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* class OBOEntry, ajout de l'attribut stanza self["stanza"]

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* class OBOTerm:
	* ajout de la propriété stanza + sa méthode getter
	* test obsolete: suppression de la contrainte 'is_a'... slot pas obligatoire pour un term obsolete
	* methode getReplaceBy renommée en getReplacedBy
This commit is contained in:
Eric Coissac
2009-07-24 11:31:44 +00:00
parent 10082b2c15
commit 8528ddeadc
1 changed files with 10 additions and 3 deletions
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13
src/obitools/obo/parser.py
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@ -526,6 +526,8 @@ class OBOEntry(dict):
if not self.isHeader: if not self.isHeader:
self.stanzaName = lines[0].strip()[1:-1] self.stanzaName = lines[0].strip()[1:-1]
lines=lines[1:] lines=lines[1:]
self["stanza"] = [stanza.strip()]
## whatever the stanza is. ## whatever the stanza is.
for line in lines: for line in lines:
## each line is a couple : tag / value ## each line is a couple : tag / value
@ -557,6 +559,7 @@ class OBOTerm(OBOEntry):
OBOEntry.__init__(self, stanza) OBOEntry.__init__(self, stanza)
assert self.stanzaName=='Term' assert self.stanzaName=='Term'
assert 'stanza' in self
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' not in self or len(self['namespace'])==1, "Only one namespace is allowed for an OBO term" assert 'namespace' not in self or len(self['namespace'])==1, "Only one namespace is allowed for an OBO term"
@ -568,7 +571,7 @@ class OBOTerm(OBOEntry):
assert 'intersection_of' not in self or len(self['intersection_of'])>=2,"Only one intersection relationship is allowed for an OBO term" assert 'intersection_of' not in self or len(self['intersection_of'])>=2,"Only one intersection relationship is allowed for an OBO term"
if self._isObsolete(): if self._isObsolete():
assert 'is_a' not in self #assert 'is_a' not in self
assert 'relationship' not in self assert 'relationship' not in self
assert 'inverse_of' not in self assert 'inverse_of' not in self
assert 'disjoint_from' not in self assert 'disjoint_from' not in self
@ -578,6 +581,9 @@ class OBOTerm(OBOEntry):
assert 'replaced_by' not in self or self._isObsolete() assert 'replaced_by' not in self or self._isObsolete()
assert 'consider' not in self or self._isObsolete() assert 'consider' not in self or self._isObsolete()
def _getStanza(self):
return self['stanza'][0]
## make-up functions. ## make-up functions.
def _getDefinition(self): def _getDefinition(self):
if 'def' in self: if 'def' in self:
@ -641,7 +647,7 @@ class OBOTerm(OBOEntry):
def _isObsolete(self): def _isObsolete(self):
return 'is_obsolete' in self and str(self['is_obsolete'][0])=='true' return 'is_obsolete' in self and str(self['is_obsolete'][0])=='true'
def _getReplaceBy(self): def _getReplacedBy(self):
if 'replaced_by' in self: if 'replaced_by' in self:
return list(set(self.get('replaced_by',None))) return list(set(self.get('replaced_by',None)))
return None return None
@ -652,6 +658,7 @@ class OBOTerm(OBOEntry):
return None return None
## automatically make-up ! ## automatically make-up !
stanza = property(_getStanza,None,None)
definition = property(_getDefinition,None,None) definition = property(_getDefinition,None,None)
id = property(_getId,None,None) id = property(_getId,None,None)
namespace = property(_getNamespace,None,None) namespace = property(_getNamespace,None,None)
@ -667,7 +674,7 @@ class OBOTerm(OBOEntry):
intersection_of = property(_getIntersection,None,None) intersection_of = property(_getIntersection,None,None)
disjoint_from = property(_getDisjonction,None,None) disjoint_from = property(_getDisjonction,None,None)
is_obsolete = property(_isObsolete,None,None) is_obsolete = property(_isObsolete,None,None)
replaced_by = property(_getReplaceBy,None,None) replaced_by = property(_getReplacedBy,None,None)
consider = property(_getConsider,None,None) consider = property(_getConsider,None,None)