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

20 Aug '15

Branch: refs/heads/release_15.07 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. Commit: a34f13a9f6eb216665ea97e1314f7b76c74c5778 https://github.com/galaxyproject/galaxy/commit/a34f13a9f6eb216665ea97e1314f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> 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 branch 'release_15.05' into release_15.07 Compare: https://github.com/galaxyproject/galaxy/compare/b4df5e944bdd...a34f13a9f6eb

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[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 20 Aug '15

20 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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[galaxyproject/galaxy] 4dc92f: expose TS version through API
by GitHub 18 Aug '15

18 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4dc92f5fb926f024865f004df3b48e760f4ea682 https://github.com/galaxyproject/galaxy/commit/4dc92f5fb926f024865f004df3b4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: 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: ----------- expose TS version through API Commit: 5d0b2b5a87283dcd4149f780ed9093dca96c313f https://github.com/galaxyproject/galaxy/commit/5d0b2b5a87283dcd4149f780ed90… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/configuration.py Log Message: ----------- feed flake8 Commit: 5c263416de4f53129bba1ef4e9947694d474d7ef https://github.com/galaxyproject/galaxy/commit/5c263416de4f53129bba1ef4e994… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: 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 pull request #613 from martenson/expose-api-ts-version expose TS version through API Compare: https://github.com/galaxyproject/galaxy/compare/b6e0ba29521b...5c263416de4f

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[galaxyproject/usegalaxy-playbook] 8e818e: update TTS
by GitHub 18 Aug '15

18 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8e818eade44799758a7db5d78bb6442279d59b28 https://github.com/galaxyproject/usegalaxy-playbook/commit/8e818eade4479975… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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[galaxyproject/galaxy] a0cd5b: [WIP] Separate upload modal and default upload vie...
by GitHub 18 Aug '15

