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Example 1 with PDAO_ROW_ID_COLUMN

use of bio.terra.common.PdaoConstant.PDAO_ROW_ID_COLUMN 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;
}
Also used : FieldValue(com.google.cloud.bigquery.FieldValue) IngestFileNotFoundException(bio.terra.service.dataset.exception.IngestFileNotFoundException) DatasetService(bio.terra.service.dataset.DatasetService) BigQueryError(com.google.cloud.bigquery.BigQueryError) ViewDefinition(com.google.cloud.bigquery.ViewDefinition) PrimaryDataAccess(bio.terra.common.PrimaryDataAccess) SnapshotDataProject(bio.terra.service.snapshot.SnapshotDataProject) PDAO_EXTERNAL_TABLE_PREFIX(bio.terra.common.PdaoConstant.PDAO_EXTERNAL_TABLE_PREFIX) TableId(com.google.cloud.bigquery.TableId) LoggerFactory(org.slf4j.LoggerFactory) Autowired(org.springframework.beans.factory.annotation.Autowired) StringUtils(org.apache.commons.lang3.StringUtils) PDAO_TEMP_TABLE(bio.terra.common.PdaoConstant.PDAO_TEMP_TABLE) DatasetTable(bio.terra.service.dataset.DatasetTable) BigQuery(com.google.cloud.bigquery.BigQuery) FieldValueList(com.google.cloud.bigquery.FieldValueList) Schema(com.google.cloud.bigquery.Schema) Map(java.util.Map) Table(bio.terra.common.Table) TableResult(com.google.cloud.bigquery.TableResult) PdaoException(bio.terra.common.exception.PdaoException) DataLocationService(bio.terra.service.resourcemanagement.DataLocationService) MismatchedRowIdException(bio.terra.service.tabulardata.exception.MismatchedRowIdException) Field(com.google.cloud.bigquery.Field) DataDeletionTableModel(bio.terra.model.DataDeletionTableModel) LoadJobConfiguration(com.google.cloud.bigquery.LoadJobConfiguration) PDAO_PREFIX(bio.terra.common.PdaoConstant.PDAO_PREFIX) SnapshotRequestRowIdTableModel(bio.terra.model.SnapshotRequestRowIdTableModel) Collection(java.util.Collection) QueryJobConfiguration(com.google.cloud.bigquery.QueryJobConfiguration) SnapshotMapColumn(bio.terra.service.snapshot.SnapshotMapColumn) Instant(java.time.Instant) SnapshotRequestContentsModel(bio.terra.model.SnapshotRequestContentsModel) Collectors(java.util.stream.Collectors) CorruptMetadataException(bio.terra.service.snapshot.exception.CorruptMetadataException) MismatchedValueException(bio.terra.service.snapshot.exception.MismatchedValueException) List(java.util.List) AssetSpecification(bio.terra.service.dataset.AssetSpecification) ST(org.stringtemplate.v4.ST) PDAO_LOAD_HISTORY_TABLE(bio.terra.common.PdaoConstant.PDAO_LOAD_HISTORY_TABLE) BadExternalFileException(bio.terra.service.tabulardata.exception.BadExternalFileException) ExternalTableDefinition(com.google.cloud.bigquery.ExternalTableDefinition) Optional(java.util.Optional) PDAO_ROW_ID_COLUMN(bio.terra.common.PdaoConstant.PDAO_ROW_ID_COLUMN) PDAO_ROW_ID_TABLE(bio.terra.common.PdaoConstant.PDAO_ROW_ID_TABLE) FormatOptions(com.google.cloud.bigquery.FormatOptions) HashMap(java.util.HashMap) Column(bio.terra.common.Column) RowIdMatch(bio.terra.service.snapshot.RowIdMatch) CsvOptions(com.google.cloud.bigquery.CsvOptions) ArrayList(java.util.ArrayList) PDAO_TABLE_ID_COLUMN(bio.terra.common.PdaoConstant.PDAO_TABLE_ID_COLUMN) AssetTable(bio.terra.service.dataset.AssetTable) Snapshot(bio.terra.service.snapshot.Snapshot) Job(com.google.cloud.bigquery.Job) InvalidQueryException(bio.terra.grammar.exception.InvalidQueryException) PdaoLoadStatistics(bio.terra.common.PdaoLoadStatistics) DatasetDataProject(bio.terra.service.dataset.DatasetDataProject) LegacySQLTypeName(com.google.cloud.bigquery.LegacySQLTypeName) Logger(org.slf4j.Logger) JobInfo(com.google.cloud.bigquery.JobInfo) Acl(com.google.cloud.bigquery.Acl) SnapshotTable(bio.terra.service.snapshot.SnapshotTable) Profile(org.springframework.context.annotation.Profile) JobStatistics(com.google.cloud.bigquery.JobStatistics) PDAO_LOAD_HISTORY_STAGING_TABLE_PREFIX(bio.terra.common.PdaoConstant.PDAO_LOAD_HISTORY_STAGING_TABLE_PREFIX) TimeUnit(java.util.concurrent.TimeUnit) BulkLoadHistoryModel(bio.terra.model.BulkLoadHistoryModel) Component(org.springframework.stereotype.Component) IngestRequestModel(bio.terra.model.IngestRequestModel) IngestFailureException(bio.terra.service.dataset.exception.IngestFailureException) ApplicationConfiguration(bio.terra.app.configuration.ApplicationConfiguration) SnapshotRequestRowIdModel(bio.terra.model.SnapshotRequestRowIdModel) PdaoConstant(bio.terra.common.PdaoConstant) BigQueryPartitionConfigV1(bio.terra.service.dataset.BigQueryPartitionConfigV1) TableInfo(com.google.cloud.bigquery.TableInfo) Dataset(bio.terra.service.dataset.Dataset) SnapshotSource(bio.terra.service.snapshot.SnapshotSource) Collections(java.util.Collections) SnapshotMapTable(bio.terra.service.snapshot.SnapshotMapTable) ST(org.stringtemplate.v4.ST) TableResult(com.google.cloud.bigquery.TableResult) SnapshotMapTable(bio.terra.service.snapshot.SnapshotMapTable) RowIdMatch(bio.terra.service.snapshot.RowIdMatch) SnapshotMapColumn(bio.terra.service.snapshot.SnapshotMapColumn) Column(bio.terra.common.Column) FieldValueList(com.google.cloud.bigquery.FieldValueList) FieldValue(com.google.cloud.bigquery.FieldValue)

