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