+
−# -*- coding: utf-8 -*-
+
−
+
−"""
+
−Diseasome data import module.
+
−Its interface is the ``entities_from_rdf`` function.
+
−"""
+
−
+
−import re
+
−RE_RELS = re.compile(r'^<(.*?)>\s<(.*?)>\s<(.*?)>\s*\.')
+
−RE_ATTS = re.compile(r'^<(.*?)>\s<(.*?)>\s"(.*)"(\^\^<(.*?)>|)\s*\.')
+
−
+
−MAPPING_ATTS = {'bio2rdfSymbol': 'bio2rdf_symbol',
+
−                'label': 'label',
+
−                'name': 'name',
+
−                'classDegree': 'class_degree',
+
−                'degree': 'degree',
+
−                'size': 'size'}
+
−
+
−MAPPING_RELS = {'geneId': 'gene_id',
+
−                'hgncId': 'hgnc_id', 
+
−                'hgncIdPage': 'hgnc_page', 
+
−                'sameAs': 'same_as', 
+
−                'class': 'classes', 
+
−                'diseaseSubtypeOf': 'subtype_of', 
+
−                'associatedGene': 'associated_genes', 
+
−                'possibleDrug': 'possible_drugs',
+
−                'type': 'types',
+
−                'omim': 'omim', 
+
−                'omimPage': 'omim_page', 
+
−                'chromosomalLocation': 'chromosomal_location'}
+
−
+
−def _retrieve_reltype(uri):
+
−    """
+
−    Retrieve a relation type from an URI.
+
−
+
−    Internal function which takes an URI containing a relation type as input
+
−    and returns the name of the relation.
+
−    If no URI string is given, then the function returns None.
+
−    """
+
−    if uri:
+
−        return uri.rsplit('/', 1)[-1].rsplit('#', 1)[-1]
+
−
+
−def _retrieve_etype(tri_uri):
+
−    """
+
−    Retrieve entity type from a triple of URIs.
+
−
+
−    Internal function whith takes a tuple of three URIs as input
+
−    and returns the type of the entity, as obtained from the
+
−    first member of the tuple.
+
−    """
+
−    if tri_uri:
+
−        return tri_uri.split('> <')[0].rsplit('/', 2)[-2].rstrip('s')
+
−
+
−def _retrieve_structure(filename, etypes):
+
−    """
+
−    Retrieve a (subject, relation, object) tuples iterator from a file.
+
−
+
−    Internal function which takes as input a file name and a tuple of 
+
−    entity types, and returns an iterator of (subject, relation, object)
+
−    tuples.
+
−    """
+
−    with open(filename) as fil:
+
−        for line in fil:
+
−            if _retrieve_etype(line) not in etypes:
+
−                continue
+
−            match = RE_RELS.match(line)
+
−            if not match:
+
−                match = RE_ATTS.match(line)
+
−            subj = match.group(1)
+
−            relation = _retrieve_reltype(match.group(2))
+
−            obj = match.group(3)
+
−            yield subj, relation, obj
+
−
+
−def entities_from_rdf(filename, etypes):
+
−    """
+
−    Return entities from an RDF file.
+
−
+
−    Module interface function which takes as input a file name and
+
−    a tuple of entity types, and returns an iterator on the 
+
−    attributes and relations of each entity. The attributes
+
−    and relations are retrieved as dictionaries.
+
−    
+
−    >>> for entities, relations in entities_from_rdf('data_file', 
+
−                                                     ('type_1', 'type_2')):
+
−        ...
+
−    """
+
−    entities = {}
+
−    for subj, rel, obj in _retrieve_structure(filename, etypes):
+
−        entities.setdefault(subj, {})
+
−        entities[subj].setdefault('attributes', {})
+
−        entities[subj].setdefault('relations', {})
+
−        entities[subj]['attributes'].setdefault('cwuri', unicode(subj))
+
−        if rel in MAPPING_ATTS:
+
−            entities[subj]['attributes'].setdefault(MAPPING_ATTS[rel], 
+
−                                                    unicode(obj))
+
−        if rel in MAPPING_RELS:
+
−            entities[subj]['relations'].setdefault(MAPPING_RELS[rel], set())
+
−            entities[subj]['relations'][MAPPING_RELS[rel]].add(unicode(obj))
+
−    return ((ent.get('attributes'), ent.get('relations')) 
+
−            for ent in entities.itervalues())