How to use the medcat.cat.CAT function in medcat

from flask import Flask
from medcat.cdb import CDB
from medcat.utils.spacy_pipe import SpacyPipe
from medcat.utils.vocab import Vocab
from medcat.cat import CAT
from flask import request
import os
import json
from spacy import displacy

vocab = Vocab()
cdb = CDB()
cdb.load_dict(os.getenv("CDB_MODEL", '/cat/models/med_ann_norm.dat'))
vocab.load_dict(path=os.getenv("VOCAB_MODEL", '/cat/models/med_ann_norm_dict.dat'))
cat = CAT(cdb, vocab=vocab)
cat.spacy_cat.train = False

app = Flask(__name__)

@app.route('/api_test', methods=['GET', 'POST'])
def api_test():
    if request.method == 'POST':
        return cat.get_json(request.form.get('text'))

    content = get_file('api_test.html')
    return content

@app.route('/doc', methods=['POST'])
def show_annotated_document():
    doc = cat(request.form.get('text'))
    return displacy.render(doc, style='ent')

from flask import Flask
from flask import Response
import json
from medcat.cdb import CDB
from medcat.utils.vocab import Vocab
from medcat.cat import CAT
from flask import request
import os


vocab = Vocab()
cdb = CDB()

cdb.load_dict(os.getenv("CDB_MODEL", '/cat/models/med_ann_norm.dat'))
vocab.load_dict(path=os.getenv("VOCAB_MODEL", '/cat/models/med_ann_norm_dict.dat'))
cat = CAT(cdb, vocab=vocab)

cat.spacy_cat.train = False

app = Flask(__name__)


app_name = 'MEDCAT'
app_lang = 'en'
app_version = os.getenv("CAT_VERSION", '0.1.0')


@app.route('/api/info', methods=['GET'])
def info():
    app_info = {'name': app_name,
                'language': app_lang,
                'version': app_version}

vocab_url = os.getenv('VOCAB_URL')
        urlretrieve(vocab_url, vocab_path)

    if not os.path.exists(cdb_path):
        cdb_url = os.getenv('CDB_URL')
        print("*"*399)
        print(cdb_url)
        urlretrieve(cdb_url, cdb_path)

    vocab = Vocab()
    vocab.load_dict(vocab_path)
    cdb = CDB()
    cdb.load_dict(cdb_path)
    mc_negated = MetaCAT(save_dir=neg_path)
    mc_negated.load()
    cat = CAT(cdb=cdb, vocab=vocab, meta_cats=[mc_negated])
    cat.spacy_cat.MIN_ACC = 0.30
    cat.spacy_cat.MIN_ACC_TH = 0.30
    cat.spacy_cat.ACC_ALWAYS = True
except Exception as e:
    print(str(e))

def get_html_and_json(text):
    doc = cat(text)

    a = json.loads(cat.get_json(text))
    for i in range(len(a['entities'])):
        ent = a['entities'][i]

        new_ent = {}
        for key in ent.keys():
            if key == 'pretty_name':

use_groups = True

    f1s = {}
    ps = {}
    rs = {}
    tps = {}
    fns = {}
    fps = {}
    cui_counts = {}
    examples = {}
    for i in range(cv):
        cdb = CDB()
        cdb.load_dict(cdb_path)
        vocab = Vocab()
        vocab.load_dict(path=vocab_path)
        cat = CAT(cdb, vocab=vocab)
        cat.train = False
        cat.spacy_cat.MIN_ACC = 0.30
        cat.spacy_cat.MIN_ACC_TH = 0.30

        # Add groups if they exist
        if groups is not None:
            for cui in cdb.cui2info.keys():
                if "group" in cdb.cui2info[cui]:
                    del cdb.cui2info[cui]['group']
            groups = json.load(open("./groups.json"))
            for k,v in groups.items():
                for val in v:
                    cat.add_cui_to_group(val, k)

        fp, fn, tp, p, r, f1, cui_counts, examples = cat.train_supervised(data_path=data_path,
                             lr=1, test_size=test_size, use_groups=use_groups, nepochs=nepochs, **kwargs)