Source code for matchms.importing.load_from_usi

import json
import logging
import numpy as np
import requests
from ..Spectrum import Spectrum

logger = logging.getLogger("matchms")

[docs]def load_from_usi(usi: str, server: str = "", metadata_harmonization: bool = True): """Load spectrum from metabolomics USI. USI returns JSON data with keys "peaks", "n_peaks" and "precuror_mz" .. code-block:: python from matchms.importing import load_from_usi spectrum = load_from_usi("mzspec:MASSBANK::accession:SM858102") print(f"Found spectrum with precursor m/z of {spectrum.get("precursor_mz"):.2f}.") Parameters ---------- usi: Provide the usi. server: string USI server metadata_harmonization : bool, optional Set to False if metadata harmonization to default keys is not desired. The default is True. """ # Create the url url = server + "/json/?usi1=" + usi metadata = {"usi": usi, "server": server} response = requests.get(url, timeout=10) if response.status_code == 404: return None # Extract data and create Spectrum object try: spectral_data = response.json() if spectral_data is None or "peaks" not in spectral_data:"Empty spectrum found (no data found). Will not be imported.") return None peaks = spectral_data["peaks"] if len(peaks) == 0:"Empty spectrum found (no peaks in 'peaks_json'). Will not be imported.") return None mz_list, intensity_list = zip(*peaks) mz_array = np.array(mz_list) intensity_array = np.array(intensity_list) metadata["precursor_mz"] = spectral_data.get("precursor_mz", None) s = Spectrum(mz_array, intensity_array, metadata, metadata_harmonization=metadata_harmonization) return s except json.decoder.JSONDecodeError: logger.warning("Failed to unpack json (JSONDecodeError).") return None