Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 6dc5f022c73d5bde3b4ef1abe31a8d3b37ade9c3 https://github.com/galaxyproject/galaxy/commit/6dc5f022c73d5bde3b4ef1abe31a8... Author: Nate Coraor <nate@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/096a1686badda620acb507deaf938... Author: Nate Coraor <nate@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/8b2387a1c1772b07473170df23bf5... Author: Martin Cech <cech.marten@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/98ec06c7d6e4d23c1e2d35fa2d045... Author: Nate Coraor <nate@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/c938e66e98512d85120c1c06d485a... Author: guerler <aysam.guerler@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/79dbff19674dbe667887b92d07016... Author: Dannon Baker <dannon.baker@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/238d908ccecd6411a3a72f7396933... Author: Nicola Soranzo <nicola.soranzo@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/a1bff672f39da8610543ba572c322... Author: Eric Rasche <rasche.eric@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/71f28c99e539acf828a03e8288e1d... Author: Dannon Baker <dannon.baker@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/01278aa956f5791badaa6e475d94f... Author: Dannon Baker <dannon.baker@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/483ea9e735bf7de22f7ce7abb6105... Author: Dannon Baker <dannon.baker@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/b4df5e944bddcbd03699a4b3b3950... Author: Dannon Baker <dannon.baker@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/a9827fae31d8826bf2426c5285fe7... Author: John Chilton <jmchilton@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/baf8fe6759fe283516c5242d42ab8... Author: Nicola Soranzo <nsoranzo@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/14a8ee95f3dd8a671ee9a1edac8fc... Author: Dannon Baker <dannon.baker@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/a34f13a9f6eb216665ea97e1314f7... Author: Nicola Soranzo <nicola.soranzo@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/737248d41d4e1d682361b85d48ea6... Author: Dannon Baker <dannon.baker@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/b8fd98979c775daf46a768572fb30... Author: Dannon Baker <dannon.baker@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/083789526105abda87a701835b8ff... Author: Nicola Soranzo <nsoranzo@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/b29e81014979d2e72d704a22560a2... Author: Dannon Baker <dannon.baker@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/4d2651a085405f2b4ba37f26fa917... Author: Dannon Baker <dannon.baker@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/e06d6a1ccae792abb45ff96d63bf8... Author: Dannon Baker <dannon.baker@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/c569f7856d41fe9b5180830256928... Author: Dannon Baker <dannon.baker@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/e8f90429e2ca3efc6dbb9f02b1d5f... Author: Dannon Baker <dannon.baker@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/d055102596d85b5a3d6da90e83970... Author: Dannon Baker <dannon.baker@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