Aggregations

ApplicationConfiguration (bio.terra.app.configuration.ApplicationConfiguration)1 Column (bio.terra.common.Column)1 PdaoConstant (bio.terra.common.PdaoConstant)1 PDAO_EXTERNAL_TABLE_PREFIX (bio.terra.common.PdaoConstant.PDAO_EXTERNAL_TABLE_PREFIX)1 PDAO_LOAD_HISTORY_STAGING_TABLE_PREFIX (bio.terra.common.PdaoConstant.PDAO_LOAD_HISTORY_STAGING_TABLE_PREFIX)1 PDAO_LOAD_HISTORY_TABLE (bio.terra.common.PdaoConstant.PDAO_LOAD_HISTORY_TABLE)1 PDAO_PREFIX (bio.terra.common.PdaoConstant.PDAO_PREFIX)1 PDAO_ROW_ID_COLUMN (bio.terra.common.PdaoConstant.PDAO_ROW_ID_COLUMN)1 PDAO_ROW_ID_TABLE (bio.terra.common.PdaoConstant.PDAO_ROW_ID_TABLE)1 PDAO_TABLE_ID_COLUMN (bio.terra.common.PdaoConstant.PDAO_TABLE_ID_COLUMN)1 PDAO_TEMP_TABLE (bio.terra.common.PdaoConstant.PDAO_TEMP_TABLE)1 PdaoLoadStatistics (bio.terra.common.PdaoLoadStatistics)1 PrimaryDataAccess (bio.terra.common.PrimaryDataAccess)1 Table (bio.terra.common.Table)1 PdaoException (bio.terra.common.exception.PdaoException)1 InvalidQueryException (bio.terra.grammar.exception.InvalidQueryException)1 BulkLoadHistoryModel (bio.terra.model.BulkLoadHistoryModel)1 DataDeletionTableModel (bio.terra.model.DataDeletionTableModel)1 IngestRequestModel (bio.terra.model.IngestRequestModel)1 SnapshotRequestContentsModel (bio.terra.model.SnapshotRequestContentsModel)1