18 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a0cd5b7410c0136c874649bdc41f5c7e6a369e46 https://github.com/galaxyproject/galaxy/commit/a0cd5b7410c0136c874649bdc41f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-16 (Thu, 16 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-button.js A client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-button.js.map A static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-button.js A static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- [WIP] Separate upload modal and default upload view, insert tabs Commit: 85fc57696f0f92014780134ade8a1482dd61dca6 https://github.com/galaxyproject/galaxy/commit/85fc57696f0f92014780134ade8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css Log Message: ----------- [WIP] Reinserting button panel Commit: f42981810af88c46da482cba940b3c580ee3b193 https://github.com/galaxyproject/galaxy/commit/f42981810af88c46da482cba940b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- [WIP] Fix button states Commit: f36f7854568462bc9615fa7edd45425c49708410 https://github.com/galaxyproject/galaxy/commit/f36f7854568462bc9615fa7edd45… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-view-default.js.map M static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js M static/style/blue/base.css Log Message: ----------- [WIP] Adjust styles Commit: ad661147e82e72641e5709dd3a131017d0227e13 https://github.com/galaxyproject/galaxy/commit/ad661147e82e72641e5709dd3a13… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-17 (Fri, 17 Jul 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: ----------- [WIP] Style adjustments Commit: 3678c111a6547cbcebc48101a39afa42601a481d https://github.com/galaxyproject/galaxy/commit/3678c111a6547cbcebc48101a39a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-18 (Sat, 18 Jul 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: ----------- Prepare composite tab Commit: 04eadf4bfcec7b1848ad4c2e6d84607b40c4eb16 https://github.com/galaxyproject/galaxy/commit/04eadf4bfcec7b1848ad4c2e6d84… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-18 (Sat, 18 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Fix uploadbox trigger for local upload Commit: dbc1bd50b425522cfc4cb22369e9efa59c5d3357 https://github.com/galaxyproject/galaxy/commit/dbc1bd50b425522cfc4cb22369e9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-18 (Sat, 18 Jul 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Code style adjustments for uploadbox code Commit: 51dca28794f68ec07647854373d94b33aed19e6e https://github.com/galaxyproject/galaxy/commit/51dca28794f68ec07647854373d9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-21 (Tue, 21 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M lib/galaxy/webapps/galaxy/api/datatypes.py M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- [WIP] Continue API integration Commit: 64a7b9e197d1c029a8846a5cbd1485972ddcab6f https://github.com/galaxyproject/galaxy/commit/64a7b9e197d1c029a8846a5cbd14… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M lib/galaxy/util/bunch.py M lib/galaxy/webapps/galaxy/api/datatypes.py Log Message: ----------- Add composite datatype details to datatypes api response Commit: a022738cf2f70555f1f8dc67026e87200e5e87a3 https://github.com/galaxyproject/galaxy/commit/a022738cf2f70555f1f8dc67026e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Move uploadbox variables to local scope Commit: 3c6a43148ab571a950b0009c1cdb43c6186841f0 https://github.com/galaxyproject/galaxy/commit/3c6a43148ab571a950b0009c1cdb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-23 (Thu, 23 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Parse composite file details to front-end, hide in regular upload view Commit: 486bbb0bf5d7a866a7205aab03d8b63279f3b3de https://github.com/galaxyproject/galaxy/commit/486bbb0bf5d7a866a7205aab03d8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: R client/galaxy/scripts/mvc/upload/upload-row.js R client/galaxy/scripts/mvc/upload/upload-view-default.js M client/galaxy/scripts/mvc/upload/upload-view.js R static/maps/mvc/upload/upload-row.js.map R static/maps/mvc/upload/upload-view-default.js.map M static/maps/mvc/upload/upload-view.js.map R static/scripts/mvc/upload/upload-row.js R static/scripts/mvc/upload/upload-view-default.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Separate regular and composite upload elements into directories Commit: a390f071cc453d7d2895ba6e30ffd025414d63b3 https://github.com/galaxyproject/galaxy/commit/a390f071cc453d7d2895ba6e30ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js A static/maps/mvc/upload/composite/composite-row.js.map A static/maps/mvc/upload/composite/composite-view.js.map A static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/upload/default/default-view.js.map A static/scripts/mvc/upload/composite/composite-row.js A static/scripts/mvc/upload/composite/composite-view.js A static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Add separated files, repack Commit: 3c372fce95c90ee1f1d5599155471f8bc16983b2 https://github.com/galaxyproject/galaxy/commit/3c372fce95c90ee1f1d559915547… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/style/blue/base.css Log Message: ----------- Fix and adjust styles for composite upload view Commit: 95ed2a2921110686a55afff909b466aa7bb7022b https://github.com/galaxyproject/galaxy/commit/95ed2a2921110686a55afff909b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 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-model.js M client/galaxy/scripts/mvc/upload/upload-settings.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 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static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/templates/panel_section.handlebars R static/scripts/templates/tool_form.handlebars R static/scripts/templates/tool_link.handlebars R static/scripts/templates/tool_search.handlebars M static/scripts/utils/config.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/masthead.css M static/style/blue/sprite-fugue.png M static/style/blue/sprite-history-buttons.png M static/style/blue/sprite-history-states.png M static/style/blue/trackster.css A templates/page_base.mako M templates/show_params.mako M templates/sorting_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/reports/jobs_specified_month_all.mako M test/api/test_dataset_collections.py M test/api/test_datasets.py M test/api/test_histories.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py M test/base/test_db_util.py M test/base/twilltestcase.py M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-history-permission-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/modules/historypanel.js M test/functional/test_admin_features.py M test/functional/test_data_managers.py M test/functional/test_data_security.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_toolbox.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py A test/functional/tools/output_collection_filter.xml M test/functional/tools/samples_tool_conf.xml M test/functional/workflow.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/tool_shed/base/test_db_util.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_rules/20_instance.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.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/test_objectstore.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tool_shed_unit_tests/test_fabric_util.py M test/unit/tool_shed_unit_tests/test_td_common_util.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tool_list.py M tools/data_source/data_source.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/stats/grouping.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/style/blue/base.css Commit: fb190f622f7a53d42e3244f47d3911043e9a6eb8 https://github.com/galaxyproject/galaxy/commit/fb190f622f7a53d42e3244f47d39… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/mvc/upload/composite/composite-row.js Log Message: ----------- Remove mode icon from row Commit: 6de2953c98cfc4ea32b8f6ae6bb6dc096c747d38 https://github.com/galaxyproject/galaxy/commit/6de2953c98cfc4ea32b8f6ae6bb6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Add 'hide_separator' attribute to modals Commit: e5503824d1c6f691b58e9d790c1c596151285a5c https://github.com/galaxyproject/galaxy/commit/e5503824d1c6f691b58e9d790c1c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Rename property to 'title_separator' Commit: bb7f9a8a51b9de8b48b15078de498f3f46515442 https://github.com/galaxyproject/galaxy/commit/bb7f9a8a51b9de8b48b15078de49… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 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/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/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/style/blue/base.css Log Message: ----------- [WIP] Further adjustments to styles and colors Commit: a9274619afcbf2d114ef07ab7759e457411d8a46 https://github.com/galaxyproject/galaxy/commit/a9274619afcbf2d114ef07ab7759… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/style/blue/base.css Log Message: ----------- Adjust icon styles Commit: 6a8fed5feed54263bac775dda908a046d9244c41 https://github.com/galaxyproject/galaxy/commit/6a8fed5feed54263bac775dda908… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-29 (Wed, 29 Jul 2015) Changed paths: M client/galaxy/style/less/upload.less M static/style/blue/base.css Log Message: ----------- Fix ftp row label style Commit: 5cdd511b7a528940090c01d4d306ccf153f2fc1f https://github.com/galaxyproject/galaxy/commit/5cdd511b7a528940090c01d4d306… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M 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branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/style/blue/base.css Commit: f83eaa8fe7a39f03c522a5b387961ac9154df9d8 https://github.com/galaxyproject/galaxy/commit/f83eaa8fe7a39f03c522a5b38796… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js M static/maps/utils/uploadbox.js.map M static/scripts/utils/uploadbox.js Log Message: ----------- Uploadbox plugin touchup Commit: 237a3d307d808d5be2e6e4d1a093a646f7d791a7 https://github.com/galaxyproject/galaxy/commit/237a3d307d808d5be2e6e4d1a093… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 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: ----------- More touchup/cleanup for upload views Commit: f753a6159e980df064d794c43b1440dd54a241dd https://github.com/galaxyproject/galaxy/commit/f753a6159e980df064d794c43b14… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-07-31 (Fri, 31 Jul 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/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-row.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-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/utils/uploadbox.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/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/utils/uploadbox.js Log Message: ----------- Fix for settings popup and more code cleanup Commit: ecd38ef6dba00cfdb94365616210690091825651 https://github.com/galaxyproject/galaxy/commit/ecd38ef6dba00cfdb94365616210… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-02 (Sun, 02 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-button-menu.js 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-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/maps/mvc/ui/ui-button-menu.js.map 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-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/ui/ui-button-menu.js 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-view.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css Log Message: ----------- Enable drag-and-drop, use dropdown instead of select, style fix uploadbox.js Commit: 1f9d5443fb5700fe47e3d57a0687f68db6508952 https://github.com/galaxyproject/galaxy/commit/1f9d5443fb5700fe47e3d57a0687… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-02 (Sun, 02 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/style/less/ui.less M static/scripts/mvc/upload/upload-settings.js M static/style/blue/base.css Log Message: ----------- Style margin fixes Commit: ea26355761cd04512d4e392f821e7d63fbfc1b53 https://github.com/galaxyproject/galaxy/commit/ea26355761cd04512d4e392f821e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-03 (Mon, 03 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 static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- More cleanup, fix model creation Commit: 13389042883fe657c6b289ba6fb2db7630ffd86e https://github.com/galaxyproject/galaxy/commit/13389042883fe657c6b289ba6fb2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-05 (Wed, 05 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/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Separate file submission from upload queue, augment and generalize send function Commit: cc46b65d16275e8f73cfceb4c1546e795146bf35 https://github.com/galaxyproject/galaxy/commit/cc46b65d16275e8f73cfceb4c154… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js M 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lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/utils/utils.js.map M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/display_base.mako M templates/search/index.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako M templates/webapps/galaxy/root/history.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M test/functional/test_toolbox.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/style/blue/base.css Commit: 42c61535d6abdf5b30a4ad10396a42b4e22eb514 https://github.com/galaxyproject/galaxy/commit/42c61535d6abdf5b30a4ad10396a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Separate upload post function, remove some unnecessary functions Commit: d85342d5097e66756900592bda86eb0bf4e5c363 https://github.com/galaxyproject/galaxy/commit/d85342d5097e66756900592bda86… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-05 (Wed, 05 Aug 2015) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix comment Commit: 8e093847f9a718de63c7ac698adadebdffc076e7 https://github.com/galaxyproject/galaxy/commit/8e093847f9a718de63c7ac698ada… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-05 (Wed, 05 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-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js 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-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.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-view.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Enable composite data submission Commit: 8eca23e4b473824d1b75635e057d018d0825d767 https://github.com/galaxyproject/galaxy/commit/8eca23e4b473824d1b75635e057d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-05 (Wed, 05 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/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/mvc/upload/composite/composite-view.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.js.map M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js Log Message: ----------- Attach success, error handlers for composite uploads, fixes Commit: 960d9e5634826ea6ef1734f9adba25c3bb72a76b https://github.com/galaxyproject/galaxy/commit/960d9e5634826ea6ef1734f9adba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-07 (Fri, 07 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-view.js M client/galaxy/style/less/ui.