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ensure a view context for background link to study tasks (#6164)
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@labkey-klum
labkey-klum authored Dec 24, 2024
1 parent bc66342 commit 84ed5d6
Showing 1 changed file with 111 additions and 92 deletions.
203 changes: 111 additions & 92 deletions study/src/org/labkey/study/assay/StudyPublishManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -136,6 +136,7 @@
import org.labkey.study.query.StudyQuerySchema;
import org.springframework.beans.MutablePropertyValues;

import java.io.Closeable;
import java.io.IOException;
import java.io.OutputStream;
import java.math.BigDecimal;
Expand Down Expand Up @@ -1173,48 +1174,52 @@ public void autoLinkDerivedSamples(ExpSampleType sampleType, List<Integer> keys,
{
if (sampleType != null && sampleType.getAutoLinkTargetContainer() != null)
{
// attempt to auto link the results
QuerySettings qs = new QuerySettings(new MutablePropertyValues(), QueryView.DATAREGIONNAME_DEFAULT);
qs.setSchemaName(SamplesSchema.SCHEMA_NAME);
qs.setQueryName(sampleType.getName());
qs.setBaseFilter(new SimpleFilter().addInClause(FieldKey.fromParts("RowId"), keys));

Map<StudyPublishService.LinkToStudyKeys, FieldKey> fieldKeyMap = StudyPublishService.get().getSamplePublishFieldKeys(user, container, sampleType, qs);
UserSchema userSchema = QueryService.get().getUserSchema(user, container, SamplesSchema.SCHEMA_NAME);
QueryView view = new QueryView(userSchema, qs, null);
// Issue 45238 - configure as API style invocation to skip setting up buttons and other items that
// rely on being invoked inside an HTTP request/ViewContext
view.setApiResponseView(true);
DataView dataView = view.createDataView();
RenderContext ctx = dataView.getRenderContext();
Map<FieldKey, ColumnInfo> selectColumns = dataView.getDataRegion().getSelectColumns();
List<Map<FieldKey, Object>> rows = new ArrayList<>();

try (Results rs = view.getResults())
// Issue 51454 : QueryView needs a view context to initialize properly. Ensure a mock view context when running in the background
try (EnsureViewContext ignore = new EnsureViewContext(container, user))
{
ctx.setResults(rs);
ResultSetRowMapFactory factory = ResultSetRowMapFactory.create(rs);
while (rs.next())
// attempt to auto link the results
QuerySettings qs = new QuerySettings(new MutablePropertyValues(), QueryView.DATAREGIONNAME_DEFAULT);
qs.setSchemaName(SamplesSchema.SCHEMA_NAME);
qs.setQueryName(sampleType.getName());
qs.setBaseFilter(new SimpleFilter().addInClause(FieldKey.fromParts("RowId"), keys));

Map<StudyPublishService.LinkToStudyKeys, FieldKey> fieldKeyMap = StudyPublishService.get().getSamplePublishFieldKeys(user, container, sampleType, qs);
UserSchema userSchema = QueryService.get().getUserSchema(user, container, SamplesSchema.SCHEMA_NAME);
QueryView view = new QueryView(userSchema, qs, null);
// Issue 45238 - configure as API style invocation to skip setting up buttons and other items that
// rely on being invoked inside an HTTP request/ViewContext
view.setApiResponseView(true);
DataView dataView = view.createDataView();
RenderContext ctx = dataView.getRenderContext();
Map<FieldKey, ColumnInfo> selectColumns = dataView.getDataRegion().getSelectColumns();
List<Map<FieldKey, Object>> rows = new ArrayList<>();

try (Results rs = view.getResults())
{
Map<FieldKey, Object> row = new HashMap<>();
ctx.setRow(factory.getRowMap(rs));
ctx.setResults(rs);
ResultSetRowMapFactory factory = ResultSetRowMapFactory.create(rs);
while (rs.next())
{
Map<FieldKey, Object> row = new HashMap<>();
ctx.setRow(factory.getRowMap(rs));

