/** 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");
}
/** 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 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;
}
