[urlpublishing] handle sub-types in RestPathEvaluator
Since commit 31a1813d53f3 "[entity/url publishing] fetch_rqlst should
use 'is_instance_of' instead of 'is'", the RestPathEvaluator's input
rset can have more than one etype, so it can't always use sameetypelist.
Related to #3825488
# -*- 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 a URI.
Internal function which takes a 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())