sierra-moxon / ctd_ingest Goto Github PK

Toy repository to try out several biolink-model predicate refactoring methods Will generate KGX formatted files

prereqs:

• must have ingest.py in two level deep directory (here: ingests/name_of_ingest)
• download and decompress manually
• make sure name in source.yaml matches name of py file and yaml file

For local development:

transform CTD csv to KGX format:

poetry install
poetry run koza transform --source ingests/ctd_chemical_to_gene/ctd_chemical_to_gene.yaml --output-format tsv

remove duplicate nodes? - results in some weird top level rows:

poetry install
poetry run python ctd_ingest/main.py merge --input-dir output --output-dir output/merged
poetry run kgx transform --transform-config neo4j-transform.yaml

load to neo4j with kgx:

docker build -t neo4j-plater .
docker images
docker run -p7474:7474 -p7687:7687  --env NEO4J_AUTH=none --name neo4j-plater 08d381cea73a
poetry run python ctd_ingest/load_neo.py --nodes output/ctd_chemical_to_gene_nodes.tsv --edges output/ctd_chemical_to_gene_edges.tsv --uri bolt://localhost:7687

spin up a TRAPI endpoint with plater

• fork plater
• fill out .env
• fill out openapi yaml
• make sure the servers param in openapi has the http version else defaults to https
• make sure to access via localhost not 0.0.0.0 (matching the servers param)
• ./main.sh navigate to localhost:port/docs to see TRAPI endpoints