vocabulon

VOCABULON loads vocabs for breakfast!

...robot breakfast ...and just CDM vocabs ...and just into PostgreSQL servers ...so watch out!

usage

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)

--key-idx KEY_IDX            enable setting primary keys, foreign keys, indexes, and constraints
                             (default: TRUE)

--cdm-schema CDM_SCHEMA                      schema to place the vocab tables in
                                             (default: omopcdm)
--cdm-schema-owner CDM_SCHEMA_OWNER          optional owner to apply to created
                                             schemas and tables
                                             (default: )
--results-schema RESULTS_SCHEMA              schema to place the vocab tables in
                                             (default: results)
--results-schema-owner RESULTS_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 omopcdm

If 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.