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

Example 1 with RowIdMatch

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

the class BigQueryPdao method matchRowIds.

// for each table in a dataset (source), collect row id matches ON the row id
public RowIdMatch matchRowIds(Snapshot snapshot, SnapshotSource source, String tableName, List<String> rowIds) throws InterruptedException {
    // One source: grab it and navigate to the relevant parts
    BigQueryProject bigQueryProject = bigQueryProjectForSnapshot(snapshot);
    Optional<SnapshotMapTable> optTable = source.getSnapshotMapTables().stream().filter(table -> table.getFromTable().getName().equals(tableName)).findFirst();
    // create a column to point to the row id column in the source table to check that passed row ids exist in it
    Column rowIdColumn = new Column().table(optTable.get().getFromTable()).name(PDAO_ROW_ID_COLUMN);
    ST sqlTemplate = new ST(mapValuesToRowsTemplate);
    sqlTemplate.add("project", bigQueryProject.getProjectId());
    sqlTemplate.add("dataset", prefixName(source.getDataset().getName()));
    sqlTemplate.add("table", tableName);
    sqlTemplate.add("column", rowIdColumn.getName());
    sqlTemplate.add("inputVals", rowIds);
    // Execute the query building the row id match structure that tracks the matching
    // ids and the mismatched ids
    RowIdMatch rowIdMatch = new RowIdMatch();
    String sql = sqlTemplate.render();
    logger.debug("mapValuesToRows sql: " + sql);
    TableResult result = bigQueryProject.query(sql);
    for (FieldValueList row : result.iterateAll()) {
        // Test getting these by name
        FieldValue rowId = row.get(0);
        FieldValue inputValue = row.get(1);
        if (rowId.isNull()) {
            rowIdMatch.addMismatch(inputValue.getStringValue());
            logger.debug("rowId=<NULL>" + "  inVal=" + inputValue.getStringValue());
        } else {
            rowIdMatch.addMatch(inputValue.getStringValue(), rowId.getStringValue());
            logger.debug("rowId=" + rowId.getStringValue() + "  inVal=" + inputValue.getStringValue());
        }
    }
    return rowIdMatch;
}

Example 2 with RowIdMatch

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

the class CreateSnapshotPrimaryDataRowIdsStep method doStep.

@Override
public StepResult doStep(FlightContext context) throws InterruptedException {
    // TODO: this assumes single-dataset snapshots, will need to add a loop for multiple
    SnapshotRequestContentsModel contentsModel = snapshotReq.getContents().get(0);
    Snapshot snapshot = snapshotDao.retrieveSnapshotByName(snapshotReq.getName());
    SnapshotSource source = snapshot.getSnapshotSources().get(0);
    SnapshotRequestRowIdModel rowIdModel = contentsModel.getRowIdSpec();
    // for each table, make sure all of the row ids match
    for (SnapshotRequestRowIdTableModel table : rowIdModel.getTables()) {
        List<String> rowIds = table.getRowIds();
        if (!rowIds.isEmpty()) {
            RowIdMatch rowIdMatch = bigQueryPdao.matchRowIds(snapshot, source, table.getTableName(), rowIds);
            if (!rowIdMatch.getUnmatchedInputValues().isEmpty()) {
                String unmatchedValues = String.join("', '", rowIdMatch.getUnmatchedInputValues());
                String message = String.format("Mismatched row ids: '%s'", unmatchedValues);
                FlightUtils.setErrorResponse(context, message, HttpStatus.BAD_REQUEST);
                return new StepResult(StepStatus.STEP_RESULT_FAILURE_FATAL, new MismatchedValueException(message));
            }
        }
    }
    bigQueryPdao.createSnapshotWithProvidedIds(snapshot, contentsModel);
    return StepResult.getStepResultSuccess();
}

Example 3 with RowIdMatch

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

the class CreateSnapshotPrimaryDataAssetStep method doStep.

@Override
public StepResult doStep(FlightContext context) throws InterruptedException {
    /*
         * map field ids into row ids and validate
         * then pass the row id array into create snapshot
         */
    SnapshotRequestContentsModel contentsModel = snapshotReq.getContents().get(0);
    SnapshotRequestAssetModel assetSpec = contentsModel.getAssetSpec();
    Snapshot snapshot = snapshotDao.retrieveSnapshotByName(snapshotReq.getName());
    SnapshotSource source = snapshot.getSnapshotSources().get(0);
    RowIdMatch rowIdMatch = bigQueryPdao.mapValuesToRows(snapshot, source, assetSpec.getRootValues());
    if (rowIdMatch.getUnmatchedInputValues().size() != 0) {
        String unmatchedValues = String.join("', '", rowIdMatch.getUnmatchedInputValues());
        String message = String.format("Mismatched input values: '%s'", unmatchedValues);
        FlightUtils.setErrorResponse(context, message, HttpStatus.BAD_REQUEST);
        return new StepResult(StepStatus.STEP_RESULT_FAILURE_FATAL, new MismatchedValueException(message));
    }
    bigQueryPdao.createSnapshot(snapshot, rowIdMatch.getMatchingRowIds());
    return StepResult.getStepResultSuccess();
}

Example 4 with RowIdMatch

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

the class BigQueryPdao method mapValuesToRows.

// compute the row ids from the input ids and validate all inputs have matches
// returns a structure with the matching row ids (suitable for calling create snapshot)
// and any mismatched input values that don't have corresponding roww.
// NOTE: In the fullness of time, we may not do this and kick the function into the UI.
// So this code assumes there is one source and one set of input values.
// The query it builds embeds data values into the query in an array. I think it will
// support about 25,000 input values. If that is not enough there is another, more
// complicated alternative:
// - create a scratch table at snapshot creation time
// - truncate before we start
// - load the values in
// - do the query
// - truncate (even tidier...)
// So if we need to make this work in the long term, we can take that approach.
@Override
public RowIdMatch mapValuesToRows(Snapshot snapshot, SnapshotSource source, List<String> inputValues) throws InterruptedException {
    // One source: grab it and navigate to the relevant parts
    BigQueryProject bigQueryProject = bigQueryProjectForSnapshot(snapshot);
    AssetSpecification asset = source.getAssetSpecification();
    Column column = asset.getRootColumn().getDatasetColumn();
    ST sqlTemplate = new ST(mapValuesToRowsTemplate);
    sqlTemplate.add("project", bigQueryProject.getProjectId());
    sqlTemplate.add("dataset", prefixName(source.getDataset().getName()));
    sqlTemplate.add("table", column.getTable().getName());
    sqlTemplate.add("column", column.getName());
    sqlTemplate.add("inputVals", inputValues);
    // Execute the query building the row id match structure that tracks the matching
    // ids and the mismatched ids
    RowIdMatch rowIdMatch = new RowIdMatch();
    String sql = sqlTemplate.render();
    logger.debug("mapValuesToRows sql: " + sql);
    TableResult result = bigQueryProject.query(sql);
    for (FieldValueList row : result.iterateAll()) {
        // Test getting these by name
        FieldValue rowId = row.get(0);
        FieldValue inputValue = row.get(1);
        if (rowId.isNull()) {
            rowIdMatch.addMismatch(inputValue.getStringValue());
            logger.debug("rowId=<NULL>" + "  inVal=" + inputValue.getStringValue());
        } else {
            rowIdMatch.addMatch(inputValue.getStringValue(), rowId.getStringValue());
            logger.debug("rowId=" + rowId.getStringValue() + "  inVal=" + inputValue.getStringValue());
        }
    }
    return rowIdMatch;
}