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[galaxyproject/galaxy] ab1549: Set allow_duplicate_entries="False" for built-in T...
by GitHub 22 Jul '16

22 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab15495b8ee4c630b7e45575cdddc2e5a6a4bd97 https://github.com/galaxyproject/galaxy/commit/ab15495b8ee4c630b7e45575cddd… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Set allow_duplicate_entries="False" for built-in Tool Data Tables. Commit: 59dd11c8bc6746c23af759e2005bc5793713a939 https://github.com/galaxyproject/galaxy/commit/59dd11c8bc6746c23af759e2005b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Fix duplicate allow_duplicate_entries Commit: 0808015c9a4255f097a1f18a28c65ae6396ff7f7 https://github.com/galaxyproject/galaxy/commit/0808015c9a4255f097a1f18a28c6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Merge pull request #2644 from blankenberg/dm-no-dupe Set allow_duplicate_entries="False" for built-in Tool Data Tables. Compare: https://github.com/galaxyproject/galaxy/compare/8dbf987e10cb...0808015c9a42

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[galaxyproject/galaxy] f2941c: Add Galactic Radio Telescope script
by GitHub 22 Jul '16

22 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f2941c47aad24b301377792843a60428099e73c9 https://github.com/galaxyproject/galaxy/commit/f2941c47aad24b301377792843a6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-03 (Fri, 03 Jun 2016) Changed paths: A scripts/grt.py Log Message: ----------- Add Galactic Radio Telescope script Commit: d032a1a4aa26b0d365418e9fb846c5fbedd3d4d1 https://github.com/galaxyproject/galaxy/commit/d032a1a4aa26b0d365418e9fb846… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Linting Commit: 6344ff40fdd843f6d6f02a9ae6956854f85ea474 https://github.com/galaxyproject/galaxy/commit/6344ff40fdd843f6d6f02a9ae695… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Make time length an option Commit: b1a07c0cfbf30968987755b3df84d9059176542d https://github.com/galaxyproject/galaxy/commit/b1a07c0cfbf30968987755b3df84… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Submit more metadata Commit: bf8f8e2d08a1d5db5831aa0f26dc584fa631ca36 https://github.com/galaxyproject/galaxy/commit/bf8f8e2d08a1d5db5831aa0f26dc… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: A doc/source/admin/grt.rst M doc/source/admin/index.rst Log Message: ----------- Document GRT Commit: 9e596cdf5fbd4e63f7811d7d82929ee2d03fc79b https://github.com/galaxyproject/galaxy/commit/9e596cdf5fbd4e63f7811d7d8292… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- E303 Commit: 012101692c9cac152f8f2a48dc6c8983375a5823 https://github.com/galaxyproject/galaxy/commit/012101692c9cac152f8f2a48dc6c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Ignore metadata setting Commit: d1d8642756a062ee6df554dc9bdc3840d6fc828b https://github.com/galaxyproject/galaxy/commit/d1d8642756a062ee6df554dc9bdc… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Change metric captured Commit: 722695a01b8531560ee5f5cb12c2b235dff53308 https://github.com/galaxyproject/galaxy/commit/722695a01b8531560ee5f5cb12c2… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Added in last_job_id_sent and removed days options so no duplicates will be sent. Commit: bb3f026bfa14d7ae77b2b50dcdaf080fa6917875 https://github.com/galaxyproject/galaxy/commit/bb3f026bfa14d7ae77b2b50dcdaf… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Removed call to args.days Commit: 473b7eadc1feb6f6ca3b216080b319174f8f1229 https://github.com/galaxyproject/galaxy/commit/473b7eadc1feb6f6ca3b216080b3… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: A scripts/grt.ini.sample M scripts/grt.py Log Message: ----------- Added in tool_blacklist Commit: c2239b1d9bed06552571de862ec2ecb2bb3b46aa https://github.com/galaxyproject/galaxy/commit/c2239b1d9bed06552571de862ec2… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.ini.sample M scripts/grt.py Log Message: ----------- Moved almost all cmd line parameters to config file. Commit: 5cd9423677ef34e417059ae0be474872fc215909 https://github.com/galaxyproject/galaxy/commit/5cd9423677ef34e417059ae0be47… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.ini.sample M scripts/grt.py Log Message: ----------- Added grt_url to grt.ini.sample and removed default from argparse Commit: db4abace58711cef08e5a48d2d06f07f17c6d0c5 https://github.com/galaxyproject/galaxy/commit/db4abace58711cef08e5a48d2d06… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Flake8 fixes Commit: 0c24b1c408defa1c0d43754521a698a16a029bbf https://github.com/galaxyproject/galaxy/commit/0c24b1c408defa1c0d43754521a6… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Fixed remaining flake8 issues Commit: 0383d47037b1e18a60e882ff6bf8e4b905ec32b2 https://github.com/galaxyproject/galaxy/commit/0383d47037b1e18a60e882ff6bf8… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Added in params reporting with initial sanitization Commit: 2fc3ffffff39acbbfca0bdd265fd61f5b80a40f6 https://github.com/galaxyproject/galaxy/commit/2fc3ffffff39acbbfca0bdd265fd… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M scripts/grt.py Log Message: ----------- Removed unused copy import Commit: 417d43fb3ed5996657b568e1d2f9b6c728594b9b https://github.com/galaxyproject/galaxy/commit/417d43fb3ed5996657b568e1d2f9… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M scripts/grt.ini.sample Log Message: ----------- Added upload1 to tool blacklist Commit: 0280daebef16e83894812a813d673e576f571806 https://github.com/galaxyproject/galaxy/commit/0280daebef16e83894812a813d67… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: R scripts/grt.ini.sample M scripts/grt.py A scripts/grt.yml.sample Log Message: ----------- grt.ini.sample is a YAML file, git it a YAML extension. Commit: 6432eae251c1a85e0c22b17d80af731a5b8a9752 https://github.com/galaxyproject/galaxy/commit/6432eae251c1a85e0c22b17d80af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M scripts/grt.py Log Message: ----------- Give grt a top-level docstring. Commit: a93874fe7b6939c32b907a6f8fdd1cc0da6ce519 https://github.com/galaxyproject/galaxy/commit/a93874fe7b6939c32b907a6f8fdd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M scripts/grt.py Log Message: ----------- Define a main() function for grt client. This is purely stylistic - but I prefer to structure code to allow testing even if there are no actual test cases yet. For more information see discussion here - http://stackoverflow.com/questions/4041238/why-use-def-main. Commit: 1f292824a161d8d62767b47424b255146edb89d4 https://github.com/galaxyproject/galaxy/commit/1f292824a161d8d62767b47424b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M scripts/grt.py Log Message: ----------- Fix some obvious Python 2isms in grt client... ... and one instance of bare exception. Commit: bbe1d7bed036499d9a60b7db9daa9a93ee9bc4ef https://github.com/galaxyproject/galaxy/commit/bbe1d7bed036499d9a60b7db9daa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M scripts/grt.py Log Message: ----------- Remove custom Galaxy config parsing in grt.py. Use existing abstractions - so things like environment variable based configuration will work. Commit: 76628c720318c43665ef0067663738d4927f291f https://github.com/galaxyproject/galaxy/commit/76628c720318c43665ef00676637… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M scripts/grt.py Log Message: ----------- Refactor grt.py method names to be clear public interface is only main(). Commit: 212f7f0d9de67afb446989ae91cae79843358360 https://github.com/galaxyproject/galaxy/commit/212f7f0d9de67afb446989ae91ca… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: R scripts/grt.ini.sample M scripts/grt.py A scripts/grt.yml.sample Log Message: ----------- Merge pull request #16 from jmchilton/grt Touch up grt.py. Commit: 8dbf987e10cb946c96b7ec82c996892d443f61ab https://github.com/galaxyproject/galaxy/commit/8dbf987e10cb946c96b7ec82c996… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: A doc/source/admin/grt.rst M doc/source/admin/index.rst A scripts/grt.py A scripts/grt.yml.sample Log Message: ----------- Merge pull request #2455 from erasche/grt Galactic Radio Telescope Compare: https://github.com/galaxyproject/galaxy/compare/5ff6d7ad194f...8dbf987e10cb

