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

[galaxyproject/galaxy] 2f6cf3: Avoid circular import when determining max metadat...
by GitHub 09 Oct '17

09 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2f6cf3b9ff72aafb35c165762d291fd7489029c8 https://github.com/galaxyproject/galaxy/commit/2f6cf3b9ff72aafb35c165762d29… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/custom_types.py Log Message: ----------- Avoid circular import when determining max metadata value size. Commit: b76c040aa6faa5b9b8dbe8ff2a43cf0766a73252 https://github.com/galaxyproject/galaxy/commit/b76c040aa6faa5b9b8dbe8ff2a43… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Hacks to set_metadata to fix previous commit. Commit: d9ddc5291c8ba9376601c59128aa5146af03c22d https://github.com/galaxyproject/galaxy/commit/d9ddc5291c8ba9376601c59128aa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/custom_types.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #4770 from jmchilton/max_metadata_setting Avoid circular import when determining max metadata value size. Compare: https://github.com/galaxyproject/galaxy/compare/5a4f625eff13...d9ddc5291c8b

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[galaxyproject/usegalaxy-playbook] 3edc55: Installed FLASH 1.2.11 on main.
by GitHub 09 Oct '17

09 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3edc55338694eabc64488bb2981c4b45ac445112 https://github.com/galaxyproject/usegalaxy-playbook/commit/3edc55338694eabc… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Installed FLASH 1.2.11 on main.

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[galaxyproject/usegalaxy-playbook] 219721: Don't gather all facts on every play (use "smart" ...
by GitHub 09 Oct '17

09 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 219721e6bb017fead8bbf9f8b1763e0d7fef71c5 https://github.com/galaxyproject/usegalaxy-playbook/commit/219721e6bb017fea… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M ansible.cfg Log Message: ----------- Don't gather all facts on every play (use "smart" fact gathering). Commit: 22644f60d8c4f35472f1074f23f6806f271ed929 https://github.com/galaxyproject/usegalaxy-playbook/commit/22644f60d8c4f354… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M roles/usegalaxy_swarmscale/files/spawn.yml M roles/usegalaxy_swarmscale/tasks/main.yml Log Message: ----------- Additional swarm scale fixes. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ebef5022b69c...…

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[galaxyproject/usegalaxy-playbook] ebef50: Ensure swarm worker node hostnames are set (recent...
by GitHub 09 Oct '17

09 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ebef5022b69ce0bfb8538da6719337d22f72b08b https://github.com/galaxyproject/usegalaxy-playbook/commit/ebef5022b69ce0bf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M roles/usegalaxy_swarmscale/files/spawn.yml Log Message: ----------- Ensure swarm worker node hostnames are set (recently spawned ones include the domain portion

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[galaxyproject/galaxy] 2f9f02: Tests for blocking path pastes and intranet URLs f...
by GitHub 09 Oct '17

09 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2f9f0211f954067f40a9e8521d62093754585e83 https://github.com/galaxyproject/galaxy/commit/2f9f0211f954067f40a9e8521d62… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-06 (Fri, 06 Oct 2017) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Tests for blocking path pastes and intranet URLs for secondary files... ... during upload. xref #4289 (blocking intranet URLs by default) xref #4404 (implementing path pastes for normal uploads with the file:// prefix). xref #4417 (initial tests for blocking file:// prefixes for non-admins added in #4404) Rebased with a small fix thanks to the ever vigilant @nsoranzo. Commit: c4048d2f80d2d04204997d86716de5b75b1816a4 https://github.com/galaxyproject/galaxy/commit/c4048d2f80d2d04204997d86716d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Put more effort into method names in test_upload_configuration_options.py. Per suggestion of @nsoranzo. Commit: 5a4f625eff139f5eac31e3b9260e8bec63d3f513 https://github.com/galaxyproject/galaxy/commit/5a4f625eff139f5eac31e3b9260e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Merge pull request #4762 from jmchilton/blocked_secondary_files_upload_urls Tests for blocking path pastes and intranet URLs for secondary files... Compare: https://github.com/galaxyproject/galaxy/compare/e03bedfb8526...5a4f625eff13

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[galaxyproject/galaxy] fe556c: Add new tab for batchmode ftp uploads
by GitHub 09 Oct '17

