From 21cc50a69a91a3f4845404bf58a666b275a14155 Mon Sep 17 00:00:00 2001 From: Pedro Nascimento Date: Mon, 19 Aug 2024 14:54:54 -0300 Subject: [PATCH 1/2] feat: Update dependencies and normalize case in clinical motivation and outcome --- app/routers/frontend.py | 6 +- app/utils.py | 28 ++++++++- poetry.lock | 126 +++++++++++++++++++++++++++++++++++++++- pyproject.toml | 1 + 4 files changed, 156 insertions(+), 5 deletions(-) diff --git a/app/routers/frontend.py b/app/routers/frontend.py index c4e4015..e49b6f0 100644 --- a/app/routers/frontend.py +++ b/app/routers/frontend.py @@ -14,7 +14,7 @@ UserInfo, ) from app.config import BIGQUERY_PROJECT -from app.utils import read_timestamp +from app.utils import read_timestamp, normalize_case router = APIRouter(prefix="/frontend", tags=["Frontend Application"]) @@ -217,8 +217,8 @@ async def get_patient_encounters( "subtype": result['subtipo'], "active_cids": [cid['descricao'] for cid in result['condicoes'] if cid['descricao']], "responsible": professional, - "clinical_motivation": result['motivo_atendimento'], - "clinical_outcome": result['desfecho_atendimento'], + "clinical_motivation": normalize_case(result['motivo_atendimento']), + "clinical_outcome": normalize_case(result['desfecho_atendimento']), "filter_tags": [unit_type], } encounters.append(encounter) diff --git a/app/utils.py b/app/utils.py index 779e1ef..8ef867e 100644 --- a/app/utils.py +++ b/app/utils.py @@ -1,8 +1,10 @@ # -*- coding: utf-8 -*- +from datetime import datetime, timedelta +import re import jwt import hashlib import json -from datetime import datetime, timedelta +import nltk from typing import Literal from loguru import logger from passlib.context import CryptContext @@ -11,6 +13,7 @@ from app.models import User +nltk.download('punkt_tab') pwd_context = CryptContext(schemes=["bcrypt"], deprecated="auto") @@ -137,3 +140,26 @@ def read_timestamp(timestamp: int, output_format=Literal['date','datetime']) -> return value.strftime("%Y-%m-%d") else: raise ValueError("Invalid format") + +def normalize_case(text): + if not text: + return None + + processed_lines = [] + for line in text.splitlines(): + pre_symbol = '' + if line.startswith('#'): + pre_symbol = '#' + line = line[1:] + if line.startswith('-'): + pre_symbol = '-' + line = line[1:] + line = line.strip() + + sentences = nltk.tokenize.sent_tokenize(line) + normalized_sentences = [sentence.capitalize() for sentence in sentences] + normalized_text = pre_symbol + ' ' + ' '.join(normalized_sentences) + + processed_lines.append(normalized_text) + + return '\n'.join(processed_lines) diff --git a/poetry.lock b/poetry.lock index 83aebe3..e0ad362 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1247,6 +1247,17 @@ files = [ [package.extras] colors = ["colorama (>=0.4.6)"] +[[package]] +name = "joblib" +version = "1.4.2" +description = "Lightweight pipelining with Python functions" +optional = false +python-versions = ">=3.8" +files = [ + {file = "joblib-1.4.2-py3-none-any.whl", hash = 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basedosdados = "^2.0.0b16" +nltk = "^3.9.1" [tool.poetry.group.dev.dependencies] From ea6671f701528825aca766ab6d00a0985fc1f776 Mon Sep 17 00:00:00 2001 From: Pedro Nascimento Date: Mon, 19 Aug 2024 15:10:43 -0300 Subject: [PATCH 2/2] refactor: Remove unused import in utils.py --- app/utils.py | 1 - 1 file changed, 1 deletion(-) diff --git a/app/utils.py b/app/utils.py index 8ef867e..82d2e81 100644 --- a/app/utils.py +++ b/app/utils.py @@ -1,6 +1,5 @@ # -*- coding: utf-8 -*- from datetime import datetime, timedelta -import re import jwt import hashlib import json