# -*- 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',

              ('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', 

                            'chromosomal_location', 'same_as', 'gene_id',

                            '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'):

        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")