August 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 238d90: Fix purging datasets whose total_size is None.
by GitHub 20 Aug '15

20 Aug '15

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: 238d908ccecd6411a3a72f7396933b3771f7e5aa https://github.com/galaxyproject/galaxy/commit/238d908ccecd6411a3a72f739693… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M scripts/cleanup_datasets/cleanup_datasets.py Log Message: ----------- Fix purging datasets whose total_size is None. Fix the error: Removing disk, file /opt/galaxy/database/files/000/dataset_192.dat Error attempting to purge data file: /opt/galaxy/database/files/000/dataset_192.dat error: unsupported operand type(s) for -=: 'Decimal' and 'NoneType' when running: python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 10 -3 -r Commit: a9827fae31d8826bf2426c5285fe789dfe61295d https://github.com/galaxyproject/galaxy/commit/a9827fae31d8826bf2426c5285fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M test/unit/test_galaxy_mapping.py Log Message: ----------- Fix failing tests for 238d908ccecd6411a3a72f7396933b3771f7e5aa. Commit: baf8fe6759fe283516c5242d42ab8274b5a3baf0 https://github.com/galaxyproject/galaxy/commit/baf8fe6759fe283516c5242d42ab… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #1 from jmchilton/release_fix Fix failing tests for 238d908ccecd6411a3a72f7396933b3771f7e5aa. Commit: 14a8ee95f3dd8a671ee9a1edac8fc3cd686a4395 https://github.com/galaxyproject/galaxy/commit/14a8ee95f3dd8a671ee9a1edac8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/model/__init__.py M scripts/cleanup_datasets/cleanup_datasets.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #616 from nsoranzo/release_15.05 [15.05] Fix purging datasets whose total_size is None. Compare: https://github.com/galaxyproject/galaxy/compare/483ea9e735bf...14a8ee95f3dd

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[galaxyproject/galaxy] d98aba: Fix ambiguous naming of item/model/row variables, ...
by GitHub 19 Aug '15

19 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d98aba9c2a335df93d1d6328edef8077529cf84b https://github.com/galaxyproject/galaxy/commit/d98aba9c2a335df93d1d6328edef… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/style/blue/base.css Log Message: ----------- Fix ambiguous naming of item/model/row variables, add drag and drop helper text and styles Commit: 7c0ad6b85720f0f6101f92061c19dfcd5947ff05 https://github.com/galaxyproject/galaxy/commit/7c0ad6b85720f0f6101f92061c19… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/style/blue/base.css Log Message: ----------- Add similar helper text to composite section Commit: f03840459b1ba61680999dd5ce77cd81d2189c66 https://github.com/galaxyproject/galaxy/commit/f03840459b1ba61680999dd5ce77… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css Log Message: ----------- Shorten title text, center drop helper labels Commit: 4ff2d913ef372bd494b3c49a3726d5cfb4e80269 https://github.com/galaxyproject/galaxy/commit/4ff2d913ef372bd494b3c49a3726… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/sharable.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/tool_shed/api/configuration.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_001 Commit: ff0b0baf0199e28fbcfd7d876b208ec1d15af4eb https://github.com/galaxyproject/galaxy/commit/ff0b0baf0199e28fbcfd7d876b20… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/style/less/upload.less M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/style/blue/base.css Log Message: ----------- Add icon to helper message Commit: 4d7b3213c940c0d743226c348828ff6ca17b6236 https://github.com/galaxyproject/galaxy/commit/4d7b3213c940c0d743226c348828… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Change label text Commit: d89450a53c45cd9aa61e78e2931ba365d7259cdb https://github.com/galaxyproject/galaxy/commit/d89450a53c45cd9aa61e78e2931b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/style/less/upload.less M static/scripts/mvc/upload/composite/composite-view.js M static/style/blue/base.css Log Message: ----------- Remove helper text from composite dialog Commit: 8cff4da9248422284f533baaf179d711a94fe739 https://github.com/galaxyproject/galaxy/commit/8cff4da9248422284f533baaf179… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/style/blue/base.css Log Message: ----------- Improve style class naming, reduce classes Commit: e3c31db51acf9084ebb3aa87435536716d05b041 https://github.com/galaxyproject/galaxy/commit/e3c31db51acf9084ebb3aa874355… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Improve button icon visibility Commit: 312242b2171bf06bd0551b7684d9a7e89a599f17 https://github.com/galaxyproject/galaxy/commit/312242b2171bf06bd0551b7684d9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/style/blue/base.css Log Message: ----------- Floating icon needs special case handling Commit: 46e47dd4cb51ed43210563cfcf8ae37c999be2d0 https://github.com/galaxyproject/galaxy/commit/46e47dd4cb51ed43210563cfcf8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/default/default-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-row.js M static/style/blue/base.css Log Message: ----------- Use shorter style name Commit: 7aa54f43c40598cc5830458985f38c2598b0dcb8 https://github.com/galaxyproject/galaxy/commit/7aa54f43c40598cc5830458985f3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- More css cleanup Commit: b19f4b217b7d12e4820c5bd1c6a2f0c6bae0b772 https://github.com/galaxyproject/galaxy/commit/b19f4b217b7d12e4820c5bd1c6a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Remove unused helper code Commit: 3c555b50e6d87f73b3e6d64bd17fae8f2e460402 https://github.com/galaxyproject/galaxy/commit/3c555b50e6d87f73b3e6d64bd17f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Update tests Commit: 62db50bfc4fbf00d415e6ea0dca0367d2ec13873 https://github.com/galaxyproject/galaxy/commit/62db50bfc4fbf00d415e6ea0dca0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Show dashed border in composite uploader to indicate drop zone Commit: c429777c93680dcee449fe410f5360afbe673758 https://github.com/galaxyproject/galaxy/commit/c429777c93680dcee449fe410f53… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Merge pull request #620 from guerler/upload_001 Improve visibility of drag and drop option, simplify upload UI Compare: https://github.com/galaxyproject/galaxy/compare/0bfc8f0041e0...c429777c9368

