- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 4da9f7: Fix fluent query log serialization when datetime t...
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4da9f70b39269e309d249c5bf44d2ff34cc16aa6 https://github.com/galaxyproject/galaxy/commit/4da9f70b39269e309d249c5bf44d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Fix fluent query log serialization when datetime types are in use. Currently queries which have raw datetime.datetime objects in the context will fail to log and throw an exception. Commit: 3bd802268dc4f024d1ea17a4721c51bd0a6d8960 https://github.com/galaxyproject/galaxy/commit/3bd802268dc4f024d1ea17a4721c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/util/log/fluent_log.py Log Message: ----------- Merge pull request #2039 from dannon/fluent_tweaks Fix fluent query log serialization when datetime types are in use. Compare: https://github.com/galaxyproject/galaxy/compare/6227156d7f57...3bd802268dc4

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[galaxyproject/galaxy] 46e430: Fix pbs runner file touch.
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 46e4308f7c68bd83a21b425bf0ea50d285e52840 https://github.com/galaxyproject/galaxy/commit/46e4308f7c68bd83a21b425bf0ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- Fix pbs runner file touch. Commit: 6227156d7f57318df5899dc0911bd299320f04f9 https://github.com/galaxyproject/galaxy/commit/6227156d7f57318df5899dc0911b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/pbs.py Log Message: ----------- Merge pull request #2074 from dannon/pbs_fix Fix pbs runner file touch. Compare: https://github.com/galaxyproject/galaxy/compare/e7d4bc306382...6227156d7f57

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[galaxyproject/galaxy] 55074c: Add Phinch as an external display application. Cur...
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55074c8f33ae27246ffbe7de7f29697078458985 https://github.com/galaxyproject/galaxy/commit/55074c8f33ae27246ffbe7de7f29… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/biom/biom_simple.xml A tool-data/biom_simple_display.loc.sample Log Message: ----------- Add Phinch as an external display application. Currently linking to a personal copy of Phinch, since it requires https://github.com/PitchInteractiveInc/Phinch/pull/54 Commit: e7d4bc306382b1a077cc7e4ed54e0b0be5f42a62 https://github.com/galaxyproject/galaxy/commit/e7d4bc306382b1a077cc7e4ed54e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/biom/biom_simple.xml A tool-data/biom_simple_display.loc.sample Log Message: ----------- Merge pull request #2069 from blankenberg/biom-phinch Add Phinch as an external display application. Compare: https://github.com/galaxyproject/galaxy/compare/3ecd4e94cf1f...e7d4bc306382

