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Merged
labkey-adam merged 3 commits into from
Oct 17, 2026
Merged

Use helper methods to create IN clauses #1087

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f22631a
Use helper methods to create IN clauses
labkey-adam Oct 15, 2026
3be3a87
Migrate away from deprecated StringUtils methods
labkey-adam Oct 15, 2026
762d7ef
Pre-compute IN clause
labkey-adam Oct 17, 2026
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4 changes: 2 additions & 2 deletions elisa/src/org/labkey/elisa/plate/BioTekPlateReader.java
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Expand Up @@ -15,7 +15,7 @@
*/
package org.labkey.elisa.plate;

import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Strings;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.CellType;
import org.apache.poi.ss.usermodel.Row;
Expand Down Expand Up @@ -43,7 +43,7 @@ protected boolean isValidStartRow(Sheet sheet, int row)
{
for (Cell cell : sheetRow)
{
if (cell.getCellType() == CellType.STRING && StringUtils.equalsIgnoreCase(cell.getStringCellValue(), "A"))
if (cell.getCellType() == CellType.STRING && Strings.CI.equals(cell.getStringCellValue(), "A"))
continue;
else if (cell.getCellType() != CellType.NUMERIC)
return false;
Expand Down
5 changes: 3 additions & 2 deletions flow/enginesrc/org/labkey/flow/analysis/model/FlowJoWorkspace.java
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Expand Up @@ -17,6 +17,7 @@
package org.labkey.flow.analysis.model;

import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Strings;
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.Nullable;
import org.junit.Assert;
Expand Down Expand Up @@ -392,8 +393,8 @@ protected double getRange(Element elParameter)

static public String ___cleanName(String name)
{
name = StringUtils.replace(name, "<", CompensationMatrix.PREFIX);
name = StringUtils.replace(name, ">", CompensationMatrix.SUFFIX);
name = Strings.CS.replace(name, "<", CompensationMatrix.PREFIX);
name = Strings.CS.replace(name, ">", CompensationMatrix.SUFFIX);
name = StringUtils.replaceChars(name, ',', ';');
// replace MacRoman em-dash and en-dash
name = StringUtils.replaceChars(name, PopulationName.MAC_EMDASH, '-');
Expand Down
6 changes: 3 additions & 3 deletions flow/src/org/labkey/flow/ScriptParser.java
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Expand Up @@ -15,7 +15,7 @@
*/
package org.labkey.flow;

import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Strings;
import org.apache.xmlbeans.XmlError;
import org.apache.xmlbeans.XmlException;
import org.apache.xmlbeans.XmlOptions;
Expand Down Expand Up @@ -83,7 +83,7 @@ public void parse(String script)
XmlOptions options = new XmlOptions();
List<XmlError> errors = new ArrayList<>();
options.setDocumentType(ScriptDocument.type);
script = StringUtils.replace(script, "<script>", "<script xmlns=\"" + ScriptDocument.type.getContentModel().getName().getNamespaceURI() + "\">");
script = Strings.CS.replace(script, "<script>", "<script xmlns=\"" + ScriptDocument.type.getContentModel().getName().getNamespaceURI() + "\">");
ScriptDocument doc = ScriptDocument.Factory.parse(new StringReader(script), options);
options.setErrorListener(errors);

Expand All @@ -92,7 +92,7 @@ public void parse(String script)
for (XmlError xmlError : errors)
{
String message = xmlError.getMessage();
message = StringUtils.replace(message, "@" + ScriptDocument.type.getContentModel().getName().getNamespaceURI(), "");
message = Strings.CS.replace(message, "@" + ScriptDocument.type.getContentModel().getName().getNamespaceURI(), "");
String location = xmlError.getCursorLocation().xmlText();
if (location.length() > 100)
location = StringUtilsLabKey.leftSurrogatePairFriendly(location, 100);
Expand Down
21 changes: 6 additions & 15 deletions flow/src/org/labkey/flow/controllers/executescript/ChooseRunsToAnalyzeForm.java
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Expand Up @@ -226,26 +226,17 @@ public SimpleFilter getBaseFilter(TableInfo table, Filter filter)
SimpleFilter ret = new SimpleFilter(filter);