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-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/style/blue/base.css Log Message: ----------- Fix ui behavior for restart, progress and result states Commit: 2d332e9b71b4ff28d228ef57c8bd46b6c8b1d2c4 https://github.com/galaxyproject/galaxy/commit/2d332e9b71b4ff28d228ef57c8bd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-07 (Fri, 07 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: ----------- Disable restart button if upload completed Commit: d76efc57523daa5cbb05200a2c6868e2eb9db228 https://github.com/galaxyproject/galaxy/commit/d76efc57523daa5cbb05200a2c68… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-07 (Fri, 07 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 static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Activate paste/fetch feature, improve behavior Commit: b0c7b736d450121528c4518880a2c6f128a4ee7c https://github.com/galaxyproject/galaxy/commit/b0c7b736d450121528c4518880a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-07 (Fri, 07 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-view.js 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-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-view.js Log Message: ----------- Add green start button, fix text field Commit: 1f3ee5f64806d41bc4166248370aab443c60c49e https://github.com/galaxyproject/galaxy/commit/1f3ee5f64806d41bc4166248370a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/default/default-view.js.map M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Adjust start button location Commit: 3fae23368b85682c99b82a855c8ddf0d28238e7b https://github.com/galaxyproject/galaxy/commit/3fae23368b85682c99b82a855c8d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-07 (Fri, 07 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 static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-view.js Log Message: ----------- Fix color to primary/blue Commit: 17b84cb7b4bd67e4b0d9941b77cbed3c60201b43 https://github.com/galaxyproject/galaxy/commit/17b84cb7b4bd67e4b0d9941b77cb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-10 (Mon, 10 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: ----------- Fix paste/fetch field style Commit: 5e4c0bcf64666b4c30fe4519479d0d7e1aee9000 https://github.com/galaxyproject/galaxy/commit/5e4c0bcf64666b4c30fe4519479d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-10 (Mon, 10 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 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 Log Message: ----------- Fix start button style Commit: 92526c834049a4b8e16f479521400542eeb503c8 https://github.com/galaxyproject/galaxy/commit/92526c834049a4b8e16f47952140… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M static/maps/mvc/upload/composite/composite-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-view.js Log Message: ----------- Fix update screen calls Commit: eaff25b6eb89bf1cd563b6a350f119e3a8371bc3 https://github.com/galaxyproject/galaxy/commit/eaff25b6eb89bf1cd563b6a350f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/upload/upload-view.js A client/galaxy/scripts/reports_webapp/run_stats.js A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/base.less A client/galaxy/style/less/reports.less M client/grunt-tasks/style.js M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/visualizations/trackster/config/trackster.xml A doc/source/api/guidelines.rst M doc/source/api_doc.rst M doc/source/index.rst M doc/source/releases/_header.rst A doc/source/ts_api_doc.rst M lib/galaxy/dataset_collections/builder.py M lib/galaxy/datatypes/registry.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py A lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/basic_util.py M scripts/tool_shed/build_ts_whoosh_index.py A static/images/reports_webapp/bases/home-icon-active.png A static/images/reports_webapp/bases/home-icon-hov.png A static/images/reports_webapp/bases/home-icon.png A static/images/reports_webapp/home-icon-active.png A static/images/reports_webapp/home-icon-hov.png A static/images/reports_webapp/home-icon.png A static/maps/libs/jquery.sparklines.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/upload/upload-view.js.map A static/maps/reports_webapp/run_stats.js.map A static/maps/utils/query-string-parsing.js.map M static/maps/viz/trackster.js.map A static/scripts/libs/jquery.sparklines.js M static/scripts/mvc/form/form-select-content.js A static/scripts/reports_webapp/run_stats.js A static/scripts/utils/query-string-parsing.js M static/scripts/viz/trackster.js M static/style/blue/base.css A static/style/blue/reports.css M templates/base.mako M templates/page_base.mako M templates/sorting_base.mako A templates/spark_base.mako M templates/webapps/galaxy/cloud/index.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako A templates/webapps/reports/run_stats.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako A templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako R templates/webapps/tool_shed/message.mako M templates/webapps/tool_shed/repository/manage_repository.mako M test/functional/test_toolbox.py A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: client/galaxy/scripts/mvc/upload/upload-view.js static/maps/mvc/upload/upload-view.js.map static/scripts/mvc/upload/upload-view.js static/style/blue/base.css Commit: 4beeeecf4c3dda5ee18c4dc928fb416a7b56de79 https://github.com/galaxyproject/galaxy/commit/4beeeecf4c3dda5ee18c4dc928fb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-10 (Mon, 10 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/upload-model.js 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/upload-model.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/upload-model.js Log Message: ----------- Fix file names and description Commit: b3c0725d97a1cf5c4229f60a46a878710c41cab5 https://github.com/galaxyproject/galaxy/commit/b3c0725d97a1cf5c4229f60a46a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-popover.js 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-ftp.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/maps/mvc/ui/ui-popover.js.map 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-ftp.js.map M static/scripts/mvc/ui/ui-popover.js 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/scripts/mvc/upload/upload-ftp.js M static/style/blue/base.css Log Message: ----------- Continue ftp popup integration Commit: c7ad46099c1118a62936d0f2df4bdb2ff920895e https://github.com/galaxyproject/galaxy/commit/c7ad46099c1118a62936d0f2df4b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js M client/galaxy/scripts/utils/utils.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-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js M static/scripts/utils/utils.js M static/style/blue/base.css Log Message: ----------- Enable ftp file selection for composite uploads Commit: a8def9a910ecae7fe5d3507ce38d235e20810038 https://github.com/galaxyproject/galaxy/commit/a8def9a910ecae7fe5d3507ce38d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/composite/composite-row.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/upload-ftp.js M static/style/blue/base.css Log Message: ----------- Style fixes, adjustments for ftp popover table Commit: 80e45d230b1ea5a3bf8a77e573ed8a33a4263f4d https://github.com/galaxyproject/galaxy/commit/80e45d230b1ea5a3bf8a77e573ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Add icons to buttons in regular view Commit: ab87393897b2948b306c86c692aaabd748abec31 https://github.com/galaxyproject/galaxy/commit/ab87393897b2948b306c86c692aa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/datatypes/genetics.py Log Message: ----------- Place string split in make_html_table call into try block Commit: 7695fec2fa217a056fa34a1cf78fcb41864549f2 https://github.com/galaxyproject/galaxy/commit/7695fec2fa217a056fa34a1cf78f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py R static/help.css R static/help.html R static/help.rst R static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/reports_webapp/bases/home-icon-active.png R static/images/reports_webapp/bases/home-icon-hov.png R static/images/reports_webapp/bases/home-icon.png R static/images/reports_webapp/home-icon-active.png R static/images/reports_webapp/home-icon-hov.png R static/images/reports_webapp/home-icon.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg M static/style/blue/base.css M static/style/blue/reports.css R static/welcome.rst M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/style/blue/base.css Commit: 4da5f1370f8bad346e1a26b913f8fab0bd567f0d https://github.com/galaxyproject/galaxy/commit/4da5f1370f8bad346e1a26b913f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/composite/composite-view.js M lib/galaxy/webapps/galaxy/api/datatypes.py M static/maps/mvc/upload/composite/composite-view.js.map M static/scripts/mvc/upload/composite/composite-view.js Log Message: ----------- Fix corner cases ie missing datatype details Commit: 82c732752f2c201ed223e46abb533ea262f9fe9e https://github.com/galaxyproject/galaxy/commit/82c732752f2c201ed223e46abb53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix unload message if queue is running/active Commit: 1686109ae8d6ac615ffdb45d1a0a6e7b5f48c786 https://github.com/galaxyproject/galaxy/commit/1686109ae8d6ac615ffdb45d1a0a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Fix sorting for upper case extension Commit: 71bcb8dc9d4b478c098e8ba2adf63e227eb3f658 https://github.com/galaxyproject/galaxy/commit/71bcb8dc9d4b478c098e8ba2adf6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map Log Message: ----------- Remove comments Commit: 2bdbe8036f93409a8a2d5b7a9b75c205201bd448 https://github.com/galaxyproject/galaxy/commit/2bdbe8036f93409a8a2d5b7a9b75… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map Log Message: ----------- Remove comments Commit: b07625b0c03045a4539b5f01a7115324f8905ff0 https://github.com/galaxyproject/galaxy/commit/b07625b0c03045a4539b5f01a711… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M static/maps/mvc/upload/upload-ftp.js.map M static/scripts/mvc/upload/upload-ftp.js Log Message: ----------- Remove unnecessary if condition in ftp uploader Commit: dd421d00076660ef368757c7871b5fa7c3ab80c9 https://github.com/galaxyproject/galaxy/commit/dd421d00076660ef368757c7871b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-12 (Wed, 12 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/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Minor fixes Commit: 304e693fd36fe5a84aeef0b1b1a2e3c909e1eb59 https://github.com/galaxyproject/galaxy/commit/304e693fd36fe5a84aeef0b1b1a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Allow safe switching between histories while queue is running Commit: 704e031f6339f63103e24805369db1c28653fd58 https://github.com/galaxyproject/galaxy/commit/704e031f6339f63103e24805369d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M CONTRIBUTING.md M client/galaxy/scripts/galaxy.menu.js M config/galaxy.ini.sample M doc/source/project/organization.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/sharable.py M lib/galaxy/model/__init__.py M lib/galaxy/quota/__init__.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/version.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/tool/tag_attribute_handler.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M static/maps/galaxy.menu.js.map M static/scripts/galaxy.menu.js R templates/webapps/galaxy/cloud/index.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Commit: 0c3fdd2d637255e61a08f4684f63bd6b097c02eb https://github.com/galaxyproject/galaxy/commit/0c3fdd2d637255e61a08f4684f63… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/utils.js M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/utils/utils.js A test/qunit/test-app.js M test/qunit/test-common.js A test/qunit/test-data/bootstrapped.js A test/qunit/test-data/fakeserver.js A test/qunit/tests/upload_dialog_tests.html A test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Add test cases for uploader, add generic Galaxy environment to qunit Commit: ed171e95190e651434927e05f67b5a65f1c84828 https://github.com/galaxyproject/galaxy/commit/ed171e95190e651434927e05f67b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M CONTRIBUTING.md M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/less/reports.less M client/grunt-tasks/scripts.js M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.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-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js M static/style/blue/base.css M static/style/blue/reports.css M templates/page_base.mako M templates/spark_base.mako A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into upload_000 Conflicts: static/maps/utils/utils.js.map static/scripts/utils/utils.js static/style/blue/base.css Commit: 89801414bbdc18f5db98c32ca462ef92f97f5647 https://github.com/galaxyproject/galaxy/commit/89801414bbdc18f5db98c32ca462… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-17 (Mon, 17 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-view.js M client/galaxy/scripts/mvc/upload/upload-view.js 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-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-view.js M static/scripts/mvc/upload/upload-view.js Log Message: ----------- Enhance FTP visibilty handling Commit: e9e3dd62d2178d391f5ba9f0c677063800b0f3a3 https://github.com/galaxyproject/galaxy/commit/e9e3dd62d2178d391f5ba9f0c677… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/datatypes.py Log Message: ----------- Use list comprehension to build composite_files array Commit: b6e0ba29521bbc382a9fe15493e55b2bbde1bfde https://github.com/galaxyproject/galaxy/commit/b6e0ba29521bbc382a9fe15493e5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-button-menu.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js R client/galaxy/scripts/mvc/upload/upload-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M lib/galaxy/datatypes/genetics.py M lib/galaxy/util/bunch.py M lib/galaxy/webapps/galaxy/api/datatypes.py M static/maps/mvc/ui/ui-button-menu.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map A static/maps/mvc/upload/composite/composite-row.js.map A static/maps/mvc/upload/composite/composite-view.js.map A static/maps/mvc/upload/default/default-row.js.map A static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-model.js.map R static/maps/mvc/upload/upload-row.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/upload/upload-view.js.map M static/maps/utils/uploadbox.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/ui/ui-button-menu.js M static/scripts/mvc/ui/ui-color-picker.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js A static/scripts/mvc/upload/composite/composite-row.js A static/scripts/mvc/upload/composite/composite-view.js A static/scripts/mvc/upload/default/default-row.js A static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-model.js R static/scripts/mvc/upload/upload-row.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/upload/upload-view.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/style/blue/base.css A test/qunit/test-app.js M test/qunit/test-common.js A test/qunit/test-data/bootstrapped.js A test/qunit/test-data/fakeserver.js A test/qunit/tests/upload_dialog_tests.html A test/qunit/tests/upload_dialog_tests.js M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #605 from guerler/upload_000 Add composite file uploader Compare: https://github.com/galaxyproject/galaxy/compare/bb7795f63c47...b6e0ba29521b

