/** {@inheritDoc} */
public Query getQuery(String action, List<String> keys) {
// classes for FROM clause
QueryClass qcDisease = new QueryClass(Disease.class);
QueryClass qcGene = new QueryClass(Gene.class);
QueryClass qcPub = new QueryClass(Publication.class);
// fields for SELECT clause
QueryField qfDiseaseName = new QueryField(qcDisease, "diseaseId");
QueryField qfGeneId = new QueryField(qcGene, "id");
QueryField qfGeneName = new QueryField(qcGene, "primaryIdentifier");
QueryField qfId = new QueryField(qcPub, "pubMedId");
QueryField qfPubTitle = new QueryField(qcPub, "title");
// constraints
ConstraintSet cs = new ConstraintSet(ConstraintOp.AND);
// constrain genes to be in list
if (!action.startsWith("population")) {
cs.addConstraint(new BagConstraint(qfGeneId, ConstraintOp.IN, bag.getOsb()));
}
// disease.publication = publication
QueryCollectionReference qcr = new QueryCollectionReference(qcGene, "diseases");
cs.addConstraint(new ContainsConstraint(qcr, ConstraintOp.CONTAINS, qcDisease));
QueryCollectionReference fin =
new QueryCollectionReference(qcDisease, "associatedPublications");
cs.addConstraint(new ContainsConstraint(fin, ConstraintOp.CONTAINS, qcPub));
Query q = new Query();
q.setDistinct(true);
// from statement
q.addFrom(qcGene);
q.addFrom(qcDisease);
q.addFrom(qcPub);
// add constraints to query
q.setConstraint(cs);
// needed for the 'not analysed' number
if ("analysed".equals(action)) {
q.addToSelect(qfGeneId);
// export query
// needed for export button on widget
} else if ("export".equals(action)) {
q.addToSelect(qfId);
q.addToSelect(qfGeneName);
q.addToOrderBy(qfId);
// total queries
// needed for enrichment calculations
} else if (action.endsWith("Total")) {
q.addToSelect(qfGeneId);
Query subQ = q;
q = new Query();
q.addFrom(subQ);
q.addToSelect(new QueryFunction()); // disease count
// needed for enrichment calculations
} else {
q.addToSelect(qfId);
q.addToGroupBy(qfId);
q.addToSelect(new QueryFunction()); // disease count
if ("sample".equals(action)) {
q.addToSelect(qfPubTitle);
q.addToGroupBy(qfPubTitle);
}
}
return q;
}
/** {@inheritDoc} */
public PathQuery generatePathQuery(
ObjectStore os, InterMineBag bag, String series, String category) {
Model model = os.getModel();
PathQuery q = new PathQuery(model);
Path geneSymbol = PathQuery.makePath(model, q, "Gene.symbol");
Path genePrimary = PathQuery.makePath(model, q, "Gene.primaryIdentifier");
Path haemAtlasSampleName =
PathQuery.makePath(model, q, "Gene.probeSets.haemAtlasResults.sampleName");
Path haemAtlasGroup = PathQuery.makePath(model, q, "Gene.probeSets.haemAtlasResults.group");
Path haemAtlasAverage =
PathQuery.makePath(model, q, "Gene.probeSets.haemAtlasResults.averageIntensity");
Path haemAtlasSample = PathQuery.makePath(model, q, "Gene.probeSets.haemAtlasResults.sample");
Path haemAtlasP =
PathQuery.makePath(model, q, "Gene.probeSets.haemAtlasResults.detectionProbabilities");
Path haemAtlasIlluId = PathQuery.makePath(model, q, "Gene.probeSets.illuId");
List<Path> view = new ArrayList<Path>();
view.add(geneSymbol);
view.add(genePrimary);
view.add(haemAtlasSampleName);
view.add(haemAtlasGroup);
view.add(haemAtlasAverage);
view.add(haemAtlasSample);
view.add(haemAtlasP);
view.add(haemAtlasIlluId);
q.setViewPaths(view);
String bagType = bag.getType();
ConstraintOp constraintOp = ConstraintOp.IN;
String constraintValue = bag.getName();
String label = null, id = null, code = q.getUnusedConstraintCode();
Constraint c = new Constraint(constraintOp, constraintValue, false, label, code, id, null);
q.addNode(bagType).getConstraints().add(c);
constraintOp = ConstraintOp.EQUALS;
code = q.getUnusedConstraintCode();
PathNode categoryNode = q.addNode("Gene.probeSets.haemAtlasResults.sampleName");
Constraint categoryConstraint =
new Constraint(constraintOp, series, false, label, code, id, null);
categoryNode.getConstraints().add(categoryConstraint);
constraintOp = ConstraintOp.LESS_THAN;
code = q.getUnusedConstraintCode();
PathNode seriesNode = q.addNode("Gene.probeSets.haemAtlasResults.detectionProbabilities");
Constraint seriesConstraint = new Constraint(constraintOp, 0.01, false, label, code, id, null);
seriesNode.getConstraints().add(seriesConstraint);
q.setConstraintLogic("A and B and C");
q.syncLogicExpression("and");
List<OrderBy> sortOrder = new ArrayList<OrderBy>();
sortOrder.add(new OrderBy(geneSymbol, "asc"));
sortOrder.add(new OrderBy(genePrimary));
q.setSortOrder(sortOrder);
return q;
}