List<FlowRun> runs = FlowRun.getRunsForContainer(getContainer(), FlowProtocolStep.keywords);
int runCount = 0;
SQLFragment sql = new SQLFragment("RowId IN (");
String comma = "";
for (FlowRun run : runs)
{
if (run.getPath() == null)
continue;
sql.append(comma);
comma = ",";
sql.appendValue(run.getRunId());
runCount ++;
}
sql.append(")");
if (runCount == 0)
List<Long> runIds = runs.stream()
.filter(run -> run.getPath() != null)
.map(FlowRun::getRunId)
.toList();
if (runIds.isEmpty())
{
ret.addWhereClause(new SQLFragment("1 = 0"));
}
else
{
ret.addWhereClause(sql, FieldKey.fromParts("RowId"));
ret.addInClause(FieldKey.fromParts("RowId"), runIds);
}
return ret;
}
Expand Down
16 changes: 4 additions & 12 deletions flow/src/org/labkey/flow/controllers/well/WellController.java
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Expand Up @@ -105,11 +105,13 @@
import java.io.IOException;
import java.net.URI;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.TreeSet;

Expand Down Expand Up @@ -756,18 +758,8 @@ public boolean handlePost(UpdateKeywordsForm form, BindException errors)
update.add(getContainer());
update.add(ObjectType.fcsKeywords.getTypeId());
update.add(_keywordid);
update.append(" AND value IN (");
String param = "?";
for (int i=0 ; i<form.from.length ; i++)
{
if (null != form.from[i])
{
update.append(param);
update.add(form.from[i]);
param = ",?";
}
}
update.append(")");
update.append(" AND value");
update.appendInClause(Arrays.stream(form.from).filter(Objects::nonNull).toList(), FlowManager.get().getSchema().getSqlDialect());

int updated = new SqlExecutor(FlowManager.get().getSchema()).execute(update);

Expand Down
6 changes: 3 additions & 3 deletions flow/src/org/labkey/flow/data/FieldSubstitution.java
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Expand Up @@ -16,7 +16,7 @@

package org.labkey.flow.data;

import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Strings;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.labkey.api.query.FieldKey;
Expand All @@ -38,10 +38,10 @@ static public FieldSubstitution fromString(String s)
int ichCur = 0;
while (true)
{
int ichExprStart = StringUtils.indexOf(s, "${", ichCur);
int ichExprStart = Strings.CS.indexOf(s, "${", ichCur);
if (ichExprStart < 0)
break;
int ichExprEnd = StringUtils.indexOf(s, "}", ichExprStart);
int ichExprEnd = Strings.CS.indexOf(s, "}", ichExprStart);
if (ichExprEnd < 0)
break;
if (ichExprStart > ichCur)
Expand Down
14 changes: 7 additions & 7 deletions flow/src/org/labkey/flow/persist/AttributeSetHelper.java
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Expand Up @@ -15,13 +15,13 @@
*/
package org.labkey.flow.persist;

import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.collections.LongHashMap;
import org.labkey.api.data.Container;
import org.labkey.api.data.DbScope;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.SqlSelector;
import org.labkey.api.data.Table;
import org.labkey.api.exp.api.ExpData;
Expand Down Expand Up @@ -254,12 +254,12 @@ private static void loadFromDb(final AttributeSet attrs, AttrObject obj, final b

if (!keywordIDs.isEmpty())
{
String sqlKeywordAliaes = "SELECT A.name AS PreferredName, B.Name AS AliasName\n" +
SQLFragment sqlKeywordAliaes = new SQLFragment("SELECT A.name AS PreferredName, B.Name AS AliasName\n" +
"FROM flow.KeywordAttr A\n" +
"INNER JOIN flow.KeywordAttr B\n" +
"ON A.RowId = B.Id\n" +
"AND B.RowId != B.Id\n" +
"AND A.RowId IN (" + StringUtils.join(keywordIDs, ", ") + ")";
"AND A.RowId").appendInClause(keywordIDs, mgr.getSchema().getSqlDialect());

new SqlSelector(mgr.getSchema(), sqlKeywordAliaes).forEach(rs -> attrs.addKeywordAlias(rs.getString(1), rs.getString(2)));
}
Expand All @@ -282,12 +282,12 @@ private static void loadFromDb(final AttributeSet attrs, AttrObject obj, final b