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[galaxyproject/galaxy] 930c37: Style fixes
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 930c37ffb10bf36d2e95cee34da35997cdf59d8d https://github.com/galaxyproject/galaxy/commit/930c37ffb10bf36d2e95cee34da3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/library/jobs.js M config/plugins/visualizations/charts/static/library/storage.js M config/plugins/visualizations/charts/static/models/chart.js M config/plugins/visualizations/charts/static/models/config.js M config/plugins/visualizations/charts/static/models/group.js M config/plugins/visualizations/charts/static/models/groups.js M config/plugins/visualizations/charts/static/views/viewer.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Style fixes Commit: 4dd33fecb7b7643e7a4e14440a56187b790219a0 https://github.com/galaxyproject/galaxy/commit/4dd33fecb7b7643e7a4e14440a56… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Align editor view style Commit: 0861bb5b946bef5f5b7bb3d6c40670ec4eb1661d https://github.com/galaxyproject/galaxy/commit/0861bb5b946bef5f5b7bb3d6c406… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Fix spacing Commit: b6914479fba31057c064fcdcfc48060760d15400 https://github.com/galaxyproject/galaxy/commit/b6914479fba31057c064fcdcfc48… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/group.js Log Message: ----------- Align group view coding style Commit: 58a237eb4597cd709f8dbd0dcf6143f0adebc7f7 https://github.com/galaxyproject/galaxy/commit/58a237eb4597cd709f8dbd0dcf61… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/group.js Log Message: ----------- Adjust group view coding styles Commit: d38a4a4f6b193aa4aae84d200cdf77916aee9038 https://github.com/galaxyproject/galaxy/commit/d38a4a4f6b193aa4aae84d200cdf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Align remaining view code styles Commit: c6e9a56a46e97c7991eb3b67084c60d0d839f81e https://github.com/galaxyproject/galaxy/commit/c6e9a56a46e97c7991eb3b67084c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/models/chart.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Adjust viewport styles Commit: ad9f8b139d77575281900997039cc3bba3d00eb5 https://github.com/galaxyproject/galaxy/commit/ad9f8b139d77575281900997039c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js Log Message: ----------- Decouple change handler for input parameters Commit: a8da228c8fddcff29c73c0900574e74290166359 https://github.com/galaxyproject/galaxy/commit/a8da228c8fddcff29c73c0900574… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Use common parameter factory for charts Commit: 0486ea4cc6aee83ea3d57f5fff0bf75b562410e2 https://github.com/galaxyproject/galaxy/commit/0486ea4cc6aee83ea3d57f5fff0b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/library/ui-table-form.js Log Message: ----------- Fadein additional options Commit: ef029042fd30c46b02e423b00f80cfb8dbf38e49 https://github.com/galaxyproject/galaxy/commit/ef029042fd30c46b02e423b00f80… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: R config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/settings.js Log Message: ----------- Combine ui-table-form and settings view Commit: 08b8cd6f00aed9554256ecf2c7eafd2e4f99ce99 https://github.com/galaxyproject/galaxy/commit/08b8cd6f00aed9554256ecf2c7ea… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/settings.js Log Message: ----------- Remove unused rendering options for settings view Commit: ce131d8b51dec8bb99571a524dc4c4f045e675d7 https://github.com/galaxyproject/galaxy/commit/ce131d8b51dec8bb99571a524dc4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css Log Message: ----------- Fix font size change caused by report styles Commit: 39c544c7742c9cc7853a9bbeac1d43c564b43e7b https://github.com/galaxyproject/galaxy/commit/39c544c7742c9cc7853a9bbeac1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/library/storage.js Log Message: ----------- Show error message if saving fails Commit: 806019bb95844569c611618e177d974bd673332e https://github.com/galaxyproject/galaxy/commit/806019bb95844569c611618e177d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/library/storage.js Log Message: ----------- Add reusable modal show to app Commit: ca4b444af481bbdbdcd495ad3a397d4e0d1812d0 https://github.com/galaxyproject/galaxy/commit/ca4b444af481bbdbdcd495ad3a39… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Fix state information rendering Commit: 9f7c392239885c9ba8fdc43e7ba3e2d4d90dc2cc https://github.com/galaxyproject/galaxy/commit/9f7c392239885c9ba8fdc43e7ba3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Revise to 3-tab mode Commit: 645727c7a520a25b2459155604ff05eb533de4dd https://github.com/galaxyproject/galaxy/commit/645727c7a520a25b2459155604ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Fix margin Commit: 539eeef5123f4adac296806ac4faf6931b24bb3c https://github.com/galaxyproject/galaxy/commit/539eeef5123f4adac296806ac4fa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Use large margin Commit: 916d2d01f788f32f126dd31ad4cf8fca1f99af85 https://github.com/galaxyproject/galaxy/commit/916d2d01f788f32f126dd31ad4cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M config/plugins/visualizations/charts/static/views/editor.js M static/maps/mvc/ui/ui-tabs.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-tabs.js Log Message: ----------- Refactor ui-tabs view Commit: b59cf74589e98c0666e1202750611a610e49826a https://github.com/galaxyproject/galaxy/commit/b59cf74589e98c0666e120275061… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M config/plugins/visualizations/charts/static/views/editor.js M static/maps/mvc/ui/ui-tabs.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-tabs.js Log Message: ----------- Add tab tooltips Commit: 78432f7d88f60564c4415253b0886fc05590e8b0 https://github.com/galaxyproject/galaxy/commit/78432f7d88f60564c4415253b088… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js R config/plugins/visualizations/charts/static/views/group.js A config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M static/maps/mvc/form/form-repeat.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-repeat.js Log Message: ----------- Add repeat style view for data groups Commit: e2ebcd40e5d1a4bee009bd647bad40698dedecd5 https://github.com/galaxyproject/galaxy/commit/e2ebcd40e5d1a4bee009bd647bad… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M static/maps/mvc/ui/ui-tabs.js.map M static/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Insert tab icons Commit: 3ca50a6b237b77cda3f7dba9acd6c151b4893b80 https://github.com/galaxyproject/galaxy/commit/3ca50a6b237b77cda3f7dba9acd6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M config/plugins/visualizations/charts/static/views/editor.js M static/maps/mvc/ui/ui-tabs.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-tabs.js Log Message: ----------- Insert tab icons Commit: e10d63cee00018ebf176976b6af4899634e87103 https://github.com/galaxyproject/galaxy/commit/e10d63cee00018ebf176976b6af4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Fix 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config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Refactor individual model files, auto add first data series Commit: e25057c0d12e4570d53f4cb5eeed213e081b850a https://github.com/galaxyproject/galaxy/commit/e25057c0d12e4570d53f4cb5eeed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/library/storage.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/groups.js M static/maps/mvc/form/form-data.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-data.js M static/style/blue/base.css Log Message: ----------- Use regular form view for groups Commit: 6ebc19aa2e4978d4bf151f5f994c54e37fa5dd25 https://github.com/galaxyproject/galaxy/commit/6ebc19aa2e4978d4bf151f5f994c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css Log Message: ----------- Fix status margin Commit: fdf7a917c440087d206890e08b39608131ace241 https://github.com/galaxyproject/galaxy/commit/fdf7a917c440087d206890e08b39… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/models/config.js Log Message: ----------- Limit query size Commit: 2ee278a20fbedd6391c015b85689d834150a3a39 https://github.com/galaxyproject/galaxy/commit/2ee278a20fbedd6391c015b85689… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Add semicolon Commit: f25e177fa55e456e0fd739f772e2a9dbc69304a0 https://github.com/galaxyproject/galaxy/commit/f25e177fa55e456e0fd739f772e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/viewport.js M static/maps/mvc/form/form-view.js.map M static/scripts/mvc/form/form-view.js Log Message: ----------- Series color Commit: 9e3a9212754da8407bf93a9078e5f61116660f38 https://github.com/galaxyproject/galaxy/commit/9e3a9212754da8407bf93a9078e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Fix chart column validation Commit: 5c0a25498b6fa9b54539ba421fcceb634f75e411 https://github.com/galaxyproject/galaxy/commit/5c0a25498b6fa9b54539ba421fcc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Relax column type matching condition Commit: d583d34d13d934230fd2645336df642b40dfb03e https://github.com/galaxyproject/galaxy/commit/d583d34d13d934230fd2645336df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M .ci/py3_sources.txt M Makefile M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/data.js M 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M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_runner.py M scripts/fetch_eggs.py M scripts/set_dataset_sizes.py M setup.cfg M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-template.js.map M static/maps/viz/trackster/painters.js.map M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-template.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M templates/admin/impersonate.mako M templates/ind_share_base.mako M templates/user/change_password.mako M test/api/helpers.py M test/api/test_datasets.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py A test/functional/tools/identifier_collection.xml M test/functional/tools/samples_tool_conf.xml M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional_tests.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_toolbox.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/gsummary.xml M tox.ini Log Message: ----------- Merge branch 'dev' into charts_revision_000 Commit: 9c1ee51e3a48c12e43071afafeb1847d66ddaa78 https://github.com/galaxyproject/galaxy/commit/9c1ee51e3a48c12e43071afafeb1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/datatypes_conf.xml.sample M config/job_conf.xml.sample_advanced A config/tool_destinations.yml.sample M doc/source/admin/interactive_environments.rst M doc/source/dev/index.rst A doc/source/dev/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/actions/post.py A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js M templates/webapps/galaxy/history/grid.mako M test/api/test_users.py M test/api/test_workflows.py A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml A test/unit/datatypes/test_data.py A test/unit/jobs/dynamic_tool_destination/__init__.py A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml A test/unit/jobs/dynamic_tool_destination/data/test.empty A test/unit/jobs/dynamic_tool_destination/data/test.fasta A test/unit/jobs/dynamic_tool_destination/data/test1.full A test/unit/jobs/dynamic_tool_destination/data/test3.full A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_conda_resolution.py M tools/stats/gsummary.xml Log Message: ----------- Merge branch 'dev' into charts_revision_000 Commit: 5ff6d7ad194f9e5145facef5c6baf2736e52c330 https://github.com/galaxyproject/galaxy/commit/5ff6d7ad194f9e5145facef5c6ba… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/library/jobs.js M config/plugins/visualizations/charts/static/library/storage.js R config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/models/chart.js M config/plugins/visualizations/charts/static/models/config.js R config/plugins/visualizations/charts/static/models/group.js R config/plugins/visualizations/charts/static/models/groups.js M config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css M config/plugins/visualizations/charts/static/views/editor.js R config/plugins/visualizations/charts/static/views/group.js A config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewer.js M config/plugins/visualizations/charts/static/views/viewport.js M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/ui/ui-tabs.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-data.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-tabs.js M static/style/blue/base.css Log Message: ----------- Merge pull request #2531 from guerler/charts_revision_000 Charts revision Compare: https://github.com/galaxyproject/galaxy/compare/2075af4de80f...5ff6d7ad194f

