Arachne Community Edition build and run manual

Upgrade

Upgrade to 1.16.x

The upgrade to version 16 is feasible only from the 15th version. If you want to upgrade from a version lesser than 15, then go first to 15, and only then to 16

Instalation

Prerequisites

For building and run the Arachne please install following applications:

• Apache Maven 3
• JDK up to 8u241
• LibreOffice 6 - for running the ArachneCentralAPI only
• Apache Solr 7
• Postgres DBMS 9.6+

Prepare databases:

Please create ohdsi user and 2 databases: arachne_portal and datanode. That can achieved by running following command in psql console:

create role ohdsi with LOGIN password 'ohdsi';
create database arachne_portal owner ohdsi;
create database datanode owner ohdsi;

Getting sources

Arachne network consists of two applications – Datanode and CentralApi. Sources are located in the github repositories. Please checkout: ArachneCentralAPI ArachneNodeAPI The latest released version can be found in the master branch.

Solr Configuration

Download solr 7 binaries. Solr configuration is stored in ArachneCentralAPI/solr-config. Please run command to create and configure cores:

solr start -c && \
    solr create_collection -c users -n arachne-config && \
    solr create_collection -c data-sources -n arachne-config && \
    solr create_collection -c studies -n arachne-config && \
    solr create_collection -c analyses -n arachne-config && \
    solr create_collection -c analysis-files -n arachne-config && \
    solr create_collection -c papers -n arachne-config && \
    solr create_collection -c paper-protocols -n arachne-config && \
    solr create_collection -c paper-files -n arachne-config && \
    solr create_collection -c submissions -n arachne-config && \
    solr create_collection -c insights -n arachne-config && \
    solr create_collection -c result-files -n arachne-config && \
    solr create_collection -c study-files -n arachne-config && \
    solr zk upconfig -n arachne-config -d /$PATHTO/ArachneCentralAPI/solr_config -z localhost:9983 && \
    solr stop -all

Start solr application by running following command in the terminal:

solr start -c && \
    solr zk upconfig -n arachne-config -d /$PATHTO/ArachneCentralAPI/solr_config -z localhost:9983 

Solr console should be available at: http://localhost:8983/solr

Build ArachneCentralAPI and ArachneNodeApi

Arachne application property files contains few configuration profiles. For this manual we use DEV. Please review available options in the:

• ArachneCentralAPI/src/main/resources
• ArachneNodeAPI/src/main/resources

1. Open command prompt terminal in the ArachneCentralAPI/ folder and run: mvn clean package -DskipTests -DskipDocker -P dev

2. Open command prompt terminal in the ArachneNodeAPI/ folder and run: mvn clean package -DskipTests -DskipDocker -P dev

Two artifacts should be created: ArachneCentralAPI/target/portal-exec.jar and ArachneNodeAPI/target/datanode-exec.jar which are spring-boot fat jars and contains all the required dependencies.

Start ArachneCentralAPI

Create folder and grant RW access: mkdir -p /var/arachne/files/jcr/workspaces. Arachne applications expect jasypt encryption for passwords. Please generate values using e.g.: jasypt online encoder

Start application using following command:

java -jar ArachneCentralAPI/target/portal-exec.jar --office.home=/usr/lib/libreoffice/ --jasypt.encryptor.password=dummy "--spring.datasource.password=ENC(3b0hKjcVNZjGGLwd85Q+tw==)" "--spring.mail.password=ENC(O8Of4J1ejz9r7tZo05CS/Q==)" --portal.urlWhiteList=https://localhost:8080

spring.mail.password and spring.mail.username contains dummy values in this example, please replace them with your settings, otherwise send mail functionality will not work. Please encrypt email and database passwords with the same jasypt password. You can do it via online or via jasypt cli

ArachneCentralAPI should be available at: https://localhost:8080

Start ArachneNodeAPI

Arachne DataNodeAPI application at start registers in ArachneCentralAPI. In current scenario it should be running on https://localhost:8080

java -jar target/datanode-exec.jar --datanode.arachneCentral.host=https://localhost --datanode.arachneCentral.port=8080 --jasypt.encryptor.password=dummy "--spring.datasource.password=ENC(3b0hKjcVNZjGGLwd85Q+tw==)" "--spring.mail.password=ENC(O8Of4J1ejz9r7tZo05CS/Q==)" --spring.datasource.url=jdbc:postgresql://localhost:5432/datanode

ArachneNodeAPI should be available at: https://localhost:8880

Supply your mail sender configuration parameters otherwise emails will not work.

You may override any configuration parameter using “--name=value” spring boot notation.