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

[galaxyproject/infrastructure-playbook] fead42: Add additional Jetstream @ IU instances
by GitHub 13 Sep '16

13 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fead42a8d278bdc92720c0155f61727eb6a946ac https://github.com/galaxyproject/infrastructure-playbook/commit/fead42a8d27… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory Log Message: ----------- Add additional Jetstream @ IU instances

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[galaxyproject/infrastructure-playbook] 27cf8f: Install supervisor on Jetstream controllers
by GitHub 13 Sep '16

13 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 27cf8f31bc20b7d1258ddc65572b6ea6c9f198c5 https://github.com/galaxyproject/infrastructure-playbook/commit/27cf8f31bc2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M jetstreamtaccenv/playbook.yml Log Message: ----------- Install supervisor on Jetstream controllers Commit: 6aa7b6fd0ff86dc948366ce88a9809b3ffcf99ad https://github.com/galaxyproject/infrastructure-playbook/commit/6aa7b6fd0ff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- Add 4 additional Jetstream instances @ TACC Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/6db7f4ea50…

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[galaxyproject/infrastructure-playbook] 6db7f4: Add cvmfs0-psu0 and schedule key resignings.
by GitHub 13 Sep '16

13 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6db7f4ea508b7af0b965451f04d9d092f63b4c44 https://github.com/galaxyproject/infrastructure-playbook/commit/6db7f4ea508… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: A galaxyenv/host_vars/cvmfs0-psu0.galaxyproject.org.yml M galaxyenv/inventory A galaxyenv/secret_host_vars/cvmfs0-psu0.galaxyproject.org.yml M roles/cvmfs/tasks/stratum0.yml Log Message: ----------- Add cvmfs0-psu0 and schedule key resignings.

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[galaxyproject/usegalaxy-playbook] 4a9b8a: Added RNA-Seq Portal public server to slides.\
by GitHub 13 Sep '16

13 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4a9b8a11cf2b4af7d04349d9e67ae6d4351d9c50 https://github.com/galaxyproject/usegalaxy-playbook/commit/4a9b8a11cf2b4af7… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: A files/galaxy/common/static/welcome_img/RNA-Seq-Portal.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Added RNA-Seq Portal public server to slides.\

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[galaxyproject/galaxy] 85c1a8: Log the resolved dependency type
by GitHub 13 Sep '16

13 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85c1a8f2e2c7e4a93a9df7c8c2a0b8aff952774d https://github.com/galaxyproject/galaxy/commit/85c1a8f2e2c7e4a93a9df7c8c2a0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Log the resolved dependency type Commit: 167286ad93bea7853eb6d95b6112bd04ff4fa20c https://github.com/galaxyproject/galaxy/commit/167286ad93bea7853eb6d95b6112… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M templates/show_params.mako M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Track used dependencies in job metadata and expose with job info. Commit: 04db0a2348e671ff0b80612d001bd62f69c2e32b https://github.com/galaxyproject/galaxy/commit/04db0a2348e671ff0b80612d001b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py Log Message: ----------- Correct comment (thanks @martenson) Commit: 63f758f9976b5e5810cae8648fa926d2d4855e5e https://github.com/galaxyproject/galaxy/commit/63f758f9976b5e5810cae8648fa9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M templates/show_params.mako M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Merge pull request #2917 from mvdbeek/log_dependency_type Log the resolved dependency type Compare: https://github.com/galaxyproject/galaxy/compare/b102e2012342...63f758f9976b

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[galaxyproject/galaxy] 4df654: Add `database/dependencies` gitignore
by GitHub 12 Sep '16

12 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4df654d7da363afad10c7dc78a35a3f6c3a3d1bf https://github.com/galaxyproject/galaxy/commit/4df654d7da363afad10c7dc78a35… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M .gitignore Log Message: ----------- Add `database/dependencies` gitignore Since the galaxy.ini.sample file is shipped with `#tool_dependency_dir = database/dependencies` as default, and we don't want anyone commiting dependencies. Commit: b102e2012342078a3b8bcab8348b2aaa485aa2a6 https://github.com/galaxyproject/galaxy/commit/b102e2012342078a3b8bcab8348b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M .gitignore Log Message: ----------- Merge pull request #2904 from nturaga/update_gitignore Add `database/dependencies` gitignore Compare: https://github.com/galaxyproject/galaxy/compare/7cc1579c5908...b102e2012342

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[galaxyproject/galaxy] c158d0: Refactor shed tool lineage registration
by GitHub 12 Sep '16

