- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] cda2b3: Fix Instance is not bound to a Session
by GitHub 10 Apr '17

10 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: cda2b32ebeb9a02c44377ded8b1727d3bd2a394d https://github.com/galaxyproject/galaxy/commit/cda2b32ebeb9a02c44377ded8b17… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-04-08 (Sat, 08 Apr 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Fix Instance is not bound to a Session by refreshing the tool_version_cache, just like we do when we reload the toolbox. Commit: 93b366d75a99b3335a92be792c89443487bfd49d https://github.com/galaxyproject/galaxy/commit/93b366d75a99b3335a92be792c89… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-09 (Sun, 09 Apr 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Merge pull request #3904 from mvdbeek/fix_instance_not_bound [17.01] Fix Instance is not bound to a Session Compare: https://github.com/galaxyproject/galaxy/compare/2396befa02df...93b366d75a99

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[galaxyproject/galaxy] 9aa023: Fix for direct message routing using a 'real' exch...
by GitHub 09 Apr '17

09 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 9aa02339e730988cc1174103e3091690f3c8a42d https://github.com/galaxyproject/galaxy/commit/9aa02339e730988cc1174103e309… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/queues.py Log Message: ----------- Fix for direct message routing using a 'real' exchange like rabbitmq -- this worked with local/database connections already, if accidentally. I want to do more refactoring of how these are configured, but am deferring that for now as it's not a priority. Commit: 2396befa02df1083da56357b9210e9d62fdb4266 https://github.com/galaxyproject/galaxy/commit/2396befa02df1083da56357b9210… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-09 (Sun, 09 Apr 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/queues.py Log Message: ----------- Merge pull request #3846 from dannon/mq_routing_fix [17.01] Fix for direct message routing using a 'real' exchange like rabbitmq Compare: https://github.com/galaxyproject/galaxy/compare/3c080cae96aa...2396befa02df

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[galaxyproject/infrastructure-playbook] 33e4f2: add ftp rewrite to hub
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 33e4f2e997cbcb986c9f25fc010a6aa9fedf9e0e https://github.com/galaxyproject/infrastructure-playbook/commit/33e4f2e997c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M common_roles M galaxyenv/templates/nginx/galaxyproject.j2 Log Message: ----------- add ftp rewrite to hub

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[galaxyproject/usegalaxy-playbook] 484c39: Fix GIE version bug
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 484c39c0d50cfe6a947da50e9afcd4d2ccc141a8 https://github.com/galaxyproject/usegalaxy-playbook/commit/484c39c0d50cfe6a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: M production/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample M production/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js M production/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako M production/files/interactive_environments/plugins/common/templates/ie.mako R production/files/interactive_environments/plugins/ethercalc/config/allowed_images.yml.sample R production/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample R production/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml R production/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js R production/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako M production/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.xml M production/files/interactive_environments/plugins/jupyter/static/js/jupyter.js M production/files/interactive_environments/plugins/jupyter/templates/jupyter.mako M production/files/interactive_environments/plugins/neo/config/neo.ini.sample M production/files/interactive_environments/plugins/neo/static/js/neo.js M production/files/interactive_environments/plugins/neo/templates/neo.mako M production/files/interactive_environments/plugins/phinch/config/phinch.ini.sample M production/files/interactive_environments/plugins/phinch/static/js/phinch.js M production/files/interactive_environments/plugins/phinch/templates/phinch.mako M production/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample M production/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M production/files/interactive_environments/plugins/rstudio/templates/rstudio.mako M production/files/interactive_environments/proxy/lib/mapper.js M roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info M roles/galaxyprojectdotorg.interactive_environments/tasks/extract_component.yml M roles/galaxyprojectdotorg.interactive_environments/tasks/synchronize_components.yml Log Message: ----------- Fix GIE version bug