1 0

[galaxyproject/galaxy] bb82ec: Merge pull request #1 from galaxyproject/dev
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb82ec5bec1fec28402768cfbd40e01a7341e2de https://github.com/galaxyproject/galaxy/commit/bb82ec5bec1fec28402768cfbd40… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: A .ci/first_startup.sh M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M .travis.yml M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui/icon-btn.less M client/grunt-tasks/style.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.xml A config/plugins/interactive_environments/phinch/static/js/phinch.js A config/plugins/interactive_environments/phinch/templates/phinch.mako M config/tool_conf.xml.main M config/tool_conf.xml.sample M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init M create_db.sh M doc/source/admin/framework_dependencies.rst M doc/source/project/organization.rst M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/managers/workflows.py R lib/galaxy/metadata M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/util/none_like.py M lib/galaxy/util/sanitize_html.py A lib/galaxy/util/ucsc.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M 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Merge pull request #1 from galaxyproject/dev pull updates from HEAD of dev Commit: d123b402303a708c2d20d83a0fbc0289d9bc65db https://github.com/galaxyproject/galaxy/commit/d123b402303a708c2d20d83a0fbc… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M .gitignore M Makefile M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js R client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M 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static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map R static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster/tracks.js.map M 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test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional_tests.py M test/unit/jobs/test_runner_local.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/test_lazy_process.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Merge pull request #2 from galaxyproject/dev Merge pull request #2 from galaxyproject/dev Commit: 1fed38b28289bee22a00fbac4b1030224dd77150 https://github.com/galaxyproject/galaxy/commit/1fed38b28289bee22a00fbac4b10… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M .gitignore M CONTRIBUTORS.md M Makefile M README.rst R buildbot_setup.sh M client/README.md M client/bower.json M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M 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[galaxyproject/galaxy] d02f1f: * Update docs on Interactive Environments
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d02f1f1d6a1a236be7619a596c35ac04d0cfebaf https://github.com/galaxyproject/galaxy/commit/d02f1f1d6a1a236be7619a596c35… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M doc/source/admin/interactive_environments.rst A doc/source/dev/interactive_environments.rst Log Message: ----------- * Update docs on Interactive Environments * Move docs on writing IEs to developer docs Commit: 19ab4f793bb1394005206cfe3deaad44636e3a60 https://github.com/galaxyproject/galaxy/commit/19ab4f793bb1394005206cfe3dea… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M doc/source/dev/index.rst Log Message: ----------- Add link to IE dev docs Commit: e73a8071f5efc0a7e19143a71bbe63eb9d617cc9 https://github.com/galaxyproject/galaxy/commit/e73a8071f5efc0a7e19143a71bbe… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Addressed @erasche's comments Commit: 63abe20ab84ff7860400e6a4d726e01f6a80b3b7 https://github.com/galaxyproject/galaxy/commit/63abe20ab84ff7860400e6a4d726… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Replace single ` with `` Commit: cd0932600f5701f2d01bc28d9f79c77de0e8ee76 https://github.com/galaxyproject/galaxy/commit/cd0932600f5701f2d01bc28d9f79… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Modified Apache/nginx settings suggestions Commit: 4860cc715613bee1ab9527d10f8a654e5a29a6be https://github.com/galaxyproject/galaxy/commit/4860cc715613bee1ab9527d10f8a… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M doc/source/dev/index.rst Log Message: ----------- Added correct link to index.rst Commit: 8b324e8f456f17ecbed22f0f19a18cb819601745 https://github.com/galaxyproject/galaxy/commit/8b324e8f456f17ecbed22f0f19a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M doc/source/admin/interactive_environments.rst M doc/source/dev/index.rst A doc/source/dev/interactive_environments.rst Log Message: ----------- Merge pull request #2543 from pvanheus/interactive_env_docs Updates to Interactive Environment docs Compare: https://github.com/galaxyproject/galaxy/compare/9291c8ae34d2...8b324e8f456f

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[galaxyproject/infrastructure-playbook] c09fc0: Proxy images through duvel since performance from ...
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c09fc029d2e83d251e1b0002e37bbc021d38fa75 https://github.com/galaxyproject/infrastructure-playbook/commit/c09fc029d2e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M galaxyenv/host_vars/duvel.galaxyproject.org.yml A galaxyenv/templates/nginx/images-proxy.j2 M galaxyenv/templates/nginx/images.j2 Log Message: ----------- Proxy images through duvel since performance from outside direct to orval is low (why??)

