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Describe TargetedMS usage metrics #1298

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Merged
labkey-jeckels merged 5 commits into from
Oct 28, 2026
Merged

Describe TargetedMS usage metrics #1298

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b94bf0f
Describe TargetedMS usage metrics
labkey-jeckels Oct 23, 2026
fa2bd7d
Claude review
labkey-jeckels Oct 24, 2026
0189b57
Fix the QC annotation usage metric query's GROUP BY so Postgres accep…
labkey-jeckels Oct 25, 2026
470909d
Skip usage metric queries when only collecting descriptions
labkey-jeckels Oct 27, 2026
0d829f1
Claude review
labkey-jeckels Oct 27, 2026
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53 changes: 31 additions & 22 deletions src/org/labkey/targetedms/TargetedMSModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,7 @@
import org.labkey.api.settings.OptionalFeatureFlag;
import org.labkey.api.settings.OptionalFeatureService;
import org.labkey.api.targetedms.TargetedMSService;
import org.labkey.api.usageMetrics.SimpleMetricsService;
import org.labkey.api.usageMetrics.UsageMetricsService;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.ActionURL;
Expand Down Expand Up @@ -95,7 +96,7 @@
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
Expand Down Expand Up @@ -561,41 +562,47 @@ protected void init()
UsageMetricsService svc = UsageMetricsService.get();
if (null != svc)
{
svc.registerUsageMetrics(MODULE_NAME, () ->
svc.registerUsageMetrics(MODULE_NAME, metrics ->
{
Map<String, Object> metric = new HashMap<>();
DbSchema schema = TargetedMSManager.getSchema();
metric.put("runCount", new SqlSelector(schema, "SELECT COUNT(*) FROM TargetedMS.Runs WHERE Deleted = ?", Boolean.FALSE).getObject(Long.class));
metric.put("guideSetCount", new SqlSelector(schema, "SELECT COUNT(*) FROM TargetedMS.GuideSet").getObject(Long.class));
metric.put("guideSetContainerCount", new SqlSelector(schema, "SELECT COUNT(DISTINCT Container) FROM TargetedMS.GuideSet").getObject(Long.class));
metrics.put("runCount", () -> new SqlSelector(schema, "SELECT COUNT(*) FROM TargetedMS.Runs WHERE Deleted = ? AND StatusId = ?", Boolean.FALSE, SkylineDocImporter.STATUS_SUCCESS).getObject(Long.class), "Successfully imported Skyline document runs across the server, excluding those marked deleted");
metrics.put("guideSetCount", () -> new SqlSelector(schema, "SELECT COUNT(*) FROM TargetedMS.GuideSet").getObject(Long.class), "QC guide sets across the server");
metrics.put("guideSetContainerCount", () -> new SqlSelector(schema, "SELECT COUNT(DISTINCT Container) FROM TargetedMS.GuideSet").getObject(Long.class), "Folders with at least one QC guide set");

SQLFragment folderTypeSQL = new SQLFragment("SELECT p.value, COUNT(*) AS FolderCount FROM ");
folderTypeSQL.append(PropertySchema.getInstance().getTableInfoProperties(), "p");
folderTypeSQL.append(" INNER JOIN ");
folderTypeSQL.append(PropertySchema.getInstance().getTableInfoPropertySets(), "ps");
folderTypeSQL.append(" ON p.\"set\" = ps.\"set\" WHERE ps.category = 'moduleProperties.TargetedMS' ");
folderTypeSQL.append(" AND p.name = ? GROUP BY value");
// The root holds the site-wide default, not a folder's setting
folderTypeSQL.append(" AND p.name = ? AND p.value IS NOT NULL AND ps.objectid <> ? GROUP BY value");
folderTypeSQL.add(FOLDER_TYPE_PROP_NAME);

Map<String, Long> folderCounts = new HashMap<>();
new SqlSelector(PropertySchema.getInstance().getSchema(), folderTypeSQL).forEach(rs ->
folderCounts.put(rs.getString("value"), rs.getLong("FolderCount")));

metric.put("folderCounts", folderCounts);

SQLFragment annotationFolderCountSQL = new SQLFragment("SELECT at.Name, COUNT(DISTINCT a.Container) AS FolderCount FROM ");
folderTypeSQL.add(ContainerManager.getRoot().getId());

metrics.put("folderCounts", () -> {
Map<String, Object> folderCounts = new LinkedHashMap<>();
new SqlSelector(PropertySchema.getInstance().getSchema(), folderTypeSQL).forEach(rs ->
folderCounts.put(rs.getString("value"), rs.getLong("FolderCount")));
return folderCounts;
}, "Folders by their TargetedMS folder type setting (Experiment, Library, QC, etc.)");

// Built-in types live in /Shared; custom names are user-entered and can repeat across folders
SQLFragment annotationFolderCountSQL = new SQLFragment("SELECT CASE WHEN at.Container = ? THEN at.Name ELSE 'custom' END AS Name, COUNT(DISTINCT a.Container) AS FolderCount FROM ");
annotationFolderCountSQL.add(ContainerManager.getSharedContainer().getId());
annotationFolderCountSQL.append(TargetedMSManager.getTableInfoQCAnnotationType(), "at");
annotationFolderCountSQL.append(" INNER JOIN " );
annotationFolderCountSQL.append(TargetedMSManager.getTableInfoQCAnnotation(), "a");
annotationFolderCountSQL.append(" ON at.Id = a.qcAnnotationTypeId GROUP BY at.Name");
// Repeating the CASE here would bind a second parameter, which Postgres won't match to the SELECT's expression
annotationFolderCountSQL.append(" ON at.Id = a.qcAnnotationTypeId GROUP BY 1");

Map<String, Long> annotationFolderCounts = new HashMap<>();
new SqlSelector(PropertySchema.getInstance().getSchema(), annotationFolderCountSQL).forEach(rs ->
annotationFolderCounts.put(rs.getString("Name"), rs.getLong("FolderCount")));
metrics.put("annotationFolderCounts", () -> {
Map<String, Object> annotationFolderCounts = new LinkedHashMap<>();
new SqlSelector(schema, annotationFolderCountSQL).forEach(rs ->
annotationFolderCounts.put(rs.getString("Name"), rs.getLong("FolderCount")));
return annotationFolderCounts;
}, "Folders with at least one QC annotation of each annotation type, by built-in type name, with all custom types under 'custom'");

metric.put("annotationFolderCounts", annotationFolderCounts);

return metric;
return metrics;
});
}
TargetedMSService.setInstance(new TargetedMSServiceImpl());
Expand Down Expand Up @@ -626,6 +633,8 @@ protected void init()
@Override
protected void startupAfterSpringConfig(ModuleContext moduleContext)
{
SimpleMetricsService.get().describeClientSideFeatureArea("panoramaQCPlot", "QC trend plot y-axis zoom use: yAxisZoom when a user zooms an axis, yAxisZoomReset when a zoom is reset");

PipelineService service = PipelineService.get();
service.registerPipelineProvider(new TargetedMSPipelineProvider(this));

Expand Down
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