Intervention_Normalizer/postprocess.py at master · WengLab-InformaticsResearch/Intervention_Normalizer · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
import configure
import os


def get_map():
    drug_types = "T116,T195,T123,T122,T103,T120,T104,T200,T196,T126,T131,T125,T129,T130,T197,T114,T109,T121,T192,T127"
    procedure_types = "T060,T065,T058,T059,T063,T062,T061"
    device_types = "T203,T074,T075"
    activity_types = "T052,T053,T056,T051,T064,T055,T066,T057,T054"
    sem_map = {}

    for item in drug_types.split(','):
        sem_map[item] = 'drug'
    for item in procedure_types.split(','):
        sem_map[item] = 'procedure'
    for item in device_types.split(','):
        sem_map[item] = 'device'
    for item in activity_types.split(','):
        sem_map[item] = 'activity'
    return sem_map


def get_semtype_id(file):
    sem_id = {}
    with open(file, 'r') as f:
        for line in f:
            tokens = line.split('|')
            sem_id[tokens[3]] = tokens[2]
    return sem_id


def convert2standard(snippets):
    sem_id = get_semtype_id(os.path.join(configure.RESOURCE_PATH, 'semGroups.txt'))

    sem_map = get_map()

    result = []

    for snippet in snippets:
        standard = {'file_id': snippet['file_id'], 'start': snippet['start_pos'], 'end': snippet['end_pos'],
                    'text': snippet['raw_text']}
        drug = []
        procedure = []
        device = []
        activity = []

        components = []
        for entity in snippet['entities']:
            components.append(entity['cui'])
            temp_entity = {'text': entity['ngram'], 'maps_to': entity['cui'] + ':' + entity['term']}
            sem_type = sem_map[sem_id[entity['semtypes'][0]]]
            del entity['ngram']
            del entity['term']
            del entity['cui']
            del entity['similarity']
            del entity['semtypes']
            del entity['preferred']
            del entity['id']

            # deal with the negation
            if 'has_negation' not in entity.keys() or len(entity['has_negation']) == 0:
                entity['has_negation'] = 'affirmed'
            else:
                entity['has_negation'] = 'negated'

            for key, value in entity.items():
                temp_entity[key] = value

            if sem_type == 'drug':
                drug.append(temp_entity)
            if sem_type == 'procedure':
                procedure.append(temp_entity)
            if sem_type == 'device':
                device.append(temp_entity)
            if sem_type == 'activity':
                activity.append(temp_entity)

        if len(drug) > 0:
            standard['has_drug'] = drug
        if len(procedure) > 0:
            standard['has_procedure'] = procedure
        if len(device) > 0:
            standard['has_device'] = device
        if len(activity) > 0:
            standard['has_activity'] = activity


        # add the relation
        if snippet['relation'] == 'N/A':
            relation = 'N/A'
        elif snippet['relation'] == 'combined_with':
            comp = '<->'.join(components)
            relation = 'combined_with (' + comp + ')'
        elif snippet['relation'] == 'before':
            comp = '->'.join(components)
            relation = 'before (' + comp + ')'
        elif snippet['relation'] == 'after':
            comp = '->'.join(reversed(components))
            relation = 'before (' + comp + ')'
        elif snippet['relation'] == 'contain':
            comp = '->'.join(components)
            relation = 'contain (' + comp + ')'
        elif snippet['relation'] == 'in':
            comp = '->'.join(reversed(components))
            relation = 'contain (' + comp + ')'
        elif snippet['relation'] == 'substituted_for':
            comp = '->'.join(components)
            relation = 'substituted_for (' + comp + ')'
        elif snippet['relation'] == 'switched_to':
            comp = '->'.join(reversed(components))
            relation = 'substituted_for (' + comp + ')'
        elif snippet['relation'] == 'without':
            comp = '->'.join(components)
            relation = 'without (' + comp + ')'
        elif snippet['relation'] == 'or':
            comp = '<->'.join(components)
            relation = 'or (' + comp + ')'

        standard['has_relation'] = relation
        result.append(standard)
    return result


def run(snippets):
    snippets = convert2standard(snippets)
    return snippets