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[galaxyproject/galaxy] a8147e: add tar to datatype_conf.xml
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8147e537cf8e894d6d5032220909d211235d72f https://github.com/galaxyproject/galaxy/commit/a8147e537cf8e894d6d503222090… Author: maria <maria.bernard(a)jouy.inra.fr> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add tar to datatype_conf.xml Commit: 9291c8ae34d225e97f03ed5b012326ccc3c9893d https://github.com/galaxyproject/galaxy/commit/9291c8ae34d225e97f03ed5b0123… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #2636 from mariabernard/tar_datatype_branch add tar to datatypes_conf.xml Compare: https://github.com/galaxyproject/galaxy/compare/423e85fc8111...9291c8ae34d2

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[galaxyproject/galaxy] a8b7c6: Smart string handling on the wsgi response -- this...
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8b7c6a8eca231b251d59ddeb5ccab88845a757e https://github.com/galaxyproject/galaxy/commit/a8b7c6a8eca231b251d59ddeb5cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Smart string handling on the wsgi response -- this fixes uwsgi blanking out when handling endpoints that return unicode. Commit: 01cdb9387e4c1b885ab474b5c0c88a05a1147ca2 https://github.com/galaxyproject/galaxy/commit/01cdb9387e4c1b885ab474b5c0c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Simplify flatten method Commit: 5ba7e5adaeda7d33d869ed71542491cb40f3c5d7 https://github.com/galaxyproject/galaxy/commit/5ba7e5adaeda7d33d869ed715424… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Make sure yielded items from a flattened iterable are properly stringified. Commit: a5f9e5b9efd287c1bce5d6f3da41f30affd511ad https://github.com/galaxyproject/galaxy/commit/a5f9e5b9efd287c1bce5d6f3da41… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Reverted the refactoring of flatten; generator wasn't unpacking (of course), and caused an infinite loop. Commit: 423e85fc81110cb800b398b485d3aacc97914500 https://github.com/galaxyproject/galaxy/commit/423e85fc81110cb800b398b485d3… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge pull request #2630 from dannon/base_framework_string_handling Smart string handling on the wsgi response -- this fixes uwsgi blanki… Compare: https://github.com/galaxyproject/galaxy/compare/f67d3cbe93e3...423e85fc8111

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[galaxyproject/galaxy] 92948b: Overload select wrapper`s concat function
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 92948b5b0fc062ce904c5987c1d48d3831730a9a https://github.com/galaxyproject/galaxy/commit/92948b5b0fc062ce904c5987c1d4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Overload select wrapper`s concat function Commit: 1de7beca98d0bc8b11b9dca46a4984ac1cee9428 https://github.com/galaxyproject/galaxy/commit/1de7beca98d0bc8b11b9dca46a49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #2623 from guerler/fix_select_value_concat [16.04] Overload select wrapper`s concat function Compare: https://github.com/galaxyproject/galaxy/compare/68a64182c14a...1de7beca98d0

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[galaxyproject/galaxy] e4a35f: Paste handles encoding automatically when thrown u...
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: e4a35f943b42401c92646d8f6b7b1c1fd515a9c1 https://github.com/galaxyproject/galaxy/commit/e4a35f943b42401c92646d8f6b7b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Paste handles encoding automatically when thrown unicode, but uwsgi does not. This was resulting in unencoded (unicode) workflow drawings (svg) not appearing at all when the gen_image was invoked. Also took the opportunity to add a correct header for a standalone svg document. Commit: 68a64182c14af9f4cc10915c466177292d24ebfc https://github.com/galaxyproject/galaxy/commit/68a64182c14af9f4cc10915c4661… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Merge pull request #2628 from dannon/workflow_svg_uwsgi_fix [16.04] Workflow SVG generation fix Compare: https://github.com/galaxyproject/galaxy/compare/132bd4dd57e0...68a64182c14a

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[galaxyproject/galaxy] d8711a: Initial DTD to Galaxy work
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d8711a121ce127cce82ed7010ed9ba1bb6ff1479 https://github.com/galaxyproject/galaxy/commit/d8711a121ce127cce82ed7010ed9… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-29 (Wed, 29 Jun 2016) Changed paths: A config/tool_destinations.yml.sample A lib/galaxy/jobs/rules/dynamic_tool_destination.py Log Message: ----------- Initial DTD to Galaxy work Commit: c053197beed35f2357c17b887ed60d218b0c7a4c https://github.com/galaxyproject/galaxy/commit/c053197beed35f2357c17b887ed6… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-04 (Mon, 04 Jul 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/rules/dynamic_tool_destination.py A test/unit/jobs/rules/__init__.py A test/unit/jobs/rules/data/dest_fail.yml A test/unit/jobs/rules/data/priority_tool_destination.yml A test/unit/jobs/rules/data/test.empty A test/unit/jobs/rules/data/test.fasta A test/unit/jobs/rules/data/test1.full A test/unit/jobs/rules/data/test3.full A test/unit/jobs/rules/data/test_no_verbose.yml A test/unit/jobs/rules/data/test_num_input_datasets.yml A test/unit/jobs/rules/data/test_users.yml A test/unit/jobs/rules/data/tool_destination.yml A test/unit/jobs/rules/mockGalaxy.py A test/unit/jobs/rules/test_dynamic_tool_destination.py A test/unit/jobs/rules/vfdb/?bact.test A test/unit/jobs/rules/ymltests.py Log Message: ----------- Added in DTD tests Commit: 99161d6074e5cae86eb5788d641511ad6e47c26a https://github.com/galaxyproject/galaxy/commit/99161d6074e5cae86eb5788d6415… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-04 (Mon, 04 Jul 2016) Changed paths: M lib/galaxy/jobs/rules/dynamic_tool_destination.py M test/unit/jobs/rules/mockGalaxy.py M test/unit/jobs/rules/test_dynamic_tool_destination.py M test/unit/jobs/rules/ymltests.py Log Message: ----------- Flake8 fixes Commit: ed48c6c28b72ef63499ff39abcce9171fb684154 https://github.com/galaxyproject/galaxy/commit/ed48c6c28b72ef63499ff39abcce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/rules/dynamic_tool_destination.py Log Message: ----------- Use more traditional Galaxy config handling for DTD. Commit: d87957e1a2030752b5617934b911da0855bae3fe https://github.com/galaxyproject/galaxy/commit/d87957e1a2030752b5617934b911… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M config/job_conf.xml.sample_advanced A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py R lib/galaxy/jobs/rules/dynamic_tool_destination.py M test/unit/jobs/rules/test_dynamic_tool_destination.py Log Message: ----------- Ease configuration and add documentation for using DTD syntax for destinations. Moving rules also means it won't conflict with other peoples custom dynamic destinations and should prevent Galaxy from reloading the Python repeatedly. Commit: 43fccc98879d17cc6c5f1833f12e4ed25cc1329e https://github.com/galaxyproject/galaxy/commit/43fccc98879d17cc6c5f1833f12e… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: A test/unit/jobs/dynamic_tool_destination/__init__.py A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml A test/unit/jobs/dynamic_tool_destination/data/test.empty A test/unit/jobs/dynamic_tool_destination/data/test.fasta A test/unit/jobs/dynamic_tool_destination/data/test1.full A test/unit/jobs/dynamic_tool_destination/data/test3.full A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py R test/unit/jobs/rules/__init__.py R test/unit/jobs/rules/data/dest_fail.yml R test/unit/jobs/rules/data/priority_tool_destination.yml R test/unit/jobs/rules/data/test.empty R test/unit/jobs/rules/data/test.fasta R test/unit/jobs/rules/data/test1.full R test/unit/jobs/rules/data/test3.full R test/unit/jobs/rules/data/test_no_verbose.yml R test/unit/jobs/rules/data/test_num_input_datasets.yml R test/unit/jobs/rules/data/test_users.yml R test/unit/jobs/rules/data/tool_destination.yml R test/unit/jobs/rules/mockGalaxy.py R test/unit/jobs/rules/test_dynamic_tool_destination.py R test/unit/jobs/rules/vfdb/?bact.test R test/unit/jobs/rules/ymltests.py Log Message: ----------- Moved dtd tests into a different folder Commit: 5ae1058272c788efcf35f37f0d927b8eaefa3b73 https://github.com/galaxyproject/galaxy/commit/5ae1058272c788efcf35f37f0d92… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M config/tool_destinations.yml.sample Log Message: ----------- Updated tool_destinations.yml.sample to include a little more information Commit: a4c713bf64851d1a2bbc99fd0102f5c506f6ecfe https://github.com/galaxyproject/galaxy/commit/a4c713bf64851d1a2bbc99fd0102… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Fix dict iteration in dtd default_destination parsing/validation Commit: f67d3cbe93e36af9809db6bb3cb3e1af64f8174a https://github.com/galaxyproject/galaxy/commit/f67d3cbe93e36af9809db6bb3cb3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/job_conf.xml.sample_advanced A config/tool_destinations.yml.sample M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py A test/unit/jobs/dynamic_tool_destination/__init__.py A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml A test/unit/jobs/dynamic_tool_destination/data/test.empty A test/unit/jobs/dynamic_tool_destination/data/test.fasta A test/unit/jobs/dynamic_tool_destination/data/test1.full A test/unit/jobs/dynamic_tool_destination/data/test3.full A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py Log Message: ----------- Merge pull request #2579 from phac-nml/add-dtd-to-galaxy Add DTD to Galaxy Compare: https://github.com/galaxyproject/galaxy/compare/47f25f1dc69b...f67d3cbe93e3

