/** Set the preferences for this import object. */
public void setPrefs(Prefs prefs, DataObject db) throws Exception {
Errors.logInfo("ImportData.setPrefs(...) started");
this.pid = Integer.valueOf(prefs.pid).toString();
this.isid = Integer.valueOf(prefs.isid).toString();
this.ifid = Integer.valueOf(prefs.ifid).toString();
this.upPath = prefs.upPath;
this.systemFileName = prefs.fileName;
this.updateMethod = prefs.updateMethod;
this.connection = prefs.connection;
this.conn_viss = prefs.connViss;
this.sampleUnitId = prefs.sampleUnitId;
this.speciesId = prefs.speciesId;
this.userId = prefs.userId;
this.db = db;
debug();
if (!updateMethod.equals("CREATE")
&& !updateMethod.equals("UPDATE")
&& !updateMethod.equals("CREATE_OR_UPDATE"))
throw new Exception("UpdateMethod is not CREATE, UPDATE, CREATE_OR_UPDATE");
Errors.logInfo("ImportData.setPrefs(...) ended");
}
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;
}
/** Prints a debug information about the knowledge of this import module. */
public void debug() {
Errors.logInfo("ImportData.debug() started");
if (connection == null) Errors.logDebug("connection is null");
else Errors.logDebug("connection is not null");
if (conn_viss == null) Errors.logDebug("conn_viss is null");
else Errors.logDebug("conn_viss is not null");
if (pid == null) Errors.logDebug("pid is null");
else Errors.logDebug("pid=" + pid);
if (isid == null) Errors.logDebug("isid is null");
else Errors.logDebug("isid=" + isid);
if (upPath == null) Errors.logDebug("upPath is null");
else Errors.logDebug("upPath=" + upPath);
Errors.logDebug("sampleUnitId=" + sampleUnitId);
Errors.logDebug("speciesId=" + speciesId);
if (userId == null) Errors.logDebug("userId is null");
else Errors.logDebug("userId=" + userId);
Errors.logDebug("level=" + level);
Errors.logDebug("maxDev=" + maxDev);
if (updateMethod == null) Errors.logDebug("updateMethod is null");
else Errors.logDebug("updateMethod=" + updateMethod);
Errors.logInfo("ImportData.debug() ended");
}
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 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;
}
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;
}