Python Criteria.get_available_criterias方法代碼示例

# 需要導入模塊: from criteria.helper.criteria import Criteria [as 別名]
# 或者: from criteria.helper.criteria.Criteria import get_available_criterias [as 別名]
    def test_available_criterias(self):
        feature = 'gene'
        available_criterias = Criteria.get_available_criterias(feature, INI_CONFIG)
        expected_dict = {'gene': ['cand_gene_in_study', 'gene_in_region', 'is_gene_in_mhc', 'cand_gene_in_region']}
        self.assertIsNotNone(available_criterias, 'Criterias as not none')
        self.assertIn('cand_gene_in_study', available_criterias['gene'])
        self.assertEqual(available_criterias.keys(), expected_dict.keys(), 'Dic keys equal')

        available_criterias = Criteria.get_available_criterias(feature=None, config=INI_CONFIG)
        self.assertIn('gene', available_criterias)
        self.assertIn('marker', available_criterias)

# 需要導入模塊: from criteria.helper.criteria import Criteria [as 別名]
# 或者: from criteria.helper.criteria.Criteria import get_available_criterias [as 別名]
    def test_gene_criteria_types(self):
        """Test if the indexes have records"""
        idx_key = "GENE_CRITERIA"
        feature_type = "gene"
        idx = ElasticSettings.idx(idx_key)

        idx_types = CriteriaDataIntegrityUtils.get_criteria_index_types(idx_key)
        gene_criterias = Criteria.get_available_criterias(feature_type)

        CriteriaDataIntegrityTestUtils().test_criteria_types(idx, idx_types, gene_criterias["gene"])
        CriteriaDataIntegrityTestUtils().test_criteria_mappings(idx, idx_types)

        # get random doc for each type ['gene_in_region', 'cand_gene_in_region', 'cand_gene_in_study', 'is_gene_in_mhc']
        idx_type = "gene_in_region"
        doc_by_idx_type = ElasticUtils.get_rdm_docs(idx, idx_type, size=1)
        self.assertTrue(len(doc_by_idx_type) == 1, "got back one document")
        gene_in_region_doc = doc_by_idx_type[0]

        #         {'score': 10, 'CRO': [{'fname': '4p11', 'fid': '4p11_005'}],
        #          '_meta': {'_type': 'gene_in_region', '_score': 0.9997835,
        #                    '_index': 'pydgin_imb_criteria_gene', '_id': 'ENSG00000250753'},
        #          'disease_tags': ['CRO'], 'qid': 'ENSG00000250753'}

        qid = getattr(gene_in_region_doc, "qid")
        print(qid)
        disease_tags = getattr(gene_in_region_doc, "disease_tags")
        #         ENSG00000248482
        #         ['IBD', 'UC']
        #         [{'fid': '5q31.1_013', 'fname': '5q31.1'}]
        #         [{'fid': '5q31.1_013', 'fname': '5q31.1'}]
        fnotes = getattr(gene_in_region_doc, disease_tags[0])
        region_id = fnotes[0]["fid"]
        print(region_id)

# 需要導入模塊: from criteria.helper.criteria import Criteria [as 別名]
# 或者: from criteria.helper.criteria.Criteria import get_available_criterias [as 別名]
    def get_available_criterias(cls, feature=None, config=None):
        'Function to get available criterias for region'
        if config is None:
            config = CriteriaManager.get_criteria_config()

        if feature is None:
            feature = cls.FEATURE_TYPE

        available_criterias = Criteria.get_available_criterias(feature, config)
        return available_criterias

# 需要導入模塊: from criteria.helper.criteria import Criteria [as 別名]
# 或者: from criteria.helper.criteria.Criteria import get_available_criterias [as 別名]
    def process_criterias(cls, feature, criteria=None, config=None, show=False, test=False):
        '''function to delegate the call to the right criteria class and build the criteria for that class
        '''
        from criteria.helper.criteria import Criteria
        from criteria.helper.gene_criteria import GeneCriteria
        from criteria.helper.marker_criteria import MarkerCriteria
        from criteria.helper.region_criteria import RegionCriteria
        from criteria.helper.study_criteria import StudyCriteria

        if config is None:
            if test:
                config = cls.get_criteria_config(ini_file='test_criteria.ini')
            else:
                config = cls.get_criteria_config(ini_file='criteria.ini')

        available_criterias = Criteria.get_available_criterias(feature, config=config, test=test)[feature]

        criterias_to_process = []
        if criteria is None:
            criterias_to_process = available_criterias
        else:
            criterias_list = criteria.split(',')
            criterias_to_process = [criteria.strip() for criteria in criterias_list
                                    if criteria.strip() in available_criterias]

        if show:
            print(criterias_to_process)
            return criterias_to_process

        logger.debug(datetime.datetime.strftime(datetime.datetime.now(), '%Y-%m-%d %H:%M:%S'))
        for section in criterias_to_process:
            if feature == 'gene':
                print('Call to build criteria gene index')
                Criteria.process_criteria(feature, section, config, GeneCriteria, test=test)
            elif feature == 'marker':
                print('Call to build criteria marker index')
                Criteria.process_criteria(feature, section, config, MarkerCriteria, test=test)
            elif feature == 'region':
                print('Call to build criteria region index')
                Criteria.process_criteria(feature, section, config, RegionCriteria, test=test)
            elif feature == 'study':
                print('Call to build criteria study index')
                Criteria.process_criteria(feature, section, config, StudyCriteria, test=test)
            else:
                logger.critical('Unsupported feature ... please check the inputs')

        logger.debug(datetime.datetime.strftime(datetime.datetime.now(), '%Y-%m-%d %H:%M:%S'))
        logger.debug('========DONE==========')

# 需要導入模塊: from criteria.helper.criteria import Criteria [as 別名]
# 或者: from criteria.helper.criteria.Criteria import get_available_criterias [as 別名]
    def test_marker_criteria_types(self):
        '''Test if the indexes have records'''
        idx_key = 'MARKER_CRITERIA'
        feature_type = 'marker'
        idx = ElasticSettings.idx(idx_key)

        idx_types = CriteriaDataIntegrityUtils.get_criteria_index_types(idx_key)
        gene_criterias = Criteria.get_available_criterias(feature_type)

        CriteriaDataIntegrityTestUtils().test_criteria_types(idx, idx_types, gene_criterias['gene'])
        CriteriaDataIntegrityTestUtils().test_criteria_mappings(idx, idx_types)

        # get random doc for each type ['gene_in_region', 'cand_gene_in_region', 'cand_gene_in_study', 'is_gene_in_mhc']
        idx_type = 'rsq_with_index_snp'
        doc_by_idx_type = ElasticUtils.get_rdm_docs(idx, idx_type, size=1)
        self.assertTrue(len(doc_by_idx_type) == 1, 'got back one document')