#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# SPDX-FileCopyrightText: 2022 Pablo Marcos <software@loreak.org>
#
# SPDX-License-Identifier: MIT
"""
A python module that leverages the functions present in the :obj:`~CanGraph.GraphifyHMDB.build\_database`
module to recreate `the HMDB database <https://hmdb.ca/>`_ using a graph forma and Neo4J, and then provides an GraphML export file.
Please note that, to work, the functions here pre-suppose you have internet access, which will be used to download
HMDB's XMLs under ```./xmlfolder/``` (please ensure you have read-write access there).
For more details on how to run this script, please consult the package's README
"""
# Import external modules necessary for the script
from neo4j import GraphDatabase # The Neo4J python driver
from alive_progress import alive_bar # A cute progress bar that shows the script is still running
import os, sys, shutil # Vital modules to interact with the filesystem
from time import sleep # A hack to avoid starving the system resources
# Import subscripts for the program
import build_database
# A hack that allows us to de-duplicate the miscleaneous script in this less-used script
sys.path.append("../")
# NOTE: Please beware that, if using this module by itself, you might need to copy "miscelaneous.py" into your path
# This is not the most elegant, but simplifies code maintenance, and this script shouldnt be used much so...
import miscelaneous as misc
[docs]def main():
"""
The function that executes the code
"""
hmdb_urls = ["https://hmdb.ca/system/downloads/current/hmdb_proteins.zip",
"https://hmdb.ca/system/downloads/current/urine_metabolites.zip",
"https://hmdb.ca/system/downloads/current/serum_metabolites.zip",
"https://hmdb.ca/system/downloads/current/csf_metabolites.zip",
"https://hmdb.ca/system/downloads/current/saliva_metabolites.zip",
"https://hmdb.ca/system/downloads/current/feces_metabolites.zip",
"https://hmdb.ca/system/downloads/current/sweat_metabolites.zip"
]
instance = f"{sys.argv[1]}"; user = f"{sys.argv[2]}"; passwd = f"{sys.argv[3]}"
driver = GraphDatabase.driver(instance, auth=(user, passwd))
Neo4JImportPath = misc.get_import_path(driver)
print("Connected to Neo4J")
with driver.session() as session:
session.run( misc.clean_database() )
print("Cleaned DataBase")
for url in hmdb_urls:
filename = f"{url.split('/')[-1].split('.')[0]}.xml"
print(f"Downloading and Unzipping: {filename}...")
misc.download_and_unzip(url, "./xmlfolder")
filepath = os.path.abspath(f"./xmlfolder/{filename}")
shutil.copyfile(filepath, f"{Neo4JImportPath}/{filename}")
if filename == "hmdb_proteins.xml":
print("File downloaded, now splitting its contents...")
total_subfiles = misc.split_xml(f"{Neo4JImportPath}/{filename}", "protein", "hmdb")
print("File splitted, now on to import its contents to Neo4J...")
sleep(5)
with alive_bar(total_subfiles*7) as bar:
for i in range(1, total_subfiles):
newfile = f"{filename.split('.')[0]}_{i}.xml"
# For each file, add its contents to the DB
build_database.build_from_protein_file(newfile, driver)
# And remove it
os.remove(f"{Neo4JImportPath}/{filename.split('.')[0]}_{i}.xml")
else:
print("File downloaded, now splitting its contents...")
total_subfiles = misc.split_xml(f"{Neo4JImportPath}/{filename}", "metabolite", "hmdb")
print("File splitted, now on to import its contents to Neo4J...")
sleep(5)
with alive_bar(total_subfiles*9) as bar:
for i in range(1, total_subfiles):
newfile = f"{filename.split('.')[0]}_{i}.xml"
# For each file, add its contents to the DB
build_database.build_from_metabolite_file(newfile, driver)
# And remove it
os.remove(f"{Neo4JImportPath}/{filename.split('.')[0]}_{i}.xml")
# At the end, we purge the database
misc.purge_database(driver)
# And export it:
with driver.session() as session:
session.write_transaction(misc.export_graphml, "graph.graphml")
bar()
print(f"You can find the exported graph at {Neo4JImportPath}/graph.graphml")
shutil.copyfile(f"{Neo4JImportPath}/graph.graphml", f"./graph.graphml")
print(f"A copy of the file has been saved in this project's work directory")
if __name__ == '__main__':
main()