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[galaxyproject/galaxy] 706a76: Add tool test for what happens when output filter ...
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 706a76ea80308aa00c0e316deaf10c8c46cd427e https://github.com/galaxyproject/galaxy/commit/706a76ea80308aa00c0e316deaf1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add tool test for what happens when output filter throws exception. Run new test with: ``` ./run_tests.sh -framework -id output_filter_exception_1 ``` xref https://github.com/galaxyproject/tools-iuc/pull/883 xref https://github.com/galaxyproject/planemo/commit/a066afb1c2c30f4ef2c3033ab9a… xref https://github.com/galaxy-iuc/standards/pull/31 Commit: 274ec0f953f61fc169bb90086d96dc4b91d45008 https://github.com/galaxyproject/galaxy/commit/274ec0f953f61fc169bb90086d96… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M test/functional/tools/output_filter_exception_1.xml Log Message: ----------- Fix typo spotted by @nsoranzo. Commit: 47f25f1dc69b77b69037b5056877a7f153c9e7e5 https://github.com/galaxyproject/galaxy/commit/47f25f1dc69b77b69037b5056877… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2631 from jmchilton/output_filter_exception Add tool test for what happens when output filter throws exception. Compare: https://github.com/galaxyproject/galaxy/compare/8d24fbe0fed3...47f25f1dc69b

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[galaxyproject/galaxy] e26930: Properly initialize reference datasets when workfl...
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e269304a0f5c563bd463aeb4d45f9b0518a17b8e https://github.com/galaxyproject/galaxy/commit/e269304a0f5c563bd463aeb4d45f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py Log Message: ----------- Properly initialize reference datasets when workflow form is loaded Commit: 8d24fbe0fed37fbc5502b15b4191df0eadde4e1c https://github.com/galaxyproject/galaxy/commit/8d24fbe0fed37fbc5502b15b4191… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2632 from guerler/fix_workflow_data_on_load Properly initialize datasets when workflow is loaded for execution Compare: https://github.com/galaxyproject/galaxy/compare/2b3a0334e0bd...8d24fbe0fed3

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[galaxyproject/galaxy] e37850: UI, HDCAs: render element_count when available
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e37850386ecc8122abeb6695ffc76eb513f34516 https://github.com/galaxyproject/galaxy/commit/e37850386ecc8122abeb6695ffc7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M static/maps/mvc/collection/collection-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/collection/collection-li.js Log Message: ----------- UI, HDCAs: render element_count when available - Adds a change event for element_count that renders the subtitle - Subtitle now renders the count or nothing if not available Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: 6b64af72deafee0382cb5b9c83ed39a3fa42e1c9 https://github.com/galaxyproject/galaxy/commit/6b64af72deafee0382cb5b9c83ed… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- UI, history: doc updates Conflicts: client/galaxy/scripts/mvc/history/history-contents.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: 654748763af10aa87d3afe9fdf9ea686520ede7e https://github.com/galaxyproject/galaxy/commit/654748763af10aa87d3afe9fdf9e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: implement list:list Conflicts: static/maps/mvc/history/history-contents.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/history/history-contents.js Commit: d550024d56c063bb78e4855395cfbf0cc440fe08 https://github.com/galaxyproject/galaxy/commit/d550024d56c063bb78e4855395cf… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: more feedback on bad collection type Conflicts: static/maps/mvc/history/history-contents.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/bundled/login.bundled.js static/scripts/bundled/login.bundled.js.map static/scripts/mvc/history/history-contents.js Commit: 0d49b06bac4a5c4a4b94e48517d1c0f5de713d42 https://github.com/galaxyproject/galaxy/commit/0d49b06bac4a5c4a4b94e48517d1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- repack Commit: 132bd4dd57e084ec8e743e1360e7d2a0faa29ac6 https://github.com/galaxyproject/galaxy/commit/132bd4dd57e084ec8e743e1360e7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- Merge branch 'backport_2613' into release_16.04 (and rebuild client) Commit: 2b3a0334e0bdfa3ef92c88c7d697eccce447083b https://github.com/galaxyproject/galaxy/commit/2b3a0334e0bdfa3ef92c88c7d697… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c6c22a977f97...2b3a0334e0bd

