[galaxy-dev] (Test) Tool Shed rending bug with non-ASCII characters in README.rst
Hello all, Another day, another bug report :( Yesterday I updated this repository, including the README file which now uses reStructuredText markup: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/fd0c284a245c After that change, I couldn't view this repository on the Test Tool Shed: return render_render_readme(context,readme,pad,parent,row_counter) Module _webapps_tool_shed_repository_common_mako:988 in render_render_readme __M_writer(unicode( rst_to_html( readme.text ) )) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1009: ordinal not in range(128) A unicode error. Sigh. As can be seen here, there was a obvious non-ASCII character in the references (Götz) listed in this README.rst file, which renders nicely on BitBucket: https://bitbucket.org/peterjc/galaxy-central/src/7f03d0b7eaa9d002c7389a94a0ee35e599537b1e/tools/blast2go/README.rst In the short term I have replaced Götz with Goetz - which I was able to do by entering the upload URL by hand, giving: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/0f2fc13ce5fc return render_render_readme(context,readme,pad,parent,row_counter) Module _webapps_tool_shed_repository_common_mako:988 in render_render_readme __M_writer(unicode( rst_to_html( readme.text ) )) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 1138: ordinal not in range(128) Progress - the error is now later in the file, which turned out to be a long-dash in a reference, also edited, and now it works: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/9b6482bd1222 The commit in my repository for 'fixing' the tool: https://bitbucket.org/peterjc/galaxy-central/commits/0d329a0e28171754c2d17da491d1ce45b479c3df My hunch is this is related to this recent commit in Galaxy, https://bitbucket.org/galaxy/galaxy-central/commits/535d8ed52369a8bf02ce5e382b488bf94a6f257b In the medium term I would like to revert back to Götz, and also replace Bjoern Gruening with Björn Grüning too (both in my README.rst files and in the RST markup within the tool XML files). Regards, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] (Test) Tool Shed rending bug with non-ASCII characters in README.rst
Peter, I've managed to duplicate that issue on my local tool shed instance, and hope to have a fix submitted soon. --Dave B. On 09/12/2013 05:51 AM, Peter Cock wrote: Hello all, Another day, another bug report :( Yesterday I updated this repository, including the README file which now uses reStructuredText markup: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/fd0c284a245c After that change, I couldn't view this repository on the Test Tool Shed: return render_render_readme(context,readme,pad,parent,row_counter) Module _webapps_tool_shed_repository_common_mako:988 in render_render_readme __M_writer(unicode( rst_to_html( readme.text ) )) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1009: ordinal not in range(128) A unicode error. Sigh. As can be seen here, there was a obvious non-ASCII character in the references (Götz) listed in this README.rst file, which renders nicely on BitBucket: https://bitbucket.org/peterjc/galaxy-central/src/7f03d0b7eaa9d002c7389a94a0ee35e599537b1e/tools/blast2go/README.rst In the short term I have replaced Götz with Goetz - which I was able to do by entering the upload URL by hand, giving: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/0f2fc13ce5fc return render_render_readme(context,readme,pad,parent,row_counter) Module _webapps_tool_shed_repository_common_mako:988 in render_render_readme __M_writer(unicode( rst_to_html( readme.text ) )) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 1138: ordinal not in range(128) Progress - the error is now later in the file, which turned out to be a long-dash in a reference, also edited, and now it works: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/9b6482bd1222 The commit in my repository for 'fixing' the tool: https://bitbucket.org/peterjc/galaxy-central/commits/0d329a0e28171754c2d17da491d1ce45b479c3df My hunch is this is related to this recent commit in Galaxy, https://bitbucket.org/galaxy/galaxy-central/commits/535d8ed52369a8bf02ce5e382b488bf94a6f257b In the medium term I would like to revert back to Götz, and also replace Bjoern Gruening with Björn Grüning too (both in my README.rst files and in the RST markup within the tool XML files). Regards, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] (Test) Tool Shed rending bug with non-ASCII characters in README.rst
On Thu, Sep 12, 2013 at 2:40 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I've managed to duplicate that issue on my local tool shed instance, and hope to have a fix submitted soon. --Dave B. Thanks Dave, Note it seems to be OK at the moment within the RST of a tools help text, e.g. the Tool Shed preview for this looks fine: e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] (Test) Tool Shed rending bug with non-ASCII characters in README.rst
On Thu, Sep 12, 2013 at 4:22 PM, Dave Bouvier d...@bx.psu.edu wrote: Thanks for the additional information, Dan has committed a fix in 10592:ea0c57f1cdf0, which is now running on the test tool shed. --Dave B. Thanks - in the short term I will try to avoid accents in my README.rst files (until the main Tool Shed is updated). Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] (Test) Tool Shed rending bug with non-ASCII characters in README.rst
Thanks for the additional information, Dan has committed a fix in 10592:ea0c57f1cdf0, which is now running on the test tool shed. --Dave B. On 09/12/2013 09:44 AM, Peter Cock wrote: On Thu, Sep 12, 2013 at 2:40 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I've managed to duplicate that issue on my local tool shed instance, and hope to have a fix submitted soon. --Dave B. Thanks Dave, Note it seems to be OK at the moment within the RST of a tools help text, e.g. the Tool Shed preview for this looks fine: e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
