Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b97c7964457010318b4639e57ca01fd6185269f2 https://github.com/galaxyproject/galaxy/commit/b97c7964457010318b4639e57ca01... Author: guerler <aysam.guerler@gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Filter missing inputs when processing data Commit: edca79a0cf4d0e6afceb0f3b3894b6b3a169bd53 https://github.com/galaxyproject/galaxy/commit/edca79a0cf4d0e6afceb0f3b3894b... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Do not encode dict items that start with 'metadata_' in return value of api/tools/create. Resolves #2423, #2137, and https://github.com/galaxyproject/tools-iuc/pull/770. However, this whole act of encoding by key.endswith('_id') is very messy. Commit: 42739c88c80d10742add92f2e3978ed65a295188 https://github.com/galaxyproject/galaxy/commit/42739c88c80d10742add92f2e3978... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test for failing handling of BIOM1 metadata. Commit: 37a491599257c4045ad9e45ae53d12b9d97be418 https://github.com/galaxyproject/galaxy/commit/37a491599257c4045ad9e45ae53d1... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #2458 from guerler/fix_process_data [16.04] Filter missing inputs when processing data Commit: 10a3f23de2f8d728780b7c1615e7d4c9afeaeeb2 https://github.com/galaxyproject/galaxy/commit/10a3f23de2f8d728780b7c1615e7d... Author: John Chilton <jmchilton@gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2459 from blankenberg/metadata-id-fix [16.04] Do not encode dict items that start with 'metadata_' in return value of api/tools/create. Commit: 9e5419f58c2af16d4cc6e8ece79c61f86a38b6cf https://github.com/galaxyproject/galaxy/commit/9e5419f58c2af16d4cc6e8ece79c6... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Delay import of DrmaaSessionFactory after runner initialization Fix issue #2463, i.e. the regression introduced in #2102 by which Galaxy no longer respects <param id="drmaa_library_path"> in config/job_conf.xml , preventing the use of multiple drmaa runners. Commit: 8983e4304060482426e8f3f2eb072eb0f071ba83 https://github.com/galaxyproject/galaxy/commit/8983e4304060482426e8f3f2eb072... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #2466 from nsoranzo/release_16.04_fix_for_2463 [16.04] Delay import of DrmaaSessionFactory after runner initialization Commit: bb5dc6e20b4e9bfe6fd971c31d5dd2f3f5301bbb https://github.com/galaxyproject/galaxy/commit/bb5dc6e20b4e9bfe6fd971c31d5dd... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c0b5a2840bc9...bb5dc6e20b4e