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[galaxyproject/galaxy] c85738: Merge ToolConfWatchers and separate from Toolbox
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c8573888232f15ef3641bfeb2f0d92a7aa80387f https://github.com/galaxyproject/galaxy/commit/c8573888232f15ef3641bfeb2f0d… Author: mvdbeek <m.vandenbeek(a)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: 1a5e337420e4832593b6e30089c0022291fd6078 https://github.com/galaxyproject/galaxy/commit/1a5e337420e4832593b6e30089c0… Author: mvdbeek <m.vandenbeek(a)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/f79fb9075a4f724d5bad95163a64… Author: mvdbeek <m.vandenbeek(a)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/63f1efd15a6903526406ff8d643f… Author: mvdbeek <m.vandenbeek(a)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/c4e6671ce50a64ba561a3ef81581… Author: mvdbeek <m.vandenbeek(a)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: b037332e943edbf9cf65f4799a1226bf53e8476a https://github.com/galaxyproject/galaxy/commit/b037332e943edbf9cf65f4799a12… Author: mvdbeek <m.vandenbeek(a)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/2c7089df46fa0a5178a1e0f72cc8… Author: mvdbeek <m.vandenbeek(a)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: e7a4ae5c154e5a9a9d2767c76ea043c5fd846fe8 https://github.com/galaxyproject/galaxy/commit/e7a4ae5c154e5a9a9d2767c76ea0… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/b5323e714726...e7a4ae5c154e

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[galaxyproject/galaxy] 82fe42: Hardklor and kronik datatypes for proteomics
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 82fe4262148ae462eb4fe5012e4c7c03ec9be7b8 https://github.com/galaxyproject/galaxy/commit/82fe4262148ae462eb4fe5012e4c… Author: Jorrit Boekel <jorrit.boekel(a)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/c10a23b924983f11565c6a8976b8… Author: Jorrit Boekel <jorrit.boekel(a)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: b5323e7147266ccd14728e5b4783350c7704be30 https://github.com/galaxyproject/galaxy/commit/b5323e7147266ccd14728e5b4783… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/f5ade2b5daab...b5323e714726

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[galaxyproject/galaxy] 2b4b43: Add missing trigger event to drop handler in conte...
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b4b431d0a4f300c1af3d9ac4a105e7887ec09c6 https://github.com/galaxyproject/galaxy/commit/2b4b431d0a4f300c1af3d9ac4a10… Author: guerler <aysam.guerler(a)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: ea17f2dacf8b00e579741676deb33a98d0c234ef https://github.com/galaxyproject/galaxy/commit/ea17f2dacf8b00e579741676deb3… Author: guerler <aysam.guerler(a)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: f5ade2b5daab6fbf3fa924cbda89fbf21e7373a9 https://github.com/galaxyproject/galaxy/commit/f5ade2b5daab6fbf3fa924cbda89… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/408906efb118...f5ade2b5daab

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[galaxyproject/galaxy] e085f8: Routes cleanup -- this adjust_hidden route is unne...
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e085f8cb41a00668efa6108b3caf9e7dbbc712f2 https://github.com/galaxyproject/galaxy/commit/e085f8cb41a00668efa6108b3caf… Author: Dannon Baker <dannon.baker(a)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/a2a64821b4511db810865e75e991… Author: Dannon Baker <dannon.baker(a)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: 408906efb118dc4f36d134c632667101d34a666e https://github.com/galaxyproject/galaxy/commit/408906efb118dc4f36d134c63266… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/5b880697c23e...408906efb118

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[galaxyproject/galaxy] ab1f7e: synchronise against latest UCSC versions
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab1f7eae4d0f1836dad4e52a75dbc18f9bd20336 https://github.com/galaxyproject/galaxy/commit/ab1f7eae4d0f1836dad4e52a75db… Author: Bjoern Gruening <bjoern.gruening(a)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: cac9c980dfce7e22d076cec4032facd1c011d33f https://github.com/galaxyproject/galaxy/commit/cac9c980dfce7e22d076cec4032f… Author: Björn Grüning <bjoern(a)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/5b880697c23e2cdf1c4339976db2… Author: Nicola Soranzo <nsoranzo(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/8ea4cf29f812...5b880697c23e

