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a 'namespace' property in the OBO format

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This commit is contained in:
Eric Coissac
2008-10-06 16:33:54 +00:00
parent fa0636029a
commit bcbbaea78c
1 changed files with 2 additions and 5 deletions
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7
src/obitools/obo/parser.py
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@ -214,7 +214,7 @@ class DefValue(TaggedValue):
dbxrefs = TaggedValue._match_bracket.search(cleanvalue).group(0) dbxrefs = TaggedValue._match_bracket.search(cleanvalue).group(0)
## recording zone ## recording zone
self.tag = "def" self.tag = 'def'
## the value of a DefValue is not the standard value but the definition. ## the value of a DefValue is not the standard value but the definition.
self.value=definition self.value=definition
self.dbxrefs=xrefFactory(dbxrefs) self.dbxrefs=xrefFactory(dbxrefs)
@ -558,7 +558,7 @@ class OBOTerm(OBOEntry):
assert self.stanzaName=='Term' assert self.stanzaName=='Term'
assert 'id' in self and len(self['id'])==1,"An OBOTerm must have an id" assert 'id' in self and len(self['id'])==1,"An OBOTerm must have an id"
assert 'name' in self and len(self['name'])==1,"An OBOTerm must have a name" assert 'name' in self and len(self['name'])==1,"An OBOTerm must have a name"
assert 'namespace' in self and len(self['namespace'])==1, "An OBOTerm must belong to one of the cell_component, molecular_function or biological_process namespace" assert 'namespace' not in self or len(self['namespace'])==1, "Only one namespace is allowed for an OBO term"
assert 'def' not in self or len(self['def'])==1,"Only one definition is allowed for an OBO term" assert 'def' not in self or len(self['def'])==1,"Only one definition is allowed for an OBO term"
assert 'comment' not in self or len(self['comment'])==1,"Only one comment is allowed for an OBO term" assert 'comment' not in self or len(self['comment'])==1,"Only one comment is allowed for an OBO term"
@ -586,9 +586,6 @@ class OBOTerm(OBOEntry):
def _getId(self): def _getId(self):
return self['id'][0] return self['id'][0]
def _getNamespace(self):
return self['namespace'][0]
def _getName(self): def _getName(self):
return self['name'][0] return self['name'][0]