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Fix flow test failure - int vs long #948

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labkey-jeckels merged 2 commits into from
Oct 31, 2025
Merged

Fix flow test failure - int vs long #948

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f1efca9
Fix flow test failure - int vs long
labkey-jeckels Oct 30, 2025
0091ced
Switch back to long
labkey-jeckels Oct 30, 2025
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6 changes: 1 addition & 5 deletions flow/src/org/labkey/flow/controllers/attribute/summary.jsp
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Original file line number Diff line number Diff line change
Expand Up @@ -45,11 +45,7 @@
Collection<FlowEntry> aliases = entry.getValue();

Map<Long, Number> counts = FlowManager.get().getUsageCount(primary._type, primary._rowId);
long totalCount = 0;
for (Number count : counts.values())
totalCount += count.longValue();

Number primaryUsages = counts.get(primary._rowId);
Number primaryUsages = counts.get((long)primary._rowId);
%>
<tr>
<td>
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54 changes: 13 additions & 41 deletions flow/src/org/labkey/flow/persist/FlowManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,6 @@
import org.labkey.api.exp.PropertyDescriptor;
import org.labkey.api.exp.api.ExpData;
import org.labkey.api.exp.api.ExpSampleType;
import org.labkey.api.exp.api.ExperimentService;
import org.labkey.api.exp.query.SamplesSchema;
import org.labkey.api.module.ModuleLoader;
import org.labkey.api.query.BatchValidationException;
Expand Down Expand Up @@ -288,12 +287,12 @@ public Collection<FlowEntry> getAttributeEntries(@NotNull String containerId, @N
public static class FlowEntry implements Comparable<FlowEntry>
{
public final AttributeType _type;
public final Integer _rowId;
public final int _rowId;
public final String _containerId;
public final String _name;
public final Integer _aliasId;
public final int _aliasId;

public FlowEntry(@NotNull AttributeType type, @NotNull Integer rowId, @NotNull String containerId, @NotNull String name, @NotNull Integer aliasId)
public FlowEntry(@NotNull AttributeType type, @NotNull int rowId, @NotNull String containerId, @NotNull String name, @NotNull Integer aliasId)
{
_type = type;
_rowId = rowId;
Expand All @@ -304,7 +303,7 @@ public FlowEntry(@NotNull AttributeType type, @NotNull Integer rowId, @NotNull S

public boolean isAlias()
{
return !_rowId.equals(_aliasId);
return _rowId != _aliasId;
}

@Override
Expand All @@ -315,7 +314,7 @@ public boolean equals(Object o)

FlowEntry flowEntry = (FlowEntry) o;

if (!_rowId.equals(flowEntry._rowId)) return false;
if (_rowId != flowEntry._rowId) return false;
if (_type != flowEntry._type) return false;

return true;
Expand All @@ -325,7 +324,7 @@ public boolean equals(Object o)
public int hashCode()
{
int result = _type.hashCode();
result = 31 * result + _rowId.hashCode();
result = 31 * result + Integer.hashCode(_rowId);
return result;
}

Expand Down Expand Up @@ -548,7 +547,7 @@ private void ensureAlias(@NotNull FlowEntry entry, @NotNull String aliasName, bo
return;

// If this existing entry is already an alias of entry, do nothing
if (existing._aliasId.equals(entry._rowId))
if (existing._aliasId == entry._rowId)
return;

// If this existing entry doesn't have any aliases, we can make this existing entry an alias of the entry.
Expand Down Expand Up @@ -628,7 +627,6 @@ private void updateAttribute(@NotNull Container container, @NotNull FlowEntry en
// Update any attribute usages of the current rowId to the new rowId, keeping the original id the same
private int updateAttributeValuesPreferredId(@NotNull String containerId, @NotNull AttributeType type, int currentRowId, int newRowId)
{
TableInfo attrTable = attributeTable(type);
TableInfo valueTable = valueTable(type);
String valueTableAttrIdColumn = valueTableAttrIdColumn(type);

Expand Down Expand Up @@ -741,20 +739,6 @@ public Collection<FlowEntry> getAliases(final FlowEntry entry)
return aliases;
}

public Collection<Integer> getAliasIds(final FlowEntry entry)
{
//_log.info("getAliasIds");
// Get the attributes that have an id equal to the entry and exclude the entry itself.
TableInfo table = attributeTable(entry._type);
SimpleFilter filter = new SimpleFilter();
filter.addCondition(table.getColumn("Container"), entry._containerId);
filter.addCondition(table.getColumn("Id"), entry._rowId);
filter.addCondition(table.getColumn("RowId"), entry._rowId, CompareType.NEQ);
TableSelector selector = new TableSelector(table, Collections.singleton("RowId"), filter, null);

return selector.getArrayList(Integer.class);
}

public Map<FlowEntry, Collection<FlowEntry>> getAliases(Container c, final AttributeType type)
{
TableInfo table = attributeTable(type);
Expand Down Expand Up @@ -879,7 +863,6 @@ public Map<Long, Number> getUsageCount(AttributeType type, int rowId)
if (entry == null)
return Collections.emptyMap();

TableInfo attrTable = attributeTable(type);
TableInfo valueTable = valueTable(type);
String valueTableAttrIdColumn = valueTableAttrIdColumn(type);
String valueTableOriginalAttrIdColumn = valueTableOriginalAttrIdColumn(type);
Expand Down Expand Up @@ -913,7 +896,6 @@ public Collection<FlowDataObject> getUsages(FlowEntry entry)
if (entry == null)
return Collections.emptyList();

