+
−# -*- coding: utf-8 -*-
+
−# copyright 2012 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
+
−# contact http://www.logilab.fr -- mailto:contact@logilab.fr
+
−#
+
−# This program is free software: you can redistribute it and/or modify it under
+
−# the terms of the GNU Lesser General Public License as published by the Free
+
−# Software Foundation, either version 2.1 of the License, or (at your option)
+
−# any later version.
+
−#
+
−# This program is distributed in the hope that it will be useful, but WITHOUT
+
−# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+
−# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+
−# details.
+
−#
+
−# You should have received a copy of the GNU Lesser General Public License along
+
−# with this program. If not, see <http://www.gnu.org/licenses/>.
+
−
+
−"""This module imports the Diseasome data into a CubicWeb instance.
+
−"""
+
−
+
−# Python imports
+
−import sys
+
−import argparse
+
−
+
−# Logilab import, for timing
+
−from logilab.common.decorators import timed
+
−
+
−# CubicWeb imports
+
−import cubicweb.dataimport as cwdi
+
−from cubes.dataio import dataimport as mcwdi
+
−
+
−# Diseasome parser import
+
−import diseasome_parser as parser
+
−
+
−def _is_of_class(instance, class_name):
+
−    """Helper function to determine whether an instance is
+
−    of a specified class or not.
+
−    Returns a True if this is the case and False otherwise.
+
−    """
+
−    if instance.__class__.__name__ == class_name:
+
−        return True
+
−    else:
+
−        return False
+
−
+
−@timed
+
−def diseasome_import(session, file_name, store):
+
−    """Main function for importing Diseasome data.
+
−
+
−    It uses the Diseasome data parser to get the contents of the
+
−    data from a file, then uses a store for importing the data
+
−    into a CubicWeb instance.
+
−
+
−    >>> diseasome_import(session, 'file_name', Store)
+
−
+
−    """
+
−    exturis = dict(session.execute('Any U, X WHERE X is ExternalUri, X uri U'))
+
−    uri_to_eid = {}
+
−    uri_to_etype = {}
+
−    all_relations = {}
+
−    etypes = {('http://www4.wiwiss.fu-berlin.de/'
+
−               'diseasome/resource/diseasome/genes'): 'Gene',
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−              ('http://www4.wiwiss.fu-berlin.de/'
+
−               'diseasome/resource/diseasome/diseases'): 'Disease'}
+
−    # Read the parsed data
+
−    for entity, relations in parser.entities_from_rdf(file_name, 
+
−                                                      ('gene', 'disease')):
+
−        uri = entity.get('cwuri', None)
+
−        types = list(relations.get('types', []))
+
−        if not types:
+
−            continue
+
−        etype = etypes.get(types[0])
+
−        if not etype:
+
−            sys.stderr.write('Entity type %s not recognized.', types[0])
+
−            sys.stderr.flush()
+
−        if _is_of_class(store, 'MassiveObjectStore'):
+
−            for relation in (set(relations).intersection(('classes', 
+
−                            'possible_drugs', 'omim', 'omim_page', 
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−                            'chromosomal_location', 'same_as', 'gene_id',
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−                            'hgnc_id', 'hgnc_page'))):
+
−                store.init_rtype_table(etype, relation, 'ExternalUri')
+
−            for relation in set(relations).intersection(('subtype_of',)):
+
−                store.init_rtype_table(etype, relation, 'Disease')
+
−            for relation in set(relations).intersection(('associated_genes',)):
+
−                store.init_rtype_table(etype, relation, 'Gene')
+
−        # Create the entities
+
−        ent = store.create_entity(etype, **entity)
+
−        if not _is_of_class(store, 'MassiveObjectStore'):
+
−            uri_to_eid[uri] = ent.eid
+
−            uri_to_etype[uri] = ent.cw_etype
+
−        else:
+
−            uri_to_eid[uri] = uri
+
−            uri_to_etype[uri] = etype
+
−        # Store relations for after
+
−        all_relations[uri] = relations
+
−    # Perform a first commit, of the entities
+
−    store.flush()
+
−    kwargs = {}
+
−    for uri, relations in all_relations.items():
+
−        from_eid = uri_to_eid.get(uri)
+
−        # ``subjtype`` should be initialized if ``SQLGenObjectStore`` is used
+
−        # and there are inlined relations in the schema.
+
−        # If ``subjtype`` is not given, while ``SQLGenObjectStore`` is used
+
−        # and there are inlined relations in the schema, the store
+
−        # tries to infer the type of the subject, but this does not always 
+
−        # work, e.g. when there are several object types for the relation.
+
−        # ``subjtype`` is ignored for other stores, or if there are no
+
−        # inlined relations in the schema.
