- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 7ca03b: Fix typos.
by GitHub 04 Mar '16

04 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ca03bbf047d989359dcf1eee460e4586e200f54 https://github.com/galaxyproject/galaxy/commit/7ca03bbf047d989359dcf1eee460… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix typos. Commit: 501a10c3f1ab7102e0a83d4afdd97f78a1a0bc21 https://github.com/galaxyproject/galaxy/commit/501a10c3f1ab7102e0a83d4afdd9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/model/metadata.py M lib/galaxy/model/search.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/workflow_util.py M scripts/functional_tests.py M scripts/transfer.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/tool_shed/base/twilltestcase.py M tools/data_source/upload.py Log Message: ----------- Do not import dumps and loads from galaxy.util.json . Commit: b4eae046cd759a906ccf1e8cd9297a5dc305f57d https://github.com/galaxyproject/galaxy/commit/b4eae046cd759a906ccf1e8cd929… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/datatypes/tabular.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/model/metadata.py M lib/galaxy/model/search.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/workflow_util.py M scripts/functional_tests.py M scripts/transfer.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/tool_shed/base/twilltestcase.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #1840 from nsoranzo/galaxy_util_json Do not import dumps and loads from galaxy.util.json . Compare: https://github.com/galaxyproject/galaxy/compare/84daaec66e87...b4eae046cd75

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[galaxyproject/galaxy] a10934: Fix repeat prefix
by GitHub 04 Mar '16

04 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a10934741dc53b545effdbd407f6b05584bc64de https://github.com/galaxyproject/galaxy/commit/a10934741dc53b545effdbd407f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix repeat prefix Commit: 84daaec66e875055e5513619e9fa4c7368bda229 https://github.com/galaxyproject/galaxy/commit/84daaec66e875055e5513619e9fa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #1848 from guerler/fix_prefix_000 Fix repeat prefix Compare: https://github.com/galaxyproject/galaxy/compare/6da3c56ec9e6...84daaec66e87

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[galaxyproject/galaxy] 1c73b8: also update rrda when repairing or updating a repo...
by GitHub 04 Mar '16

04 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1c73b8c1a335881d2b1573cc954d1c0ed1438c65 https://github.com/galaxyproject/galaxy/commit/1c73b8c1a335881d2b1573cc954d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- also update rrda when repairing or updating a repository Commit: 887e2577c98244a223cbc8ef0523fa8d1a4ae352 https://github.com/galaxyproject/galaxy/commit/887e2577c98244a223cbc8ef0523… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add logging before removing outdated dependencies Commit: 6da3c56ec9e6e644847eee417e2b3f4b5b5078c0 https://github.com/galaxyproject/galaxy/commit/6da3c56ec9e6e644847eee417e2b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1850 from mvdbeek/old_rrda_fix also update rrda when repairing or updating a repository Compare: https://github.com/galaxyproject/galaxy/compare/45bffbcd1915...6da3c56ec9e6

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[galaxyproject/galaxy] 26d556: Update more scripts to respect GALAXY_VIRTUAL_ENV.
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 26d5561b4ff48eb770970bee5f2ba49d425e9902 https://github.com/galaxyproject/galaxy/commit/26d5561b4ff48eb770970bee5f2b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M manage_tools.sh M run_reports.sh M run_tool_shed.sh Log Message: ----------- Update more scripts to respect GALAXY_VIRTUAL_ENV. Drop explicit sourcing in run_reports and run_tool_shed since they source common_startup. Commit: 97793ab81ab5601466fa89bba7b3250118e95de4 https://github.com/galaxyproject/galaxy/commit/97793ab81ab5601466fa89bba7b3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M manage_tools.sh M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1847 from jmchilton/more_virtualenv_fixes [16.01] Update more scripts to respect GALAXY_VIRTUAL_ENV. Compare: https://github.com/galaxyproject/galaxy/compare/0fbd22c9a306...97793ab81ab5

