This is a server application which accepts IHE PCD-01 HL7v2 ORU01 messages (see references below) through the Minimal Lower Layer Protocol. These can for example be sent by a medical device or gateway. The application then validates and persists these messages in a database along with the ACK response messages sent out by the server itself.
The application will listen on port 8870 for accepting HL7v2 messages through MLLP.
If a message fails structural validation according to IHE PCD01 profile, the server will respond with an error-ACK message containing an ERR segment with a description of the error for each error found.
The ingested HL7v2 ORU-01 message will be saved in 3 different formats for ease of analysis.
- The following formats are used to store messages as XML fields in an SQL database.
- A custom XML format (T5 XML) which has a structure that follows the IHE PCD01-specified containment tree.
- HL7v2 standard XML format.
- The following format is used for storage in an RDF triple store.
- HL7v2 XML converted to RDF triples.
Observation data is also extracted from messages and stored driectly in SQL tables with separate fields for value, timestamp and a handfull of other data.
The ACK-messages sent in response by the server is also persisted as HL7v2 XML and optionally as RDF triples.
The application requires access to a PostgerSQL>=v9.4 database in which to store ingested messages as well as outgoing ACK-messages. The database must have the PLv8 version of Fhirbase installed, see fhirbase-plv8. This software is at the time of writing in rapid change. The version in use has commit id 128de806c25f60ccf80180dbd20d5439a8a5fbb1, later versions may contain breaking changes. The PLv8 itself is pre-installed on some distributions of PostgreSQL, see (this page )[http://pgxn.org/dist/plv8/] for more information on PLv8 and installation instructions.
A script for initializing all required database schema can be found at sql/initialize.sql. Make sure the database user has the correct permissions in order to create tables.
Example usage:
psql [database name or connection uri] < sql/initialize.sql
See the private infrastructure repository for setting up a basic set of data for demo-purpouses.
Optionally, the application can also store messages as RDF triples to aid further analysis and validation. This requires access to an OpenLink Virtuoso triple store. It has been tested with Virtuoso Open-Source Edition 7.2.1.
The application is written in Java version 8 and uses Gradle for automatic building and dependency management.
Before building the project, make sure to download the virtjena_2.jar and virtjdbc4.jar for Jena 2.10 and later from OpenLink's Vituoso Open-Source Edition download page and put them in the lib/ folder.
Assuming that Java EE 8 development kit is installed and exist on the PATH environment variable, the project can be built with the following command from the project root folder:
./gradlew build
This outputs a .war-file into the build/lib directory.
The build process produces a servlet contained in a .war-file which can be deployed on any compatible Java servlet container. It has been tested with Apache Tomcat 8.0.
The application uses the following environment variables:
JDBC_CONNECTION_STRING- A string containing connection information such as hostname/IP, username, password and other connection settings accepted by the Postgres JDBC driver. All application data will be stored in this database.T5_RDF_HOST- (Optional) IP/hostname of the triple store.T5_RDF_PORT- (Optional) Port number of the triple store.T5_RDF_GRAPH- (Optional) Graph name prefix to use for storing triplified HL7 messages.T5_RDF_USER- (Optional) Triple store username.T5_RDF_PASSWORD- (Optional) Triple store password.T5_DATA_INJECTION_ENABLED- Enable/Disable device identification injection. Valid values aretrueandfalse.T5_TIME_ADJUSTMENT_ENABLED- (Optional) Enable/disable assumption of a time zone other than that of the machine on which the application is running when dealing with messages that does not specify a time zone. Valid values aretrueandfalse.T5_DEFAULT_TIME_ZONE- (Optional) The time zone to assume for incoming message that does not specify a time zone.