09 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fe556c8425859e2c0866b215d4f91e680590a935 https://github.com/galaxyproject/galaxy/commit/fe556c8425859e2c0866b215d4f9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 Log Message: ----------- Add new tab for batchmode ftp uploads Commit: 40f3ac3e6b53344d092827bc4bd86c7969101956 https://github.com/galaxyproject/galaxy/commit/40f3ac3e6b53344d092827bc4bd8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 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/admin.bundled.js M static/scripts/bundled/admin.bundled.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/upload/collection/collection-view.js Log Message: ----------- Load ftp file list view into ftp specific tab Commit: 985b17f1f67d9b108e3972e3b69eeba951f82c9a https://github.com/galaxyproject/galaxy/commit/985b17f1f67d9b108e3972e3b69e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/style/less/upload.less 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 M static/style/blue/base.css Log Message: ----------- Adjust styles for view of ftp list Commit: b677bb1e467713745c11db69906bdc1e87190a28 https://github.com/galaxyproject/galaxy/commit/b677bb1e467713745c11db69906b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Remove important tag from css style adjustment Commit: 6d11c856f8b2893ede15776b9251dc39de643ecf https://github.com/galaxyproject/galaxy/commit/6d11c856f8b2893ede15776b9251… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 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: ----------- Fix extensions and genome build styles, align with default uploader view Commit: 4f5b574412b7a988c912be13c8080ca3a55ad0c7 https://github.com/galaxyproject/galaxy/commit/4f5b574412b7a988c912be13c808… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/style/less/upload.less M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/style/blue/base.css Log Message: ----------- Align style of composite uploader to all other upload modes Commit: 7a2c1cdb0ecc481ae376df07cff732a922b9ad03 https://github.com/galaxyproject/galaxy/commit/7a2c1cdb0ecc481ae376df07cff7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 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: ----------- Add handlers to add and remove selected ftp files Commit: 47d7357d87c528665a05060931a9e1e5b650f11f https://github.com/galaxyproject/galaxy/commit/47d7357d87c528665a05060931a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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: ----------- Add extension info popup Commit: 668c268775ddf630221098adbbfa654e22b9c35d https://github.com/galaxyproject/galaxy/commit/668c268775ddf630221098adbbfa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Add reusable extension info popup Commit: 4637e4e392baa19452bb7bbbf9f6aeb16357f84b https://github.com/galaxyproject/galaxy/commit/4637e4e392baa19452bb7bbbf9f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: A client/galaxy/scripts/mvc/upload/ftp/ftp-view.js A client/galaxy/scripts/mvc/upload/upload-extension.js A static/maps/mvc/upload/ftp/ftp-view.js.map A static/maps/mvc/upload/upload-extension.js.map A static/scripts/mvc/upload/ftp/ftp-view.js A static/scripts/mvc/upload/upload-extension.js Log Message: ----------- Add packed files Commit: e38ecb4b11f28840b51bee922a46dbbc4f764140 https://github.com/galaxyproject/galaxy/commit/e38ecb4b11f28840b51bee922a46… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/ftp/ftp-view.js M static/maps/mvc/upload/ftp/ftp-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/upload/ftp/ftp-view.js Log Message: ----------- Add listener to adjust start button activity Commit: bac5299a4556592e453140d9be4c60c9ebe94ba5 https://github.com/galaxyproject/galaxy/commit/bac5299a4556592e453140d9be4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/ftp/ftp-view.js M static/maps/mvc/upload/ftp/ftp-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.map M static/scripts/mvc/upload/ftp/ftp-view.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix upload submission, refresh history after success Commit: 7496d66628cf754ffafa2264d06b6df701fae0d6 https://github.com/galaxyproject/galaxy/commit/7496d66628cf754ffafa2264d06b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/ftp/ftp-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/ftp/ftp-view.js.map 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/ftp/ftp-view.js M static/scripts/mvc/upload/upload-ftp.js M static/style/blue/base.css Log Message: ----------- Augment ftp popover view, add refresh button to ftp view Commit: 779a3418053e1c3bd17eb6f06089ebf0aef6427f https://github.com/galaxyproject/galaxy/commit/779a3418053e1c3bd17eb6f06089… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/ftp/ftp-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/ftp/ftp-view.js.map 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/ftp/ftp-view.js M static/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Fix select all event handler Commit: aca251dd7939718e4f292504ff20611c77e129e9 https://github.com/galaxyproject/galaxy/commit/aca251dd7939718e4f292504ff20… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/ftp/ftp-view.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 submission of multiple ftp files Commit: 911bb2b52473c684f28faed5048856d1437c9afe https://github.com/galaxyproject/galaxy/commit/911bb2b52473c684f28faed50488… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.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: ----------- Order tab alphabatically Commit: d6221bf339e73ef186e0e11c7036810a9fcdfff4 https://github.com/galaxyproject/galaxy/commit/d6221bf339e73ef186e0e11c7036… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/ftp/ftp-view.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: ----------- Show proper message if files are selected twice Commit: 459bd881529fd742bbeb9fe9e6e04b45bb8cf1db https://github.com/galaxyproject/galaxy/commit/459bd881529fd742bbeb9fe9e6e0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/datatypes/data.py M lib/galaxy/workflow/modules.py M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 branch 'dev' into ftp_uploader Commit: e4cb4912d9e09e96c78261318a0e18d8b1ea32dc https://github.com/galaxyproject/galaxy/commit/e4cb4912d9e09e96c78261318a0e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/ftp/ftp-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.