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DDIB should not output two subject columns. #2263

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merged 2 commits into from May 19, 2021
Merged

DDIB should not output two subject columns. #2263

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a1df236
DDIB should not output two subject columns.
labkey-matthewb May 17, 2021
d2bb2fd
Update api/src/org/labkey/api/dataiterator/ExistingRecordDataIterator…
labkey-matthewb May 18, 2021
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9 changes: 7 additions & 2 deletions api/src/org/labkey/api/dataiterator/ExistingRecordDataIterator.java
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Expand Up @@ -39,6 +39,7 @@ public abstract class ExistingRecordDataIterator extends WrapperDataIterator
{
public static final String EXISTING_RECORD_COLUMN_NAME = "_" + ExistingRecordDataIterator.class.getName() + "#EXISTING_RECORD_COLUMN_NAME";

final CachingDataIterator _unwrapped;
final TableInfo target;
final ArrayList<ColumnInfo> pkColumns = new ArrayList<>();
final ArrayList<Supplier<Object>> pkSuppliers = new ArrayList<>();
Expand All @@ -52,6 +53,10 @@ public abstract class ExistingRecordDataIterator extends WrapperDataIterator
ExistingRecordDataIterator(DataIterator in, TableInfo target, @Nullable Set<String> keys, boolean useMark)
{
super(in);

// NOTE in might get wrapped with a LoggingDataIterator, so remember the original DataIterator
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this._unwrapped = useMark ? (CachingDataIterator)in : null;

this.target = target;
this.existingColIndex = in.getColumnCount()+1;
this.useMark = useMark;
Expand Down Expand Up @@ -130,7 +135,7 @@ public boolean next() throws BatchValidationException
{
// NOTE: we have to call mark() before we call next() if we want the 'next' row to be cached
if (useMark)
((CachingDataIterator)_delegate).mark();
_unwrapped.mark(); // unwrapped _delegate
boolean ret = super.next();
if (ret && !pkColumns.isEmpty())
prefetchExisting();
Expand Down Expand Up @@ -251,7 +256,7 @@ protected void prefetchExisting() throws BatchValidationException
existingRecords.put(r,(Map<String,Object>)map);
});
// backup to where we started so caller can iterate through them one at a time
((CachingDataIterator)_delegate).reset();
_unwrapped.reset(); // unwrapped _delegate
_delegate.next();
}
}
Expand Down
35 changes: 20 additions & 15 deletions study/src/org/labkey/study/model/DatasetDataIteratorBuilder.java
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Expand Up @@ -198,6 +198,22 @@ public DataIterator getDataIterator(DataIteratorContext context)
continue;
}

if (match == subjectCol)
{
try
{
// translate the incoming participant column
// do a conversion for PTID aliasing
it.translatePtid(in, user);
continue;
}
catch (ValidationException e)
{
setupError(e.getMessage());
return it;
}
}

int out;
if (DefaultStudyDesignWriter.isColumnNumericForeignKeyToDataspaceTable(match.getFk(), true))
{
Expand Down Expand Up @@ -249,19 +265,8 @@ else if (match.getPropertyType() == PropertyType.FILE_LINK)
Integer indexContainer = outputMap.get(containerColumn);
Integer indexReplace = outputMap.get("replace");

// do a conversion for PTID aliasing
Integer translatedIndexPTID = indexPTID;
try
{
translatedIndexPTID = it.translatePtid(indexPTIDInput, user);
}
catch (ValidationException e)
{
context.getErrors().addRowError(e);
}

// For now, just specify null for sequence num index... we'll add it below
it.setSpecialOutputColumns(translatedIndexPTID, null, indexVisitDate, indexKeyProperty, indexContainer);
it.setSpecialOutputColumns(indexPTID, null, indexVisitDate, indexKeyProperty, indexContainer);
it.setTimepointType(timetype);

/* NOTE: these columns must be added in dependency order
Expand Down Expand Up @@ -411,11 +416,11 @@ else if (_datasetDefinition.getUseTimeKeyField())
{
Integer indexVisit = timetype.isVisitBased() ? it.indexSequenceNumOutput : indexVisitDate;
// no point if required columns are missing
if (null != translatedIndexPTID && null != indexVisit)
if (null != indexPTID && null != indexVisit)
{
ScrollableDataIterator scrollable = DataIteratorUtil.wrapScrollable(ret);
_datasetDefinition.checkForDuplicates(scrollable, indexLSID,
translatedIndexPTID, null == indexVisit ? -1 : indexVisit, null == indexKeyProperty ? -1 : indexKeyProperty, null == indexReplace ? -1 : indexReplace,
indexPTID, null == indexVisit ? -1 : indexVisit, null == indexKeyProperty ? -1 : indexKeyProperty, null == indexReplace ? -1 : indexReplace,
context, null,
checkDuplicates);
scrollable.beforeFirst();
Expand Down Expand Up @@ -612,7 +617,7 @@ int translateSequenceNum(Integer indexSequenceNumInput, Integer indexVisitDateIn

int translatePtid(Integer indexPtidInput, User user) throws ValidationException
{
ColumnInfo col = new BaseColumnInfo("ParticipantId", JdbcType.VARCHAR);
ColumnInfo col = new BaseColumnInfo(_datasetDefinition.getStudy().getSubjectColumnName(), JdbcType.VARCHAR);
ParticipantIdImportHelper piih = new ParticipantIdImportHelper(_datasetDefinition.getStudy(), user, _datasetDefinition);
Callable call = piih.getCallable(getInput(), indexPtidInput);
return addColumn(col, call);
Expand Down