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[galaxyproject/galaxy] e1672f: Changed refresh time on reports homepage
by GitHub 18 Aug '15

18 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e1672f37b9bb0be4506b0df4610c14c3289df212 https://github.com/galaxyproject/galaxy/commit/e1672f37b9bb0be4506b0df4610c… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js Log Message: ----------- Changed refresh time on reports homepage Commit: e7a753bb6f67082b2a70ec122a2113becebad046 https://github.com/galaxyproject/galaxy/commit/e7a753bb6f67082b2a70ec122a21… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Ran grunt Commit: 3ba118621d54b2b115281198a28576140507d7b0 https://github.com/galaxyproject/galaxy/commit/3ba118621d54b2b115281198a285… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map Log Message: ----------- Added documentation Commit: bb7795f63c478c69e2671b2e5b4f2b12e1ff812a https://github.com/galaxyproject/galaxy/commit/bb7795f63c478c69e2671b2e5b4f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M client/galaxy/scripts/reports_webapp/run_stats.js M static/maps/reports_webapp/run_stats.js.map M static/scripts/reports_webapp/run_stats.js Log Message: ----------- Merge pull request #609 from Airistotal/dev Changed refresh time on reports homepage Compare: https://github.com/galaxyproject/galaxy/compare/9c8edf106bd6...bb7795f63c47

