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

Use helper methods to create IN clauses #1023

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abc0990
Use helper methods to create IN clauses
labkey-adam Oct 15, 2026
1ce0c46
Migrate away from deprecated StringUtils methods
labkey-adam Oct 15, 2026
432b1f8
More reliable NOT InClause generation
labkey-adam Oct 16, 2026
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69 changes: 13 additions & 56 deletions snd/src/org/labkey/snd/SNDManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,6 @@
import java.sql.SQLException;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayDeque;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
Expand All @@ -104,7 +103,6 @@
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.LongSummaryStatistics;
import java.util.Map;
Expand Down Expand Up @@ -717,12 +715,7 @@ private Map<Integer, Map<Integer, String>> getBulkPackageCategories(Container c,
sql.append(schema.getTable(SNDSchema.PKGCATEGORIES__TABLE_NAME), "ca");
sql.append(" ON cj.CategoryId = ca.CategoryId");
if (pkgIds != null) {
sql.append(" WHERE PkgId IN ( ");
ArrayDeque<Integer> pkgIdsQueue = new ArrayDeque<>(pkgIds);
while (pkgIdsQueue.size() > 1) {
sql.append("?, ").add(pkgIdsQueue.pop());
}
sql.append("?) ").add(pkgIdsQueue.pop());
sql.append(" WHERE PkgId").appendInClause(pkgIds, schema.getDbSchema().getSqlDialect()).append(" ");
}
SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql);

Expand Down Expand Up @@ -874,9 +867,7 @@ public static List<SuperPackage> getSuperPkgs(Container c, User u, List<Integer>

SQLFragment sql = new SQLFragment("SELECT sp.SuperPkgId, sp.ParentSuperPkgId, sp.PkgId, sp.SuperPkgPath, sp.SortOrder, sp.Required FROM ");
sql.append(schema.getTable(SNDSchema.SUPERPKGS_TABLE_NAME), "sp");
sql.append(" WHERE sp.SuperPkgId IN (");
addSubPkgParameters(sql, superPackageIds.iterator());
sql.append(")");
sql.append(" WHERE sp.SuperPkgId").appendInClause(superPackageIds, schema.getDbSchema().getSqlDialect());
SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql);

if (!selector.getArrayList(SuperPackage.class).isEmpty())
Expand All @@ -899,9 +890,8 @@ public static List<SuperPackage> convertToTopLevelSuperPkgs(Container c, User u,
sql.append(schema.getTable(SNDSchema.SUPERPKGS_TABLE_NAME), "sp2");
sql.append(" ON sp2.PkgId = sp.PkgId");

sql.append(" WHERE sp.SuperPkgId IN (");
addSubPkgParameters(sql, superPackageIds.iterator());
sql.append(") AND sp2.ParentSuperPkgId IS NULL");
sql.append(" WHERE sp.SuperPkgId").appendInClause(superPackageIds, schema.getDbSchema().getSqlDialect());
sql.append(" AND sp2.ParentSuperPkgId IS NULL");
SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql);

if (!selector.getArrayList(SuperPackage.class).isEmpty())
Expand All @@ -923,9 +913,8 @@ public static List<SuperPackage> filterTopLevelSuperPkgs(Container c, User u, Li

SQLFragment sql = new SQLFragment("SELECT sp.SuperPkgId, sp.ParentSuperPkgId, sp.PkgId, sp.SuperPkgPath, sp.SortOrder, sp.Required FROM ");
sql.append(schema.getTable(SNDSchema.SUPERPKGS_TABLE_NAME), "sp");
sql.append(" WHERE sp.SuperPkgId IN (");
addSubPkgParameters(sql, superPackageIds.iterator());
sql.append(") AND sp.ParentSuperPkgId IS NULL");
sql.append(" WHERE sp.SuperPkgId").appendInClause(superPackageIds, schema.getDbSchema().getSqlDialect());
sql.append(" AND sp.ParentSuperPkgId IS NULL");
SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql);

if (!selector.getArrayList(SuperPackage.class).isEmpty())
Expand Down Expand Up @@ -966,9 +955,8 @@ public static List<SuperPackage> filterChildSuperPkgs(Container c, User u, List<

