PhenopacketLab

This Maven project is a project to show how an Angular/Springboot application can provide UIs that could be used for the Phenopacket software. The project is made of an Angular part (Frontend) and a Java Spring Boot part (phenopacketlab-restapi).

The Single-page application can be accessed at the following URL (dev version): https://phenopacketlab-dev.jax.org The Spring Boot RESTful API which serves the application with all the necessary ontologies can be found at this URL: https://phenopacketlab-dev.jax.org/swagger-ui/index.html

The project can be deployed in multiple ways:

• frontend dist folder can be deployed by being copied in a Web server and the backend can be deployed as a war file.
• frontend and backend can be both deployed in a single war file on a server.
• frontend and backend can be packaged in an executable file that contains a Tomcat EE instance and that is used to serve the application.

Below are some screenshots of the running application:

The welcome screen:

The phenopacket table with a list of phenopackets:

The Phenopacket creator stepper:

The phenotypic feature creation step with text mining feature:

The disease creation step with text search:

Build from sources

Build the source code by running:

cd PhenopacketLab
./mvnw clean package

Setup PhenopacketLab data directory

PhenopacketLab backend requires several data files to be present to run. The data directory is set up in two steps:

• download non-ontology resources
• preprocess ontologies

Note, an obographs-cli and robot JAR files are required for setup. Check out Obographs and ROBOT to get ahold of the executable JARs.

Run the following to set up the data directory:

OBOGRAPHS_JAR=/Users/elkasb/software-dep/obographs-cli-0.3.0.jar
ROBOT_JAR=/Users/elkasb/software-dep/robot-1.9.1.jar
PLAB_DATADIR=/Users/elkasb/data/phenopacket-lab
PLAB_VERSION=0.1-SNAPSHOT

# 0 - Build the app
#cd PhenopacketLab
./mvnw --projects phenopacketlab-restapi --also-make --batch-mode package

# 1 - Download non-ontology resources
java -jar phenopacketlab-ingest/target/phenopacketlab-ingest-${PLAB_VERSION}.jar ingest ${PLAB_DATADIR}

# 2 - Preprocess ontologies
bash scripts/preprocess-ontologies.sh --data-directory ${PLAB_DATADIR} --obographs-jar ${OBOGRAPHS_JAR} --robot-jar ${ROBOT_JAR}

If not already present, the command will create the path/to/phenopacket-lab folder including missing parent directories. The and download the data files into the folder.

Run PhenopacketLab backend

If using any environment besides local (datastore-emulator) and not on a cloud service you need to set google application credentials for svc-jax-phenopacket for datastore:

GOOGLE_APPLICATION_CREDENTIALS="/path/to/private/key"

Spool up the backend by running:

./mvnw clean package

PL_VERSION=0.1-SNAPSHOT
PL_JAR=phenopacketlab-restapi/target/phenopacketlab-restapi-${PL_VERSION}.jar
PL_DATADIR=path/to/phenopacket-lab
PL_PROFILE=development
java -Dspring.profiles.active=${PL_PROFILE} -Dphenopacketlab.data-directory=${PL_DATADIR} -jar ${PL_JAR} 

By default, backend serves requests at localhost:8080, and the frontend will be at localhost:4200.