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Fix issue with lowercasing in datatypes/registry.py #2361

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merged 2 commits into from
May 16, 2016
Merged

Fix issue with lowercasing in datatypes/registry.py #2361

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cd96a50
Fix an issue about not-lowercasing extensions in load_display_applica…
remimarenco May 14, 2016
5d47c79
Handle the case where extension is None
remimarenco May 14, 2016
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20 changes: 16 additions & 4 deletions lib/galaxy/datatypes/registry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,9 +119,7 @@ def __import_module( full_path, datatype_module, datatype_class_name ):
for elem in registration.findall( 'datatype' ):
# Keep a status of the process steps to enable stopping the process of handling the datatype if necessary.
ok = True
extension = elem.get( 'extension', None )
if extension:
extension = extension.lower()
extension = self.get_extension( elem )
dtype = elem.get( 'type', None )
type_extension = elem.get( 'type_extension', None )
mimetype = elem.get( 'mimetype', None )
Expand Down Expand Up @@ -552,7 +550,7 @@ def load_display_applications( self, app, installed_repository_dict=None, deacti
# Load display applications defined by local datatypes_conf.xml.
datatype_elems = self.display_app_containers
for elem in datatype_elems:
extension = elem.get( 'extension', None )
extension = self.get_extension( elem )
for display_app in elem.findall( 'display' ):
display_file = display_app.get( 'file', None )
if installed_repository_dict:
Expand Down Expand Up @@ -861,3 +859,17 @@ def to_xml_file( self ):
os.write( fd, '</datatypes>\n' )
os.close( fd )
os.chmod( self.xml_filename, 0o644 )

def get_extension( self, elem ):
"""
Function which returns the extension lowercased
:param elem:
:return extension:
"""
extension = elem.get('extension', None)
# If extension is not None and is uppercase or mixed case, we need to lowercase it
if extension is not None and not extension.islower():
self.log.debug( "%s is not lower case, that could cause troubles in the future. \
Please change it to lower case" % extension )
extension = extension.lower()
return extension