example_main_get_samplesMetadata_from_MGnifystudy.py

# Date: 09-12-2023
# Description: This script is an example of how to use the functions from the Functions_get_samplesMetadata_from_MGnifystudy.py script.
# Version: 1.0
# License: MIT License
# Usage: python example_main_get_samplesMetadata_from_MGnifystudy.py
# Warning: The external script relies on the MGnify API, which could have high traffic. If the script fails, try again later.
# References: https://github.com/Multiomics-Analytics-Group/Retrieve_info_MGnifyAPI/blob/main/Scripts/example_main_get_samplesMetadata_from_MGnifystudy.py
# ------------------------------------------------------------------------------------------------------------------------------------
# Import external functions
import pandas as pd
import json
from Functions_get_samplesMetadata_from_MGnifystudy import get_samples_metadata_from_MGnifystudy

# Set the study accession for the MGnify study
study_accession = "MGYS00001392"

# Retrieve the results info for the MGnify study
samples_metadata = get_samples_metadata_from_MGnifystudy(study_accession)

# Export the result of the request to a JSON file
with open(f"../Output/{study_accession}_samples_metadata.json", "w") as outfile:
    json.dump(samples_metadata, outfile)

# Extract the desired attributes and create a DataFrame
sample_list = []

for sample in samples_metadata:
    attributes = sample["attributes"]
    sample_list.append({
        "sample_id": sample["id"],
        "sample_name": attributes["sample-name"],
        "biosample": attributes["biosample"],
        "sample_description": attributes["sample-desc"],
        "latitude": attributes["latitude"],
        "longitude": attributes["longitude"],
        "geolocation": attributes["geo-loc-name"],
        "biome": attributes["environment-biome"],
        "biome_feature": attributes["environment-feature"],
        "biome_material": attributes["environment-material"],
    })

# Create a DataFrame from the list of dictionaries
samples_metadata_df = pd.DataFrame(sample_list)

# Export the dataframe to a CSV file
samples_metadata_df.to_csv(f"../Output/{study_accession}_samples_metadata.csv", index=False)