This docker container will load UMLS data into a PostgreSQL database and also provide PgAdmin for postgres.

• docker 18.06.1-ce or higer
• docker-compose 1.22.0 or higher
• The UMLS data prepared using MetamorphoSys

1. Place all your .RRF files from META into a folder, e.g. /data/META/<all .RRF files>
2. Run the preparation script that will escape some characters in the .RRF data

cd <umls github repo>
./escape.sh "/data/META"    # Path to the META folder with .RRF files
# If the path to your data is /data/META  all is ready. If non open the docker-compose.yml and edit the bind for the /data directory
docker-compose build
docker-compose up     # Optional add -d 

3. Once the data import is done (it can take hours depending on your machine), you can access the PgAdmin on IP:1234 and PostgreSQL on IP:1234

Note: Username and password for PgAdmin are the ones in docker-compose.yml

To fix some bugs when importing, escape all the \ in input data.

chmod a+x escape.sh
./escape.sh "<path to the folder containing RRF files>"

#e.g.
./escape.sh "/data/META"

Take care not to run this script multiple times, as it will escape the escaped chars.

Importing the data can be sometimes problematic:

• There are some problems with the \ - escape chars, easiest solution is to run the small bash script that will escape the \ chars.
• RRF format has bugs and missing rows/columns, sometimes, depending on the UMLS version. You will have to manually check the log of the container to be sure everything was imported nicely
• All tables are not always present, be sure to remove the tables you don't need from the ./postgres/scripts/1_pgsql_all_tables.sql. If you don't do that the improt tends to fail. Or you will have to manually run the scripts using psql.

Some parts of the import sql scripts were taken from: PostgreSQL load & index scripts - by Steve Bedrick, Yeb Havinga available at umls