Examples with Column bio.terra.common.Column used on opensource projects

Example 6 with Column

use of bio.terra.common.Column in project jade-data-repo by DataBiosphere.

the class SnapshotMapTableDao method retrieveMapColumns.

public List<SnapshotMapColumn> retrieveMapColumns(UUID mapTableId, Table fromTable, Table toTable) {
    String sql = "SELECT id, from_column_id, to_column_id" + " FROM snapshot_map_column WHERE map_table_id = :map_table_id";
    List<SnapshotMapColumn> mapColumns = jdbcTemplate.query(sql, new MapSqlParameterSource().addValue("map_table_id", mapTableId), (rs, rowNum) -> {
        UUID fromId = rs.getObject("from_column_id", UUID.class);
        Optional<Column> datasetColumn = fromTable.getColumnById(fromId);
        if (!datasetColumn.isPresent()) {
            throw new CorruptMetadataException("Dataset column referenced by snapshot source map column was not found");
        }
        UUID toId = rs.getObject("to_column_id", UUID.class);
        Optional<Column> snapshotColumn = toTable.getColumnById(toId);
        if (!snapshotColumn.isPresent()) {
            throw new CorruptMetadataException("Snapshot column referenced by snapshot source map column was not found");
        }
        return new SnapshotMapColumn().id(rs.getObject("from_column_id", UUID.class)).fromColumn(datasetColumn.get()).toColumn(snapshotColumn.get());
    });
    return mapColumns;
}

Example 7 with Column

use of bio.terra.common.Column in project jade-data-repo by DataBiosphere.

the class SnapshotService method createSnapshotRelationships.

/**
 * Map from a list of source relationships (from a dataset or asset) into snapshot relationships.
 *
 * @param sourceRelationships relationships from a dataset or asset
 * @param snapshotSource source with mapping between dataset tables and columns -> snapshot tables and columns
 * @return a list of relationships tied to the snapshot tables
 */
public List<Relationship> createSnapshotRelationships(List<Relationship> sourceRelationships, SnapshotSource snapshotSource) {
    // We'll copy the asset relationships into the snapshot.
    List<Relationship> snapshotRelationships = new ArrayList<>();
    // Create lookups from dataset table and column ids -> snapshot tables and columns, respectively
    Map<UUID, Table> tableLookup = new HashMap<>();
    Map<UUID, Column> columnLookup = new HashMap<>();
    for (SnapshotMapTable mapTable : snapshotSource.getSnapshotMapTables()) {
        tableLookup.put(mapTable.getFromTable().getId(), mapTable.getToTable());
        for (SnapshotMapColumn mapColumn : mapTable.getSnapshotMapColumns()) {
            columnLookup.put(mapColumn.getFromColumn().getId(), mapColumn.getToColumn());
        }
    }
    for (Relationship sourceRelationship : sourceRelationships) {
        UUID fromTableId = sourceRelationship.getFromTable().getId();
        UUID fromColumnId = sourceRelationship.getFromColumn().getId();
        UUID toTableId = sourceRelationship.getToTable().getId();
        UUID toColumnId = sourceRelationship.getToColumn().getId();
        if (tableLookup.containsKey(fromTableId) && tableLookup.containsKey(toTableId) && columnLookup.containsKey(fromColumnId) && columnLookup.containsKey(toColumnId)) {
            Table fromTable = tableLookup.get(fromTableId);
            Column fromColumn = columnLookup.get(fromColumnId);
            Table toTable = tableLookup.get(toTableId);
            Column toColumn = columnLookup.get(toColumnId);
            snapshotRelationships.add(new Relationship().name(sourceRelationship.getName()).fromTable(fromTable).fromColumn(fromColumn).toTable(toTable).toColumn(toColumn));
        }
    }
    return snapshotRelationships;
}

Example 8 with Column

use of bio.terra.common.Column in project jade-data-repo by DataBiosphere.

the class SnapshotTableDao method createColumns.

private void createColumns(UUID tableId, Collection<Column> columns) {
    MapSqlParameterSource params = new MapSqlParameterSource();
    params.addValue("table_id", tableId);
    DaoKeyHolder keyHolder = new DaoKeyHolder();
    for (Column column : columns) {
        params.addValue("name", column.getName());
        params.addValue("type", column.getType());
        params.addValue("array_of", column.isArrayOf());
        jdbcTemplate.update(sqlInsertColumn, params, keyHolder);
        UUID columnId = keyHolder.getId();
        column.id(columnId);
    }
}

