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Molecule and PS bulk import by file #7651

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Molecule and PS bulk import by file
XingY May 7, 2026
100427b
crlf
XingY May 7, 2026
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10 changes: 6 additions & 4 deletions audit/src/org/labkey/audit/AuditController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@
import org.labkey.api.settings.AdminConsole;
import org.labkey.api.settings.LookAndFeelProperties;
import org.labkey.api.util.DateUtil;
import org.labkey.api.util.Pair;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.JspView;
Expand Down Expand Up @@ -382,17 +383,18 @@ public void validateForm(AuditTransactionForm form, Errors errors)
@Override
public Object execute(AuditTransactionForm form, BindException errors)
{
List<Long> rowIds;
Pair<List<Long>, Map<Long, Long>> results;
User elevatedUser = ElevatedUser.ensureCanSeeAuditLogRole(getContainer(), getUser());
ContainerFilter cf = ContainerFilter.getContainerFilterByName(form.getContainerFilter(), getContainer(), elevatedUser);
if (form.isSampleType())
rowIds = AuditLogImpl.get().getTransactionSampleIds(form.getTransactionAuditId(), elevatedUser, getContainer(), cf);
results = AuditLogImpl.get().getTransactionSampleIds(form.getTransactionAuditId(), elevatedUser, getContainer(), cf);
else
rowIds = AuditLogImpl.get().getTransactionSourceIds(form.getTransactionAuditId(), elevatedUser, getContainer(), cf);
results = AuditLogImpl.get().getTransactionSourceIds(form.getTransactionAuditId(), elevatedUser, getContainer(), cf);

ApiSimpleResponse response = new ApiSimpleResponse();
response.put("success", true);
response.put("rowIds", rowIds);
response.put("rowIds", results.first);
response.put("dataTypeIds", results.second);

return response;
}
Expand Down
89 changes: 44 additions & 45 deletions audit/src/org/labkey/audit/AuditLogImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
Expand Down Expand Up @@ -247,70 +248,68 @@ public ActionURL getAuditUrl()
return new ActionURL(AuditController.ShowAuditLogAction.class, ContainerManager.getRoot());
}

public List<Long> getTransactionSampleIds(long transactionAuditId, User user, Container container, @Nullable ContainerFilter containerFilter)
public Pair<List<Long>, Map<Long, Long>> getTransactionSampleIds(long transactionAuditId, User user, Container container, @Nullable ContainerFilter containerFilter)
{
List<AuditTypeEvent> transactionEvents = TRANSACTION_EVENT_CACHE.get(transactionAuditId).second;
if (!transactionEvents.isEmpty())
List<SampleTimelineAuditEvent> events;
if (transactionEvents.isEmpty())
{
List<Long> ids = new ArrayList<>();
transactionEvents.forEach(event -> {
if (event instanceof SampleTimelineAuditEvent stEvent)
ids.add(stEvent.getSampleId());
});
return ids;
SimpleFilter filter = new SimpleFilter();
filter.addCondition(FieldKey.fromParts("TransactionID"), transactionAuditId);
events = AuditLogService.get().getAuditEvents(container, user, SampleTimelineAuditEvent.EVENT_TYPE, filter, null, containerFilter);
}

SimpleFilter filter = new SimpleFilter();
filter.addCondition(FieldKey.fromParts("TransactionID"), transactionAuditId);

List<SampleTimelineAuditEvent> events = AuditLogService.get().getAuditEvents(container, user, SampleTimelineAuditEvent.EVENT_TYPE, filter, null, containerFilter);
return events.stream().map(SampleTimelineAuditEvent::getSampleId).collect(Collectors.toList());
else
{
events = transactionEvents.stream()
.filter(SampleTimelineAuditEvent.class::isInstance)
.map(SampleTimelineAuditEvent.class::cast)
.toList();
}
Map<Long, Long> dataTypeRowCounts = new HashMap<>();
List<Long> sampleIds = new ArrayList<>();
events.forEach(event -> {
dataTypeRowCounts.merge(event.getSampleTypeId(), 1L, Long::sum);
sampleIds.add(event.getSampleId());
});
return Pair.of(sampleIds, dataTypeRowCounts);
}

