use of org.pmiops.workbench.config.CdrBigQuerySchemaConfig.ColumnConfig in project workbench by all-of-us.
the class FieldSetQueryBuilder method extractResults.
public Map<String, Object> extractResults(TableQueryAndConfig tableQueryAndConfig, List<FieldValue> row) {
TableQuery tableQuery = tableQueryAndConfig.getTableQuery();
List<ColumnConfig> columnConfigs = tableQuery.getColumns().stream().map(columnName -> tableQueryAndConfig.getColumn(columnName)).collect(Collectors.toList());
Map<String, Object> results = new HashMap<>(tableQuery.getColumns().size());
for (int i = 0; i < columnConfigs.size(); i++) {
FieldValue fieldValue = row.get(i);
ColumnConfig columnConfig = columnConfigs.get(i);
if (!fieldValue.isNull()) {
Object value;
switch(columnConfig.type) {
case DATE:
value = fieldValue.getStringValue();
break;
case FLOAT:
value = fieldValue.getDoubleValue();
break;
case INTEGER:
value = fieldValue.getLongValue();
break;
case STRING:
value = fieldValue.getStringValue();
break;
case TIMESTAMP:
value = DATE_TIME_FORMAT.print(fieldValue.getTimestampValue() / 1000L);
break;
default:
throw new IllegalStateException("Unrecognized column type: " + columnConfig.type);
}
results.put(columnConfig.name, value);
}
}
return results;
}
use of org.pmiops.workbench.config.CdrBigQuerySchemaConfig.ColumnConfig 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);
}
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