/** {@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;
}
