@Test
public void test_equals_overriden() {
FileHeader header1 = new FileHeader("hello", '%') {};
FileHeader header2 = new FileHeader("hello", '%') {};
assertTrue(header1.equals(header2));
}
void configureNewFile() {
blockSize(configImpl().blockSize());
_fileHeader = FileHeader.newCurrentFileHeader();
setRegularEndAddress(_fileHeader.length());
newSystemData(configImpl().freespaceSystem(), configImpl().idSystemType());
systemData().converterVersion(Converter.VERSION);
createStringIO(_systemData.stringEncoding());
createIdSystem();
initializeClassMetadataRepository();
initalizeWeakReferenceSupport();
generateNewIdentity();
AbstractFreespaceManager blockedFreespaceManager = AbstractFreespaceManager.createNew(this);
installFreespaceManager(blockedFreespaceManager);
initNewClassCollection();
initializeEssentialClasses();
_fileHeader.initNew(this);
blockedFreespaceManager.start(0);
}
@Test
public void test_hashCode_overriden() {
FileHeader header1 = new FileHeader("hello", '%') {};
FileHeader header2 = new FileHeader("hello", '%') {};
assertEquals(header1.hashCode(), header2.hashCode());
}
@Test
public void test_getRawContent_replaces_classname() throws ContentSyntaxErrorException {
final String headerStr = "/* constant \n" + " * %classname% */";
FileHeader header = new FileHeader(headerStr, '%') {};
assertEquals(
"/* constant \n * MyClass */",
header.getRawContent(new HashMap<String, List<String>>(), "MyClass.cs"));
}
@Test
public void test_getContent_does_not_replace_id_of_alternating_part() {
final String headerStr = "/* constant \n" + " * <description>%description%0%</description>*/";
FileHeader header = new FileHeader(headerStr, '%') {};
assertEquals(
"/* constant \n * <description>%description%0%</description>*/", header.getContent());
}
/**
* To call this method the FileLogReader must have been created as writable.
*
* @param size
* @throws IOException
*/
public synchronized void truncate(long size) throws IOException {
if (size < mRAF.length()) {
mRAF.setLength(size);
FileHeader hdr = getHeader();
hdr.setFileSize(size);
hdr.write(mRAF);
mRAF.seek(size);
}
}
void readThis() throws OldFormatException {
newSystemData(AbstractFreespaceManager.FM_LEGACY_RAM, StandardIdSystemFactory.LEGACY);
blockSizeReadFromFile(1);
_fileHeader = FileHeader.read(this);
if (config().generateCommitTimestamps().isUnspecified()) {
config().generateCommitTimestamps(_systemData.idToTimestampIndexId() != 0);
}
createStringIO(_systemData.stringEncoding());
createIdSystem();
initializeClassMetadataRepository();
initalizeWeakReferenceSupport();
setNextTimeStampId(systemData().lastTimeStampID());
classCollection().setID(_systemData.classCollectionID());
classCollection().read(systemTransaction());
Converter.convert(new ConversionStage.ClassCollectionAvailableStage(this));
_fileHeader.readIdentity(this);
if (_config.isReadOnly()) {
return;
}
if (!configImpl().commitRecoveryDisabled()) {
_fileHeader.completeInterruptedTransaction(this);
}
FreespaceManager blockedFreespaceManager =
AbstractFreespaceManager.createNew(this, _systemData.freespaceSystem());
installFreespaceManager(blockedFreespaceManager);
blockedFreespaceManager.read(this, _systemData.inMemoryFreespaceSlot());
blockedFreespaceManager.start(_systemData.bTreeFreespaceId());
_fileHeader = _fileHeader.convert(this);
if (freespaceMigrationRequired(blockedFreespaceManager)) {
migrateFreespace(blockedFreespaceManager);
}
writeHeader(true, false);
if (Converter.convert(new ConversionStage.SystemUpStage(this))) {
_systemData.converterVersion(Converter.VERSION);
_fileHeader.writeVariablePart(this);
transaction().commit();
}
}
public void print() {
FileHeader hdr = new FileHeader();
System.out.println("Directory contents:");
for (int i = 0; i < tableSize; i++)
if (table[i].inUse) {
Debug.printf('+', "Name: %s, Sector: %d\n", table[i].name, new Integer(table[i].sector));
hdr.fetchFrom(table[i].sector);
hdr.print();
}
System.out.println("");
}
public void writeHeader(boolean startFileLockingThread, boolean shuttingDown) {
if (shuttingDown) {
_freespaceManager.write(this);
_freespaceManager = null;
}
StatefulBuffer writer = createStatefulBuffer(systemTransaction(), 0, _fileHeader.length());
