private void addLink(
Study study,
Map<Integer, Term> stageForNode,
Map<Integer, String> taxonForNode,
LabeledCSVParser links,
Location location)
throws StudyImporterException, NodeFactoryException {
Integer consumerNodeID = Integer.parseInt(links.getValueByLabel("ConsumerNodeID"));
Integer resourceNodeID = Integer.parseInt(links.getValueByLabel("ResourceNodeID"));
String linkType = links.getValueByLabel("LinkType");
InteractType interactType =
interactionMapping.get(StringUtils.trim(StringUtils.lowerCase(linkType)));
if (interactType == null) {
throw new StudyImporterException(
"failed to map interaction type ["
+ linkType
+ "] in line ["
+ links.lastLineNumber()
+ "]");
}
Specimen consumer = nodeFactory.createSpecimen(study, taxonForNode.get(consumerNodeID));
consumer.setLifeStage(stageForNode.get(consumerNodeID));
consumer.setExternalId(getNamespace() + ":NodeID:" + consumerNodeID);
consumer.caughtIn(location);
String resourceName = taxonForNode.get(resourceNodeID);
Specimen resource = nodeFactory.createSpecimen(study, resourceName);
resource.setLifeStage(stageForNode.get(resourceNodeID));
resource.setExternalId(getNamespace() + ":NodeID:" + resourceNodeID);
resource.caughtIn(location);
consumer.interactsWith(resource, interactType);
}
