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Collect unique set of sequence IDs for SequenceIdentity table #7146

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Merged
labkey-adam merged 1 commit into from
Oct 24, 2025
Merged

Collect unique set of sequence IDs for SequenceIdentity table #7146

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2 changes: 0 additions & 2 deletions api/src/org/labkey/api/data/DatabaseMigrationService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.collections.CopyOnWriteCaseInsensitiveHashMap;
import org.labkey.api.data.DatabaseMigrationConfiguration.DefaultDatabaseMigrationConfiguration;
import org.labkey.api.data.SimpleFilter.AndClause;
import org.labkey.api.data.SimpleFilter.FilterClause;
Expand All @@ -22,7 +21,6 @@
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;

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33 changes: 32 additions & 1 deletion experiment/src/org/labkey/experiment/ExperimentModule.java
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Expand Up @@ -27,6 +27,7 @@
import org.labkey.api.audit.SampleTimelineAuditEvent;
import org.labkey.api.collections.CsvSet;
import org.labkey.api.collections.LongHashMap;
import org.labkey.api.collections.Sets;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerFilter;
import org.labkey.api.data.ContainerManager;
Expand Down Expand Up @@ -936,20 +937,50 @@ public void afterTable(TableInfo sourceTable, TableInfo targetTable, SimpleFilte
}
});

// Data classes have a built-in Flag field
DatabaseMigrationService.get().registerSchemaHandler(new DefaultMigrationSchemaHandler(DataClassDomainKind.getSchema()) {
@Override
public void addDomainDataFilter(OrClause orClause, DomainFilter filter, TableInfo sourceTable, FieldKey fKey, Set<String> selectColumnNames)
{
// Data classes have a built-in Flag field
addDomainDataFlagFilter(orClause, filter, sourceTable, fKey, selectColumnNames);
}

private static final Set<String> SEQUENCE_TABLES = Sets.newCaseInsensitiveHashSet("protsequence", "nucsequence", "molecule");
private static final Set<Long> SEQUENCE_IDS = new HashSet<>();

@Override
public void afterTable(TableInfo sourceTable, TableInfo targetTable, SimpleFilter notCopiedFilter)
{
Collection<String> notCopiedLsids = new TableSelector(sourceTable, Collections.singleton("LSID"), notCopiedFilter, null).getCollection(String.class);
if (!notCopiedLsids.isEmpty())
LOG.info(" {} rows not copied", Formats.commaf0.format(notCopiedLsids.size()));

String name = sourceTable.getName();
int idx = name.indexOf('_');
name = name.substring(idx + 1);

if (SEQUENCE_TABLES.contains(name))
{
new TableSelector(targetTable, Collections.singleton("Ident")).stream(String.class)
.map(ident -> {
int i = ident.indexOf(':');
try
{
return Long.parseLong(ident.substring(i + 1));
}
catch (Exception e)
{
throw new RuntimeException("Exception trying to split ident on ':' (" + ident + ")", e);
}
})
.forEach(SEQUENCE_IDS::add);
}
}

@Override
public void afterSchema()
{
LOG.info("This is where we'll copy {} sequences into biologics.SequenceIdentity", SEQUENCE_IDS.size());
}
});
}
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