"""SBML report using https://sbml4humans.de."""
import http.server
import socketserver
import threading
import time
import webbrowser
from pathlib import Path
from sbmlutils import __version__
from sbmlutils.log import get_logger
[docs]logger = get_logger(__name__)
[docs]def start_server(path: Path, port: int = 5115) -> None:
"""Start a simple webserver serving path on port."""
class Handler(http.server.SimpleHTTPRequestHandler):
def __init__(self, *args, **kwargs): # type: ignore
"""Initialize handler for requests."""
super().__init__(directory=path, *args, **kwargs)
with socketserver.TCPServer(("", port), Handler) as httpd:
httpd.serve_forever()
[docs]def create_online_report(
sbml_path: Path,
server: str = "https://sbml4humans.de",
fileserver_duration: int = 10,
fileserver_port: int = 5115,
) -> None:
"""Create sbml4humans report.
The SBML file can be validated during report generation.
Local parameters can be promoted during report generation.
:param sbml_path: path to SBML file
:param server: server to use for report, for local development use `localhost:3456`
:param fileserver_duration: duration of file server in seconds
:param fileserver_port: port of file server
:return: None
"""
# validate and check arguments
if not isinstance(sbml_path, Path):
logger.warning(
f"All paths should be of type 'Path', "
f"but '{type(sbml_path)}' found for: {sbml_path}"
)
sbml_path = Path(sbml_path)
if not sbml_path.exists():
raise IOError(f"'sbml_path' does not exist: '{sbml_path}'")
# serve files
daemon = threading.Thread(
name="daemon_server",
target=start_server,
args=(sbml_path.parent, fileserver_port),
)
# Set as a daemon so it will be killed once the main thread is dead.
daemon.setDaemon(True)
daemon.start()
# post file via url to sbml4humans server
url = f"http://0.0.0.0:{fileserver_port}/{sbml_path.name}"
url_encoded = url.replace(":", "%253A")
url_encoded = url_encoded.replace("/", "%252F")
sbml4humans_url = f"{server}/model_url?url={url_encoded}"
logger.info(f"Create report: `{sbml4humans_url}`")
# open in browser
webbrowser.open(sbml4humans_url, new=0)
# give some time to render report (the fileserver must stay alive)
time.sleep(fileserver_duration)
if __name__ == "__main__":
from sbmlutils.resources import REPRESSILATOR_SBML
# create_online_report(sbml_path=REPRESSILATOR_SBML)
create_online_report(sbml_path=REPRESSILATOR_SBML, server="localhost:3456")