b2cde36d8d1687c003 https://github.com/galaxyproject/galaxy/commit/009e2cbf5e9592fd8af782b2cde36... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/datasets.py M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Improve interaction between job state and purged datasets. There are two basic behavior changes here and bunch of testing to verify the new behaviors. 1) Previously purging a dataset would cause a creating job to be cancelled but all outputs would need to be "deleted" in order to cause the creating job to be cancelled. After this change the behavior is the same for both deletion and purging - the job will run until all outputs are deleted or purged. 2) Previously Galaxy jobs wouldn't attempt to cleanup purged datasets that were created by a running tool - this cleanup now occurs. These are tackled as a pair because I assume the difference in the behaviors between deletion and purging was a hack around tools populating datasets that had been purged while running. Cancelling the job wasn't a sure fix - but it would reduce the likelihood of such problems. I think the new approach is a bit more robust and explicit. Commit: 0d95b4e2079aa0d442a2e030fe7606c7627bd1e6 https://github.com/galaxyproject/galaxy/commit/0d95b4e2079aa0d442a2e030fe760... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding graph traversal types Commit: cbc7dd17fcf3bfe9eecdd8a0577a6d63e565f509 https://github.com/galaxyproject/galaxy/commit/cbc7dd17fcf3bfe9eecdd8a0577a6... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Removing unused if else Commit: 5440889bf6a7c5f278860760cd8c4ba18708c263 https://github.com/galaxyproject/galaxy/commit/5440889bf6a7c5f278860760cd8c4... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/watcher.py R lib/galaxy/util/postfork.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Merge pull request #3759 from natefoo/abstract-app-stack Abstract uWSGI handling into new galaxy.web.stack package Commit: 18cb50ecea80b3feeac02a2ef07c4cbd816c39d4 https://github.com/galaxyproject/galaxy/commit/18cb50ecea80b3feeac02a2ef07c4... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js A static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/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 A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Abstraction for re-use between collection creators. The new mixin reduces the duplication between the list and list of paired collection creators. I'd like to add functionality related to hiding the original datasets (especially useful for direct upload of collections but previously requested also) but I'd like to reduce the duplication related to doing that first. This is a start in that direction. Commit: d9f21fd34c059d422e63d31e9fb94660e826c4ff https://github.com/galaxyproject/galaxy/commit/d9f21fd34c059d422e63d31e9fb94... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Only fail through to client mapping when it exists. Commit: 3921aa573c0fa7b900316cdad4d06e23c02b19b2 https://github.com/galaxyproject/galaxy/commit/3921aa573c0fa7b900316cdad4d06... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M scripts/api/README Log Message: ----------- Merge pull request #3777 from martenson/dedup-readme deduplicate obsolete API readme Commit: 5428d39adb6bf37c61b8c17efb1b3157e0b242d2 https://github.com/galaxyproject/galaxy/commit/5428d39adb6bf37c61b8c17efb1b3... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py Log Message: ----------- Merge pull request #3753 from blankclemens/webhook_tool_list Webhook plugin: tool_list Commit: 61677d2026f155868ad57a1289609c1aad1044e6 https://github.com/galaxyproject/galaxy/commit/61677d2026f155868ad57a1289609... Author: nekrut <anton@nekrut.org> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml Log Message: ----------- made collection ops help sections slightly more readable Commit: 9ecb71ecf76df08fee7829e28db081ec2dc3fb0a https://github.com/galaxyproject/galaxy/commit/9ecb71ecf76df08fee7829e28db08... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Build toolbox_requirements_status only once (thanks for the review @nsoranzo) Commit: 69e2af50317abefa98748b8fc84db2870552b589 https://github.com/galaxyproject/galaxy/commit/69e2af50317abefa98748b8fc84db... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Restore render_tool_centric_table function Commit: a5b0e760503dc09ac99d47bbcde1524c7f3e37a4 https://github.com/galaxyproject/galaxy/commit/a5b0e760503dc09ac99d47bbcde15... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js A static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/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 A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #3781 from jmchilton/collection-builders Abstraction for re-use between collection creators. Commit: 7a6579878a09862e1cd5919ba7d94c527f3b0e56 https://github.com/galaxyproject/galaxy/commit/7a6579878a09862e1cd5919ba7d94... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix markup and add a stylistic space Commit: a8d0c46ee97b37df20ac2022af4309890ca0c6e0 https://github.com/galaxyproject/galaxy/commit/a8d0c46ee97b37df20ac2022af430... Author: Anton Nekrutenko <anekrut@gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/unzip_collection.xml Log Message: ----------- Update unzip_collection.xml fixed typos identified by @mvdbeek Commit: 234361253a168eaf4b4c86fe4a1963a511271c86 https://github.com/galaxyproject/galaxy/commit/234361253a168eaf4b4c86fe4a196... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M 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lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/mapper.js A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py R lib/galaxy_utils/__init__.py R lib/galaxy_utils/sequence/__init__.py R lib/galaxy_utils/sequence/fasta.py R lib/galaxy_utils/sequence/fastq.py R lib/galaxy_utils/sequence/sequence.py R lib/galaxy_utils/sequence/transform.py R lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M scripts/api/README M scripts/bootstrap_history.py A scripts/secret_decoder_ring.py M scripts/slideshow/slideshow_template.html A static/maps/analysis.js.map A static/maps/app.js.map A static/maps/app/analysis.js.map M static/maps/galaxy.interactive_environments.js.map M static/maps/layout/menu.js.map M static/maps/libs/jquery/jquery.autocomplete.js.map A static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map R 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static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/layout/menu.js M static/scripts/libs/jquery/jquery.autocomplete.js A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/user/user-quotameter.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/ui/autocom_tagging.js M static/style/blue/base.css M templates/admin/reload_tool.mako M templates/grid_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/tool_form.mako M test/TESTING.md M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/populators.py M test/docker/base/run_test_wrapper.sh A test/functional/tools/mulled_example_multi_incomplete.xml A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/integration/test_resolvers.py M test/qunit/tests/form_tests.js M test/selenium_tests/framework.py A test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_uploads.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into add_hdca_to_library Commit: 3dcd174f2b2f0e78d58b3e9d7e19103bd299b128 https://github.com/galaxyproject/galaxy/commit/3dcd174f2b2f0e78d58b3e9d7e191... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- repack Commit: eadbb16462f2bd6f6f8f8cf71d992f0c5389c80f https://github.com/galaxyproject/galaxy/commit/eadbb16462f2bd6f6f8f8cf71d992... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml Log Message: ----------- Merge pull request #3784 from nekrut/collection_ops_help_fixes made collection ops help sections slightly more readable Commit: 279548574136817c226fad61c52168cfab199fb8 https://github.com/galaxyproject/galaxy/commit/279548574136817c226fad61c5216... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js M test/api/test_libraries.py Log Message: ----------- Merge pull request #3559 from mvdbeek/add_hdca_to_library Add possibility to load collection into library Commit: 7873aac2edb003fa073efc1249884d7b25c9028f https://github.com/galaxyproject/galaxy/commit/7873aac2edb003fa073efc1249884... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M .ci/py3_sources.txt M README.rst A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py A doc/source/admin/authentication.md R doc/source/admin/chat-0.png R doc/source/admin/chat-1.png R doc/source/admin/chat-2.png R doc/source/admin/chat-3.png R doc/source/admin/chat-4.png R doc/source/admin/chat.rst R doc/source/admin/communication_server.png R doc/source/admin/communication_server_rooms.png R doc/source/admin/grt.rst R doc/source/admin/images_webhooks/history-menu.png R doc/source/admin/images_webhooks/masthead.png R doc/source/admin/images_webhooks/masthead_trans_object.png R doc/source/admin/images_webhooks/tool.png R doc/source/admin/images_webhooks/workflow.png M doc/source/admin/index.rst R doc/source/admin/interactive_environments.png R doc/source/admin/interactive_environments.rst R doc/source/admin/interactive_environments.svg R doc/source/admin/mulled_containers.rst A doc/source/admin/special_topics/chat-0.png A doc/source/admin/special_topics/chat-1.png A doc/source/admin/special_topics/chat-2.png A doc/source/admin/special_topics/chat-3.png A doc/source/admin/special_topics/chat-4.png A doc/source/admin/special_topics/chat.rst A doc/source/admin/special_topics/communication_server.png A doc/source/admin/special_topics/communication_server_rooms.png A doc/source/admin/special_topics/grt.rst A doc/source/admin/special_topics/images_webhooks/history-menu.png A doc/source/admin/special_topics/images_webhooks/masthead.png A 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lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml R lib/galaxy/util/postfork.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/tool_shed/galaxy_install/update_repository_manager.py M run_tests.sh M scripts/api/README M scripts/secret_decoder_ring.py A static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/library/library-foldertoolbar-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 A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M test/api/test_libraries.py M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako Commit: 2872a31881f2f404b2962464ffb734065e96d1b3 https://github.com/galaxyproject/galaxy/commit/2872a31881f2f404b2962464ffb73... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/style/less/ui.less M static/maps/mvc/user/user-custom-builds.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-custom-builds.js M static/style/blue/base.css Log Message: ----------- Move styles out of code file Commit: 79b26d2273d46250b55f04eb6c1e0a0c03bf65bf https://github.com/galaxyproject/galaxy/commit/79b26d2273d46250b55f04eb6c1e0... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Fix collection operations not having a history. Fixes #3437. Commit: 269aac614b5d19ffbfc3ec1ad7e4330ba9c0b847 https://github.com/galaxyproject/galaxy/commit/269aac614b5d19ffbfc3ec1ad7e43... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Apply some suggested FR localization wording changes. Commit: 3036df35f0f5089cfbfc69ecdc46dcf057a3d6bf https://github.com/galaxyproject/galaxy/commit/3036df35f0f5089cfbfc69ecdc46d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Avoid potential inconsistencies between differently stored labels Commit: 54af1979676c817b00044e645383e638b86fdcfa https://github.com/galaxyproject/galaxy/commit/54af1979676c817b00044e645383e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- Add more translation points for localization. Commit: 8eb40ae7fb9d59586e40a7a85abdf5e222c903bd https://github.com/galaxyproject/galaxy/commit/8eb40ae7fb9d59586e40a7a85abdf... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-21 (Tue, 21 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Correct 'Get Data' usage, since we won't be translating that in the first pass Commit: 3ed60db5ce9bf2acb954c843c14f8983b11ffbd9 https://github.com/galaxyproject/galaxy/commit/3ed60db5ce9bf2acb954c843c14f8... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: lib/galaxy/tools/deps/container_resolvers/__init__.py static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Commit: 10ddd3d3bdb238f1ff0de26326fcaca07c81a316 https://github.com/galaxyproject/galaxy/commit/10ddd3d3bdb238f1ff0de26326fca... Author: lecorguille <lecorguille@users.noreply.github.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- new points Commit: 2eefe8571a00497c6faefff64cf86224bae05825 https://github.com/galaxyproject/galaxy/commit/2eefe8571a00497c6faefff64cf86... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Fix usage of _.extend in joint collection builder templates. Fixes bug introduced in #3781. #minor Commit: 390adffb988ff4f1c6b723e4f5776ed5186c26bb https://github.com/galaxyproject/galaxy/commit/390adffb988ff4f1c6b723e4f5776... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #17 from lecorguille/i18n_history_options new points history options Commit: f8950feb30ca3caa94d48f487d9d7079839143a0 https://github.com/galaxyproject/galaxy/commit/f8950feb30ca3caa94d48f487d9d7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #3799 from jmchilton/fix_extend_usage Fix usage of _.extend in joint collection builder templates. Commit: c58fa9a349ce4432f1febd5f530fc4afdd4893bd https://github.com/galaxyproject/galaxy/commit/c58fa9a349ce4432f1febd5f530fc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M .ci/py3_sources.txt M README.rst A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py R lib/galaxy/tags/__init__.py R lib/galaxy/tags/tag_handler.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/filter_failed_collection.xml M lib/galaxy/tools/flatten_collection.xml M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/unzip_collection.xml M lib/galaxy/tools/zip_collection.xml R lib/galaxy/util/postfork.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/sentry.py A lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/util.py M lib/tool_shed/galaxy_install/update_repository_manager.py M run_tests.sh M scripts/api/README M scripts/secret_decoder_ring.py A static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/nls/fr/locale.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 A static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/nls/fr/locale.js R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/api/test_libraries.py M test/docker/base/run_test_wrapper.sh M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Rebuild client and merge from upstream. Commit: 9d736dd42eba2e8bd116d575c7d1278e15183ba3 https://github.com/galaxyproject/galaxy/commit/9d736dd42eba2e8bd116d575c7d12... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py Log Message: ----------- Fix container resolution. Without these decorators swapped - resolving containers results in the following Exception: ``` TypeError: unbound method __str__() must be called with ContainerResolver instance as first argument (got nothing instead) ``` I think this recent merge commit 3ed60db5ce9bf2acb954c843c14f8983b11ffbd9 introduced this problem as it merged the two decorators together. Commit: 2fc18675dbfd66a296006bb4ef90d57bdde4d5dc https://github.com/galaxyproject/galaxy/commit/2fc18675dbfd66a296006bb4ef90d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Debug Commit: 8a033b720b370a7e7e9049fa22a5c7a78f0d5a85 https://github.com/galaxyproject/galaxy/commit/8a033b720b370a7e7e9049fa22a5c... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py Log Message: ----------- Merge pull request #3805 from jmchilton/container_resolution_fix Fix container resolution. Commit: 71b09b49a7541789909b1617e661e0252573453a https://github.com/galaxyproject/galaxy/commit/71b09b49a7541789909b1617e661e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Fix label, fix dataset id parsing Commit: ef2353a1423586845da9d19c5780f298db742b1c https://github.com/galaxyproject/galaxy/commit/ef2353a1423586845da9d19c5780f... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Add len id for converted datasets to dbkey attributes Commit: afbb3b5a1e26a0a3e9698cec71ed5d733189d451 https://github.com/galaxyproject/galaxy/commit/afbb3b5a1e26a0a3e9698cec71ed5... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Add additional error message for fasta conversions Commit: 368b276ded599e7f0c206b852cdd901199b16b7e https://github.com/galaxyproject/galaxy/commit/368b276ded599e7f0c206b852cdd9... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Parse correct dataset id Commit: 50283125ea37f313afdfd0d69b92a0380fc77e17 https://github.com/galaxyproject/galaxy/commit/50283125ea37f313afdfd0d69b92a... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M test/shed_functional/functional/test_1150_datatype_converters.py Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako Commit: 76bd515879d4353bff066d0b2526d68d86cdff56 https://github.com/galaxyproject/galaxy/commit/76bd515879d4353bff066d0b2526d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix lint Commit: b0325cef02f995a589dc14425d1ae73d7ef4cfee https://github.com/galaxyproject/galaxy/commit/b0325cef02f995a589dc14425d1ae... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Post determine fasta results Commit: 7457b7611513159551a604afe13927a1a50dc6da https://github.com/galaxyproject/galaxy/commit/7457b7611513159551a604afe1392... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #3807 from galaxyproject/release_17.01 Merge Release 17.01 in Dev Commit: 9e807dab3f7b98e77ca2358e1204a6220879764c https://github.com/galaxyproject/galaxy/commit/9e807dab3f7b98e77ca2358e1204a... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M static/maps/layout/menu.js.map A static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js A static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js Log Message: ----------- Merge pull request #3762 from dannon/i18n i18n improvements and French localization Commit: 7fdb4064c6194534cb654f1afd5d9b5e9dd98ef3 https://github.com/galaxyproject/galaxy/commit/7fdb4064c6194534cb654f1afd5d9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Trim down one translation, thanks @mvdbeek Commit: 3a52d07a900f4d4fa9933bbccce1efe76708988d https://github.com/galaxyproject/galaxy/commit/3a52d07a900f4d4fa9933bbccce1e... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Merge pull request #3809 from dannon/minor_wording_tweak One minor translation followup tweak to French Localization Commit: a3b16bf69a4d6f09b9693ffbc6a54ed0910918e9 https://github.com/galaxyproject/galaxy/commit/a3b16bf69a4d6f09b9693ffbc6a54... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M run_tests.sh M test/qunit/package.json Log Message: ----------- Small improvements to Qunit tests. - Drop explicit requirement on phantomjs since we are moving away from explicit phantomjs testing (it is still pulled in by QUnit which is fine). - If ``npm install .`` has previously been executed from the ``test/qunit``, don't require globally available grunt to run the tests via ``run_tests.sh -q``. Commit: ca36c0dbfd438708e35e18d06c603f2cc2ce7047 https://github.com/galaxyproject/galaxy/commit/ca36c0dbfd438708e35e18d06c603... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js 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.map M static/scripts/mvc/tool/tools.js Log Message: ----------- Have tool-search listen to change as well as keyup Commit: 0ced044897bc40f28b758e53b1019c422ea0410a https://github.com/galaxyproject/galaxy/commit/0ced044897bc40f28b758e53b1019... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_uploads.py Log Message: ----------- Flush out upload tests for Selenium. - Use newer abstraction in the simplest upload test - verify the default extension (auto -> sam) and dbkey (?) also. - Add a test case that explicitly sets the extension of an upload and verifies. - Add a test case that explicitly sets a genome and verifies. - Add a test case that tests setting ext for all uploads and verifies. - Add a test case that tests setting genome for all uploads and verifies. Commit: 9e61aff69314606bff4ad16d502295cfdcb0ed07 https://github.com/galaxyproject/galaxy/commit/9e61aff69314606bff4ad16d50229... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M run_tests.sh M test/qunit/package.json Log Message: ----------- Merge pull request #3810 from jmchilton/qunit_touchup Small improvements for driving Qunit tests. Commit: 3b7d44e6f7b773218fad0820464efa4610130938 https://github.com/galaxyproject/galaxy/commit/3b7d44e6f7b773218fad0820464ef... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix message margin in left column Commit: 4a0f00fc1e3f383450968a9732edb479378f82ac https://github.com/galaxyproject/galaxy/commit/4a0f00fc1e3f383450968a9732edb... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/users.py M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Trigger jobs when custom build has been added, check for linecount file on reload Commit: 95be12787ace869bf01f6c30e4b62ba7a4739c96 https://github.com/galaxyproject/galaxy/commit/95be12787ace869bf01f6c30e4b62... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M lib/galaxy/jobs/runners/__init__.py M run_tests.sh M static/maps/layout/menu.js.map A static/maps/nls/fr/locale.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/nls/zh/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js A static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M test/qunit/package.json Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako Commit: fbd8507e3a34e8f46545c1bf4869f179e03dde4e https://github.com/galaxyproject/galaxy/commit/fbd8507e3a34e8f46545c1bf4869f... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3793 from guerler/store_label_in_step Avoid potential inconsistencies between differently stored labels Commit: b82d7311c1034afa32a5ce3caa8aaa44b63d4bb9 https://github.com/galaxyproject/galaxy/commit/b82d7311c1034afa32a5ce3caa8aa... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Merge pull request #3786 from jmchilton/zip_edit Fix collection operations not having a history. Commit: 5e97c017b980cb7d478b5d17837f7438727e7551 https://github.com/galaxyproject/galaxy/commit/5e97c017b980cb7d478b5d17837f7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-23 (Thu, 23 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #3811 from jmchilton/upload_tests Implement more upload testing in Selenium. Commit: 18a26c5f376b9c7be07f0998e817ef6262fc22c2 https://github.com/galaxyproject/galaxy/commit/18a26c5f376b9c7be07f0998e817e... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako Log Message: ----------- Merge pull request #3699 from shiltemann/ethercalc Ethercalc Interactive Environment Commit: d270a21908a8b1d203ac653d96177ae921cb5a5d https://github.com/galaxyproject/galaxy/commit/d270a21908a8b1d203ac653d96177... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/history/history-view-edit.js M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/selenium_tests/test_collection_builders.py Log Message: ----------- Allow non-ready jobs in collection builder. This includes two parallel changes to the Selenium tests. - It adds a decorator to allow retrying certain atomic actions that may occur during jQuery transitions automatically. - It refactors things to allow waiting on HIDs to become visible instead of just green. Commit: 3d13a2bb4f75f2224f24511aa96c9f97d8ff3e44 https://github.com/galaxyproject/galaxy/commit/3d13a2bb4f75f2224f24511aa96c9... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Fix transiently failing Selenium test of tool form re-running. Reworks addition of staleness checkers introduced in #3780. Commit: c9d06aeb41d9e15c07dddf4fff67630f2ee2237d https://github.com/galaxyproject/galaxy/commit/c9d06aeb41d9e15c07dddf4fff676... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M test/api/test_history_contents.py Log Message: ----------- Allow collection creation API to hide original datasets during creation. Commit: 5fa546749bcc7b5a8c2579c46a1360217d4883c8 https://github.com/galaxyproject/galaxy/commit/5fa546749bcc7b5a8c2579c46a136... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/style/less/ui/paired-collection-creator.less M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/style/blue/base.css Log Message: ----------- Allow collection builders to hide original datasets. Commit: 82ca6931c02b1a4b13fe9dc4e86c7ace6029f5d5 https://github.com/galaxyproject/galaxy/commit/82ca6931c02b1a4b13fe9dc4e86c7... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py Log Message: ----------- More test cases for collection builders. - Add test case for building paired lists. - Add tests for new hide original datasets functionality for lists and paired lists. Commit: ad68b154d4cbecdbc2e96e58d9d3c4153e014eeb https://github.com/galaxyproject/galaxy/commit/ad68b154d4cbecdbc2e96e58d9d3c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M test/unit/tools/test_toolbox.py Log Message: ----------- Make ToolConfWatcher watch ToolCache If any item in the tool cache has changed (local tool update, repository update, tool deleted) the toolbox will be reloaded and any tool changes are applied. Should fix https://github.com/galaxyproject/galaxy/issues/3813. Commit: c91c988c852e5a30e1c7c69168b5df770933dcd5 https://github.com/galaxyproject/galaxy/commit/c91c988c852e5a30e1c7c69168b5d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M test/unit/tools/test_watcher.py Log Message: ----------- Fix ToolConfWatcher test: can only watch existing files Commit: 5be7ebe780b487175563eb4661955a07df1d30cd https://github.com/galaxyproject/galaxy/commit/5be7ebe780b487175563eb4661955... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py M test/unit/tools/test_toolbox.py Log Message: ----------- Only call tool_cache.cleanup if tool_cache exists Commit: 4d9cf642a80025e28ea0276f8c41fcd9d9a53903 https://github.com/galaxyproject/galaxy/commit/4d9cf642a80025e28ea0276f8c41f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix toolshed startup by setting tool_cache to `None` (the toolshed loads an empty toolbox) Commit: 0bf2493233fd0afbc07da6620740536938d8d059 https://github.com/galaxyproject/galaxy/commit/0bf2493233fd0afbc07da66207405... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Wrap tool_cache cleanup in try/except clause Commit: 50417de1b4971db4fe42b1c797024081c66deef5 https://github.com/galaxyproject/galaxy/commit/50417de1b4971db4fe42b1c797024... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding A* search algorithm for finding shortest distance between root and destination Commit: 197aa402d72895d370307ce9724c86b892cded96 https://github.com/galaxyproject/galaxy/commit/197aa402d72895d370307ce9724c8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-25 (Sat, 25 Mar 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Improve ToolCache cleanup logic Pull `removed_tool_ids` out of try/except, so that we can return `removed_tool_ids` even if an exception occured. Fix a typo in the `_should_cleanup` docstring. Many thanks for the suggestions @nsoranzo. Commit: a47828bf892f8e1627bcb5f00ae63be56c9b6fcf https://github.com/galaxyproject/galaxy/commit/a47828bf892f8e1627bcb5f00ae63... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2017-03-25 (Sat, 25 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py Log Message: ----------- Merge pull request #3814 from mvdbeek/repository_updates Awesome, thanks @mvdbeek ! Commit: 50a51575f1d4f0a7ccc8c476ab0ad7de2ffca3c8 https://github.com/galaxyproject/galaxy/commit/50a51575f1d4f0a7ccc8c476ab0ad... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-26 (Sun, 26 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tools.js 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static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/user/user-preferences.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js A static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/nls/zh/locale.js M static/style/blue/base.css R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/grid_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/tool_shed/repository/common.mako M test/TESTING.md M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/populators.py M test/docker/base/run_test_wrapper.sh M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/integration/test_resolvers.py M test/qunit/package.json A test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py Log Message: ----------- Merging with dev Commit: 086dfd71ca4b82a7aeb2421cb2a08e76975639b3 https://github.com/galaxyproject/galaxy/commit/086dfd71ca4b82a7aeb2421cb2a08... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-26 (Sun, 26 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Removing tabs and updating time out for path animation Commit: 371d277c5514d0e7d033c8724f8d5cc58878f6bc https://github.com/galaxyproject/galaxy/commit/371d277c5514d0e7d033c8724f8d5... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-26 (Sun, 26 Mar 2017) Changed paths: M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Disable tool shed test function that fails frequently on Jenkins. Commit: c8573888232f15ef3641bfeb2f0d92a7aa80387f https://github.com/galaxyproject/galaxy/commit/c8573888232f15ef3641bfeb2f0d9... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge ToolConfWatchers and separate from Toolbox This should avoid some complexities associated with managing threads. I would also like to eliminate the separate reload_tool_data_tables and reload_data_managers callbacks and do this when reloading the toolbox, but every tool data table reload triggers twice the download of http://igv.broadinstitute.org/genomes/genomes.txt, which each time takes 2 seconds. Commit: 04941d0aea0be51fd169cb332070f6a420b71d0c https://github.com/galaxyproject/galaxy/commit/04941d0aea0be51fd169cb332070f... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/utils.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Fixing review comments- removing sliders for colors and zoom and adding color pickers, updating values for min and max zoom and replacing logo of the plugin Commit: f1206a8e352b9ef4288aa08bd18ac6b3387c790e https://github.com/galaxyproject/galaxy/commit/f1206a8e352b9ef4288aa08bd18ac... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map Log Message: ----------- Updating library files Commit: 229c0a2339b38f6481a489e5a8454018458297d2 https://github.com/galaxyproject/galaxy/commit/229c0a2339b38f6481a489e5a8454... Author: Hans-Rudolf Hotz <hrhotz@users.noreply.github.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update __init__.py using the lagacy python environemnt is also required for "CONVERTER_bed_to_fli_0" when displaying a bed file in trackster Commit: 37fd039bd5bf0ca2beda8183e298cd1454b16544 https://github.com/galaxyproject/galaxy/commit/37fd039bd5bf0ca2beda8183e298c... Author: Hans-Rudolf Hotz <hrhotz@users.noreply.github.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update __init__.py Commit: a6240c4b8c7477d2aca39ef97217139962fd5848 https://github.com/galaxyproject/galaxy/commit/a6240c4b8c7477d2aca39ef972171... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3822 from hrhotz/patch-1 fix bedfile display in trackster Commit: 21e5731355ebcbba2bb4280844091576c7700abf https://github.com/galaxyproject/galaxy/commit/21e5731355ebcbba2bb4280844091... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample Log Message: ----------- Fix for EtherCalc IE image specification. Will allow EtherCalc to work in 17.05. Commit: b4feb85f11280935b0ce13ea5d3693122f4319e8 https://github.com/galaxyproject/galaxy/commit/b4feb85f11280935b0ce13ea5d369... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/ts_api_doc.rst Log Message: ----------- improve accessibility of API docs for both Galaxy and TS Commit: bdcf4807ce5f2d3c1f12cd23120f4f5ec55f0067 https://github.com/galaxyproject/galaxy/commit/bdcf4807ce5f2d3c1f12cd23120f4... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A doc/source/admin/reports.md Log Message: ----------- add basic Reports documentation Commit: 1c716eb9da355864bd0116ce2579be3f03482e7c https://github.com/galaxyproject/galaxy/commit/1c716eb9da355864bd0116ce2579b... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js 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.map M static/scripts/mvc/tool/tools.js Log Message: ----------- Merge pull request #3808 from dannon/trigger-search-input Have tool-search listen to change as well as keyup Commit: 90c534570876c0f76a02458433960d9923a96ec3 https://github.com/galaxyproject/galaxy/commit/90c534570876c0f76a02458433960... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Fixing an issue with JSON data 'elements' attribute Commit: 967d0b6c0aef6fe331c4e9c92bc1b902363e660a https://github.com/galaxyproject/galaxy/commit/967d0b6c0aef6fe331c4e9c92bc1b... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/datasets.py M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3619 from jmchilton/purge_jobs_rework Improve interaction between job state and purged datasets. Commit: 810a96caef678462369604afd2a52b5c25c9268c https://github.com/galaxyproject/galaxy/commit/810a96caef678462369604afd2a52... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/datasets.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py 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.map M static/scripts/mvc/tool/tools.js M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py Log Message: ----------- Merge branch 'dev' into collection_builder_enhancements Commit: db09acb0263751560714c74d9f7c9ea6fed649ae https://github.com/galaxyproject/galaxy/commit/db09acb0263751560714c74d9f7c9... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/style/less/ui/paired-collection-creator.less M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/style/blue/base.css M test/api/test_history_contents.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #3806 from jmchilton/collection_builder_enhancements Small enhancements for collection builders Commit: 7964c7d1d0564422131760d1c6a1b9334954ca48 https://github.com/galaxyproject/galaxy/commit/7964c7d1d0564422131760d1c6a1b... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding styles for selected nodes and updating default colors for nodes, edges and higlighted elements Commit: 0809c19c36cf5f73f60928bd11c6a091c96e06b2 https://github.com/galaxyproject/galaxy/commit/0809c19c36cf5f73f60928bd11c6a... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/ui/paired-collection-creator.less M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/tools/__init__.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/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.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/tool/tools.js M static/style/blue/base.css M test/api/test_history_contents.py M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merging with dev Commit: cfd8ec776e692fe2706c1bd7cc40dcf1a8c56832 https://github.com/galaxyproject/galaxy/commit/cfd8ec776e692fe2706c1bd7cc40d... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #3817 from bgruening/cytoscape Cytoscape as the Galaxy charts plugin Commit: c24ed4f8fa2f277757eccb8e5cdb7d324a3a3521 https://github.com/galaxyproject/galaxy/commit/c24ed4f8fa2f277757eccb8e5cdb7... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A doc/source/admin/reports.md M doc/source/admin/useful_scripts.rst A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/releases/_header.rst M doc/source/ts_api_doc.rst Log Message: ----------- Merge pull request #3812 from martenson/admin-docs-imp api & reports documentation improvements Commit: 2839153eb4b08f0b9a536059912d39fd3ee902a0 https://github.com/galaxyproject/galaxy/commit/2839153eb4b08f0b9a536059912d3... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding Phylocanvas visualization for the Galaxy charts Commit: 606c32998f94a5e94921315a1be66d570e68c63d https://github.com/galaxyproject/galaxy/commit/606c32998f94a5e94921315a1be66... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py Log Message: ----------- Allow upload to collections. - New upload tab for "Collections". - This has a new option to select "Collection Type" in footer. - Collection upload geared toward homogeneous datasets - must specify genome and file format for all files. - New button "Build" after all individual datasets have finished their upload to the server. - Clicking "Build" launches the appropriate collection builder for selected collection type. - By default, uploading a collection hides the original uploaded datasets (can be unchecked). Implement tests for all uploaded collection types. Commit: 07be669ed0d392fde70a79aa442bae028cfe3fcd https://github.com/galaxyproject/galaxy/commit/07be669ed0d392fde70a79aa442ba... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample Log Message: ----------- Merge pull request #3825 from blankenberg/ethercalc Fix for EtherCalc IE image specification. Commit: 66ca698f5aa4e897a792fe47f81526ed703bc154 https://github.com/galaxyproject/galaxy/commit/66ca698f5aa4e897a792fe47f8152... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3829 from galaxyproject/release_17.01 Merge Release 17.01 Commit: 876c7a2d3df70b1c4edcf4fe738eb51c6e76bcfa https://github.com/galaxyproject/galaxy/commit/876c7a2d3df70b1c4edcf4fe738eb... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js Log Message: ----------- Adding more features like colors, collapse, prune and resize of the tree Commit: 8e1d761beccfc301129070f2c5c0a79939d290a0 https://github.com/galaxyproject/galaxy/commit/8e1d761beccfc301129070f2c5c0a... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M display_applications/igv/bigwig.xml M doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A doc/source/admin/reports.md M doc/source/admin/useful_scripts.rst A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/releases/_header.rst M doc/source/ts_api_doc.rst M lib/galaxy/tools/__init__.py Log Message: ----------- Merging with dev Commit: f88d893562112223553ba069eff2a1f42fe7d69b https://github.com/galaxyproject/galaxy/commit/f88d893562112223553ba069eff2a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Add HistoryDatasetCollectionAssociation as a possible tagged item in the galaxy tag manager. Should refactor this down the road, feels weird to register everything here in the manager. Commit: 73bfb57abf5ba728e4145731f91d0b222d74f5df https://github.com/galaxyproject/galaxy/commit/73bfb57abf5ba728e4145731f91d0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Use the correct tag manager instance from the Collections manager. Commit: 64f8e1cf3c27d86f625736ecd0438df7d329ca2d https://github.com/galaxyproject/galaxy/commit/64f8e1cf3c27d86f625736ecd0438... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Stricter checks for GFF/GFF3/GTF sniffing Check frame column in Gff.sniff() and Gtf.sniff() . Parse attributes column in Gff3.sniff() with a specific function to prevent non-compliant GTF files being recognised as GFF3. Commit: 32e8a2023deef55db60c61910321e366f40396d6 https://github.com/galaxyproject/galaxy/commit/32e8a2023deef55db60c61910321e... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Fix import order for lib/galaxy/datatypes/util/gff_util.py Commit: 5ceca34344b92d6bfa63ad1eb433a1cdea893f4f https://github.com/galaxyproject/galaxy/commit/5ceca34344b92d6bfa63ad1eb433a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M lib/galaxy/managers/collections.py M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js Log Message: ----------- Add basic tag rendering to expanded collection Commit: 821ee5bbcbfdd9a79c52ac60a20a51e20898b573 https://github.com/galaxyproject/galaxy/commit/821ee5bbcbfdd9a79c52ac60a20a5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M static/maps/mvc/collection/collection-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-view-edit.js Log Message: ----------- Simplify tags usage, since this editor's display is static. Commit: 4a45c9097e5c7d19977196d3ade1cd949af5af03 https://github.com/galaxyproject/galaxy/commit/4a45c9097e5c7d19977196d3ade1c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M client/package.json M client/webpack.config.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Add babel loader. Commit: 2a86f8e54c95da45b59fe166d515fc40b06f3c26 https://github.com/galaxyproject/galaxy/commit/2a86f8e54c95da45b59fe166d515f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/managers/hdcas.py Log Message: ----------- Add tags to hdca serializer. TODO: Details only. Commit: 225393a30006ca0313585de1a4bd93b3f0d88566 https://github.com/galaxyproject/galaxy/commit/225393a30006ca0313585de1a4bd9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M lib/galaxy/managers/hdcas.py Log Message: ----------- Add nametags to dataset collection serializer Commit: 2f66d4563e02e8b585e5c1529b4e414117846858 https://github.com/galaxyproject/galaxy/commit/2f66d4563e02e8b585e5c1529b4e4... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js Log Message: ----------- Adding shapes for leaves of phylogenetic tree Commit: f369ab0668fcedf572346553d3e0b70564f81796 https://github.com/galaxyproject/galaxy/commit/f369ab0668fcedf572346553d3e0b... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add login redirect for backbone router Commit: e431af074f4bb8a0d70f6a387af2654bfa21790b https://github.com/galaxyproject/galaxy/commit/e431af074f4bb8a0d70f6a387af26... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Redirect through push Commit: 81824fa0446a6f4f5c372961528609d362e5fbfa https://github.com/galaxyproject/galaxy/commit/81824fa0446a6f4f5c37296152860... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/ui/paired-collection-creator.less A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M display_applications/igv/bigwig.xml M doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A doc/source/admin/reports.md M doc/source/admin/useful_scripts.rst A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/releases/_header.rst M doc/source/ts_api_doc.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/workflows.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/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.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/tool/tools.js M static/style/blue/base.css M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_tools.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako Commit: 11860d55fb7a51985d4027e35b6a6ead78748cfa https://github.com/galaxyproject/galaxy/commit/11860d55fb7a51985d4027e35b6a6... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Attempt to improve the robustness and verboseness of the test_sharing_valid Selenium test. - When registering, put a little pause in after clicking to ensure the browser has a chance to submit the request before continuing to check if indeed the user is logged in. - If the user doesn't appear to be logged in, dump the contents of the user menu out so we can see if a different user is logged in or if there is no log in. - Attempt to be more robust about conditions being waited on when clicking history option menu - in case clicks were being fired during jQuery transitions or something. xref #3838 Commit: ab11adfa501ababc2d1f20e731727b8df787b803 https://github.com/galaxyproject/galaxy/commit/ab11adfa501ababc2d1f20e731727... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Merge pull request #3819 from jmchilton/disable_pesky_ts_test Disable tool shed test function that fails frequently on Jenkins. Commit: 790a35ea2e605c3b15e3e59df07f3febc9688f8d https://github.com/galaxyproject/galaxy/commit/790a35ea2e605c3b15e3e59df07f3... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Properly handle multiple hidden datasets when populating data select options Commit: a0b4ab63d288d04ddd7b4372090c1e956653f4e6 https://github.com/galaxyproject/galaxy/commit/a0b4ab63d288d04ddd7b4372090c1... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3842 from guerler/fix_hidden_datasets Properly handle multiple hidden datasets when populating data select options Commit: 777db9829b41a0ffde892ac9fe11846f5af93b91 https://github.com/galaxyproject/galaxy/commit/777db9829b41a0ffde892ac9fe118... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #3696 from jmchilton/upload_collection Allow uploading to collections. Commit: 10e89cfc851526973b8234257ba9039b5961160f https://github.com/galaxyproject/galaxy/commit/10e89cfc851526973b8234257ba90... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #3841 from jmchilton/selenium_fixes_7 Attempt to improve the robustness and verboseness of the test_sharing_valid Selenium test. Commit: 452683998293d525e4c999d6ebf6f5eb85adca2e https://github.com/galaxyproject/galaxy/commit/452683998293d525e4c999d6ebf6f... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Annotate new api endpoints Commit: 31a8ebe9d5e6595ea0299546b59c07ce32931ac0 https://github.com/galaxyproject/galaxy/commit/31a8ebe9d5e6595ea0299546b59c0... Author: guerler <aysam.guerler@gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Merge branch 'dev' into remove_custom_builds_mako Commit: 185aa3968bd38cfe021f7bcec9bae02c12ae4c0b https://github.com/galaxyproject/galaxy/commit/185aa3968bd38cfe021f7bcec9bae... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Log when workflow scheduling is delayed about why. Currently the logs contain fairly uninformative step delayed messages that don't allow admins to understand why parts of the workflow are being delayed during scheduling. Here are some examples of before and after. When running the test: ``` ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_pause ``` Before these lines would show up: ``` galaxy.workflow.run DEBUG 2017-03-30 09:23:47,327 Workflow step 2 of invocation 1 invoked (174.149 ms) galaxy.workflow.run DEBUG 2017-03-30 09:23:47,347 Workflow step 3 of invocation 1 invoked (19.355 ms) galaxy.workflow.run DEBUG 2017-03-30 09:23:47,364 Workflow step 4 of invocation 1 delayed (16.262 ms) ``` Now these same lines are as follows: ``` galaxy.workflow.run DEBUG 2017-03-30 09:19:28,601 Workflow step 2 of invocation 1 invoked (172.849 ms) galaxy.workflow.run DEBUG 2017-03-30 09:19:28,619 Marking step 3 outputs delayed (executing pause step) galaxy.workflow.run DEBUG 2017-03-30 09:19:28,620 Workflow step 3 of invocation 1 invoked (17.999 ms) galaxy.workflow.run DEBUG 2017-03-30 09:19:28,633 Workflow step 4 of invocation 1 delayed (dependent step [3] delayed, so this step must be delayed) (13.398 ms) ``` Also, when running the test: ``` ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_run_dynamic_output_collections_3 ``` Before these lines would be printed: ``` galaxy.workflow.run DEBUG 2017-03-30 09:25:35,910 Workflow step 4 of invocation 1 invoked (281.479 ms) galaxy.workflow.run DEBUG 2017-03-30 09:25:35,937 Workflow step 5 of invocation 1 delayed (25.904 ms) galaxy.workflow.run DEBUG 2017-03-30 09:25:35,970 Workflow step 6 of invocation 1 delayed (32.597 ms) ``` Now these same lines are as follows: ``` galaxy.workflow.run DEBUG 2017-03-30 09:27:54,270 Workflow step 4 of invocation 1 invoked (295.826 ms) galaxy.workflow.run DEBUG 2017-03-30 09:27:54,315 Workflow step 5 of invocation 1 delayed (dependent collection [1] not yet populated with datasets) (44.581 ms) galaxy.workflow.run DEBUG 2017-03-30 09:27:54,326 Workflow step 6 of invocation 1 delayed (dependent step [5] delayed, so this step must be delayed) (10.804 ms) ``` When running workflows with steps that depend explicitly on other steps (instead of implicitly between dataset connections), lines such as: ``` galaxy.workflow.run DEBUG 2017-03-30 09:33:52,966 Marking step 3 outputs delayed (workflow paused at this step waiting for review) galaxy.workflow.run DEBUG 2017-03-30 09:33:53,001 Workflow step 4 of invocation 1 delayed (dependent step [3] delayed, so this step must be delayed) (0.157 ms) galaxy.workflow.run DEBUG 2017-03-30 09:33:53,001 Workflow step 5 of invocation 1 delayed (depends on step [4] but that step has not been invoked yet) (0.084 ms) ``` and ``` galaxy.workflow.run DEBUG 2017-03-30 09:33:57,090 Workflow step 5 of invocation 1 delayed (depends on step [4] but one or more jobs created from that step have not finished yet) (0.144 ms) ``` now may appear. Commit: c4fd96092bcabd869f8c4a4427489d0b2c6209a3 https://github.com/galaxyproject/galaxy/commit/c4fd96092bcabd869f8c4a4427489... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/tag.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/tag.js Log Message: ----------- Make TagEditor label optional. Commit: e67dc45c26e77d3f2b85ac7e2ab80ac5fdab0cf9 https://github.com/galaxyproject/galaxy/commit/e67dc45c26e77d3f2b85ac7e2ab80... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-view-edit.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into phylocanvas Commit: b8692309484c3a671145684277201ed7aaf444dd https://github.com/galaxyproject/galaxy/commit/b8692309484c3a671145684277201... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Re-arrange workflow scheduling logic according to @nsoranzo's suggestions. Commit: 94c357f608f93ccf9c0494e07599cae85c15782d https://github.com/galaxyproject/galaxy/commit/94c357f608f93ccf9c0494e07599c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- Merge branch 'release_17.01' into dev Commit: 3d2833fdb72b9d967d4ec05581c7e0c1aa3a81a1 https://github.com/galaxyproject/galaxy/commit/3d2833fdb72b9d967d4ec05581c7e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/web/base/controllers/admin.py M templates/webapps/galaxy/admin/manage_dependencies.mako Log Message: ----------- Merge pull request #3750 from mvdbeek/remove_unused_envs Add the possibility to uninstall conda environments that are not in u… Commit: 90ac2f43566220cd82a771afd2040a1410addb4a https://github.com/galaxyproject/galaxy/commit/90ac2f43566220cd82a771afd2040... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/util/gff_util.py Log Message: ----------- Merge pull request #3832 from nsoranzo/gff_sniff_fix Stricter checks for GFF/GFF3/GTF sniffing Commit: 200e475bc7cd340401f46028fc234a1e7c2ad87c https://github.com/galaxyproject/galaxy/commit/200e475bc7cd340401f46028fc234... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-30 (Thu, 30 Mar 2017) Changed paths: M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3849 from jmchilton/improved_scheduling_delay_logging Log reason when workflow scheduling of a step is delayed. Commit: fa086edf22c725b8a98cff92ac6ca6a4ab210237 https://github.com/galaxyproject/galaxy/commit/fa086edf22c725b8a98cff92ac6ca... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js Log Message: ----------- Adding support for .nhx files (Newick) and removing txt files support Commit: c9f602d434104423078d2f0661e6acd8aa5c359b https://github.com/galaxyproject/galaxy/commit/c9f602d434104423078d2f0661e6a... Author: Gildas Le Corguillé <lecorguille@users.noreply.github.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Update datatypes_conf.xml.sample Oups, I did it again :) Just add the sniffer for the mzData datatype Commit: dfbb80dd8b21f87af217fce49d14df396517c6d9 https://github.com/galaxyproject/galaxy/commit/dfbb80dd8b21f87af217fce49d14d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3852 from lecorguille/patch-1 Update datatypes_conf.xml.sample Commit: 190d1901a43a284c478876d2ec3567a1cc1af5a5 https://github.com/galaxyproject/galaxy/commit/190d1901a43a284c478876d2ec356... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/workflow/scheduling_manager.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into dev Commit: ad2e6473bc07a5b229d50f85c28cad0363a40f11 https://github.com/galaxyproject/galaxy/commit/ad2e6473bc07a5b229d50f85c28ca... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into dev Commit: c452af01bd16cf85e7459f767ee77c381e527a9a https://github.com/galaxyproject/galaxy/commit/c452af01bd16cf85e7459f767ee77... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Render 'nametags' for hdcas Commit: 2f4aa1a763146e980f9c1c929f07ffd4b7bf7ff3 https://github.com/galaxyproject/galaxy/commit/2f4aa1a763146e980f9c1c929f07f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M static/maps/mvc/collection/collection-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-view-edit.js Log Message: ----------- Toggle tags prompt on collection view Commit: 01655895174eb14530d27452789682335b2f7197 https://github.com/galaxyproject/galaxy/commit/01655895174eb14530d2745278968... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M static/maps/mvc/collection/collection-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-view.js Log Message: ----------- Tags editor location/styling fix for collection view. Commit: 5dcc0ed04376d08deb960f309e21fc14a6d29ce8 https://github.com/galaxyproject/galaxy/commit/5dcc0ed04376d08deb960f309e21f... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M test/api/test_users.py Log Message: ----------- Clean up old TODO into history tests. We upgraded the module a long time ago now that was referenced in the Trello card. Commit: 6af5334f125461fba1ea1735bf06eed516bd6754 https://github.com/galaxyproject/galaxy/commit/6af5334f125461fba1ea1735bf06e... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M test/api/test_users.py Log Message: ----------- Merge pull request #3855 from jmchilton/user_api_tests Clean up old TODO into history tests. Commit: b5fe42c462ebcbf4fb9f0a09fd63e11c2a68fd7e https://github.com/galaxyproject/galaxy/commit/b5fe42c462ebcbf4fb9f0a09fd63e... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-04-01 (Sat, 01 Apr 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- Small changes to links and add gitter Commit: ffce14e65d70441827086c1eccdae46a28819df3 https://github.com/galaxyproject/galaxy/commit/ffce14e65d70441827086c1eccdae... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- change devteam to iuc Commit: 224a5b39004e93c7ced8a6ce317e2ac85b553b40 https://github.com/galaxyproject/galaxy/commit/224a5b39004e93c7ced8a6ce317e2... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- fix contribute pdf link Commit: 5169fbe917c90ee6b13a345e869bf88bf51f6512 https://github.com/galaxyproject/galaxy/commit/5169fbe917c90ee6b13a345e869bf... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-03-31 (Fri, 31 Mar 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- Merge pull request #3861 from galaxyproject/contrib_changes Small changes to links and add gitter Commit: 1a5e337420e4832593b6e30089c0022291fd6078 https://github.com/galaxyproject/galaxy/commit/1a5e337420e4832593b6e30089c00... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/app.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Move ConfigWatchers into galaxy.webapps.galaxy.config_watchers Commit: f79fb9075a4f724d5bad95163a6450c9ffb89b84 https://github.com/galaxyproject/galaxy/commit/f79fb9075a4f724d5bad95163a645... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/tools/test_toolbox.py Log Message: ----------- Move ToolWatcher from Toolbox to ConfigWatchers class Commit: 63f1efd15a6903526406ff8d643fb3d6f4a5e678 https://github.com/galaxyproject/galaxy/commit/63f1efd15a6903526406ff8d643fb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix toolshed startup Commit: c4e6671ce50a64ba561a3ef815816426183adf4d https://github.com/galaxyproject/galaxy/commit/c4e6671ce50a64ba561a3ef815816... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Fix import order in config_watchers.py Commit: 0c3f7989bb913842e28a8fbb267d1280420caa92 https://github.com/galaxyproject/galaxy/commit/0c3f7989bb913842e28a8fbb267d1... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M .ci/flake8_lint_include_list.txt M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M templates/webapps/galaxy/admin/manage_dependencies.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/data/test_workflow_pause.ga M test/base/populators.py A test/integration/test_maximum_worklfow_invocation_duration.py Log Message: ----------- Merging wtih dev Commit: b037332e943edbf9cf65f4799a1226bf53e8476a https://github.com/galaxyproject/galaxy/commit/b037332e943edbf9cf65f4799a122... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/config_watchers.py Log Message: ----------- Avoid race-condition between multiple instances of ToolConfWatchers Commit: 2c7089df46fa0a5178a1e0f72cc87514e8a97142 https://github.com/galaxyproject/galaxy/commit/2c7089df46fa0a5178a1e0f72cc87... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix TS tests Commit: 1e70211fa4827badf4bd3fe1f1703004d369afec https://github.com/galaxyproject/galaxy/commit/1e70211fa4827badf4bd3fe1f1703... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M test/api/test_libraries.py Log Message: ----------- Touch up #3559 based on post-merge discussions. Commit: 339566bc03f1a51c7a4c60c2d6a100f43e1d3c15 https://github.com/galaxyproject/galaxy/commit/339566bc03f1a51c7a4c60c2d6a10... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M CONTRIBUTING.md M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/scheduling_manager.py M test/api/test_users.py M test/api/test_workflows.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml Log Message: ----------- Merging with dev Commit: 6f4e242b16487b6032347dad3f60fef00f60464f https://github.com/galaxyproject/galaxy/commit/6f4e242b16487b6032347dad3f60f... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js Log Message: ----------- Merge pull request #3850 from bgruening/phylocanvas Phylocanvas as a BioJS component for the Galaxy charts Commit: 5d810d5908ac851e398ebc7fcd7d54c5a892fd04 https://github.com/galaxyproject/galaxy/commit/5d810d5908ac851e398ebc7fcd7d5... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M test/api/test_libraries.py Log Message: ----------- Merge pull request #3857 from jmchilton/3559_touchups Touch up #3559 based on post-merge discussions. Commit: 29331b36cf4ad350d4919679deeca6f342b1e182 https://github.com/galaxyproject/galaxy/commit/29331b36cf4ad350d4919679deeca... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt A config/containers_conf.yml.sample M config/galaxy.ini.sample M lib/galaxy/config.py R lib/galaxy/container/__init__.py R lib/galaxy/container/docker_swarm.py A lib/galaxy/containers/__init__.py A lib/galaxy/containers/docker.py A lib/galaxy/containers/docker_decorators.py A lib/galaxy/containers/docker_model.py A lib/galaxy/containers/docker_swarm.py A lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/util/submodules.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Container interface abstraction. Support Docker and Docker Swarm mode (>1.12 SwarmKit). Container interface configuration is performed via the containers_conf.yml config file, for which a documented sample is provided. The GIE launcher has been modified to use the container interface if the `enable_beta_containers_interface` option is set in galaxy.ini. This removes some of the previous GIE-specific swarm mode work that was done. The Galaxy docker swarm manager also uses the container interface now. TODO: The API docker interfaces should be done fairly soon before we have many consumers of the docker model objects, because they'll probably be changed to more closely reflect their API representations. Commit: 41a88de7527c4e5f38070fe31e0dfe78ad817603 https://github.com/galaxyproject/galaxy/commit/41a88de7527c4e5f38070fe31e0df... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/actions/__init__.py M static/maps/mvc/ui/ui-options.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-options.js M test/api/test_tools.py A test/functional/tools/identifier_multiple_in_conditional.xml A test/functional/tools/identifier_multiple_in_repeat.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Commit: c9bbaa30f7400f547e8549ae8d0d3bed5ccbf0c5 https://github.com/galaxyproject/galaxy/commit/c9bbaa30f7400f547e8549ae8d0d3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M .ci/flake8_lint_include_list.txt M CONTRIBUTING.md M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-options.js A client/galaxy/scripts/mvc/upload/collection/collection-row.js A client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/ui/paired-collection-creator.less M client/galaxy/style/less/upload.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js M config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A 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lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/scheduling_manager.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-options.js.map A static/maps/mvc/upload/collection/collection-row.js.map A static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-options.js A static/scripts/mvc/upload/collection/collection-row.js A static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M templates/webapps/galaxy/admin/manage_dependencies.mako M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/api_asserts.py M test/base/data/test_workflow_pause.ga M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml A test/functional/tools/identifier_multiple_in_conditional.xml A test/functional/tools/identifier_multiple_in_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py A test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_job_conf.xml M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into tags_improvements Commit: d1974a42e5787ef06d4c4d25dbe7178eb26284d5 https://github.com/galaxyproject/galaxy/commit/d1974a42e5787ef06d4c4d25dbe71... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M tools/filters/trimmer.py M tools/filters/trimmer.xml Log Message: ----------- Use detect_errors="exit_code" in Trim tool Prevent job failures due to spurious messages on stderr from the cluster scheduler. Commit: 405dbd3b7f3022332fb6c660f88e67361fbb5429 https://github.com/galaxyproject/galaxy/commit/405dbd3b7f3022332fb6c660f88e6... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-custom-builds.js M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-custom-builds.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-custom-builds.js Log Message: ----------- Move custom build metadata endpoint to histories Commit: a16c5320fd647b45dbad197714fc52d2a5254548 https://github.com/galaxyproject/galaxy/commit/a16c5320fd647b45dbad197714fc5... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/api/histories.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Wait for history panel, workaround until overall ui has been visited Commit: 439444e65ad9c79a0a2553a5eb916405b1910e93 https://github.com/galaxyproject/galaxy/commit/439444e65ad9c79a0a2553a5eb916... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Preserve tags for collection outputs. This is one step forward, also need to address non-output handled collectinos, like those automatically created in workflow execution with collection inputs. Commit: bfbca68b4e70cc380398e364dd8abdd5ac1a360e https://github.com/galaxyproject/galaxy/commit/bfbca68b4e70cc380398e364dd8ab... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Don't wrap tags up in element_kwds -- this prevents them being sent to non-hda collections. Commit: 6ce47ddbf4ed0046f52cd6c7d4f140c893d9b1e3 https://github.com/galaxyproject/galaxy/commit/6ce47ddbf4ed0046f52cd6c7d4f14... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Also include implicit_collection_info in collection tag creation logic. Commit: 5937a677d57e6180aaeabcd737e70aac0809fbd5 https://github.com/galaxyproject/galaxy/commit/5937a677d57e6180aaeabcd737e70... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M tools/filters/trimmer.py M tools/filters/trimmer.xml Log Message: ----------- Merge pull request #3869 from nsoranzo/trimmer Use detect_errors="exit_code" in Trim tool Commit: 2b0ac9a098b7ca2c207c3d00be698a993e4130ff https://github.com/galaxyproject/galaxy/commit/2b0ac9a098b7ca2c207c3d00be698... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js Log Message: ----------- Enable drag drop for history items Commit: 97d5a86a585b2c9ac159c9db255dd0389f83ab3b https://github.com/galaxyproject/galaxy/commit/97d5a86a585b2c9ac159c9db255dd... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Catch drag and drop basic event handlers for content selector Commit: aa7bed3b7270db18505e1dc7a8f84600482114cb https://github.com/galaxyproject/galaxy/commit/aa7bed3b7270db18505e1dc7a8f84... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Add basic styles to highlight drop area on drag over Commit: f56651b9ea8b20e34d1cb0604888d3de2e49e2c4 https://github.com/galaxyproject/galaxy/commit/f56651b9ea8b20e34d1cb0604888d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Access drop data Commit: 642002854c2abd312e917632191c7db638234ad7 https://github.com/galaxyproject/galaxy/commit/642002854c2abd312e917632191c7... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Move drop handler, support datasets and collections Commit: 5bbc91289b0d5cd69a00a487751f4782f298932a https://github.com/galaxyproject/galaxy/commit/5bbc91289b0d5cd69a00a487751f4... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Display success and error colors Commit: 039f706bd7395f8b0350453936f2e82f98fa4e93 https://github.com/galaxyproject/galaxy/commit/039f706bd7395f8b0350453936f2e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix style color on inital dragover Commit: af066197b9b9a4ff6f804fe4cc588611eab0ddd9 https://github.com/galaxyproject/galaxy/commit/af066197b9b9a4ff6f804fe4cc588... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Improve validation Commit: da0d53728be70d26123a748546a8c0d6cb8d67c3 https://github.com/galaxyproject/galaxy/commit/da0d53728be70d26123a748546a8c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Move delay timer value to attributes, rename status handler Commit: e05036a6a02c396c207c9ea80dc056a58c9f7f08 https://github.com/galaxyproject/galaxy/commit/e05036a6a02c396c207c9ea80dc05... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Avoid flickering due to bubbling events from children without masking div Commit: 5c85fe1c9821a12caaef30df37eeac3c1fcb2a66 https://github.com/galaxyproject/galaxy/commit/5c85fe1c9821a12caaef30df37eea... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Remove unused default behavior blockers Commit: 2c3cdfb6d0355667909a40a79c8e02a76b6dca97 https://github.com/galaxyproject/galaxy/commit/2c3cdfb6d0355667909a40a79c8e0... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Fix code style, improve readability Commit: 071186d520fdd0069b182dd77aeaad4bddd1e323 https://github.com/galaxyproject/galaxy/commit/071186d520fdd0069b182dd77aeaa... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Improve support for multiple dataset selector Commit: 383db9bb3bedef57f490dff4feb1bd74188c798b https://github.com/galaxyproject/galaxy/commit/383db9bb3bedef57f490dff4feb1b... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-04 (Tue, 04 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Trigger change to update current selection if value has not actually changed Commit: ab1f7eae4d0f1836dad4e52a75dbc18f9bd20336 https://github.com/galaxyproject/galaxy/commit/ab1f7eae4d0f1836dad4e52a75dbc... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- synchronise against latest UCSC versions Commit: 6251b51aebc8719b64122e1311175e683e55bbb3 https://github.com/galaxyproject/galaxy/commit/6251b51aebc8719b64122e1311175... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Merge pull request #3871 from guerler/history_drag_drop Allows to drag-and-drop history items into the content selector Commit: 200994536e6110fffb586a968edf7edd3c04e4f2 https://github.com/galaxyproject/galaxy/commit/200994536e6110fffb586a968edf7... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Revert "Allows to drag-and-drop history items into the content selector" Commit: c27dac65c882906aa87c364961ac7783f1babd17 https://github.com/galaxyproject/galaxy/commit/c27dac65c882906aa87c364961ac7... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge pull request #3783 from dannon/routing_bug_exception_propagation Layered routing fix for when controller route fails and client route does not exist. Commit: 8bbd423909d7ed524b2f73cdc7f7bf42b49c43f2 https://github.com/galaxyproject/galaxy/commit/8bbd423909d7ed524b2f73cdc7f7b... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Merge pull request #3877 from galaxyproject/revert-3871-history_drag_drop Revert "Allows to drag-and-drop history items into the content selector" Commit: d607c7e0b134ac81faf0648af6e8a48d8941c938 https://github.com/galaxyproject/galaxy/commit/d607c7e0b134ac81faf0648af6e8a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-table.js A client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/ui.less M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py A static/GruntFile.js A static/GruntFile.js.map M static/maps/layout/menu.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-table.js.map A static/maps/mvc/user/user-custom-builds.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/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-table.js A static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css R templates/user/dbkeys.mako Log Message: ----------- Merge remote-tracking branch 'guerler/remove_custom_builds_mako' into dev Commit: 676b5cb2779eda3f87d62d2ee5dd74244aaa8071 https://github.com/galaxyproject/galaxy/commit/676b5cb2779eda3f87d62d2ee5dd7... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Fix inability to raise errors if OS in non en_US Commit: bdcc474d3666fd08f0032629e1882a4441b35244 https://github.com/galaxyproject/galaxy/commit/bdcc474d3666fd08f0032629e1882... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-table.js A client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/ui.less M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py A static/GruntFile.js A static/GruntFile.js.map M static/maps/layout/menu.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-table.js.map A static/maps/mvc/user/user-custom-builds.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/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-table.js A static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css R templates/user/dbkeys.mako M tools/filters/trimmer.py M tools/filters/trimmer.xml Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into tags_improvements Commit: 82fe4262148ae462eb4fe5012e4c7c03ec9be7b8 https://github.com/galaxyproject/galaxy/commit/82fe4262148ae462eb4fe5012e4c7... Author: Jorrit Boekel <jorrit.boekel@scilifelab.se> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Hardklor and kronik datatypes for proteomics Commit: c10a23b924983f11565c6a8976b80f6c65b97955 https://github.com/galaxyproject/galaxy/commit/c10a23b924983f11565c6a8976b80... Author: Jorrit Boekel <jorrit.boekel@scilifelab.se> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- More recognizable naming for datatype extensions Commit: 54b7c32bd2913c236c4eacfaf45bdef3ba4c2e7d https://github.com/galaxyproject/galaxy/commit/54b7c32bd2913c236c4eacfaf45bd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Render nametags from core tag data instead of a different field. This actually should be somewhat faster, along with being easier to track/update. Commit: 74f97a8942cd13572293ff79aec600fcdab4ed88 https://github.com/galaxyproject/galaxy/commit/74f97a8942cd13572293ff79aec60... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Fix for dropping into run workflow iframe Commit: 7304d5bdc4997da727747f86cf7049bb2452050a https://github.com/galaxyproject/galaxy/commit/7304d5bdc4997da727747f86cf704... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-table.js A client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/ui.less M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py A static/GruntFile.js A static/GruntFile.js.map M static/maps/layout/menu.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-table.js.map A static/maps/mvc/user/user-custom-builds.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/form/form-parameters.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-table.js A static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css R templates/user/dbkeys.mako Log Message: ----------- Merge branch 'dev' into history_drag_drop_000 Commit: ba91462362c59a1a0dbbfdc80920642de10dbd20 https://github.com/galaxyproject/galaxy/commit/ba91462362c59a1a0dbbfdc809206... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add delay attribute to time success/error highlighting Commit: 37b6d907cbc338793f950d33904421faf376f2c3 https://github.com/galaxyproject/galaxy/commit/37b6d907cbc338793f950d3390442... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Remove unused cursor style Commit: d9d4ce0ad349d506eb8e902f079453dd4cf9ba16 https://github.com/galaxyproject/galaxy/commit/d9d4ce0ad349d506eb8e902f07945... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Looks like this was always using trans.hsitory instead of the id that was passed to the endpoint. Commit: c9863b251ee831f0a7f97935f86e3d46f692ae9f https://github.com/galaxyproject/galaxy/commit/c9863b251ee831f0a7f97935f86e3... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Merge pull request #3887 from dannon/fix_broken_jenkins Fix new history endpoint providing custom builds metadata Commit: 6f95ba9c2c7637fef29d639b19cde81cc3f0ec74 https://github.com/galaxyproject/galaxy/commit/6f95ba9c2c7637fef29d639b19cde... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Merge branch 'dev' into history_drag_drop_000 Commit: 2215869f2d68c1839091dc23cf303bf43fa29078 https://github.com/galaxyproject/galaxy/commit/2215869f2d68c1839091dc23cf303... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tag.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tag.js Log Message: ----------- Listen to tag change events, rerender list item for nametags. Commit: d9bb8a7d300c723a172ecc288e332c2a2763f872 https://github.com/galaxyproject/galaxy/commit/d9bb8a7d300c723a172ecc288e332... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Remove unused model import from users api Commit: c6ce56dd0a2ddb7b5e4760b3bab7be80ef367ba3 https://github.com/galaxyproject/galaxy/commit/c6ce56dd0a2ddb7b5e4760b3bab7b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #3888 from guerler/remove_unused_model Remove unused model import from users api Commit: 5a513b20bbc371cf9a51483b1cf468d9126a45fe https://github.com/galaxyproject/galaxy/commit/5a513b20bbc371cf9a51483b1cf46... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/tag.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/tag.js Log Message: ----------- Remove (previously) never-invoked change code which now double-invokes. Parents will handle this. Commit: d2205c4167aa543be633721b6650098bca6835b4 https://github.com/galaxyproject/galaxy/commit/d2205c4167aa543be633721b66500... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge branch 'dev' into history_drag_drop_000 Commit: 72a3fea37f3cb622f0b509a72921ad11ecabf99f https://github.com/galaxyproject/galaxy/commit/72a3fea37f3cb622f0b509a72921a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Unused glob in buildapp Commit: 5055172e64bb48ec0eb6d3e4b4ec6461cbc19162 https://github.com/galaxyproject/galaxy/commit/5055172e64bb48ec0eb6d3e4b4ec6... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3889 from dannon/unused_glob Unused glob in buildapp Commit: 6a625b2c6116992bd475cffe4f11a8ced41110fe https://github.com/galaxyproject/galaxy/commit/6a625b2c6116992bd475cffe4f11a... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge branch 'dev' into history_drag_drop_000 Commit: d41a4efd8822c46aa9f236937d4fc74678ba0dfd https://github.com/galaxyproject/galaxy/commit/d41a4efd8822c46aa9f236937d4fc... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- For datasets, only rerender title bar if tags have changed (for nametags) Commit: 2ab68fea8b20c256c30afd7e18bcf2647c978396 https://github.com/galaxyproject/galaxy/commit/2ab68fea8b20c256c30afd7e18bcf... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/hda-li.js M static/maps/mvc/history/hda-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/hda-li.js Log Message: ----------- Remove redundant listener, handled in parent. Commit: 9e9a2d8312990c11ff7d9df6e71927bdc3210514 https://github.com/galaxyproject/galaxy/commit/9e9a2d8312990c11ff7d9df6e7192... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Rerender specifically subtitle iff it's the only changed attribute. Commit: bcd24e845477d72761072baf014119b3dda2372d https://github.com/galaxyproject/galaxy/commit/bcd24e845477d72761072baf01411... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Merge pull request #3886 from guerler/history_drag_drop_000 History drag-and-drop feature with iframe support for run workflow form Commit: af37dd55de283602338f07452c92224eb0490fa6 https://github.com/galaxyproject/galaxy/commit/af37dd55de283602338f07452c922... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M config/tool_destinations.yml.sample M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Merge pull request #3657 from lecorguille/dynamic_tool_nest_param Allow nest param in the dynamic_tool rule -> argument Commit: eb0ff254a59196499e7c714b4fc8d744ef463df9 https://github.com/galaxyproject/galaxy/commit/eb0ff254a59196499e7c714b4fc8d... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M run_tests.sh Log Message: ----------- Update to a new Docker test image to fix dependency bugs. Hopefully this will fix tests for #3179. Commit: 232e8096925dd7739b98120c172b5cb092192f3e https://github.com/galaxyproject/galaxy/commit/232e8096925dd7739b98120c172b5... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Python3: Use shlex_quote() from six.moves instead of pipes.quote() Commit: 334f4d7a19882ad97aec75f50b61fda5eb807974 https://github.com/galaxyproject/galaxy/commit/334f4d7a19882ad97aec75f50b61f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py R lib/galaxy/webapps/galaxy/controllers/search.py Log Message: ----------- Remove old, unused search controller. This would be implemented as a clientside route if we ever pursued development. Commit: e085f8cb41a00668efa6108b3caf9e7dbbc712f2 https://github.com/galaxyproject/galaxy/commit/e085f8cb41a00668efa6108b3caf9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Routes cleanup -- this adjust_hidden route is unnecessary and is handled by the normal controller logic. Commit: a2a64821b4511db810865e75e991e19fc365f6f9 https://github.com/galaxyproject/galaxy/commit/a2a64821b4511db810865e75e991e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- This login route is also unnecessary Commit: d19be8bf46c41d12e0a4d6c34454cc150cc06378 https://github.com/galaxyproject/galaxy/commit/d19be8bf46c41d12e0a4d6c34454c... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #3891 from nsoranzo/python3 Python3: Use shlex_quote() from six.moves instead of pipes.quote() Commit: dc80d8c7dcb194300b622d8cfc9fd2dd5d11a811 https://github.com/galaxyproject/galaxy/commit/dc80d8c7dcb194300b622d8cfc9fd... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #3890 from jmchilton/fix_docker_testing Update to a new Docker test image to fix dependency bugs. Commit: 69ff6ab906d94fdb4da3bd0b858fce2de3b349fa https://github.com/galaxyproject/galaxy/commit/69ff6ab906d94fdb4da3bd0b858fc... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py R lib/galaxy/webapps/galaxy/controllers/search.py Log Message: ----------- Merge pull request #3894 from dannon/search_controller_removal Remove old, unused search controller. Commit: cad62b1f8b5d289dc27ec88303118dadddbbbc52 https://github.com/galaxyproject/galaxy/commit/cad62b1f8b5d289dc27ec88303118... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/less/ui.less M config/tool_destinations.yml.sample M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py R lib/galaxy/webapps/galaxy/controllers/search.py M run_tests.sh M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/ui/ui-select-content.js M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into tags_improvements Commit: 1a5d570704da50bdca0ca3194f5549f1338f2c6b https://github.com/galaxyproject/galaxy/commit/1a5d570704da50bdca0ca3194f554... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M static/maps/mvc/collection/collection-view-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove comment, rebuild. Commit: 95fd21230b7f73434a4af60b6624b499efcaa1af https://github.com/galaxyproject/galaxy/commit/95fd21230b7f73434a4af60b6624b... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js Log Message: ----------- Adding bug fix for SIF files Commit: ee66994c44cda791ab4c0d5c8fe72dff4edd2710 https://github.com/galaxyproject/galaxy/commit/ee66994c44cda791ab4c0d5c8fe72... Author: anuprulez <anup.rulez@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/buildapp.py R lib/galaxy/webapps/galaxy/controllers/search.py M run_tests.sh Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into bugfix_cytoscape Commit: 483f25c5c2c8d375d6096d9ca239618e413dde45 https://github.com/galaxyproject/galaxy/commit/483f25c5c2c8d375d6096d9ca2396... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js Log Message: ----------- Merge pull request #3896 from bgruening/bugfix_cytoscape Cytoscape bugfix for SIF files Commit: 2b4b431d0a4f300c1af3d9ac4a105e7887ec09c6 https://github.com/galaxyproject/galaxy/commit/2b4b431d0a4f300c1af3d9ac4a105... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Add missing trigger event to drop handler in content selector Commit: 8ea4cf29f812d8ce29b31efa18495aad5d5fca44 https://github.com/galaxyproject/galaxy/commit/8ea4cf29f812d8ce29b31efa18495... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tag.js M client/package.json M client/webpack.config.js M lib/galaxy/managers/collections.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/tags.py M lib/galaxy/tools/actions/__init__.py M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tag.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/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tag.js Log Message: ----------- Merge pull request #3868 from dannon/tags_improvements Adding tagging to collections. Commit: ea17f2dacf8b00e579741676deb33a98d0c234ef https://github.com/galaxyproject/galaxy/commit/ea17f2dacf8b00e579741676deb33... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tag.js M client/package.json M client/webpack.config.js M lib/galaxy/managers/collections.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/tags.py M lib/galaxy/tools/actions/__init__.py M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tag.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/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tag.js Log Message: ----------- Merge branch 'dev' into fix_refresh_trigger Commit: cac9c980dfce7e22d076cec4032facd1c011d33f https://github.com/galaxyproject/galaxy/commit/cac9c980dfce7e22d076cec4032fa... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- remove obsolete line Commit: 5b880697c23e2cdf1c4339976db2bf7d6a9a1c62 https://github.com/galaxyproject/galaxy/commit/5b880697c23e2cdf1c4339976db2b... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge pull request #3874 from bgruening/new_ucsc synchronise against latest UCSC versions Commit: 408906efb118dc4f36d134c632667101d34a666e https://github.com/galaxyproject/galaxy/commit/408906efb118dc4f36d134c632667... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3895 from dannon/routes_cleanup Routes cleanup Commit: f5ade2b5daab6fbf3fa924cbda89fbf21e7373a9 https://github.com/galaxyproject/galaxy/commit/f5ade2b5daab6fbf3fa924cbda89f... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Merge pull request #3897 from guerler/fix_refresh_trigger Add missing trigger event to drop handler in content selector Commit: b5323e7147266ccd14728e5b4783350c7704be30 https://github.com/galaxyproject/galaxy/commit/b5323e7147266ccd14728e5b47833... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3884 from glormph/kronik_proteomics_datatype Hardklor and kronik datatypes for proteomics Commit: e7a4ae5c154e5a9a9d2767c76ea043c5fd846fe8 https://github.com/galaxyproject/galaxy/commit/e7a4ae5c154e5a9a9d2767c76ea04... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/webapps/galaxy/config_watchers.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #3821 from mvdbeek/repository_updates Merge ToolConfWatchers and separate from Toolbox Commit: c4cf4164b31249457a4cdb92405006136193b1bb https://github.com/galaxyproject/galaxy/commit/c4cf4164b31249457a4cdb9240500... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M lib/galaxy/jobs/__init__.py A lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py M test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml Log Message: ----------- Allow explicit workflow scheduler handler process configuration. Refactor job handler stuff to allow this with re-use. Commit: fd216163aec719314fb328b87e5bea6f871a3b0a https://github.com/galaxyproject/galaxy/commit/fd216163aec719314fb328b87e5be... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Initial workflow scheduling handler fixes caught by :eagle::eyes:. Commit: 414abb00d1e5b25516d9ad714575b591ea503c2c https://github.com/galaxyproject/galaxy/commit/414abb00d1e5b25516d9ad714575b... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Add a validator that ensures a dataset's extra_files_path directory exists and is non-empty Commit: c134dac9d5f2ec86f0194d114d42c4742f63e6b9 https://github.com/galaxyproject/galaxy/commit/c134dac9d5f2ec86f0194d114d42c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Identify and handle runtime values when generating displayed text Commit: 7439d03bafe6fad42db950e85c0e329a8f0c8bff https://github.com/galaxyproject/galaxy/commit/7439d03bafe6fad42db950e85c0e3... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove optional app parameter for text conversion caller Commit: 278030638c50e51e18f712d19a2b8e71c2efc4a1 https://github.com/galaxyproject/galaxy/commit/278030638c50e51e18f712d19a2b8... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use new runtime value identifier for select field context values Commit: 18b006cb75ba8f8c088e17ebc7adc52a7b0e11f8 https://github.com/galaxyproject/galaxy/commit/18b006cb75ba8f8c088e17ebc7adc... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Remove app parameter from text conversion caller Commit: 8ef55bca36673a79974f9f2579543ed6cd15ef3d https://github.com/galaxyproject/galaxy/commit/8ef55bca36673a79974f9f2579543... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M templates/show_params.mako M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Remove app parameter from callers used in makos Commit: 9c9a7b97c557444e564c2de6669c28c02226f857 https://github.com/galaxyproject/galaxy/commit/9c9a7b97c557444e564c2de6669c2... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Remove parsing of app parameter from select field wrapper Commit: 7f111eea528b0be4ad6dfd59bb69076c899ce6aa https://github.com/galaxyproject/galaxy/commit/7f111eea528b0be4ad6dfd59bb690... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add missing spaces Commit: 735e38d1a3c582727476f8223cdd7c4606e5b413 https://github.com/galaxyproject/galaxy/commit/735e38d1a3c582727476f8223cdd7... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-11 (Tue, 11 Apr 2017) Changed paths: M test/unit/tools/test_wrappers.py Log Message: ----------- Adjust unit test cases Commit: 3e191c7ff4457ce4723c914d3ae9ad8157beecb5 https://github.com/galaxyproject/galaxy/commit/3e191c7ff4457ce4723c914d3ae9a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-12 (Wed, 12 Apr 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/queues.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into dev Commit: 4f4efe6405b866c419760af465500458d8dafdba https://github.com/galaxyproject/galaxy/commit/4f4efe6405b866c419760af465500... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-12 (Wed, 12 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix library parameter style width to avoid second line Commit: 23895e9ef0a001d4dafdedc8aee4846f8c7505d7 https://github.com/galaxyproject/galaxy/commit/23895e9ef0a001d4dafdedc8aee48... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #3926 from guerler/fix_library_parameter_style Fix library parameter style width to avoid second line Commit: d6336b712592809aabef507802d7ce8179a9d2d7 https://github.com/galaxyproject/galaxy/commit/d6336b712592809aabef507802d7c... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Remove unnecessary print Commit: d21c8dc8f11c2d4c40967ab9f532a5ce6364f2ea https://github.com/galaxyproject/galaxy/commit/d21c8dc8f11c2d4c40967ab9f532a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Merge pull request #3881 from erasche/unicode-viz-errors Fix inability for viz to raise loading with non-ascii messages Commit: 8599dff7a0098e121ddb244345a1c478f0a05cee https://github.com/galaxyproject/galaxy/commit/8599dff7a0098e121ddb244345a1c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Standardize usage of log.exception in datatypes registry. Commit: d303cf5ffbea29ad9d0d96b167f20606a022a488 https://github.com/galaxyproject/galaxy/commit/d303cf5ffbea29ad9d0d96b167f20... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Strip exception strings from being included in log.exception statements across the project. Commit: c46e36bdee354a879d2770b0ec9e22b00ec1c104 https://github.com/galaxyproject/galaxy/commit/c46e36bdee354a879d2770b0ec9e2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/managers/citations.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/__init__.py Log Message: ----------- Overhaul string templating in log.exception statements -- should apply to all logs, eventually. Commit: 55c4d52455763f516aed03795b4a6550ae5744c6 https://github.com/galaxyproject/galaxy/commit/55c4d52455763f516aed03795b4a6... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M templates/show_params.mako M templates/webapps/galaxy/workflow/display.mako M test/unit/tools/test_wrappers.py Log Message: ----------- Merge pull request #3920 from guerler/fix_display_to_text_for_runtime_values Identify and handle runtime values when generating displayed text Commit: 040635d3dcee4c13960170010c8a7c10319c4fd5 https://github.com/galaxyproject/galaxy/commit/040635d3dcee4c13960170010c8a7... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/jobs/__init__.py A lib/galaxy/util/handlers.py M lib/galaxy/workflow/scheduling_manager.py M test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml Log Message: ----------- Merge pull request #3844 from jmchilton/dev_workflow_conf Allow explicit configuration of handlers for workflow scheduling. Commit: 695293f01563f56637ee6b63db2c96bfd0204f9f https://github.com/galaxyproject/galaxy/commit/695293f01563f56637ee6b63db2c9... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt A config/containers_conf.yml.sample M config/galaxy.ini.sample M lib/galaxy/config.py R lib/galaxy/container/__init__.py R lib/galaxy/container/docker_swarm.py A lib/galaxy/containers/__init__.py A lib/galaxy/containers/docker.py A lib/galaxy/containers/docker_decorators.py A lib/galaxy/containers/docker_model.py A lib/galaxy/containers/docker_swarm.py A lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/util/submodules.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Merge pull request #3863 from natefoo/containers-abstraction Container interface abstraction Commit: 9b6a9dc0c73dfc0625e55a3db4c262174bda0dff https://github.com/galaxyproject/galaxy/commit/9b6a9dc0c73dfc0625e55a3db4c26... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_1.txt M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Start work on a relabelling collection operation. I think it needs to be touched up but the basic operation seems to work so far. I think what remains to be done is: - Validate uniqueness of identifiers and provide nice messages if they are not unique. - Validate that at least the required number of lines are present in the file and provide a nice message if not. - Add strict mode to ensure exactly the correct number of lines is added. - Find where validation of identifiers happens in the API and apply same validation here - try not to let unsafe identifiers be created. - Consider more advanced modes - selecting a column, apply a regex replace, pick two columns for nested lists, etc.... None of this may need to be needed in the first iteration. - Consider another mode where a collection is labelled against an existing collection - should that be a separate tool of the same tool. Commit: d21c14f0096b1fa7954396e7e9878b1d1e712331 https://github.com/galaxyproject/galaxy/commit/d21c14f0096b1fa7954396e7e9878... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_2.txt Log Message: ----------- Add possibility to rename collection items from a tabular file Commit: 338130a979c99f60a171ba6b9ffca5db0a0e16a8 https://github.com/galaxyproject/galaxy/commit/338130a979c99f60a171ba6b9ffca... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Fix failing test case in relable_from_file based on comment from @mvdbeek. Commit: 09bcdd9185e969c0eec34770faf8cb418c0f3e47 https://github.com/galaxyproject/galaxy/commit/09bcdd9185e969c0eec34770faf8c... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_bad_1.txt Log Message: ----------- Various improvements to relabel from file collection operation. - Better error handling (check for bad characters when creating collections). - Implement a strict mode parameter to do even more validation. - Rework tabular vs txt mode to be explicit user choice. - Mirror fix in release_17.01 for datasets not having a history, Commit: d43d7aa140f399fbaa65308fe842c9afba8c44a3 https://github.com/galaxyproject/galaxy/commit/d43d7aa140f399fbaa65308fe842c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-14 (Fri, 14 Apr 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/tools/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/utility_containers/__init__.py Log Message: ----------- Fix E241, F841 from exception refactoring. Commit: 77caed9861d3666150c49442df9374b63660c2e5 https://github.com/galaxyproject/galaxy/commit/77caed9861d3666150c49442df937... Author: Jim Johnson <jj@umn.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Update text.py Add interaction annotations to SnpEffDb metadata Interaction annotations are now included in SnpEff v4.3 Commit: e9011488f2f5bfe91f542d173a9f7b3132e414ad https://github.com/galaxyproject/galaxy/commit/e9011488f2f5bfe91f542d173a9f7... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #3938 from jj-umn/patch-6 Update text.py Add interaction annotations to SnpEffDb metadata Commit: 2288a88ab793198147fdb5a1050d0325a831d9f8 https://github.com/galaxyproject/galaxy/commit/2288a88ab793198147fdb5a1050d0... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_bad_2.txt Log Message: ----------- Fix relabel_from_file collection operation error handling if duplicate identifiers. Commit: abe6434916812a8236052560d58ab184b98b3ccb https://github.com/galaxyproject/galaxy/commit/abe6434916812a8236052560d58ab... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako Log Message: ----------- Update ethercalc GIE for readiness checking Commit: a2b8b43179cbf880f1e16ab43172545e4309c058 https://github.com/galaxyproject/galaxy/commit/a2b8b43179cbf880f1e16ab431725... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Generate proper url for readiness endpoint Commit: 154530994f979070fe8c94c7730a99d11164c7fc https://github.com/galaxyproject/galaxy/commit/154530994f979070fe8c94c7730a9... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Error handling for GIE container readiness check Commit: 1e536e4ec7325b8d61394ea4091d8285eff24315 https://github.com/galaxyproject/galaxy/commit/1e536e4ec7325b8d61394ea4091d8... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Add an ignore_volumes option for swarm_mode containers Commit: 49abfced0918e2722ad0325aa7df6abbd2c5019e https://github.com/galaxyproject/galaxy/commit/49abfced0918e2722ad0325aa7df6... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_from_file.xml M lib/galaxy/tools/relabel_from_file.xml A test-data/filter_labels_1.txt M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement collection operation for filtering lists from a file. Commit: c0fd3c7c6ddef01b0546b485a1a4e88d215042e2 https://github.com/galaxyproject/galaxy/commit/c0fd3c7c6ddef01b0546b485a1a4e... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-19 (Wed, 19 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Display input parameters default value for runtime values Commit: fba860f689d1af5e6727a946e20e1521f83620ed https://github.com/galaxyproject/galaxy/commit/fba860f689d1af5e6727a946e20e1... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-19 (Wed, 19 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Use local flag to handle runtime values Commit: 989b6be3390e35d896122ef044ffe114f8959949 https://github.com/galaxyproject/galaxy/commit/989b6be3390e35d896122ef044ffe... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-19 (Wed, 19 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Change to only inheriting 'name' tags -- we may want to branch this out further in the future, but we'll start conservatively. Commit: 9f4fd7c449646f8c3da9ba90d642a99b9cec386c https://github.com/galaxyproject/galaxy/commit/9f4fd7c449646f8c3da9ba90d642a... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/containers_conf.yml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M lib/galaxy/containers/docker_swarm.py M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Merge pull request #3941 from natefoo/containers-bugfixes Containers interface and GIE bugfixes Commit: 01b3eb42d88b1900b73a8dfb9eecdbce49e531e0 https://github.com/galaxyproject/galaxy/commit/01b3eb42d88b1900b73a8dfb9eecd... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_from_file.xml A lib/galaxy/tools/relabel_from_file.xml A test-data/filter_labels_1.txt A test-data/new_labels_1.txt A test-data/new_labels_2.txt A test-data/new_labels_bad_1.txt A test-data/new_labels_bad_2.txt M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3940 from jmchilton/collection_op_filter_from_file Collection Operation - Filtering from a File Commit: 4adda20b0b75ba68ebc69b4aefc86adea68299d4 https://github.com/galaxyproject/galaxy/commit/4adda20b0b75ba68ebc69b4aefc86... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M config/openid_conf.xml.sample R openid/google.xml Log Message: ----------- Remove Google from OpenID providers in the sample. Google dropped OpenID support a while back. Commit: 386afbb4f6ac703c60d2ffd975a1c3740f67457b https://github.com/galaxyproject/galaxy/commit/386afbb4f6ac703c60d2ffd975a1c... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/managers/citations.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/__init__.py Log Message: ----------- Merge pull request #3933 from dannon/exception_logging_fixes Standardize usage of log.exception Commit: 0bc8d1f4ceb8bf3a212c5d17ddc2a1aa3e096191 https://github.com/galaxyproject/galaxy/commit/0bc8d1f4ceb8bf3a212c5d17ddc2a... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M config/openid_conf.xml.sample Log Message: ----------- move genomespace as the first shown provider in selection Commit: e04ac61003787ea7c99bc524017ae8afaec1decf https://github.com/galaxyproject/galaxy/commit/e04ac61003787ea7c99bc524017ae... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M config/openid_conf.xml.sample R openid/google.xml Log Message: ----------- Merge pull request #3953 from dannon/openid_sample_nogoogle Remove Google from OpenID providers in the sample. Commit: 0fc0a49b4bb7de0f95bdd8f594a22515243cd4a7 https://github.com/galaxyproject/galaxy/commit/0fc0a49b4bb7de0f95bdd8f594a22... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/layout/menu.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.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/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- change 'user' menu to login or register for anons Commit: 1fa8c837accda3d8120538da98ef200ab0250453 https://github.com/galaxyproject/galaxy/commit/1fa8c837accda3d8120538da98ef2... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- improve french localization of the new menu item Commit: 439579298acbe2f85d79dd484ba1dca9cb15eee3 https://github.com/galaxyproject/galaxy/commit/439579298acbe2f85d79dd484ba1d... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3956 from galaxyproject/release_17.01 merge Release 17.01 Commit: 9c44ae01cd99e8d23335bbf5846d1a777b777969 https://github.com/galaxyproject/galaxy/commit/9c44ae01cd99e8d23335bbf5846d1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/repository_registry.py Log Message: ----------- Followup to exception refactoring, fixes a few issues @nsoranzo noticed with my semiautomatic refactorings. Commit: 0bd59518a6411858a44f1fe5a4bd8082df74353d https://github.com/galaxyproject/galaxy/commit/0bd59518a6411858a44f1fe5a4bd8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Unused exception, templates. Commit: e842a265875909a0bead4e6e3e9f8006170067c3 https://github.com/galaxyproject/galaxy/commit/e842a265875909a0bead4e6e3e9f8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/layout/menu.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.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/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- Merge pull request #3955 from martenson/user-menu-ux change 'user' menu to login or register for anons Commit: aa024f6d23389dd8868ce85f7544f1c7b3f58a8e https://github.com/galaxyproject/galaxy/commit/aa024f6d23389dd8868ce85f7544f... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/repository_registry.py Log Message: ----------- Merge pull request #3959 from dannon/exception_refactor_tweaks Followup to exception refactoring Commit: c9087fe21e650892af647940915f3bcfbac693cc https://github.com/galaxyproject/galaxy/commit/c9087fe21e650892af647940915f3... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt A lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Graphite support Commit: d41ad577617da2577b5dabadb47cb37a7edc5cb1 https://github.com/galaxyproject/galaxy/commit/d41ad577617da2577b5dabadb47cb... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix margin style values for color picker element Commit: a6a920cb5ebb71a8f0349e733b31ffdd70ffab27 https://github.com/galaxyproject/galaxy/commit/a6a920cb5ebb71a8f0349e733b31f... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-color-picker.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-color-picker.js M static/style/blue/base.css Log Message: ----------- Remove unused label attribute, fix styles within color selector, remove encoded style attributes Commit: 9aa7c6d2e905fc83bb9aee2c06f85f6aa7e1ad8c https://github.com/galaxyproject/galaxy/commit/9aa7c6d2e905fc83bb9aee2c06f85... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/repository_registry.py M static/maps/layout/menu.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.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/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- Merge branch 'dev' into fix_color_input_style Commit: 26c06880c2d49bda0c03c0ec11f39e6a529a962b https://github.com/galaxyproject/galaxy/commit/26c06880c2d49bda0c03c0ec11f39... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- flake8 Commit: e9eba8625d7922a9e7e7f759fc797d4fab8ddb7d https://github.com/galaxyproject/galaxy/commit/e9eba8625d7922a9e7e7f759fc797... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Small selenium hack. Commit: 388bb42ba067a1464c1393208c3d6eea7eff0315 https://github.com/galaxyproject/galaxy/commit/388bb42ba067a1464c1393208c3d6... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: A doc/source/admin/special_topics/grafana.png M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/performance_tracking.rst Log Message: ----------- Stats docs Commit: 060dc7379e4a74c33a19e82c6a160f97bab1cf9e https://github.com/galaxyproject/galaxy/commit/060dc7379e4a74c33a19e82c6a160... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'release_17.01' into dev Commit: ade550f9527fd1651d79a9d01f1a4dc798585bcf https://github.com/galaxyproject/galaxy/commit/ade550f9527fd1651d79a9d01f1a4... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml Log Message: ----------- Fix some selectors in tours Commit: 898f22c75d5a0afeeb30df113f304e66a5b4c70b https://github.com/galaxyproject/galaxy/commit/898f22c75d5a0afeeb30df113f304... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- More fixes for History Intro tour - Remove unnecessary quotes that end up in the pop-up - Fix one pop-up title - Remove one step that is broken if the user is already logged-in Commit: feb31685f63f6805d2e5953697b9ed531a44379d https://github.com/galaxyproject/galaxy/commit/feb31685f63f6805d2e5953697b9e... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Do not click on the section name, it is already expanded Introduced in commit ca36c0dbfd438708e35e18d06c603f2cc2ce7047 . Commit: 2b05fd050a3e1b517ca992a37f5d574521a37dd2 https://github.com/galaxyproject/galaxy/commit/2b05fd050a3e1b517ca992a37f5d5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #3970 from nsoranzo/tour_fixes Tour fixes Commit: 908dd2d342bbd5467b52211ba6fcbf02788d2371 https://github.com/galaxyproject/galaxy/commit/908dd2d342bbd5467b52211ba6fcb... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Fix some typos in config/galaxy.ini.sample Commit: 57c4020518f05221c118c9254111f789f4fe2116 https://github.com/galaxyproject/galaxy/commit/57c4020518f05221c118c9254111f... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3971 from nsoranzo/galaxy.ini_typos Fix some typos in config/galaxy.ini.sample Commit: 722c294165eb40aad9d8f4a3d02e383563064b3e https://github.com/galaxyproject/galaxy/commit/722c294165eb40aad9d8f4a3d02e3... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Use first/last child selector Commit: 6c51f5232a7af4b0a73d803b4a3e7c64b23ec9c7 https://github.com/galaxyproject/galaxy/commit/6c51f5232a7af4b0a73d803b4a3e7... Author: guerler <aysam.guerler@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M static/maps/mvc/ui/ui-color-picker.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-color-picker.js Log Message: ----------- Remove unused classes from code file Commit: b9effa4a2b7ccad8e210243853d0e9429b3b034d https://github.com/galaxyproject/galaxy/commit/b9effa4a2b7ccad8e210243853d0e... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt A lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3964 from erasche/graphite Graphite support Commit: 45e40a184a416e28d771c3cca4f487b06b6e284e https://github.com/galaxyproject/galaxy/commit/45e40a184a416e28d771c3cca4f48... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: A doc/source/admin/special_topics/grafana.png M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/performance_tracking.rst Log Message: ----------- Merge pull request #3968 from erasche/stats-docs Stats docs Commit: 399c7f061ceff36c355536abd499362edc6f90d5 https://github.com/galaxyproject/galaxy/commit/399c7f061ceff36c355536abd4993... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-color-picker.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-color-picker.js M static/style/blue/base.css Log Message: ----------- Merge pull request #3965 from guerler/fix_color_input_style Fix margin style values for color picker element Commit: 2f518e5ee4444e3a95b6f4967366a1b38b1ca3b4 https://github.com/galaxyproject/galaxy/commit/2f518e5ee4444e3a95b6f4967366a... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #3967 from jmchilton/selenium_fixes_8 Small selenium hack to fix occasionally failing collection upload tests. Commit: 80324d08a5270b4961f706b1951c3b0f8c7ffe57 https://github.com/galaxyproject/galaxy/commit/80324d08a5270b4961f706b1951c3... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- 17.01 version of rstudio Commit: b1c6d3363d6bccbc53c689543efa4460d796c814 https://github.com/galaxyproject/galaxy/commit/b1c6d3363d6bccbc53c689543efa4... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample Log Message: ----------- remove old versions Commit: 60a05c1811c3716e47c28ecec6f2ab25d3b56d97 https://github.com/galaxyproject/galaxy/commit/60a05c1811c3716e47c28ecec6f2a... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: 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 Log Message: ----------- more touch-ups and easier vimdiffing with jupyter configs Commit: 42734350d2e44fce1b2e699f643d755e7e4441be https://github.com/galaxyproject/galaxy/commit/42734350d2e44fce1b2e699f643d7... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: f3c8edea83e537281e830fe8fa6d9de3da836489 https://github.com/galaxyproject/galaxy/commit/f3c8edea83e537281e830fe8fa6d9... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Use abstract dataset functions for testing Commit: ec22b1d3ecd85cff65d232d0997703ee096d5ce1 https://github.com/galaxyproject/galaxy/commit/ec22b1d3ecd85cff65d232d099770... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Fixes to get IEs working on Mac OS X. - Fix logic error related to config parsing (OS non-specific). - Don't trust GatewayAddress from Docker if on Mac OS X - it is probably a Docker host VM specific address. - Update sqlite dependency for the newest version of Node available from Mac OS X Homebrew. - Add a little blurb about how to configure galaxy_infrastructure_url in this case. Commit: d082f1c334f3079249ed4d2404c52ac96850dc4b https://github.com/galaxyproject/galaxy/commit/d082f1c334f3079249ed4d2404c52... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/tag.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tag.js Log Message: ----------- Purely clientside implementation of hashtag shortcut for nametags. These are translated to 'name:nametag_value' prior to saving and are persisted in that form. Commit: f3dbf55aad06c64e26fd7dd44db9a87c73835153 https://github.com/galaxyproject/galaxy/commit/f3dbf55aad06c64e26fd7dd44db9a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/tag.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/tag.js Log Message: ----------- Render 'name:' as hashtags. I personally like the display better and it'll nudge people towards using them I think, while still giving us the 'real' tagging hierarchy to work with. Commit: 4a5c8823173a125fd3eade1693a23ba6e6b73aa5 https://github.com/galaxyproject/galaxy/commit/4a5c8823173a125fd3eade1693a23... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Remove unused import Commit: 910c22b7a1c759a651186f13e6c6707d91becfec https://github.com/galaxyproject/galaxy/commit/910c22b7a1c759a651186f13e6c67... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Merge pull request #3978 from jmchilton/ie_for_mac_os_x_fixes Fixes to get GIEs working on Mac OS X. Commit: c84b5725e63a3b93b5c798d23b277df27d63cd6f https://github.com/galaxyproject/galaxy/commit/c84b5725e63a3b93b5c798d23b277... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #3977 from nsoranzo/travis Use container-based infrastructure (sudo: false) in TravisCI Commit: 740d85a6a6f8b3877faf75fa3488a1a1d2a10c1e https://github.com/galaxyproject/galaxy/commit/740d85a6a6f8b3877faf75fa3488a... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3975 from erasche/17.05-gie-fixes 17.05 rstudio fixes / one small gie fix Commit: d398c90dbd70fff91a672935997bc21e949e8767 https://github.com/galaxyproject/galaxy/commit/d398c90dbd70fff91a672935997bc... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M test/api/test_workflows.py M test/qunit/tests/ui_tests.js Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: static/maps/mvc/ui/ui-select-content.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/ui/ui-select-content.js Commit: 647b4901c30d356f13f851a76c2a7c7ed8bfd808 https://github.com/galaxyproject/galaxy/commit/647b4901c30d356f13f851a76c2a7... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M Makefile M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- move reqs to dev-requirements and touch makefile Commit: d42fc9ae71b26caed30d6b904681a6b2065febbc https://github.com/galaxyproject/galaxy/commit/d42fc9ae71b26caed30d6b904681a... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .ci/py3_sources.txt M .gitignore M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js A client/galaxy/scripts/mvc/collection/base-creator.js M 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tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.xml M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_binned_scores_in_intervals.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' into fix_documentation_build Commit: be7d1294fd69618cbd415df4c562ce2c4ef88808 https://github.com/galaxyproject/galaxy/commit/be7d1294fd69618cbd415df4c562c... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M tox.ini Log Message: ----------- Fix Travix builds which use flake8-docstrings flake8-docstrings is broken due to the release of pydocstyle 2.0.0 (see https://gitlab.com/pycqa/flake8-docstrings/issues/19 ), so temporarily add an extra dep in tox.ini to pin it. Commit: 9f36bea7f1aa25bc193ec1bcc243d303cbfff1bc https://github.com/galaxyproject/galaxy/commit/9f36bea7f1aa25bc193ec1bcc243d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/tag.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/tag.js Log Message: ----------- Slight refactoring, also name->hash for recommended tags. Commit: a2b8a7d26ab748d7565ef9245a678bc2740d1bdd https://github.com/galaxyproject/galaxy/commit/a2b8a7d26ab748d7565ef9245a678... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/ui/ui-select-content.js M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/js/package.json M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M test/api/test_workflows.py M test/qunit/tests/ui_tests.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into hashtags Commit: 7edfe39f20024f161a30be14406c0baa2a9807bf https://github.com/galaxyproject/galaxy/commit/7edfe39f20024f161a30be14406c0... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M Makefile Log Message: ----------- fix makefile help for docs thanks nsoranzo Commit: b7a8bea3cd67b8e889f44fd88b8529e47fe53cbc https://github.com/galaxyproject/galaxy/commit/b7a8bea3cd67b8e889f44fd88b852... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #3981 from nsoranzo/fix_py27-lint_build Fix Travix builds which use flake8-docstrings Commit: ea3796152a01aad87f0585bf83ceb661392ba4d4 https://github.com/galaxyproject/galaxy/commit/ea3796152a01aad87f0585bf83ceb... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Replace wiki.galaxyproject.org links in /lib Commit: 04a32064f1d553c01828092b445175a9c7d8a53d https://github.com/galaxyproject/galaxy/commit/04a32064f1d553c01828092b44517... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/viz/phyloviz.js M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/viz/phyloviz.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/citation/citation-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/viz/phyloviz.js Log Message: ----------- Update wiki.galaxyproject.org links in client Commit: a5143ce7a86cb64c81b0ffa36a90742b872cec15 https://github.com/galaxyproject/galaxy/commit/a5143ce7a86cb64c81b0ffa36a907... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/data_manager/index.mako Log Message: ----------- Convert wiki.galaxyproject.org links in templates Commit: 29aa00e42129bec564a9f1009547e3b740b29709 https://github.com/galaxyproject/galaxy/commit/29aa00e42129bec564a9f1009547e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .travis.yml M CONTRIBUTING.md M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/grid/grid-template.js M 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test/integration/workflow_handler_configuration_job_conf.xml A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml M test/qunit/package.json M test/qunit/test-data/paired-collection-creator.data.js M test/qunit/tests/ui_tests.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/filters/trimmer.py M tools/filters/trimmer.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into wiki-to-hub Commit: 0dd75e6cdd985ec3711987ef8adb3fe6365b8501 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Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako A templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Attempt to rectify bad merge. Commit: 05e81192bd91559876da1a82b734c7e49e15f43e https://github.com/galaxyproject/galaxy/commit/05e81192bd91559876da1a82b734c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M test/qunit/tests/form_tests.js Log Message: ----------- Update tool form qunit test text. Commit: 291426a5dcd7941e1d6711b5926418bf0dab0c4c https://github.com/galaxyproject/galaxy/commit/291426a5dcd7941e1d6711b592641... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3943 from guerler/show_default_value_for_runtime_values Show default value for runtime values Commit: 92d93c7ef96452ba343a43502fe519e0dea3f8bf https://github.com/galaxyproject/galaxy/commit/92d93c7ef96452ba343a43502fe51... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge pull request #3263 from zfrenchee/patch-1 Azure - Leasing container sometimes breaks things in docker galaxy Commit: 78c263ac7c6beb1b93269f252897b0dd6336b450 https://github.com/galaxyproject/galaxy/commit/78c263ac7c6beb1b93269f252897b... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Udpate Babel to a version compat. with sphinx. Commit: 3e14cd532074d190def283ed2cce61ae22c0eee9 https://github.com/galaxyproject/galaxy/commit/3e14cd532074d190def283ed2cce6... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #3986 from jmchilton/babel_update Udpate Babel to a version compat. with sphinx. Commit: b12b951e91e6b8472f81d73f184c40aac7f9aad8 https://github.com/galaxyproject/galaxy/commit/b12b951e91e6b8472f81d73f184c4... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Attempted fix for transiently failing API test_jobs introduced in #3619. A couple things need to occur while the jobs are "running" and it seems that 60 seconds wasn't enough time to sleep for all that to happen on Jenkins. I checked the timing in the raw logs (they are for some reasons being filtered out in the Jenkins display of the XUnit) - and indeed the jobs are properly sleeping the correct amount of time but the client API calls need some more time it seems. My initial thought was maybe the jobs were being interrupted or something - and that does not appear to be the case. Commit: 26afd36a4d1336825fa47e2e8f3921c4ee8e1486 https://github.com/galaxyproject/galaxy/commit/26afd36a4d1336825fa47e2e8f392... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge remote-tracking branch 'guerler/login_routes' into dev Commit: 54b9d7ac10535e56caf9389da00125664a9a779e https://github.com/galaxyproject/galaxy/commit/54b9d7ac10535e56caf9389da0012... Author: Dave B <dave@bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Use the configured tool_path when loading data managers. Commit: 7ba3662d29f0f8d9c6a24ea3fa66eee421f6059d https://github.com/galaxyproject/galaxy/commit/7ba3662d29f0f8d9c6a24ea3fa66e... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M Makefile M lib/galaxy/dependencies/dev-requirements.txt Log Message: ----------- Merge pull request #3104 from athos-ribeiro/fix_documentation_build Add missing imports for documentation builds Commit: 92f3841bee3a473b85661779790a40f773b0f86d https://github.com/galaxyproject/galaxy/commit/92f3841bee3a473b85661779790a4... Author: Dave B <dave@bx.psu.edu> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Remove dev remnant. Commit: 8b21e651969fff8cff41f736c47312f099cc5ee9 https://github.com/galaxyproject/galaxy/commit/8b21e651969fff8cff41f736c4731... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Improve implicit workflow connection test case. I think https://jenkins.galaxyproject.org/job/docker-api/7316/testReport/junit/api.t... may be the first time I have seen it fail - but still it has some other problems. - Eliminate the sleep - instead wait on explicitly on the desired condition (first two jobs are complete and the workflow is ready for unpause). This is likely why the test case failed. - Improve the other assertions to provide more details in the test case ever fails again. Commit: 1d9b7d592b131b69b91c40eeed3e844df65f67e4 https://github.com/galaxyproject/galaxy/commit/1d9b7d592b131b69b91c40eeed3e8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into hashtags Commit: 6e1daab992c27fa22b7682bcf5609fcea75aa800 https://github.com/galaxyproject/galaxy/commit/6e1daab992c27fa22b7682bcf5609... Author: Dave B <dave@bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Fix errors discovered by Nicola. Commit: 89e692d980965f5a1963818180ccaf62ae2c207f https://github.com/galaxyproject/galaxy/commit/89e692d980965f5a1963818180cca... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M CITATION M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M config/galaxy.ini.sample M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/workflow/workflow-forms.js M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Tweaks for @nsoranzo. Commit: 5fe7b7208c8668b7d4dd9dc31568c77a0a8c2562 https://github.com/galaxyproject/galaxy/commit/5fe7b7208c8668b7d4dd9dc31568c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M templates/admin/tool_shed_repository/select_tool_panel_section.mako Log Message: ----------- Fix support link Commit: a26991b2a8bea94a98eae38bdacc4739a818f57a https://github.com/galaxyproject/galaxy/commit/a26991b2a8bea94a98eae38bdacc4... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Selenium workflow run test case fix. The ``with self.main_panel():`` construct wasn't cleaning up properly - I've fixed this and eliminated the terrible workarounds in the execution test case that I guess I had added trying to figure out how to make things work. It should be more stable now. (This test case has been failing 1 out 9 times I'd say.) Commit: 760160a02cd925168eefb0b05a4471bd5dbc7b61 https://github.com/galaxyproject/galaxy/commit/760160a02cd925168eefb0b05a447... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #3991 from jmchilton/workflow_connection_test_case_improvement Improve implicit workflow connection test case. Commit: 85a9b37d80fcc503d674e4f3322b9e618f5e87c5 https://github.com/galaxyproject/galaxy/commit/85a9b37d80fcc503d674e4f3322b9... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M run_tests.sh M test/selenium_tests/framework.py Log Message: ----------- Setup framework for retrying failed Selenium tests. - By default this won't occur locally, but you can set GALAXY_TEST_SELENIUM_RETRIES to a non-zero number to enable auto retrying tests that many times. - Capture the stack trace in the Selenium test error report directory - this will be useful for debugging problems that may fail once but pass on a subsequence attempt. Jenkins now captures these directories and includes their content in the test reports. - Document the Selenium test error report directory in run_tests.sh as well as this new retry variable. - Update the Jenkins test script to set this new variable to 1 so transient failures break the build much less frequently. Commit: 5fd7f8bdf728356ee1aeafb36996392dd91b9e46 https://github.com/galaxyproject/galaxy/commit/5fd7f8bdf728356ee1aeafb369963... Author: Dave B <dave@bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Explicit is better than implicit. Commit: f0740136831623adf8b2c1fe9ed17dbf4327ebc4 https://github.com/galaxyproject/galaxy/commit/f0740136831623adf8b2c1fe9ed17... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M config/galaxy.ini.sample Log Message: ----------- Small tweaks for data-libraries URLS Commit: dab18fb2387d737f859637bbd37d9b0ce3ec658c https://github.com/galaxyproject/galaxy/commit/dab18fb2387d737f859637bbd37d9... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M CITATION M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/viz/phyloviz.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/viz/phyloviz.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/citation/citation-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/viz/phyloviz.js M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako M test/qunit/tests/form_tests.js Log Message: ----------- Merge branch 'wiki-to-hub' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: 5a6e53f728858d14064c984956c5c24666395da3 https://github.com/galaxyproject/galaxy/commit/5a6e53f728858d14064c984956c5c... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Rework Jupyter IE for additional_ids handling. - Add a new option ``use_volumes`` to the Docker config. - If using volumes, do nothing differently. - If not using volumes, set ADDITIONAL_IDS in the environment for the IE itself to fetch (requires https://github.com/bgruening/docker-jupyter-notebook/pull/17). Commit: 9bc24aeef06b3536a6f69ddc23ac1ede4fb9b7a0 https://github.com/galaxyproject/galaxy/commit/9bc24aeef06b3536a6f69ddc23ac1... Author: John Chilton <jmchilton@gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Update rstudio to match additional hid handling of Jupyter. Ping @erasche - does this work? I'm not sure how rstudio handles the existing DATASET_HID. Commit: 5b9bc76cac7f8ad4dd859af97e9ae1199cf6e62a https://github.com/galaxyproject/galaxy/commit/5b9bc76cac7f8ad4dd859af97e9ae... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Change validator name Commit: 2b09fe149dc7b65718f4a74f288cfe27cf6fcf82 https://github.com/galaxyproject/galaxy/commit/2b09fe149dc7b65718f4a74f288cf... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Merge pull request #3989 from davebx/fix_managers Use the configured tool_path when loading data managers Commit: a32e78585c843517d5ae091ce03e08427214f2ff https://github.com/galaxyproject/galaxy/commit/a32e78585c843517d5ae091ce03e0... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Merge pull request #3918 from gregvonkuster/fpv Add a validator that ensures a dataset's extra_files_path Commit: c93afcec64d5f4036bf75011c35b4c8497068238 https://github.com/galaxyproject/galaxy/commit/c93afcec64d5f4036bf75011c35b4... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh M run_tests.sh M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #3993 from jmchilton/selenium_fixes_10 Setup framework for retrying failed Selenium tests. Commit: ffed281c33be5bcb1006cd3e94055fa01e5c3d18 https://github.com/galaxyproject/galaxy/commit/ffed281c33be5bcb1006cd3e94055... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-04-30 (Sun, 30 Apr 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Merge pull request #3988 from jmchilton/job_test_timing_improvements Attempted fix for transiently failing API test_jobs introduced in #3619. Commit: 7b385c2b849fc091a477b75a9194a99934454f8e https://github.com/galaxyproject/galaxy/commit/7b385c2b849fc091a477b75a9194a... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #3992 from jmchilton/selenium_fixes_9 Fixes for Selenium workflow run test case. Commit: 313a006ae3ea9d383ad102ceda17f657275ff5bf https://github.com/galaxyproject/galaxy/commit/313a006ae3ea9d383ad102ceda17f... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add entry for empty_extra_files_path validator Commit: 41cbe242991eb69bc821a9f2d0b8ab599b73aa9a https://github.com/galaxyproject/galaxy/commit/41cbe242991eb69bc821a9f2d0b8a... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Use floating point to log toolox reload times Commit: 4d1cae41cb7ce0d3aa10d413de8ec4000e50444a https://github.com/galaxyproject/galaxy/commit/4d1cae41cb7ce0d3aa10d413de8ec... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Add timing information for Data Manager reload Commit: c06b4c92658563fda4efe8b1dcf6045113b664fd https://github.com/galaxyproject/galaxy/commit/c06b4c92658563fda4efe8b1dcf60... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/toolbox/cache.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Add a short-lived (1s) ToolShedRepositoryCache This will speed up repeated ToolShedRepositories lookups, like when building the Toolbox for the first time, or when loading a shed_tool_conf.xml file with many deactivated tools. Commit: 43c9c287a9a3520d77cc9235dfbfa6ac6cf33227 https://github.com/galaxyproject/galaxy/commit/43c9c287a9a3520d77cc9235dfbfa... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Speed up tool-data table reloads by doing a os.walk and caching the result for 1s instead of repeatedly calling os.path.exists. Commit: 34ed9b48ddc2fdd0e2456b959fed5eedec9b92c1 https://github.com/galaxyproject/galaxy/commit/34ed9b48ddc2fdd0e2456b959fed5... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/cache.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Only index changed tools when re-indexing the toolbox This speeds up repeated toolbox reloads enourmously (from 1 second on my test-instance to 0.1 seconds). Commit: c6429bff1c38b2196fece8155449ba62723242ee https://github.com/galaxyproject/galaxy/commit/c6429bff1c38b2196fece8155449b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Always use cache to fetch tool_version objects Commit: 96cb87431402454fa52db35547fb3028c5aae807 https://github.com/galaxyproject/galaxy/commit/96cb87431402454fa52db35547fb3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Use cElementTree for light xml parsing speedup Commit: 2906f0c0857fc958f7e9049e2e7134065908852f https://github.com/galaxyproject/galaxy/commit/2906f0c0857fc958f7e9049e2e713... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/lineages/tool_shed.py Log Message: ----------- Update ToolVersionCache when adding a new ToolShedLineage Commit: 6c22726db082cedee9884bde9aa913bbb93dea05 https://github.com/galaxyproject/galaxy/commit/6c22726db082cedee9884bde9aa91... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py Log Message: ----------- Move tool_cache.reset_status() calls to reload toolbox/data managers, so that we can use information about whether tools are new during reloads Commit: 431a4824abf91b7a10e5417d63a990ba0a5f916d https://github.com/galaxyproject/galaxy/commit/431a4824abf91b7a10e5417d63a99... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py Log Message: ----------- Make sure re-indexing the toolbox occurs on the new toolbox Commit: ea9ecdf57150e800115ae28f6e80d80a7bfef249 https://github.com/galaxyproject/galaxy/commit/ea9ecdf57150e800115ae28f6e80d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Remove `replace_existing` option for data managers If a data manager is defined twice for the same data manager id in the shed_tool_conf.xml the first data manager will be loaded. This is not a problem when updating a data manager through the toolshed, because the outdated data manager will be removed from the tool cache and a new toolbox is being built. Commit: db910f4f81771f91f9a5b96bfc5fb9bd6d506e2b https://github.com/galaxyproject/galaxy/commit/db910f4f81771f91f9a5b96bfc5fb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Reset the tool cache once all tools are loaded after starting up galaxy Commit: 9aa5556dedb35b748ed17b20fd26348fdcdea829 https://github.com/galaxyproject/galaxy/commit/9aa5556dedb35b748ed17b20fd263... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Reduce logging during toolbox reloads We don't log loading of tools that have not changed when reloading the toolbox. Commit: 475b8866bad2a58b314354ae73ee1e5ccd94b8cb https://github.com/galaxyproject/galaxy/commit/475b8866bad2a58b314354ae73ee1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py Log Message: ----------- Fix unittests that access app.tool_cache Commit: beae93bf766fc48a3a2f2edcd275d13ae0fe8ba2 https://github.com/galaxyproject/galaxy/commit/beae93bf766fc48a3a2f2edcd275d... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Re-use ExecutionTimer abstractions for consistent log patterns. Commit: a83ef0b86c0acbfb7c0bf1b40579e5102c78ad29 https://github.com/galaxyproject/galaxy/commit/a83ef0b86c0acbfb7c0bf1b40579e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py Log Message: ----------- Log startup time Commit: 3ff2a7832a949d300d9cddab0fea05fa74b1a403 https://github.com/galaxyproject/galaxy/commit/3ff2a7832a949d300d9cddab0fea0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Fix cElementTree imports Commit: c905c4217b0397f92b2eb1019308851da043682f https://github.com/galaxyproject/galaxy/commit/c905c4217b0397f92b2eb10193088... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Fix import order in lib/galaxy/tools/data/__init__.py Commit: b72994fe0294326f99df880e3ba7e248f1ffe145 https://github.com/galaxyproject/galaxy/commit/b72994fe0294326f99df880e3ba7e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Add possibility explicitly rebuild ToolShedRepositoryCache Commit: 84c1559d473f7d9234173aeb802f30067fe0ffe6 https://github.com/galaxyproject/galaxy/commit/84c1559d473f7d9234173aeb802f3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Fix path checking for files that are not in the tool_data_path directory Commit: 0504dcd2997bc4673ded5c7fdc1e2b28a85dcb18 https://github.com/galaxyproject/galaxy/commit/0504dcd2997bc4673ded5c7fdc1e2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Use generator instead of list comprehenesion followed converting it to a set. (Thanks @nsoranzo) Commit: cbed78fbfbcb1c381af5be9442c8ce6af1a3a554 https://github.com/galaxyproject/galaxy/commit/cbed78fbfbcb1c381af5be9442c8c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Don't return toolbox (thx @nsoranzo) Commit: 4dd49c938d2c7bcfac37fe475eccb1e32653b6b4 https://github.com/galaxyproject/galaxy/commit/4dd49c938d2c7bcfac37fe475eccb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py Log Message: ----------- Use ExecutionTimer abstraction to report startup time Commit: dc1617596e47c384b8a88de395fe41a681145ffd https://github.com/galaxyproject/galaxy/commit/dc1617596e47c384b8a88de395fe4... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Remove unused time import Commit: 4c44338144763819f78f99b84d5816ded18de372 https://github.com/galaxyproject/galaxy/commit/4c44338144763819f78f99b84d581... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Be more defesive when accessing app.tool_cache Commit: 5069815c0eba0a7c4c406ec0f781f138f7aee291 https://github.com/galaxyproject/galaxy/commit/5069815c0eba0a7c4c406ec0f781f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Rebuild repo cache when deciding if repository should be created. Commit: d15813cb2a489e1de8771886e9df8ebb69fc079e https://github.com/galaxyproject/galaxy/commit/d15813cb2a489e1de8771886e9df8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Avoid having tools in tool_cache marked as new when they have rapidly shifted from new to expired. Commit: 586f49486cf4c1f4597237d3df95562bb477c6f8 https://github.com/galaxyproject/galaxy/commit/586f49486cf4c1f4597237d3df955... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Don't crash if a tool has not been added to the cache properly Commit: 3d6bc1d56372b5853fdddd08362d8f57b4026adb https://github.com/galaxyproject/galaxy/commit/3d6bc1d56372b5853fdddd08362d8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Refresh tool_data_path_files if we know that a new table has been written Commit: 07da123e9d311e5ec453399024ef992859770234 https://github.com/galaxyproject/galaxy/commit/07da123e9d311e5ec453399024ef9... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Reference old_toolbox earlier, since reloading can happen in a different thread, which will lead to a hang when waiting for another toolbox reload Commit: 677d98622dfa30a65d8a8fc392c25077abdcc0e9 https://github.com/galaxyproject/galaxy/commit/677d98622dfa30a65d8a8fc392c25... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/tool_shed/util/repository_util.py Log Message: ----------- Always refresh tool_shed_repository_cache before fetching repositories by ids (since that is only called from admin_toolshed.py and installed_repository_metadata_manager.py) Commit: f940c797ff981c3f0a12b6a3abeee61e05ff2436 https://github.com/galaxyproject/galaxy/commit/f940c797ff981c3f0a12b6a3abeee... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix import order in lib/galaxy/config.py Commit: 89f57f2aa753f5de9673cd3dcf5c13ca3d3f6639 https://github.com/galaxyproject/galaxy/commit/89f57f2aa753f5de9673cd3dcf5c1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Allow looking up repositories by repository_id via ToolShedRepositoryCache Commit: 456d1b47b62d05d3fc5180d4f9da525317efc28c https://github.com/galaxyproject/galaxy/commit/456d1b47b62d05d3fc5180d4f9da5... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/util/tool_dependency_util.py Log Message: ----------- Refresh TSR cache when needed Commit: 8411b0253adc947838af760e4614611ac8183464 https://github.com/galaxyproject/galaxy/commit/8411b0253adc947838af760e46146... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Restore deactivate/activate functionality Commit: 15e2c9b61aae9476b519a8c2e1c233e134e3ebbc https://github.com/galaxyproject/galaxy/commit/15e2c9b61aae9476b519a8c2e1c23... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Revert "Fix cElementTree imports" This reverts commit 6d365f03e888ef12527105119f0a7adebae23b95. Commit: 7e61f8c047ce3cb29f5d9999a93b2c7bd0ee1cde https://github.com/galaxyproject/galaxy/commit/7e61f8c047ce3cb29f5d9999a93b2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Revert "Use cElementTree for light xml parsing speedup" This reverts commit 556469f5171ef9897a5c40de9d661d2d4f4deb86. Commit: 141f15256e8ef39baf457be1e8ef1cdf5414f5aa https://github.com/galaxyproject/galaxy/commit/141f15256e8ef39baf457be1e8ef1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Use ExecutionTimer Commit: 73c7c364a25caf519dfd4cfea17b500077510a74 https://github.com/galaxyproject/galaxy/commit/73c7c364a25caf519dfd4cfea17b5... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use tool_shed_repository_cache in populate_tool_shed_info Commit: 869d7bf481e77aca420cc3970844650f7ad6ff20 https://github.com/galaxyproject/galaxy/commit/869d7bf481e77aca420cc39708446... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/auth/__init__.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/util/plugin_config.py Log Message: ----------- Replace getchildren(), which has been deprecated (https://docs.python.org/2/library/xml.etree.elementtree.html#xml.etree.Eleme...) Commit: 3079d0c239bf7c46d872e65d107eaab4b3741b46 https://github.com/galaxyproject/galaxy/commit/3079d0c239bf7c46d872e65d107ea... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Write out the datatype registry only once Commit: f88304b65b430da0a3db67e25e457044c373bf99 https://github.com/galaxyproject/galaxy/commit/f88304b65b430da0a3db67e25e457... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/search/__init__.py Log Message: ----------- Build toolbox search in a local control task Commit: 5e7da2c910e28e13b5a79c3ad794d6f40446694a https://github.com/galaxyproject/galaxy/commit/5e7da2c910e28e13b5a79c3ad794d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py M test/base/driver_util.py Log Message: ----------- Don't fail tests without internet connectivity Commit: 5a26896745c16e25ce951ee3a85bdc2cd81087e1 https://github.com/galaxyproject/galaxy/commit/5a26896745c16e25ce951ee3a85bd... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/parser/xml.py M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Write out datatype registry when loading set_metadata tool Commit: f199d5b434da500330520f891a3188ee69eccce4 https://github.com/galaxyproject/galaxy/commit/f199d5b434da500330520f891a318... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Keep cache thread-local Commit: b4e4f3ce7a9bc6ef06b4191bf8f8f2fef493d844 https://github.com/galaxyproject/galaxy/commit/b4e4f3ce7a9bc6ef06b4191bf8f8f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Use current session Commit: ff1b66afb325ebe68a2d174503980b03100ca6d4 https://github.com/galaxyproject/galaxy/commit/ff1b66afb325ebe68a2d174503980... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Fix thread local cache use Commit: 84351de20bef488022cf82ac2610e2e5c0b369cd https://github.com/galaxyproject/galaxy/commit/84351de20bef488022cf82ac2610e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Send control task as postfork function Commit: b666649c8159316eaa22bc4c89575fda38e9838d https://github.com/galaxyproject/galaxy/commit/b666649c8159316eaa22bc4c89575... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Work around InstanceDetached errors Commit: 86684df5ef235b6390f0cfa838927cf6e5b67330 https://github.com/galaxyproject/galaxy/commit/86684df5ef235b6390f0cfa838927... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Skip time-based reloading, rely on detecting DetachedInstanceErrors to trigger cache rebuild Commit: cdad5bee9b1f9761a5b3ab56cbdc3c3eb6e63e14 https://github.com/galaxyproject/galaxy/commit/cdad5bee9b1f9761a5b3ab56cbdc3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py Log Message: ----------- Attempt to speedup proprietary datatype loading Commit: 2587ab55b8743ae626f977961e4f3c8e7cb0eb05 https://github.com/galaxyproject/galaxy/commit/2587ab55b8743ae626f977961e4f3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/util/tool_util.py Log Message: ----------- Remove operations from custom_datatype_manager Updating the upload file formats is handled when loading the datatype into the registry, and reloading the upload tool seems unnecessary and insufficient, since this would only affect the current web handler. In any case removed and added datatypes are immediately propagated to the upload tool. Commit: af156a8f7496dc9a9e70d3992f227c626aec7fa2 https://github.com/galaxyproject/galaxy/commit/af156a8f7496dc9a9e70d3992f227... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/search/__init__.py Log Message: ----------- Build search index at startup, rebuild repository cache during toolbox or datamanager reload Commit: 4c1f9c8f0d8ea2a58264fdbcb53accf3f7b52dac https://github.com/galaxyproject/galaxy/commit/4c1f9c8f0d8ea2a58264fdbcb53ac... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3994 from gregvonkuster/xsd Add entry for empty_extra_files_path validator Commit: 7a6961e30d013d5c3bfa53118e6fb2cc1fd1d35f https://github.com/galaxyproject/galaxy/commit/7a6961e30d013d5c3bfa53118e6fb... Author: guerler <aysam.guerler@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Undo dataset renaming Commit: 2586df45637d794c63252838573b2d1e6d692243 https://github.com/galaxyproject/galaxy/commit/2586df45637d794c63252838573b2... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M .ci/flake8_wrapper_docstrings.sh M setup.cfg M tox.ini Log Message: ----------- Remove pydocstyle pins - there was an update to flake8-docstrings. Commit: 6201c61d72df9b3b0a1af454d52e4462c02fc587 https://github.com/galaxyproject/galaxy/commit/6201c61d72df9b3b0a1af454d52e4... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Add a note about use_volumes to Jupyter and RStudio GIEs. Commit: 09404117b9d45e73650665a612fa7001ce5006f2 https://github.com/galaxyproject/galaxy/commit/09404117b9d45e73650665a612fa7... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3980 from jmchilton/ie_for_mac_os_x_fixes Rework Jupyter IE for additional_ids handling. Commit: 37c7425eae98c8cc39b7a0d9ca6b8cf5c4e0cbcd https://github.com/galaxyproject/galaxy/commit/37c7425eae98c8cc39b7a0d9ca6b8... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M .ci/flake8_wrapper_docstrings.sh M setup.cfg M tox.ini Log Message: ----------- Merge pull request #3995 from jmchilton/flake8fixes Remove pydocstyle pins - there was an update to flake8-docstrings. Commit: d638e377054893554e31f93d009c3bb153c6ddf5 https://github.com/galaxyproject/galaxy/commit/d638e377054893554e31f93d009c3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.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: ----------- Quick fix for displaying a message instead of just redirecting on clientside routes when login is required. TODO: refactor both message display and the decoration of routes. Commit: edff1e65b9bd08b09ac864c93cbec867be23b444 https://github.com/galaxyproject/galaxy/commit/edff1e65b9bd08b09ac864c93cbec... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.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: ----------- Merge pull request #4000 from dannon/error_message_for_login_required Displaying a message instead of just redirecting Commit: 7b50ae39b0d4ad5208e97f86c60e16bfa9fcfbff https://github.com/galaxyproject/galaxy/commit/7b50ae39b0d4ad5208e97f86c60e1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M CITATION M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/viz/phyloviz.js M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/tool_shed/galaxy_install/tools/data_manager.py M run_tests.sh M setup.cfg M static/maps/mvc/citation/citation-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/viz/phyloviz.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/citation/citation-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/viz/phyloviz.js M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/user/index.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_jobs.py M test/api/test_workflows.py M test/galaxy_selenium/navigates_galaxy.py M test/qunit/tests/form_tests.js M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into hashtags Commit: 06e2e67872b8de486c189fd513ac5458c91dc2e5 https://github.com/galaxyproject/galaxy/commit/06e2e67872b8de486c189fd513ac5... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M static/maps/mvc/tag.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/tag.js Log Message: ----------- Merge pull request #3979 from dannon/hashtags Hashtags Commit: 86ebe28667008d65f0c4223e22df1e74837baf11 https://github.com/galaxyproject/galaxy/commit/86ebe28667008d65f0c4223e22df1... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M lib/galaxy/datatypes/data.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Enhance filenames with collection context when downloading datasets from GUI. - Reduce duplication related to calculating filename. - Formalized pattern for normal dataset download using string.Tempalte - "Galaxy${hid}-[${name}].${ext}". - In the context of collections, hid and name of the datasets are pretty worthless so I used a second pattern for collections based on where it is in the current GUI frame. The new pattern is "Galaxy${hdca_hid}-[${hdca_name}__${element_identifier}].${ext}". - The patterns make this a little more tweakable - for people who want something different it should be pretty straight forward to make these patterns configurable. Fixes #2140 I think. Commit: ef92904afaa0222e66e0861dbb37fdf07e541a88 https://github.com/galaxyproject/galaxy/commit/ef92904afaa0222e66e0861dbb37f... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Repack client. Commit: 4b7d5e32d4a0cd6ffa72e6551b57022a4d2dc6d2 https://github.com/galaxyproject/galaxy/commit/4b7d5e32d4a0cd6ffa72e6551b570... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M lib/galaxy/datatypes/data.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Merge pull request #3985 from jmchilton/fix_collection_download_name Enhance filenames with collection context when downloading datasets from GUI. Commit: a6415b25fdb9661504505ba9c5016f7645720d30 https://github.com/galaxyproject/galaxy/commit/a6415b25fdb9661504505ba9c5016... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/registry.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/util/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M test/base/driver_util.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #3909 from mvdbeek/speedup_toolbox Speedup startup and toolbox operations Commit: 1c8370cf33a0bba05019397677c2b0a386b5136b https://github.com/galaxyproject/galaxy/commit/1c8370cf33a0bba05019397677c2b... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Restore line accidentally removed as part of #3985. Commit: 1a733864842ba8c1af3591b4d1aaa85fb3152a9a https://github.com/galaxyproject/galaxy/commit/1a733864842ba8c1af3591b4d1aaa... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #3996 from guerler/undo_url_upload_renaming Undo dataset renaming for URL uploads Commit: 0680a29a7992de0e606ec7047da845d5686d8029 https://github.com/galaxyproject/galaxy/commit/0680a29a7992de0e606ec7047da84... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #4004 from jmchilton/filename_fixup Restore line accidentally removed as part of #3985. Commit: d224bedd3992e413363f345d64488e13d63518fe https://github.com/galaxyproject/galaxy/commit/d224bedd3992e413363f345d64488... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Implicitly set use_volumes = False if using Docker swarm Commit: 4b3a361a887d02e1944fd092b1c3a84b7da13f95 https://github.com/galaxyproject/galaxy/commit/4b3a361a887d02e1944fd092b1c3a... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Update Jupyter image to 17.05 Commit: afc4fbcc38292c90641dcac737fd08ad0c253201 https://github.com/galaxyproject/galaxy/commit/afc4fbcc38292c90641dcac737fd0... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample Log Message: ----------- Merge pull request #4007 from natefoo/jupyer-17.05 Update Jupyter image to 17.05 Commit: ecf634a619e93ffe98b5b785e3de10125940adce https://github.com/galaxyproject/galaxy/commit/ecf634a619e93ffe98b5b785e3de1... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #4006 from natefoo/implicit-use-volumes Implicitly set use_volumes = False if using Docker swarm Commit: 06d0e4fce57fa29e6d7fb02c455b77f6855f783c https://github.com/galaxyproject/galaxy/commit/06d0e4fce57fa29e6d7fb02c455b7... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/tools/__init__.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.01' into dev Commit: 8db51db70258463df762e6ed70f621f56d1a8d74 https://github.com/galaxyproject/galaxy/commit/8db51db70258463df762e6ed70f62... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.05.rc1 Commit: 609842e558da5f60eef94809204b48204fc8158a https://github.com/galaxyproject/galaxy/commit/609842e558da5f60eef94809204b4... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M tox.ini Log Message: ----------- [17.05] Pin dependencies for linting Galaxy. Commit: aeed375c0286315c2b893d7b807d3522c5c21a36 https://github.com/galaxyproject/galaxy/commit/aeed375c0286315c2b893d7b807d3... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M tox.ini Log Message: ----------- Merge pull request #4012 from jmchilton/17.05_pin_release_linting [17.05] Pin dependencies for linting Galaxy. Commit: ce8f0dec0532266bff5d277f8acc50a4c6a9b2b5 https://github.com/galaxyproject/galaxy/commit/ce8f0dec0532266bff5d277f8acc5... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-02 (Tue, 02 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #4009 from jmchilton/version-17.05 [17.05] Update version to 17.05.rc1 Commit: 460d1737beb5d6e3e966c33998a7d5d046ac3e87 https://github.com/galaxyproject/galaxy/commit/460d1737beb5d6e3e966c33998a7d... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- typo Commit: 8dd5b153ed728591d3e44acb4271afc0210981f2 https://github.com/galaxyproject/galaxy/commit/8dd5b153ed728591d3e44acb4271a... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- Pass hdca and element_identifier to _serve_raw This is necessary for getting the new filenames introduced in #3985 if downloading tabular datatypes. Closes #4016. Commit: 99317c77557ed4daec4c36619ec90a45a51e35eb https://github.com/galaxyproject/galaxy/commit/99317c77557ed4daec4c36619ec90... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #4017 from mvdbeek/fix_new_download_names_tabular Pass hdca and element_identifier to _serve_raw Commit: 6ef7b9977a3ed936c02b3e7fadfd105bbaea9595 https://github.com/galaxyproject/galaxy/commit/6ef7b9977a3ed936c02b3e7fadfd1... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-03 (Wed, 03 May 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #4015 from erasche/remote-user-bug [17.05] Typo in remote user / user preferences exception Commit: 3332dfb6717e9bd368341e0bc0aa51d3b53fa861 https://github.com/galaxyproject/galaxy/commit/3332dfb6717e9bd368341e0bc0aa5... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/util/plugin_config.py Log Message: ----------- [17.05] Fix setting up explicit container resolution from a container resolution config file. Commit: f26e358321481500d0f993e0d7b2be9bdd1047b8 https://github.com/galaxyproject/galaxy/commit/f26e358321481500d0f993e0d7b2b... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/jobs/rule_helper.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix docker_dispatch dynamic destination rule for container resolvers. Commit: a9faa4873e4509a60822019afe3faa4cab3f8336 https://github.com/galaxyproject/galaxy/commit/a9faa4873e4509a60822019afe3fa... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Do not attempt to use mulled containers if tool requires legacy Galaxy environment. Commit: be7dea47d556823abfab7a369b3ac466f6dea494 https://github.com/galaxyproject/galaxy/commit/be7dea47d556823abfab7a369b3ac... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Sanitize container names sending to Kubernetes. Commit: a0c59d8f05c011f6c7b002599ed09c3fe091c340 https://github.com/galaxyproject/galaxy/commit/a0c59d8f05c011f6c7b002599ed09... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Try activating conda environment again if previous activation failed Commit: c38c0276afb88ed5b1403ede53ae35247307890d https://github.com/galaxyproject/galaxy/commit/c38c0276afb88ed5b1403ede53ae3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-07 (Sun, 07 May 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Exit with error message when conda environemnt could not be activated (thx @nsoranzo). Commit: 9e6c1529929132414e240e306d2b244ef6853944 https://github.com/galaxyproject/galaxy/commit/9e6c1529929132414e240e306d2b2... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-08 (Mon, 08 May 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #4035 from mvdbeek/retry_conda_activation [17.05] Try activating conda environment again if previous activation failed Commit: ced568a9e5974d0a4944abce99a64f1b8eb6e6f6 https://github.com/galaxyproject/galaxy/commit/ced568a9e5974d0a4944abce99a64... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-10 (Wed, 10 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Fix destructive tag rerender to be a simple replacement. Left the original template/render in place, we could refactor as this becomes more standardized. Commit: 650691c943c096ee15233c61e4459982b2c6928d https://github.com/galaxyproject/galaxy/commit/650691c943c096ee15233c61e4459... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Merge pull request #4052 from dannon/1705_fix_tag_drag [17.05] Fix destructive tag rerender to be a simpler, more precise html replacement. Commit: 9940ae70309a56013200d3e30ced5bf9437c75c7 https://github.com/galaxyproject/galaxy/commit/9940ae70309a56013200d3e30ced5... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: 04bb1e85cd16a04d6968c8d10755bd5e142831b1 https://github.com/galaxyproject/galaxy/commit/04bb1e85cd16a04d6968c8d10755b... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-view.js M static/maps/mvc/upload/collection/collection-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/upload/collection/collection-view.js Log Message: ----------- [17.05] Fix FTP upload of multiple files in collection uploader. Commit: aa1e4cea148ba6a1683d905704191e64ee64a46c https://github.com/galaxyproject/galaxy/commit/aa1e4cea148ba6a1683d905704191... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-view.js M static/maps/mvc/upload/collection/collection-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/upload/collection/collection-view.js Log Message: ----------- Merge pull request #4058 from jmchilton/upload_ftp_fix [17.05] Fix FTP upload of multiple files in collection uploader. Commit: 0bafd683f152f28a193ee39a415018e4a8952767 https://github.com/galaxyproject/galaxy/commit/0bafd683f152f28a193ee39a41501... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/util/plugin_config.py Log Message: ----------- Merge pull request #4020 from jmchilton/fix_explicit_container_resolver_from_config [17.05] Fix setting up explicit container resolution... Commit: 185c76605f2d0da1d8e261b9b3b3a626b8ba6226 https://github.com/galaxyproject/galaxy/commit/185c76605f2d0da1d8e261b9b3b3a... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #4033 from jmchilton/dispatch_fix [17.05] Fixes for containerized job executions. Commit: 5e880815ade8756964017a446c6ceaa5cbb72f1a https://github.com/galaxyproject/galaxy/commit/5e880815ade8756964017a446c6ce... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-05-14 (Sun, 14 May 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Use galaxy.root by default Commit: 88c0635ef70d8054b50dcbfae2788a9cfa7bd973 https://github.com/galaxyproject/galaxy/commit/88c0635ef70d8054b50dcbfae2788... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-05-14 (Sun, 14 May 2017) Changed paths: M doc/source/admin/special_topics/webhooks.rst Log Message: ----------- Link has already rotted Commit: 6dd145ed1a97263eb9cca42f26613e28b22f177d https://github.com/galaxyproject/galaxy/commit/6dd145ed1a97263eb9cca42f26613... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2017-05-14 (Sun, 14 May 2017) Changed paths: M doc/source/admin/special_topics/webhooks.rst Log Message: ----------- Try and document a bit Commit: bd83608a2fb9ac6e8ec0391ab803f569e134d4fa https://github.com/galaxyproject/galaxy/commit/bd83608a2fb9ac6e8ec0391ab803f... Author: guerler <aysam.guerler@gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M static/maps/mvc/grid/grid-template.js.map M static/scripts/mvc/grid/grid-template.js Log Message: ----------- Fix global grid action events Commit: d3427a1344d165cf6b76b3e2ef4c2113f5ea1916 https://github.com/galaxyproject/galaxy/commit/d3427a1344d165cf6b76b3e2ef4c2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Rebuild Commit: 6614e94a4953a8352515edded517d060cd6265c7 https://github.com/galaxyproject/galaxy/commit/6614e94a4953a8352515edded517d... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M doc/source/admin/special_topics/webhooks.rst M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Merge pull request #4065 from erasche/fix-4064 [17.05] Correct webhooks to use Galaxy.root and be compatible with proxy_prefix Commit: 8c126a87579f89a3689cdcacf467ee01bbe6793a https://github.com/galaxyproject/galaxy/commit/8c126a87579f89a3689cdcacf467e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Update contributors, diff of 17.01->17.05. Commit: 3807b5d3037d569138366c44659d9ee955a5590f https://github.com/galaxyproject/galaxy/commit/3807b5d3037d569138366c44659d9... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- 16.10 -> 17.01 contributor diff. Commit: b88097ae395968d562c1847189fae0b129f6ce4b https://github.com/galaxyproject/galaxy/commit/b88097ae395968d562c1847189fae... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- 16.07 -> 16.10 contributors update. Commit: 5b27ad4cb47b5b250db3cf0cf2624b09a05b40ed https://github.com/galaxyproject/galaxy/commit/5b27ad4cb47b5b250db3cf0cf2624... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- CONTRIBUTORS update 16.04 -> 16.07 Commit: d1ce1a623772d19f5fe9039c81e47fc08e2624e7 https://github.com/galaxyproject/galaxy/commit/d1ce1a623772d19f5fe9039c81e47... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: A doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst Log Message: ----------- initial version of RN Commit: 4cb13b2404e4562c3d79e8707640624514fed3d5 https://github.com/galaxyproject/galaxy/commit/4cb13b2404e4562c3d79e87076406... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- add 17.05 to the release list Commit: 5aaf95e0459bc2331492df9423d2cfe9121ff22b https://github.com/galaxyproject/galaxy/commit/5aaf95e0459bc2331492df9423d2c... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/_thanks.rst M doc/source/releases/older_releases.rst Log Message: ----------- fix links to wiki/hub Commit: 56874e163086b89d97dae17d59afa004777936bd https://github.com/galaxyproject/galaxy/commit/56874e163086b89d97dae17d59afa... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst Log Message: ----------- rn improvements Commit: c8250ae68aea09fb7a1f15109aa5f28027b50966 https://github.com/galaxyproject/galaxy/commit/c8250ae68aea09fb7a1f15109aa5f... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- add new options from galaxy.ini diff Commit: f0570a20a8aab422aa6e3674a5aed98803d7dd89 https://github.com/galaxyproject/galaxy/commit/f0570a20a8aab422aa6e3674a5aed... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- link to proper release-bound sample config Commit: c459cd66ba7ebb5fbd0bb49557eabca4bd39433b https://github.com/galaxyproject/galaxy/commit/c459cd66ba7ebb5fbd0bb49557eab... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- add new datatypes section to the announce Commit: 4125f79161e584aa98098016e6a540111c7b5e2a https://github.com/galaxyproject/galaxy/commit/4125f79161e584aa98098016e6a54... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #4034 from jmchilton/k8_name_fixed [17.05] Sanitize container names sending to Kubernetes. Commit: 3d6dfa4f60741743507c259da6d5610ab6fa14ff https://github.com/galaxyproject/galaxy/commit/3d6dfa4f60741743507c259da6d56... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- For people without a commit-signing email, just use the github username (for now -- they can of course change this via PR) Commit: b1e9552e1b13c36c8d9ec7343e2f4cd11817cbef https://github.com/galaxyproject/galaxy/commit/b1e9552e1b13c36c8d9ec7343e2f4... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #4070 from dannon/contrib_update [17.05] CONTRIBUTORS update Commit: f1d4ceeb304783801b96a579900e3b0e5da4010d https://github.com/galaxyproject/galaxy/commit/f1d4ceeb304783801b96a579900e3... Author: Hans-Rudolf Hotz <hrhotz@users.noreply.github.com> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Update CONTRIBUTORS.md completing the email address Commit: 73bf5b4f7502e8e8f4d7701bd9ab77770968d396 https://github.com/galaxyproject/galaxy/commit/73bf5b4f7502e8e8f4d7701bd9ab7... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #4086 from hrhotz/patch-1 Update CONTRIBUTORS.md Commit: a1c14ee8faca1e47ac8fca3691d734f47b587f6b https://github.com/galaxyproject/galaxy/commit/a1c14ee8faca1e47ac8fca3691d73... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Do not modify self.app.config.tool_data_path and self.app.config.tool_data_table_config_path during metadata setting. xref https://github.com/galaxyproject/tools-iuc/issues/1315. I suspect multiple threads installing tool simultaneously may have led to self.app.config.tool_data_path and/or self.app.config.tool_data_table_config_path being set to a temporary directory. Initial testing looks like this is not necessary. Commit: 9ec6c13fa9196b87e30ed5a97769526b1c4a0cd0 https://github.com/galaxyproject/galaxy/commit/9ec6c13fa9196b87e30ed5a977695... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-05-21 (Sun, 21 May 2017) Changed paths: 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/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/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/mol_to_smi_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 Log Message: ----------- update openbabel to version 2.4.1 Commit: d5f298baa59c05015fa19967443915e1c4faf595 https://github.com/galaxyproject/galaxy/commit/d5f298baa59c05015fa1996744391... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- add Thoba's email Commit: f94fa8edbe12c8af3e2deb62c5c65cf9b437ca00 https://github.com/galaxyproject/galaxy/commit/f94fa8edbe12c8af3e2deb62c5c65... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #4095 from martenson/contrib-email [17.05] add Thoba's email to contributors Commit: f9f206ca45e21a72c96ddaa7f0b2f0751ffb7950 https://github.com/galaxyproject/galaxy/commit/f9f206ca45e21a72c96ddaa7f0b2f... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst Log Message: ----------- polish release notes, add links to tutorials Commit: 15556c0a71eb7bbdf33f35158239b4a243441510 https://github.com/galaxyproject/galaxy/commit/15556c0a71eb7bbdf33f35158239b... Author: John Chilton <jmchilton@gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: A doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M doc/source/releases/older_releases.rst Log Message: ----------- Merge pull request #4075 from martenson/17.05_release_notes [17.05] release notes Commit: 1bdd1620fe16a7036fae04d7131356e7c80a1ccf https://github.com/galaxyproject/galaxy/commit/1bdd1620fe16a7036fae04d713135... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- listify new contributors Commit: 0b3e29199f33ad2f8ec0db3c9a750b4b16fc9415 https://github.com/galaxyproject/galaxy/commit/0b3e29199f33ad2f8ec0db3c9a750... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: 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/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/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/mol_to_smi_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 Log Message: ----------- Merge pull request #4094 from bgruening/openbabel_update [17.05] Open Babel update for datatype converters Commit: 9ebc464ba3f4d78822603638df00331864a1acf9 https://github.com/galaxyproject/galaxy/commit/9ebc464ba3f4d78822603638df003... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- Merge pull request #4100 from martenson/17.05_release_notes [17.05] release notes- listify new contributors Commit: 6f8472e525345b74fb6818bd2d89cd486435c822 https://github.com/galaxyproject/galaxy/commit/6f8472e525345b74fb6818bd2d89c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fixes repeat handling in workflow editor, store values as passed from ui Commit: aa8aafb10958d555874d4288c6a3bedffcac1f25 https://github.com/galaxyproject/galaxy/commit/aa8aafb10958d555874d4288c6a3b... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #4104 from dannon/tags_continued [17.05] Change to only inheriting 'name' tags Commit: 3d1da8e11d5acfebddda760ea2de74b22b3856eb https://github.com/galaxyproject/galaxy/commit/3d1da8e11d5acfebddda760ea2de7... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Merge pull request #4089 from mvdbeek/no_global_changes [17.05] Do not modify self.app.config.tool_data_path Commit: 0268f5078c28d5cfb05845fd09aaab783ad015c7 https://github.com/galaxyproject/galaxy/commit/0268f5078c28d5cfb05845fd09aaa... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #4107 from guerler/fix_repeats_in_workflows [17.05] Fixes repeat handling in workflow editor, store values as passed from ui Commit: 31015a83af9b3622498dd63276ffe93c45f5d6c6 https://github.com/galaxyproject/galaxy/commit/31015a83af9b3622498dd63276ffe... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-05-24 (Wed, 24 May 2017) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Remove residual comment Follow-up on https://github.com/galaxyproject/galaxy/pull/4089 Commit: 4294663d5379555c8c6ab12eb520430379941701 https://github.com/galaxyproject/galaxy/commit/4294663d5379555c8c6ab12eb5204... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-05-24 (Wed, 24 May 2017) Changed paths: M doc/source/releases/17.05.rst Log Message: ----------- Improve 17.05 release notes Also add 4 pull requests merged in the last few days. Commit: d8c21e1fd9a1c9058ffa9efa9db2984c807e84af https://github.com/galaxyproject/galaxy/commit/d8c21e1fd9a1c9058ffa9efa9db29... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-24 (Wed, 24 May 2017) Changed paths: M doc/source/releases/17.05.rst M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Merge pull request #4110 from nsoranzo/release_17.05 [17.05] Improve 17.05 release notes Commit: 18ef6a6ab0dcba1a1254a9d9f4273c346fdd1478 https://github.com/galaxyproject/galaxy/commit/18ef6a6ab0dcba1a1254a9d9f4273... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-24 (Wed, 24 May 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.05 Commit: 68433b1eff0a93704544a49f3d8f3a912d97c285 https://github.com/galaxyproject/galaxy/commit/68433b1eff0a93704544a49f3d8f3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-25 (Thu, 25 May 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Force uniqueness of preserved tags (so, don't allow many inputs with a 'name:foo' tag to add a ton of 'name:foo' tags to a dataset; just use one) Commit: b6e8d3e8acd00c1a595f15f2654c1b7809ecc831 https://github.com/galaxyproject/galaxy/commit/b6e8d3e8acd00c1a595f15f2654c1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Slight refactoring to use a dict for unique'ing preserved tags. TODO: enhance object builtins to compare correctly so we can use a set, maybe. Not a big deal unless/until we have a second type of preserved tag though. Commit: dd06a01746f2ace048b9e1e604756e648a6ef1fd https://github.com/galaxyproject/galaxy/commit/dd06a01746f2ace048b9e1e604756... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Handle *both* paths for tag appending using the now-dict correctly. Commit: 2ac04bbf095573f2621ffeea0e2fdeb59b21da53 https://github.com/galaxyproject/galaxy/commit/2ac04bbf095573f2621ffeea0e2fd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Uniqueify hashtag display Commit: 3d16319a15b7ac2f947eca24c36957894ae00afe https://github.com/galaxyproject/galaxy/commit/3d16319a15b7ac2f947eca24c3695... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-05-27 (Sat, 27 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge pull request #4114 from dannon/force_uniqueness_preserved_tags [17.05] Force uniqueness of preserved tags Commit: 42e274d3342720037d441222b9fb1bbcbce2d7c1 https://github.com/galaxyproject/galaxy/commit/42e274d3342720037d441222b9fb1... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #4122 from galaxyproject/release_17.01 [17.05] merge Release 17.01 Commit: c409572ef8510e0c4322d835c5ba90f32bc9c653 https://github.com/galaxyproject/galaxy/commit/c409572ef8510e0c4322d835c5ba9... Author: guerler <aysam.guerler@gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js.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/tool/tool-form-composite.js Log Message: ----------- Handle potential regex expression in workflow parameter names Commit: a9d0d3671afc2be90509517b53b96af694ff22e5 https://github.com/galaxyproject/galaxy/commit/a9d0d3671afc2be90509517b53b96... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M lib/galaxy/util/compression_utils.py Log Message: ----------- Fix for returning a fileobject in compression_utils.py when handling a zipfile. Will return the first named object in the archive. zipfile.os_zipfile does not exist... Commit: f6ced00ef0de0fa67e2ecd06fa2db204e73f25ad https://github.com/galaxyproject/galaxy/commit/f6ced00ef0de0fa67e2ecd06fa2db... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M lib/galaxy/util/compression_utils.py Log Message: ----------- Merge pull request #4135 from blankenberg/17.05_zipfile [17.05] Fix for returning a fileobject in compression_utils.py when handling a zipfile. Commit: 75028ac1eec7de53a197217921ebd5b7dac4daac https://github.com/galaxyproject/galaxy/commit/75028ac1eec7de53a197217921ebd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js.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/tool/tool-form-composite.js Log Message: ----------- Merge pull request #4133 from guerler/escape_regex [17.05] Properly escape potential regex expression in workflow parameters Commit: c260e0b0c8ec1b8c479ab2aa2f60b7dfd533b324 https://github.com/galaxyproject/galaxy/commit/c260e0b0c8ec1b8c479ab2aa2f60b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Sort tags for display (note, this is stupid to have in 3 places -- refactor) Commit: 967c363786f36a4d4aab020a073b7c5e7eefbce6 https://github.com/galaxyproject/galaxy/commit/967c363786f36a4d4aab020a073b7... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Filter tags for empties (fixes #4127) Commit: 0c43954e8d09f9f6dc7ac3af02b14821e8fc53ae https://github.com/galaxyproject/galaxy/commit/0c43954e8d09f9f6dc7ac3af02b14... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Slight tweak of logic in tag filtering PJA Commit: 12905321ca8083e4b41eb0fe03193463b8efb019 https://github.com/galaxyproject/galaxy/commit/12905321ca8083e4b41eb0fe03193... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Allow hashtag usage in workflow PJA tag addition mechanism Commit: 0954290e5dfe74ab4d7a658dca9e2896e7aa020e https://github.com/galaxyproject/galaxy/commit/0954290e5dfe74ab4d7a658dca9e2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Combine list comprehensions, slightly tweak logic. Commit: c2348340cfa865ac33ed38311f22c0e8043c89ae https://github.com/galaxyproject/galaxy/commit/c2348340cfa865ac33ed38311f22c... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Fix for Data Tables loaded from a URL. Commit: b0c46cc4d0ec554d10186050c91a5c8a4880a8ff https://github.com/galaxyproject/galaxy/commit/b0c46cc4d0ec554d10186050c91a5... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-01 (Thu, 01 Jun 2017) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #4140 from blankenberg/17.05_data_tables_URL_fix [17.05] Fix for Data Tables loaded from a URL. Commit: 0272e188a81b89d743c22956c88e6cdac433b8db https://github.com/galaxyproject/galaxy/commit/0272e188a81b89d743c22956c88e6... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/jobs/actions/post.py M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge pull request #4139 from dannon/tag_sorting [17.05] Tag fixes Commit: fdc712fb8884ada20373eab548144d4179aa0461 https://github.com/galaxyproject/galaxy/commit/fdc712fb8884ada20373eab548144... Author: guerler <aysam.guerler@gmail.com> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Hide error highlighting if user interacts with highlighted field Commit: 9d0f9efbbaf52b81baed355e9b88afd9b29a7472 https://github.com/galaxyproject/galaxy/commit/9d0f9efbbaf52b81baed355e9b88a... Author: guerler <aysam.guerler@gmail.com> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Disable feature for forms which auto refresh with a server validation Commit: cbe9944815d0e543247824969b2c6aa5212b971b https://github.com/galaxyproject/galaxy/commit/cbe9944815d0e543247824969b2c6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-04 (Sun, 04 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-input.js Log Message: ----------- Merge pull request #4147 from martenson/fix_hide_error [17.05] Hide error highlighting if user interacts with highlighted field Commit: 0b1eaf3269ed5ccbfba7807826e822b38f57778e https://github.com/galaxyproject/galaxy/commit/0b1eaf3269ed5ccbfba7807826e82... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- fix - remove extra slash Commit: d39b955e8a5d6c54852d3b32cd9cd1e7e2d3e519 https://github.com/galaxyproject/galaxy/commit/d39b955e8a5d6c54852d3b32cd9cd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-06 (Tue, 06 Jun 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Merge pull request #4158 from martenson/webhooks-fix-prefix [17.05] fix webhooks loading url Commit: c90b94311e5427da95a36a9661c1d0eb19e16fc2 https://github.com/galaxyproject/galaxy/commit/c90b94311e5427da95a36a9661c1d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py Log Message: ----------- Instead of setting the tags from a list, workflow PJAs will now append tags, so propagating tags will work alongside this feature. Commit: 01510af8f57508877dda205cb0afdc144bfa73c2 https://github.com/galaxyproject/galaxy/commit/01510af8f57508877dda205cb0afd... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Consistent spacing (not a fan of the rule, but consistency is better) Commit: 472ff8ce520a6327179dd54c301db763ea7e979b https://github.com/galaxyproject/galaxy/commit/472ff8ce520a6327179dd54c301db... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Fix for when item.tags is undefined Commit: b32c1cf1a3143804b0c4f12f6f7235a87801a74d https://github.com/galaxyproject/galaxy/commit/b32c1cf1a3143804b0c4f12f6f723... Author: guerler <aysam.guerler@gmail.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Check name export in legacy export section Commit: f7ba7295102c9ce9969c634ee89e26f02c2801ea https://github.com/galaxyproject/galaxy/commit/f7ba7295102c9ce9969c634ee89e2... Author: John Chilton <jmchilton@gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #4203 from guerler/fix_name_export [17.05] Check name type in legacy export section Commit: 268ee7f1b7e65dde514098e0779b80b7589d26b5 https://github.com/galaxyproject/galaxy/commit/268ee7f1b7e65dde514098e0779b8... Author: guerler <aysam.guerler@gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Improve resilience of tool url building Commit: 69e76f98fa90782c37a2697de0204e4ff7945f09 https://github.com/galaxyproject/galaxy/commit/69e76f98fa90782c37a2697de0204... Author: guerler <aysam.guerler@gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Remove redundancy of tool_id parameter Commit: a498390bef74301816945551a9832f38747fd4fc https://github.com/galaxyproject/galaxy/commit/a498390bef74301816945551a9832... Author: guerler <aysam.guerler@gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix basic version changes for reloaded tools Commit: 9dca211e2fe59eaad1f7b95c8d51608b2afa05af https://github.com/galaxyproject/galaxy/commit/9dca211e2fe59eaad1f7b95c8d516... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #4214 from guerler/revise_tool_url [17.05] Improve resilience of tool url building Commit: 368be188d0918adaa0d7f752883c24bb79f261ec https://github.com/galaxyproject/galaxy/commit/368be188d0918adaa0d7f752883c2... Author: guerler <aysam.guerler@gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Unescape tool id before parsing to tool form builder Commit: f439fd30eb1f803daf8e1898bc1648c8cee131f8 https://github.com/galaxyproject/galaxy/commit/f439fd30eb1f803daf8e1898bc164... Author: Andrea Bagnacani <andrea.bagnacani@uni-rostock.de> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tours.js.map 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/tool/tool-form-base.js M static/scripts/mvc/tours.js Log Message: ----------- conditional postclick execution onNext Commit: c8eff858d68cdbea85524c4e366cc479ba556dcd https://github.com/galaxyproject/galaxy/commit/c8eff858d68cdbea85524c4e366cc... Author: guerler <aysam.guerler@gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Remove float style from color picker label Commit: bd2d52800e7776ead1c8c7af53995d13cd288397 https://github.com/galaxyproject/galaxy/commit/bd2d52800e7776ead1c8c7af53995... Author: John Chilton <jmchilton@gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #4233 from guerler/fix_color_picker_release [17.05] Remove float style from color picker label Commit: d0893b91ae281a17b3ae1bc210f197c6f259103c https://github.com/galaxyproject/galaxy/commit/d0893b91ae281a17b3ae1bc210f19... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: fc613d2d60c126b3b37c9ebe3ddbd9cc58803643 https://github.com/galaxyproject/galaxy/commit/fc613d2d60c126b3b37c9ebe3ddbd... Author: John Chilton <jmchilton@gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py Log Message: ----------- Merge pull request #4188 from dannon/workflow_pja_add_not_set_tags [17.05] Hashtags w/ workflow-defined tags fix Commit: e58b24db6133720edf442ca85702e4bba050e9c9 https://github.com/galaxyproject/galaxy/commit/e58b24db6133720edf442ca85702e... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tours.js.map 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/tool/tool-form-base.js M static/scripts/mvc/tours.js Log Message: ----------- Merge pull request #4228 from bagnacan/release_17.05_backport_4062 [17.05] conditional postclick execution onNext Commit: d4d558b27a09f684be8311f3cfb659b16545e167 https://github.com/galaxyproject/galaxy/commit/d4d558b27a09f684be8311f3cfb65... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge remote-tracking branch 'guerler/fix_id_encoding' into release_17.05 Includes client rebuild. Commit: 6c6c804ab63866c6239299f4221fa436dd4a9591 https://github.com/galaxyproject/galaxy/commit/6c6c804ab63866c6239299f4221fa... Author: E Rasche <hxr@hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- When a page is involved, the ID will be wrong Commit: 33a0c7fac3a0624d26efd8d08dabbca5f7e8c226 https://github.com/galaxyproject/galaxy/commit/33a0c7fac3a0624d26efd8d08dabb... Author: E Rasche <hxr@hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Make client Commit: a2229783177b76786f581cc78040b059cbd2aab5 https://github.com/galaxyproject/galaxy/commit/a2229783177b76786f581cc78040b... Author: John Chilton <jmchilton@gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4355 from erasche/patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Commit: ecfb90ef9f8037575db2e62ae49d8bbb7e4e427b https://github.com/galaxyproject/galaxy/commit/ecfb90ef9f8037575db2e62ae49d8... Author: John Chilton <jmchilton@gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js R static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "[release_17.05] Patch bug preventing creation of dataset library folders" Commit: 163e4ebbe1fbfc5f1f97b5aabc804621fdd426c9 https://github.com/galaxyproject/galaxy/commit/163e4ebbe1fbfc5f1f97b5aabc804... Author: John Chilton <jmchilton@gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js R static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4356 from galaxyproject/revert-4355-patch-wrong-folder-id Revert "[release_17.05] Patch bug preventing creation of dataset library folders" Commit: 12f0acba1dc1b81bb621ea130a75ec7dfac0fdaa https://github.com/galaxyproject/galaxy/commit/12f0acba1dc1b81bb621ea130a75e... Author: John Chilton <jmchilton@gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "Revert "[release_17.05] Patch bug preventing creation of dataset library folders"" Commit: 10efd7fac6e38c5ca07d94c351d10473811c7d6c https://github.com/galaxyproject/galaxy/commit/10efd7fac6e38c5ca07d94c351d10... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4357 from galaxyproject/revert-4356-revert-4355-patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Commit: d0b06a3b1da09ff3394e9ea036d788676817b58f https://github.com/galaxyproject/galaxy/commit/d0b06a3b1da09ff3394e9ea036d78... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Don't cast tool_version to string if tool_version is None-type If a version is not specifically requested a wrong version (`None` cast to `'None'`) of a tool will be loaded in the workflow editor instead of the latest version. That should address @martenson's remark in https://github.com/galaxyproject/galaxy/pull/4373#issuecomment-321896674 (and maybe also https://github.com/galaxyproject/galaxy/issues/557#issuecomment-213498153). Commit: 6ad6fd9252bf5ec44beb00cb434876e170dc9548 https://github.com/galaxyproject/galaxy/commit/6ad6fd9252bf5ec44beb00cb43487... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Rebuild tool_version_cache on DetachedInstanceError Commit: 4faf496c9898786e8f504bd36b28dc70df4e3e26 https://github.com/galaxyproject/galaxy/commit/4faf496c9898786e8f504bd36b28d... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Conflicts: tox.ini Commit: 7f78ee7b18b83961b305cac19aa8949a4452710d https://github.com/galaxyproject/galaxy/commit/7f78ee7b18b83961b305cac19aa89... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4420 from mvdbeek/fix_wrong_tool_version_cast [17.05] Don't cast tool_version to string if tool_version is None-type Commit: 685b9de09bca5a2973de336b93865273c9fa975c https://github.com/galaxyproject/galaxy/commit/685b9de09bca5a2973de336b93865... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into release_17.05 Commit: ce7d8a2fc1bcc1f9241028b3d437c653edccda0c https://github.com/galaxyproject/galaxy/commit/ce7d8a2fc1bcc1f9241028b3d437c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Validate workflow step after step argument injection Commit: 3ef39b390c8d2f66ff890a29b712f785b6376601 https://github.com/galaxyproject/galaxy/commit/3ef39b390c8d2f66ff890a29b712f... Author: guerler <aysam.guerler@gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Fix drag and drop from history for firefox Commit: cf897795fe8b544bc4cb5899585b1be2ee0063e6 https://github.com/galaxyproject/galaxy/commit/cf897795fe8b544bc4cb5899585b1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Merge pull request #4496 from guerler/fix_drag_drop_firefox [17.05] Fix drag and drop from history for Firefox Commit: c70926445fb7518e1f2ebf755477ca3327dea6a3 https://github.com/galaxyproject/galaxy/commit/c70926445fb7518e1f2ebf755477c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4483 from guerler/fix_workflow_validation [17.05] Validate workflow step after step argument injection Commit: 1d485390b0af80441c4e577f8fb7ddde265f9618 https://github.com/galaxyproject/galaxy/commit/1d485390b0af80441c4e577f8fb7d... Author: E Rasche <hxr@hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 41fe55129a3af95d7ef84ecb387b954b14509843 https://github.com/galaxyproject/galaxy/commit/41fe55129a3af95d7ef84ecb387b9... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Conflicts: lib/galaxy/datatypes/data.py Commit: b17fbfb968b8921729798c909220e522abfb29fd https://github.com/galaxyproject/galaxy/commit/b17fbfb968b8921729798c909220e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Fix startup of galaxy when wehbooks dir is empty Reported by @alpapan on gitter. Commit: c86bf78c6a966b52d3c9e21ffae71bbf134ecdb4 https://github.com/galaxyproject/galaxy/commit/c86bf78c6a966b52d3c9e21ffae71... Author: Eric Rasche <hxr@hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Merge pull request #4570 from mvdbeek/webhook_loading_fix [17.05] Bug: Fix startup of galaxy when wehbooks dir is empty Commit: 83b363d5207625b916523b7d08b4fff26e8379ed https://github.com/galaxyproject/galaxy/commit/83b363d5207625b916523b7d08b4f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: fc90aec7fe4a3267868fdf3cc2c2123f935f15a2 https://github.com/galaxyproject/galaxy/commit/fc90aec7fe4a3267868fdf3cc2c21... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Fix virtualenv activation for some scripts In particular add virtualenv activation to extract_dataset_parts.sh to fix the following error when running tools which use `<parallelism>`: ``` Fatal error: /tmp/tmpOoQ01k/job_working_directory/000/12/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 17, in <module> import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module> from six import string_types ModuleNotFoundError: No module named 'six' ``` Commit: 97e8e36185312ff6e1afea15fec7e83aadafd25b https://github.com/galaxyproject/galaxy/commit/97e8e36185312ff6e1afea15fec7e... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Merge pull request #4624 from nsoranzo/release_17.05_fix_scripts [17.05] Backport of #4616 Commit: 2c77d386def0dc21b8aa40d5d7cf5f8934c16a74 https://github.com/galaxyproject/galaxy/commit/2c77d386def0dc21b8aa40d5d7cf5... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Write out registry once per job Commit: e03ee53f3c398fe429ba1fe8693782a06b20cd73 https://github.com/galaxyproject/galaxy/commit/e03ee53f3c398fe429ba1fe869378... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py Log Message: ----------- Remove references to integrated_datatypes_config Commit: 03d9a9c6fba0e26fae080a7ebb65fd6f0676477e https://github.com/galaxyproject/galaxy/commit/03d9a9c6fba0e26fae080a7ebb65f... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-09-16 (Sat, 16 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Merge pull request #4633 from mvdbeek/backport_registry_to_working_dir [17.05] Backport #4600: Write datatypes registry xml to working directory Commit: a3ff1297435721d3f687052382b75a2a2f2f9b25 https://github.com/galaxyproject/galaxy/commit/a3ff1297435721d3f687052382b75... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Explicitly write registry.xml when creating a job for the upload tool Commit: d980dfa162b340423ffd8822ac9dcdf6f1997e80 https://github.com/galaxyproject/galaxy/commit/d980dfa162b340423ffd8822ac9dc... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Write registry.xml for all tools that require galaxy's python env This should cover the upload and data_source tools. Commit: b7b3ffb1813f31b7811bdbb35602743294356f66 https://github.com/galaxyproject/galaxy/commit/b7b3ffb1813f31b7811bdbb356027... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Fix unit test failure Commit: 5d7b524b5785fcb483dbc7381c871595a070b1b0 https://github.com/galaxyproject/galaxy/commit/5d7b524b5785fcb483dbc7381c871... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Merge pull request #4644 from mvdbeek/upload_tool_registry_xml_failure [17.05] BUG: Explicitly write registry.xml when creating a job for the upload tool Commit: cfabe37d69549e919d3fce15cbcca108fdcf1597 https://github.com/galaxyproject/galaxy/commit/cfabe37d69549e919d3fce15cbcca... Author: Nate Coraor <nate@bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: 2eed478545857ab2c3b4c958bc3e2c360656af42 https://github.com/galaxyproject/galaxy/commit/2eed478545857ab2c3b4c958bc3e2... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Update conda channel order to sync with Bioconda Commit: a5b7dce09fb690f09d25f1b806d3339bdf2171c9 https://github.com/galaxyproject/galaxy/commit/a5b7dce09fb690f09d25f1b806d33... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove _ensure_conda_context() function and make conda_context argument mandatory in functions/methods. This should help making sure the correct context (e.g. channels) is used for all Conda operations. Also remove unused is_target_available() function. Conflicts: lib/galaxy/tools/deps/conda_util.py Commit: 3551386a1ac667e0d2f7c6e82256d180aa5100f7 https://github.com/galaxyproject/galaxy/commit/3551386a1ac667e0d2f7c6e82256d... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Override channel list on the command line instead of modifying condarc The way we were modifying condarc in the ensure_channels_configured() method was broken because we were appending the missing channels at the end, so the final order may not be the one specified in conda_ensure_channels . Also: - not modifying the user condarc is a much better approach - overriding the channel list on the command line will make debugging easier Commit: 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071 https://github.com/galaxyproject/galaxy/commit/81ece2551cea27cbd0e718ef5b7a2... Author: John Chilton <jmchilton@gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #4731 from nsoranzo/release_17.05_backport_4409 [17.05] Backport #4409 Commit: 1348a604e6943af5cdf56c67454b79eec325d2e4 https://github.com/galaxyproject/galaxy/commit/1348a604e6943af5cdf56c67454b7... Author: Martin Cech <marten@bx.psu.edu> Date: 2017-10-10 (Tue, 10 Oct 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CITATION M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/citation/citation-view.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M 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tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge branch 'release_17.05' into release_17.01 Compare: https://github.com/galaxyproject/galaxy/compare/f64b7fcfb124...1348a604e694