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[galaxyproject/galaxy] 8dd247: Minor followup to 1846
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8dd24734e3fd9dd64bc4bd93736c9ef571930cbf https://github.com/galaxyproject/galaxy/commit/8dd24734e3fd9dd64bc4bd93736c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Minor followup to 1846 Commit: 45bffbcd19158e6f147398d07d3f691f18d50247 https://github.com/galaxyproject/galaxy/commit/45bffbcd19158e6f147398d07d3f… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Merge pull request #1853 from dannon/style_nits Minor style followup to 1846 Compare: https://github.com/galaxyproject/galaxy/compare/02ed07ca82e1...45bffbcd1915

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[galaxyproject/galaxy] 6e13c3: Cherry-picked changes from pull request #1392.
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6e13c3999a6d54b40b2910d5ce95da724f133122 https://github.com/galaxyproject/galaxy/commit/6e13c3999a6d54b40b2910d5ce95… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py Log Message: ----------- Cherry-picked changes from pull request #1392. Commit: 3ec58fd1da5f7122752627eef581d5826190bc13 https://github.com/galaxyproject/galaxy/commit/3ec58fd1da5f7122752627eef581… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Update API endpoint names in code comments. Commit: b15a7ff06df23d7004f670f34638fe9ee5d33f92 https://github.com/galaxyproject/galaxy/commit/b15a7ff06df23d7004f670f34638… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/categories.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Include repository metadata when browsing repositories in a category. Commit: 02ed07ca82e19e20b37e50e9f6294069240d9ed1 https://github.com/galaxyproject/galaxy/commit/02ed07ca82e19e20b37e50e9f629… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/web/form_builder.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py Log Message: ----------- Merge pull request #1821 from davebx/toolshed_decouple_api Cherry-picked changes from pull request #1392. Compare: https://github.com/galaxyproject/galaxy/compare/779793810d1f...02ed07ca82e1

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[galaxyproject/galaxy] e0ce68: Fix lack of output when discovering large collecti...
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: e0ce68cc58a6d6eeb306f5c0445563e71bcc1d12 https://github.com/galaxyproject/galaxy/commit/e0ce68cc58a6d6eeb306f5c04455… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix lack of output when discovering large collections... Example log statement collected for each dataset: ``` galaxy.tools.parameters.output_collect DEBUG 2016-03-03 11:47:31,302 (8) Created dynamic collection dataset for path [/home/john/workspace/galaxy/database/job_working_directory/000/8/oe2_ie2.fq] with element identifier [oe2:ie2] for output [list_output]. ``` Commit: 0fbd22c9a30686afe62de1e1f23ff309dd6374a8 https://github.com/galaxyproject/galaxy/commit/0fbd22c9a30686afe62de1e1f23f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #1852 from jmchilton/dataset_collection_log [16.01] Fix lack of log output when discovering large collections... Compare: https://github.com/galaxyproject/galaxy/compare/de70306407c0...0fbd22c9a306

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[galaxyproject/usegalaxy-playbook] 2841ee: remove border around carousel so it matches twitte...
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2841ee2db805198cb43356c92f75bf5090761919 https://github.com/galaxyproject/usegalaxy-playbook/commit/2841ee2db805198c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- remove border around carousel so it matches twitter borderless widget

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[galaxyproject/galaxy] 159e5f: Do not create text values for failed inputs
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 159e5fd5d55dac24541189bea24e6f977c10a1d6 https://github.com/galaxyproject/galaxy/commit/159e5fd5d55dac24541189bea24e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Do not create text values for failed inputs Commit: 779793810d1f742dd1fd161c3eec1695df152d4d https://github.com/galaxyproject/galaxy/commit/779793810d1f742dd1fd161c3eec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1844 from guerler/fix_text_value_handling_000 Do not create text values for failed inputs Compare: https://github.com/galaxyproject/galaxy/compare/80bcb987c84a...779793810d1f

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[galaxyproject/galaxy] 1220e2: Prevent tours from kicking off within iframes, cau...
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1220e2e9788026af7b7047720d03f7bb097f5762 https://github.com/galaxyproject/galaxy/commit/1220e2e9788026af7b7047720d03… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Prevent tours from kicking off within iframes, causing duplicate tour step display. Commit: 80bcb987c84a8331c84db864a557f326594afd91 https://github.com/galaxyproject/galaxy/commit/80bcb987c84a8331c84db864a557… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-03 (Thu, 03 Mar 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js Log Message: ----------- Merge pull request #1846 from dannon/tour_iframe_bug Prevent tours from kicking off within iframes Compare: https://github.com/galaxyproject/galaxy/compare/9b0c491729de...80bcb987c84a

