1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/a4c7aeb61c7b/ changeset: a4c7aeb61c7b user: jgoecks date: 2012-08-27 21:44:01 summary: Comment out phyloviz XML parser until native Python XML parsing is used. affected #: 2 files

diff -r 75a03bacdc7a3dc5b1c03f8b02df0ab383366955 -r a4c7aeb61c7b8e76fcf3fd96d0d351be88d1c1d1 lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py --- a/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py +++ b/lib/galaxy/visualization/phyloviz/phyloviz_dataprovider.py @@ -1,6 +1,6 @@ from newickparser import Newick_Parser from nexusparser import Nexus_Parser -from phyloxmlparser import Phyloxml_Parser +#from phyloxmlparser import Phyloxml_Parser

class Phyloviz_DataProvider(object):

@@ -16,9 +16,9 @@ if fileExt == "nhx": # parses newick files newickParser = Newick_Parser() jsonDicts, parseMsg = newickParser.parseFile(filepath) - elif fileExt == "phyloxml": # parses phyloXML files - phyloxmlParser = Phyloxml_Parser() - jsonDicts, parseMsg = phyloxmlParser.parseFile(filepath) + #elif fileExt == "phyloxml": # parses phyloXML files + # phyloxmlParser = Phyloxml_Parser() + # jsonDicts, parseMsg = phyloxmlParser.parseFile(filepath) elif fileExt == "nex": # parses nexus files nexusParser = Nexus_Parser() jsonDicts, parseMsg = nexusParser.parseFile(filepath)

diff -r 75a03bacdc7a3dc5b1c03f8b02df0ab383366955 -r a4c7aeb61c7b8e76fcf3fd96d0d351be88d1c1d1 lib/galaxy/visualization/phyloviz/phyloxmlparser.py --- a/lib/galaxy/visualization/phyloviz/phyloxmlparser.py +++ b/lib/galaxy/visualization/phyloviz/phyloxmlparser.py @@ -1,4 +1,7 @@ from baseparser import Base_Parser, PhyloTree, Node + +''' +TOD0: use native Python XML parser. from lxml import etree

class Phyloxml_Parser(Base_Parser): @@ -143,3 +146,4 @@ # filepath = "../data/" +"bcl_2.xml" # filepath = "../data/" +"reducedXml.xml" parser.parseFile(filepath) +''' \ No newline at end of file

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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