SQLFragment sql = new SQLFragment("SELECT sp.SuperPkgId, sp.ParentSuperPkgId, sp.PkgId, sp.SuperPkgPath, sp.SortOrder, sp.Required FROM ");
sql.append(schema.getTable(SNDSchema.SUPERPKGS_TABLE_NAME), "sp");
sql.append(" WHERE sp.SuperPkgId IN (");
addSubPkgParameters(sql, superPackageIds.iterator());
sql.append(") AND sp.ParentSuperPkgId = ?").add(parentSuperPackageId);
sql.append(" WHERE sp.SuperPkgId").appendInClause(superPackageIds, schema.getDbSchema().getSqlDialect());
sql.append(" AND sp.ParentSuperPkgId = ?").add(parentSuperPackageId);
SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql);

if (!selector.getArrayList(SuperPackage.class).isEmpty())
Expand All @@ -988,19 +976,10 @@ public static List<Integer> getDeletedChildSuperPkgs(Container c, User u, List<S
SQLFragment sql = new SQLFragment("SELECT sp.SuperPkgId FROM ");
sql.append(schema.getTable(SNDSchema.SUPERPKGS_TABLE_NAME), "sp");
sql.append(" WHERE");
if ((superPackages != null) && (!superPackages.isEmpty()))
if (superPackages != null)
{
sql.append(" sp.SuperPkgId NOT IN (");
Iterator<SuperPackage> superPackageIterator = superPackages.iterator();
while (superPackageIterator.hasNext())
{
Integer superPkgId = superPackageIterator.next().getSuperPkgId();
if (!superPackageIterator.hasNext())
sql.append("?").add(superPkgId);
else
sql.append("?,").add(superPkgId);
}
sql.append(") AND");
sql.append(" ").appendNotInClause("sp.SuperPkgId", superPackages.stream().map(SuperPackage::getSuperPkgId).toList(), schema.getDbSchema().getSqlDialect());
sql.append(" AND");
}
sql.append(" sp.ParentSuperPkgId = ?").add(parentSuperPackageId);
SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql);
Expand All @@ -1011,21 +990,6 @@ public static List<Integer> getDeletedChildSuperPkgs(Container c, User u, List<S
return null;
}

/**
* Used for building sql statements when adding subpackages to parameters
*/
private static void addSubPkgParameters(SQLFragment sql, Iterator<Integer> subPkgIterator)
{
while (subPkgIterator.hasNext())
{
Integer superPkgId = subPkgIterator.next();
if (!subPkgIterator.hasNext())
sql.append("?").add(superPkgId);
else
sql.append("?,").add(superPkgId);
}
}

/**
* Checks if package is descendent of a super package
*/
Expand Down Expand Up @@ -3656,9 +3620,7 @@ public List<Category> getCategories(Container c, User u, List<Integer> categoryI

SQLFragment sql = new SQLFragment("SELECT CategoryId, Description, Active, ObjectId, Container FROM ");
sql.append(pkgCategoriesTable, "ed");
sql.append(" WHERE CategoryId IN (");
sql.append(StringUtils.join(categoryIds, ","));
sql.append(")");
sql.append(" WHERE CategoryId").appendInClause(categoryIds, schema.getDbSchema().getSqlDialect());

SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql);
return selector.getArrayList(Category.class);
Expand Down Expand Up @@ -4032,12 +3994,7 @@ private Map<Integer, SuperPackage> getBulkSuperPkgs(Container c, User u, List<GW
if (eventIds != null) {
sql.append(" INNER JOIN " + SNDSchema.NAME + "." + SNDSchema.EVENTDATA_TABLE_NAME + " ed");
sql.append(" ON ed.SuperPkgId = sp.SuperPkgId ");
sql.append(" WHERE ed.EventId IN ( ");
ArrayDeque<Integer> eventIdsQueue = new ArrayDeque<>(eventIds);
while (eventIdsQueue.size() > 1) {
sql.append("?, ").add(eventIdsQueue.pop());
}
sql.append("?) ").add(eventIdsQueue.pop());
sql.append(" WHERE ed.EventId").appendInClause(eventIds, schema.getDbSchema().getSqlDialect()).append(" ");
}
sql.append(" ORDER BY sp.SuperPkgId ");