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[galaxyproject/infrastructure-playbook] 3a24bb: Docker SSL fixes (distribute from playbook if nece...
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3a24bb310885f6a529e28aa6c8424e991223a45d https://github.com/galaxyproject/infrastructure-playbook/commit/3a24bb31088… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-07 (Fri, 07 Apr 2017) Changed paths: A common_env/group_vars/dockersslclients.yml A common_env/secret_group_vars/dockersslclients.yml M roles/docker/defaults/main.yml M roles/docker/tasks/ssl-ca.yml M roles/docker/tasks/ssl-client.yml M roles/docker/tasks/ssl-server.yml A taccenv/group_vars/dockersslclients.yml M taccenv/host_vars/galaxy07.tacc.utexas.edu.yml M taccenv/inventory M taccenv/playbook.yml A taccenv/secret_group_vars/dockersslclients.yml Log Message: ----------- Docker SSL fixes (distribute from playbook if necessary, e.g. for cases where the docker ssl master cannot ssh directly to ansible_user@client).

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[galaxyproject/galaxy] f88d89: Add HistoryDatasetCollectionAssociation as a possi...
by GitHub 07 Apr '17

07 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f88d893562112223553ba069eff2a1f42fe7d69b https://github.com/galaxyproject/galaxy/commit/f88d893562112223553ba069eff2… Author: Dannon Baker <dannon.baker(a)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/73bfb57abf5ba728e4145731f91d… Author: Dannon Baker <dannon.baker(a)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: 5ceca34344b92d6bfa63ad1eb433a1cdea893f4f https://github.com/galaxyproject/galaxy/commit/5ceca34344b92d6bfa63ad1eb433… Author: Dannon Baker <dannon.baker(a)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/821ee5bbcbfdd9a79c52ac60a20a… Author: Dannon Baker <dannon.baker(a)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/4a45c9097e5c7d19977196d3ade1… Author: Dannon Baker <dannon.baker(a)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/2a86f8e54c95da45b59fe166d515… Author: Dannon Baker <dannon.baker(a)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/225393a30006ca0313585de1a4bd… Author: Dannon Baker <dannon.baker(a)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: c4fd96092bcabd869f8c4a4427489d0b2c6209a3 https://github.com/galaxyproject/galaxy/commit/c4fd96092bcabd869f8c4a442748… Author: Dannon Baker <dannon.baker(a)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: c452af01bd16cf85e7459f767ee77c381e527a9a https://github.com/galaxyproject/galaxy/commit/c452af01bd16cf85e7459f767ee7… Author: Dannon Baker <dannon.baker(a)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/2f4aa1a763146e980f9c1c929f07… Author: Dannon Baker <dannon.baker(a)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/01655895174eb14530d274527896… Author: Dannon Baker <dannon.baker(a)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: c9bbaa30f7400f547e8549ae8d0d3bed5ccbf0c5 https://github.com/galaxyproject/galaxy/commit/c9bbaa30f7400f547e8549ae8d0d… Author: Dannon Baker <dannon.baker(a)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 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/config.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/util/gff_util.py 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/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: 439444e65ad9c79a0a2553a5eb916405b1910e93 https://github.com/galaxyproject/galaxy/commit/439444e65ad9c79a0a2553a5eb91… Author: Dannon Baker <dannon.baker(a)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/bfbca68b4e70cc380398e364dd8a… Author: Dannon Baker <dannon.baker(a)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/6ce47ddbf4ed0046f52cd6c7d4f1… Author: Dannon Baker <dannon.baker(a)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: bdcc474d3666fd08f0032629e1882a4441b35244 https://github.com/galaxyproject/galaxy/commit/bdcc474d3666fd08f0032629e188… Author: Dannon Baker <dannon.baker(a)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: 54b7c32bd2913c236c4eacfaf45bdef3ba4c2e7d https://github.com/galaxyproject/galaxy/commit/54b7c32bd2913c236c4eacfaf45b… Author: Dannon Baker <dannon.baker(a)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: 2215869f2d68c1839091dc23cf303bf43fa29078 https://github.com/galaxyproject/galaxy/commit/2215869f2d68c1839091dc23cf30… Author: Dannon Baker <dannon.baker(a)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: 5a513b20bbc371cf9a51483b1cf468d9126a45fe https://github.com/galaxyproject/galaxy/commit/5a513b20bbc371cf9a51483b1cf4… Author: Dannon Baker <dannon.baker(a)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: d41a4efd8822c46aa9f236937d4fc74678ba0dfd https://github.com/galaxyproject/galaxy/commit/d41a4efd8822c46aa9f236937d4f… Author: Dannon Baker <dannon.baker(a)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/2ab68fea8b20c256c30afd7e18bc… Author: Dannon Baker <dannon.baker(a)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/9e9a2d8312990c11ff7d9df6e719… Author: Dannon Baker <dannon.baker(a)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: cad62b1f8b5d289dc27ec88303118dadddbbbc52 https://github.com/galaxyproject/galaxy/commit/cad62b1f8b5d289dc27ec8830311… Author: Dannon Baker <dannon.baker(a)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/1a5d570704da50bdca0ca3194f55… Author: Dannon Baker <dannon.baker(a)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: 8ea4cf29f812d8ce29b31efa18495aad5d5fca44 https://github.com/galaxyproject/galaxy/commit/8ea4cf29f812d8ce29b31efa1849… Author: Aysam Guerler <aysam.guerler(a)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. Compare: https://github.com/galaxyproject/galaxy/compare/483f25c5c2c8...8ea4cf29f812