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[galaxyproject/galaxy] e37850: UI, HDCAs: render element_count when available
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: e37850386ecc8122abeb6695ffc76eb513f34516 https://github.com/galaxyproject/galaxy/commit/e37850386ecc8122abeb6695ffc7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M static/maps/mvc/collection/collection-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/collection/collection-li.js Log Message: ----------- UI, HDCAs: render element_count when available - Adds a change event for element_count that renders the subtitle - Subtitle now renders the count or nothing if not available Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: 6b64af72deafee0382cb5b9c83ed39a3fa42e1c9 https://github.com/galaxyproject/galaxy/commit/6b64af72deafee0382cb5b9c83ed… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- UI, history: doc updates Conflicts: client/galaxy/scripts/mvc/history/history-contents.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: 654748763af10aa87d3afe9fdf9ea686520ede7e https://github.com/galaxyproject/galaxy/commit/654748763af10aa87d3afe9fdf9e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: implement list:list Conflicts: static/maps/mvc/history/history-contents.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/history/history-contents.js Commit: d550024d56c063bb78e4855395cfbf0cc440fe08 https://github.com/galaxyproject/galaxy/commit/d550024d56c063bb78e4855395cf… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- UI, history: more feedback on bad collection type Conflicts: static/maps/mvc/history/history-contents.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/bundled/login.bundled.js static/scripts/bundled/login.bundled.js.map static/scripts/mvc/history/history-contents.js Commit: 0d49b06bac4a5c4a4b94e48517d1c0f5de713d42 https://github.com/galaxyproject/galaxy/commit/0d49b06bac4a5c4a4b94e48517d1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js Log Message: ----------- repack Commit: 132bd4dd57e084ec8e743e1360e7d2a0faa29ac6 https://github.com/galaxyproject/galaxy/commit/132bd4dd57e084ec8e743e1360e7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-contents.js M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- Merge branch 'backport_2613' into release_16.04 (and rebuild client) Compare: https://github.com/galaxyproject/galaxy/compare/95c64c0ba917...132bd4dd57e0

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[galaxyproject/galaxy] 0303ec: Optimize get_file_peek()
by GitHub 21 Jul '16

21 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0303ec33ae2044b9e0f2482cd4cd56a5db6f2664 https://github.com/galaxyproject/galaxy/commit/0303ec33ae2044b9e0f2482cd4cd… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Optimize get_file_peek() last_line was always the empty string because line is read with readline() and therefore '\n' is always its last character (if it is present). Follow-up to #2556. Commit: 9b5f6d60c6dd66a556f22202abcd90c5c2d4858f https://github.com/galaxyproject/galaxy/commit/9b5f6d60c6dd66a556f22202abcd… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix smart_str doctest Docstrings should start with 'u"""' if containing Unicode characters (see also PEP 257). Backslashes should be doubled in docstrings (or raw strings should be used, but the 'ur' prefix is not supported in Python3). Commit: c6c22a977f97208ad1196bdc07b53f9e89313123 https://github.com/galaxyproject/galaxy/commit/c6c22a977f97208ad1196bdc07b5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #2637 from nsoranzo/get_file_peek Optimize get_file_peek() Compare: https://github.com/galaxyproject/galaxy/compare/715441df84a8...c6c22a977f97

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[galaxyproject/galaxy] 4fabf5: typo in summary statistics tool
by GitHub 20 Jul '16

20 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fabf51f4bfa9d7e8392706bdbedc302ca402544 https://github.com/galaxyproject/galaxy/commit/4fabf51f4bfa9d7e8392706bdbed… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- typo in summary statistics tool Commit: 715441df84a8cd49d283ec5d800bae8dc982de86 https://github.com/galaxyproject/galaxy/commit/715441df84a8cd49d283ec5d800b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M tools/stats/gsummary.xml Log Message: ----------- Merge pull request #2639 from nturaga/typo_summary_stats_tool typo in summary statistics tool Compare: https://github.com/galaxyproject/galaxy/compare/5fe4bea3aecd...715441df84a8

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[galaxyproject/galaxy] 30fd1e: Test case for dynamically creating `list:list:list...
by GitHub 20 Jul '16

20 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30fd1e0e64788b0e08c668b1b48e13e5b4ef4afb https://github.com/galaxyproject/galaxy/commit/30fd1e0e64788b0e08c668b1b48e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case for dynamically creating `list:list:list`s. This could check the outputs ideally, but it was failing to simply execute the workflow so this does serve as check that some bugs are fixed. Commit: 39c095aa6a4fe73fe6e224698b77775dc015f511 https://github.com/galaxyproject/galaxy/commit/39c095aa6a4fe73fe6e224698b77… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Improved logging and error message when mapping over an empty* collection. *actually empty or accidentally empty. Commit: 85d7784b18b6199911aee3b7dd6e0389016b87d9 https://github.com/galaxyproject/galaxy/commit/85d7784b18b6199911aee3b7dd6e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix concepts "populated" & "waiting_for_elements" for nested collections. Commit: 54b8ae00dbe71dd9d47496b59b88270e43a09823 https://github.com/galaxyproject/galaxy/commit/54b8ae00dbe71dd9d47496b59b88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M test/api/test_workflows.py Log Message: ----------- Rework test case that fails occasionally on Jenkins. Should be a little more robust now. Commit: 5fe4bea3aecd69ebfc2867bf31658fd8d635c3b3 https://github.com/galaxyproject/galaxy/commit/5fe4bea3aecd69ebfc2867bf3165… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-20 (Wed, 20 Jul 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/execute.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #2634 from jmchilton/list_list_list_problem Fix certain combos of dynamic deeply nested collections in workflows. Compare: https://github.com/galaxyproject/galaxy/compare/f36095a9fb64...5fe4bea3aecd

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[galaxyproject/galaxy] bc79e9: UI, history: replace copy dialog on grid refresh
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bc79e9cc4a0f5597d6243f946e034f88106141d1 https://github.com/galaxyproject/galaxy/commit/bc79e9cc4a0f5597d6243f946e03… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- UI, history: replace copy dialog on grid refresh Fixes #2624 init_grid is called from update_grid to rebuild the grid. This patches that call to replace the copy links with the dialog. Note: - related to #1303 which was an effort to make a single code path for copying histories. - Uses monkey patching to keep from porting build artifacts. Commit: 5f24afb1b3eebb7e30cee3958015b972b0bf2b1d https://github.com/galaxyproject/galaxy/commit/5f24afb1b3eebb7e30cee3958015… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix off by one error, causing only first line of file to be rendered in peek. Commit: 09b9339569d688e89b6f6fb9abc32b8e2b465e28 https://github.com/galaxyproject/galaxy/commit/09b9339569d688e89b6f6fb9abc3… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py A test/unit/datatypes/test_data.py Log Message: ----------- Fixed to only line_count not line_count + 1 lines and added in really basic test Commit: 7e389c7d54da91298c4b5970314c7e5040902952 https://github.com/galaxyproject/galaxy/commit/7e389c7d54da91298c4b5970314c… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fixed E226 Commit: 85671bd466e8bfca0dc22c8fbdc6385a3e9dcf1e https://github.com/galaxyproject/galaxy/commit/85671bd466e8bfca0dc22c8fbdc6… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M test/unit/datatypes/test_data.py Log Message: ----------- Fixed E302 Commit: f4631d2e59af6596afbf571e5cb983e5ce734115 https://github.com/galaxyproject/galaxy/commit/f4631d2e59af6596afbf571e5cb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- Merge pull request #2629 from carlfeberhard/fix.saved-copy [16.01] UI, history: replace copy dialog on grid refresh Commit: ac64c0162ef5f9c68529ee730326c985f4430280 https://github.com/galaxyproject/galaxy/commit/ac64c0162ef5f9c68529ee730326… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 95c64c0ba917bfbc5d04ff603ec3ca2a58f6c54f https://github.com/galaxyproject/galaxy/commit/95c64c0ba917bfbc5d04ff603ec3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild as a part of merging from 16.01. Commit: f36095a9fb647eaa6333c3696e37cdaeb945e5bb https://github.com/galaxyproject/galaxy/commit/f36095a9fb647eaa6333c3696e37… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1e36eba631b2...f36095a9fb64