_fileHeader.writeFixedPart(this, startFileLockingThread, shuttingDown, writer, blockSize());
if (shuttingDown) {
ensureLastSlotWritten();
}
syncFiles();
}
@Test
public void test_getRawContent_replaces_back_alternating_parts()
throws ContentSyntaxErrorException {
Map<String, List<String>> altData = new HashMap<String, List<String>>();
List<String> value = new Vector<String>();
value.add("real-value");
altData.put("description", value);
final String headerStr = "/* constant \n" + " * <description>%description%0%</description>*/";
FileHeader header = new FileHeader(headerStr, '%') {};
assertEquals(
"/* constant \n * <description>real-value</description>*/", header.getRawContent(altData));
}
/** Check if object support this format. If a match is found return true else return false */
public boolean supportFormat(FileHeader hdr) {
boolean out = false;
try {
for (int i = 0; i < headers.size(); i++) {
if ((headers.get(i).formatTypeName().equals(hdr.formatTypeName()))
&& (headers.get(i).objectTypeName().equals(hdr.objectTypeName()))
&& (headers.get(i).version() == hdr.version())) {
return true;
}
}
} catch (Exception e) {
e.printStackTrace();
}
return false;
}
public synchronized void open() throws IOException {
mRAF = new RandomAccessFile(mFile, mReadOnly ? "r" : "rw");
mIN = new RedoLogInput(mRAF, mFile.getPath());
mHeader.read(mRAF);
mHeaderRead = true;
mFileSizeAtOpen = mRAF.length();
}
/**
* Store to file.
*
* @param out
* @throws Throwable
*/
public void toFile(File fout) throws Throwable {
List<File> files = new ArrayList<File>();
files.add(header.getF1());
for (FileDataOutputBlock<?> b : header.getBlocks()) {
if (b instanceof TripleFileDataOutputBlock<?>) {
files.add(b.getF1());
files.add(((TripleFileDataOutputBlock<?>) b).getF2());
files.add(((TripleFileDataOutputBlock<?>) b).getF3());
} else if (b instanceof HeterogenousFileDataOutputBlock<?>) {
files.add(b.getF1());
files.add(((HeterogenousFileDataOutputBlock<?>) b).getF2());
} else {
files.add(b.getF1());
}
}
// System.out.println("Concatenate: " +
// Arrays.toString(files.toArray()));
FileUtils.concatenateFile(fout, false, files);
}
public void setIdentity(Db4oDatabase identity) {
synchronized (lock()) {
_systemData.identity(identity);
// The dirty TimeStampIdGenerator triggers writing of
// the variable part of the systemdata. We need to
// make it dirty here, so the new identity is persisted:
_timeStampIdGenerator.generate();
_fileHeader.writeVariablePart(this);
}
}
@Test
public void tets_getRawContent_replaces_two_block_with_same_id_correctly()
throws ContentSyntaxErrorException {
Map<String, List<String>> altData = new HashMap<String, List<String>>();
List<String> value = new Vector<String>();
value.add("real-value");
value.add("real-value2");
altData.put("description", value);
final String headerStr =
"/* constant \n"
+ " * <description>%description%1%</description> \n"
+ " * <description>%description%0%</description> */";
FileHeader header = new FileHeader(headerStr, '%') {};
assertEquals(
"/* constant \n"
+ " * <description>real-value2</description> \n"
+ " * <description>real-value</description> */",
header.getRawContent(altData));
}
private void migrateFreespace(FreespaceManager oldFreespaceManager) {
FreespaceManager newFreespaceManager =
AbstractFreespaceManager.createNew(this, configImpl().freespaceSystem());
newFreespaceManager.start(0);
systemData().freespaceSystem(configImpl().freespaceSystem());
installFreespaceManager(newFreespaceManager);
AbstractFreespaceManager.migrate(oldFreespaceManager, newFreespaceManager);
_fileHeader.writeVariablePart(this);
}
public Runnable commitHook() {
_systemData.lastTimeStampID(_timeStampIdGenerator.last());
return _fileHeader.commit(false);
}
public final void writeTransactionPointer(int pointer) {
_fileHeader.writeTransactionPointer(systemTransaction(), pointer);
}
@Test
public void test_getNewlinesCount() throws ContentSyntaxErrorException {
FileHeader header1 = new FileHeader("lin1\n line2 \n adsadasd \n", '%') {};
assertEquals(3, header1.getNewlinesCount(new Hashtable<String, List<String>>()));
}
@Override
protected FileHeader getNewHeader(FileHeader oldHeader) {
FileHeader result = new FileHeader();
