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Merge pull request #174 from jburke-cadc/CADC-13452
CADC-13452 ingest an existing table into the tap_schema
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cadc-tap-schema/src/intTest/java/ca/nrc/cadc/tap/db/TableIngesterTest.java
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cadc-tap-schema/src/main/java/ca/nrc/cadc/tap/db/TableIngester.java
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| /* | ||
| ************************************************************************ | ||
| ******************* CANADIAN ASTRONOMY DATA CENTRE ******************* | ||
| ************** CENTRE CANADIEN DE DONNÉES ASTRONOMIQUES ************** | ||
| * | ||
| * (c) 2024. (c) 2024. | ||
| * Government of Canada Gouvernement du Canada | ||
| * National Research Council Conseil national de recherches | ||
| * Ottawa, Canada, K1A 0R6 Ottawa, Canada, K1A 0R6 | ||
| * All rights reserved Tous droits réservés | ||
| * | ||
| * NRC disclaims any warranties, Le CNRC dénie toute garantie | ||
| * expressed, implied, or énoncée, implicite ou légale, | ||
| * statutory, of any kind with de quelque nature que ce | ||
| * respect to the software, soit, concernant le logiciel, | ||
| * including without limitation y compris sans restriction | ||
| * any warranty of merchantability toute garantie de valeur | ||
| * or fitness for a particular marchande ou de pertinence | ||
| * purpose. NRC shall not be pour un usage particulier. | ||
| * liable in any event for any Le CNRC ne pourra en aucun cas | ||
| * damages, whether direct or être tenu responsable de tout | ||
| * indirect, special or general, dommage, direct ou indirect, | ||
| * consequential or incidental, particulier ou général, | ||
| * arising from the use of the accessoire ou fortuit, résultant | ||
| * software. Neither the name de l'utilisation du logiciel. Ni | ||
| * of the National Research le nom du Conseil National de | ||
| * Council of Canada nor the Recherches du Canada ni les noms | ||
| * names of its contributors may de ses participants ne peuvent | ||
| * be used to endorse or promote être utilisés pour approuver ou | ||
| * products derived from this promouvoir les produits dérivés | ||
| * software without specific prior de ce logiciel sans autorisation | ||
| * written permission. préalable et particulière | ||
| * par écrit. | ||
| * | ||
| * This file is part of the Ce fichier fait partie du projet | ||
| * OpenCADC project. OpenCADC. | ||
| * | ||
| * OpenCADC is free software: OpenCADC est un logiciel libre ; | ||
| * you can redistribute it and/or vous pouvez le redistribuer ou le | ||
| * modify it under the terms of modifier suivant les termes de | ||
| * the GNU Affero General Public la “GNU Affero General Public | ||
| * License as published by the License” telle que publiée | ||
| * Free Software Foundation, par la Free Software Foundation | ||
| * either version 3 of the : soit la version 3 de cette | ||
| * License, or (at your option) licence, soit (à votre gré) | ||
| * any later version. toute version ultérieure. | ||
| * | ||
| * OpenCADC is distributed in the OpenCADC est distribué | ||
| * hope that it will be useful, dans l’espoir qu’il vous | ||
| * but WITHOUT ANY WARRANTY; sera utile, mais SANS AUCUNE | ||
| * without even the implied GARANTIE : sans même la garantie | ||
| * warranty of MERCHANTABILITY implicite de COMMERCIALISABILITÉ | ||
| * or FITNESS FOR A PARTICULAR ni d’ADÉQUATION À UN OBJECTIF | ||
| * PURPOSE. See the GNU Affero PARTICULIER. Consultez la Licence | ||
| * General Public License for Générale Publique GNU Affero | ||
| * more details. pour plus de détails. | ||
| * | ||