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[galaxyproject/galaxy] 95fd21: Adding bug fix for SIF files
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 95fd21230b7f73434a4af60b6624b499efcaa1af https://github.com/galaxyproject/galaxy/commit/95fd21230b7f73434a4af60b6624… Author: anuprulez <anup.rulez(a)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/ee66994c44cda791ab4c0d5c8fe7… Author: anuprulez <anup.rulez(a)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/483f25c5c2c8d375d6096d9ca239… Author: Dannon Baker <dannon.baker(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/69ff6ab906d9...483f25c5c2c8

1 0

[galaxyproject/ansible-galaxy]
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/tags/0.7 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] c9f923: Remove a lot of cruft, switch to yaml-style task p...
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: c9f923ad2691df71df75658cebd87f4249ab268c https://github.com/galaxyproject/ansible-galaxy/commit/c9f923ad2691df71df75… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-06 (Thu, 06 Apr 2017) Changed paths: M README.md M defaults/main.yml M files/makepyc.py M handlers/main.yml M tasks/clone.yml M tasks/database.yml M tasks/dependencies.yml M tasks/download.yml M tasks/main.yml M tasks/mutable_setup.yml M tasks/static_setup.yml M tasks/virtualenv.yml Log Message: ----------- Remove a lot of cruft, switch to yaml-style task params, and update for Ansible 2.2 compatibility

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[galaxyproject/galaxy] 334f4d: Remove old, unused search controller. This would ...
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 334f4d7a19882ad97aec75f50b61fda5eb807974 https://github.com/galaxyproject/galaxy/commit/334f4d7a19882ad97aec75f50b61… Author: Dannon Baker <dannon.baker(a)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: 69ff6ab906d94fdb4da3bd0b858fce2de3b349fa https://github.com/galaxyproject/galaxy/commit/69ff6ab906d94fdb4da3bd0b858f… Author: Martin Cech <marten(a)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. Compare: https://github.com/galaxyproject/galaxy/compare/dc80d8c7dcb1...69ff6ab906d9