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: ----------- Hide ftp tab if ftp is unavailable, use info header of ftp tab to display ftp help Commit: 1b9a6275b2d1decd6f76b6cfb96a34dab2297f79 https://github.com/galaxyproject/galaxy/commit/1b9a6275b2d1decd6f76b6cfb96a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/ftp/ftp-view.js 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: ----------- Use model and consistently named attributes Commit: 694f58651e225748dfd8bb0e3a84230074289fe6 https://github.com/galaxyproject/galaxy/commit/694f58651e225748dfd8bb0e3a84… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/ftp/ftp-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/ftp/ftp-view.js.map 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/ftp/ftp-view.js M static/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Indicate job submission in start button Commit: 6757d047a0804005c63984d71ee6c779c75585bb https://github.com/galaxyproject/galaxy/commit/6757d047a0804005c63984d71ee6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js 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.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Rename tab label Commit: 2ecd18e769c7e180da4e5374758dcb9f5b0f42b1 https://github.com/galaxyproject/galaxy/commit/2ecd18e769c7e180da4e5374758d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/ftp/ftp-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/ftp/ftp-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/utils/uploadbox.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/collection/collection-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/ftp/ftp-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/utils/uploadbox.js Log Message: ----------- Index ftp files instead of using backbones filtering function Commit: de3bf8e46fb7df80ef050a6e3a97f3eb60f06634 https://github.com/galaxyproject/galaxy/commit/de3bf8e46fb7df80ef050a6e3a97… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M config/datatypes_conf.xml.sample M config/error_report.yml.sample M doc/source/admin/special_topics/bug_reports.rst M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/item_attrs.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/requirements.py A lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tag.js.map A static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/tag.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-terminals.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M test/api/test_jobs.py M test/api/test_workflows.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/selenium_tests/framework.py A test/selenium_tests/test_published_histories_grid.py A test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge branch 'dev' into ftp_uploader Commit: dc3218eab2f971e4d3f13e16389ea480caf74af7 https://github.com/galaxyproject/galaxy/commit/dc3218eab2f971e4d3f13e16389e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-04 (Mon, 04 Sep 2017) Changed paths: M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Fix ftp test Commit: 55486381a6701f748bb8b051bcd70a20a526fca6 https://github.com/galaxyproject/galaxy/commit/55486381a6701f748bb8b051bcd7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/less/ui.less M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-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/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/style/blue/base.css Log Message: ----------- Use lazy loader to handle uploader row construction Commit: 4de5c95866b2264b6d3ea36f0e313bac1417edb8 https://github.com/galaxyproject/galaxy/commit/4de5c95866b2264b6d3ea36f0e31… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/less/ui.less M static/maps/mvc/upload/default/default-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/upload/default/default-view.js M static/style/blue/base.css Log Message: ----------- Use limit loader Fix reset call Commit: 5b16f0974f5f1af737f639ddcaa17ebe77a7bdae https://github.com/galaxyproject/galaxy/commit/5b16f0974f5f1af737f639ddcaa1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: R client/galaxy/scripts/mvc/upload/ftp/ftp-view.js M client/galaxy/scripts/mvc/upload/upload-view.js R static/maps/mvc/upload/ftp/ftp-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map R static/scripts/mvc/upload/ftp/ftp-view.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Remove separate ftp tab Commit: 45ec3a9568a0c7102dfcc2b16cf01c428c5bfcdc https://github.com/galaxyproject/galaxy/commit/45ec3a9568a0c7102dfcc2b16cf0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: A client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/upload/default/default-view.js A static/maps/mvc/lazy/lazy-limited.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/lazy/lazy-limited.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Put lazy loader into separate file for reusability Commit: 9977d85d0bf238064ceb75009917a86c4156490d https://github.com/galaxyproject/galaxy/commit/9977d85d0bf238064ceb75009917… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 Log Message: ----------- Add support to submit ftp files before queueing remaining files Commit: edd6bcbe41071d276912944cb6bac6752c532e49 https://github.com/galaxyproject/galaxy/commit/edd6bcbe41071d276912944cb6ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.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: ----------- Use consistent names Commit: 7816b6b4430fd96ce311fd64ac7352f833cb595d https://github.com/galaxyproject/galaxy/commit/7816b6b4430fd96ce311fd64ac73… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.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: ----------- Move render function Commit: f24fda5301de8f3cb4c033cb6dd1036f19409d89 https://github.com/galaxyproject/galaxy/commit/f24fda5301de8f3cb4c033cb6dd1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/upload/default/default-view.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 collection listener to govern lazy loader Commit: 33414be9e4b3aad9eb1338a9600b8789aaaea7e8 https://github.com/galaxyproject/galaxy/commit/33414be9e4b3aad9eb1338a9600b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.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: ----------- Move ftp helper to separate function Commit: a7108b63c1b037c1b45aef56650996bbe919330e https://github.com/galaxyproject/galaxy/commit/a7108b63c1b037c1b45aef566509… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.