12 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c158d0b0611ed233b4b3d39fd23822e38d69d4db https://github.com/galaxyproject/galaxy/commit/c158d0b0611ed233b4b3d39fd238… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py Log Message: ----------- Refactor shed tool lineage registration to avoid using tool.tool_shed_repository if possible, since this is a property of the tool instance, which results in a database query. These sequential queries slow down reloading a large number of tools. Commit: 7cc1579c5908186d02aa04f9e72495530d63fe75 https://github.com/galaxyproject/galaxy/commit/7cc1579c5908186d02aa04f9e724… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-12 (Mon, 12 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py Log Message: ----------- Merge pull request #2909 from mvdbeek/last_speed_fix Refactor shed tool lineage registration Compare: https://github.com/galaxyproject/galaxy/compare/48a841c0d9c8...7cc1579c5908

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[galaxyproject/galaxy] 9b414c: Minor fixes to shed tool lineage
by GitHub 09 Sep '16

09 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b414cd1fa2eb87187daff9677d5b0d552355009 https://github.com/galaxyproject/galaxy/commit/9b414cd1fa2eb87187daff9677d5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M test/unit/tools_support.py Log Message: ----------- Minor fixes to shed tool lineage get_installed_tool_version needs to look up the tool_version object using the tool_id, not the tool_version id. Make sure toolshed tools in cache have toolshed attribute. Commit: 48a841c0d9c80f03512314d31ac9f63358a186dc https://github.com/galaxyproject/galaxy/commit/48a841c0d9c80f03512314d31ac9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-09 (Fri, 09 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #2905 from mvdbeek/minor_lineage_bug Minor fixes to shed tool lineage Compare: https://github.com/galaxyproject/galaxy/compare/5c45da362ad2...48a841c0d9c8

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[galaxyproject/galaxy] d5ba73: Fix hang when installing data managers
by GitHub 08 Sep '16

08 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5ba73b0c84f6bfa297d4b75296e5614d25a07cf https://github.com/galaxyproject/galaxy/commit/d5ba73b0c84f6bfa297d4b75296e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py Log Message: ----------- Fix hang when installing data managers Commit: 82c1da4709a5ae5b52ee60b2b197f91d64c5d5d3 https://github.com/galaxyproject/galaxy/commit/82c1da4709a5ae5b52ee60b2b197… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Add data managers to new toolbox before replacing the old toolbox, to avoid 'Tool not found or not accessible.' while installing new tools Commit: a8f794290dc1e529dd9564a95a55f4b808b2e6d9 https://github.com/galaxyproject/galaxy/commit/a8f794290dc1e529dd9564a95a55… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Handle xml ParseError Occasionally the following Traceback can be seen in the log files: ``` Traceback (most recent call last): File "lib/galaxy/tools/toolbox/base.py", line 112, in _init_tools_from_configs self._init_tools_from_config( config_filename ) File "lib/galaxy/tools/toolbox/base.py", line 136, in _init_tools_from_config tool_conf_source = get_toolbox_parser(config_filename) File "lib/galaxy/tools/toolbox/parser.py", line 152, in get_toolbox_parser return XmlToolConfSource(config_filename) File "lib/galaxy/tools/toolbox/parser.py", line 40, in __init__ tree = parse_xml(config_filename) File "lib/galaxy/util/__init__.py", line 210, in parse_xml root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: unclosed token: line 2636, column 0 ``` We just try parsing again, which seems to solve the issue. This may be a problem with concurrently reading/writing to the file. Commit: 89bafff06170c02e5089800a5062e3de0421ad23 https://github.com/galaxyproject/galaxy/commit/89bafff06170c02e5089800a5062… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/tool_shed/galaxy_install/tools/data_manager.py Log Message: ----------- Whitespace fix Commit: c3886b373e8954c1f7bb193cf28357aebd8cd459 https://github.com/galaxyproject/galaxy/commit/c3886b373e8954c1f7bb193cf283… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/queue_worker.py Log Message: ----------- Specifically index new toolbox Commit: 6fd4c5a5be75a39e941ab4b4b4df95c9456ca1e9 https://github.com/galaxyproject/galaxy/commit/6fd4c5a5be75a39e941ab4b4b4df… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Keep track of toolbox reload time Commit: 230e7df4ae293e46e4f15bf2cf811f788a9f811d https://github.com/galaxyproject/galaxy/commit/230e7df4ae293e46e4f15bf2cf81… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py Log Message: ----------- Use cache to get the repository containing a tool when reloading toolbox. This should prevent lots of (slow) database requests when reloading the toolbox. Commit: c5406eb192a0e2355602e5e5d7eb1e218a632d07 https://github.com/galaxyproject/galaxy/commit/c5406eb192a0e2355602e5e5d7eb… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Improve logic handling of loading tools Commit: ab9be8c311a7943d778842522a706451e9996943 https://github.com/galaxyproject/galaxy/commit/ab9be8c311a7943d778842522a70… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fetch cached tools repository Commit: 894b77ba23fa66a8852b554aacf18cc123f5d7cd https://github.com/galaxyproject/galaxy/commit/894b77ba23fa66a8852b554aacf1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/lineages/factory.py Log Message: ----------- Simplify lineage registration Commit: acc5b4ceb6525a9cf53bf39c3d6c00abf9069990 https://github.com/galaxyproject/galaxy/commit/acc5b4ceb6525a9cf53bf39c3d6c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py Log Message: ----------- Load all versions in a single request Commit: 971227c59dd1d32b537c04c59a16e7572aa7acbd https://github.com/galaxyproject/galaxy/commit/971227c59dd1d32b537c04c59a16… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/util/profiling.py Log Message: ----------- Use tool version cache to boost tool panel loading Commit: 833af5e8c2121947e16bdfb99b2794b7a130d045 https://github.com/galaxyproject/galaxy/commit/833af5e8c2121947e16bdfb99b27… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/util/profiling.py Log Message: ----------- Restore peacemeal tool registration Commit: 8bed867fcfcf249838b6b24a1b5985af401b9b5a https://github.com/galaxyproject/galaxy/commit/8bed867fcfcf249838b6b24a1b59… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Reload tool_version_cache after new installs in the unit-testing code. Commit: 894ac295207430d5ec1b02a0be7ee76ce4dc2cc0 https://github.com/galaxyproject/galaxy/commit/894ac295207430d5ec1b02a0be7e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Reload tool_version_cache when adding new tool version relationships to the database. Commit: 09173cc6070bc914759f15854367d62ca6323c79 https://github.com/galaxyproject/galaxy/commit/09173cc6070bc914759f15854367… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/profiling.py M lib/tool_shed/tools/tool_version_manager.py Log Message: ----------- Rebase and linting fixes Commit: c08db31ab22aefa23a0e6472c4f115cff537668f https://github.com/galaxyproject/galaxy/commit/c08db31ab22aefa23a0e6472c4f1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/tools/toolbox/lineages/tool_shed.py R lib/galaxy/util/profiling.py Log Message: ----------- Document ToolVersionCache class Commit: 92d028cbae55d120326cfac61f2fd4fb5d425b35 https://github.com/galaxyproject/galaxy/commit/92d028cbae55d120326cfac61f2f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M test/unit/tools_support.py Log Message: ----------- Remove unnecessary self.install_model from unittest app Commit: 5c45da362ad27c788fe5f7e62fd5c779b7fa24bf https://github.com/galaxyproject/galaxy/commit/5c45da362ad27c788fe5f7e62fd5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/tools/tool_version_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #2901 from mvdbeek/fix_data_manager_hangs All-around improvements to toolbox loading/reloading Compare: https://github.com/galaxyproject/galaxy/compare/0c3b5272eb53...5c45da362ad2