if (!statisticIDs.isEmpty())
{
String sqlStatisticAliaes = "SELECT A.name AS PreferredName, B.Name AS AliasName\n" +
SQLFragment sqlStatisticAliaes = new SQLFragment("SELECT A.name AS PreferredName, B.Name AS AliasName\n" +
"FROM flow.StatisticAttr A\n" +
"INNER JOIN flow.StatisticAttr B\n" +
"ON A.RowId = B.Id\n" +
"AND B.RowId != B.Id\n" +
"AND A.RowId IN (" + StringUtils.join(statisticIDs, ", ") + ")";
"AND A.RowId").appendInClause(statisticIDs, mgr.getSchema().getSqlDialect());

new SqlSelector(mgr.getSchema(), sqlStatisticAliaes).forEach(rs -> attrs.addStatisticAlias(new StatisticSpec(rs.getString(1)), new StatisticSpec(rs.getString(2))));
}
Expand Down Expand Up @@ -330,12 +330,12 @@ private static void loadFromDb(final AttributeSet attrs, AttrObject obj, final b

if (!graphIDs.isEmpty())
{
String sqlGraphAliaes = "SELECT A.name AS PreferredName, B.Name AS AliasName\n" +
SQLFragment sqlGraphAliaes = new SQLFragment("SELECT A.name AS PreferredName, B.Name AS AliasName\n" +
"FROM flow.GraphAttr A\n" +
"INNER JOIN flow.GraphAttr B\n" +
"ON A.RowId = B.Id\n" +
"AND B.RowId != B.Id\n" +
"AND A.RowId IN (" + StringUtils.join(graphIDs, ", ") + ")";
"AND A.RowId").appendInClause(graphIDs, mgr.getSchema().getSqlDialect());

new SqlSelector(mgr.getSchema(), sqlGraphAliaes).forEach(rs -> attrs.addGraphAlias(new GraphSpec(rs.getString(1)), new GraphSpec(rs.getString(2))));
}
Expand Down
53 changes: 16 additions & 37 deletions flow/src/org/labkey/flow/persist/FlowManager.java
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Expand Up @@ -17,7 +17,6 @@
package org.labkey.flow.persist;

import jakarta.servlet.http.HttpServletResponse;
import org.apache.commons.collections4.iterators.ArrayIterator;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
Expand All @@ -44,6 +43,7 @@
import org.labkey.api.data.Table;
import org.labkey.api.data.TableInfo;
import org.labkey.api.data.TableSelector;
import org.labkey.api.data.dialect.SqlDialect;
import org.labkey.api.dataiterator.DataIteratorContext;
import org.labkey.api.dataiterator.MapDataIterator;
import org.labkey.api.exp.Handler;
Expand Down Expand Up @@ -96,8 +96,6 @@
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
Expand Down Expand Up @@ -953,14 +951,8 @@ public List<AttrObject> getAttrObjects(Collection<ExpData> datas)
{
if (datas.isEmpty())
return Collections.emptyList();
SQLFragment sql = new SQLFragment ("SELECT * FROM " + getTinfoObject().toString() + " WHERE DataId IN (");
String comma = "";
for (ExpData data : datas)
{
sql.append(comma).appendValue(data.getRowId());
comma = ",";
}
sql.append(")");
SQLFragment sql = new SQLFragment ("SELECT * FROM " + getTinfoObject().toString() + " WHERE DataId");
sql.appendInClause(datas.stream().map(ExpData::getRowId).toList(), getSchema().getSqlDialect());
AttrObject[] array = new SqlSelector(getSchema(), sql).getArray(AttrObject.class);
return Arrays.asList(array);
}
Expand Down Expand Up @@ -1023,31 +1015,27 @@ public AttrObject createAttrObject(@NotNull ExpData data, ObjectType type, URI u

int MAX_BATCH = 1000;

private String join(Integer[] oids, int from, int to)
{
Iterator<Integer> i = new ArrayIterator<>(oids, from, to);
return StringUtils.join(i, ',');
}

private void deleteAttributes(Integer[] oids)
{
if (oids.length == 0)
return;

SqlExecutor executor = new SqlExecutor(getSchema());
SqlDialect dialect = getSchema().getSqlDialect();

for (int from = 0, to; from < oids.length; from = to)
{
to = from + MAX_BATCH;
if (to > oids.length)
to = oids.length;