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[galaxyproject/galaxy] 0609fe: Need to make changes to consolidate sharing.mako f...
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0609fe056f360e8f1eb6f542ee32bd1c89522c3d https://github.com/galaxyproject/galaxy/commit/0609fe056f360e8f1eb6f542ee32… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/webapps/galaxy/workflow/list.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Need to make changes to consolidate sharing.mako file Commit: 2c4cb334c0b215c23e617a035f2b2062f10afa1d https://github.com/galaxyproject/galaxy/commit/2c4cb334c0b215c23e617a035f2b… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Making a single mako file for sharing and export. "sharing_base.mako" also needs to be re written. Commit: 20ef047dc150f361328d393edfe64e6556aaa0ff https://github.com/galaxyproject/galaxy/commit/20ef047dc150f361328d393edfe6… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- more mako mixing Commit: d402df68822bafa3fd6b21e61f7eb99da07e45e8 https://github.com/galaxyproject/galaxy/commit/d402df68822bafa3fd6b21e61f7e… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/sharing_base.mako M templates/webapps/galaxy/workflow/export.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- more changes in sharing.mako Commit: ebda79c2ebbc88370d80ee32029149f831f4f3d6 https://github.com/galaxyproject/galaxy/commit/ebda79c2ebbc88370d80ee320291… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Scrolly fix Commit: f526a7c2b438b3a1781e92c52826d448563ac71e https://github.com/galaxyproject/galaxy/commit/f526a7c2b438b3a1781e92c52826… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #1 from dannon/workflow_sharing_menu Scrolly fix Commit: ccbc3e0045d0e46460004fe8b6c4123b837491f9 https://github.com/galaxyproject/galaxy/commit/ccbc3e0045d0e46460004fe8b6c4… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: R templates/webapps/galaxy/workflow/export.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- This commit addresses issue #1782 and simplifies the workflow sharing/publish and Download/Export options Commit: 0ea13c957a6efbb7812f828e1f550eb676659a2f https://github.com/galaxyproject/galaxy/commit/0ea13c957a6efbb7812f828e1f55… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/webapps/galaxy/workflow/list.mako Log Message: ----------- cleaning comments Commit: 827d175e431b9f2344293d3de47ac663cb56f17b https://github.com/galaxyproject/galaxy/commit/827d175e431b9f2344293d3de47a… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- removed commeted code Commit: dbfa39e3618bfc7706eac8108faa768d659a07f6 https://github.com/galaxyproject/galaxy/commit/dbfa39e3618bfc7706eac8108faa… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/list.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Made some small UI fixes as suggested by @martenson Commit: 4618e4cb87d2035d52c2b0022859d4951d945931 https://github.com/galaxyproject/galaxy/commit/4618e4cb87d2035d52c2b0022859… Author: nitesh1989 <nitesh.turaga(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- removed descriptions Commit: 36a8eb27eca34b0bfb6fc7106b61b3571b91949e https://github.com/galaxyproject/galaxy/commit/36a8eb27eca34b0bfb6fc7106b61… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- styling changes to share and download page hide myexperiment export as it does not work now Commit: dd2d62065c817008368df8fce094af3a6da993a8 https://github.com/galaxyproject/galaxy/commit/dd2d62065c817008368df8fce094… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- re-add my experiment export; some styling tweaks Commit: a3a2e0d07b7154839b9375e31b9fcc935f88fd06 https://github.com/galaxyproject/galaxy/commit/a3a2e0d07b7154839b9375e31b9f… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #3 from martenson/workflow_changes styling changes to share and download page Commit: 5939b6d6952df9602d1294a81d13ca44dc33dfb9 https://github.com/galaxyproject/galaxy/commit/5939b6d6952df9602d1294a81d13… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- restyle the sharing page template a bit more Commit: 263e7b28495f7975787d6f868a1bf891293948f1 https://github.com/galaxyproject/galaxy/commit/263e7b28495f7975787d6f868a1b… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #4 from martenson/workflow_changes more style Workflow changes Commit: 1ca33b1d5dbac64fc0607b974be249718869e5a4 https://github.com/galaxyproject/galaxy/commit/1ca33b1d5dbac64fc0607b974be2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- sharing page cleanup; remove invalid html tags; indentation Commit: 0abd920d0bb389a670e0f3ad943d73386f63e09e https://github.com/galaxyproject/galaxy/commit/0abd920d0bb389a670e0f3ad943d… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #5 from martenson/workflow_changes sharing page cleanup; remove invalid html tags; indentation Commit: 3ecd4e94cf1f310d09ece4b69369b4340891c3d7 https://github.com/galaxyproject/galaxy/commit/3ecd4e94cf1f310d09ece4b69369… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/sharing_base.mako R templates/webapps/galaxy/workflow/export.mako M templates/webapps/galaxy/workflow/list.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #2060 from nitesh1989/workflow_sharing_menu Simplify Workflow sharing menu Compare: https://github.com/galaxyproject/galaxy/compare/463de48d7fdb...3ecd4e94cf1f

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[galaxyproject/galaxy] 20f61e: workaround for error message in case original tool...
by GitHub 04 Apr '16

04 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 20f61e6a2f36967e16a92cbcf8ad7f81ca76fb29 https://github.com/galaxyproject/galaxy/commit/20f61e6a2f36967e16a92cbcf8ad… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- workaround for error message in case original toolshed had been disabled Commit: 65a7ebee23364a89d72e528bfcde6b1f6b3c5cd9 https://github.com/galaxyproject/galaxy/commit/65a7ebee23364a89d72e528bfcde… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2072 from mvdbeek/backport_1738 [16.01] backport #1738 Compare: https://github.com/galaxyproject/galaxy/compare/90b95dc665bd...65a7ebee2336

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[galaxyproject/galaxy] 7ae007: Add the Roadmap of the project
by GitHub 03 Apr '16

03 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ae007bf435820217822d945be50fa639f589628 https://github.com/galaxyproject/galaxy/commit/7ae007bf435820217822d945be50… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-04-03 (Sun, 03 Apr 2016) Changed paths: M README.rst Log Message: ----------- Add the Roadmap of the project I was reading an article from Trello: http://blog.trello.com/tips-for-making-a-public-roadmap/ and thought it could be useful for people to have direct access to the roadmap instead of looking for it in the issues. :) Commit: 114ef7336944e2e256936cc1d02d1befc9e80e40 https://github.com/galaxyproject/galaxy/commit/114ef7336944e2e256936cc1d02d… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-04-03 (Sun, 03 Apr 2016) Changed paths: M README.rst Log Message: ----------- Update README.rst Commit: 463de48d7fdbfebaf4cc7215b2c3c95ae0656818 https://github.com/galaxyproject/galaxy/commit/463de48d7fdbfebaf4cc7215b2c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-03 (Sun, 03 Apr 2016) Changed paths: M README.rst Log Message: ----------- Merge pull request #2071 from remimarenco/patch-4 Add the Roadmap of the project Compare: https://github.com/galaxyproject/galaxy/compare/e3cbc63def36...463de48d7fdb

