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Describe Specimen usage metrics #289

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labkey-jeckels merged 3 commits into from
Oct 28, 2026
Merged

Describe Specimen usage metrics #289

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Describe Specimen usage metrics
labkey-jeckels Oct 23, 2026
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Claude review
labkey-jeckels Oct 24, 2026
a8ade52
Claude review
labkey-jeckels Oct 27, 2026
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29 changes: 22 additions & 7 deletions specimen/src/org/labkey/specimen/SpecimenModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -107,13 +107,24 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;

public class SpecimenModule extends SpringModule
{
private static final Logger LOG = LogHelper.getLogger(SpecimenModule.class, "Specimen metrics");
public static final String NAME = "Specimen";

// Counts are reported only when non-zero
private static final Map<String, String> SPECIMEN_COUNT_DESCRIPTIONS = Map.of(
"simple", "Studies using a simple specimen repository",
"simpleSpecimens", "Specimens across all simple specimen repositories",
"advanced", "Studies using an advanced specimen repository",
"events", "Specimen events across all advanced specimen repositories",
"vials", "Vials across all advanced specimen repositories",
"specimens", "Specimens (vial groupings) across all advanced specimen repositories",
"locations", "Specimen locations summed across all studies",
"locationsInUse", "Specimen locations flagged in use or referenced by specimen requests or other study data, summed across all studies"
);

@Override
public String getName()
{
Expand Down Expand Up @@ -299,7 +310,7 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)

if (null != ss)
{
svc.registerUsageMetrics(NAME, () -> {
svc.registerUsageMetrics(NAME, metrics -> {
// Collect and add specimen repository statistics: simple vs. advanced study count, event/vial/specimen count, count of studies with requests enabled, request count by status
MultiSet<String> specimenMultiSet = new HashMultiSet<>();
MutableInt requestsEnabled = new MutableInt(0);
Expand Down Expand Up @@ -340,13 +351,17 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
LOG.debug(specimenMultiSet.toString());
});

Map<String, Object> specimensMap = specimenMultiSet.uniqueSet().stream().collect(Collectors.toMap(s -> s, specimenMultiSet::getCount));
SPECIMEN_COUNT_DESCRIPTIONS.forEach((key, description) -> {
int count = specimenMultiSet.getCount(key);
metrics.reportedIf(count > 0).put(key, count, description);
});
Map<String, Object> requestsMap = new SqlSelector(SpecimenSchema.get().getSchema(), new SQLFragment("SELECT Label, COUNT(*) FROM study.SampleRequest INNER JOIN study.SampleRequestStatus srs ON StatusId = srs.RowId GROUP BY Label")).getValueMap(String.class);
requestsMap.put("enabled", requestsEnabled);
specimensMap.put("requests", requestsMap);
specimensMap.put("hasLocations", hasLocations.intValue());
metrics.group("requests", "Specimen requests across the server, by status label")
.putAll(requestsMap)
.put("enabled", requestsEnabled.intValue(), "Studies with specimen requests enabled");
metrics.put("hasLocations", hasLocations.intValue(), "Studies with at least one specimen location");

return specimensMap;
return metrics;
});
}
}
Expand Down
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