| * You should have received Vous devriez avoir reçu une | ||
| * a copy of the GNU Affero copie de la Licence Générale | ||
| * General Public License along Publique GNU Affero avec | ||
| * with OpenCADC. If not, see OpenCADC ; si ce n’est | ||
| * <http://www.gnu.org/licenses/>. pas le cas, consultez : | ||
| * <http://www.gnu.org/licenses/>. | ||
| * | ||
| * : 5 $ | ||
| * | ||
| ************************************************************************ | ||
| */ | ||
|
|
||
| package ca.nrc.cadc.tap.db; | ||
|
|
||
| import ca.nrc.cadc.auth.AuthenticationUtil; | ||
| import ca.nrc.cadc.db.DatabaseTransactionManager; | ||
| import ca.nrc.cadc.tap.PluginFactory; | ||
| import ca.nrc.cadc.tap.schema.ADQLIdentifierException; | ||
| import ca.nrc.cadc.tap.schema.ColumnDesc; | ||
| import ca.nrc.cadc.tap.schema.SchemaDesc; | ||
| import ca.nrc.cadc.tap.schema.TableDesc; | ||
| import ca.nrc.cadc.tap.schema.TapDataType; | ||
| import ca.nrc.cadc.tap.schema.TapPermissions; | ||
| import ca.nrc.cadc.tap.schema.TapSchemaDAO; | ||
| import ca.nrc.cadc.tap.schema.TapSchemaUtil; | ||
| import java.sql.DatabaseMetaData; | ||
| import java.sql.ResultSet; | ||
| import java.sql.SQLException; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import javax.security.auth.Subject; | ||
| import javax.sql.DataSource; | ||
| import org.apache.log4j.Logger; | ||
|
|
||
| public class TableIngester { | ||
| private static final Logger log = Logger.getLogger(TableIngester.class); | ||
|
|
||
| private final DataSource dataSource; | ||
| private final DatabaseDataType databaseDataType; | ||
| private final TapSchemaDAO tapSchemaDAO; | ||
|
|
||
| public TableIngester(DataSource dataSource) { | ||
| this.dataSource = dataSource; | ||
| PluginFactory pluginFactory = new PluginFactory(); | ||
| this.tapSchemaDAO = pluginFactory.getTapSchemaDAO(); | ||
| this.tapSchemaDAO.setDataSource(dataSource); | ||
| this.databaseDataType = pluginFactory.getDatabaseDataType(); | ||
| log.debug("loaded: " + databaseDataType.getClass().getName()); | ||
| } | ||
|
|
||
| public void ingest(String schemaName, String tableName) { | ||
| // create the table description | ||
| TableDesc ingestTable; | ||
| try { | ||
| ingestTable = createTableDesc(schemaName, tableName); | ||
| } catch (SQLException e) { | ||
| throw new IllegalArgumentException(String.format("error getting database metadata for %s because: %s", | ||
| tableName, e.getMessage())); | ||
| } | ||
|
|
||
| // check the table is valid ADQL | ||
| try { | ||
| TapSchemaUtil.checkValidTableName(ingestTable.getTableName()); | ||
| } catch (ADQLIdentifierException ex) { | ||
| throw new IllegalArgumentException("invalid table name: " + ingestTable.getTableName(), ex); | ||
| } | ||
| try { | ||
| for (ColumnDesc cd : ingestTable.getColumnDescs()) { | ||
| TapSchemaUtil.checkValidIdentifier(cd.getColumnName()); | ||
| } | ||
| } catch (ADQLIdentifierException ex) { | ||
| throw new IllegalArgumentException(ex.getMessage()); | ||
| } | ||
|
|
||
| // make caller the table owner | ||
| Subject caller = AuthenticationUtil.getCurrentSubject(); | ||
| TapPermissions tapPermissions = new TapPermissions(); | ||
| tapPermissions.owner = caller; | ||
| ingestTable.tapPermissions = tapPermissions; | ||
|
|
||
| DatabaseTransactionManager tm = new DatabaseTransactionManager(dataSource); | ||
| try { | ||
| tm.startTransaction(); | ||
|
|
||
| // TODO: change getSchema() above to lockSchema() once implemented to prevent duplicate put | ||
| // add the schema to the tap_schema if it doesn't exist | ||
| SchemaDesc schemaDesc = tapSchemaDAO.getSchema(schemaName, true); | ||
| if (schemaDesc != null) { | ||
| log.debug(String.format("existing schema '%s' in tap_schema", schemaDesc.getSchemaName())); | ||
