doc/tutorials/dataimport/diseasome_parser.py
author Sylvain Thénault <sylvain.thenault@logilab.fr>
Wed, 20 Jan 2016 08:26:30 +0100
changeset 11219 0796b6191cea
parent 10663 54b8a1f249fb
permissions -rw-r--r--
[pylint] more work on the pylint support * uniformize usage of ClassDef and simplify related import * don't insert in the ast a python function but an astroid representation of that function * ignore __pkginfo__ file * drop attr-rgx, variable-rgx and argument-rgx, put the name in good-names instead * drop additional-builtins * add cell_call to the list of methods for which we don't want 'abstract-method'
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# -*- coding: utf-8 -*-
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"""
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Diseasome data import module.
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Its interface is the ``entities_from_rdf`` function.
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"""
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import re
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RE_RELS = re.compile(r'^<(.*?)>\s<(.*?)>\s<(.*?)>\s*\.')
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RE_ATTS = re.compile(r'^<(.*?)>\s<(.*?)>\s"(.*)"(\^\^<(.*?)>|)\s*\.')
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MAPPING_ATTS = {'bio2rdfSymbol': 'bio2rdf_symbol',
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                'label': 'label',
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                'name': 'name',
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                'classDegree': 'class_degree',
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                'degree': 'degree',
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                'size': 'size'}
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MAPPING_RELS = {'geneId': 'gene_id',
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                'hgncId': 'hgnc_id', 
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                'hgncIdPage': 'hgnc_page', 
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                'sameAs': 'same_as', 
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                'class': 'classes', 
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                'diseaseSubtypeOf': 'subtype_of', 
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                'associatedGene': 'associated_genes', 
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                'possibleDrug': 'possible_drugs',
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                'type': 'types',
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                'omim': 'omim', 
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                'omimPage': 'omim_page', 
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                'chromosomalLocation': 'chromosomal_location'}
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def _retrieve_reltype(uri):
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    """
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    Retrieve a relation type from a URI.
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    Internal function which takes a URI containing a relation type as input
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    and returns the name of the relation.
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    If no URI string is given, then the function returns None.
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    """
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    if uri:
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        return uri.rsplit('/', 1)[-1].rsplit('#', 1)[-1]
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def _retrieve_etype(tri_uri):
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    """
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    Retrieve entity type from a triple of URIs.
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    Internal function whith takes a tuple of three URIs as input
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    and returns the type of the entity, as obtained from the
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    first member of the tuple.
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    """
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    if tri_uri:
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        return tri_uri.split('> <')[0].rsplit('/', 2)[-2].rstrip('s')
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def _retrieve_structure(filename, etypes):
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    """
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    Retrieve a (subject, relation, object) tuples iterator from a file.
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    Internal function which takes as input a file name and a tuple of 
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    entity types, and returns an iterator of (subject, relation, object)
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    tuples.
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    """
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    with open(filename) as fil:
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        for line in fil:
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            if _retrieve_etype(line) not in etypes:
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                continue
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            match = RE_RELS.match(line)
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            if not match:
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                match = RE_ATTS.match(line)
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            subj = match.group(1)
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            relation = _retrieve_reltype(match.group(2))
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            obj = match.group(3)
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            yield subj, relation, obj
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def entities_from_rdf(filename, etypes):
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    """
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    Return entities from an RDF file.
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    Module interface function which takes as input a file name and
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    a tuple of entity types, and returns an iterator on the 
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    attributes and relations of each entity. The attributes
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    and relations are retrieved as dictionaries.
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    >>> for entities, relations in entities_from_rdf('data_file', 
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                                                     ('type_1', 'type_2')):
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        ...
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    """
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    entities = {}
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    for subj, rel, obj in _retrieve_structure(filename, etypes):
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        entities.setdefault(subj, {})
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        entities[subj].setdefault('attributes', {})
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        entities[subj].setdefault('relations', {})
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        entities[subj]['attributes'].setdefault('cwuri', unicode(subj))
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        if rel in MAPPING_ATTS:
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            entities[subj]['attributes'].setdefault(MAPPING_ATTS[rel], 
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                                                    unicode(obj))
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        if rel in MAPPING_RELS:
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            entities[subj]['relations'].setdefault(MAPPING_RELS[rel], set())
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            entities[subj]['relations'][MAPPING_RELS[rel]].add(unicode(obj))
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    return ((ent.get('attributes'), ent.get('relations')) 
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            for ent in entities.values())