getColumnValue(fieldKeyMap.get(LinkToStudyKeys.ParticipantId), ctx, selectColumns, row);
getColumnValue(fieldKeyMap.get(LinkToStudyKeys.VisitId), ctx, selectColumns, row);
getColumnValue(fieldKeyMap.get(LinkToStudyKeys.VisitLabel), ctx, selectColumns, row);
getColumnValue(fieldKeyMap.get(LinkToStudyKeys.Date), ctx, selectColumns, row);
getColumnValue(FieldKey.fromParts(StudyPublishService.ROWID_PROPERTY_NAME), ctx, selectColumns, row);
getColumnValue(fieldKeyMap.get(LinkToStudyKeys.ParticipantId), ctx, selectColumns, row);
getColumnValue(fieldKeyMap.get(LinkToStudyKeys.VisitId), ctx, selectColumns, row);
getColumnValue(fieldKeyMap.get(LinkToStudyKeys.VisitLabel), ctx, selectColumns, row);
getColumnValue(fieldKeyMap.get(LinkToStudyKeys.Date), ctx, selectColumns, row);
getColumnValue(FieldKey.fromParts(StudyPublishService.ROWID_PROPERTY_NAME), ctx, selectColumns, row);

rows.add(row);
rows.add(row);
}
}
catch (Exception e)
{
throw new ExperimentException(e);
}
}
catch (Exception e)
{
throw new ExperimentException(e);
}

if (!rows.isEmpty())
autoLinkSamples(sampleType, rows, container, user);
if (!rows.isEmpty())
autoLinkSamples(sampleType, rows, container, user);
}
}
}

Expand Down Expand Up @@ -1254,58 +1259,62 @@ public void autoLinkSamples(ExpSampleType sampleType, List<Map<FieldKey, Object>
Set<Study> validStudies = StudyPublishService.get().getValidPublishTargets(user, InsertPermission.class);
if (validStudies.contains(study))
{
LOG.debug(String.format("Resolved target study in container %s for auto-linking with %s from container %s", targetContainerPath, sampleTypeName, containerPath));
List<Map<String, Object>> dataMaps = new ArrayList<>();
// Issue 49253 : QueryView needs a view context to initialize properly. Ensure a mock view context when running in the background
try (EnsureViewContext ignore = new EnsureViewContext(container, user))
{
LOG.debug(String.format("Resolved target study in container %s for auto-linking with %s from container %s", targetContainerPath, sampleTypeName, containerPath));
List<Map<String, Object>> dataMaps = new ArrayList<>();

// attempt to match up the subject/timepoint information even if the sample has not been published to
// a study yet, this includes traversing any parent lineage samples for corresponding information
QuerySettings qs = new QuerySettings(new MutablePropertyValues(), QueryView.DATAREGIONNAME_DEFAULT);
qs.setSchemaName(SamplesSchema.SCHEMA_NAME);
qs.setQueryName(sampleType.getName());
// attempt to match up the subject/timepoint information even if the sample has not been published to
// a study yet, this includes traversing any parent lineage samples for corresponding information
QuerySettings qs = new QuerySettings(new MutablePropertyValues(), QueryView.DATAREGIONNAME_DEFAULT);
qs.setSchemaName(SamplesSchema.SCHEMA_NAME);
qs.setQueryName(sampleType.getName());

Map<LinkToStudyKeys, FieldKey> publishKeys = StudyPublishService.get().getSamplePublishFieldKeys(user, container, sampleType, qs);
final boolean visitBased = study.getTimepointType().isVisitBased();
Map<String, BigDecimal> translateMap = Collections.emptyMap();
Map<LinkToStudyKeys, FieldKey> publishKeys = StudyPublishService.get().getSamplePublishFieldKeys(user, container, sampleType, qs);
final boolean visitBased = study.getTimepointType().isVisitBased();
Map<String, BigDecimal> translateMap = Collections.emptyMap();

if (visitBased && publishKeys.containsKey(LinkToStudyKeys.VisitLabel))
{
// try visit label if we don't have visit ID
translateMap = StudyService.get().getVisitImportMap(study, true);
}
if (visitBased && publishKeys.containsKey(LinkToStudyKeys.VisitLabel))
{
// try visit label if we don't have visit ID
translateMap = StudyService.get().getVisitImportMap(study, true);
}

