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

[galaxyproject/galaxy] 6dc5f0: Merge branch 'security-20150812-xss' into release_...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/master 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: 8b2387a1c1772b07473170df23bf5eea2aed0e54 https://github.com/galaxyproject/galaxy/commit/8b2387a1c1772b07473170df23bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M lib/tool_shed/metadata/repository_metadata_manager.py Log Message: ----------- fix regenerating repo metadata when coming from batch interface it used to create only single instalable revision (the latest) Commit: 98ec06c7d6e4d23c1e2d35fa2d04511bae8ab90c https://github.com/galaxyproject/galaxy/commit/98ec06c7d6e4d23c1e2d35fa2d04… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-08-13 (Thu, 13 Aug 2015) Changed paths: M lib/tool_shed/metadata/repository_metadata_manager.py Log Message: ----------- Merge pull request #600 from martenson/ts-metadata-batch-reset [release_15.07] fix regenerating repo metadata when coming from batch interface 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: 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: 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: 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 Commit: 737248d41d4e1d682361b85d48ea65574367e59d https://github.com/galaxyproject/galaxy/commit/737248d41d4e1d682361b85d48ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: b8fd98979c775daf46a768572fb30f4467fd7458 https://github.com/galaxyproject/galaxy/commit/b8fd98979c775daf46a768572fb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: 083789526105abda87a701835b8ff44e0ec89405 https://github.com/galaxyproject/galaxy/commit/083789526105abda87a701835b8f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge pull request #625 from dannon/release_15.07 [release_15.07] Fix for valid height/width definitions in workflow rendering code, and fix identifiers. Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: e06d6a1ccae792abb45ff96d63bf8ab51e685231 https://github.com/galaxyproject/galaxy/commit/e06d6a1ccae792abb45ff96d63bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: c569f7856d41fe9b51808302569283c800a4eb93 https://github.com/galaxyproject/galaxy/commit/c569f7856d41fe9b518083025692… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: e8f90429e2ca3efc6dbb9f02b1d5fbe8afc446a5 https://github.com/galaxyproject/galaxy/commit/e8f90429e2ca3efc6dbb9f02b1d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: d055102596d85b5a3d6da90e8397016f6daf2271 https://github.com/galaxyproject/galaxy/commit/d055102596d85b5a3d6da90e8397… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/render.py M lib/tool_shed/metadata/repository_metadata_manager.py M scripts/cleanup_datasets/cleanup_datasets.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/130004feb10f...d055102596d8

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[galaxyproject/galaxy] b29e81: Fix for valid height/width definitions in workflow...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: e06d6a1ccae792abb45ff96d63bf8ab51e685231 https://github.com/galaxyproject/galaxy/commit/e06d6a1ccae792abb45ff96d63bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: c569f7856d41fe9b51808302569283c800a4eb93 https://github.com/galaxyproject/galaxy/commit/c569f7856d41fe9b518083025692… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: e8f90429e2ca3efc6dbb9f02b1d5fbe8afc446a5 https://github.com/galaxyproject/galaxy/commit/e8f90429e2ca3efc6dbb9f02b1d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Compare: https://github.com/galaxyproject/galaxy/compare/083789526105...e8f90429e2ca

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[galaxyproject/galaxy] b29e81: Fix for valid height/width definitions in workflow...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.05 Home: https://github.com/galaxyproject/galaxy Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: e06d6a1ccae792abb45ff96d63bf8ab51e685231 https://github.com/galaxyproject/galaxy/commit/e06d6a1ccae792abb45ff96d63bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: c569f7856d41fe9b51808302569283c800a4eb93 https://github.com/galaxyproject/galaxy/commit/c569f7856d41fe9b518083025692… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Compare: https://github.com/galaxyproject/galaxy/compare/14a8ee95f3dd...c569f7856d41

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[galaxyproject/galaxy] b29e81: Fix for valid height/width definitions in workflow...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.03 Home: https://github.com/galaxyproject/galaxy Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: e06d6a1ccae792abb45ff96d63bf8ab51e685231 https://github.com/galaxyproject/galaxy/commit/e06d6a1ccae792abb45ff96d63bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Compare: https://github.com/galaxyproject/galaxy/compare/01278aa956f5...e06d6a1ccae7

