commit/galaxy-central: 25 new changesets
25 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aae74ee09e46/ Changeset: aae74ee09e46 Branch: stable User: jmchilton Date: 2015-01-15 21:01:03+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r 19e56e66b0b344c6e2afa4541f6988e4fdb9af29 -r aae74ee09e4667e270750711327c8167e1dfae05 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2575,7 +2575,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.template_macro_params.keys() if not self.options or self.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/f15cc980e3ca/ Changeset: f15cc980e3ca Branch: stable User: jmchilton Date: 2015-01-15 21:01:05+00:00 Summary: Update tag latest_2013.06.03 for changeset aae74ee09e46 Affected #: 1 file diff -r f7235d0ad14fd90b8977e88f68715a7dedc5bab9 -r f15cc980e3ca5bf1f15fe9a11d420e3022c787de .hgtags --- a/.hgtags +++ b/.hgtags @@ -13,7 +13,7 @@ 9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 -19e56e66b0b344c6e2afa4541f6988e4fdb9af29 latest_2013.06.03 +aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 cee903b8b3eee9145627ee89742555dac581791e latest_2013.08.12 7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 https://bitbucket.org/galaxy/galaxy-central/commits/8b183b869448/ Changeset: 8b183b869448 Branch: stable User: jmchilton Date: 2015-01-15 21:01:11+00:00 Summary: Merge head created for backport bug fix on latest_2013.06.03 Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/db967a25c5db/ Changeset: db967a25c5db Branch: stable User: jmchilton Date: 2015-01-15 21:01:13+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r cee903b8b3eee9145627ee89742555dac581791e -r db967a25c5db969ee4b3e138fe2be4d979665bdf lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2585,7 +2585,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.template_macro_params.keys() if not self.options or self.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/f405d17de085/ Changeset: f405d17de085 Branch: stable User: jmchilton Date: 2015-01-15 21:01:15+00:00 Summary: Update tag latest_2013.08.12 for changeset db967a25c5db Affected #: 1 file diff -r 8b183b869448efd44c5e4dd452421392bcfdd295 -r f405d17de085663dc0392dadfa51d20956c39bfa .hgtags --- a/.hgtags +++ b/.hgtags @@ -14,7 +14,7 @@ b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 -cee903b8b3eee9145627ee89742555dac581791e latest_2013.08.12 +db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 https://bitbucket.org/galaxy/galaxy-central/commits/cb12cb063a9b/ Changeset: cb12cb063a9b Branch: stable User: jmchilton Date: 2015-01-15 21:01:17+00:00 Summary: Merge head created for backport bug fix on latest_2013.08.12 Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/52a18b44474f/ Changeset: 52a18b44474f Branch: stable User: jmchilton Date: 2015-01-15 21:01:18+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r 7d5aa19a166cba9039e15f338a1e3fc924c43d3a -r 52a18b44474f017fce92850fb3892a4f76a7374a lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2592,7 +2592,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.template_macro_params.keys() if not self.options or self.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/9ae14630ca77/ Changeset: 9ae14630ca77 Branch: stable User: jmchilton Date: 2015-01-15 21:01:20+00:00 Summary: Update tag latest_2013.11.04 for changeset 52a18b44474f Affected #: 1 file diff -r cb12cb063a9b326fc435189264c4fb6fa66cffb6 -r 9ae14630ca7716e6a7eef34865c65356a9abb4d5 .hgtags --- a/.hgtags +++ b/.hgtags @@ -15,7 +15,7 @@ dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 -7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 +52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 https://bitbucket.org/galaxy/galaxy-central/commits/4dc0e41df66e/ Changeset: 4dc0e41df66e Branch: stable User: jmchilton Date: 2015-01-15 21:01:22+00:00 Summary: Merge head created for backport bug fix on latest_2013.11.04 Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/746db2bf4da0/ Changeset: 746db2bf4da0 Branch: stable User: jmchilton Date: 2015-01-15 21:01:23+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r 0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 -r 746db2bf4da081a7491b5a4602aeadd2611b3b1d lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -323,7 +323,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys() if not self.tool or not self.tool.options or self.tool.