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[galaxyproject/galaxy] eb0ff2: Update to a new Docker test image to fix dependenc...
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eb0ff254a59196499e7c714b4fc8d744ef463df9 https://github.com/galaxyproject/galaxy/commit/eb0ff254a59196499e7c714b4fc8… Author: John Chilton <jmchilton(a)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: dc80d8c7dcb194300b622d8cfc9fd2dd5d11a811 https://github.com/galaxyproject/galaxy/commit/dc80d8c7dcb194300b622d8cfc9f… Author: Björn Grüning <bjoern(a)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. Compare: https://github.com/galaxyproject/galaxy/compare/d19be8bf46c4...dc80d8c7dcb1

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[galaxyproject/galaxy] 232e80: Python3: Use shlex_quote() from six.moves instead ...
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 232e8096925dd7739b98120c172b5cb092192f3e https://github.com/galaxyproject/galaxy/commit/232e8096925dd7739b98120c172b… Author: Nicola Soranzo <nicola.soranzo(a)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: d19be8bf46c41d12e0a4d6c34454cc150cc06378 https://github.com/galaxyproject/galaxy/commit/d19be8bf46c41d12e0a4d6c34454… Author: Björn Grüning <bjoern(a)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() Compare: https://github.com/galaxyproject/galaxy/compare/af37dd55de28...d19be8bf46c4

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[galaxyproject/galaxy]
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/revert-3871-history_drag_drop Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] d19a15: Allow nest param in the dynamic_tool rule -> argum...
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d19a158e10ada652fb1bf1549dac4f1f3446aa5a https://github.com/galaxyproject/galaxy/commit/d19a158e10ada652fb1bf1549dac… Author: lecorguille <lecorguille(a)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: 73921a21e9164bad342269ed3fe3c347d42a5c8d https://github.com/galaxyproject/galaxy/commit/73921a21e9164bad342269ed3fe3… Author: lecorguille <lecorguille(a)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/705eb17b02b748ce76b5644386c7… Author: lecorguille <lecorguille(a)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/d624b04f25510475bd1cb48fbcbd… Author: lecorguille <lecorguille(a)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: af37dd55de283602338f07452c92224eb0490fa6 https://github.com/galaxyproject/galaxy/commit/af37dd55de283602338f07452c92… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/bcd24e845477...af37dd55de28

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[galaxyproject/galaxy] 74f97a: Fix for dropping into run workflow iframe
by GitHub 06 Apr '17

06 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 74f97a8942cd13572293ff79aec600fcdab4ed88 https://github.com/galaxyproject/galaxy/commit/74f97a8942cd13572293ff79aec6… Author: guerler <aysam.guerler(a)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/7304d5bdc4997da727747f86cf70… Author: guerler <aysam.guerler(a)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/ba91462362c59a1a0dbbfdc80920… Author: guerler <aysam.guerler(a)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/37b6d907cbc338793f950d339044… Author: guerler <aysam.guerler(a)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: 6f95ba9c2c7637fef29d639b19cde81cc3f0ec74 https://github.com/galaxyproject/galaxy/commit/6f95ba9c2c7637fef29d639b19cd… Author: guerler <aysam.guerler(a)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: d2205c4167aa543be633721b6650098bca6835b4 https://github.com/galaxyproject/galaxy/commit/d2205c4167aa543be633721b6650… Author: guerler <aysam.guerler(a)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: 6a625b2c6116992bd475cffe4f11a8ced41110fe https://github.com/galaxyproject/galaxy/commit/6a625b2c6116992bd475cffe4f11… Author: guerler <aysam.guerler(a)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: bcd24e845477d72761072baf014119b3dda2372d https://github.com/galaxyproject/galaxy/commit/bcd24e845477d72761072baf0141… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/5055172e64bb...bcd24e845477

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[galaxyproject/galaxy] 72a3fe: Unused glob in buildapp
by GitHub 05 Apr '17

05 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72a3fea37f3cb622f0b509a72921ad11ecabf99f https://github.com/galaxyproject/galaxy/commit/72a3fea37f3cb622f0b509a72921… Author: Dannon Baker <dannon.baker(a)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/5055172e64bb48ec0eb6d3e4b4ec… Author: Aysam Guerler <aysam.guerler(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/c6ce56dd0a2d...5055172e64bb

