Examples with SnapshotMapColumn bio.terra.service.snapshot.SnapshotMapColumn used on opensource projects

Example 1 with SnapshotMapColumn

use of bio.terra.service.snapshot.SnapshotMapColumn in project jade-data-repo by DataBiosphere.

the class BigQueryPdao method sourceSelectSql.

private String sourceSelectSql(String snapshotId, Column targetColumn, SnapshotMapTable mapTable) {
    // In the future, there may not be a column map for a given target column; it might not exist
    // in the table. The logic here covers these cases:
    // 1) no source column: supply NULL
    // 2) source is simple datatype FILEREF or DIRREF:
    // generate the expression to construct the DRS URI: supply AS target name
    // 3) source is a repeating FILEREF or DIRREF:
    // generate the unnest/re-nest to construct array of DRS URI: supply AS target name
    // 4) source and target column with same name, just list source name
    // 5) If source and target column with different names: supply AS target name
    String targetColumnName = targetColumn.getName();
    SnapshotMapColumn mapColumn = lookupMapColumn(targetColumn, mapTable);
    if (mapColumn == null) {
        return "NULL AS " + targetColumnName;
    } else {
        String colType = mapColumn.getFromColumn().getType();
        String mapName = mapColumn.getFromColumn().getName();
        if (StringUtils.equalsIgnoreCase(colType, "FILEREF") || StringUtils.equalsIgnoreCase(colType, "DIRREF")) {
            String drsPrefix = "'drs://" + datarepoDnsName + "/v1_" + snapshotId + "_'";
            if (targetColumn.isArrayOf()) {
                return "ARRAY(SELECT CONCAT(" + drsPrefix + ", x) " + "FROM UNNEST(" + mapName + ") AS x) AS " + targetColumnName;
            } else {
                return "CONCAT(" + drsPrefix + ", " + mapName + ") AS " + targetColumnName;
            }
        } else if (StringUtils.equalsIgnoreCase(mapName, targetColumnName)) {
            return targetColumnName;
        } else {
            return mapName + " AS " + targetColumnName;
        }
    }
}

Example 2 with SnapshotMapColumn

use of bio.terra.service.snapshot.SnapshotMapColumn in project jade-data-repo by DataBiosphere.

the class CreateSnapshotFireStoreDataStep method doStep.

@Override
public StepResult doStep(FlightContext context) throws InterruptedException {
    // We need a complete snapshot; use the snapshotService to get one.
    Snapshot snapshot = snapshotService.retrieveByName(snapshotReq.getName());
    // bounds the intermediate size in a way.
    for (SnapshotSource snapshotSource : snapshot.getSnapshotSources()) {
        for (SnapshotMapTable mapTable : snapshotSource.getSnapshotMapTables()) {
            for (SnapshotMapColumn mapColumn : mapTable.getSnapshotMapColumns()) {
                String fromDatatype = mapColumn.getFromColumn().getType();
                if (StringUtils.equalsIgnoreCase(fromDatatype, "FILEREF") || StringUtils.equalsIgnoreCase(fromDatatype, "DIRREF")) {
                    List<String> refIds = bigQueryPdao.getSnapshotRefIds(snapshotSource.getDataset(), snapshot.getName(), mapTable.getFromTable().getName(), mapTable.getFromTable().getId().toString(), mapColumn.getFromColumn());
                    Dataset dataset = datasetService.retrieve(snapshotSource.getDataset().getId());
                    fileDao.addFilesToSnapshot(dataset, snapshot, refIds);
                    dependencyDao.storeSnapshotFileDependencies(dataset, snapshot.getId().toString(), refIds);
                }
            }
        }
    }
    return StepResult.getStepResultSuccess();
}