+
−        kwargs['subjtype'] = uri_to_etype.get(uri)
+
−        if not from_eid:
+
−            continue
+
−        for rtype, rels in relations.items():
+
−            if rtype in ('classes', 'possible_drugs', 'omim', 'omim_page',
+
−                         'chromosomal_location', 'same_as', 'gene_id',
+
−                         'hgnc_id', 'hgnc_page'):
+
−                for rel in list(rels):
+
−                    if rel not in exturis:
+
−                        # Create the "ExternalUri" entities, which are the
+
−                        # objects of the relations
+
−                        extu = store.create_entity('ExternalUri', uri=rel)
+
−                        if not _is_of_class(store, 'MassiveObjectStore'):
+
−                            rel_eid = extu.eid
+
−                        else:
+
−                            # For the "MassiveObjectStore", the EIDs are 
+
−                            # in fact the URIs.
+
−                            rel_eid = rel
+
−                        exturis[rel] = rel_eid
+
−                    else:
+
−                        rel_eid = exturis[rel]
+
−                    # Create the relations that have "ExternalUri"s as objects
+
−                    if not _is_of_class(store, 'MassiveObjectStore'):
+
−                        store.relate(from_eid, rtype, rel_eid, **kwargs)
+
−                    else:
+
−                        store.relate_by_iid(from_eid, rtype, rel_eid)
+
−            elif rtype in ('subtype_of', 'associated_genes'):
+
−                for rel in list(rels):
+
−                    to_eid = uri_to_eid.get(rel)
+
−                    if to_eid:
+
−                        # Create relations that have objects of other type 
+
−                        # than "ExternalUri"
+
−                        if not _is_of_class(store, 'MassiveObjectStore'):
+
−                            store.relate(from_eid, rtype, to_eid, **kwargs)
+
−                        else:
+
−                            store.relate_by_iid(from_eid, rtype, to_eid)
+
−                    else:
+
−                        sys.stderr.write('Missing entity with URI %s '
+
−                                         'for relation %s' % (rel, rtype))
+
−                        sys.stderr.flush()
+
−    # Perform a second commit, of the "ExternalUri" entities.
+
−    # when the stores in the CubicWeb ``dataimport`` module are used,
+
−    # relations are also committed.
+
−    store.flush()
+
−    # If the ``MassiveObjectStore`` is used, then entity and relation metadata
+
−    # are pushed as well. By metadata we mean information on the creation
+
−    # time and author.
+
−    if _is_of_class(store, 'MassiveObjectStore'):
+
−        store.flush_meta_data()
+
−        for relation in ('classes', 'possible_drugs', 'omim', 'omim_page', 
+
−                         'chromosomal_location', 'same_as'):
+
−            # Afterwards, relations are actually created in the database.
+
−            store.convert_relations('Disease', relation, 'ExternalUri',
+
−                                    'cwuri', 'uri')
+
−        store.convert_relations('Disease', 'subtype_of', 'Disease', 
+
−                                'cwuri', 'cwuri')
+
−        store.convert_relations('Disease', 'associated_genes', 'Gene', 
+
−                                'cwuri', 'cwuri')
+
−        for relation in ('gene_id', 'hgnc_id', 'hgnc_page', 'same_as'):
+
−            store.convert_relations('Gene', relation, 'ExternalUri', 
+
−                                    'cwuri', 'uri')
+
−        # Clean up temporary tables in the database
+
−        store.cleanup()
+
−
+
−if __name__ == '__main__':
+
−    # Change sys.argv so that ``cubicweb-ctl shell`` can work out the options
+
−    # we give to our ``diseasome_import.py`` script.
+
−    sys.argv = [arg for 
+
−                arg in sys.argv[sys.argv.index("--") - 1:] if arg != "--"]
+
−    PARSER = argparse.ArgumentParser(description="Import Diseasome data")
+
−    PARSER.add_argument("-df", "--datafile", type=str,
+
−                        help="RDF data file name")
+
−    PARSER.add_argument("-st", "--store", type=str,
+
−                        default="RQLObjectStore",
+
−                        help="data import store")
+
−    ARGS = PARSER.parse_args()
+
−    if ARGS.datafile:
+
−        FILENAME = ARGS.datafile
+
−        if ARGS.store in (st + "ObjectStore" for 
+
−                          st in ("RQL", "NoHookRQL", "SQLGen")):
+
−            IMPORT_STORE = getattr(cwdi, ARGS.store)(session)
+
−        elif ARGS.store == "MassiveObjectStore":
+
−            IMPORT_STORE = mcwdi.MassiveObjectStore(session)
+
−        else:
+
−            sys.exit("Import store unknown")
+
−        diseasome_import(session, FILENAME, IMPORT_STORE)
+
−    else:
+
−        sys.exit("Data file not found or not specified")