VOCABULON loads vocabs for breakfast!
...robot breakfast ...and just CDM vocabs ...and just into PostgreSQL servers ...so watch out!
Behold: VOCABULON produces the following help text when started with the -h or --help arguments:
vocabulon is for creating vocab tables and populating them (over the network)
configuration is by envvar or command-line arguments
Usage: vocabulon [-h|--help] [options]
-h / --help show this message
-v / --version print the version number and exit
-d / --debug print additional debugging messages
--pghost PGHOST database server address to connect to (default: 127.0.0.1)
--pgport PGPORT port number to connect to the database server on (default: 5432)
--pguser PGUSER username to use when authenticating to the server (default: user)
--pgpassword PGPASSWORD password to use when authenticating to the server (default: empty string)
--pgdatabase PGDATABASE database name to access on the database server (default: user)
--schema SCHEMA schema to place the vocab tables in (default: vocab)
--schema-owner SCHEMA_OWNER optional owner to apply to created schemas and tables (default: )
--vocab-dir VOCAB_DIR directory where vocab CSV files can be found (default: /vocab)
--scratch-dir SCRATCH_DIR directory where scratch files can be written (default: /work)
Calling forth VOCABULON's awesome power goes like this (assuming you have a directory called vocab with some CSV files in it):
docker run --rm --volume "$(pwd)/vocab:/vocab:ro" edence/vocabulon:1 \
--pghost db.example.com \
--pguser calculon \
--pgpassword all-my-circuits2 \
--pgdatabase omopcdmIf needed, VOCABULON will create the concept, concept_ancestor, concept_class, concept_relationship, concept_synonym, domain, drug_strength, and relationship tables in the chosen schema (vocab by default). It will even create the schema if it's missing.
Next, VOCABULON will unrelentingly populate those tables with data from your puny-barely-a-challenge-at-all CSV files.