1 0

[galaxyproject/galaxy] fe251e: Ensure removal of temporary files.
by GitHub 18 Aug '15

18 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fe251e3c2de4d986b3654130b317fe5fe9b2cffb https://github.com/galaxyproject/galaxy/commit/fe251e3c2de4d986b3654130b317… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Ensure removal of temporary files. Specifically, export_info.xml and manifest.xml were not being deleted after the capsule was created. Commit: ed4bb86c3355cad578354696394dd6364b5a898d https://github.com/galaxyproject/galaxy/commit/ed4bb86c3355cad578354696394d… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Also delete uploaded file data after processing. API uploads, e.g. with planemo, would leave upload_file_data_XXXXXX lying around in the configured temporary directory. Forever. Commit: 9c8edf106bd61851b0668ceb6047104784f2cb1a https://github.com/galaxyproject/galaxy/commit/9c8edf106bd61851b0668ceb6047… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Merge pull request #607 from davebx/ts_tempfiles Ensure removal of temporary files. Compare: https://github.com/galaxyproject/galaxy/compare/634799803ef3...9c8edf106bd6

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[galaxyproject/galaxy] c938e6: Fix output collection terminal base class
by GitHub 17 Aug '15

17 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c938e66e98512d85120c1c06d485a13000ff82c1 https://github.com/galaxyproject/galaxy/commit/c938e66e98512d85120c1c06d485… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix output collection terminal base class Commit: 79dbff19674dbe667887b92d070165ade85ae834 https://github.com/galaxyproject/galaxy/commit/79dbff19674dbe667887b92d0701… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #602 from guerler/fix_collections_000 [15.07] Fix output collection terminal base class Commit: 4463676e2cf70989b4a036f155356418ef22b049 https://github.com/galaxyproject/galaxy/commit/4463676e2cf70989b4a036f15535… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge branch 'release_15.07' into dev Commit: 634799803ef36b9ea1a615bc980425f224d5d958 https://github.com/galaxyproject/galaxy/commit/634799803ef36b9ea1a615bc9804… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge from release and rebuild. Compare: https://github.com/galaxyproject/galaxy/compare/c0119de12eee...634799803ef3

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[galaxyproject/galaxy] 646086: Add a --develop flag to grunt that is compatible w...
by GitHub 17 Aug '15