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[galaxyproject/galaxy] 6968cf: Using node 5.7, 'grunt style' fails with the error...
by GitHub 03 Mar '16

03 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6968cf0158f6b14ebbeaac3655151b5f67c393de https://github.com/galaxyproject/galaxy/commit/6968cf0158f6b14ebbeaac365515… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M client/grunt-tasks/style.js Log Message: ----------- Using node 5.7, 'grunt style' fails with the error: "ERROR Warning: Cannot delete files outside the current working directory. Use --force to continue. " This re-enables deletion of the temporary file. Commit: 9b0c491729de2945dc78b1766f520160c846c5d3 https://github.com/galaxyproject/galaxy/commit/9b0c491729de2945dc78b1766f52… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M client/grunt-tasks/style.js Log Message: ----------- Merge pull request #1841 from dannon/grunt_style Using node 5.7, 'grunt style' fails with the error: Compare: https://github.com/galaxyproject/galaxy/compare/158732edb6ce...9b0c491729de

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[galaxyproject/usegalaxy-playbook] 5aea44: mutable confs for Main; add labels
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5aea4451d1e354f1d0783d24cffe4a70bcf5ba91 https://github.com/galaxyproject/usegalaxy-playbook/commit/5aea4451d1e354f1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- mutable confs for Main; add labels

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[galaxyproject/galaxy] 499268: Hide tools that have been replaced.
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4992684d1fc58d4774e5d6a6c1df9c193218c460 https://github.com/galaxyproject/galaxy/commit/4992684d1fc58d4774e5d6a6c1df… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Hide tools that have been replaced. Commit: de70306407c0682834814c479c91f8b8adc615ce https://github.com/galaxyproject/galaxy/commit/de70306407c0682834814c479c91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M config/tool_conf.xml.main Log Message: ----------- Merge pull request #1837 from davebx/release_16.01 [16.01] Hide tools that have been replaced. Compare: https://github.com/galaxyproject/galaxy/compare/dfef64db75c4...de70306407c0

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[galaxyproject/infrastructure-playbook] 66421a: Change access list on leeroy
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 66421a2b51af676da937f5608b8200fdfd0bf8b1 https://github.com/galaxyproject/infrastructure-playbook/commit/66421a2b51a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- Change access list on leeroy

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[galaxyproject/galaxy] a49401: Improve dataset error log message
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: a49401189735daa55e44dec7af6b84a646e8bbc9 https://github.com/galaxyproject/galaxy/commit/a49401189735daa55e44dec7af6b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Improve dataset error log message Commit: dfef64db75c43cd4001a67cf48143e28df3efe60 https://github.com/galaxyproject/galaxy/commit/dfef64db75c43cd4001a67cf4814… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #1836 from natefoo/dataset-error-log [16.01] Improve dataset error log message Compare: https://github.com/galaxyproject/galaxy/compare/0051cab4f352...dfef64db75c4

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[galaxyproject/galaxy] 9aefb9: Fix workflow saving broken in dev.
by GitHub 02 Mar '16

02 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9aefb989e660e1e6e48e28338471e5642bb65236 https://github.com/galaxyproject/galaxy/commit/9aefb989e660e1e6e48e28338471… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix workflow saving broken in dev. Broken with PR #1735 (kind of accross two non-atomic commits I think - 92d978dd9d9b15bab7b3852787c2ce094880f97d and 0dac0c207757cf160901df387214dcfc56016469). Testing: Try to save a workflow. \#minor Commit: 158732edb6ceb1ed073d058b3a71c4c26e4887d2 https://github.com/galaxyproject/galaxy/commit/158732edb6ceb1ed073d058b3a71… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-02 (Wed, 02 Mar 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1835 from jmchilton/from_editor_fix Fix workflow saving broken in dev. Compare: https://github.com/galaxyproject/galaxy/compare/45bd65f85e22...158732edb6ce