TableInfo attrTable = attributeTable(entry._type);
TableInfo valueTable = valueTable(entry._type);
String valueTableAttrIdColumn = valueTableAttrIdColumn(entry._type);
String valueTableOriginalAttrIdColumn = valueTableOriginalAttrIdColumn(entry._type);
Expand Down Expand Up @@ -949,7 +931,6 @@ public Map<Integer, Collection<FlowDataObject>> getAllUsages(AttributeType type,
if (entry == null)
return Collections.emptyMap();

TableInfo attrTable = attributeTable(type);
TableInfo valueTable = valueTable(type);
String valueTableAttrIdColumn = valueTableAttrIdColumn(type);
String valueTableOriginalAttrIdColumn = valueTableOriginalAttrIdColumn(type);
Expand Down Expand Up @@ -1094,15 +1075,6 @@ private void deleteAttributes(SQLFragment sqlObjectIds)
}
}

public void deleteAttributes(ExpData data)
{
AttrObject obj = getAttrObject(data);
if (obj == null)
return;
deleteAttributes(new Integer[] {obj.getRowId()});
}


private void deleteObjectIds(Integer[] oids, Set<Container> containers)
{
DbScope scope = getSchema().getScope();
Expand Down Expand Up @@ -1212,7 +1184,7 @@ public void setKeyword(Container c, User user, ExpData data, String keyword, Str
String sampleLabel = data.getName();
ensureKeywordName(c, sampleLabel, keyword, true);

AttributeCache.Entry a = AttributeCache.KEYWORDS.byAttribute(c, keyword);
AttributeCache.Entry<?, ?> a = AttributeCache.KEYWORDS.byAttribute(c, keyword);
assert a != null : "Expected to find keyword entry for '" + keyword + "'";
int preferredId = a.getAliasedId() == null ? a.getRowId() : a.getAliasedId();
int originalId = a.getRowId();
Expand Down Expand Up @@ -1478,7 +1450,7 @@ public int getFCSFileCount(User user, Container container)

// count(fcsfile)
TableInfo table = schema.getTable(FlowTableType.FCSFiles, null);
List<Aggregate> aggregates = Collections.singletonList(new Aggregate("RowId", Aggregate.BaseType.COUNT));
List<Aggregate> aggregates = Collections.singletonList(new Aggregate(FieldKey.fromParts("RowId"), Aggregate.BaseType.COUNT));
List<ColumnInfo> columns = Collections.singletonList(table.getColumn("RowId"));

// filter to those wells that were imported from a Keywords run
Expand All @@ -1489,8 +1461,8 @@ public int getFCSFileCount(User user, Container container)
Map<String, List<Aggregate.Result>> agg = new TableSelector(table, columns, filter, null).getAggregates(aggregates);
//TODO: multiple aggregates
Aggregate.Result result = agg.get(aggregates.get(0).getColumnName()).get(0);
if (result != null && result.getValue() instanceof Number)
return ((Number)result.getValue()).intValue();
if (result != null && result.getValue() instanceof Number n)
return n.intValue();

return 0;
}
Expand All @@ -1503,7 +1475,7 @@ public int getFCSFileOnlyRunsCount(User user, Container container)
filter.addCondition(FieldKey.fromParts("FCSFileCount"), 0, CompareType.NEQ);
filter.addCondition(FieldKey.fromParts("ProtocolStep"), "Keywords", CompareType.EQUAL);
TableInfo table = schema.getTable(FlowTableType.Runs, null);
List<Aggregate> aggregates = Collections.singletonList(new Aggregate("RowId", Aggregate.BaseType.COUNT));
List<Aggregate> aggregates = Collections.singletonList(new Aggregate(FieldKey.fromParts("RowId"), Aggregate.BaseType.COUNT));
List<ColumnInfo> columns = Collections.singletonList(table.getColumn("RowId"));
Map<String, List<Aggregate.Result>> agg = new TableSelector(table, columns, filter, null).getAggregates(aggregates);
Aggregate.Result result = agg.get("RowId").get(0);
Expand Down Expand Up @@ -1629,7 +1601,7 @@ public void setFileDateForAllFCSFiles(@NotNull Container c, @NotNull User user)
final OntologyManager.ImportHelper helper = new OntologyManager.ImportHelper()
{
@Override
public String beforeImportObject(Map<String, Object> map) throws SQLException
public String beforeImportObject(Map<String, Object> map)
{
String lsid = (String)map.get("lsid");
assert lsid != null;
Expand Down
2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/persist/PersistTests.java
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Expand Up @@ -140,7 +140,7 @@ public void keywordAliases() throws Exception
AttributeCache.KeywordEntry cacheEntry = AttributeCache.KEYWORDS.byName(c, "keyword1");
assertEquals("keyword1", cacheEntry.getAttribute());
assertEquals(c, cacheEntry.getContainer());
assertEquals(entry._rowId.intValue(), cacheEntry.getRowId());
assertEquals(entry._rowId, cacheEntry.getRowId());

// verify cached keyword alias
Collection<AttributeCache.KeywordEntry> cacheAliases = cacheEntry.getAliases();
Expand Down