17 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 64608685393a235bad5c161421861af6c5609048 https://github.com/galaxyproject/galaxy/commit/64608685393a235bad5c16142186… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/grunt-tasks/scripts.js Log Message: ----------- Add a --develop flag to grunt that is compatible with both standard build *and* watch to allow for easier debugging instead of requiring the 'decompress' task -- though this still works. This makes it possible to drop in 'debugger' statements, etc., and should help when working on the client. Additionally enable drop_console for the compressor, since it's now much easier to use local development tweaks. Commit: 63d6c37a39a53bae6806e3bb9267a1659313f878 https://github.com/galaxyproject/galaxy/commit/63d6c37a39a53bae6806e3bb9267… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.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-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Rebuild client w/ new options. Commit: 2666499da649fdbb3524d11ceab90b9af86205da https://github.com/galaxyproject/galaxy/commit/2666499da649fdbb3524d11ceab9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M client/grunt-tasks/scripts.js Log Message: ----------- One minor styling issue Commit: c0119de12eeeba5308c72b98811a2d140cdccbd4 https://github.com/galaxyproject/galaxy/commit/c0119de12eeeba5308c72b98811a… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-08-17 (Mon, 17 Aug 2015) Changed paths: M client/grunt-tasks/scripts.js M static/maps/galaxy.interactive_environments.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/toastr.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/data.js.map M static/maps/mvc/dataset/dataset-choice.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-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-select.js.map M static/maps/utils/deferred.js.map M static/maps/utils/graph.js.map M static/maps/utils/metrics-logger.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/filters.js.map M static/maps/viz/visualization.js.map M static/scripts/galaxy.interactive_environments.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/toastr.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/data.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/visualization.js Log Message: ----------- Merge pull request #601 from dannon/grunt_develop_mode Grunt develop mode Compare: https://github.com/galaxyproject/galaxy/compare/ed54c343e66d...c0119de12eee

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[galaxyproject/galaxy] 0f2e21: Cleanup of the toolshed's url handling methods.
by GitHub 17 Aug '15

17 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0f2e2152ee17532488a8231cf1220ed9ddddb3aa https://github.com/galaxyproject/galaxy/commit/0f2e2152ee17532488a8231cf122… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Cleanup of the toolshed's url handling methods. Commit: 9f975e85067c1c5f695979f13d26ae4d132cb36f https://github.com/galaxyproject/galaxy/commit/9f975e85067c1c5f695979f13d26… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Make travis happier. Commit: 624cf19ba5bec88dfee58380722720fc47d68eb3 https://github.com/galaxyproject/galaxy/commit/624cf19ba5bec88dfee583807227… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/common_util.py Log Message: ----------- More linting. Commit: d7e6d627d0679a5cc95f30e71f5a9d30cc753802 https://github.com/galaxyproject/galaxy/commit/d7e6d627d0679a5cc95f30e71f5a… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Correct errors found by Nicola. Commit: 84329f8f3d7423106f197fb880fc12aee2d2b71d https://github.com/galaxyproject/galaxy/commit/84329f8f3d7423106f197fb880fc… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/util/common_util.py Log Message: ----------- Remove debug output. Commit: 0efc866a07699067beb930dc0275aab7dfb40cd5 https://github.com/galaxyproject/galaxy/commit/0efc866a07699067beb930dc0275… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Correct additional errors discovered by Nicola. Commit: 5ddd2c92a3caeb75bcb379f297f2967af26afc47 https://github.com/galaxyproject/galaxy/commit/5ddd2c92a3caeb75bcb379f297f2… Author: Dave B. <dave(a)bx.psu.edu> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Fix missing parameter. Commit: ed54c343e66d7dee79dd785da837f2ce55f69138 https://github.com/galaxyproject/galaxy/commit/ed54c343e66d7dee79dd785da837… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-16 (Sun, 16 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/scripts/api/common.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #586 from davebx/ts_url_cleanup Cleanup of the toolshed's url handling methods. Compare: https://github.com/galaxyproject/galaxy/compare/2da0083cdfdf...ed54c343e66d

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[galaxyproject/galaxy] d6ef04: Applied paging to all pages
by GitHub 15 Aug '15

15 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d6ef0458309a9cfea12cb33b9d0931fd75eeb04a https://github.com/galaxyproject/galaxy/commit/d6ef0458309a9cfea12cb33b9d09… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/page_base.mako M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_in_error.mako Log Message: ----------- Applied paging to all pages Commit: 21ab4d2dbfa8576f89a13018d962cd8dc3738239 https://github.com/galaxyproject/galaxy/commit/21ab4d2dbfa8576f89a13018d962… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-view.js A client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/style/less/reports.less M config/datatypes_conf.xml.sample M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M lib/galaxy/dataset_collections/builder.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/history.py A lib/galaxy/webapps/reports/controllers/home.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/basic_util.py R static/help.css R static/help.html R static/help.rst R static/images/SetAttr.png R static/images/SetGenome.png R static/images/brochure.pdf R static/images/galaxy.png R static/images/galaxyLogo_small.png R static/images/lock.jpg R static/images/qk/quickie1_small.png R static/images/qk/quickie2_small.png R static/images/qk/quickie3_small.png R static/images/qk/quickie4_small.png R static/images/qk/quickie5_small.png R static/images/qk/quickie6_small.png R static/images/qk/quickie7_small.png R static/images/screencast.png R static/images/sequencer.png R static/images/tools.gif R static/images/toolsExpandingMenu.gif R static/images/welcomePhoto.jpg M static/maps/mvc/upload/upload-view.js.map A static/maps/reports_webapp/run_stats.js.map M static/scripts/mvc/upload/upload-view.js A static/scripts/reports_webapp/run_stats.js M static/style/blue/base.css M static/style/blue/reports.css R static/welcome.rst M templates/base.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako A templates/webapps/reports/run_stats.mako R templates/webapps/tool_shed/message.mako M templates/webapps/tool_shed/repository/manage_repository.mako M test/functional/test_toolbox.py A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml M test/functional/tools/samples_tool_conf.xml M tool-data/all_fasta.loc.sample M tool-data/faseq.loc.sample M tool-data/liftOver.loc.sample M tool-data/mosaik_index.loc.sample M tool-data/ngs_sim_fasta.loc.sample M tool-data/perm_base_index.loc.sample M tool-data/perm_color_index.loc.sample M tool-data/picard_index.loc.sample M tool-data/regions.loc.sample M tool-data/srma_index.loc.sample Log Message: ----------- Merge branch 'dev' of https://github.com/Airistotal/galaxy into Reports_pages Commit: dd51cfe6e0ae23e8faab7b43673f9f3bc6cc6dcf https://github.com/galaxyproject/galaxy/commit/dd51cfe6e0ae23e8faab7b43673f… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/workflows.py M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Added Paging to Workflows Commit: a27ff9b2922aff5f863cf7d2e84094e236d8c6bb https://github.com/galaxyproject/galaxy/commit/a27ff9b2922aff5f863cf7d2e840… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M lib/galaxy/webapps/reports/controllers/workflows.py M static/style/blue/base.css M static/style/blue/reports.css Log Message: ----------- Added limits to queries (bug fix) Changed homepage button location (small style change) Changes for CI Commit: 1d3e304644f0f5b7b3cb828a9016e2b679791f46 https://github.com/galaxyproject/galaxy/commit/1d3e304644f0f5b7b3cb828a9016… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-11 (Tue, 11 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/webapps/reports/jobs_per_user.mako Log Message: ----------- Timing of the queries on the jobs per user page. Commit: 266d96bcb0c34365b1f3ea136909abad7180a118 https://github.com/galaxyproject/galaxy/commit/266d96bcb0c34365b1f3ea136909… Author: Airistotal <danieltos.bouchard(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py M templates/webapps/reports/jobs_per_user.mako Log Message: ----------- Changed for CI, added total time for page load Commit: 2da0083cdfdfc268229d730ef2a8f5432da781f1 https://github.com/galaxyproject/galaxy/commit/2da0083cdfdfc268229d730ef2a8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-15 (Sat, 15 Aug 2015) Changed paths: M client/galaxy/style/less/reports.less M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M static/style/blue/base.css M static/style/blue/reports.css M templates/page_base.mako M templates/spark_base.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako M templates/webapps/reports/workflows_per_workflow.mako Log Message: ----------- Merge pull request #576 from Airistotal/Reports_pages Reports: Applied paging to all pages Compare: https://github.com/galaxyproject/galaxy/compare/5b2e208b775f...2da0083cdfdf

