In [ ]:

from biokb_taxtree import DbManager, TurtleCreator, Neo4jImporter
import os

from biokb_taxtree import DbManager, TurtleCreator, Neo4jImporter import os

In [ ]:

# to make sure no environment variable is set
os.environ.pop("CONNECTION_STR", None)
os.environ.pop("NEO4J_USER", None)
os.environ.pop("NEO4J_PASSWORD", None)
os.environ.pop("NEO4J_URI", None)
pass

# to make sure no environment variable is set os.environ.pop("CONNECTION_STR", None) os.environ.pop("NEO4J_USER", None) os.environ.pop("NEO4J_PASSWORD", None) os.environ.pop("NEO4J_URI", None) pass

Workflow without podman-compose¶

Default settings import the data into ~/.biokb/biokb.db

In [ ]:

DbManager().import_data()
# TurtleCreator().create_ttls()
# you can start from a specific list of tax_id like this: 3193(Embryophyta) and 40674 (Mammalia)
TurtleCreator().create_ttls(start_from_tax_ids=[3193, 40674])

DbManager().import_data() # TurtleCreator().create_ttls() # you can start from a specific list of tax_id like this: 3193(Embryophyta) and 40674 (Mammalia) TurtleCreator().create_ttls(start_from_tax_ids=[3193, 40674])

Before starting the import into neo4j start a test container with:

podman run --replace --rm --name biokb-neo4j-test -p7474:7474 -p7687:7687 -e NEO4J_AUTH=neo4j/neo4j_password neo4j:latest

In [ ]:

Neo4jImporter().import_ttls()

Neo4jImporter().import_ttls()

Open Neo4j browser, login with neo4j/neo4j_password