author | Julien Cristau <julien.cristau@logilab.fr> |
Mon, 24 Nov 2014 17:43:29 +0100 | |
changeset 10047 | a1fde2d343b6 |
parent 9702 | c2108dbfb508 |
child 10663 | 54b8a1f249fb |
permissions | -rw-r--r-- |
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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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|
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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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|
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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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99 |
return ((ent.get('attributes'), ent.get('relations')) |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
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100 |
for ent in entities.itervalues()) |