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[galaxyproject/galaxy] 6dc5f0: Merge branch 'security-20150812-xss' into release_...
by GitHub 19 Aug '15

19 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6dc5f022c73d5bde3b4ef1abe31a8d3b37ade9c3 https://github.com/galaxyproject/galaxy/commit/6dc5f022c73d5bde3b4ef1abe31a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into release_15.01 Commit: 096a1686badda620acb507deaf9382ccee37086a https://github.com/galaxyproject/galaxy/commit/096a1686badda620acb507deaf93… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into release_15.01 Commit: a1bff672f39da8610543ba572c322d53eda88b4f https://github.com/galaxyproject/galaxy/commit/a1bff672f39da8610543ba572c32… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix bug in tool reloading API where ID not passed Commit: 71f28c99e539acf828a03e8288e1de4af40a887e https://github.com/galaxyproject/galaxy/commit/71f28c99e539acf828a03e8288e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #622 from erasche/tool-reloading-fix [15.01] Tool reloading fix Commit: 01278aa956f5791badaa6e475d94f679adab10b1 https://github.com/galaxyproject/galaxy/commit/01278aa956f5791badaa6e475d94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 483ea9e735bf7de22f7ce7abb6105c9b929ea928 https://github.com/galaxyproject/galaxy/commit/483ea9e735bf7de22f7ce7abb610… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: b4df5e944bddcbd03699a4b3b395044cc3c4886c https://github.com/galaxyproject/galaxy/commit/b4df5e944bddcbd03699a4b3b395… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Resolve merge conflict merging forward 15.05-15.07 Commit: 0bfc8f0041e0ae94d46a0ea028e8683a6387e6cf https://github.com/galaxyproject/galaxy/commit/0bfc8f0041e0ae94d46a0ea028e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Log Message: ----------- Merge branch 'release_15.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/8c75438a5f75...0bfc8f0041e0

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[galaxyproject/galaxy] 6dc5f0: Merge branch 'security-20150812-xss' into release_...
by GitHub 19 Aug '15