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[galaxyproject/galaxy] d06e2a: XSD discovered tool problems.
by GitHub 08 Sep '16

08 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d06e2a672b0c81e5391e077288bf36001f72dbb5 https://github.com/galaxyproject/galaxy/commit/d06e2a672b0c81e5391e077288bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M test/functional/tools/column_multi_param.xml M test/functional/tools/column_param.xml M test/functional/tools/identifier_collection.xml M test/functional/tools/identifier_multiple.xml M test/functional/tools/identifier_single.xml M test/functional/tools/inputs_as_json.xml M test/functional/tools/multi_output.xml M test/functional/tools/multi_output_assign_primary.xml M test/functional/tools/multi_output_configured.xml M test/functional/tools/tool_directory.xml M test/functional/tools/validation_repeat.xml M tools/data_source/upload.xml Log Message: ----------- XSD discovered tool problems. Commit: 0c3b5272eb53256b892a313aa6fcc4d5d5b5daa0 https://github.com/galaxyproject/galaxy/commit/0c3b5272eb53256b892a313aa6fc… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-09-08 (Thu, 08 Sep 2016) Changed paths: M test/functional/tools/column_multi_param.xml M test/functional/tools/column_param.xml M test/functional/tools/identifier_collection.xml M test/functional/tools/identifier_multiple.xml M test/functional/tools/identifier_single.xml M test/functional/tools/inputs_as_json.xml M test/functional/tools/multi_output.xml M test/functional/tools/multi_output_assign_primary.xml M test/functional/tools/multi_output_configured.xml M test/functional/tools/tool_directory.xml M test/functional/tools/validation_repeat.xml M tools/data_source/upload.xml Log Message: ----------- Merge pull request #2903 from jmchilton/format_fixes XSD discovered tool problems. Compare: https://github.com/galaxyproject/galaxy/compare/d98dcd75db30...0c3b5272eb53

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