--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/tutorials/dataimport/diseasome_parser.py	Tue Mar 12 18:31:15 2013 +0100
@@ -0,0 +1,100 @@
+# -*- 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())