// the schema supports the subject/timepoint fields
if (publishKeys.containsKey(LinkToStudyKeys.ParticipantId))
{
String timePointPropName = visitBased ? StudyPublishService.SEQUENCENUM_PROPERTY_NAME : StudyPublishService.DATE_PROPERTY_NAME;
for (Map<FieldKey, Object> row : results)
// the schema supports the subject/timepoint fields
if (publishKeys.containsKey(LinkToStudyKeys.ParticipantId))
{
Object timePointValue = getTimepointValue(row, publishKeys, visitBased, translateMap);
if (row.containsKey(publishKeys.get(LinkToStudyKeys.ParticipantId)) && timePointValue != null)
String timePointPropName = visitBased ? StudyPublishService.SEQUENCENUM_PROPERTY_NAME : StudyPublishService.DATE_PROPERTY_NAME;
for (Map<FieldKey, Object> row : results)
{
dataMaps.add(Map.of(
LinkToStudyKeys.ParticipantId.name(), row.get(publishKeys.get(LinkToStudyKeys.ParticipantId)),
timePointPropName, timePointValue,
StudyPublishService.ROWID_PROPERTY_NAME, row.get(FieldKey.fromParts(StudyPublishService.ROWID_PROPERTY_NAME)),
StudyPublishService.SOURCE_LSID_PROPERTY_NAME, sampleType.getLSID()
));
Object timePointValue = getTimepointValue(row, publishKeys, visitBased, translateMap);
if (row.containsKey(publishKeys.get(LinkToStudyKeys.ParticipantId)) && timePointValue != null)
{
dataMaps.add(Map.of(
LinkToStudyKeys.ParticipantId.name(), row.get(publishKeys.get(LinkToStudyKeys.ParticipantId)),
timePointPropName, timePointValue,
StudyPublishService.ROWID_PROPERTY_NAME, row.get(FieldKey.fromParts(StudyPublishService.ROWID_PROPERTY_NAME)),
StudyPublishService.SOURCE_LSID_PROPERTY_NAME, sampleType.getLSID()
));
}
}
}
}

StudyPublishService.get().publishData(
user,
container,
targetContainer,
sampleType.getAutoLinkCategory(),
sampleTypeName,
Pair.of(Dataset.PublishSource.SampleType, sampleType.getRowId()),
dataMaps,
ExpMaterialTable.Column.RowId.toString(),
publishErrors
);

if (!publishErrors.isEmpty())
publishErrors.forEach(LOG::error);
StudyPublishService.get().publishData(
user,
container,
targetContainer,
sampleType.getAutoLinkCategory(),
sampleTypeName,
Pair.of(Dataset.PublishSource.SampleType, sampleType.getRowId()),
dataMaps,
ExpMaterialTable.Column.RowId.toString(),
publishErrors
);

if (!publishErrors.isEmpty())
publishErrors.forEach(LOG::error);
}
}
else
{
Expand Down Expand Up @@ -1745,19 +1754,7 @@ public Map<LinkToStudyKeys, FieldKey> getSamplePublishFieldKeys(User user, Conta

// optionally add columns added through a view, useful for picking up any lineage fields
if (qs != null)
{
if (HttpView.hasCurrentView())
getViewColumns(userSchema, qs, columns);
else
{
// Issue 49253 : the QueryView needs a view context to initialize properly. If we are running in a background job
// push a fake view context onto the stack and remove it when we are done
try (ViewContext.StackResetter ignored = ViewContext.pushMockViewContext(user, container, new ActionURL()))
{
getViewColumns(userSchema, qs, columns);
}
}
}
getViewColumns(userSchema, qs, columns);

for (ColumnInfo ci : columns.values())
{
Expand Down Expand Up @@ -1806,4 +1803,26 @@ private void getViewColumns(UserSchema userSchema, QuerySettings qs, Map<FieldKe
columns.put(entry.getKey(), entry.getValue());
}
}

private static class EnsureViewContext implements Closeable
{
private final boolean _hasCurrentView;
private final int _stackSize;

private EnsureViewContext(Container container, User user)
{
_hasCurrentView = HttpView.hasCurrentView();
_stackSize = HttpView.getStackSize();

if (!_hasCurrentView)
ViewContext.getMockViewContext(user, container, new ActionURL(), true);
}

@Override
public void close()
{
if (!_hasCurrentView)
HttpView.resetStackSize(_stackSize);
}
}
}

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