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[galaxyproject/galaxy] b3881f: For non-shed tool data - read loc from sample if a...
by GitHub 02 Apr '16

02 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b3881f86c1fcbb98405d5a316baaf99f247ae741 https://github.com/galaxyproject/galaxy/commit/b3881f86c1fcbb98405d5a316baa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/data/__init__.py M scripts/common_startup.sh Log Message: ----------- For non-shed tool data - read loc from sample if available. Commit: e3cbc63def3607fb7a0a646000d2b12ed728a579 https://github.com/galaxyproject/galaxy/commit/e3cbc63def3607fb7a0a646000d2… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-02 (Sat, 02 Apr 2016) Changed paths: M lib/galaxy/tools/data/__init__.py M scripts/common_startup.sh Log Message: ----------- Merge pull request #2070 from jmchilton/tool_loc_sample For non-shed tool data - read loc from sample if available. Compare: https://github.com/galaxyproject/galaxy/compare/e02e97dc798d...e3cbc63def36

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[galaxyproject/galaxy] 4c216f: Adjust testing directories so no python root is ev...
by GitHub 02 Apr '16

02 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4c216f1077f4f44b459397f085c26a54c2da547b https://github.com/galaxyproject/galaxy/commit/4c216f1077f4f44b459397f085c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M run_tests.sh A test/shed_functional/__init__.py A test/shed_functional/base/__init__.py A test/shed_functional/base/common.py A test/shed_functional/base/test_db_util.py A test/shed_functional/base/twilltestcase.py A test/shed_functional/functional/__init__.py A test/shed_functional/functional/test_0000_basic_repository_features.py A test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py A test/shed_functional/functional/test_0020_basic_repository_dependencies.py A test/shed_functional/functional/test_0030_repository_dependency_revisions.py A test/shed_functional/functional/test_0040_repository_circular_dependencies.py A test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py A test/shed_functional/functional/test_0060_workflows.py A test/shed_functional/functional/test_0070_invalid_tool.py A test/shed_functional/functional/test_0080_advanced_circular_dependencies.py A test/shed_functional/functional/test_0090_tool_search.py A test/shed_functional/functional/test_0100_complex_repository_dependencies.py A test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py A test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_0130_datatype_converters.py A test/shed_functional/functional/test_0140_tool_help_images.py A test/shed_functional/functional/test_0150_prior_installation_required.py A test/shed_functional/functional/test_0160_circular_prior_installation_required.py A test/shed_functional/functional/test_0170_complex_prior_installation_required.py A 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test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py A test/shed_functional/functional/test_1090_repository_dependency_handling.py A test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py A test/shed_functional/functional/test_1110_install_tool_from_tool_search.py A test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py A test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_1150_datatype_converters.py A test/shed_functional/functional/test_1160_tool_help_images.py A test/shed_functional/functional/test_1170_prior_installation_required.py A test/shed_functional/functional/test_1180_circular_prior_installation_required.py A test/shed_functional/functional/test_1190_complex_prior_installation_required.py A 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test/shed_functional/test_data/package_matplotlib/tool_dependencies.xml A test/shed_functional/test_data/package_numpy/package_numpy_1_7.tar A test/shed_functional/test_data/proteomics_datatypes/proteomics_datatypes.tar A test/shed_functional/test_data/readme.txt A test/shed_functional/test_data/repository_capsules/0490_filtering.tar.gz A test/shed_functional/test_data/repository_capsules/0500_emboss_5.tar.gz A test/shed_functional/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz A test/shed_functional/test_data/repository_capsules/0520_filtering.tar.gz R test/tool_shed/__init__.py R test/tool_shed/base/__init__.py R test/tool_shed/base/common.py R test/tool_shed/base/test_db_util.py R test/tool_shed/base/twilltestcase.py R test/tool_shed/functional/__init__.py R test/tool_shed/functional/test_0000_basic_repository_features.py R test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py R 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test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/filtering/README R test/tool_shed/test_data/filtering/filtering_0000.txt R test/tool_shed/test_data/filtering/filtering_1.1.0.tar R test/tool_shed/test_data/filtering/filtering_2.2.0.tar R test/tool_shed/test_data/filtering/filtering_test_data.tar R test/tool_shed/test_data/filtering/readme.txt R test/tool_shed/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga R test/tool_shed/test_data/freebayes/freebayes.tar R test/tool_shed/test_data/freebayes/freebayes.xml R test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml R test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml R test/tool_shed/test_data/freebayes/sam_fa_indices.loc.sample R test/tool_shed/test_data/freebayes/tool_data_table_conf.xml.sample R test/tool_shed/test_data/freebayes/tool_dependencies.xml R test/tool_shed/test_data/htseq_count/htseq_count.tar R test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar R test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml R test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar R test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar R test/tool_shed/test_data/readme.txt R test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz R test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz R test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz R test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz A test/unit/shed_unit/__init__.py A test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_td_common_util.py A test/unit/shed_unit/test_tool_panel_manager.py R test/unit/tool_shed_unit_tests/__init__.py R test/unit/tool_shed_unit_tests/test_fabric_util.py R test/unit/tool_shed_unit_tests/test_td_common_util.py R test/unit/tool_shed_unit_tests/test_tool_panel_manager.py Log Message: ----------- Adjust testing directories so no python root is ever "tool_shed". We have a tool_shed directory in lib, so if we enter a test case from some path and test/tool_shed happens to be a valid python top-level module - it blocks out lib/tool_shed and Galaxy doesn't work properly in the test. A similar problem was encountered with unit tests and fixed with https://github.com/galaxyproject/galaxy/commit/df442a06382f23bdf0401bdd632b… - but I have decided that directory name was a bit log and so this commit unifies the approach to unit and functional test names for tool shed tests. Commit: 27f99cdf4014dbf1d70d6cb2a98a957fe38d7a42 https://github.com/galaxyproject/galaxy/commit/27f99cdf4014dbf1d70d6cb2a98a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M test/base/driver_util.py Log Message: ----------- Fix test data path. Commit: c04d200dc77ecc67d85ae1a41f709cfcf84cfaae https://github.com/galaxyproject/galaxy/commit/c04d200dc77ecc67d85ae1a41f70… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M test/base/driver_util.py Log Message: ----------- Merge pull request #46 from davebx/shed_tests Fix test data path. Commit: e02e97dc798dcb3c153ae46ece382ddd44917b8a https://github.com/galaxyproject/galaxy/commit/e02e97dc798dcb3c153ae46ece38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M run_tests.sh M test/base/driver_util.py A test/shed_functional/__init__.py A test/shed_functional/base/__init__.py A test/shed_functional/base/common.py A test/shed_functional/base/test_db_util.py A test/shed_functional/base/twilltestcase.py A test/shed_functional/functional/__init__.py A test/shed_functional/functional/test_0000_basic_repository_features.py A test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py A test/shed_functional/functional/test_0020_basic_repository_dependencies.py A test/shed_functional/functional/test_0030_repository_dependency_revisions.py A test/shed_functional/functional/test_0040_repository_circular_dependencies.py A test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py A test/shed_functional/functional/test_0060_workflows.py A test/shed_functional/functional/test_0070_invalid_tool.py A test/shed_functional/functional/test_0080_advanced_circular_dependencies.py A test/shed_functional/functional/test_0090_tool_search.py A test/shed_functional/functional/test_0100_complex_repository_dependencies.py A test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py A test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_0130_datatype_converters.py A test/shed_functional/functional/test_0140_tool_help_images.py A test/shed_functional/functional/test_0150_prior_installation_required.py A test/shed_functional/functional/test_0160_circular_prior_installation_required.py A test/shed_functional/functional/test_0170_complex_prior_installation_required.py A test/shed_functional/functional/test_0300_reset_all_metadata.py A test/shed_functional/functional/test_0310_hg_api_features.py A test/shed_functional/functional/test_0400_repository_component_reviews.py A test/shed_functional/functional/test_0410_repository_component_review_access_control.py A test/shed_functional/functional/test_0420_citable_urls_for_repositories.py A test/shed_functional/functional/test_0430_browse_utilities.py A test/shed_functional/functional/test_0440_deleting_dependency_definitions.py A test/shed_functional/functional/test_0450_skip_tool_tests.py A test/shed_functional/functional/test_0460_upload_to_repository.py A test/shed_functional/functional/test_0470_tool_dependency_repository_type.py A test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py A test/shed_functional/functional/test_0490_export_import_repositories.py A test/shed_functional/functional/test_0500_export_repository_simple_dependency.py A test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py A 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test/tool_shed/test_data/freebayes/tool_data_table_conf.xml.sample R test/tool_shed/test_data/freebayes/tool_dependencies.xml R test/tool_shed/test_data/htseq_count/htseq_count.tar R test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar R test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml R test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar R test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar R test/tool_shed/test_data/readme.txt R test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz R test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz R test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz R test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz A test/unit/shed_unit/__init__.py A test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_td_common_util.py A test/unit/shed_unit/test_tool_panel_manager.py R test/unit/tool_shed_unit_tests/__init__.py R test/unit/tool_shed_unit_tests/test_fabric_util.py R test/unit/tool_shed_unit_tests/test_td_common_util.py R test/unit/tool_shed_unit_tests/test_tool_panel_manager.py Log Message: ----------- Merge pull request #2067 from jmchilton/shed_tests Adjust testing directories so no python root is ever "tool_shed". Compare: https://github.com/galaxyproject/galaxy/compare/1c201a863067...e02e97dc798d

