JarCastingProtempa Neo4j Tools
Department of Biomedical Informatics, Emory University, Atlanta, GA
What does it do?
It provides a Protempa destination for loading data into a Neo4j graph database. Protempa destinations implement the org.protempa.dest.Destination interface and process output from the temporal abstraction process. See the Protempa project's README for more details on Protempa's architecture.
Latest release:
Version 4.0
Updated Protempa dependency.
Version 3.0
Updated Protempa dependency.
Version 2.0
Updated Protempa dependency.
Version 1.0
Supports loading and updating a Neo4j database with the output of Protempa.
Build requirements
Runtime requirements
Building it
The project uses the maven build tool. Typically, you build it by invoking mvn clean install at the command line. For simple file changes, not additions or deletions, you can usually use mvn install. See https://github.com/eurekaclinical/dev-wiki/wiki/Building-Eureka!-Clinical-projects for more details.
Maven dependency
<dependency>
<groupId>org.eurekaclinical</groupId>
<artifactId>aiw-neo4j-etl</artifactId>
<version>version</version>
</dependency>
Installation
Just put the aiw-neo4j-etl jarfile and its dependencies in the classpath, and Protempa will automatically register it.
Using it
Here is an example:
import org.protempa.SourceFactory;
import org.protempa.backend.Configurations;
import org.protempa.bconfigs.ini4j.INIConfigurations;
import org.protempa.Protempa;
import org.protempa.dest.Destination;
import org.protempa.dest.map.MapDestination;
import org.protempa.query.DefaultQueryBuilder;
import org.protempa.query.Query;
import edu.emory.cci.aiw.neo4jetl.Neo4jDestination;
// An implementation of org.protempa.backend.Configurations provides the backends to use.
Configurations backends = new INIConfigurations(new File("src/test/resources"));
SourceFactory sourceFactory = new SourceFactory(backends.load("protempa-config.ini"));
// Use try-with-resources to ensure resources are cleaned up.
try (Protempa protempa = Protempa.newInstance(sourceFactory)) {
DefaultQueryBuilder q = new DefaultQueryBuilder();
q.setName("My test query");
q.setPropositionIds(new String[]{"ICD9:Diagnoses", "ICD9:Procedures", "LAB:LabTest", "Encounter", "MED:medications", "VitalSign",
"PatientDetails"}); // an array of the concept ids of the data to retrieve and/or temporal patterns to compute
Query query = protempa.buildQuery(q);
// An implementation of org.protempa.dest.Destination processes output from the temporal abstraction process.
Configuration neo4jConfig = //implementation of edu.emory.cci.aiw.neo4jetl.config.Configuration
Destination dest = new Neo4jDestination(neo4jConfig);
protempa.execute(query, dest);
}
This Protempa destination loads data into Neo4j using Neo4j's embedded mode for performance. It will shut Neo4j server down at the beginning of the data load, and start it after the data load has ended.
License
Unlike other Eureka! Clinical projects, this one is available under GNU General Public License version 3 due to the licensing of the Neo4j libraries on which this project depends.