FileHeader newHeader = getFileHeader();
FileHeaderTransformer transformer = getTransformer();
boolean modified = false;
// by default, reuse the old header
result.setDescription(oldHeader.getDescription());
result.setCopyrightFirstYear(oldHeader.getCopyrightFirstYear());
result.setCopyrightLastYear(oldHeader.getCopyrightLastYear());
result.setCopyrightHolder(oldHeader.getCopyrightHolder());
result.setLicense(oldHeader.getLicense());
if (isUpdateDescription() && !transformer.isDescriptionEquals(oldHeader, newHeader)) {
// can update description and it has changed
if (log.isDebugEnabled()) {
log.debug(
"description has changed from ["
+ oldHeader.getDescription()
+ "] to ["
+ newHeader.getDescription()
+ "]");
}
// description has changed, mark header to be updated
modified = true;
// use the new description
result.setDescription(newHeader.getDescription());
}
if (isUpdateCopyright() && !transformer.isCopyrightEquals(oldHeader, newHeader)) {
// can update copyright and it has changed
if (log.isDebugEnabled()) {
log.debug(
"copyright has changed from ["
+ oldHeader.getCopyright()
+ "] to ["
+ newHeader.getCopyright()
+ "]");
}
// description has changed, mark header to be updated
modified = true;
// use the new copyright
result.setCopyrightFirstYear(result.getCopyrightFirstYear());
result.setCopyrightLastYear(result.getCopyrightLastYear());
result.setCopyrightHolder(result.getCopyrightHolder());
}
if (isUpdateLicense() && !transformer.isLicenseEquals(oldHeader, newHeader)) {
// can update license and it has changed
if (log.isDebugEnabled()) {
log.debug(
"license has changed from ["
+ oldHeader.getLicense()
+ "] to ["
+ newHeader.getLicense()
+ "]");
}
// description has changed, mark header to be updated
modified = true;
// use the new license
result.setLicense(newHeader.getLicense());
}
if (!modified) {
// nothing has to be updated, so return a {@code null} result
result = null;
}
return result;
}
public boolean check() {
Errors.logDebug("CheckVariables started");
boolean res = false;
DbImportFile dbInFile = new DbImportFile();
String fullFileName = "";
String checkFileName = "";
String errMessage = null;
try {
// Create the variable
DbVariable dbVariable = new DbVariable();
dbInFile.setStatus(conn_viss, ifid, "0%");
// Store the file on server filesystem
fullFileName = dbInFile.storeImportFileBLOB(conn_viss, ifid);
checkFileName = fullFileName + "_checked";
FileHeader header = FileParser.scanFileHeader(fullFileName);
String type = header.formatTypeName().toUpperCase();
char delimiter = header.delimiter().charValue();
FileParser fileParser = new FileParser(fullFileName);
fileParser.Parse(
FileTypeDefinitionList.matchingDefinitions(
FileTypeDefinition.VARIABLE, FileTypeDefinition.LIST));
// Write out the result to a new file
FileWriter fileOut = new FileWriter(checkFileName);
fileOut.write(
header.objectTypeName()
+ "/"
+ header.formatTypeName()
+ "/"
+ header.version()
+ "/"
+ header.delimiter()
+ "\n");
String titles[] = fileParser.columnTitles();
for (int j = 0; j < titles.length; j++) {
fileOut.write(titles[j] + delimiter);
}
fileOut.write("\n");
String errorMsg = "";
errorMsg = checkList(fileParser, fileOut, delimiter);
fileOut.close();
/*
* Save the file to database
*/
dbInFile.saveCheckedFile(conn_viss, ifid, checkFileName);
if (errorMsg.startsWith("ERROR:")) {
res = false;
dbInFile.setStatus(conn_viss, ifid, "ERROR");
// Add a message to the log
dbInFile.addErrMsg(
conn_viss,
ifid,
"File checked failed for sampling unit "
+ DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId))
+ ". <br>"
+ errorMsg);
Errors.logDebug("ErrorMsg=" + errorMsg);
} else if (errorMsg.startsWith("WARNING:")) {
dbInFile.setStatus(conn_viss, ifid, "WARNING");
res = true;
// Add a message to the log
dbInFile.addErrMsg(conn_viss, ifid, "Warnings exists: " + errorMsg);
} else {
dbInFile.setStatus(conn_viss, ifid, "CHECKED");
res = true;
// Add a message to the log
dbInFile.addErrMsg(
conn_viss,
ifid,
"File checked for sampling unit "
+ DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId))
+ ".<br>"
+ errorMsg);
}
/*
if (errorMsg.length()>0)
{
res = false;
dbInFile.setStatus(conn_viss,ifid,"ERROR");