Example 9 with Column

use of bio.terra.common.Column in project jade-data-repo by DataBiosphere.

the class SnapshotTableDao method retrieveTables.

public List<SnapshotTable> retrieveTables(UUID parentId) {
    MapSqlParameterSource params = new MapSqlParameterSource().addValue("parent_id", parentId);
    return jdbcTemplate.query(sqlSelectTable, params, (rs, rowNum) -> {
        SnapshotTable table = new SnapshotTable().id(rs.getObject("id", UUID.class)).name(rs.getString("name")).rowCount(rs.getLong("row_count"));
        List<Column> columns = retrieveColumns(table);
        return table.columns(columns);
    });
}

Example 10 with Column

use of bio.terra.common.Column in project jade-data-repo by DataBiosphere.

the class SnapshotDaoTest method happyInOutTest.

@Test
public void happyInOutTest() throws Exception {
    snapshotRequest.name(snapshotRequest.getName() + UUID.randomUUID().toString());
    String flightId = "happyInOutTest_flightId";
    Snapshot snapshot = snapshotService.makeSnapshotFromSnapshotRequest(snapshotRequest);
    snapshotId = snapshotDao.createAndLock(snapshot, flightId);
    snapshotDao.unlock(snapshotId, flightId);
    Snapshot fromDB = snapshotDao.retrieveSnapshot(snapshotId);
    assertThat("snapshot name set correctly", fromDB.getName(), equalTo(snapshot.getName()));
    assertThat("snapshot description set correctly", fromDB.getDescription(), equalTo(snapshot.getDescription()));
    assertThat("correct number of tables created", fromDB.getTables().size(), equalTo(2));
    assertThat("correct number of sources created", fromDB.getSnapshotSources().size(), equalTo(1));
    // verify source and map
    SnapshotSource source = fromDB.getSnapshotSources().get(0);
    assertThat("source points back to snapshot", source.getSnapshot().getId(), equalTo(snapshot.getId()));
    assertThat("source points to the asset spec", source.getAssetSpecification().getId(), equalTo(dataset.getAssetSpecifications().get(0).getId()));
    assertThat("correct number of map tables", source.getSnapshotMapTables().size(), equalTo(2));
    // Verify map table
    SnapshotMapTable mapTable = source.getSnapshotMapTables().stream().filter(t -> t.getFromTable().getName().equals("thetable")).findFirst().orElseThrow(AssertionError::new);
    Table datasetTable = dataset.getTables().stream().filter(t -> t.getName().equals("thetable")).findFirst().orElseThrow(AssertionError::new);
    Table snapshotTable = snapshot.getTables().stream().filter(t -> t.getName().equals("thetable")).findFirst().orElseThrow(AssertionError::new);
    assertThat("correct map table dataset table", mapTable.getFromTable().getId(), equalTo(datasetTable.getId()));
    assertThat("correct map table snapshot table", mapTable.getToTable().getId(), equalTo(snapshotTable.getId()));
    assertThat("correct number of map columns", mapTable.getSnapshotMapColumns().size(), equalTo(1));
    // Verify map columns
    SnapshotMapColumn mapColumn = mapTable.getSnapshotMapColumns().get(0);
    // Why is dataset columns Collection and not List?
    Column datasetColumn = datasetTable.getColumns().iterator().next();
    Column snapshotColumn = snapshotTable.getColumns().get(0);
    assertThat("correct map column dataset column", mapColumn.getFromColumn().getId(), equalTo(datasetColumn.getId()));
    assertThat("correct map column snapshot column", mapColumn.getToColumn().getId(), equalTo(snapshotColumn.getId()));
    List<Relationship> relationships = fromDB.getRelationships();
    assertThat("a relationship comes back", relationships.size(), equalTo(1));
    Relationship relationship = relationships.get(0);
    Table fromTable = relationship.getFromTable();
    Column fromColumn = relationship.getFromColumn();
    Table toTable = relationship.getToTable();
    Column toColumn = relationship.getToColumn();
    assertThat("from table name matches", fromTable.getName(), equalTo("thetable"));
    assertThat("from column name matches", fromColumn.getName(), equalTo("thecolumn"));
    assertThat("to table name matches", toTable.getName(), equalTo("anothertable"));
    assertThat("to column name matches", toColumn.getName(), equalTo("anothercolumn"));
    assertThat("relationship points to the snapshot table", fromTable.getId(), equalTo(snapshotTable.getId()));
}