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[BI-2803] Create new obsVarCount stat for both Experiment creation and appends use case #502

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[BI-2803] Create new obsVarCount stat for both Experiment creation and appends use case #502

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8 changes: 7 additions & 1 deletion ...er/services/processors/experiment/appendoverwrite/middleware/process/AppendStatistic.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
package org.breedinginsight.brapps.importer.services.processors.experiment.appendoverwrite.middleware.process;

import io.micronaut.context.annotation.Prototype;
import lombok.Setter;
import org.breedinginsight.brapps.importer.model.response.ImportPreviewStatistics;

import java.util.HashSet;
Expand All @@ -32,6 +33,8 @@ public class AppendStatistic {
private int newCount;
private int existingCount;
private int mutatedCount;
@Setter
private int obsVarCount;

public AppendStatistic() {
this.clearData();
Expand All @@ -44,6 +47,7 @@ public void clearData() {
this.newCount = 0;
this.existingCount = 0;
this.mutatedCount = 0;
this.obsVarCount = 0;
}
public int incrementNewCount(Integer value) {
int increment = 0;
Expand Down Expand Up @@ -94,14 +98,16 @@ public Map<String, ImportPreviewStatistics> constructPreviewMap() {
ImportPreviewStatistics newStats = ImportPreviewStatistics.builder().newObjectCount(newCount).build();
ImportPreviewStatistics existingStats = ImportPreviewStatistics.builder().newObjectCount(existingCount).build();
ImportPreviewStatistics mutatedStats = ImportPreviewStatistics.builder().newObjectCount(mutatedCount).build();
ImportPreviewStatistics obsVarStats = ImportPreviewStatistics.builder().newObjectCount(obsVarCount).build();

return Map.of(
"Environments", environmentStats,
"Observation_Units", observationUnitsStats,
"GIDs", gidStats,
"Observations", newStats,
"Existing_Observations", existingStats,
"Mutated_Observations", mutatedStats
"Mutated_Observations", mutatedStats,
"Observation_Variables", obsVarStats
);
}
}
8 changes: 5 additions & 3 deletions ...services/processors/experiment/appendoverwrite/middleware/process/ImportTableProcess.java
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Expand Up @@ -218,7 +218,7 @@ public AppendOverwriteMiddlewareContext process(AppendOverwriteMiddlewareContext
*/
if (phenotypeCols.isEmpty()) {
processedData = processedDataFactory.undefinedDatasetBean();
updatePreviewStatistics(processedData, context, studyName, unitId);
updatePreviewStatistics(processedData, context, studyName, unitId, phenotypeCols.size());
}

// Assemble the pending observation data for all phenotypes
Expand Down Expand Up @@ -332,7 +332,7 @@ public AppendOverwriteMiddlewareContext process(AppendOverwriteMiddlewareContext
processedData.getValidationErrors().ifPresent(errList -> errList.forEach(e -> validationErrors.addError(rowNum + 2, e))); // +2 to account for header row and excel file 1-based row index

// Update import preview statistics and set in the context
updatePreviewStatistics(processedData, context, studyName, unitId);
updatePreviewStatistics(processedData, context, studyName, unitId, varNames.size());

// Construct a pending observation
Optional<PendingImportObject<BrAPIObservation>> pendingProcessedData = Optional.ofNullable(processedData.constructPendingObservation());
Expand Down Expand Up @@ -395,12 +395,14 @@ private boolean isChanged(String cellData, BrAPIObservation observation, String
private void updatePreviewStatistics(VisitedObservationData processedData,
AppendOverwriteMiddlewareContext context,
String studyName,
String unitId) {
String unitId,
int obsVarCount) {
// Update import preview statistics and set in the context
processedData.updateTally(statistic);
statistic.addEnvironmentName(studyName);
statistic.addObservationUnitId(unitId);
statistic.addGid(context.getAppendOverwriteWorkflowContext().getPendingGermplasmByOUId().get(unitId).getBrAPIObject().getAccessionNumber());
statistic.setObsVarCount(obsVarCount);
context.getAppendOverwriteWorkflowContext().setStatistic(statistic);
}
}
15 changes: 14 additions & 1 deletion .../importer/services/processors/experiment/create/workflow/CreateNewExperimentWorkflow.java
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Expand Up @@ -258,6 +258,15 @@ private Map<String, ImportPreviewStatistics> generateStatisticsMap(PendingData p
.count()
);

// Assume observationVariableName is set when pending observations are created.
int obsVarCount = Math.toIntExact(
observationByHash.values()
.stream()
.map(o -> o.getBrAPIObject().getObservationVariableName())
.distinct()
.count()
);

ImportPreviewStatistics environmentStats = ImportPreviewStatistics.builder()
.newObjectCount(environmentNameCounter.size())
.build();
Expand All @@ -276,14 +285,18 @@ private Map<String, ImportPreviewStatistics> generateStatisticsMap(PendingData p
ImportPreviewStatistics mutatedObservationStats = ImportPreviewStatistics.builder()
.newObjectCount(numMutatedObservations)
.build();
ImportPreviewStatistics obsVarStats = ImportPreviewStatistics.builder()
.newObjectCount(obsVarCount)
.build();

return Map.of(
"Environments", environmentStats,
"Observation_Units", obdUnitStats,
"GIDs", gidStats,
"Observations", observationStats,
"Existing_Observations", existingObservationStats,
"Mutated_Observations", mutatedObservationStats
"Mutated_Observations", mutatedObservationStats,
"Observation_Variables", obsVarStats
);
}

Expand Down
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