Python Criteria.get_feature_idx_n_idxtypes方法代码示例

# 需要导入模块: from criteria.helper.criteria import Criteria [as 别名]
# 或者: from criteria.helper.criteria.Criteria import get_feature_idx_n_idxtypes [as 别名]
    def test_get_feature_idx_n_idxtypes(self):

        (idx, idx_types) = Criteria.get_feature_idx_n_idxtypes('gene')
        self.assertEqual('pydgin_imb_criteria_gene', idx, 'Got the right idx back')
        self.assertIn('cand_gene_in_study', idx_types, 'Got the right idx type back')
        self.assertIn('cand_gene_in_region', idx_types, 'Got the right idx type back')

        (idx, idx_types) = Criteria.get_feature_idx_n_idxtypes('marker')
        self.assertEqual('pydgin_imb_criteria_marker', idx, 'Got the right idx back')

        self.assertIn('is_an_index_snp', idx_types, 'Got the right idx type back')
        self.assertIn('marker_is_gwas_significant_in_study', idx_types, 'Got the right idx type back')
        self.assertIn('is_marker_in_mhc', idx_types, 'Got the right idx type back')

# 需要导入模块: from criteria.helper.criteria import Criteria [as 别名]
# 或者: from criteria.helper.criteria.Criteria import get_feature_idx_n_idxtypes [as 别名]
def show_feature_criteria_details(feature_id, feature_type, feature_doc=None, section='criteria',
                                  section_title="criteria"):
    ''' Template inclusion tag to render criteria details bar. '''
    print('===================')
    print(feature_id)
    print(feature_type)
    print('====================')
    (idx, idx_types) = Criteria.get_feature_idx_n_idxtypes(feature_type)
    criteria_disease_tags = Criteria.get_all_criteria_disease_tags([feature_id], idx, idx_types)
    print(criteria_disease_tags)
    return {'criteria': criteria_disease_tags, 'feature_id': feature_id, 'appname': feature_type,
            'f': feature_doc, 'section': section, 'section_title': section_title}

# 需要导入模块: from criteria.helper.criteria import Criteria [as 别名]
# 或者: from criteria.helper.criteria.Criteria import get_feature_idx_n_idxtypes [as 别名]
    def filter_queryset(self, request, queryset, view):
        ''' Override this method to request just the documents required from elastic. '''
        q_size = view.paginator.get_limit(request)
        q_from = view.paginator.get_offset(request)

        filterable = getattr(view, 'filter_fields', [])
        filters = dict([(k, v) for k, v in request.GET.items() if k in filterable])
        criteria_idx = self._get_index(filters.get('feature_type', 'GENE_CRITERIA'))

        feature_type = filters.get('feature_type')
        feature_id = filters.get('feature_id')
        aggregate = filters.get('aggregate')
        detail = filters.get('detail')

        idx = criteria_idx
        if type(criteria_idx) == list:
            idx = ','.join(ElasticSettings.idx(name) for name in criteria_idx)
        else:
            idx = ElasticSettings.idx(criteria_idx)

        results = []
        if feature_id and aggregate == 'true':
            disease_doc_tags = Criteria.get_disease_tags(feature_id, idx=idx)
            disease_tags = [getattr(d, 'code') for d in disease_doc_tags]
            new_obj = ElasticObject()
            new_obj.qid = feature_id
            new_obj.disease_tags = disease_tags
            new_obj.criteria_type = None
            results.append(new_obj)
            return results
        elif feature_id and detail == 'true':
            (idx, idx_types) = Criteria.get_feature_idx_n_idxtypes(feature_type.lower())
            criteria_details = Criteria.get_criteria_details(feature_id, idx=idx, idx_type=idx_types)
            criteria_list = idx_types.split(',')
            criteria_details_expanded = Criteria.add_meta_info(idx, criteria_list, criteria_details)

            feature_details = self._get_feature_details(criteria_details_expanded)

            for criteria, details in feature_details.items():
                print(criteria)
                new_obj = ElasticObject()
                new_obj.qid = details['qid']
                new_obj.criteria_type = criteria
                disease_tags = details['disease_tags']
                fdetails = list(details['fdetails'])
                print('+++++++++++++++')
                print(disease_tags)
                print(fdetails)
                print('+++++++++++++++')
                new_obj.disease_tags = disease_tags
                new_obj.feature_details = fdetails
                results.append(new_obj)

            return results
        else:
            q = ElasticQuery(Query.match_all())
            s = Search(search_query=q, idx=idx, size=q_size, search_from=q_from)
            json_results = s.get_json_response()

            for result in json_results['hits']['hits']:
                new_obj = ElasticObject(initial=result['_source'])
                new_obj.uuid = result['_id']
                new_obj.criteria_type = result['_type']
                results.append(new_obj)

            view.es_count = json_results['hits']['total']
            return results