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[galaxyproject/galaxy] 4ea881: Fix old bug in non-allowed_images.yml GIEs
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 4ea881caa21602c5562224fa268ff87788eee0dd https://github.com/galaxyproject/galaxy/commit/4ea881caa21602c5562224fa268f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fix old bug in non-allowed_images.yml GIEs Commit: b713fff00d7c1a6c50e72f69647a6b5cbe3629dd https://github.com/galaxyproject/galaxy/commit/b713fff00d7c1a6c50e72f69647a… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix off by one error, causing only first line of file to be rendered in peek. Commit: 997fa1577b19d9daa31768731e7cd5f4a19db1e6 https://github.com/galaxyproject/galaxy/commit/997fa1577b19d9daa31768731e7c… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/datatypes/data.py A test/unit/datatypes/test_data.py Log Message: ----------- Fixed to only line_count not line_count + 1 lines and added in really basic test Commit: 157da746d8c5da8985d71fee578ba68dc104a11f https://github.com/galaxyproject/galaxy/commit/157da746d8c5da8985d71fee578b… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fixed E226 Commit: a68381777df3e6c8165f5b9bdc4d4abf9bee41db https://github.com/galaxyproject/galaxy/commit/a68381777df3e6c8165f5b9bdc4d… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M test/unit/datatypes/test_data.py Log Message: ----------- Fixed E302 Commit: 1069a69ae08a4a2db609aebb03c4a8fa53162777 https://github.com/galaxyproject/galaxy/commit/1069a69ae08a4a2db609aebb03c4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #2550 from erasche/asdf [16.04] Fix old bug in non-allowed_images.yml GIEs Commit: c3bf89f75093bfe73f09d0f33dff8df6d60f9269 https://github.com/galaxyproject/galaxy/commit/c3bf89f75093bfe73f09d0f33dff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-28 (Tue, 28 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Fix tag_autocomplete issue. When we swapped to tag manager the signature changed and some of these were missed. Commit: 1507bd37fe8cb872975e46a6e7be468e984db0d8 https://github.com/galaxyproject/galaxy/commit/1507bd37fe8cb872975e46a6e7be… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- More defensive proxying Commit: f8e40bb5951cc38dce118cebcc09a5cc3ca96930 https://github.com/galaxyproject/galaxy/commit/f8e40bb5951cc38dce118cebcc09… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Merge pull request #2585 from erasche/backport-proxy-fix [16.04] Backport proxy fixes Commit: 7c2c2ca62a069700725c67e08053389b583680e7 https://github.com/galaxyproject/galaxy/commit/7c2c2ca62a069700725c67e08053… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Tabular dataset chunking fix which should prevent duplicated lines. Skipping to the newline previously shifted the chunk past where it should read. Commit: acdfd2423f3e8764375d0b7a23dad3c919db47fc https://github.com/galaxyproject/galaxy/commit/acdfd2423f3e8764375d0b7a23da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Rename vars to be sensible, add comment to clarify what this is doing. Commit: 84d152082009418f2fd5dfe0e9001e8924a678fc https://github.com/galaxyproject/galaxy/commit/84d152082009418f2fd5dfe0e900… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Absolute positioning for tabular dataset chunking, vs abstract chunk. Ships a minimum of one line regardless of size, and relies on client to know position. Commit: ca4b51b390d14077188b5226e4c83ed0991dcbb5 https://github.com/galaxyproject/galaxy/commit/ca4b51b390d14077188b5226e4c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M static/maps/mvc/dataset/data.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/data.js Log Message: ----------- Make client with new tabular display. Commit: a65faa961ca434901baaaeffe2e5926d4ac523c1 https://github.com/galaxyproject/galaxy/commit/a65faa961ca434901baaaeffe2e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fix tabular chunked display offset=0 request, pass through ck_size to allow client specification of chunk size overriding the app defaults (neither of these are used by the js client currently though) Commit: d7cdf74bdf2690ab1d83cb262021251ae3e28d14 https://github.com/galaxyproject/galaxy/commit/d7cdf74bdf2690ab1d83cb262021… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Handle the case when the last character of the initial read is a newline. Commit: b7718a0f9ae3a626ab88080e0798a451597984c8 https://github.com/galaxyproject/galaxy/commit/b7718a0f9ae3a626ab88080e0798… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Swap ck_size default from 0 to None to indicate unset. This does not change any behavior at all, but @nsoranzo requested the change to make usage more clear. Commit: 1d8f39d987217c09048e05e1d5443173eb02a9f2 https://github.com/galaxyproject/galaxy/commit/1d8f39d987217c09048e05e1d544… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Remove old, unused arguments from some display_dataset methods, minor argument tweaks. Commit: 4da2119c2560c68cb716270933959eb8cf3d48ed https://github.com/galaxyproject/galaxy/commit/4da2119c2560c68cb71627093395… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-07 (Thu, 07 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- Remove explicit 'chunk' parameter passthrough in datasets API Commit: ab2e48bae7395661ce1112363fe167968582e919 https://github.com/galaxyproject/galaxy/commit/ab2e48bae7395661ce1112363fe1… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tag.py Log Message: ----------- Merge pull request #2569 from dannon/workflow_tag_fixes [16.04] Fix tag_autocomplete issue in workflow editor. Commit: 05c063b13a3fb4acf99af4ecbeb5d2350369301d https://github.com/galaxyproject/galaxy/commit/05c063b13a3fb4acf99af4ecbeb5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-08 (Fri, 08 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/data.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/data.js Log Message: ----------- Merge pull request #2587 from dannon/backport_tabular_fix [16.04] Tabular Dataset Display Fixes Commit: aa7ead6dccd2c80152664c31bbf9b27f2f463799 https://github.com/galaxyproject/galaxy/commit/aa7ead6dccd2c80152664c31bbf9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-14 (Thu, 14 Jul 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Strip whitespaces when processing <url_template> content Otherwise download_binary action tries to save the file to an invalid filename. Reported by @remimarenco on IRC. Fix typo. Commit: 8c59d1c953c61b6d73d9bef5c4dda8a8056240b7 https://github.com/galaxyproject/galaxy/commit/8c59d1c953c61b6d73d9bef5c4dd… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-07-15 (Fri, 15 Jul 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #2618 from nsoranzo/release_16.04_fix_download_binary [16.04] Strip whitespaces when processing <url_template> content Commit: dfce1a973012d430823a3dfad6edad08a31df747 https://github.com/galaxyproject/galaxy/commit/dfce1a973012d430823a3dfad6ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- This is an extra hammer swing at #1531 / #1542, which @rmarenco encountered. He said this resolves it. Commit: f9416573325139c6449d9a8959a138d5681d00d8 https://github.com/galaxyproject/galaxy/commit/f9416573325139c6449d9a8959a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Extra debugging to hopefully shed light on the PJA Async issue with delete intermediates action and new(ish) workflow scheduling. Clarified a few vars. Commit: bc79e9cc4a0f5597d6243f946e034f88106141d1 https://github.com/galaxyproject/galaxy/commit/bc79e9cc4a0f5597d6243f946e03… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- UI, history: replace copy dialog on grid refresh Fixes #2624 init_grid is called from update_grid to rebuild the grid. This patches that call to replace the copy links with the dialog. Note: - related to #1303 which was an effort to make a single code path for copying histories. - Uses monkey patching to keep from porting build artifacts. Commit: 8a5042d15b5b94fb804a1b1488375939dd88c3d2 https://github.com/galaxyproject/galaxy/commit/8a5042d15b5b94fb804a1b148837… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #2626 from dannon/backport_hammerthrow [16.04] Backport workflow fix Commit: 10ac6ee132642e19b8bf0bd60903a85336337571 https://github.com/galaxyproject/galaxy/commit/10ac6ee132642e19b8bf0bd60903… Author: Carl Eberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py A test/unit/datatypes/test_data.py Log Message: ----------- Merge pull request #2556 from ericenns/fix-2461-dataset-peek [16.04] Fix off by one error, causing only first line of file to be rendered … Commit: 5f24afb1b3eebb7e30cee3958015b972b0bf2b1d https://github.com/galaxyproject/galaxy/commit/5f24afb1b3eebb7e30cee3958015… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix off by one error, causing only first line of file to be rendered in peek. Commit: 09b9339569d688e89b6f6fb9abc32b8e2b465e28 https://github.com/galaxyproject/galaxy/commit/09b9339569d688e89b6f6fb9abc3… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py A test/unit/datatypes/test_data.py Log Message: ----------- Fixed to only line_count not line_count + 1 lines and added in really basic test Commit: 7e389c7d54da91298c4b5970314c7e5040902952 https://github.com/galaxyproject/galaxy/commit/7e389c7d54da91298c4b5970314c… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fixed E226 Commit: 85671bd466e8bfca0dc22c8fbdc6385a3e9dcf1e https://github.com/galaxyproject/galaxy/commit/85671bd466e8bfca0dc22c8fbdc6… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M test/unit/datatypes/test_data.py Log Message: ----------- Fixed E302 Commit: f4631d2e59af6596afbf571e5cb983e5ce734115 https://github.com/galaxyproject/galaxy/commit/f4631d2e59af6596afbf571e5cb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- Merge pull request #2629 from carlfeberhard/fix.saved-copy [16.01] UI, history: replace copy dialog on grid refresh Commit: ac64c0162ef5f9c68529ee730326c985f4430280 https://github.com/galaxyproject/galaxy/commit/ac64c0162ef5f9c68529ee730326… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 95c64c0ba917bfbc5d04ff603ec3ca2a58f6c54f https://github.com/galaxyproject/galaxy/commit/95c64c0ba917bfbc5d04ff603ec3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild as a part of merging from 16.01. Commit: a5b836e9eeead2eab752d79b0e15197b82cb0720 https://github.com/galaxyproject/galaxy/commit/a5b836e9eeead2eab752d79b0e15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/data.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/dataset/data.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/data.js M templates/webapps/galaxy/history/grid.mako A test/unit/datatypes/test_data.py Log Message: ----------- Merge branch 'release_16.04' Compare: https://github.com/galaxyproject/galaxy/compare/0ba99fe24609...a5b836e9eeea

