Examples with CdrBigQuerySchemaConfig org.pmiops.workbench.config.CdrBigQuerySchemaConfig used on opensource projects

Example 1 with CdrBigQuerySchemaConfig

use of org.pmiops.workbench.config.CdrBigQuerySchemaConfig in project workbench by all-of-us.

the class CohortMaterializationService method getTableQueryAndConfig.

private TableQueryAndConfig getTableQueryAndConfig(FieldSet fieldSet) {
    TableQuery tableQuery;
    if (fieldSet == null) {
        tableQuery = new TableQuery();
        tableQuery.setTableName(PERSON_TABLE);
        tableQuery.setColumns(ImmutableList.of(PERSON_ID));
    } else {
        tableQuery = fieldSet.getTableQuery();
        if (tableQuery == null) {
            // TODO: support other kinds of field sets besides tableQuery
            throw new BadRequestException("tableQuery must be specified in field sets");
        }
        String tableName = tableQuery.getTableName();
        if (Strings.isNullOrEmpty(tableName)) {
            throw new BadRequestException("Table name must be specified in field sets");
        }
    }
    CdrBigQuerySchemaConfig cdrSchemaConfig = cdrSchemaConfigProvider.get();
    TableConfig tableConfig = cdrSchemaConfig.cohortTables.get(tableQuery.getTableName());
    if (tableConfig == null) {
        throw new BadRequestException("Table " + tableQuery.getTableName() + " is not a valid " + "cohort table; valid tables are: " + cdrSchemaConfig.cohortTables.keySet().stream().sorted().collect(Collectors.joining(",")));
    }
    Map<String, ColumnConfig> columnMap = Maps.uniqueIndex(tableConfig.columns, columnConfig -> columnConfig.name);
    List<String> columnNames = tableQuery.getColumns();
    if (columnNames == null || columnNames.isEmpty()) {
        // By default, return all columns on the table in question in our configuration.
        tableQuery.setColumns(columnMap.keySet().stream().collect(Collectors.toList()));
    } else {
        for (String columnName : columnNames) {
            // TODO: handle columns on foreign key tables
            if (!columnMap.containsKey(columnName)) {
                throw new BadRequestException("Unrecognized column name: " + columnName);
            }
        }
    }
    List<String> orderBy = tableQuery.getOrderBy();
    if (orderBy == null || orderBy.isEmpty()) {
        ColumnConfig primaryKey = findPrimaryKey(tableConfig);
        if (PERSON_ID.equals(primaryKey)) {
            tableQuery.setOrderBy(ImmutableList.of(PERSON_ID));
        } else {
            // TODO: consider having per-table default sort order based on e.g. timestamp
            tableQuery.setOrderBy(ImmutableList.of(PERSON_ID, primaryKey.name));
        }
    } else {
        for (String columnName : orderBy) {
            if (columnName.toUpperCase().endsWith(DESCENDING_SUFFIX)) {
                columnName = columnName.substring(0, columnName.length() - DESCENDING_SUFFIX.length());
            }
            if (!columnMap.containsKey(columnName)) {
                throw new BadRequestException("Invalid column in orderBy: " + columnName);
            }
        }
    }
    return new TableQueryAndConfig(tableQuery, tableConfig, columnMap);
}