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[galaxyproject/galaxy] 78b1f9: Dockerfile testing improvements.
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78b1f9af3741889a542d881cf242a12acc932a7e https://github.com/galaxyproject/galaxy/commit/78b1f9af3741889a542d881cf242… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Dockerfile testing improvements. - Use wheel from inside container. - Update to the latest pre-release phantom and casper dependencies (they seem more stable). Commit: dc897cf86a25a834455db4c16c6d99f7d0c6e7cd https://github.com/galaxyproject/galaxy/commit/dc897cf86a25a834455db4c16c6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M create_db.sh M manage_db.sh Log Message: ----------- Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Commit: 6135d7ea5634255242e13bea87075fb7422a2656 https://github.com/galaxyproject/galaxy/commit/6135d7ea5634255242e13bea8707… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Update to phantomjs 2.1 and official sources. Commit: 45bd65f85e22e5abe3ea77249e45730cff71ef02 https://github.com/galaxyproject/galaxy/commit/45bd65f85e22e5abe3ea77249e45… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #1449 from jmchilton/updated_client_test_deps Docker Testing - Newer versions of phantomjs and casperjs, in container wheels. Compare: https://github.com/galaxyproject/galaxy/compare/97c2fa3c0f97...45bd65f85e22

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[galaxyproject/galaxy] f67cbe: revert escaping added in a24e206ff7762d5b86d3dc724...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f67cbe72d571f87a87e868161650e5965e681881 https://github.com/galaxyproject/galaxy/commit/f67cbe72d571f87a87e868161650… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- revert escaping added in a24e206ff7762d5b86d3dc7240190f043dc532b5 that prevented line endings and spaces to be rendered properly Commit: 0051cab4f35240ff8b85f010b1ae0d66de7273c0 https://github.com/galaxyproject/galaxy/commit/0051cab4f35240ff8b85f010b1ae… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Merge pull request #1830 from martenson/revert-ts-repo-rendering [16.01] revert ts repo long desc escaping Compare: https://github.com/galaxyproject/galaxy/compare/cf91ab451189...0051cab4f352

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[galaxyproject/galaxy] 9d4722: Improved logging during tool executions.
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d4722c7e99b669da09a014f994c011e2f8552be https://github.com/galaxyproject/galaxy/commit/9d4722c7e99b669da09a014f994c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py Log Message: ----------- Improved logging during tool executions. Haven't a hard time untangling what messages belong to what job/tool during workflow executions. Commit: 97c2fa3c0f9735167e5cf2446b5c5e7bde72999e https://github.com/galaxyproject/galaxy/commit/97c2fa3c0f9735167e5cf2446b5c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py Log Message: ----------- Merge pull request #1832 from jmchilton/job_log_1 Improved logging during tool executions. Compare: https://github.com/galaxyproject/galaxy/compare/eb2005e7a224...97c2fa3c0f97

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[galaxyproject/galaxy] d3b343: Use visit_inputs for check_and_update_param_values
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3b343acab7567ce80f9a427f0e61afc55ba4005 https://github.com/galaxyproject/galaxy/commit/d3b343acab7567ce80f9a427f0e6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M test/api/test_workflows.py Log Message: ----------- Use visit_inputs for check_and_update_param_values Commit: d32c6b90210a6481d829eb1f7a050e1a48ee1405 https://github.com/galaxyproject/galaxy/commit/d32c6b90210a6481d829eb1f7a05… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/workflow/extract.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Move job resource parameter xml to job config Commit: 0b5651a5ed6553c1ddb3d9c25dd3b0019fc97ad7 https://github.com/galaxyproject/galaxy/commit/0b5651a5ed6553c1ddb3d9c25dd3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M lib/galaxy/tools/parameters/grouping.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py Log Message: ----------- Do not rely on __current_case__ Commit: 02187afb57a3b212c4e9a05b153e117bc8778866 https://github.com/galaxyproject/galaxy/commit/02187afb57a3b212c4e9a05b153e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-27 (Sat, 27 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/workflow/extract.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Handle missing parameters Commit: eb2005e7a2245e2e3e09ccbf7489081da393e57e https://github.com/galaxyproject/galaxy/commit/eb2005e7a2245e2e3e09ccbf7489… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/workflow/extract.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/run.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py Log Message: ----------- Merge pull request #1764 from guerler/fix_check_and_update_000 Use visit inputs for check_and_update_param_values Compare: https://github.com/galaxyproject/galaxy/compare/18128fa97d07...eb2005e7a224

