Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c49e7803fa1814abd04afb26b54965fb7af612ac https://github.com/galaxyproject/galaxy/commit/c49e7803fa1814abd04afb26b5496... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- fix biomart url Commit: 7bed69ba17b4ce633c621ee34a7544115eb95970 https://github.com/galaxyproject/galaxy/commit/7bed69ba17b4ce633c621ee34a754... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- Specify Ensembl biomart server in descriptions. Commit: 1e7edf0bd7a003e0abc63c4f0a17fdfac535ade3 https://github.com/galaxyproject/galaxy/commit/1e7edf0bd7a003e0abc63c4f0a17f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- no parens Commit: 81cf234576bc1f52f93a11b193f6cc9c26130c28 https://github.com/galaxyproject/galaxy/commit/81cf234576bc1f52f93a11b193f6c... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- Merge pull request #14 from dannon/fix_biomart Specify Ensembl biomart server in descriptions. Commit: cc4911019077c5c6e1b4ec293670020f34aed596 https://github.com/galaxyproject/galaxy/commit/cc4911019077c5c6e1b4ec2936700... Author: guerler <aysam.guerler@gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Enhance to_json such that it can be safely called multiple times Commit: f5060628d2de4802be610fd6caf5c878afdb4312 https://github.com/galaxyproject/galaxy/commit/f5060628d2de4802be610fd6caf5c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/util/sanitize_html.py Log Message: ----------- Fix pages encoding. Using str on previously unicodify'd extended set values does not work. ``` In [2]: str("Blah blah blah, this breaks the page: ಠ_ಠ") Out[2]: 'Blah blah blah, this breaks the page: \xe0\xb2\xa0_\xe0\xb2\xa0' In [3]: str(unicodify("Blah blah blah, this breaks the page: ಠ_ಠ")) --------------------------------------------------------------------------- UnicodeEncodeError Traceback (most recent call last) <ipython-input-3-4a83f5e5f5c8> in <module>() ----> 1 str(unicodify("Blah blah blah, this breaks the page: ಠ_ಠ")) UnicodeEncodeError: 'ascii' codec can't encode character u'\u0ca0' in position 38: ordinal not in range(128) ``` Commit: 659a900693b72886fd27731a2568ce71657c4401 https://github.com/galaxyproject/galaxy/commit/659a900693b72886fd27731a2568c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/util/sanitize_html.py Log Message: ----------- Simplify expression, trust upstream pieces. Commit: e13738868519d8c7c6f7dec8cfd598f7929b8828 https://github.com/galaxyproject/galaxy/commit/e13738868519d8c7c6f7dec8cfd59... Author: guerler <aysam.guerler@gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Apply parameter translation for data source tools Commit: 7c7d6edbfd94e5b3e187778b89ac1febb5690cb9 https://github.com/galaxyproject/galaxy/commit/7c7d6edbfd94e5b3e187778b89ac1... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/util/validation.py Log Message: ----------- Swap validate_and_sanitize_basestring to use unicodify Commit: a9280649b201dc8c1ce6e1601c5baaae211acbd7 https://github.com/galaxyproject/galaxy/commit/a9280649b201dc8c1ce6e1601c5ba... Author: John Chilton <jmchilton@gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Sync job_script module with Pulsar to fix doctest. Following test fails without this change and is fixed by it. ``` nosetests --with-doctest lib/galaxy/jobs/runners/util/job_script ``` I'm not sure why Travis doesn't pick this up - I should figure that out. Commit: 0cde386a2cfec1c18f68f1dfd939843328f8046f https://github.com/galaxyproject/galaxy/commit/0cde386a2cfec1c18f68f1dfd9398... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/util/validation.py Log Message: ----------- Remove more unnecessary unicode/text_type, since sanitize_html will always return unicode. Commit: eac0fb9b26c6c52ab695d58cef13c73d3d2566b4 https://github.com/galaxyproject/galaxy/commit/eac0fb9b26c6c52ab695d58cef13c... Author: John Chilton <jmchilton@gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #2201 from guerler/fix_parameters_000 [16.04] Translate data source tool parameters on parameter expansion Commit: 4ea53d99aaa20b15e1d09f7140dff14336360686 https://github.com/galaxyproject/galaxy/commit/4ea53d99aaa20b15e1d09f7140dff... Author: John Chilton <jmchilton@gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2196 from guerler/extend_to_json_000 [16.04] Extend to_json for dataset tool parameters Commit: e5290e1964fcfc49fb5f57a232e4bcc35c28a52a https://github.com/galaxyproject/galaxy/commit/e5290e1964fcfc49fb5f57a232e4b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M tools/data_source/biomart.xml Log Message: ----------- Merge pull request #2149 from martenson/fix-biomart [16.04] fix/replace biomart data source Commit: adbc66873a13dc3c6cbcbf86181f935d09fed490 https://github.com/galaxyproject/galaxy/commit/adbc66873a13dc3c6cbcbf86181f9... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Merge pull request #2203 from jmchilton/doctest_fix [16.04] Sync job_script module with Pulsar to fix doctest. Commit: 8749c82bef4789d810313a3fd853202a1748c63a https://github.com/galaxyproject/galaxy/commit/8749c82bef4789d810313a3fd8532... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py Log Message: ----------- Merge pull request #2197 from dannon/pages_parser_fix [16.04] Pages parser fix Commit: 97110e2655255bf752bb00ca7df046f9c9e016cb https://github.com/galaxyproject/galaxy/commit/97110e2655255bf752bb00ca7df04... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M tools/data_source/biomart.xml Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c79d057ca459...97110e265525