#!/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.MeSHandMetaNetX.build\_database`
module to recreate `the MetaNetX database <https://www.metanetx.org/>`_ using a graph format and Neo4J,
and then provides an GraphML export file. It also annotates related MeSH_IDs and KEGG Pathway IDs
Please note that, to work, the functions here pre-suppose you have internet access, which will be used to download
MetaNetX's TSVs under a folder provided as ```sys.argv[4]```. (please ensure you have read-write access there)
and query some web SPARQL and REST web services.
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
# 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
"""
mnx_urls = ["https://www.metanetx.org/cgi-bin/mnxget/mnxref/chem_xref.tsv",
"https://www.metanetx.org/cgi-bin/mnxget/mnxref/chem_prop.tsv",
"https://www.metanetx.org/cgi-bin/mnxget/mnxref/chem_isom.tsv",
"https://www.metanetx.org/cgi-bin/mnxget/mnxref/comp_xref.tsv",
"https://www.metanetx.org/cgi-bin/mnxget/mnxref/comp_prop.tsv"
]
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")
datafolder = os.path.abspath(sys.argv[4])
# We download all the necessary DB files
#for index, url in enumerate(mnx_urls):
#print(f"Downloading files: {index + 1}/{len(mnx_urls)}")
#misc.download(url, f"{datafolder}")
#print(f"Splitting files: {index + 1}/{len(mnx_urls)}")
#misc.split_csv(f"{url.split('/')[-1]}", f"{datafolder}", sep='\t', sep_out='\t', startFrom=351, withStepsOf=1000)
all_files = []
for root,dirs,files in os.walk(sys.argv[4]):
for filename in files:
all_files.append( os.path.abspath(os.path.join(root, filename)) )
print("Database ready for import. Commencing process...")
with alive_bar(len(all_files) + 26) as bar:
# First, we import all the files
for filename in os.listdir(datafolder):
#shutil.copyfile(f"{os.path.abspath(sys.argv[4])}/{filename}", f"{Neo4JImportPath}/{filename}")
#build_database.build_from_file(filename, driver)
#os.remove(f"{Neo4JImportPath}/{filename}")
bar()
# Then, we add proteins and their properties:
with driver.session() as session:
#session.run(build_database.add_pept())
bar(); bar(); bar(); bar(); bar() # Add some bulk bars because this will take forever
#session.run(build_database.find_protein_data_in_metanetx())
bar(); bar(); bar(); bar(); bar()
# And their interactions with other MetaNetX metabolites
with driver.session() as session:
session.run(build_database.find_protein_interactions_in_metanetx())
bar(); bar(); bar(); bar(); bar()
# Finally, we try to find KEGG Patways for all metabolites in the DB
with driver.session() as session:
#session.run(build_database.get_kegg_pathways_for_metabolites())
bar(); bar(); bar(); bar(); bar()
# And MeSH IDs, too (by name):
with driver.session() as session:
#session.run(build_database.add_mesh_by_name())
bar(); bar(); bar(); bar(); bar()
# At the end, purge the database
#misc.purge_database(driver)
# And export it:
with driver.session() as session:
session.manage_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()