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[galaxyproject/galaxy] b29e81: Fix for valid height/width definitions in workflow...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.01 Home: https://github.com/galaxyproject/galaxy Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Compare: https://github.com/galaxyproject/galaxy/compare/71f28c99e539...4d2651a08540

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[galaxyproject/galaxy] 737248: Fix for valid height/width definitions in workflow...
by GitHub 21 Aug '15

21 Aug '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 737248d41d4e1d682361b85d48ea65574367e59d https://github.com/galaxyproject/galaxy/commit/737248d41d4e1d682361b85d48ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: b8fd98979c775daf46a768572fb30f4467fd7458 https://github.com/galaxyproject/galaxy/commit/b8fd98979c775daf46a768572fb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: 083789526105abda87a701835b8ff44e0ec89405 https://github.com/galaxyproject/galaxy/commit/083789526105abda87a701835b8f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge pull request #625 from dannon/release_15.07 [release_15.07] Fix for valid height/width definitions in workflow rendering code, and fix identifiers. Compare: https://github.com/galaxyproject/galaxy/compare/a34f13a9f6eb...083789526105

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[galaxyproject/galaxy] 9fb615: Change FTP icon to open folder icon
by GitHub 20 Aug '15

20 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9fb615f83a15ae31cbc4376733831604d0d4d04b https://github.com/galaxyproject/galaxy/commit/9fb615f83a15ae31cbc437673383… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-20 (Thu, 20 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/scripts/mvc/upload/default/default-view.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/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 Log Message: ----------- Change FTP icon to open folder icon Commit: 94dfbaa10a783a98e7488e0aa28e7551497657db https://github.com/galaxyproject/galaxy/commit/94dfbaa10a783a98e7488e0aa28e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-20 (Thu, 20 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/scripts/mvc/upload/default/default-view.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/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 Log Message: ----------- Change pencil icon to edit icon Commit: 8be164f92c6896f2d9d0297d96c8073bd2612ec6 https://github.com/galaxyproject/galaxy/commit/8be164f92c6896f2d9d0297d96c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Fix tests Commit: 795e30171149e65d14e1031b2f4d652da8f5f25c https://github.com/galaxyproject/galaxy/commit/795e30171149e65d14e1031b2f4d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-20 (Thu, 20 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/scripts/mvc/upload/default/default-view.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/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 test/qunit/tests/upload_dialog_tests.js Log Message: ----------- Merge pull request #628 from guerler/upload_002 Change uploader icons Compare: https://github.com/galaxyproject/galaxy/compare/6ead1de53c17...795e30171149

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[galaxyproject/galaxy] aceb82: Remove fastx_clipper_sequences.txt, moved to tools...
by GitHub 20 Aug '15

20 Aug '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aceb82247003c71565d57794d5572858d21a7712 https://github.com/galaxyproject/galaxy/commit/aceb82247003c71565d57794d557… Author: Lance Parsons <lparsons(a)genomics.princeton.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: R tool-data/fastx_clipper_sequences.txt Log Message: ----------- Remove fastx_clipper_sequences.txt, moved to toolshed Commit: 6ead1de53c17cb0e3e1465f2076b3c43ea81cbc4 https://github.com/galaxyproject/galaxy/commit/6ead1de53c17cb0e3e1465f2076b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: R tool-data/fastx_clipper_sequences.txt Log Message: ----------- Merge pull request #611 from lparsons/fastx_clipper_sequences Remove fastx_clipper_sequences.txt, moved to toolshed Compare: https://github.com/galaxyproject/galaxy/compare/0f883ef776bd...6ead1de53c17

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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/dev 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 Commit: 0f883ef776bd71348b82be29221abbbc1751d45f https://github.com/galaxyproject/galaxy/commit/0f883ef776bd71348b82be29221a… 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_15.07' into dev Conflicts: lib/galaxy/model/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/c429777c9368...0f883ef776bd

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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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