/** Setup - Set up a test BEL {@link Document}. */
@Before
public void setupTest() {
NamespaceGroup namespaceGroup = new NamespaceGroup();
Namespace entrezGeneNs = new Namespace("EG", "http://www.belscript.org/ns/entrez-gene");
Namespace hgncNs = new Namespace("HGNC", "http://www.belscript.org/ns/hgnc");
namespaceGroup.setNamespaces(asList(entrezGeneNs, hgncNs));
StatementGroup statementGroup = new StatementGroup();
AnnotationDefinition speciesDefinition =
new AnnotationDefinition("species", "Description", "Usage", asList("9606"));
AnnotationDefinition tissueDefinition =
new AnnotationDefinition("tissue", "Description", "Usage", asList("TH1", "TH2", "AB3"));
AnnotationGroup annotationGroup = new AnnotationGroup();
annotationGroup.setAnnotations(
asList(
CommonModelFactory.getInstance().createAnnotation("9606", speciesDefinition),
CommonModelFactory.getInstance().createAnnotation("TH1", tissueDefinition)));
annotationGroup.setEvidence(
CommonModelFactory.getInstance()
.createEvidence(
"the elevation of intracellular cAMP concentration that results from increased glucagon production also plays a role in the down-regulation process"));
statementGroup.setAnnotationGroup(annotationGroup);
FunctionEnum p = FunctionEnum.PROTEIN_ABUNDANCE;
List<BELObject> args = new ArrayList<BELObject>();
args.add(CommonModelFactory.getInstance().createParameter(hgncNs, "NFKB"));
Term t = new Term(p, args);
FunctionEnum r = FunctionEnum.RNA_ABUNDANCE;
args = new ArrayList<BELObject>();
args.add(CommonModelFactory.getInstance().createParameter(hgncNs, "FAS"));
Term t2 = new Term(r, args);
Statement simpleIncrease =
new Statement(
t,
"",
annotationGroup,
new org.openbel.framework.common.model.Statement.Object(t2),
RelationshipType.INCREASES);
statementGroup.setStatements(asList(simpleIncrease));
Header header = new Header("", asList("Unladen"), asList("Swallow"), "", "", "", "", "");
Document document = new Document(header, statementGroup);
document.setDefinitions(asList(speciesDefinition, tissueDefinition));
document.setNamespaceGroup(namespaceGroup);
protoNetwork = new ProtoNetworkBuilder(document).buildProtoNetwork();
}
/** {@inheritDoc} */
@Override
public Citation clone() {
Calendar newdate = null;
if (date != null) {
newdate = (Calendar) date.clone();
}
return CommonModelFactory.getInstance()
.createCitation(name, reference, comment, newdate, authors, type);
}