Source code for modos.remote

"""Functions related to server storage handling"""

from dataclasses import field
from typing import Mapping, Optional

from pydantic import HttpUrl, validate_call
from pydantic.dataclasses import dataclass
import requests


@dataclass(frozen=True)
[docs] class EndpointManager: """Handle modos server endpoints. If a modos server url is provided, it is used to detect available service urls. Alternatively, service urls can be provided explicitely if no modos server is available. Parameters ---------- modos URL to the modos server. services Mapping of services to their urls. Examples -------- >>> ex = EndpointManager(modos="http://modos.example.org") # doctest: +SKIP >>> ex.list() # doctest: +SKIP { 's3: Url('http://s3.example.org/'), 'htsget': Url('http://htsget.example.org/') } >>> ex.htsget # doctest: +SKIP Url('http://htsget.example.org/') >>> ex = EndpointManager(services={"s3": "http://s3.example.org"}) >>> ex.s3 Url('http://s3.example.org/') """
[docs] modos: Optional[HttpUrl] = None
[docs] services: dict[str, HttpUrl] = field(default_factory=dict)
[docs] def list(self) -> dict[str, HttpUrl]: """List available endpoints.""" if self.modos: return requests.get(url=str(self.modos)).json() elif self.services: return self.services else: return {}
@property
[docs] def s3(self) -> Optional[HttpUrl]: return self.list().get("s3")
@property
[docs] def fuzon(self) -> Optional[HttpUrl]: return self.list().get("fuzon")
@property
[docs] def htsget(self) -> Optional[HttpUrl]: return self.list().get("htsget")
@validate_call
[docs] def list_remote_items(url: HttpUrl) -> list[HttpUrl]: return requests.get(url=f"{url}/list").json()["modos"]
@validate_call
[docs] def get_metadata_from_remote( url: HttpUrl, modo_id: Optional[str] = None ) -> Mapping: """Function to access metadata from one specific or all modos on a remote server Parameters ---------- server_url Url to the remote modo server id id of the modo to retrieve metadata from. Will return all if not specified (default). """ meta = requests.get(url=f"{url}/meta").json() if modo_id is not None: try: return meta[modo_id] except KeyError as e: raise ValueError( f"Could not find metadata for modo with id: {modo_id}" ) from e else: return meta
[docs] def is_s3_path(path: str): """Check if a path is an S3 path""" return path.startswith("s3://")
@validate_call
[docs] def get_s3_path(url: HttpUrl, query: str, exact_match: bool = False) -> list: """Request public S3 path of a specific modo or all modos matching the query string Parameters ---------- remote_url Url to the remote modo server query query string to specify the modo of interest exact_match if True only modos with exactly that id will be returned, otherwise (default) all matching modos """ return requests.get( url=f"{url}/get", params={"query": query, "exact_match": exact_match}, ).json()