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Testing

Database

The main requirement for testing is a postgres database, preferably populated with some sample (or real!) data. The options are:

  • a locally installed copy of postgres
  • postgres running in a docker container
  • the whole annotation service running in a docker container

If you have a local copy of postgres running then you also have the postgres user and the psql command line tool. You can run the database initialisation scripts normally.

If you have postgres running in a docker container then you won't have the postgres user (so sudo postgres won't work) and you won't have the psql command. First, install your operating system package which provides psql (probably postgresql-client or similar). Then you can run the database initialisation scripts with the --docker option.

If you are using the whole annotation service in a docker container (see CogStack-SemEHR/Dockerfile.md) then you don't interact with postgres itself, only the externally-visible API, and it already has some sample documents loaded.

Starting postgresql

To use the standard postgresql docker run

sudo docker run -d --rm --name=pg -p 5432:5432 -e POSTGRES_PASSWORD=semehr postgres

To use the annotation_server docker run

sudo docker run -d --rm --name=pg -p 8485:8485 -p 5432:5432 howff/annotation_server

Database creation

First run StructuredReports/src/tools/postgres_init_01.sh [--docker] to create the database and tables.

Ancillary data

Run CogStack-SemEHR/umls/umls_create_postgres.sh [--docker] to populate the UMLS database. Before running this uncompress the supplied CSV files, tar xf umls_20210905.tar.xz

Sample data

Uncompress the supplied data files:

cd StructuredReports/src/data
tar xf mtsamples_ihi_semehr_results.tar.xz

Populate the database with the samples: ./semehr_to_postgres.py -t ../data/mtsamples_ihi_docs -j ../data/mtsamples_ihi_semehr_results -m ../data/mtsamples_ihi_meta

Query

See the script to check if postgres_query_cui restricts to a range of dates, then

./semehr_to_postgres.py -q cui:C0205076