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 submission function using current format Commit: 728087ed530f27698a0c9634ca0c1e5d471d24cb https://github.com/galaxyproject/galaxy/commit/728087ed530f27698a0c9634ca0c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/docker-compose.yml M .travis.yml M CITATION M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M 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static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/mvc/groups/group-listrow-view.js.map M static/toolshed/maps/mvc/groups/group-model.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js M static/toolshed/scripts/mvc/groups/group-model.js R templates/admin/forms/create_form.mako R templates/admin/forms/edit_form_definition.mako R templates/admin/forms/grid.mako R templates/admin/forms/view_form_definition.mako R templates/admin/tool_shed_repository/browse_category.mako M templates/display_base.mako M templates/display_common.mako R templates/export_base.mako R templates/rss.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako R templates/webapps/galaxy/admin/toolsheds.mako R templates/webapps/galaxy/history/permissions.mako R templates/webapps/galaxy/history/rename.mako R templates/webapps/galaxy/page/create.mako R templates/webapps/galaxy/visualization/create.mako M templates/webapps/galaxy/workflow/editor.mako A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/populators.py R test/base/test_db_util.py A test/base/testcase.py M test/base/tool_shed_util.py R test/base/twilltestcase.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py R test/functional/database_contexts.py R test/functional/test_library_templates.py M test/functional/test_toolbox.py M test/functional/tools/composite.xml M test/functional/tools/composite_output.xml M test/functional/tools/composite_output_tests.xml M test/functional/tools/metadata.xml A test/functional/twilltestcase.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py A test/integration/test_data_manager_table_reload.py M test/integration/test_resolvers.py M test/integration/test_upload_configuration_options.py A test/integration/tool_sheds_conf.xml M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py A test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_published_histories_grid.py A test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py A test/unit/__init__.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_HistoryManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools_support.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py R test/unit/web/base/__init__.py R test/unit/web/base/test_HookPluginManager.py R test/unit/web/base/test_PageServingPluginManager.py R test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/workflow_support.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/extract/liftOver_wrapper.xml M tools/filters/join.py M tools/filters/joiner.xml M tools/sr_assembly/velvetg.xml Log Message: ----------- Merge remote-tracking branch 'jmchilton/multiple_files_per_upload' into ftp_uploader Commit: 5c4ae1e319e08f72de146783b1e4adab1b1b41eb https://github.com/galaxyproject/galaxy/commit/5c4ae1e319e08f72de146783b1e4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js 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.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Specify file type and dbkey per entry Commit: 833554a42eea0686f608efc9dd2c4e2f83013a9b https://github.com/galaxyproject/galaxy/commit/833554a42eea0686f608efc9dd2c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Make sure that column count and lines are defined Commit: 10196dd2e46614a9c366fa95afae7bd360233f4b https://github.com/galaxyproject/galaxy/commit/10196dd2e46614a9c366fa95afae… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/postgresql_fake.tar.bz2 M lib/galaxy/model/__init__.py M lib/galaxy/tools/toolbox/base.py M static/maps/mvc/history/history-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-view.js A test-data/selenium-test-notebook.ipynb M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py A test/selenium_tests/test_jupyter.py A test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_landing.py A test/selenium_tests/test_navigates_galaxy.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge branch 'dev' into ftp_uploader Commit: 6081c0bc8392320ecb865af9f58f5726fa40fcdf https://github.com/galaxyproject/galaxy/commit/6081c0bc8392320ecb865af9f58f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/onload.js M config/galaxy.ini.sample M lib/galaxy/__init__.py M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py R lib/galaxy/util/backports/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/image_util.py R lib/galaxy/util/log/__init__.py R lib/galaxy/util/log/fluent_log.py A lib/galaxy/util/logging/__init__.py A lib/galaxy/util/logging/fluent_log.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/streamball.py M lib/galaxy/util/submodules.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/tool_shed/model/__init__.py M run.sh M setup.cfg M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/onload.js M test/api/test_tools.py A test/api/test_tools_upload.py M test/base/api.py M test/base/api_util.py A test/base/constants.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M test/unit/test_security_helper.py M tools/filters/joiner.xml Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into ftp_uploader Conflicts: static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Commit: e03bedfb8526e55d34fd66348fc78e1a397abbd7 https://github.com/galaxyproject/galaxy/commit/e03bedfb8526e55d34fd66348fc7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-09 (Mon, 09 Oct 2017) Changed paths: A client/galaxy/scripts/mvc/lazy/lazy-limited.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js A client/galaxy/scripts/mvc/upload/upload-extension.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M lib/galaxy/datatypes/text.py A static/maps/mvc/lazy/lazy-limited.js.map M static/maps/mvc/upload/collection/collection-view.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map A static/maps/mvc/upload/upload-extension.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/lazy/lazy-limited.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js A static/scripts/mvc/upload/upload-extension.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Merge pull request #4513 from guerler/ftp_uploader Allow users to upload multiple FTP files within a single request Compare: https://github.com/galaxyproject/galaxy/compare/5edc4235bb23...e03bedfb8526