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[galaxyproject/galaxy] d62982: Docstring fixes for lib/galaxy/jobs/runners/pulsar...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d629822912d861db60de7e97a8c264442c37c495 https://github.com/galaxyproject/galaxy/commit/d629822912d861db60de7e97a8c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Docstring fixes for lib/galaxy/jobs/runners/pulsar.py. Commit: 32b945f06321538f8aed36d4d542f0395f4cd192 https://github.com/galaxyproject/galaxy/commit/32b945f06321538f8aed36d4d542… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix pulsar import order. Commit: cc17d5304cc9ca9910162f5dd83640d31175bbad https://github.com/galaxyproject/galaxy/commit/cc17d5304cc9ca9910162f5dd836… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Implement a Pulsar embedded job runner. Closes #1378. Commit: 1c201a8630672524ad217959af9a1bdd3a67d16f https://github.com/galaxyproject/galaxy/commit/1c201a8630672524ad217959af9a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #2057 from jmchilton/pulsar_overhaul Implement an Embedded Pulsar Job Runner Compare: https://github.com/galaxyproject/galaxy/compare/991d7282c7b0...1c201a863067

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[galaxyproject/galaxy] 51f63a: Replace embedded Pulsar code with dependency.
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51f63a7d3e545db1e7c89621418523356fb1bdee https://github.com/galaxyproject/galaxy/commit/51f63a7d3e545db1e7c896214185… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M doc/source/lib/modules.rst R doc/source/lib/pulsar.client.rst R doc/source/lib/pulsar.client.staging.rst R doc/source/lib/pulsar.client.transport.rst R doc/source/lib/pulsar.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt R lib/pulsar/__init__.py R lib/pulsar/client/__init__.py R lib/pulsar/client/action_mapper.py R lib/pulsar/client/amqp_exchange.py R lib/pulsar/client/amqp_exchange_factory.py R lib/pulsar/client/client.py R lib/pulsar/client/config_util.py R lib/pulsar/client/decorators.py R lib/pulsar/client/destination.py R lib/pulsar/client/interface.py R lib/pulsar/client/job_directory.py R lib/pulsar/client/manager.py R lib/pulsar/client/object_client.py R lib/pulsar/client/path_mapper.py R lib/pulsar/client/setup_handler.py R lib/pulsar/client/staging/__init__.py R lib/pulsar/client/staging/down.py R lib/pulsar/client/staging/up.py R lib/pulsar/client/transport/__init__.py R lib/pulsar/client/transport/curl.py R lib/pulsar/client/transport/poster.py R lib/pulsar/client/transport/requests.py R lib/pulsar/client/transport/ssh.py R lib/pulsar/client/transport/standard.py R lib/pulsar/client/util.py Log Message: ----------- Replace embedded Pulsar code with dependency. Pulsar's setup.py has been parameterized to allow it build a special wheel that doesn't depend on galaxy-lib (https://github.com/galaxyproject/pulsar/commit/ce9d4f9e80936407fe4f793afa66…) and instead expects it to come from the environment. This special dependency has been published to PyPI here (https://pypi.python.org/pypi/pulsar-galaxy-lib) and added to StarForge here (https://github.com/galaxyproject/starforge/pull/79) These are now available on wheels.galaxyproject.org. In addition to removing the source dirctories - I have removed doc and CI references to these directories. Commit: 07eb322e8c06e91095fe418c0d71bf725b682db5 https://github.com/galaxyproject/galaxy/commit/07eb322e8c06e91095fe418c0d71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix Pulsar effective working directory for #1688. Commit: 991d7282c7b045edc57710f2acddde9f83816e89 https://github.com/galaxyproject/galaxy/commit/991d7282c7b045edc57710f2acdd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M doc/source/lib/modules.rst R doc/source/lib/pulsar.client.rst R doc/source/lib/pulsar.client.staging.rst R doc/source/lib/pulsar.client.transport.rst R doc/source/lib/pulsar.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py R lib/pulsar/__init__.py R lib/pulsar/client/__init__.py R lib/pulsar/client/action_mapper.py R lib/pulsar/client/amqp_exchange.py R lib/pulsar/client/amqp_exchange_factory.py R lib/pulsar/client/client.py R lib/pulsar/client/config_util.py R lib/pulsar/client/decorators.py R lib/pulsar/client/destination.py R lib/pulsar/client/interface.py R lib/pulsar/client/job_directory.py R lib/pulsar/client/manager.py R lib/pulsar/client/object_client.py R lib/pulsar/client/path_mapper.py R lib/pulsar/client/setup_handler.py R lib/pulsar/client/staging/__init__.py R lib/pulsar/client/staging/down.py R lib/pulsar/client/staging/up.py R lib/pulsar/client/transport/__init__.py R lib/pulsar/client/transport/curl.py R lib/pulsar/client/transport/poster.py R lib/pulsar/client/transport/requests.py R lib/pulsar/client/transport/ssh.py R lib/pulsar/client/transport/standard.py R lib/pulsar/client/util.py Log Message: ----------- Merge pull request #2052 from jmchilton/pulsar-deps Pulsar-As-A-Dependency Compare: https://github.com/galaxyproject/galaxy/compare/a03e64268a9e...991d7282c7b0

