June 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] e370c5: Re-add get_updated_changeset_revisions_from_tool_s...
by GitHub 08 Jun '16

08 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e370c556498c45b9533276182aa7158aa730d83c https://github.com/galaxyproject/galaxy/commit/e370c556498c45b9533276182aa7… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/tool_shed/util/metadata_util.py Log Message: ----------- Re-add get_updated_changeset_revisions_from_tool_shed() method It was accidentally removed in PR #2269. Fix toolshed tests Commit: b7108cfb8b622d2212505a1f55bc8b063d545723 https://github.com/galaxyproject/galaxy/commit/b7108cfb8b622d2212505a1f55bc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/tool_shed/util/metadata_util.py Log Message: ----------- Merge pull request #2472 from nsoranzo/fix_for_2269 Re-add get_updated_changeset_revisions_from_tool_shed() method Compare: https://github.com/galaxyproject/galaxy/compare/66e4750589db...b7108cfb8b62

1 0

[galaxyproject/galaxy] d2be9d: Prevent missing display to text values in workflow...
by GitHub 08 Jun '16

08 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d2be9dc98dbee387bec377a9c89685bb0011c85f https://github.com/galaxyproject/galaxy/commit/d2be9dc98dbee387bec377a9c896… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Prevent missing display to text values in workflow preview Commit: befe35456a606cab03c3119c013c5983323c16e3 https://github.com/galaxyproject/galaxy/commit/befe35456a606cab03c3119c013c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge pull request #2471 from guerler/fix_workflow_display [16.04] Prevent missing display to text values in workflow preview Commit: 4cd2af860ffc31ee574e6f81c941840ae603efe5 https://github.com/galaxyproject/galaxy/commit/4cd2af860ffc31ee574e6f81c941… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Avoid empty strings when converting values to display text Commit: 04863c833bb1de9c298600be7c2de44d2b6b694b https://github.com/galaxyproject/galaxy/commit/04863c833bb1de9c298600be7c2d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2473 from martenson/port-value-to-display [16.04] Avoid empty strings when converting values to display text Commit: 66e4750589db3e05163ad47323e6aee9ed7a2d4c https://github.com/galaxyproject/galaxy/commit/66e4750589db3e05163ad47323e6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/27a2a36657ae...66e4750589db

1 0

[galaxyproject/galaxy] 4cd2af: Avoid empty strings when converting values to disp...
by GitHub 08 Jun '16

08 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 4cd2af860ffc31ee574e6f81c941840ae603efe5 https://github.com/galaxyproject/galaxy/commit/4cd2af860ffc31ee574e6f81c941… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Avoid empty strings when converting values to display text Commit: 04863c833bb1de9c298600be7c2de44d2b6b694b https://github.com/galaxyproject/galaxy/commit/04863c833bb1de9c298600be7c2d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2473 from martenson/port-value-to-display [16.04] Avoid empty strings when converting values to display text Compare: https://github.com/galaxyproject/galaxy/compare/befe35456a60...04863c833bb1

1 0

[galaxyproject/galaxy] d2be9d: Prevent missing display to text values in workflow...
by GitHub 08 Jun '16

08 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: d2be9dc98dbee387bec377a9c89685bb0011c85f https://github.com/galaxyproject/galaxy/commit/d2be9dc98dbee387bec377a9c896… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Prevent missing display to text values in workflow preview Commit: befe35456a606cab03c3119c013c5983323c16e3 https://github.com/galaxyproject/galaxy/commit/befe35456a606cab03c3119c013c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge pull request #2471 from guerler/fix_workflow_display [16.04] Prevent missing display to text values in workflow preview Compare: https://github.com/galaxyproject/galaxy/compare/8983e4304060...befe35456a60

1 0

[galaxyproject/galaxy] ed9198: Add parameter expansion caller and test cases as p...
by GitHub 08 Jun '16

08 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ed919805c8e14cfe74fd45280fb472bf68ade022 https://github.com/galaxyproject/galaxy/commit/ed919805c8e14cfe74fd45280fb4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Add parameter expansion caller and test cases as preparation for workflow api extension Commit: 27a2a36657aec410b56a38dced69282976fb7aaa https://github.com/galaxyproject/galaxy/commit/27a2a36657aec410b56a38dced69… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/meta.py Log Message: ----------- Merge pull request #2464 from guerler/add_workflow_parameter_expansion_caller Add parameter expansion caller and test cases as preparation for workflow api extension Compare: https://github.com/galaxyproject/galaxy/compare/e8c469a62fd8...27a2a36657ae

