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
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
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
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
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