public List<Long> getTransactionSourceIds(long transactionAuditId, User user, Container container, @Nullable ContainerFilter containerFilter)
public Pair<List<Long>, Map<Long, Long>> getTransactionSourceIds(long transactionAuditId, User user, Container container, @Nullable ContainerFilter containerFilter)
{
List<String> lsids = new ArrayList<>();
List<Long> sourceIds = new ArrayList<>();
Map<Long, Long> dataTypeRowCounts = new HashMap<>();
List<AuditTypeEvent> transactionEvents = TRANSACTION_EVENT_CACHE.get(transactionAuditId).second;
if (!transactionEvents.isEmpty())
{
transactionEvents.forEach(event -> {
if (event instanceof DetailedAuditTypeEvent detailedEvent)
{
if (detailedEvent.getNewRecordMap() != null)
{
Map<String, String> newRecord = new CaseInsensitiveHashMap<>(AbstractAuditTypeProvider.decodeFromDataMap(detailedEvent.getNewRecordMap()));
if (newRecord.containsKey("RowId") && !StringUtils.isEmpty(newRecord.get("RowId")))
sourceIds.add(Long.valueOf(newRecord.get("RowId")));
else if (newRecord.containsKey("LSID") && !StringUtils.isEmpty(newRecord.get("LSID")))
lsids.add(newRecord.get("LSID"));
}
}
});
}
else
{
List<DetailedAuditTypeEvent> events = QueryService.get().getQueryUpdateAuditRecords(user, container, transactionAuditId, containerFilter);
List<DetailedAuditTypeEvent> detailedEvents = transactionEvents.isEmpty()
? QueryService.get().getQueryUpdateAuditRecords(user, container, transactionAuditId, containerFilter)
: transactionEvents.stream()
.filter(DetailedAuditTypeEvent.class::isInstance)
.map(DetailedAuditTypeEvent.class::cast)
.toList();

detailedEvents.forEach(event -> {
if (event.getNewRecordMap() != null)
{
Map<String, String> newRecord = new CaseInsensitiveHashMap<>(AbstractAuditTypeProvider.decodeFromDataMap(event.getNewRecordMap()));
if (newRecord.containsKey("RowId") && !StringUtils.isEmpty(newRecord.get("RowId")))
sourceIds.add(Long.valueOf(newRecord.get("RowId")));
else if (newRecord.containsKey("LSID") && !StringUtils.isEmpty(newRecord.get("LSID")))
lsids.add(newRecord.get("LSID"));

events.forEach((event) -> {
if (event.getNewRecordMap() != null)
if (newRecord.containsKey("ClassId") && !StringUtils.isEmpty(newRecord.get("ClassId")))
{
Map<String, String> newRecord = new CaseInsensitiveHashMap<>(AbstractAuditTypeProvider.decodeFromDataMap(event.getNewRecordMap()));
if (newRecord.containsKey("RowId") && !StringUtils.isEmpty(newRecord.get("RowId")))
sourceIds.add(Long.valueOf(newRecord.get("RowId")));
else if (newRecord.containsKey("LSID") && !StringUtils.isEmpty(newRecord.get("LSID")))
lsids.add(newRecord.get("LSID"));

Long classId = Long.valueOf(newRecord.get("ClassId"));
dataTypeRowCounts.merge(classId, 1L, Long::sum);
}
});
}
}
});
if (!lsids.isEmpty())
{
SimpleFilter filter = SimpleFilter.createContainerFilter(container);
filter.addCondition(FieldKey.fromParts("LSID"), lsids, CompareType.IN);
TableSelector selector = new TableSelector(ExperimentService.get().getTinfoData(), Collections.singleton("RowId"), filter, null);
sourceIds.addAll(selector.getArrayList(Long.class));
}
return sourceIds;
return Pair.of(sourceIds, dataTypeRowCounts);
}
}
6 changes: 5 additions & 1 deletion experiment/src/org/labkey/experiment/ExpDataIterators.java
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Original file line number Diff line number Diff line change
Expand Up @@ -96,6 +96,7 @@
import org.labkey.api.exp.query.SamplesSchema;
import org.labkey.api.qc.DataState;
import org.labkey.api.qc.SampleStatusService;
import org.labkey.api.query.AbstractQueryImportAction;
import org.labkey.api.query.BatchValidationException;
import org.labkey.api.query.FieldKey;
import org.labkey.api.query.FileColumnValueMapper;
Expand Down Expand Up @@ -2379,7 +2380,10 @@ public DataIterator getDataIterator(DataIteratorContext context)

// useTransactionAuditCache already set for import and merge in AbstractQueryImportAction.createDataIteratorContext
if (context.getInsertOption() == QueryUpdateService.InsertOption.INSERT)
context.setUseTransactionAuditCache(true);
{
if (context.getConfigParameters().isEmpty() || context.getConfigParameterBoolean(AbstractQueryImportAction.Params.useTransactionAuditCache))
context.setUseTransactionAuditCache(true);
}

// add FileLink DataIterator if any input columns are of type FILE_LINK
if (null != _fileLinkDirectory)
Expand Down
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