1 # -*- coding: utf-8 -*-

     2 

     3 """

     4 Diseasome data import module.

     5 Its interface is the ``entities_from_rdf`` function.

     6 """

     7 

     8 import re

     9 RE_RELS = re.compile(r'^<(.*?)>\s<(.*?)>\s<(.*?)>\s*\.')

    10 RE_ATTS = re.compile(r'^<(.*?)>\s<(.*?)>\s"(.*)"(\^\^<(.*?)>|)\s*\.')

    11 

    12 MAPPING_ATTS = {'bio2rdfSymbol': 'bio2rdf_symbol',

    13                 'label': 'label',

    14                 'name': 'name',

    15                 'classDegree': 'class_degree',

    16                 'degree': 'degree',

    17                 'size': 'size'}

    18 

    19 MAPPING_RELS = {'geneId': 'gene_id',

    20                 'hgncId': 'hgnc_id', 

    21                 'hgncIdPage': 'hgnc_page', 

    22                 'sameAs': 'same_as', 

    23                 'class': 'classes', 

    24                 'diseaseSubtypeOf': 'subtype_of', 

    25                 'associatedGene': 'associated_genes', 

    26                 'possibleDrug': 'possible_drugs',

    27                 'type': 'types',

    28                 'omim': 'omim', 

    29                 'omimPage': 'omim_page', 

    30                 'chromosomalLocation': 'chromosomal_location'}

    31 

    32 def _retrieve_reltype(uri):

    33     """

    34     Retrieve a relation type from an URI.

    35 

    36     Internal function which takes an URI containing a relation type as input

    37     and returns the name of the relation.

    38     If no URI string is given, then the function returns None.

    39     """

    40     if uri:

    41         return uri.rsplit('/', 1)[-1].rsplit('#', 1)[-1]

    42 

    43 def _retrieve_etype(tri_uri):

    44     """

    45     Retrieve entity type from a triple of URIs.

    46 

    47     Internal function whith takes a tuple of three URIs as input

    48     and returns the type of the entity, as obtained from the

    49     first member of the tuple.

    50     """

    51     if tri_uri:

    52         return tri_uri.split('> <')[0].rsplit('/', 2)[-2].rstrip('s')

    53 

    54 def _retrieve_structure(filename, etypes):

    55     """

    56     Retrieve a (subject, relation, object) tuples iterator from a file.

    57 

    58     Internal function which takes as input a file name and a tuple of 

    59     entity types, and returns an iterator of (subject, relation, object)

    60     tuples.

    61     """

    62     with open(filename) as fil:

    63         for line in fil:

    64             if _retrieve_etype(line) not in etypes:

    65                 continue

    66             match = RE_RELS.match(line)

    67             if not match:

    68                 match = RE_ATTS.match(line)

    69             subj = match.group(1)

    70             relation = _retrieve_reltype(match.group(2))

    71             obj = match.group(3)

    72             yield subj, relation, obj

    73 

    74 def entities_from_rdf(filename, etypes):

    75     """

    76     Return entities from an RDF file.

    77 

    78     Module interface function which takes as input a file name and

    79     a tuple of entity types, and returns an iterator on the 

    80     attributes and relations of each entity. The attributes

    81     and relations are retrieved as dictionaries.

    82     

    83     >>> for entities, relations in entities_from_rdf('data_file', 

    84                                                      ('type_1', 'type_2')):

    85         ...

    86     """

    87     entities = {}

    88     for subj, rel, obj in _retrieve_structure(filename, etypes):

    89         entities.setdefault(subj, {})

    90         entities[subj].setdefault('attributes', {})

    91         entities[subj].setdefault('relations', {})

    92         entities[subj]['attributes'].setdefault('cwuri', unicode(subj))

    93         if rel in MAPPING_ATTS:

    94             entities[subj]['attributes'].setdefault(MAPPING_ATTS[rel], 

    95                                                     unicode(obj))

    96         if rel in MAPPING_RELS:

    97             entities[subj]['relations'].setdefault(MAPPING_RELS[rel], set())

    98             entities[subj]['relations'][MAPPING_RELS[rel]].add(unicode(obj))

    99     return ((ent.get('attributes'), ent.get('relations')) 

   100             for ent in entities.itervalues())