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[galaxyproject/galaxy] d5ed68: Fix docstring linting.
by GitHub 08 Oct '17

08 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5ed68560f817a130ade340f6dab591709a73d44 https://github.com/galaxyproject/galaxy/commit/d5ed68560f817a130ade340f6dab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-08 (Sun, 08 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Fix docstring linting. The module we used added new issues D106 and D107 (lack of docstring in __init__ methods) which we fail extensively - so adding it to the ignore list. Commit: 5edc4235bb2352fd67175a5ca323ecf50047878a https://github.com/galaxyproject/galaxy/commit/5edc4235bb2352fd67175a5ca323… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-08 (Sun, 08 Oct 2017) Changed paths: M setup.cfg Log Message: ----------- Merge pull request #4766 from jmchilton/fix_docstring_linting Fix docstring linting. Compare: https://github.com/galaxyproject/galaxy/compare/58e4884b52c3...5edc4235bb23

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[galaxyproject/usegalaxy-playbook] 690b8c: Update Main
by GitHub 05 Oct '17

05 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 690b8c9ff1a359ce9235810730ec36a9558d1f68 https://github.com/galaxyproject/usegalaxy-playbook/commit/690b8c9ff1a359ce… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/usegalaxy-playbook] 340408: Restore Jetstream@TACC usage
by GitHub 05 Oct '17

05 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 340408659fa3246d52f6c6a652f03ded7058e966 https://github.com/galaxyproject/usegalaxy-playbook/commit/340408659fa3246d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/main/group_vars/galaxywebservers.yml Log Message: ----------- Restore Jetstream@TACC usage Commit: 87d23249af49e7dbc9e5cefceef49064213bca44 https://github.com/galaxyproject/usegalaxy-playbook/commit/87d23249af49e7db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: f888ca3cf6853eeaba26a98032574e1f868b358b https://github.com/galaxyproject/usegalaxy-playbook/commit/f888ca3cf6853eea… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs from Main Commit: 4dd21e09bef98db526d7ea211ef1a1bd28a756a7 https://github.com/galaxyproject/usegalaxy-playbook/commit/4dd21e09bef98db5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M env/main/group_vars/galaxywebservers.yml M roles/usegalaxy_swarmscale/files/inventory.spawn Log Message: ----------- Update Jupyter GIE image to 17.09 and set a 5 minute container timeout. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/c937b14b0bee...…

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[galaxyproject/galaxy] 1b7b4d: GIEs: Grandfather automatic uppercasing of some en...
by GitHub 05 Oct '17

05 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1b7b4da9a266fac29486aef3b3a290e1c9749199 https://github.com/galaxyproject/galaxy/commit/1b7b4da9a266fac29486aef3b3a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- GIEs: Grandfather automatic uppercasing of some env_override variables. Commit: f9eae90944790530274a9079d7eb76fc10ce68eb https://github.com/galaxyproject/galaxy/commit/f9eae90944790530274a9079d7eb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #4760 from natefoo/gie-upper-grandfather [17.09] GIEs: Grandfather automatic uppercasing of some env_override variables Commit: 58e4884b52c3f04b28d575447533a21512613770 https://github.com/galaxyproject/galaxy/commit/58e4884b52c3f04b28d575447533… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9de98a6a9fd9...58e4884b52c3

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