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[galaxyproject/galaxy] 93494a: This silences logging when display whitelist isn't...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 93494a833ee390811bdc1d13c1ef54b52ed005f2 https://github.com/galaxyproject/galaxy/commit/93494a833ee390811bdc1d13c1ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- This silences logging when display whitelist isn't explicitly defined and the default file doesn't exist. Explicit usage still logs a failure. Commit: 16280c63236621082ce4c3b3d93eb679294cd515 https://github.com/galaxyproject/galaxy/commit/16280c63236621082ce4c3b3d93e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Only attempt to read/load sanitize_whitelist_file when starting an actual galaxy application. Commit: 7534182d7afd8c997df7d919d0633345ee5c4dfa https://github.com/galaxyproject/galaxy/commit/7534182d7afd8c997df7d919d063… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py Log Message: ----------- Add a default logger prior to full logging configuration. We currently attempt to log at various places in config parsing/etc that fail with 'No handlers could be found for logger ...', and this resolves that. Commit: cf91ab4511897ef5ac4beb8d56219119073073c4 https://github.com/galaxyproject/galaxy/commit/cf91ab4511897ef5ac4beb8d5621… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Merge pull request #1828 from dannon/cherrypick_logging [16.01] Fix startup logging Commit: 18128fa97d076bd42959435a004a0ee70ea63a04 https://github.com/galaxyproject/galaxy/commit/18128fa97d076bd42959435a004a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py Log Message: ----------- Manually merge to resolve conflict, 16.01->dev Compare: https://github.com/galaxyproject/galaxy/compare/6b800a291dcf...18128fa97d07

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[galaxyproject/galaxy] 93494a: This silences logging when display whitelist isn't...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 93494a833ee390811bdc1d13c1ef54b52ed005f2 https://github.com/galaxyproject/galaxy/commit/93494a833ee390811bdc1d13c1ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- This silences logging when display whitelist isn't explicitly defined and the default file doesn't exist. Explicit usage still logs a failure. Commit: 16280c63236621082ce4c3b3d93eb679294cd515 https://github.com/galaxyproject/galaxy/commit/16280c63236621082ce4c3b3d93e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Only attempt to read/load sanitize_whitelist_file when starting an actual galaxy application. Commit: 7534182d7afd8c997df7d919d0633345ee5c4dfa https://github.com/galaxyproject/galaxy/commit/7534182d7afd8c997df7d919d063… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py Log Message: ----------- Add a default logger prior to full logging configuration. We currently attempt to log at various places in config parsing/etc that fail with 'No handlers could be found for logger ...', and this resolves that. Commit: cf91ab4511897ef5ac4beb8d56219119073073c4 https://github.com/galaxyproject/galaxy/commit/cf91ab4511897ef5ac4beb8d5621… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Merge pull request #1828 from dannon/cherrypick_logging [16.01] Fix startup logging Compare: https://github.com/galaxyproject/galaxy/compare/50bc127a3b55...cf91ab451189

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[galaxyproject/galaxy] ae6548: Add license and repository information to package....
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ae654873e211b4263430cce6419817fe3f1c59b9 https://github.com/galaxyproject/galaxy/commit/ae654873e211b4263430cce64198… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M client/package.json Log Message: ----------- Add license and repository information to package.json. This fixes a couple warnings for recent npm versions. Commit: 6b800a291dcfc4347b76f3b960e05e4a223777eb https://github.com/galaxyproject/galaxy/commit/6b800a291dcfc4347b76f3b960e0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M client/package.json Log Message: ----------- Merge pull request #1829 from dannon/packagejson_license_repo Add license and repository information to package.json. Compare: https://github.com/galaxyproject/galaxy/compare/9f590b8a0ec7...6b800a291dcf

