class QueryGetter:
def __init__(self):
self.query_handler = QueryHandler()
def search(self, query_str):
response = self.query_handler.search_sources(query_str,
keyed=True,
incl='omim')
return response['source_matches'][SourceName.OMIM]
def test_emit_warnings():
"""Test that emit_warnings works correctly."""
expected_warnings = {
'nbsp': 'Query contains non breaking space characters.'
}
query_handler = QueryHandler()
# Test emit no warnings
actual_warnings = query_handler._emit_warnings('CISPLATIN')
assert actual_warnings is None
# Test emit warnings
actual_warnings = query_handler._emit_warnings('CIS PLATIN')
assert actual_warnings == actual_warnings
actual_warnings = query_handler._emit_warnings('CIS\u00A0platin')
assert expected_warnings == actual_warnings
actual_warnings = query_handler._emit_warnings('CIS platin')
assert expected_warnings == actual_warnings
actual_warnings = query_handler._emit_warnings('CIS\xa0platin')
assert expected_warnings == actual_warnings
"""Main application for FastAPI"""
from disease import __version__
from disease.query import QueryHandler, InvalidParameterException
from disease.schemas import SearchService, NormalizationService
from fastapi import FastAPI, HTTPException, Query
from fastapi.openapi.utils import get_openapi
import html
from typing import Optional
query_handler = QueryHandler()
app = FastAPI(docs_url='/disease', openapi_url='/disease/openapi.json')
def custom_openapi():
"""Generate custom fields for OpenAPI response"""
if app.openapi_schema:
return app.openapi_schema
openapi_schema = get_openapi(title="The VICC Disease Normalizer",
version=__version__,
openapi_version="3.0.3",
description="Normalize disease terms.",
routes=app.routes)
# openapi_schema['info']['license'] = { # TODO
# "name": "Name-of-license",
# "url": "http://www.to-be-determined.com"
# }
openapi_schema['info']['contact'] = {
"name": "Alex H. Wagner",
"email": "*****@*****.**"
}
app.openapi_schema = openapi_schema
def __init__(self):
self.query_handler = QueryHandler()