hibernate/hibernate-orm · error · SchemaExtractionException

Primary Key information was missing for KEY_SEQ = %s

Error message

Primary Key information was missing for KEY_SEQ = %s

What it means

Primary-key rows are slotted into a column list indexed by KEY_SEQ (column position minus one). After the resultset is consumed, any remaining null slot means no row supplied that ordinal — the driver reported non-contiguous sequence numbers — and Hibernate throws SchemaExtractionException naming the missing KEY_SEQ rather than producing a primary key with a hole in it.

Source

Thrown at hibernate-core/src/main/java/org/hibernate/tool/schema/extract/internal/AbstractInformationExtractorImpl.java:971

			final int columnPosition = resultSet.getInt( getResultSetColumnPositionColumn() );
			final int index = columnPosition - 1;
			// Fill up the array list with nulls up to the desired index, because some JDBC drivers don't return results ordered by column position
			while ( columns.size() <= index ) {
				columns.add( null );
			}
			final Identifier columnIdentifier =
					toIdentifier( resultSet.getString( getResultSetColumnNameLabel() ) );
			columns.set( index, tableInformation.getColumn( columnIdentifier ) );
		}
		if ( firstPass ) {
			// we did not find any results (no pk)
			return null;
		}
		else {
			// validate column list is properly contiguous
			for ( int i = 0; i < columns.size(); i++ ) {
				if ( columns.get( i ) == null ) {
					throw new SchemaExtractionException( "Primary Key information was missing for KEY_SEQ = " + ( i+1) );
				}
			}
			// build the return
			return new PrimaryKeyInformationImpl( primaryKeyIdentifier, columns );
		}
	}

	@Override
	public NameSpacePrimaryKeysInformation getPrimaryKeys(Identifier catalog, Identifier schema) {
		if ( !supportsBulkPrimaryKeyRetrieval() ) {
			throw new UnsupportedOperationException( "Database doesn't support extracting all primary keys at once" );
		}
		else {
			try {
				return processPrimaryKeysResultSet(
						catalog == null ? "" : catalog.getText(),
						schema == null ? "" : schema.getText(),
						(String) null,

View on GitHub (pinned to fad1729dce)

Solutions

1. Switch to a JDBC driver version that follows the KEY_SEQ contract (1-based, contiguous, one row per PK column).
2. Avoid the broken path when possible: use hbm2ddl none, or manage the schema with tooling that does not need PK extraction on that driver.
3. Report it to the Hibernate tracker (HHH) with the driver name and version — extraction quirks get dialect-specific workarounds.

try {
    schemaValidator.validate(metadata, databaseModel);
} catch (SchemaExtractionException e) {
    if (e.getMessage() != null && e.getMessage().contains("KEY_SEQ")) {
        // driver returned non-contiguous PK positions — switch or upgrade the driver
    }
    throw e;
}

When it happens

Trigger: A driver that returns KEY_SEQ starting at zero, with gaps, or with duplicate positions; or rows whose position column could not be read correctly, leaving an index uninitialized while a later row enlarged the list.

Common situations: Niche or third-party drivers (SQLite wrappers, legacy SQL Server drivers, pool/proxy layers rewriting metadata) violating the JDBC KEY_SEQ contract; behavior appearing after a driver upgrade.

Related errors

• Encountered primary keys differing name on table %s
• Database doesn't support extracting all primary keys at once
• Could not locate table information for %s
• Primary Key information was missing for key [%s] on table [%
• No add primary key syntax supported by SQLiteDialect

AI-assisted analysis of hibernate/hibernate-orm@fad1729dce (2026-08-22). Data as JSON: /api/errors/0cedeb6aea5d30cb. Report an issue: GitHub.