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[galaxyproject/galaxy] d9d86e: Update contact email address for security issues.
by GitHub 15 Aug '15

15 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9d86ee8a749550d052ef4f7dc3ff4be51e00734 https://github.com/galaxyproject/galaxy/commit/d9d86ee8a749550d052ef4f7dc3f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Update contact email address for security issues. Commit: 55e0f109fcebbee3da19e0d5a568ff5b4cedcddb https://github.com/galaxyproject/galaxy/commit/55e0f109fcebbee3da19e0d5a568… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Mention GitHub issues. Commit: 86aa07d87e61a980b98cf6fa6e6360e7d649f5e5 https://github.com/galaxyproject/galaxy/commit/86aa07d87e61a980b98cf6fa6e63… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Require PRs to pass the CI tests. Commit: 3df58181cdf13f6a8e7e41fb813c49de4c5a6dd6 https://github.com/galaxyproject/galaxy/commit/3df58181cdf13f6a8e7e41fb813c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Small fixes for CONTRIBUTING.md . Commit: 5b2e208b775f8284c651f67dad86fd55929456ac https://github.com/galaxyproject/galaxy/commit/5b2e208b775f8284c651f67dad86… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-15 (Sat, 15 Aug 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- Merge pull request #574 from nsoranzo/dev [PROCEDURES] GitHub issues, security email contact and CI testing Compare: https://github.com/galaxyproject/galaxy/compare/cb1538588d8a...5b2e208b775f

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[galaxyproject/usegalaxy-playbook] e989ab: update MTS
by GitHub 14 Aug '15

14 Aug '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e989abf5130cfc80c69b50260ce2d5a3b5f276f1 https://github.com/galaxyproject/usegalaxy-playbook/commit/e989abf5130cfc80… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS

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[galaxyproject/galaxy] 1383ce: flake8 lib/galaxy_utils/
by GitHub 14 Aug '15

14 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1383ced0bdf55d3355a2927db42b584d3b00b15f https://github.com/galaxyproject/galaxy/commit/1383ced0bdf55d3355a2927db42b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py Log Message: ----------- flake8 lib/galaxy_utils/ Commit: cb1538588d8a7632dcb29232bbad1b299173a84c https://github.com/galaxyproject/galaxy/commit/cb1538588d8a7632dcb29232bbad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/galaxy_utils/sequence/sequence.py M lib/galaxy_utils/sequence/transform.py M lib/galaxy_utils/sequence/vcf.py Log Message: ----------- Merge pull request #604 from nsoranzo/flake8_fixes flake8 lib/galaxy_utils/ Compare: https://github.com/galaxyproject/galaxy/compare/4459e9411b61...cb1538588d8a

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[galaxyproject/galaxy] bf8d74: UI, Histories: move unhide_datasets and delete_hid...
by GitHub 14 Aug '15

