/** 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 isDeprecated() {
boolean deprecated = false;
if (!mDeprecatedKnown) {
boolean commentDeprecated = comment().isDeprecated();
boolean annotationDeprecated = false;
for (AnnotationInstanceInfo annotation : annotations()) {
if (annotation.type().qualifiedName().equals("java.lang.Deprecated")) {
annotationDeprecated = true;
break;
}
}
if (commentDeprecated != annotationDeprecated) {
Errors.error(
Errors.DEPRECATION_MISMATCH,
position(),
"Method "
+ mContainingClass.qualifiedName()
+ "."
+ name()
+ ": @Deprecated annotation and @deprecated doc tag do not match");
}
mIsDeprecated = commentDeprecated | annotationDeprecated;
mDeprecatedKnown = true;
}
return mIsDeprecated;
}
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;
}
//
// Visitor generation methods
//
public void generateDepthFirstVisitor() throws FileExistsException {
try {
File file = new File(visitorDir, outFilename);
if (Globals.noOverwrite && file.exists()) throw new FileExistsException(outFilename);
PrintWriter out = new PrintWriter(new FileOutputStream(file), false);
Spacing spc = new Spacing(INDENT_AMT);
out.println(Globals.fileHeader(spc));
out.println();
out.println(spc.spc + "package " + Globals.visitorPackage + ";");
if (!Globals.visitorPackage.equals(Globals.nodePackage))
out.println(spc.spc + "import " + Globals.nodePackage + ".*;");
out.println(spc.spc + "import java.util.*;\n");
out.println(spc.spc + "/**");
out.println(
spc.spc
+ " * Provides default methods which visit each "
+ "node in the tree in depth-first");
out.println(spc.spc + " * order. Your visitors may extend this class.");
out.println(spc.spc + " */");
out.println(
spc.spc
+ "public class "
+ visitorName
+ "<R,A> implements "
+ Globals.GJVisitorName
+ "<R,A> {");
printAutoVisitorMethods(out);
spc.updateSpc(+1);
out.println(spc.spc + "//");
out.println(spc.spc + "// User-generated visitor methods below");
out.println(spc.spc + "//");
out.println();
for (Enumeration e = classList.elements(); e.hasMoreElements(); ) {
ClassInfo cur = (ClassInfo) e.nextElement();
String name = cur.getName();
out.println(spc.spc + "/**");
if (Globals.javaDocComments) out.println(spc.spc + " * <PRE>");
out.println(cur.getEbnfProduction(spc));
if (Globals.javaDocComments) out.println(spc.spc + " * </PRE>");
out.println(spc.spc + " */");
out.print(spc.spc + "public R visit");
out.println("(" + name + " n, A argu) {");
spc.updateSpc(+1);
out.println(spc.spc + "R _ret=null;");
for (Enumeration f = cur.getNameList().elements(); f.hasMoreElements(); )
out.println(spc.spc + "n." + (String) f.nextElement() + ".accept(this, argu);");
out.println(spc.spc + "return _ret;");
spc.updateSpc(-1);
out.println(spc.spc + "}\n");
}
spc.updateSpc(-1);
out.println(spc.spc + "}");
out.flush();
out.close();
} catch (IOException e) {
Errors.hardErr("Could not generate " + outFilename);
}
}
public boolean isConsistent(MethodInfo mInfo) {
boolean consistent = true;
if (this.mReturnType != mInfo.mReturnType && !this.mReturnType.equals(mInfo.mReturnType)) {
if (!mReturnType.isPrimitive() && !mInfo.mReturnType.isPrimitive()) {
// Check to see if our class extends the old class.
ApiInfo infoApi = mInfo.containingClass().containingPackage().containingApi();
ClassInfo infoReturnClass = infoApi.findClass(mInfo.mReturnType.qualifiedTypeName());
// Find the classes.
consistent =
infoReturnClass != null
&& infoReturnClass.isAssignableTo(mReturnType.qualifiedTypeName());
} else {
consistent = false;
}
if (!consistent) {
Errors.error(
Errors.CHANGED_TYPE,
mInfo.position(),
"Method "
+ mInfo.qualifiedName()
+ " has changed return type from "
+ mReturnType
+ " to "
+ mInfo.mReturnType);
}
}
if (mIsAbstract != mInfo.mIsAbstract) {
consistent = false;
Errors.error(
Errors.CHANGED_ABSTRACT,
mInfo.position(),
"Method " + mInfo.qualifiedName() + " has changed 'abstract' qualifier");
}
if (mIsNative != mInfo.mIsNative) {
consistent = false;
Errors.error(
Errors.CHANGED_NATIVE,
mInfo.position(),
"Method " + mInfo.qualifiedName() + " has changed 'native' qualifier");
}
if (!mIsStatic) {
// Compiler-generated methods vary in their 'final' qualifier between versions of
// the compiler, so this check needs to be quite narrow. A change in 'final'
// status of a method is only relevant if (a) the method is not declared 'static'
// and (b) the method is not already inferred to be 'final' by virtue of its class.