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[galaxyproject/galaxy] 1aa1d6: Fix workflow parameters not rendered when tool par...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1aa1d6164a63438b49beb2fd6cc4b80a57bbdb5d https://github.com/galaxyproject/galaxy/commit/1aa1d6164a63438b49beb2fd6cc4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix workflow parameters not rendered when tool parameter wrapped in conditional. Commit: dad1784a087623c990e0b3f05d1c8026f7bd957c https://github.com/galaxyproject/galaxy/commit/dad1784a087623c990e0b3f05d1c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1799 from mvdbeek/fix_workflow_parameters_conditional [16.01] Fix workflow parameters not rendered when tool parameter wrapped in conditional. Commit: 56076db848459cb1da39b04dc635538ff013d3a9 https://github.com/galaxyproject/galaxy/commit/56076db848459cb1da39b04dc635… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Disable command isolation for Pulsar... ... it builds its own job script - no need to have Galaxy do this isolation on the Galaxy end. The more Pulsar can handle the better. Commit: cb19630bd4e04b21653a2cb9848e888805dfabcc https://github.com/galaxyproject/galaxy/commit/cb19630bd4e04b21653a2cb9848e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Fix unit tests for 56076db848459cb1da39b04dc635538ff013d3a9 Commit: 47c93180708eb138c1fa0393cd18b24d27249359 https://github.com/galaxyproject/galaxy/commit/47c93180708eb138c1fa0393cd18… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-28 (Sun, 28 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #1812 from jmchilton/pulsar_16.01_fixes [16.01] Disable command isolation for Pulsar... Commit: 865f2d49bd04b636552002cd0e4830f2dbad5c75 https://github.com/galaxyproject/galaxy/commit/865f2d49bd04b636552002cd0e48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M create_db.sh M manage_db.sh Log Message: ----------- Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Commit: 5bc55f9fa2fd6af9142df644bf82e830b56f9ce4 https://github.com/galaxyproject/galaxy/commit/5bc55f9fa2fd6af9142df644bf82… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Add js for mako based masthead Commit: 281f5b734610963b437b72837e7b71cebbb3c5bd https://github.com/galaxyproject/galaxy/commit/281f5b734610963b437b72837e7b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/galaxy/style/less/ui/icon-btn.less M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/config.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/version.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/shed_util_common.py M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/workflow/workflow-terminals.js M static/style/blue/base.css R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M test/functional/tools/output_format.xml M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge branch 'release_16.01' of https://github.com/galaxyproject/galaxy into release_16.01 Commit: fa8beb225004d27da24065f8f633c7917b5be942 https://github.com/galaxyproject/galaxy/commit/fa8beb225004d27da24065f8f633… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge pull request #1823 from martenson/port-masthead-fix [16.01] Port masthead fix Commit: 50bc127a3b55432884ed6350bee3e0ea67beb95f https://github.com/galaxyproject/galaxy/commit/50bc127a3b55432884ed6350bee3… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M create_db.sh M manage_db.sh Log Message: ----------- Merge pull request #1820 from jmchilton/db_script_fixes [16.01] Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Commit: 9f590b8a0ec755403f84f0fff1978530ee306ef8 https://github.com/galaxyproject/galaxy/commit/9f590b8a0ec755403f84f0fff197… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M create_db.sh M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M manage_db.sh M templates/webapps/galaxy/workflow/run.mako M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/19a58f745089...9f590b8a0ec7

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[galaxyproject/galaxy] 6dbdc4: Loading a Job object eagerloads a lot of mappings ...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6dbdc430bd9d9281407e73988511f5e355d7f537 https://github.com/galaxyproject/galaxy/commit/6dbdc430bd9d9281407e73988511… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Loading a Job object eagerloads a lot of mappings down to the dataset level. For Jobs with many outputs with large metadata, this can consume many GB of memory. Attempt to lazy load instead such that only one row should be returned for querying jobs (but this could negatively impact performance in other places). Commit: 19a58f745089eea730674158153bf77adbf2bbbc https://github.com/galaxyproject/galaxy/commit/19a58f745089eea730674158153b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #1809 from natefoo/lazyload-job Change many job mapped properties to lazy loads Compare: https://github.com/galaxyproject/galaxy/compare/a01ff73c7b0d...19a58f745089

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