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[galaxyproject/usegalaxy-playbook] ea5155: Update common_roles (didn't I already do this?)
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ea5155cf8f2d043970af4324dafb7c0c5fd37c00 https://github.com/galaxyproject/usegalaxy-playbook/commit/ea5155cf8f2d0439… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M common_roles Log Message: ----------- Update common_roles (didn't I already do this?) Commit: 19e5407e35304b2cd5162dd587612e3eff923f7a https://github.com/galaxyproject/usegalaxy-playbook/commit/19e5407e35304b2c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: R galaxy.yml M galaxy_infrastructure.yml A galaxy_main.yml M galaxy_static.yml A galaxy_test.yml M production/group_vars/galaxyservers.yml M roles/usegalaxy_privileged/tasks/main.yml M roles/usegalaxy_static/tasks/main.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/common/config/reports.ini.j2 M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/supervisor/galaxy.j2 M templates/supervisor/galaxy_datamanager.j2 M templates/supervisor/galaxy_impersonate.j2 M templates/supervisor/galaxy_installer.j2 M templates/supervisor/galaxy_reports.j2 Log Message: ----------- Move Test to CVMFS Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/0f19d175ed68...…

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[galaxyproject/usegalaxy-playbook] 0f19d1: Mutable configs on Test
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0f19d175ed688ad92f64f5aaf81045891bf2c8d9 https://github.com/galaxyproject/usegalaxy-playbook/commit/0f19d175ed688ad9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs on Test

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[galaxyproject/infrastructure-playbook] 3cf641: Additional CVMFS improvements
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3cf64197a761322e9cfda55d6dbc386c712c6219 https://github.com/galaxyproject/infrastructure-playbook/commit/3cf64197a76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M galaxyenv/inventory M galaxyenv/playbook.yml M roles/cvmfs/tasks/server.yml M roles/cvmfs/vars/main.yml M taccenv/group_vars/galaxyservers.yml M taccenv/inventory M taccenv/playbook.yml Log Message: ----------- Additional CVMFS improvements

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[galaxyproject/galaxy] 71f473: Disable install button if changeset is installed.
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71f473b16593c317d2387c647860b1442eb9ab5a https://github.com/galaxyproject/galaxy/commit/71f473b16593c317d2387c647860… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Disable install button if changeset is installed. Commit: 0651872f6473ec3efc30c924b872c2d4d8796b2c https://github.com/galaxyproject/galaxy/commit/0651872f6473ec3efc30c924b872… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Remove debug logging. Commit: a03e64268a9ef41fc738fb0027203fc9eda13b51 https://github.com/galaxyproject/galaxy/commit/a03e64268a9ef41fc738fb002720… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Merge pull request #2061 from davebx/api_install_performance Disable install button if changeset is installed. Compare: https://github.com/galaxyproject/galaxy/compare/26569c3ec4b6...a03e64268a9e

