class QueryGetter:
def __init__(self):
self.query_handler = QueryHandler()
def search(self, query_str, keyed=False, incl='', excl=''):
return self.query_handler.search(query_str=query_str,
keyed=keyed,
incl=incl,
excl=excl)
def normalize(self, query_str):
return self.query_handler.normalize(query_str)
class QueryGetter:
def __init__(self):
self.query_handler = QueryHandler()
def search(self, query_str, incl='hgnc'):
resp = self.query_handler.search(query_str, keyed=True, incl=incl)
return resp.source_matches[SourceName.HGNC]
class QueryGetter:
def __init__(self):
self.query_handler = QueryHandler()
def search(self, query_str, incl="ensembl"):
resp = self.query_handler.search(query_str, keyed=True, incl=incl)
return resp.source_matches[SourceName.ENSEMBL.value]
def test_emit_warnings():
"""Test that emit_warnings works correctly."""
expected_warnings = [{
"non_breaking_space_characters":
"Query contains non-breaking space characters"
}]
query_handler = QueryHandler()
# Test emit no warnings
actual_warnings = query_handler.emit_warnings('spry3')
assert actual_warnings == []
# Test emit warnings
actual_warnings = query_handler.emit_warnings('sp ry3')
assert actual_warnings == actual_warnings
actual_warnings = query_handler.emit_warnings('sp\u00A0ry3')
assert expected_warnings == actual_warnings
actual_warnings = query_handler.emit_warnings('sp ry3')
assert expected_warnings == actual_warnings
actual_warnings = query_handler.emit_warnings('sp\xa0ry3')
assert expected_warnings == actual_warnings
def __init__(self):
self.query_handler = QueryHandler()
"""Main application for FastAPI"""
from fastapi import FastAPI, HTTPException, Query
from fastapi.openapi.utils import get_openapi
from typing import Optional
from gene import __version__
from gene.query import QueryHandler, InvalidParameterException
from gene.schemas import SearchService, NormalizeService, \
UnmergedNormalizationService
import html
query_handler = QueryHandler()
app = FastAPI(docs_url="/gene",
openapi_url="/gene/openapi.json",
swagger_ui_parameters={"tryItOutEnabled": True})
def custom_openapi():
"""Generate custom fields for OpenAPI response"""
if app.openapi_schema:
return app.openapi_schema
openapi_schema = get_openapi(title="The VICC Gene Normalizer",
version=__version__,
openapi_version="3.0.3",
description="Normalize gene terms.",
routes=app.routes)
# openapi_schema['info']['license'] = { # TODO
# "name": "name of our license",
# "url": "http://www.our-license-tbd.com"
# }
openapi_schema['info']['contact'] = {
"name":