테크니컬 스토리

CDM 기반의 의료 데이터 분석/설계 오픈소스 OHDSI Atlas 의료 데이터 분석/설계를 위한 OHDSI OHDSI? CDM? OHDSI는 OMOP CDM 기반의 분산 연구망을 표준 및 관련 소프트웨어 도구를 만들고 유지 관리하는 국제적인 비영리 단체입니다. CDM 기반의 오픈소스를 운영하고 있습니다. OHDSI와 누적된 의료 데이터를 활용하여 여러 분석 설계 및 실행을 진행할 수 있습니다. OHDSI Atlas 사용 환경 구성을 위해 OHDSI에서 제공하는 컨테이너를 활용하여 구성하였고, 이를 공유합니다. DB는 PostgreSQL로 구성하였고, 사용자를 위한 Jupyter와 R 등의 분석 컨테이너를 포함하였습니다. 필요 패키지 ●OHDSI WEBAPI ●OHDSI Atlas ●OHDSI Achilles ●R ●PostgreSQL ●Jupyter ●Docker OS 설치 CentOS 7.9 (최소설치) 방화벽 해제 (local)$ systemctl disable firewalld (local)$ systemctl stop firewalld Docker 설치 (local)$ yum -y update (local)$ yum install yum-utils device-mapper-persistent-data lvm2 (local)$ yum-config-manager --add-repo https://download.docker.com/linux/centos/docker-ce.repo (local)$ yum install docker-ce (local)$ systemctl start docker&&systemctl enable docker 작업 폴더 생성 (local)$ mkdir /sourcedata (local)$ mkdir /sourcedata/data (local)$ mkdir /workspace1 (local)$ mkdir /workspace2 (local)$ mkdir /db1 (local)$ mkdir /db2 docker-compose 설치 (local)$ curl -L "https://github.com/docker/compose/releases/download/1.24.1/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose (local)$ chmod +x /usr/local/bin/docker-compose (local)$ ln -s /usr/local/bin/docker-compose /usr/bin/docker-compose SQL 테이블 데이터 다운로드 (local)$ yum install -y git (local)$ cd /sourcedata (local)$ git clone -b v5.3.2 https://github.com/OHDSI/CommonDataModel.git ATLAS webtool compose 파일 다운로드 (local)$ cd /sourcedata (local)$ git clone https://github.com/OHDSI/Broadsea.git PostgreSQL 컨테이너 생성 (local)$ docker run --name postgres1 -d --restart unless-stopped --shm-size=1g \ -p 1040:5432 -e POSTGRES_PASSWORD=Itmaya2009! \ -v /db1:/var/lib/postgresql/data \ -v /sourcedata:/sourcedata \ -v /workspace1:/workspace postgres **--shm-size-=1g 옵션을 실 서버에 구성할때는 32g로 구성하여 성능 확보 필요함 PostgreSQL DB 구성 (local)$ docker exec -ti postgres1 bash (postgres1)$ psql -U postgres (postgres1 #)# CREATE USER atlas PASSWORD 'Itmaya2009!' SUPERUSER; (postgres1 #)# CREATE DATABASE atlasdb OWNER atlas; (postgres1 #)# \c atlasdb (postgres1 #DB)# CREATE SCHEMA cdm; (postgres1 #DB)# CREATE SCHEMA ohdsi; (postgres1 #DB)# CREATE SCHEMA results; (postgres1 #DB)# exit DB 테이블 생성 및 데이터 복사 (local)$ docker exec -ti postgres1 bash 테이블 쿼리 생성 (postgres1)$ cd /sourcedata/CommonDataModel/inst/ddl/5.3/postgresql/ (postgres1)$ echo 'SET search_path to cdm;' | cat - OMOPCDM_postgresql_5.3_ddl.sql > 1.sql (postgres1)$ echo 'SET search_path to cdm;' | cat - OMOPCDM_postgresql_5.3_primary_keys.sql > 2.sql (postgres1)$ echo 'SET search_path to cdm;' | cat - OMOPCDM_postgresql_5.3_constraints.sql > 3.sql (postgres1)$ echo 'SET search_path to cdm;' | cat - OMOPCDM_postgresql_5.3_indices.sql > 4.sql (postgres1)$ sed -i 's/\@cdmDatabaseSchema/cdm/g' /sourcedata/CommonDataModel/inst/ddl/5.3/postgresql/1.sql (postgres1)$ sed -i 's/\@cdmDatabaseSchema/cdm/g' /sourcedata/CommonDataModel/inst/ddl/5.3/postgresql/2.sql (postgres1)$ sed -i 's/\@cdmDatabaseSchema/cdm/g' /sourcedata/CommonDataModel/inst/ddl/5.3/postgresql/3.sql (postgres1)$ sed -i 