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[galaxyproject/galaxy] 95c64c: Rebuild as a part of merging from 16.01.
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 95c64c0ba917bfbc5d04ff603ec3ca2a58f6c54f https://github.com/galaxyproject/galaxy/commit/95c64c0ba917bfbc5d04ff603ec3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild as a part of merging from 16.01.

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[galaxyproject/galaxy] bc79e9: UI, history: replace copy dialog on grid refresh
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: bc79e9cc4a0f5597d6243f946e034f88106141d1 https://github.com/galaxyproject/galaxy/commit/bc79e9cc4a0f5597d6243f946e03… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- UI, history: replace copy dialog on grid refresh Fixes #2624 init_grid is called from update_grid to rebuild the grid. This patches that call to replace the copy links with the dialog. Note: - related to #1303 which was an effort to make a single code path for copying histories. - Uses monkey patching to keep from porting build artifacts. Commit: 5f24afb1b3eebb7e30cee3958015b972b0bf2b1d https://github.com/galaxyproject/galaxy/commit/5f24afb1b3eebb7e30cee3958015… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix off by one error, causing only first line of file to be rendered in peek. Commit: 09b9339569d688e89b6f6fb9abc32b8e2b465e28 https://github.com/galaxyproject/galaxy/commit/09b9339569d688e89b6f6fb9abc3… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py A test/unit/datatypes/test_data.py Log Message: ----------- Fixed to only line_count not line_count + 1 lines and added in really basic test Commit: 7e389c7d54da91298c4b5970314c7e5040902952 https://github.com/galaxyproject/galaxy/commit/7e389c7d54da91298c4b5970314c… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fixed E226 Commit: 85671bd466e8bfca0dc22c8fbdc6385a3e9dcf1e https://github.com/galaxyproject/galaxy/commit/85671bd466e8bfca0dc22c8fbdc6… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M test/unit/datatypes/test_data.py Log Message: ----------- Fixed E302 Commit: f4631d2e59af6596afbf571e5cb983e5ce734115 https://github.com/galaxyproject/galaxy/commit/f4631d2e59af6596afbf571e5cb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- Merge pull request #2629 from carlfeberhard/fix.saved-copy [16.01] UI, history: replace copy dialog on grid refresh Commit: ac64c0162ef5f9c68529ee730326c985f4430280 https://github.com/galaxyproject/galaxy/commit/ac64c0162ef5f9c68529ee730326… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/10ac6ee13264...ac64c0162ef5

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[galaxyproject/galaxy] bc79e9: UI, history: replace copy dialog on grid refresh
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: bc79e9cc4a0f5597d6243f946e034f88106141d1 https://github.com/galaxyproject/galaxy/commit/bc79e9cc4a0f5597d6243f946e03… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- UI, history: replace copy dialog on grid refresh Fixes #2624 init_grid is called from update_grid to rebuild the grid. This patches that call to replace the copy links with the dialog. Note: - related to #1303 which was an effort to make a single code path for copying histories. - Uses monkey patching to keep from porting build artifacts. Commit: f4631d2e59af6596afbf571e5cb983e5ce734115 https://github.com/galaxyproject/galaxy/commit/f4631d2e59af6596afbf571e5cb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M templates/webapps/galaxy/history/grid.mako Log Message: ----------- Merge pull request #2629 from carlfeberhard/fix.saved-copy [16.01] UI, history: replace copy dialog on grid refresh Compare: https://github.com/galaxyproject/galaxy/compare/85671bd466e8...f4631d2e59af

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[galaxyproject/galaxy] 5f24af: Fix off by one error, causing only first line of f...
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 5f24afb1b3eebb7e30cee3958015b972b0bf2b1d https://github.com/galaxyproject/galaxy/commit/5f24afb1b3eebb7e30cee3958015… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix off by one error, causing only first line of file to be rendered in peek. Commit: 09b9339569d688e89b6f6fb9abc32b8e2b465e28 https://github.com/galaxyproject/galaxy/commit/09b9339569d688e89b6f6fb9abc3… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py A test/unit/datatypes/test_data.py Log Message: ----------- Fixed to only line_count not line_count + 1 lines and added in really basic test Commit: 7e389c7d54da91298c4b5970314c7e5040902952 https://github.com/galaxyproject/galaxy/commit/7e389c7d54da91298c4b5970314c… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fixed E226 Commit: 85671bd466e8bfca0dc22c8fbdc6385a3e9dcf1e https://github.com/galaxyproject/galaxy/commit/85671bd466e8bfca0dc22c8fbdc6… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M test/unit/datatypes/test_data.py Log Message: ----------- Fixed E302 Compare: https://github.com/galaxyproject/galaxy/compare/67c4df712a0d...85671bd466e8

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[galaxyproject/galaxy]
by GitHub 19 Jul '16

19 Jul '16

Branch: refs/heads/16.04 Home: https://github.com/galaxyproject/galaxy

1 0