19 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 6dc5f022c73d5bde3b4ef1abe31a8d3b37ade9c3 https://github.com/galaxyproject/galaxy/commit/6dc5f022c73d5bde3b4ef1abe31a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into release_15.01 Commit: 096a1686badda620acb507deaf9382ccee37086a https://github.com/galaxyproject/galaxy/commit/096a1686badda620acb507deaf93… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into release_15.01 Commit: a1bff672f39da8610543ba572c322d53eda88b4f https://github.com/galaxyproject/galaxy/commit/a1bff672f39da8610543ba572c32… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix bug in tool reloading API where ID not passed Commit: 71f28c99e539acf828a03e8288e1de4af40a887e https://github.com/galaxyproject/galaxy/commit/71f28c99e539acf828a03e8288e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #622 from erasche/tool-reloading-fix [15.01] Tool reloading fix Commit: 01278aa956f5791badaa6e475d94f679adab10b1 https://github.com/galaxyproject/galaxy/commit/01278aa956f5791badaa6e475d94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 483ea9e735bf7de22f7ce7abb6105c9b929ea928 https://github.com/galaxyproject/galaxy/commit/483ea9e735bf7de22f7ce7abb610… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: b4df5e944bddcbd03699a4b3b395044cc3c4886c https://github.com/galaxyproject/galaxy/commit/b4df5e944bddcbd03699a4b3b395… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Resolve merge conflict merging forward 15.05-15.07 Compare: https://github.com/galaxyproject/galaxy/compare/79dbff19674d...b4df5e944bdd

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[galaxyproject/galaxy] 6dc5f0: Merge branch 'security-20150812-xss' into release_...
by GitHub 19 Aug '15

19 Aug '15

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: 6dc5f022c73d5bde3b4ef1abe31a8d3b37ade9c3 https://github.com/galaxyproject/galaxy/commit/6dc5f022c73d5bde3b4ef1abe31a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into release_15.01 Commit: 096a1686badda620acb507deaf9382ccee37086a https://github.com/galaxyproject/galaxy/commit/096a1686badda620acb507deaf93… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into release_15.01 Commit: a1bff672f39da8610543ba572c322d53eda88b4f https://github.com/galaxyproject/galaxy/commit/a1bff672f39da8610543ba572c32… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix bug in tool reloading API where ID not passed Commit: 71f28c99e539acf828a03e8288e1de4af40a887e https://github.com/galaxyproject/galaxy/commit/71f28c99e539acf828a03e8288e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #622 from erasche/tool-reloading-fix [15.01] Tool reloading fix Commit: 01278aa956f5791badaa6e475d94f679adab10b1 https://github.com/galaxyproject/galaxy/commit/01278aa956f5791badaa6e475d94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: 483ea9e735bf7de22f7ce7abb6105c9b929ea928 https://github.com/galaxyproject/galaxy/commit/483ea9e735bf7de22f7ce7abb610… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Compare: https://github.com/galaxyproject/galaxy/compare/f01300d7da56...483ea9e735bf

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[galaxyproject/galaxy] 6dc5f0: Merge branch 'security-20150812-xss' into release_...
by GitHub 19 Aug '15

19 Aug '15

Branch: refs/heads/release_15.03 Home: https://github.com/galaxyproject/galaxy Commit: 6dc5f022c73d5bde3b4ef1abe31a8d3b37ade9c3 https://github.com/galaxyproject/galaxy/commit/6dc5f022c73d5bde3b4ef1abe31a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge branch 'security-20150812-xss' into release_15.01 Commit: 096a1686badda620acb507deaf9382ccee37086a https://github.com/galaxyproject/galaxy/commit/096a1686badda620acb507deaf93… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge branch 'security-20150812-shed' into release_15.01 Commit: a1bff672f39da8610543ba572c322d53eda88b4f https://github.com/galaxyproject/galaxy/commit/a1bff672f39da8610543ba572c32… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix bug in tool reloading API where ID not passed Commit: 71f28c99e539acf828a03e8288e1de4af40a887e https://github.com/galaxyproject/galaxy/commit/71f28c99e539acf828a03e8288e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #622 from erasche/tool-reloading-fix [15.01] Tool reloading fix Commit: 01278aa956f5791badaa6e475d94f679adab10b1 https://github.com/galaxyproject/galaxy/commit/01278aa956f5791badaa6e475d94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Compare: https://github.com/galaxyproject/galaxy/compare/a6a85cbc4ccb...01278aa956f5

