comparison get_infos.py @ 14:7a57f54c130f draft default tip

planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit dda8b49daae051df39f4a58d5c0d81fbc393cdf4

13:6bcd8f09158d

from argparse import ArgumentParser
from libsbml import readSBMLFromFile
from taxonid import get_taxonid
from requests import get as r_get


def get_biomass_rxn(sbml_doc):
    """
    Returns the biomass reaction of the model

            data = response.json()
            organism = data.get("organism")
            return organism
    except Exception as e:
        print(f"Error querying BiGG: {e}")
    return None

def get_taxon_id(input_name):
    """Try BiGG model name first, then NCBI directly."""
    print(f"Trying input: {input_name}")
    
    # Try resolving as a BiGG model
    organism = get_organism_from_bigg_model(input_name)
    if organism:
        print(f"Model '{input_name}' maps to organism: {organism}")
        taxon_id = get_taxonid(organism)

14:7a57f54c130f

from argparse import ArgumentParser
from libsbml import readSBMLFromFile
from requests import RequestException, get as r_get


def get_biomass_rxn(sbml_doc):
    """
    Returns the biomass reaction of the model

            data = response.json()
            organism = data.get("organism")
            return organism
    except Exception as e:
        print(f"Error querying BiGG: {e}")
    return -1


def get_taxonid(organism_name: str) -> str:
    """Query NCBI Taxonomy for a given organism name and return its Taxon ID."""
    url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
    params = {
        "db": "taxonomy",
        "term": organism_name,
        "retmode": "json"
    }
    try:
        response = r_get(url, params=params, timeout=10)
        response.raise_for_status()
        data = response.json()
        ids = data.get("esearchresult", {}).get("idlist", [])
        return ids[0] if ids else -1
    except RequestException as e:
        print(f"Error querying NCBI for '{organism_name}': {e}")
        return -1


def get_taxon_id(input_name: str) -> str:
    """Try BiGG model name first, then NCBI directly."""
    print(f"Trying input: {input_name}")

    # Try resolving as a BiGG model
    organism = get_organism_from_bigg_model(input_name)
    if organism:
        print(f"Model '{input_name}' maps to organism: {organism}")
        taxon_id = get_taxonid(organism)