// Add a message to the log
dbInFile.addErrMsg(conn_viss,ifid,"File failed the check for sampling unit "+DbSamplingUnit.getSUName(conn_viss,Integer.toString(sampleUnitId)) +"<br>"+errorMsg);
}
else
{
res = true;
dbInFile.setStatus(conn_viss,ifid,"CHECKED");
// Add a message to the log
dbInFile.addErrMsg(conn_viss,ifid,"File checked for sampling unit "+DbSamplingUnit.getSUName(conn_viss,Integer.toString(sampleUnitId)) +"<br>"+errorMsg);
}*/
} catch (Exception e) {
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();
}
} finally {
try {
/*
* Delete files uploaded
*/
File tmp = new File(checkFileName);
tmp.delete();
tmp = new File(fullFileName);
tmp.delete();
} catch (Exception ignore) {
}
}
Errors.logDebug("CheckVariables completed");
return res;
}
public boolean check() {
Errors.logDebug("CheckPhenotype started");
boolean res = false;
String errMessage = null;
FileWriter fileOut = null;
DbImportFile dbInFile = new DbImportFile();
String fullFileName = "";
String checkFileName = "";
try {
dbInFile.setStatus(conn_viss, ifid, "0%");
fullFileName = dbInFile.storeImportFileBLOB(conn_viss, ifid);
checkFileName = fullFileName + "_checked";
// Create the Phenotype
DbPhenotype dbPhenotype = new DbPhenotype();
FileHeader header = FileParser.scanFileHeader(fullFileName);
String type = header.formatTypeName().toUpperCase();
char delimiter = header.delimiter().charValue();
// AbstractValueFileParser fp = null;
FileParser fp = null;
if (type.equals("LIST")) {
fp = new FileParser(fullFileName);
fp.Parse(
FileTypeDefinitionList.matchingDefinitions(
FileTypeDefinition.PHENOTYPE, FileTypeDefinition.LIST));
} else if (type.equals("MATRIX")) {
fp = new FileParser(fullFileName);
fp.Parse(
FileTypeDefinitionList.matchingDefinitions(
FileTypeDefinition.PHENOTYPE, FileTypeDefinition.MATRIX));
}
// Write out the result to a new file
fileOut = new FileWriter(checkFileName);
fileOut.write(
header.objectTypeName()
+ "/"
+ header.formatTypeName()
+ "/"
+ header.version()
+ "/"
+ header.delimiter()
+ "\n");
String titles[] = fp.columnTitles();
for (int j = 0; j < titles.length; j++) {
fileOut.write(titles[j] + delimiter);
}
fileOut.write("\n");
// Garbage collect the unused variables
header = null;
// fullFileName = null;
// checkFileName = null;
// Fix to upper case
updateMethod = updateMethod.toUpperCase();
Vector fatalErrors = new Vector();
if (type.equals("LIST")) checkListTitles(titles, fatalErrors);
else checkMatrixTitles(titles, fatalErrors);
writeTitleErrors(fileOut, fatalErrors);
String indId;
if (titles[0].equals("IDENTITY")) indId = "IDENTITY";
else indId = "Alias";
String errMsg = "";
if (type.equals("LIST")) errMsg = checkList((FileParser) fp, fileOut, delimiter, indId);
// errMsg = checkList((FileParser)fp, fatalErrors,fileOut,delimiter,indId);
else if (type.equals("MATRIX"))
errMsg = checkMatrix((FileParser) fp, fatalErrors, fileOut, delimiter, indId);
// Close the file
fileOut.close();
/*
* Save the file to database
*/
dbInFile.saveCheckedFile(conn_viss, ifid, checkFileName);
// Get the error message from the database object. If it is set an
// error occured during the operation so an error is thrown.
// errMessage = dbIndividual.getErrorMessage();
// Assertion.assertMsg(errMessage == null ||
// errMessage.trim().equals(""), errMessage);
if (errMsg.startsWith("ERROR:")) {
dbInFile.setStatus(conn_viss, ifid, "ERROR");
res = false;
} else if (errMsg.startsWith("WARNING:")) {
dbInFile.setStatus(conn_viss, ifid, "WARNING");
res = true;
} else {
dbInFile.setStatus(conn_viss, ifid, "CHECKED");
res = true;
}
// Add a message to the log
dbInFile.addErrMsg(
conn_viss,
ifid,
"File checked for sampling unit "
+ DbSamplingUnit.getSUName(conn_viss, Integer.toString(sampleUnitId))
+ "<br>\n"
+ errMsg);
} catch (Exception e) {
// Flag for error and set the errMessage if it has not been set
// isOk = false;
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 temporary file
*/
File tmp = new File(fullFileName);
tmp.delete();
tmp = null;
tmp = new File(checkFileName);
tmp.delete();
tmp = null;
} catch (Exception ignore) {
}
}
Errors.logDebug("CheckPhenotype completed");
return res;
}
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;
}