14 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf8d74da29ba02c08cc1debed38dbf63a13dd686 https://github.com/galaxyproject/galaxy/commit/bf8d74da29ba02c08cc1debed38d… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, Histories: move unhide_datasets and delete_hidden_datasets to the client, remove them from the web controller Commit: d20add4ff8abe54cbc15704edc0222935631c767 https://github.com/galaxyproject/galaxy/commit/d20add4ff8abe54cbc15704edc02… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-30 (Thu, 30 Jul 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako Log Message: ----------- UI, Histories: use /history/view with current to replace /history, move history_as_xml to /history/as_xml Commit: ff13fb85cc46cdf8399e3477ba8808dfc6078ed5 https://github.com/galaxyproject/galaxy/commit/ff13fb85cc46cdf8399e3477ba88… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-07 (Fri, 07 Aug 2015) Changed paths: M client/bower.json M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/mvc/ui/ui-select-library.js A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/base.less M client/galaxy/style/less/history.less A client/galaxy/style/less/reports.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js M config/galaxy.ini.sample M config/plugins/visualizations/trackster/config/trackster.xml A doc/source/api/guidelines.rst M doc/source/api_doc.rst M doc/source/index.rst M doc/source/releases/_header.rst A doc/source/ts_api_doc.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/libs/d3.js.map M static/maps/libs/farbtastic.js.map A static/maps/libs/jquery.sparklines.js.map M static/maps/libs/jquery/jqtouch.js.map M static/maps/libs/raven.js.map M static/maps/libs/require.js.map M static/maps/libs/tracekit.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel-edit.js.map M static/maps/mvc/ui/ui-select-library.js.map A static/maps/utils/query-string-parsing.js.map M static/maps/utils/utils.js.map M static/maps/viz/trackster.js.map M static/scripts/libs/d3.js M static/scripts/libs/farbtastic.js A static/scripts/libs/jquery.sparklines.js M static/scripts/libs/jquery/jqtouch.js M static/scripts/libs/raven.js M static/scripts/libs/require.js M static/scripts/libs/tracekit.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel-edit.js M static/scripts/mvc/ui/ui-select-library.js A static/scripts/utils/query-string-parsing.js M static/scripts/utils/utils.js M static/scripts/viz/trackster.js M static/style/blue/base.css A static/style/blue/reports.css M templates/base.mako M templates/display_base.mako M templates/page_base.mako M templates/search/index.mako M templates/sorting_base.mako A templates/spark_base.mako M templates/webapps/galaxy/cloud/index.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/library/common/ldda_info.mako M templates/webapps/galaxy/library/common/ldda_permissions.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako M templates/webapps/reports/base_panels.mako M templates/webapps/reports/index.mako M templates/webapps/reports/jobs_errors_per_tool.mako M templates/webapps/reports/jobs_per_month_all.mako M templates/webapps/reports/jobs_per_month_in_error.mako M templates/webapps/reports/jobs_per_tool.mako M templates/webapps/reports/jobs_per_user.mako M templates/webapps/reports/jobs_specified_month_all.mako M templates/webapps/reports/jobs_specified_month_in_error.mako M templates/webapps/reports/jobs_tool_per_month.mako M templates/webapps/reports/jobs_user_per_month.mako M templates/webapps/reports/registered_users_per_month.mako M templates/webapps/reports/registered_users_specified_month.mako M templates/webapps/reports/requests_per_month_all.mako M templates/webapps/reports/requests_per_user.mako M templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/users_last_access_date.mako M templates/webapps/reports/users_user_disk_usage.mako M templates/webapps/reports/workflows_per_month_all.mako M templates/webapps/reports/workflows_per_user.mako A templates/webapps/reports/workflows_per_workflow.mako M templates/webapps/reports/workflows_user_per_month.mako R templates/webapps/tool_shed/message.mako M test/functional/test_toolbox.py A test/functional/tool-data/fasta_indexes.loc M test/functional/tool-data/sample_tool_data_tables.xml A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml A test/functional/tools/collection_creates_dynamic_nested.xml A test/functional/tools/collection_creates_list_of_pairs.xml A test/functional/tools/dbkey_filter_input.xml A test/functional/tools/dbkey_filter_multi_input.xml M test/functional/tools/samples_tool_conf.xml M tools/extract/extract_genomic_dna.py M tools/extract/extract_genomic_dna.xml Log Message: ----------- Merge conflicts Commit: 971b96ddd6855e0e2fd61b89499a15d9e6fb3b93 https://github.com/galaxyproject/galaxy/commit/971b96ddd6855e0e2fd61b89499a… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, Histories: when calling 'Delete hidden', both delete *and* unhide the datasets (preventing them from being both deleted and hidden) Commit: 3e212507defb88e91799883754d4a1d1ae8c0876 https://github.com/galaxyproject/galaxy/commit/3e212507defb88e91799883754d4… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py M templates/webapps/galaxy/history/view.mako Log Message: ----------- UI, Histories: fix view.mako json ref, remove unused import in root Commit: b0a8c6f52bfda10244e12b08ff3143c1f4ef0d45 https://github.com/galaxyproject/galaxy/commit/b0a8c6f52bfda10244e12b08ff31… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-08-10 (Mon, 10 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/options-menu.js Log Message: ----------- UI, Histories: use renderItems for batched changes in options menu Commit: 4459e9411b610ea106fe2db74d20dfd27363aa23 https://github.com/galaxyproject/galaxy/commit/4459e9411b610ea106fe2db74d20… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/options-menu.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/options-menu.js A templates/webapps/galaxy/history/as_xml.mako M templates/webapps/galaxy/history/view.mako R templates/webapps/galaxy/root/history.mako R templates/webapps/galaxy/root/history_as_xml.mako Log Message: ----------- Merge pull request #578 from carlfeberhard/history.s-n-d Remove more history UIController methods. Compare: https://github.com/galaxyproject/galaxy/compare/d0a053608582...4459e9411b61

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[galaxyproject/galaxy] c00196: Fix StockLineage.get_versions() when reverse=True ...
by GitHub 14 Aug '15

14 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c00196fd2cb4eb7f999bd2176c570b0834c81c2d https://github.com/galaxyproject/galaxy/commit/c00196fd2cb4eb7f999bd2176c57… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/tools/toolbox/lineages/stock.py Log Message: ----------- Fix StockLineage.get_versions() when reverse=True . Commit: 4b3a34f1d25cd00c12a5ee3815f609f238f83aa5 https://github.com/galaxyproject/galaxy/commit/4b3a34f1d25cd00c12a5ee3815f6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Simplify ToolVersion.get_version_ids() . Commit: 9c318ac1f7dac48e25e8b1c315c372e36dc0323e https://github.com/galaxyproject/galaxy/commit/9c318ac1f7dac48e25e8b1c315c3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Remove existing wrong tool version associations in ToolVersionManager.handle_tool_versions() . Fix #552. To fix a tool with a wrong lineage, click on "Set tool versions" on the "Repository Actions" menu. Commit: d0a0536085821e667d39cc30423d7bdcbc8e5115 https://github.com/galaxyproject/galaxy/commit/d0a0536085821e667d39cc30423d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-08-14 (Fri, 14 Aug 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/lineages/stock.py M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Merge pull request #596 from nsoranzo/lineage_fixes Tool lineage fixes. Compare: https://github.com/galaxyproject/galaxy/compare/cafe872bfb20...d0a053608582

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