from typing import Any, Dict, Optional, Union
import requests
import uvicorn
from fastapi import FastAPI, Request, Response
from fastapi.middleware.cors import CORSMiddleware
from pymetadata.core.annotation import RDFAnnotation, RDFAnnotationData
from pymetadata.identifiers.miriam import BQB
from pymetadata.omex import EntryFormat, Manifest, ManifestEntry, Omex
from sbmlutils import log
from sbmlutils.console import console
from sbmlutils.report.api_examples import ExampleMetaData, examples_info
from sbmlutils.report.sbmlinfo import SBMLDocumentInfo
logger = log.get_logger(__name__)
api = FastAPI(
title="sbml4humans",
description="sbml4humans backend api",
version="0.1.2",
terms_of_service=
"https://github.com/matthiaskoenig/sbmlutils/blob/develop/sbml4humans/privacy_notice.md",
contact={
"name": "Matthias König",
"url": "https://livermetabolism.com",
"email": "*****@*****.**",
},
license_info={
"name": "LGPLv3",
"url": "http://opensource.org/licenses/LGPL-3.0",
from typing import Dict, Iterable, List, Optional, Tuple, Union
import libsbml
import pandas as pd
from pymetadata.core.annotation import RDFAnnotation as Annotation
from pymetadata.identifiers.miriam import BQB, BQM
from sbmlutils import utils
from sbmlutils.console import console
from sbmlutils.io.sbml import read_sbml, write_sbml
from sbmlutils.log import get_logger
from ..validation import check
logger = get_logger(__name__)
def annotate_sbml(
source: Union[Path, str], annotations_path: Path, filepath: Path
) -> libsbml.SBMLDocument:
"""
Annotate a given SBML file with the provided annotations.
:param source: SBML to annotation
:param annotations_path: external file with annotations
:param filepath: annotated SBML file
:return: annotated SBMLDocument
"""
doc: libsbml.SBMLDocument = read_sbml(source=source)