Expand Down
16 changes: 8 additions & 8 deletions snprc_ehr/src/org/labkey/snprc_ehr/helpers/CustomizerQueryProvider.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
package org.labkey.snprc_ehr.helpers;

import org.apache.commons.lang.text.StrSubstitutor;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Strings;
import org.apache.commons.text.CaseUtils;
import org.labkey.api.data.AbstractTableInfo;
import org.labkey.api.data.ColumnInfo;
Expand Down Expand Up @@ -137,19 +137,19 @@ private WrappedColumn getWrappedCalculatedColumn(CalculatedColumnQueryInfo query
*/
private String mapQueryStringValues(String queryString, CalculatedColumnQueryInfo queryInfo, String dateColumnName) {
Map<String, String> queryByValues = new HashMap<>();
if(StringUtils.contains(queryString, PRIMARY_KEY_VARIABLE))
if(Strings.CS.contains(queryString, PRIMARY_KEY_VARIABLE))
queryByValues.put(PRIMARY_KEY_VARIABLE, queryInfo.getPrimaryKeyColumn().getFieldKey().toSQLString());
if(StringUtils.contains(queryString, SCHEMA_VARIABLE))
if(Strings.CS.contains(queryString, SCHEMA_VARIABLE))
queryByValues.put(SCHEMA_VARIABLE, queryInfo.getTableInfo().getPublicSchemaName());
if(StringUtils.contains(queryString, QUERY_VARIABLE))
if(Strings.CS.contains(queryString, QUERY_VARIABLE))
queryByValues.put(QUERY_VARIABLE, queryInfo.getTableInfo().getName());
if(StringUtils.contains(queryString, EHR_PATH_VARIABLE))
if(Strings.CS.contains(queryString, EHR_PATH_VARIABLE))
queryByValues.put(EHR_PATH_VARIABLE, queryInfo.getEhrSchema().getContainer().getPath());
if(StringUtils.contains(queryString, ID_COLUMN_VARIABLE))
if(Strings.CS.contains(queryString, ID_COLUMN_VARIABLE))
queryByValues.put(ID_COLUMN_VARIABLE, queryInfo.getIdColumn().getFieldKey().toSQLString());
if(StringUtils.contains(queryString, TARGET_CONTAINER_VARIABLE))
if(Strings.CS.contains(queryString, TARGET_CONTAINER_VARIABLE))
queryByValues.put(TARGET_CONTAINER_VARIABLE, queryInfo.getTableInfo().getUserSchema().getName());
if(StringUtils.contains(queryString, DATE_COLUMN_VARIABLE))
if(Strings.CS.contains(queryString, DATE_COLUMN_VARIABLE))
queryByValues.put(DATE_COLUMN_VARIABLE, dateColumnName);
return StrSubstitutor.replace(queryString, queryByValues);
}
Expand Down
25 changes: 5 additions & 20 deletions snprc_ehr/src/org/labkey/snprc_ehr/services/AnimalsGroupAssignor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -91,21 +91,6 @@ private List<Integer> getCategoryGroups()

}

private String getCategoryGroupsString()
{
StringBuilder sb = new StringBuilder();
sb.append("(");
this.getCategoryGroups().forEach(group -> {
sb.append(group.toString());
sb.append(",");
}
);
sb.setCharAt(sb.lastIndexOf(","), ' ');
sb.append(")");

return sb.toString();
}

/**
* @param groupMembers: Animals to be assigned (animalId, start date, and end date)
* returns - Nothing - Animals are either assigned or an exception is thrown
Expand Down Expand Up @@ -219,16 +204,16 @@ public void assign(List<GroupMember> groupMembers) throws ValidationException
sql.append("inner join ehr_lookups.calendar as c\n "); //;
sql.append ("on c.targetDate between agm.date and COALESCE(agm.enddate, CURRENT_TIMESTAMP + INTERVAL '10 years')\n");
sql.append("where agm.participantid = ? \n");
sql.append(" and agm.groupId in " + getCategoryGroupsString() + "\n");
sql.append(" and c.targetDate between ? and ?\n");
if (groupMember.getObjectid() != null )
sql.append(" and agm.objectId <> ?"); // ignore the record being updated

sql.add(groupMember.getParticipantid());
sql.append(" and agm.groupId").appendInClause(getCategoryGroups(), dbStudySchema.getSqlDialect()).append("\n");
sql.append(" and c.targetDate between ? and ?\n");
sql.add(groupMember.getDate());
sql.add(endDate);
if (groupMember.getObjectid() != null )
{
sql.append(" and agm.objectId <> ?"); // ignore the record being updated
sql.add(groupMember.getObjectid());
}

selector = new SqlSelector(dbStudySchema, sql);
if (selector.exists())
Expand Down
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