's/\@cdmDatabaseSchema/cdm/g' /sourcedata/CommonDataModel/inst/ddl/5.3/postgresql/4.sql 테이블 생성 (1.sql) (postgres1)$ psql -U atlas -d atlasdb -a -f 1.sql 권한 변경 (2.sql) (postgres1)$ psql -U atlas -d atlasdb -a -f 2.sql 권한 변경 (3.sql) (postgres1)$ psql -U atlas -d atlasdb -a -f 3.sql 테이블 인덱스 생성 (4.sql) (postgres1)$ psql -U atlas -d atlasdb -a -f 4.sql (postgres1)$ exit webtools, atlas, rstudio 컨테이너 생성 docker compose 구성 (local)$ echo "version: '2' services: broadsea-methods-library: image: ohdsi/broadsea-methodslibrary container_name: achilles1 ports: - "1020:8787" - "1050:6311" - "1060:1444" volumes: - /workspace1:/workspace environment: -PASSWORD=Itmaya2009! broadsea-webtools: image: ohdsi/broadsea-webtools container_name: atlas1 ports: - "1010:8080" volumes: - .:/tmp/drivers/:ro - /workspace1:/workspace - /sourcedata/Broadsea/config-local.js:/usr/local/tomcat/webapps/atlas/js/config-local.js:ro environment: -WEBAPI_URL=http://192.168.0.249:1010 - env=webapi-postgresql - security_enabled=false - security_origin=* - datasource_driverClassName=org.postgresql.Driver - datasource_url=jdbc:postgresql://192.168.0.249:1040/atlasdb - datasource.cdm.schema=cdm - datasource.ohdsi.schema=ohdsi - datasource_username=atlas - datasource_password=Itmaya2009! - spring.jpa.properties.hibernate.default_schema=ohdsi - spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect - spring.batch.repository.tableprefix=ohdsi.BATCH_ - flyway_datasource_driverClassName=org.postgresql.Driver - flyway_datasource_url=jdbc:postgresql://192.168.0.249:1040/atlasdb - flyway_schemas=ohdsi - flyway.placeholders.ohdsiSchema=ohdsi - flyway_datasource_username=atlas - flyway_datasource_password=Itmaya2009! - flyway.locations=classpath:db/migration/postgresql" > /sourcedata/Broadsea/postgresql/docker-compose.yml (local)$ cd /sourcedata/Broadsea/postgresql/ (local)$ docker-compose up -d achilles 컨테이너 ssh 구성 (local)$ docker exec -ti achilles1 bash (achilles1)$ apt update (achilles1)$ apt install -y openssh-server vim (achilles1)$ sed -i 's/\#PermitRootLogin prohibit-password/PermitRootLogin yes/g' /etc/ssh/sshd_config (achilles1)$ sed -i 's/\#Port 22/Port 1444/g' /etc/ssh/sshd_config (achilles1)$ passwd root (achilles1)> 패스워드 입력 (Itmaya2009!) (achilles1)$ service ssh start (achilles1)$ exit atlas DB 연동 (local)$ echo "ALTER TABLE ohdsi.source ALTER COLUMN is_cache_enabled SET DEFAULT true; truncate ohdsi.source; truncate ohdsi.source_daimon; INSERT INTO ohdsi.source( source_id, source_name, source_key, source_connection, source_dialect) VALUES (1, 'OHDSI CDM V5 Database', 'OHDSI-CDMV5', 'jdbc:postgresql://192.168.0.249:1040/atlasdb?user=atlas&password=Itmaya2009!', 'postgresql'); INSERT INTO ohdsi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, priority) VALUES (1, 1, 0, 'cdm', 2); INSERT INTO ohdsi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, priority) VALUES (2, 1, 1, 'cdm', 2); INSERT INTO ohdsi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, priority) VALUES (3, 1, 2, 'results', 2); INSERT INTO ohdsi.source_daimon( source_daimon_id, source_id, daimon_type, table_qualifier, priority) VALUES (4, 