if (!isEffectivelyFinal() && mInfo.isEffectivelyFinal()) {
consistent = false;
Errors.error(
Errors.ADDED_FINAL,
mInfo.position(),
"Method " + mInfo.qualifiedName() + " has added 'final' qualifier");
} else if (isEffectivelyFinal() && !mInfo.isEffectivelyFinal()) {
consistent = false;
Errors.error(
Errors.REMOVED_FINAL,
mInfo.position(),
"Method " + mInfo.qualifiedName() + " has removed 'final' qualifier");
}
}
if (mIsStatic != mInfo.mIsStatic) {
consistent = false;
Errors.error(
Errors.CHANGED_STATIC,
mInfo.position(),
"Method " + mInfo.qualifiedName() + " has changed 'static' qualifier");
}
if (!scope().equals(mInfo.scope())) {
consistent = false;
Errors.error(
Errors.CHANGED_SCOPE,
mInfo.position(),
"Method "
+ mInfo.qualifiedName()
+ " changed scope from "
+ scope()
+ " to "
+ mInfo.scope());
}
if (!isDeprecated() == mInfo.isDeprecated()) {
Errors.error(
Errors.CHANGED_DEPRECATED,
mInfo.position(),
"Method "
+ mInfo.qualifiedName()
+ " has changed deprecation state "
+ isDeprecated()
+ " --> "
+ mInfo.isDeprecated());
consistent = false;
}
// see JLS 3 13.4.20 "Adding or deleting a synchronized modifier of a method does not break "
// "compatibility with existing binaries."
/*
if (mIsSynchronized != mInfo.mIsSynchronized) {
Errors.error(Errors.CHANGED_SYNCHRONIZED, mInfo.position(), "Method " + mInfo.qualifiedName()
+ " has changed 'synchronized' qualifier from " + mIsSynchronized + " to "
+ mInfo.mIsSynchronized);
consistent = false;
}
*/
for (ClassInfo exception : thrownExceptions()) {
if (!mInfo.throwsException(exception)) {
// exclude 'throws' changes to finalize() overrides with no arguments
if (!name().equals("finalize") || (!mParameters.isEmpty())) {
Errors.error(
Errors.CHANGED_THROWS,
mInfo.position(),
"Method "
+ mInfo.qualifiedName()
+ " no longer throws exception "
+ exception.qualifiedName());
consistent = false;
}
}
}
for (ClassInfo exec : mInfo.thrownExceptions()) {
// exclude 'throws' changes to finalize() overrides with no arguments
if (!throwsException(exec)) {
if (!name().equals("finalize") || (!mParameters.isEmpty())) {
Errors.error(
Errors.CHANGED_THROWS,
mInfo.position(),
"Method "
+ mInfo.qualifiedName()
+ " added thrown exception "
+ exec.qualifiedName());
consistent = false;
}
}
}
return consistent;
}
public ParamTagInfo[] paramTags() {
if (mParamTags == null) {
final int N = mParameters.size();
String[] names = new String[N];
String[] comments = new String[N];
SourcePositionInfo[] positions = new SourcePositionInfo[N];
// get the right names so we can handle our names being different from
// our parent's names.
int i = 0;
for (ParameterInfo param : mParameters) {
names[i] = param.name();
comments[i] = "";
positions[i] = param.position();
i++;
}
// gather our comments, and complain about misnamed @param tags
for (ParamTagInfo tag : comment().paramTags()) {
int index = indexOfParam(tag.parameterName(), names);
if (index >= 0) {
comments[index] = tag.parameterComment();
positions[index] = tag.position();
} else {
Errors.error(
Errors.UNKNOWN_PARAM_TAG_NAME,
tag.position(),
"@param tag with name that doesn't match the parameter list: '"
+ tag.parameterName()
+ "'");
}
}
// get our parent's tags to fill in the blanks
MethodInfo overridden = this.findOverriddenMethod(name(), signature());
if (overridden != null) {
ParamTagInfo[] maternal = overridden.paramTags();
for (i = 0; i < N; i++) {
if (comments[i].equals("")) {
comments[i] = maternal[i].parameterComment();
positions[i] = maternal[i].position();
}
}
}
// construct the results, and cache them for next time
mParamTags = new ParamTagInfo[N];
for (i = 0; i < N; i++) {
mParamTags[i] =
new ParamTagInfo(
"@param", "@param", names[i] + " " + comments[i], parent(), positions[i]);
// while we're here, if we find any parameters that are still undocumented at this
// point, complain. (this warning is off by default, because it's really, really
// common; but, it's good to be able to enforce it)
if (comments[i].equals("")) {
Errors.error(
Errors.UNDOCUMENTED_PARAMETER,
positions[i],
"Undocumented parameter '" + names[i] + "' on method '" + name() + "'");
}
}
}
return mParamTags;
}
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;
}