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[galaxyproject/infrastructure-playbook] b03e49: Additional CVMFS improvements (including configura...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b03e493eac7e5f9051cd9ef04c8cd6c285233b7f https://github.com/galaxyproject/infrastructure-playbook/commit/b03e493eac7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M roles/cvmfs/handlers/main.yml M roles/cvmfs/tasks/client.yml A roles/cvmfs/tasks/localproxy.yml M roles/cvmfs/tasks/main.yml A roles/cvmfs/tasks/server.yml A roles/cvmfs/templates/squid.conf.j2 M roles/cvmfs/vars/main.yml M taccenv/inventory M taccenv/playbook.yml Log Message: ----------- Additional CVMFS improvements (including configuration for stratum1)

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[galaxyproject/galaxy] 4b7e86: Clean up docstrings in lib/galaxy/tools/toolbox/pa...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b7e86fa4323426e954270f2eb6d83b13d6c2752 https://github.com/galaxyproject/galaxy/commit/4b7e86fa4323426e954270f2eb6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/parser.py Log Message: ----------- Clean up docstrings in lib/galaxy/tools/toolbox/parser.py. Commit: cb5e786aa906e0bfedb3a4bd85716e46c77a4e13 https://github.com/galaxyproject/galaxy/commit/cb5e786aa906e0bfedb3a4bd8571… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/parser.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/upload_tool_conf.xml Log Message: ----------- Allow tool confs with a tool_path to not be interpreted as shed confs. Commit: 34e3b7f1c2e3797dcb7afac49125b9f33accad8c https://github.com/galaxyproject/galaxy/commit/34e3b7f1c2e3797dcb7afac49125… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/parser.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/upload_tool_conf.xml Log Message: ----------- Rename shed_conf attribute to is_shed_conf. Per discussion with @nsoranzo. Commit: 26569c3ec4b64a31f4827168cb042572ede28de0 https://github.com/galaxyproject/galaxy/commit/26569c3ec4b64a31f4827168cb04… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/parser.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/upload_tool_conf.xml Log Message: ----------- Merge pull request #2066 from jmchilton/static_tool_conf Allow tool confs with a tool_path to not be interpreted as shed confs. Compare: https://github.com/galaxyproject/galaxy/compare/18596a2bb47d...26569c3ec4b6

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[galaxyproject/infrastructure-playbook] b17443: Finish splitting the CVMFS tasks into a client inc...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b17443d5333b931871ac619a1ed69c4848017566 https://github.com/galaxyproject/infrastructure-playbook/commit/b17443d5333… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M roles/cvmfs/tasks/client.yml M roles/cvmfs/tasks/main.yml M taccenv/inventory Log Message: ----------- Finish splitting the CVMFS tasks into a client include as I'd started and then forgot

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[galaxyproject/galaxy] 7d3787: Replace common_util.url_join with util.build_url.
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7d378792cc697ded34a40c2ed6783cc27d534e81 https://github.com/galaxyproject/galaxy/commit/7d378792cc697ded34a40c2ed678… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Replace common_util.url_join with util.build_url. Commit: 494384171f260a924517844f4ff30db40a7dddbc https://github.com/galaxyproject/galaxy/commit/494384171f260a924517844f4ff3… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Do the same for tool_shed_get. Commit: d885367955a0aa1a6a389ae7d67a6829002f8254 https://github.com/galaxyproject/galaxy/commit/d885367955a0aa1a6a389ae7d67a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix indent broken with search/replace. Commit: 18596a2bb47d31b04e214c31b96a60b8a92fd70b https://github.com/galaxyproject/galaxy/commit/18596a2bb47d31b04e214c31b96a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Merge pull request #2055 from davebx/url_join Replace common_util.url_join with util.build_url. Compare: https://github.com/galaxyproject/galaxy/compare/1dc2524e0970...18596a2bb47d

