Skip to content

Improve plate assay import performance #7124

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
labkey-alan merged 2 commits into from
Oct 16, 2025
Merged

Improve plate assay import performance #7124

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
2cd782d
Improve plate assay import performance
labkey-alan Oct 15, 2025
b3867b4
PR feedback
labkey-alan Oct 15, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
19 changes: 17 additions & 2 deletions api/src/org/labkey/api/assay/AbstractAssayTsvDataHandler.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,7 @@
import java.util.Objects;
import java.util.Set;
import java.util.function.Function;
import java.util.stream.Collectors;

import static java.util.stream.Collectors.toList;
import static org.labkey.api.assay.AssayRunUploadContext.ReImportOption.MERGE_DATA;
Expand Down Expand Up @@ -1084,13 +1085,27 @@ else if (validatorMap.containsKey(pd))

if (plateId != null && wellLocation != null)
{
Map<String, Long> wellSampleCache = plateWellCache.computeIfAbsent(plateId, (id) -> AssayPlateMetadataService.get().getWellLocationToSampleIdMap(container, user, plateId));
boolean loadMaterialsCache = !plateWellCache.containsKey(plateId);
Map<String, Long> wellSampleCache = plateWellCache.computeIfAbsent(plateId, (id) -> AssayPlateMetadataService.get().getWellLocationToSampleIdMap(plateId));

// If we had to load the wellSampleCache we should also preload the ExpMaterials into the
// materialCache, so we don't need to fetch them with individual queries. This has a large
// impact on performance.
if (loadMaterialsCache)
{
Set<Long> samplesToFetch = wellSampleCache.values().stream()
.filter(id -> !materialCache.containsKey(id))
.collect(Collectors.toSet());

for (ExpMaterial m : exp.getExpMaterials(samplesToFetch))
materialCache.put(m.getRowId(), m);
}
sampleId = wellSampleCache.get(wellLocation);
}

if (sampleId != null)
{
material = materialCache.computeIfAbsent(sampleId, (id) -> exp.getExpMaterial(id, containerFilter));
material = materialCache.get(sampleId);
}

if (material != null)
Expand Down
2 changes: 1 addition & 1 deletion api/src/org/labkey/api/assay/plate/AssayPlateMetadataService.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -187,7 +187,7 @@ void applyHitSelectionCriteria(
/**
* Returns a Map of Well Location to Sample RowID for a given Plate ID.
*/
Map<String, Long> getWellLocationToSampleIdMap(Container container, User user, Long plateId);
Map<String, Long> getWellLocationToSampleIdMap(Long plateId);

boolean isWellLookup(ColumnInfo col);

Expand Down
17 changes: 13 additions & 4 deletions assay/src/org/labkey/assay/plate/AssayPlateMetadataServiceImpl.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1518,14 +1518,23 @@ public String format(FieldKey fieldKey)
return new PlateSchema(querySchema, contextualRoles);
}

record WellSampleData(Long sampleId, Integer row, Integer col) {}

@Override
public Map<String, Long> getWellLocationToSampleIdMap(Container container, User user, Long plateId)
public Map<String, Long> getWellLocationToSampleIdMap(Long plateId)
{
// Note: this method intentionally does not use PlateManager.get().getWellData, by selecting only the columns
// we need there is a small but measurable performance boost when importing plate assay data
SimpleFilter filter = new SimpleFilter(WellTable.Column.PlateId.fieldKey(), plateId);
Set<String> columns = Set.of(WellTable.Column.SampleID.name(), WellTable.Column.Row.name(), WellTable.Column.Col.name());
List<WellSampleData> wells = new TableSelector(AssayDbSchema.getInstance().getTableInfoWell(), columns, filter, null).getArrayList(WellSampleData.class);
Map<String, Long> wellLocationToSampleIdMap = new HashMap<>();
List<WellData> wellData = PlateManager.get().getWellData(container, user, plateId, true, false);

for (WellData data : wellData)
wellLocationToSampleIdMap.put(data.getPosition(), data.getSampleId());
for (WellSampleData well : wells)
{
PositionImpl pos = new PositionImpl(null, well.row, well.col);
wellLocationToSampleIdMap.put(pos.getDescription(), well.sampleId);
}

return wellLocationToSampleIdMap;
}
Expand Down