private Query getExtraQuery() {
Query query = new Query();
query.setOn(project);
query.addDefine("g", genesCollection);
return query;
}
@Override
public IEntity getEntity(ORI collectionURI) {
collectionURI = collectionURI.toAbsolute(query.getOn());
Collection collection = store.getCollection(collectionURI);
SqlEntity entity = new SqlEntity(collection);
store
.getSqlDialect()
.loadEntity(
query,
store.getDDL(collectionURI),
dataRS,
entity,
QueryUtils.newCollectionAlias(query, collectionURI));
return entity;
}
public Mutation(IEntity entity, ICollectionManager collectionManager, Parameters parameters) {
super();
// Parameters
String fieldChr = parameters.get(ImpactDecoratorParameters.FIELD_CHR);
String fieldPosition = parameters.get(ImpactDecoratorParameters.FIELD_POSITION);
String fieldAllele = parameters.get(ImpactDecoratorParameters.FIELD_ALLELE);
String fieldGeneid = parameters.get(ImpactDecoratorParameters.FIELD_GENEID);
String fieldImpact = parameters.get(ImpactDecoratorParameters.FIELD_IMPACT);
// Load mutation values
this.collectionUri = entity.getCollection().getORI();
Object value = entity.get(fieldChr);
if (value != null) {
this.chromosome = String.valueOf(value);
}
if ((value = entity.get(fieldPosition)) != null) {
this.position = Long.valueOf(String.valueOf(value));
}
if ((value = entity.get(fieldAllele)) != null) {
this.allele = String.valueOf(value);
}
this.impact = entity.get(fieldImpact);
project = new ORI(collectionUri.getProjectUrl(), null);
genesCollection = new ORI(parameters.get(ImpactDecoratorParameters.COLLECTION_GENES));
ctCollection =
new ORI(
collectionUri.getProjectUrl(), parameters.get(ImpactDecoratorParameters.COLLECTION_CT));
if ((value = entity.get(fieldGeneid)) != null) {
this.ensembl = String.valueOf(value);
IEntity gene = new EntityModel(genesCollection, this.ensembl).getObject();
Object symbol = gene.get("SYMBOL");
this.symbol = (symbol == null ? "" : "(" + String.valueOf(symbol) + ")");
}
// TODO Load mutation extra query
this.externalId = "";
this.recurrence = 0;
this.samples = 0;
this.frequency = 0.0;
// Load mutation consequences
this.consequences = new HashMap<String, Set<Consequence>>();
String fromAlias = "c";
Query query = new Query();
query.setOn(project);
query.addDefine(fromAlias, ctCollection);
query.setFrom(fromAlias);
query.addSelect(fromAlias, null);
if (getPosition() != null) {
query.setWhere(
new And(
new Equal(fromAlias, fieldChr, getChromosome()),
new And(
new Equal(fromAlias, fieldPosition, getPosition()),
new And(
new Equal(fromAlias, fieldAllele, getAllele()),
new Equal(fromAlias, fieldGeneid, ensembl)))));
} else {
String cellLine = String.valueOf(entity.get("CELLLINEID"));
String cancerSite = String.valueOf(entity.get("PROJECTID"));
query.setWhere(
new And(
new Equal(fromAlias, "PROJECTID", cancerSite),
new And(
new Equal(fromAlias, fieldGeneid, ensembl),
new Equal(fromAlias, "SAMPLEID", cellLine))));
}
IEntityTable ctTable = collectionManager.load(query);
while (ctTable.next()) {
Consequence ct = new Consequence(ctCollection, ctTable);
if (!consequences.containsKey(ct.getSnv())) {
consequences.put(ct.getSnv(), new HashSet<Consequence>());
}
consequences.get(ct.getSnv()).add(ct);
}
}