| } | ||
|
|
||
| // add the table to the tap_schema | ||
| TableDesc tableDesc = tapSchemaDAO.getTable(tableName, true); | ||
| if (tableDesc != null) { | ||
| throw new IllegalStateException(String.format("table already exists in tap_schema: %s", tableName)); | ||
| } | ||
| tapSchemaDAO.put(ingestTable); | ||
| log.debug(String.format("added table '%s' to tap_schema", tableName)); | ||
|
|
||
| tm.commitTransaction(); | ||
| } catch (Exception ex) { | ||
| try { | ||
| log.error("update tap_schema failed - rollback", ex); | ||
| tm.rollbackTransaction(); | ||
| log.error("update tap_schema failed - rollback: OK"); | ||
| } catch (Exception oops) { | ||
| log.error("update tap_schema failed - rollback : FAIL", oops); | ||
| } | ||
| throw new RuntimeException(String.format("failed to update tap_schema with %s", tableName), ex); | ||
| } finally { | ||
| if (tm.isOpen()) { | ||
| log.error("BUG: open transaction in finally - trying to rollback"); | ||
| try { | ||
| tm.rollbackTransaction(); | ||
| log.error("BUG: rollback in finally: OK"); | ||
| } catch (Exception oops) { | ||
| log.error("BUG: rollback in finally: FAIL", oops); | ||
| } | ||
| throw new RuntimeException("BUG: open transaction in finally"); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| protected TableDesc createTableDesc(String schemaName, String tableName) | ||
| throws SQLException { | ||
| log.debug(String.format("creating TableDesc for %s %s", schemaName, tableName)); | ||
| // get the table metadata | ||
| String unqualifiedTableName = getUnqualifiedTableNameFromTable(tableName); | ||
| DatabaseMetaData databaseMetaData = dataSource.getConnection().getMetaData(); | ||
| log.debug(String.format("querying DatabaseMetadata for schema=%s table=%s", schemaName, unqualifiedTableName)); | ||
| //TODO too pg specific? table names are stored lower case in the system tables queried for the metadata | ||
| ResultSet columnInfo = databaseMetaData.getColumns(null, schemaName, unqualifiedTableName.toLowerCase(), null); | ||
| ResultSet indexInfo = databaseMetaData.getIndexInfo(null, schemaName, unqualifiedTableName.toLowerCase(), false, false); | ||
| // get column names for indexed columns | ||
| List<String> indexedColumns = new ArrayList<String>(); | ||
| while (indexInfo.next()) { | ||
| String indexedColumn = indexInfo.getString("COLUMN_NAME"); | ||
| indexedColumns.add(indexedColumn); | ||
| log.debug("indexed column: " + indexedColumn); | ||
| } | ||
|
|
||
| // build TableDesc | ||
| TableDesc tableDesc = new TableDesc(schemaName, tableName); | ||
| tableDesc.tableType = TableDesc.TableType.TABLE; | ||
| tableDesc.apiCreated = true; | ||
| log.debug(String.format("creating TableDesc %s %s", schemaName, tableName)); | ||
| while (columnInfo.next()) { | ||
| String columnName = columnInfo.getString("COLUMN_NAME"); | ||
| String columnType = columnInfo.getString("TYPE_NAME"); | ||
| TapDataType tapDataType = this.databaseDataType.getTapDataType(columnType); | ||
| log.debug(String.format("creating ColumnDesc %s %s %s", tableName, columnName, tapDataType)); | ||
| ColumnDesc columnDesc = new ColumnDesc(tableName, columnName, tapDataType); | ||
| columnDesc.indexed = indexedColumns.contains(columnName); | ||
| tableDesc.getColumnDescs().add(columnDesc); | ||
| } | ||
| return tableDesc; | ||
| } | ||
|
|
||
| String getUnqualifiedTableNameFromTable(String tableName) { | ||
| String[] st = tableName.split("[.]"); | ||
| if (st.length == 2) { | ||
| return st[1]; | ||
| } | ||
| throw new IllegalArgumentException("invalid table name: " + tableName + " (expected: <schema>.<table>)"); | ||
| } | ||
|
|
||
| } |
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