1, 3, 'cdm', 2);" > /sourcedata/CommonDataModel/inst/ddl/5.3/postgresql/5.sql (local)$ docker exec -ti postgres1 bash (postgres1)$ psql -U atlas -d atlasdb -a -f /sourcedata/CommonDataModel/inst/ddl/5.3/postgresql/5.sql (postgres1)$ exit Atlas 컨테이너 재시작 (local)$ docker restart atlas1 Achilles 버전 변경 (local)$ docker exec -ti achilles1 bash (achilles1)$ R (achilles1)> remotes::install_github('OHDSI/OhdsiRTools@v2.0.2') (achilles1)>> skip Enter (achilles1)> remotes::install_github('OHDSI/Achilles@v1.7.0') (achilles1)>> skip Enter *** 분석 결과 테이블 생성 (데이터 부재로 오류 발생함. 데이터 없이는 진행하지 말 것) (achilles1)> library(Achilles) (achilles1)> connectionDetails achilles(connectionDetails, cdmDatabaseSchema = "cdm", resultsDatabaseSchema="results", cdmVersion = "5.3.2") (achilles1)> quit() (achilles1)$ exit Jupyter Notebook 구성 jupyter 컨테이너 생성 (local)$ docker run -v /sourcedata:/sourcedata -v /workspace1:/workspace --name=jupyter1 -e GRANT_SUDO=yes --user root -p 1030:8888 -d jupyter/datascience-notebook 패스워드 로그인 설정 (local)$ docker exec -ti jupyter1 bash (jupyter1)$ apt update (jupyter1)$ apt install -y vim (jupyter1)$ ipython (jupyter1)> from notebook.auth import passwd (jupyter1)> passwd() (jupyter1)> Itmaya2009! (jupyter1)> Itmaya2009! (jupyter1)> exit (출력되는 password 보안키를 복사) (jupyter1)$ echo "c.NotebookApp.password_required = True" >> ~/.jupyter/jupyter_notebook_config.py (jupyter1)$ echo "c.NotebookApp.password = '복사한 보안키'" >> ~/.jupyter/jupyter_notebook_config.py (보안키 잘 들어갔는지 vi 로 ~/.jupyter/jupyter_notebook_config.py 파일 마지막줄 확인) (jupyter1)$ exit (local)$ docker restart jupyter1 서비스 인프라 확인 Port 22 : Server Local (CentOS 7.9 Base) ( user:root / password:Itmaya2009! ) atlas config #1 공용볼륨 : /workspace1:/workspace Port 1010 : Atlas (atlas1 container) Port 1020 : R studio (achilles1 container) ( user:rstudio / password:Itmaya2009! ) Port 1030 : Jupyter Notebook (jupyter1 container) ( password:Itmaya2009! ) Port 1040 : PostgreSQL (postgres1 container) ( DB:atlasdb / user:atlas / password:Itmaya2009! ) - schema (cdm, ohdsi, results) Port 1050 : R Serve (achilles1 container) Port 1060 : Dev SSH (achilles1 container) ( user:root / password:Itmaya2009! ) atlas config #2 공용볼륨 : /workspace2:/workspace Port 2010 : Atlas (atlas2 container) Port 2020 : R studio (achilles2 container) ( user:rstudio / password:Itmaya2009! ) Port 2030 : Jupyter Notebook (jupyter2 container) ( password:Itmaya2009! ) Port 2040 : PostgreSQL (postgres2 container) ( DB:atlasdb / user:atlas / password:Itmaya2009! ) - schema (cdm, ohdsi, results) Port 2050 : R Serve (achilles1 container) Port 2060 : Dev SSH (achilles1 container) ( user:root / password:Itmaya2009! ) 서비스 동작 확인 WebAPI : http://192.168.0.249:1010/WebAPI/source/sources atlas : http://192.168.0.249:1010/atlas rStudio : http://192.168.0.249:1020/ ( user:rstudio / password:Itmaya2009! ) Jupyter : http://192.168.0.249:1030/ ( password:Itmaya2009! ) SSH : ssh root@192.168.0.249 -p 1060 ( user:root / password:Itmaya2009! ) DB : jdbc:postgresql://192.168.0.249:1040/atlasdb ( user:atlas / password:Itmaya2009! ) - schema (cdm, ohdsi, results)