package org.ensembl.healthcheck.testcase.funcgen;
import java.util.Map;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.Team;
public class ComparePreviousVersionGenomicProbeFeaturesByArrayWithProbeSets extends ComparePreviousVersionProbeFeaturesFromProbeSetsByArrayBase {
public ComparePreviousVersionGenomicProbeFeaturesByArrayWithProbeSets() {
setTeamResponsible(Team.FUNCGEN);
setDescription("Checks for loss of probes features from genomic mappings for each array that is organised into probe sets.");
}
protected Map<String, Integer> getRawProbeFeaturePerArrayCounts(DatabaseRegistryEntry dbre) {
return getCountsBySQL(dbre, "select array.name, count(distinct probe_feature.probe_feature_id) from array join array_chip using (array_id) join probe using (array_chip_id) join probe_feature using (probe_id) join analysis using (analysis_id) where analysis.logic_name not like \"%transcript%\" group by analysis.logic_name, array.name");
}
@Override
protected String entityDescription() {
return "probe features (normalised count) from genomic mapping";
}
}