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[galaxyproject/galaxy] a1bff6: Fix bug in tool reloading API where ID not passed
by GitHub 19 Aug '15

19 Aug '15

Branch: refs/heads/release_15.01 Home: https://github.com/galaxyproject/galaxy Commit: a1bff672f39da8610543ba572c322d53eda88b4f https://github.com/galaxyproject/galaxy/commit/a1bff672f39da8610543ba572c32… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix bug in tool reloading API where ID not passed Commit: 71f28c99e539acf828a03e8288e1de4af40a887e https://github.com/galaxyproject/galaxy/commit/71f28c99e539acf828a03e8288e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #622 from erasche/tool-reloading-fix [15.01] Tool reloading fix Compare: https://github.com/galaxyproject/galaxy/compare/096a1686badd...71f28c99e539

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[galaxyproject/galaxy] 4f7e59: Fix bug in reload API where id wasn't recognised
by GitHub 19 Aug '15

19 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f7e59aa445d1294906406f0497991e41198c6bc https://github.com/galaxyproject/galaxy/commit/4f7e59aa445d1294906406f04979… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Fix bug in reload API where id wasn't recognised Commit: 8c75438a5f7513c44fca8fc55ef19637122c77fd https://github.com/galaxyproject/galaxy/commit/8c75438a5f7513c44fca8fc55ef1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #619 from erasche/reload_api Fix bug in reload API where id wasn't recognised Compare: https://github.com/galaxyproject/galaxy/compare/fb11d7198448...8c75438a5f75

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[galaxyproject/galaxy] d44de6: linting broke the functionality of this module
by GitHub 19 Aug '15

19 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d44de6a4099d2d338d604f412c5b3dbf2765838f https://github.com/galaxyproject/galaxy/commit/d44de6a4099d2d338d604f412c5b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/util/jstree.py Log Message: ----------- linting broke the functionality of this module probably this commit: https://github.com/galaxyproject/galaxy/commit/5cd3e3a7e02eee03a24006b47dfb… putting it back to the former state, we did not write most of the code, we should not be linting it Commit: f47dcdda3a64d32cdb8404a78a385aea91124df2 https://github.com/galaxyproject/galaxy/commit/f47dcdda3a64d32cdb8404a78a38… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- add jstree to flake8 blacklist Commit: fb11d71984486c82eb8cec7086a86f05e7f1e1f4 https://github.com/galaxyproject/galaxy/commit/fb11d71984486c82eb8cec7086a8… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/util/jstree.py Log Message: ----------- Merge pull request #617 from martenson/remove-broken-linting-jstree remove linting that broke the functionality of jstree module Compare: https://github.com/galaxyproject/galaxy/compare/ed6174a84313...fb11d7198448

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[galaxyproject/galaxy] 5ce4f2: Managers, sharable: implement list_shared_with; AP...
by GitHub 19 Aug '15

19 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ce4f2f24d6cc6dc40318f0034e4a62ae6a2f40b https://github.com/galaxyproject/galaxy/commit/5ce4f2f24d6cc6dc40318f0034e4… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/sharable.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Managers, sharable: implement list_shared_with; API, histories: implement api/histories/shared_with_me (with order, limit, offset, and filters as index) Commit: ed6174a8431342aa1677311ed3c3ce8806acbf9d https://github.com/galaxyproject/galaxy/commit/ed6174a8431342aa1677311ed3c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-19 (Wed, 19 Aug 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/sharable.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #614 from carlfeberhard/api.histories-shared-with-me Managers, sharable: implement list_shared_with; API, histories: imple… Compare: https://github.com/galaxyproject/galaxy/compare/5c263416de4f...ed6174a84313

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