Documentation under development.
Given an AnalysisEngine, this package can help set the analysis engine as a server that can be accessed from Python.
From Java, you can start the server from the AnnotationApplication starServer function:
(new AnnotationApplication(ConceptMapperFactory.create(dictionaryFileName), 1))
.startServer(Integer.parseInt(portNumber));
From Python, you can call the server, annotate text using the annotation engine and access the list of annotation.
from py4j.java_gateway import JavaGateway
# Connect to JVM
gateway = JavaGateway()
annotation_app = gateway.entry_point
# Annotate
l = annotation_app.annotate("Example with ConceptMapper for Streptomyces albospinus")
[print(i, i.getBegin(), i.getEnd(), i.getCoveredText()) for i in l.iterator() if str(i.getClass()).endswith("DictTerm")]
This package has been tested with Java 11 and Maven 3.6.3 and Python 3.9
There is a dependency with our ConceptMapper wrapper, that needs to be installed first, please visit:
https://github.com/READ-BioMed/readbiomed-conceptmapper
To install readbiomed-uima-python-interface, first clone it and then run mvn install
Py4j needs to be installed
pip install py4j