In [1]:

from biokb_coconut import DbManager, TurtleCreator, Neo4jImporter
import os
from dotenv import load_dotenv

from biokb_coconut import DbManager, TurtleCreator, Neo4jImporter import os from dotenv import load_dotenv

In [2]:

load_dotenv(os.path.join("..", "..", ".env_template"), override=True)

load_dotenv(os.path.join("..", "..", ".env_template"), override=True)

Out[2]:

True

Workflow with podman-compose¶

In production you should copy .env_template to .env and change passwords! For testing we are using .env_template.

podman-compose -f docker-compose.yml --env-file .env_template up -d

Tip: Before running the following command, please close all other applications that might use significant system resources, as running containers can be resource-intensive.

In [3]:

# DbManager().import_data()
TurtleCreator().create_ttls()

# DbManager().import_data() TurtleCreator().create_ttls()

INFO:root:Starting turtle file generation process.
INFO:root:Creating RDF compounds turtle file.

Creating compounds triples: 100%|██████████| 715822/715822 [02:41<00:00, 4424.91it/s]
INFO:root:Creating RDF ChemicalClass classifiers turtle file.
Creating ChemicalClass triples: 100%|██████████| 461/461 [00:00<00:00, 29156.10it/s]
Creating compound/ChemicalClass link triples: 100%|██████████| 687032/687032 [00:06<00:00, 101581.34it/s]
INFO:root:Creating RDF ChemicalSubClass classifiers turtle file.
Creating ChemicalSubClass triples: 100%|██████████| 1108/1108 [00:00<00:00, 27557.29it/s]
Creating compound/ChemicalSubClass link triples: 100%|██████████| 687032/687032 [00:34<00:00, 19901.66it/s] 
INFO:root:Creating RDF ChemicalSuperClass classifiers turtle file.
Creating ChemicalSuperClass triples: 100%|██████████| 23/23 [00:00<00:00, 24780.12it/s]
Creating compound/ChemicalSuperClass link triples: 100%|██████████| 687032/687032 [00:13<00:00, 49512.09it/s]
INFO:root:Creating RDF DirectParentClassification classifiers turtle file.
Creating DirectParentClassification triples: 100%|██████████| 2103/2103 [00:00<00:00, 25235.59it/s]
Creating compound/DirectParentClassification link triples: 100%|██████████| 687032/687032 [00:10<00:00, 64211.21it/s]
INFO:root:Creating RDF NpClassifierPathway classifiers turtle file.
Creating NpClassifierPathway triples: 100%|██████████| 7/7 [00:00<00:00, 13142.40it/s]
Creating compound/NpClassifierPathway link triples: 100%|██████████| 687032/687032 [00:12<00:00, 54979.87it/s]
INFO:root:Creating RDF NpClassifierSuperclass classifiers turtle file.
Creating NpClassifierSuperclass triples: 100%|██████████| 76/76 [00:00<00:00, 29193.80it/s]
Creating compound/NpClassifierSuperclass link triples: 100%|██████████| 687032/687032 [00:12<00:00, 56003.90it/s]
INFO:root:Creating RDF NpClassifierClass classifiers turtle file.
Creating NpClassifierClass triples: 100%|██████████| 679/679 [00:00<00:00, 26787.43it/s]
Creating compound/NpClassifierClass link triples: 100%|██████████| 687032/687032 [00:11<00:00, 57739.73it/s]
INFO:root:Creating RDF organisms turtle file.
Creating organisms triples: 100%|██████████| 69112/69112 [00:06<00:00, 10133.14it/s]
Creating compound/organism link triples: 100%|██████████| 1243891/1243891 [00:17<00:00, 72502.36it/s] 
INFO:biokb_coconut.rdf.turtle:Packaging turtle files into zip archive.
INFO:root:Turtle files successfully packaged in /home/ceb/.biokb/coconut/data/ttls.zip

Out[3]:

'/home/ceb/.biokb/coconut/data/ttls.zip'

Open Neo4j browser, login with neo4j/neo4j_password

In [4]:

Neo4jImporter().import_ttls()

Neo4jImporter().import_ttls()

INFO:biokb_coconut.rdf.neo4j_importer:Start importing all turtle file in Neo4J.
INFO:biokb_coconut.rdf.neo4j_importer:Delete an existing graph in Neo4J with node label DbCoconut.

Uniqueness constraint on :Resource(uri) found. 
                
                
The store is now: Open

Processing coconut_np_classifier_class.ttl: 100%|██████████| 9/9 [13:08<00:00, 87.62s/it]         

The store is now: Closed
IMPORTED 14936360 TRIPLES

Out[4]:

True