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/30fe131b672e/ Changeset: 30fe131b672e Branch: stable User: jmchilton Date: 2015-01-15 21:01:25+00:00 Summary: Update tag latest_2014.02.10 for changeset 746db2bf4da0 Affected #: 1 file diff -r 4dc0e41df66ecbb2b5c7e9e8fe39295d5eb7ad09 -r 30fe131b672e6ea459459f8cabab81118e551e3b .hgtags --- a/.hgtags +++ b/.hgtags @@ -16,7 +16,7 @@ aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 -0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 +746db2bf4da081a7491b5a4602aeadd2611b3b1d latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 https://bitbucket.org/galaxy/galaxy-central/commits/d9cdccfc0225/ Changeset: d9cdccfc0225 Branch: stable User: jmchilton Date: 2015-01-15 21:01:25+00:00 Summary: Merge head created for backport bug fix on latest_2014.02.10 Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/b2c0570f52e1/ Changeset: b2c0570f52e1 Branch: stable User: jmchilton Date: 2015-01-15 21:01:27+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r 8f9dcac033694e4cabcf5daae5cca1cfefbe967f -r b2c0570f52e18d8661ca1d80c42867e4b036f22b lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -323,7 +323,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys() if not self.tool or not self.tool.options or self.tool.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/05c5df09ecba/ Changeset: 05c5df09ecba Branch: stable User: jmchilton Date: 2015-01-15 21:01:28+00:00 Summary: Update tag latest_2014.04.14 for changeset b2c0570f52e1 Affected #: 1 file diff -r d9cdccfc0225023736550f66b2da46f2abc47767 -r 05c5df09ecbac4adb5b32c24a55f9f056a72fc7c .hgtags --- a/.hgtags +++ b/.hgtags @@ -9,7 +9,7 @@ 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 9bce3f426863f8ba88062f67c7efc1836e82ee7c latest_2014.06.02 -8f9dcac033694e4cabcf5daae5cca1cfefbe967f latest_2014.04.14 +b2c0570f52e18d8661ca1d80c42867e4b036f22b latest_2014.04.14 9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 https://bitbucket.org/galaxy/galaxy-central/commits/ae4d7fb3f647/ Changeset: ae4d7fb3f647 Branch: stable User: jmchilton Date: 2015-01-15 21:01:29+00:00 Summary: Merge head created for backport bug fix on latest_2014.04.14 Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/c52dc4c72b77/ Changeset: c52dc4c72b77 Branch: stable User: jmchilton Date: 2015-01-15 21:01:30+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r 9bce3f426863f8ba88062f67c7efc1836e82ee7c -r c52dc4c72b77e4b0849a596b6d05e4341236642a lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -348,7 +348,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys() if not self.tool or not self.tool.options or self.tool.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/a430a10e3db9/ Changeset: a430a10e3db9 Branch: stable User: jmchilton Date: 2015-01-15 21:01:31+00:00 Summary: Update tag latest_2014.06.02 for changeset c52dc4c72b77 Affected #: 1 file diff -r ae4d7fb3f6478e32b46eddbfc3b5f7f10c6ee246 -r a430a10e3db976c0981a782d54593923f00a20d7 .hgtags --- a/.hgtags +++ b/.hgtags @@ -8,7 +8,7 @@ 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -9bce3f426863f8ba88062f67c7efc1836e82ee7c latest_2014.06.02 +c52dc4c72b77e4b0849a596b6d05e4341236642a latest_2014.06.02 b2c0570f52e18d8661ca1d80c42867e4b036f22b latest_2014.04.14 9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 https://bitbucket.org/galaxy/galaxy-central/commits/4b8e3b14abc5/ Changeset: 4b8e3b14abc5 Branch: stable User: jmchilton Date: 2015-01-15 21:01:32+00:00 Summary: Merge head created for backport bug fix on latest_2014.06.02 Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/6d6d7f8b3217/ Changeset: 6d6d7f8b3217 Branch: stable User: jmchilton Date: 2015-01-15 21:01:33+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r f3fc4602e22b39468d780b955a1a05caf867a7e9 -r 6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -348,7 +348,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys() if not self.tool or not self.tool.options or self.tool.