String list = join(oids, from, to);
// XXX: delete no longer referenced statattr afterwards?
executor.execute("DELETE FROM flow.Statistic WHERE ObjectId IN (" + list + ")");
executor.execute("DELETE FROM flow.Keyword WHERE ObjectId IN (" + list + ")");
executor.execute("DELETE FROM flow.Graph WHERE ObjectId IN (" + list + ")");
executor.execute("DELETE FROM flow.Script WHERE ObjectId IN (" + list + ")");
List<Integer> list = Arrays.asList(oids).subList(from, to);
Comment thread
labkey-adam marked this conversation as resolved.
var inList = new SQLFragment().appendInClause(list, dialect);
// XXX: delete no longer referenced statattr afterward?
executor.execute(new SQLFragment("DELETE FROM flow.Statistic WHERE ObjectId").append(inList));
executor.execute(new SQLFragment("DELETE FROM flow.Keyword WHERE ObjectId").append(inList));
executor.execute(new SQLFragment("DELETE FROM flow.Graph WHERE ObjectId").append(inList));
executor.execute(new SQLFragment("DELETE FROM flow.Script WHERE ObjectId").append(inList));
}
}

Expand All @@ -1069,9 +1057,8 @@ private void deleteObjectIds(Integer[] oids, Set<Container> containers)
try (DbScope.Transaction transaction = scope.ensureTransaction())
{
deleteAttributes(oids);
SQLFragment sqlf = new SQLFragment("DELETE FROM flow.Object WHERE RowId IN (" );
sqlf.append(StringUtils.join(oids,','));
sqlf.append(")");
SQLFragment sqlf = new SQLFragment("DELETE FROM flow.Object WHERE RowId");
sqlf.appendInClause(Arrays.asList(oids), getSchema().getSqlDialect());
new SqlExecutor(getSchema()).execute(sqlf);
transaction.commit();
}
Expand Down Expand Up @@ -1109,17 +1096,9 @@ public void deleteData(List<ExpData> datas)
{
if (datas.isEmpty())
return;
StringBuilder sqlGetOIDs = new StringBuilder("SELECT flow.Object.RowId FROM flow.Object WHERE flow.Object.DataId IN (");
String comma = "";
Set<Container> containers = new HashSet<>();
for (ExpData data : datas)
{
sqlGetOIDs.append(comma);
comma = ", ";
sqlGetOIDs.append(data.getRowId());
containers.add(data.getContainer());
}
sqlGetOIDs.append(")");
SQLFragment sqlGetOIDs = new SQLFragment("SELECT flow.Object.RowId FROM flow.Object WHERE flow.Object.DataId");
sqlGetOIDs.appendInClause(datas.stream().map(ExpData::getRowId).toList(), getSchema().getSqlDialect());
Set<Container> containers = datas.stream().map(ExpData::getContainer).collect(Collectors.toSet());
Integer[] objectIds = new SqlSelector(getSchema(), sqlGetOIDs).getArray(Integer.class);
if (objectIds.length == 0)
return;
Expand Down
6 changes: 2 additions & 4 deletions flow/src/org/labkey/flow/query/FlowSchema.java
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Expand Up @@ -17,7 +17,6 @@
package org.labkey.flow.query;

import jakarta.servlet.http.HttpServletRequest;
import org.apache.commons.lang3.StringUtils;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.assay.AbstractAssayProvider;
Expand Down Expand Up @@ -1927,9 +1926,8 @@ private void filterTable(FilteredTable table, Map<? extends Object, Integer> map
}
else
{
SQLFragment sqlCondition = new SQLFragment("RowId IN (");
sqlCondition.append(StringUtils.join(map.values().iterator(), ","));
sqlCondition.append(")");
SQLFragment sqlCondition = new SQLFragment("RowId");
sqlCondition.appendInClause(map.values(), table.getSqlDialect());
table.addCondition(sqlCondition);
}
}
Expand Down
3 changes: 2 additions & 1 deletion flow/src/org/labkey/flow/reports/FilterFlowReport.java
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Expand Up @@ -19,6 +19,7 @@
import com.fasterxml.jackson.annotation.JsonManagedReference;
import org.apache.commons.beanutils.ConversionException;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Strings;
import org.labkey.api.data.CachedResultSet;
import org.labkey.api.data.CachedResultSetBuilder;
import org.labkey.api.data.ColumnInfo;
Expand Down Expand Up @@ -437,7 +438,7 @@ public void updateFilterProperties(PropertyValues pvs)

public String toSQL(String s)
{
return null == s ? "''" : "'" + StringUtils.replace(s, "'", "\'\'") + "'";
return null == s ? "''" : "'" + Strings.CS.replace(s, "'", "\'\'") + "'";
}

public String toSQL(FieldKey fieldKey)
Expand Down
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