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[galaxyproject/galaxy] d9bb8a: Remove unused model import from users api
by GitHub 05 Apr '17

05 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9bb8a7d300c723a172ecc288e332c2a2763f872 https://github.com/galaxyproject/galaxy/commit/d9bb8a7d300c723a172ecc288e33… Author: guerler <aysam.guerler(a)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/c6ce56dd0a2ddb7b5e4760b3bab7… Author: Dannon Baker <dannon.baker(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/c9863b251ee8...c6ce56dd0a2d

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[galaxyproject/galaxy] d9d4ce: Looks like this was always using trans.hsitory ins...
by GitHub 05 Apr '17

05 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9d4ce0ad349d506eb8e902f079453dd4cf9ba16 https://github.com/galaxyproject/galaxy/commit/d9d4ce0ad349d506eb8e902f0794… Author: Dannon Baker <dannon.baker(a)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/c9863b251ee831f0a7f97935f86e… Author: Aysam Guerler <aysam.guerler(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/d607c7e0b134...c9863b251ee8

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[galaxyproject/galaxy] d32317: Add build endpoints to user api
by GitHub 05 Apr '17

05 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d32317438c407799c2b33364af6e553fa03fbdfa https://github.com/galaxyproject/galaxy/commit/d32317438c407799c2b33364af6e… Author: guerler <aysam.guerler(a)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/814d58f9810283c1e851b6c6ec06… Author: guerler <aysam.guerler(a)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/c12c2d1dff45afe1a62321f45a26… Author: guerler <aysam.guerler(a)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/72fb0d6f043e5085323059f80a39… Author: guerler <aysam.guerler(a)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/32a8633f4e0b4fc06ba3b61027ae… Author: guerler <aysam.guerler(a)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/2153ef5b76a1958c0067abb6c549… Author: guerler <aysam.guerler(a)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: d42848ec9b73a89e1cbe20a3250481bd1b41a93a https://github.com/galaxyproject/galaxy/commit/d42848ec9b73a89e1cbe20a32504… Author: guerler <aysam.guerler(a)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/0b26d561aabdb5af6e21e8d845f1… Author: guerler <aysam.guerler(a)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: 689560d7db23240df193fc913d8165643eea8cac https://github.com/galaxyproject/galaxy/commit/689560d7db23240df193fc913d81… Author: guerler <aysam.guerler(a)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/06f61927b5f9f6d35c7c0bdebdd3… Author: guerler <aysam.guerler(a)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/8b5e27aaeae1ac9b35b0959f2ccc… Author: guerler <aysam.guerler(a)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/d2692dc77bdd4db48cbcc77d9cd7… Author: guerler <aysam.guerler(a)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/b1b87358e7fdb991cf1ef1b90aab… Author: guerler <aysam.guerler(a)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: 200b3837c7956e4ee5b19b01eb67e62375e58e97 https://github.com/galaxyproject/galaxy/commit/200b3837c7956e4ee5b19b01eb67… Author: guerler <aysam.guerler(a)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: 15273ad1489c9cdc216126ff36c2ec2d912e4165 https://github.com/galaxyproject/galaxy/commit/15273ad1489c9cdc216126ff36c2… Author: guerler <aysam.guerler(a)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/bb5b8cf525562e1a930ad03a4071… Author: guerler <aysam.guerler(a)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/474b0c1d2ceade095fd995d19ba3… Author: guerler <aysam.guerler(a)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/39c9f79970579556eac63c12d401… Author: guerler <aysam.guerler(a)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/4180d2e08841628753a65966143c… Author: guerler <aysam.guerler(a)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: f5844252ae9feee554342e69562c3ae65985bb82 https://github.com/galaxyproject/galaxy/commit/f5844252ae9feee554342e69562c… Author: guerler <aysam.guerler(a)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/aea96855bb5da18623c51ab6e688… Author: guerler <aysam.guerler(a)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: e78e1607db1eacc175c8f731cdb879fe3e293476 https://github.com/galaxyproject/galaxy/commit/e78e1607db1eacc175c8f731cdb8… Author: guerler <aysam.guerler(a)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/b557e31a4c29fcab875837c1ccc3… Author: guerler <aysam.guerler(a)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/abe156783a7305a8341e217ece31… Author: guerler <aysam.guerler(a)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: 95b6f033a447d25b5826a4e368caf2fc15201d10 https://github.com/galaxyproject/galaxy/commit/95b6f033a447d25b5826a4e368ca… Author: guerler <aysam.guerler(a)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/6b2a4ebd3653f25ef01e109ac7bd… Author: guerler <aysam.guerler(a)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: 39c1b1b24998d9ce77d660ad5dee525f71156720 https://github.com/galaxyproject/galaxy/commit/39c1b1b24998d9ce77d660ad5dee… Author: guerler <aysam.guerler(a)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: 76bcf23b434984cd45002192a72bb90d3c06ade5 https://github.com/galaxyproject/galaxy/commit/76bcf23b434984cd45002192a72b… Author: guerler <aysam.guerler(a)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/ad73c7d39d93683aba1b065b6660… Author: guerler <aysam.guerler(a)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/5ee585c681326072c489f26d2d2b… Author: guerler <aysam.guerler(a)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/ff5166c2930f54a05601ab9a9343… Author: guerler <aysam.guerler(a)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/a89a4f726ba60110810c99b372a5… Author: guerler <aysam.guerler(a)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 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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/2872a31881f2f404b2962464ffb7… Author: guerler <aysam.guerler(a)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: 2fc18675dbfd66a296006bb4ef90d57bdde4d5dc https://github.com/galaxyproject/galaxy/commit/2fc18675dbfd66a296006bb4ef90… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-22 (Wed, 22 Mar 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Debug Commit: 71b09b49a7541789909b1617e661e0252573453a https://github.com/galaxyproject/galaxy/commit/71b09b49a7541789909b1617e661… Author: guerler <aysam.guerler(a)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/ef2353a1423586845da9d19c5780… Author: guerler <aysam.guerler(a)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/afbb3b5a1e26a0a3e9698cec71ed… Author: guerler <aysam.guerler(a)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/368b276ded599e7f0c206b852cdd… Author: guerler <aysam.guerler(a)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/50283125ea37f313afdfd0d69b92… Author: guerler <aysam.guerler(a)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/76bd515879d4353bff066d0b2526… Author: guerler <aysam.guerler(a)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/b0325cef02f995a589dc14425d1a… Author: guerler <aysam.guerler(a)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: 3b7d44e6f7b773218fad0820464efa4610130938 https://github.com/galaxyproject/galaxy/commit/3b7d44e6f7b773218fad0820464e… Author: guerler <aysam.guerler(a)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/4a0f00fc1e3f383450968a9732ed… Author: guerler <aysam.guerler(a)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 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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 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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: 405dbd3b7f3022332fb6c660f88e67361fbb5429 https://github.com/galaxyproject/galaxy/commit/405dbd3b7f3022332fb6c660f88e… Author: guerler <aysam.guerler(a)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/a16c5320fd647b45dbad197714fc… Author: guerler <aysam.guerler(a)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: 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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 Compare: https://github.com/galaxyproject/galaxy/compare/8bbd423909d7...d607c7e0b134

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[galaxyproject/galaxy] 200994: Revert "Allows to drag-and-drop history items into...
by GitHub 05 Apr '17

05 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 200994536e6110fffb586a968edf7edd3c04e4f2 https://github.com/galaxyproject/galaxy/commit/200994536e6110fffb586a968edf… Author: Martin Cech <marten(a)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: 8bbd423909d7ed524b2f73cdc7f7bf42b49c43f2 https://github.com/galaxyproject/galaxy/commit/8bbd423909d7ed524b2f73cdc7f7… Author: John Chilton <jmchilton(a)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" Compare: https://github.com/galaxyproject/galaxy/compare/c27dac65c882...8bbd423909d7

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