1 0

[galaxyproject/galaxy] 4147fe: Make pykube an optional dependency since we don't ...
by GitHub 08 Jun '16

08 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4147fe6ca5b485ccf02a81ed8e6d87f525489220 https://github.com/galaxyproject/galaxy/commit/4147fe6ca5b485ccf02a81ed8e6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Make pykube an optional dependency since we don't have wheels for it. I should have requested this as a change to https://github.com/galaxyproject/galaxy/pull/2314. Rebased with improved job conf sample comment thanks to suggestions by @nsoranzo. Commit: e8c469a62fd88026ee8908f2e4ae5d2b4f77812d https://github.com/galaxyproject/galaxy/commit/e8c469a62fd88026ee8908f2e4ae… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #2468 from jmchilton/pykube_optional Make pykube an optional dependency since we don't have wheels for it. Compare: https://github.com/galaxyproject/galaxy/compare/beed45a3c787...e8c469a62fd8

1 0

[galaxyproject/galaxy] bcf250: Fix py34-lint tox test
by GitHub 08 Jun '16

08 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bcf25027aa48eb2e9ee3fb2e5a37ef5898d8d1ec https://github.com/galaxyproject/galaxy/commit/bcf25027aa48eb2e9ee3fb2e5a37… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/tool_shed/util/repository_util.py Log Message: ----------- Fix py34-lint tox test Broken with the merge of #2269. Commit: beed45a3c787415c5ac1b2d2b8cc13a0973f495c https://github.com/galaxyproject/galaxy/commit/beed45a3c787415c5ac1b2d2b8cc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/tool_shed/util/repository_util.py Log Message: ----------- Merge pull request #2469 from nsoranzo/python3 Fix py34-lint tox test Compare: https://github.com/galaxyproject/galaxy/compare/bb5dc6e20b4e...beed45a3c787

1 0

[galaxyproject/infrastructure-playbook] f52543: Install subversion on orval
by GitHub 08 Jun '16

08 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: f5254387f2bb2d116b9c990949f42ebb0e102d06 https://github.com/galaxyproject/infrastructure-playbook/commit/f5254387f2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M galaxyenv/host_vars/orval.galaxyproject.org.yml Log Message: ----------- Install subversion on orval

1 0

[galaxyproject/galaxy] b97c79: Filter missing inputs when processing data
by GitHub 08 Jun '16

08 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b97c7964457010318b4639e57ca01fd6185269f2 https://github.com/galaxyproject/galaxy/commit/b97c7964457010318b4639e57ca0… Author: guerler <aysam.guerler(a)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/edca79a0cf4d0e6afceb0f3b3894… Author: Daniel Blankenberg <dan.blankenberg(a)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/42739c88c80d10742add92f2e397… Author: Daniel Blankenberg <dan.blankenberg(a)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/37a491599257c4045ad9e45ae53d… Author: Martin Cech <cech.marten(a)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/10a3f23de2f8d728780b7c1615e7… Author: John Chilton <jmchilton(a)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/9e5419f58c2af16d4cc6e8ece79c… Author: Nicola Soranzo <nicola.soranzo(a)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/8983e4304060482426e8f3f2eb07… Author: Martin Cech <cech.marten(a)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/bb5dc6e20b4e9bfe6fd971c31d5d… Author: Nicola Soranzo <nicola.soranzo(a)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

1 0

[galaxyproject/galaxy] 9e5419: Delay import of DrmaaSessionFactory after runner i...
by GitHub 08 Jun '16

08 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 9e5419f58c2af16d4cc6e8ece79c61f86a38b6cf https://github.com/galaxyproject/galaxy/commit/9e5419f58c2af16d4cc6e8ece79c… Author: Nicola Soranzo <nicola.soranzo(a)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/8983e4304060482426e8f3f2eb07… Author: Martin Cech <cech.marten(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/10a3f23de2f8...8983e4304060

1 0