Startup script for OHDSI Broadsee

broadsee-start.sh

#!/bin/bash

PGSCHEMA=${1:-public}; PGDATABASE=${PGDATABASE:-postgres}
PGHOST=${PGHOST:-localhost}; PGPORT=${PGPORT:-5432}
PGUSER=${PGUSER:-postgres}; PGPASSWORD=${PGPASSWORD:-postgres}

PGURI="postgresql://${PGHOST}:${PGPORT}/${PGDATABASE}"

tmp_docker_compose="docker-compose.yml"
cat > ${tmp_docker_compose} <<EOB
version: '2'
services:
  "methods_library":
    image: "ohdsi/broadsea-methodslibrary"
    ports:
      - "8787:8787"
      - "6311:6311"
  "webtools":
    image: "ohdsi/broadsea-webtools"
    ports:
      - "8080:8080"
    volumes:
      - .:/tmp/drivers/:ro
      - .:/tmp/achilles-data-reports/:ro
    environment:
      - WEBAPI_URL="http://localhost:8080"
      - env="webapi-postgresql"
      - datasource.driverClassName="org.postgresql.Driver"
      - datasource.url="jdbc:postgresql://${PGHOST}:${PGPORT}/${PGDATABASE}"
      - datasource.cdm.schema="${PGSCHEMA}"
      - datasource.ohdsi.schema="ohdsi"
      - datasource.username="${PGUSER}"
      - datasource.password="${PGPASSWORD}"
      - spring.jpa.properties.hibernate.default_schema="ohdsi"
      - spring.batch.repository.tableprefix=ohdsi.BATCH_
      - flyway.datasource.driverClassName="org.postgresql.Driver"
      - flyway.datasource.url="jdbc:${PGURI}"
      - flyway.schemas="ohdsi"
      - flyway.placeholders.ohdsiSchema="ohdsi"
      - flyway.datasource.username="${PGUSER}"
      - flyway.datasource.password="${PGPASSWORD}"
      - flyway.locations="classpath:db/migration/postgresql"
EOB

tmp_source_daimon="source_source_daimon.sql"
cat > ${tmp_source_daimon} <<EOB
-- remove any previously added database connection configuration data
TRUNCATE ohdsi.source;
TRUNCATE ohdsi.source_daimon;

-- OHDSI CDM source
INSERT INTO ohdsi.source(
                source_id,
                source_name,
                source_key,
                source_connection,
                source_dialect)
     VALUES (1, 'OHDSI CDM V5 Database', 'OHDSI-CDMV5',
                'jdbc:${PGURI}?user=${PGUSER}&password=${PGPASSWORD}',
                'postgresql');

-- CDM daimon
INSERT INTO ohdsi.source_daimon(
                source_daimon_id,
                source_id,
                daimon_type,
                table_qualifier,
                priority)
     VALUES (1, 1, 0, '${PGSCHEMA}', 2);

-- VOCABULARY daimon
INSERT INTO ohdsi.source_daimon(
                source_daimon_id,
                source_id,
                daimon_type,
                table_qualifier,
                priority)
    VALUES (2, 1, 1, '${PGSCHEMA}', 2);

-- RESULTS daimon
INSERT INTO ohdsi.source_daimon(
                source_daimon_id,
                source_id,
                daimon_type,
                table_qualifier,
                priority)
     VALUES (3, 1, 2, 'ohdsi', 2);

-- EVIDENCE daimon
INSERT INTO ohdsi.source_daimon(
                source_daimon_id,
                source_id,
                daimon_type,
                table_qualifier,
                priority)
     VALUES (4, 1, 3, 'ohdsi', 2);
EOB

docker-compose --file ${tmp_docker_compose} --project-name "broadsee" up

rm ${tmp_docker_compose}
rm ${tmp_source_daimon}