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[galaxyproject/galaxy] 205850: Use a stricter regexp for microseconds.
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 205850586e87af4fb3a9d7779eb1f2852ccf45c3 https://github.com/galaxyproject/galaxy/commit/205850586e87af4fb3a9d7779eb1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/managers/base.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Use a stricter regexp for microseconds. Commit: 1dc2524e0970b9c2e8b55045c19dd8f6586892a6 https://github.com/galaxyproject/galaxy/commit/1dc2524e0970b9c2e8b55045c19d… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/managers/base.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Merge pull request #2065 from nsoranzo/stricter_microseconds_re Use a stricter regexp for microseconds. Compare: https://github.com/galaxyproject/galaxy/compare/569b87dc002f...1dc2524e0970

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[galaxyproject/galaxy] 78c839: Add a dictionary to params_dict that maps datasets...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78c839cccdd09f9eb79467e77f1ad247783efa58 https://github.com/galaxyproject/galaxy/commit/78c839cccdd09f9eb79467e77f1a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-29 (Tue, 29 Mar 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Add a dictionary to params_dict that maps datasets to identifier keys, so that element_identifiers for datasets in repeats are passed correctly to the tool wrapper. Commit: 569b87dc002f5fe09cb34496a71deda1e6678d1b https://github.com/galaxyproject/galaxy/commit/569b87dc002f5fe09cb34496a71d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Merge pull request #2029 from mvdbeek/element_identifier_in_repeat Better element_identifier handling in repeat sections Compare: https://github.com/galaxyproject/galaxy/compare/ff48ad9b54fc...569b87dc002f

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[galaxyproject/infrastructure-playbook] 7812fd: Install CVMFS on nodes
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 7812fd520eee03ffae2ef0bb9b1e7f4a31b0d06e https://github.com/galaxyproject/infrastructure-playbook/commit/7812fd520ee… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: A .gitignore A roles/cvmfs/handlers/main.yml A roles/cvmfs/tasks/client.yml A roles/cvmfs/tasks/main.yml A roles/cvmfs/vars/main.yml M taccenv/inventory M taccenv/playbook.yml Log Message: ----------- Install CVMFS on nodes

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[galaxyproject/galaxy] ec83fb: Change user disk usage pgcalc function up a bit to...
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ec83fb64942647218f6cd56929b13405527af686 https://github.com/galaxyproject/galaxy/commit/ec83fb64942647218f6cd56929b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/model/util.py Log Message: ----------- Change user disk usage pgcalc function up a bit to make a slightly safer dry-run, since it doesn't appear that in some environments (not sure why) the rollback isn't actually happening. Commit: ff48ad9b54fca66d4abb21f83e56ee57a2eb6f1c https://github.com/galaxyproject/galaxy/commit/ff48ad9b54fca66d4abb21f83e56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/model/util.py Log Message: ----------- Merge pull request #2063 from dannon/dryrun Change user disk usage pgcalc function up a bit to make a slightly sa… Compare: https://github.com/galaxyproject/galaxy/compare/1c2b2a5c71d1...ff48ad9b54fc

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[galaxyproject/galaxy] 46b4e8: Managers: remove UTC zone when parsing dates
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 46b4e8d94cf989f429039a63e38cc739c14e6a76 https://github.com/galaxyproject/galaxy/commit/46b4e8d94cf989f429039a63e38c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/managers/base.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Managers: remove UTC zone when parsing dates This change creates a more complete regex for parsing dates used in filters. MySQL in particular errored when the UTC zone character 'Z' was appended to a valid iso 8601 date (because it's MySQL). The FilterParser.parse_date method now: - strips both the separator 'T' and any ending 'Z' - one space are allowed as the date/time separator - milliseconds are permitted - both time and time with milliseconds are optional - any added timezone (besides the UTC Z) will cause an error - feedback was made more clear - tests were added (and should make the above more clear) Commit: 1c2b2a5c71d105f0f2d9ac64d7a502f81b4297ec https://github.com/galaxyproject/galaxy/commit/1c2b2a5c71d105f0f2d9ac64d7a5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/managers/base.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Merge pull request #2062 from carlfeberhard/fix.date_filter_parsing Managers: remove UTC zone when parsing dates Compare: https://github.com/galaxyproject/galaxy/compare/5fd5343d07f2...1c2b2a5c71d1

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[galaxyproject/usegalaxy-playbook] d11e5f: update MTS
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d11e5f83f7145c997e7355db0cbfda02b2e24bd4 https://github.com/galaxyproject/usegalaxy-playbook/commit/d11e5f83f7145c99… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS

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[galaxyproject/usegalaxy-playbook] 8d33c8: update TTS
by GitHub 31 Mar '16

31 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8d33c888362f023c8f48c744b8fbc11856cccd17 https://github.com/galaxyproject/usegalaxy-playbook/commit/8d33c888362f023c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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