@Override
public List<Assertion> getAssertions() throws SyntaxError {
if (table.getRowCount() < 2) throw new SyntaxError("Query tables must have at least two rows.");
assignColumns();
Assertion make = constructFixture(getFixtureName());
Assertion ti =
makeAssertion(
callFunction(getTableName(), "table", tableAsList()),
new SilentReturnExpectation(0, 0));
Assertion qi =
makeAssertion(callFunction(getTableName(), "query"), new QueryTableExpectation());
tableInstruction = ti.getInstruction().getId();
queryId = qi.getInstruction().getId();
// addExpectation(new QueryTableExpectation());
return list(make, ti, qi);
}
public boolean imp() {
boolean res = false;
DbVariable dbVariable = null;
String fullFileName = "";
String errMessage = null;
DbImportFile dbInFile = new DbImportFile();
try {
dbVariable = new DbVariable();
// Store the file on server filesystem
fullFileName = dbInFile.storeImportFileBLOB(conn_viss, ifid);
FileParser fileParser = new FileParser(fullFileName);
fileParser.Parse(
FileTypeDefinitionList.matchingDefinitions(
FileTypeDefinition.VARIABLE, FileTypeDefinition.LIST));
dbVariable.CreateVariables(fileParser, connection, sampleUnitId, Integer.parseInt(userId));
errMessage = dbVariable.getErrorMessage();
Assertion.assertMsg(errMessage == null || errMessage.trim().equals(""), errMessage);
dbInFile.setStatus(conn_viss, ifid, "IMPORTED");
// dbInFile.UpdateImportFile(connection,null,null,"Done",Integer.parseInt(ifid),Integer.parseInt(userId));
// Add a message to the log
dbInFile.addErrMsg(
conn_viss,
ifid,
"File imported to sampling unit "
+ DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId))
+ "Note: Markers is always imported in Create mode.");
res = true;
} catch (Exception e) {
Errors.logError("ImportVariables.imp(...)" + e.getMessage());
dbInFile.setStatus(conn_viss, ifid, "ERROR");
// dbInFile.UpdateImportFile(connection,null,null,e.getMessage(),Integer.parseInt(ifid),Integer.parseInt(userId));
// Add a message to the log
dbInFile.addErrMsg(conn_viss, ifid, e.getMessage());
e.printStackTrace(System.err);
if (errMessage == null) {
errMessage = e.getMessage();
}
} finally {
try {
/*
* Delete files uploaded
*/
File tmp = new File(fullFileName);
tmp.delete();
} catch (Exception ignore) {
}
}
return res;
}
private void directory_to_directory(
String source_base_name, String destination_base_name, String directory_name)
throws IOException, InterruptedException {
// E.g.
// source_base_name: /foo/bar
// destination_base_name: /x/y
// directory_name: abc
//
// - Create /x/y/abc
// - Copy /foo/bar/abc/* to /x/y/abc/*
// Get source directory.
String source_directory_name = Path.concatenate(source_base_name, directory_name);
File source_directory = File.create(source_directory_name);
Assertion.check(source_directory.isDirectory());
// Get destination directory, creating it if
// necessary.
String destination_directory_name = Path.concatenate(destination_base_name, directory_name);
File destination_directory = File.create(destination_directory_name);
destination_directory.mkdirs();
// Get files in source directory
String[] source_file_names = source_directory.list();
Vector source_files = new Vector();
for (int i = 0; i < source_file_names.length; i++)
source_files.addElement(File.create(source_directory_name, source_file_names[i]));
// Copy
to_directory(source_files, destination_directory);
}
private void to_directory(Vector sources, File destination_directory)
throws IOException, InterruptedException {
Assertion.check(destination_directory.exists());
for (Enumeration source_scan = sources.elements(); source_scan.hasMoreElements(); ) {
File source = (File) source_scan.nextElement();
if (source.isFile()) {
File destination = File.create(destination_directory.getPath(), source.getName());
file_to_file(source, destination);
} else if (_recursive) {
String source_base = source.getParent();
if (source_base == null) source_base = ".";
String destination_base = destination_directory.getCanonicalPath();
directory_to_directory(source_base, destination_base, source.getName());
}
}
}
public boolean imp() {
boolean res = false;
String errMessage = null;
DbImportFile dbInFile = new DbImportFile();
DbPhenotype dbp = new DbPhenotype();
String fullFileName = null;
try {
Errors.logInfo("CheckPhenotype started");
// connection.setAutoCommit(false);
dbInFile.setStatus(conn_viss, ifid, "0%");
fullFileName = dbInFile.storeImportFileBLOB(conn_viss, ifid);
FileHeader header = FileParser.scanFileHeader(fullFileName);
FileParser fileParser = new FileParser(fullFileName);
// Set status
dbInFile.setStatus(conn_viss, ifid, "10%");
// Ensure file format is list or matrix
Assertion.assertMsg(
header.formatTypeName().equalsIgnoreCase(FileTypeDefinition.LIST)
|| header.formatTypeName().equalsIgnoreCase(FileTypeDefinition.MATRIX),
"Format type name should be list or matrix "
+ "but found found "
+ header.formatTypeName());
// If file is a list
if (header.formatTypeName().equalsIgnoreCase(FileTypeDefinition.LIST)) {
fileParser.Parse(
FileTypeDefinitionList.matchingDefinitions(
FileTypeDefinition.PHENOTYPE, FileTypeDefinition.LIST));
dbInFile.setStatus(conn_viss, ifid, "20%");
if (updateMethod.equals("CREATE")) {
dbp.CreatePhenotypesList(
fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue());
} else if (updateMethod.equals("UPDATE")) {
dbp.UpdatePhenotypesList(
fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue());
} else if (updateMethod.equals("CREATE_OR_UPDATE")) {
dbp.CreateOrUpdatePhenotypesList(
fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue());
}
}
// If file is a matrix
else if (header.formatTypeName().equalsIgnoreCase(FileTypeDefinition.MATRIX)) {
fileParser.Parse(
FileTypeDefinitionList.matchingDefinitions(
FileTypeDefinition.PHENOTYPE, FileTypeDefinition.MATRIX));
dbInFile.setStatus(conn_viss, ifid, "20%");
if (updateMethod.equals("CREATE")) {
dbp.CreatePhenotypesMatrix(
fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue());
} else if (updateMethod.equals("UPDATE")) {
dbp.UpdatePhenotypesMatrix(
fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue());
} else if (updateMethod.equals("CREATE_OR_UPDATE")) {
dbp.CreateOrUpdatePhenotypesMatrix(
fileParser, connection, sampleUnitId, Integer.valueOf(userId).intValue());
}
}
errMessage = dbp.getErrorMessage();
Assertion.assertMsg(errMessage == null || errMessage.trim().equals(""), errMessage);
dbInFile.setStatus(conn_viss, ifid, "IMPORTED");
// Add a message to the log
dbInFile.addErrMsg(
conn_viss,
ifid,
"File imported for sampling unit "
+ DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId)));
res = true;
Errors.logInfo("Check Phenotype ended");
} catch (Exception e) {
// Flag for error and set the errMessage if it has not been set
// isOk = false;
dbInFile.setStatus(conn_viss, ifid, "ERROR");
// Add a message to the log
dbInFile.addErrMsg(conn_viss, ifid, e.getMessage());
e.printStackTrace(System.err);
if (errMessage == null) {
errMessage = e.getMessage();
}
}
return res;
}