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/93eeb569386c/ Changeset: 93eeb569386c Branch: stable User: jmchilton Date: 2015-01-15 21:01:34+00:00 Summary: Update tag latest_2014.08.11 for changeset 6d6d7f8b3217 Affected #: 1 file diff -r 4b8e3b14abc5e18d14985f8736ee652796e4f782 -r 93eeb569386c4af71a211e58621d180a5f3e963e .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,7 +18,7 @@ 52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 746db2bf4da081a7491b5a4602aeadd2611b3b1d latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 +6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 https://bitbucket.org/galaxy/galaxy-central/commits/464f7083f431/ Changeset: 464f7083f431 Branch: stable User: jmchilton Date: 2015-01-15 21:01:34+00:00 Summary: Merge head created for backport bug fix on latest_2014.08.11 Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/782fa60fc654/ Changeset: 782fa60fc654 Branch: stable User: jmchilton Date: 2015-01-15 21:01:35+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r 9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 -r 782fa60fc65488aea0c618d723e9a63d42caf865 lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -348,7 +348,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys() if not self.tool or not self.tool.options or self.tool.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/cfdcc366831c/ Changeset: cfdcc366831c Branch: stable User: jmchilton Date: 2015-01-15 21:01:36+00:00 Summary: Update tag latest_2014.10.06 for changeset 782fa60fc654 Affected #: 1 file diff -r 464f7083f43112e1676af0271329eb4fe820bb25 -r cfdcc366831c310ef3eb413d9611dfac1b27b4d0 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,6 +20,6 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 +782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 3b559c4b9399236ae2a76ea1f061fcd660e76ed5 latest_2015.01.13 https://bitbucket.org/galaxy/galaxy-central/commits/cd6c14de33c5/ Changeset: cd6c14de33c5 Branch: stable User: jmchilton Date: 2015-01-15 21:01:37+00:00 Summary: Merge head created for backport bug fix on latest_2014.10.06 Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/fd75aaee91cf/ Changeset: fd75aaee91cf Branch: stable User: jmchilton Date: 2015-02-02 14:10:43+00:00 Summary: Merged in jmchilton/galaxy-central-backport-2/stable (pull request #638) [STABLE] Backport pull request #636 to all relevant latest_* releases Affected #: 3 files diff -r a7ae7afffa8fa7551ea760ca01e9c1808809391b -r fd75aaee91cf3e8a0916689dfea72e0c752c447c .hgtags --- a/.hgtags +++ b/.hgtags @@ -8,18 +8,18 @@ 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -9bce3f426863f8ba88062f67c7efc1836e82ee7c latest_2014.06.02 -8f9dcac033694e4cabcf5daae5cca1cfefbe967f latest_2014.04.14 +c52dc4c72b77e4b0849a596b6d05e4341236642a latest_2014.06.02 +b2c0570f52e18d8661ca1d80c42867e4b036f22b latest_2014.04.14 9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 -19e56e66b0b344c6e2afa4541f6988e4fdb9af29 latest_2013.06.03 -cee903b8b3eee9145627ee89742555dac581791e latest_2013.08.12 -7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 -0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 +aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 +db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 +52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 +746db2bf4da081a7491b5a4602aeadd2611b3b1d latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 +6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 +782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 c5e7535b4d229dbbe52d48ea35a27ab601205b7b latest_2015.01.13 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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