doc/tutorials/dataimport/diseasome_parser.py
author Sylvain Thénault <sylvain.thenault@logilab.fr>
Mon, 20 Jun 2016 17:59:43 +0200
changeset 11359 2da2dd60331c
parent 10663 54b8a1f249fb
permissions -rw-r--r--
[sql gen] Explicitly name unique index This patch hotfix logilab database for https://www.logilab.org/6662663 and fix database creation to stop using UNIQUE in the table schema but rather create the index later on, so its name is under control. Also consider this change in schema synchronization hooks. This is preliminary work related to #13822045

# -*- 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.values())