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Make MS2 codepaths supply fieldMap for Sort.getOrderByClause() #894

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Merged
labkey-matthewb merged 2 commits into from
Jun 11, 2025
Merged

Make MS2 codepaths supply fieldMap for Sort.getOrderByClause() #894

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ab9f530
Reinstate unchecked version of Sort.getOrderByClause() to fix MS2 sql…
labkey-matthewb Jun 10, 2025
c9879f8
Always pass a column list to get sort clause
labkey-jeckels Jun 11, 2025
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29 changes: 12 additions & 17 deletions ms2/src/org/labkey/ms2/compare/CompareQuery.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
import org.labkey.api.data.DataRegion;
import org.labkey.api.data.DisplayColumn;
import org.labkey.api.data.ExcelWriter;
import org.labkey.api.data.JdbcType;
import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.SimpleFilter;
Expand All @@ -48,8 +49,11 @@
import java.sql.ResultSetMetaData;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

/**
Expand All @@ -68,7 +72,7 @@ public class CompareQuery extends SQLFragment
private String _header;
protected final User _user;

private final Set<FieldKey> _columns = new HashSet<>();
private final Map<FieldKey, ColumnInfo> _columns = new HashMap<>();
protected static final String HEADER_PREFIX = "Numbers below represent ";

public CompareQuery(ActionURL currentUrl, List<MS2Run> runs, User user)
Expand Down Expand Up @@ -153,7 +157,12 @@ protected void generateSql(BindException errors)

protected void addColumn(String name)
{
_columns.add(FieldKey.fromParts(name));
// Fake up a column map so we can use Sort.getOrderByClause()
FieldKey fk = FieldKey.fromParts(name);
BaseColumnInfo col = new BaseColumnInfo(fk, JdbcType.VARCHAR);
col.setSortFieldKeys(Collections.singletonList(fk));
col.setAlias(MS2Manager.getSqlDialect().makeDatabaseIdentifier(name));
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@labkey-matthewb labkey-matthewb Jun 11, 2025

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Since names are mixed-case, we just have to make sure our usages are consistent. But it would be obvious if there were a problem.

_columns.put(fk, col);
}

protected void selectColumns()
Expand Down Expand Up @@ -357,28 +366,14 @@ protected void sort()
Sort sort = new Sort("-RunCount,-Pattern," + getLabelColumn());
sort.addURLSort(_currentUrl, MS2Manager.getDataRegionNameCompare());

// Filter out bogus URL sort columns
int index = 0;
while (sort.getSortList().size() > index)
{
if (!_columns.contains(sort.getSortList().get(index).getFieldKey()))
{
sort.deleteSortColumn(index);
}
else
{
index++;
}
}

// TODO: If there are more than three columns in the sort list, then it may be that "BestName" and "Protein"
// are in the list, in which case SQL server will fail to execute the query. Therefore, we restrict the number
// of columns you can sort on to 3.
while (sort.getSortList().size() > 3)
{
sort.deleteSortColumn(sort.getSortList().size() - 1);
}
append(sort.getOrderByClause(MS2Manager.getSqlDialect()));
append(sort.getOrderByClause(MS2Manager.getSqlDialect(), _columns));
}

protected void appendNewLine()
Expand Down
14 changes: 0 additions & 14 deletions ms2/src/org/labkey/ms2/peptideview/MS2ResultSet.java
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Expand Up @@ -19,15 +19,12 @@
import org.labkey.api.data.ResultSetWrapper;
import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.Sort;
import org.labkey.ms2.MS2Manager;
import org.labkey.ms2.MS2Run;

import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Iterator;
import java.util.List;

/**
* User: adam
Expand All @@ -37,22 +34,12 @@
public abstract class MS2ResultSet extends ResultSetWrapper
{
protected Iterator<MS2Run> _iter;
protected SimpleFilter _filter;
protected Sort _sort;

protected MS2ResultSet()
{
super(null);
}

MS2ResultSet(List<MS2Run> runs, SimpleFilter filter, Sort sort)
{
super(null);
_iter = runs.iterator();
_filter = filter;
_sort = sort;
}

// Subclasses should call at the end of their constructors -- this pre-fetches the first result set which ensures
// that calls to getMetaData(), etc. will work before next() is called.
protected void init()
Expand Down Expand Up @@ -91,7 +78,6 @@ private boolean prepareNextResultSet() throws SQLException

/**
* Wraps the join of Peptides, PeptidesData, & SpectraData in a subselect to disambiguate scan & fraction column references in filters/sorts
*
*/
protected SQLFragment getBaseResultSetSql()
{
Expand Down
35 changes: 0 additions & 35 deletions ms2/src/org/labkey/ms2/peptideview/ResultSetSpectrumIterator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,15 +17,9 @@
package org.labkey.ms2.peptideview;

import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.Sort;
import org.labkey.api.data.SqlSelector;
import org.labkey.api.util.Pair;
import org.labkey.api.util.ResultSetUtil;
import org.labkey.ms2.MS2Manager;
import org.labkey.ms2.MS2Run;
import org.labkey.ms2.PeptideManager;
import org.labkey.ms2.Spectrum;
import org.labkey.ms2.SpectrumException;
import org.labkey.ms2.SpectrumImporter;
Expand All @@ -34,7 +28,6 @@
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;

/**
Expand All @@ -61,11 +54,6 @@ protected ResultSetSpectrumIterator()
{
}

public ResultSetSpectrumIterator(List<MS2Run> runs, SimpleFilter filter, Sort sort)
{
_rs = new SpectrumResultSet(runs, filter, sort);
}

@Override
public boolean hasNext()
{
Expand Down Expand Up @@ -302,27 +290,4 @@ public double getPrecursorMass()
}
}
}


private static class SpectrumResultSet extends MS2ResultSet
{
public SpectrumResultSet(List<MS2Run> runs, SimpleFilter filter, Sort sort)
{
super(runs, filter, sort);
}

@Override
public ResultSet getNextResultSet()
{
PeptideManager.replaceRunCondition(_filter, null, _iter.next());

SQLFragment sql = getBaseResultSetSql();
sql.append(") X\n");
sql.append(_filter.getWhereSQL(MS2Manager.getTableInfoPeptides()));
sql.append('\n');
sql.append(_sort.getOrderByClause(MS2Manager.getSqlDialect()));

return new SqlSelector(MS2Manager.getSchema(), sql.getSQL(), _filter.getWhereParams(MS2Manager.getTableInfoPeptides())).getResultSet(false);
}
}
}