edu.pitt.dbmi.data.reader.validation.covariance.LowerCovarianceDataFileValidation Maven / Gradle / Ivy
/*
* Copyright (C) 2018 University of Pittsburgh.
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
* MA 02110-1301 USA
*/
package edu.pitt.dbmi.data.reader.validation.covariance;
import edu.pitt.dbmi.data.reader.DataFileReader;
import edu.pitt.dbmi.data.reader.Delimiter;
import edu.pitt.dbmi.data.reader.validation.*;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.StandardOpenOption;
import java.util.LinkedList;
import java.util.List;
/**
* Dec 12, 2018 11:04:58 AM
*
* @author Kevin V. Bui ([email protected])
* @version $Id: $Id
*/
public class LowerCovarianceDataFileValidation extends AbstractDataFileValidation implements CovarianceValidation {
/**
* Constructor.
*
* @param dataFile the data file.
* @param delimiter the delimiter.
*/
public LowerCovarianceDataFileValidation(Path dataFile, Delimiter delimiter) {
super(dataFile, delimiter);
}
/**
* {@inheritDoc}
*
* Validate the covariance.
*/
@Override
public List validate() {
List validationResults = new LinkedList<>();
try {
int numOfCases = validateNumberOfCases(validationResults);
int numOfVars = validateVariables(validationResults);
validateData(numOfVars, validationResults);
if (validationResults.size() <= this.maxNumOfMsg) {
String infoMsg = String.format("There are %d cases and %d variables.", numOfCases, numOfVars);
ValidationResult result = new ValidationResult(ValidationCode.INFO, MessageType.FILE_SUMMARY, infoMsg);
result.setAttribute(ValidationAttribute.ROW_NUMBER, numOfCases);
result.setAttribute(ValidationAttribute.COLUMN_NUMBER, numOfVars);
validationResults.add(result);
}
} catch (IOException exception) {
if (validationResults.size() <= this.maxNumOfMsg) {
String errMsg = String.format("Unable to read file %s.", this.dataFile.getFileName());
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_IO_ERROR, errMsg);
result.setAttribute(ValidationAttribute.FILE_NAME, this.dataFile.getFileName());
validationResults.add(result);
}
}
return validationResults;
}
private void validateData(int numOfVars, List results) throws IOException {
try (InputStream in = Files.newInputStream(this.dataFile, StandardOpenOption.READ)) {
boolean skip = false;
boolean hasSeenNonblankChar = false;
boolean hasQuoteChar = false;
byte delimChar = this.delimiter.getByteValue();
// comment marker check
byte[] comment = this.commentMarker.getBytes();
int cmntIndex = 0;
boolean checkForComment = comment.length > 0;
int lineDataNum = 1;
int lineNum = 1;
int colNum = 0;
int rowNum = 1;
StringBuilder dataBuilder = new StringBuilder();
byte prevChar = -1;
byte[] buffer = new byte[DataFileReader.BUFFER_SIZE];
int len;
while ((len = in.read(buffer)) != -1 && results.size() <= this.maxNumOfMsg && !Thread.currentThread().isInterrupted()) {
for (int i = 0; i < len && !Thread.currentThread().isInterrupted(); i++) {
byte currChar = buffer[i];
if (currChar == DataFileReader.CARRIAGE_RETURN || currChar == DataFileReader.LINE_FEED) {
if (currChar == DataFileReader.LINE_FEED && prevChar == DataFileReader.CARRIAGE_RETURN) {
prevChar = DataFileReader.LINE_FEED;
continue;
}
if (hasSeenNonblankChar && !skip) {
if (lineDataNum >= 3) {
colNum++;
String value = dataBuilder.toString().trim();
if (colNum > rowNum) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format(
"Line %d: Excess data. Expect %d value(s) but encounter %d.",
lineNum, rowNum, colNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_EXCESS_DATA, errMsg);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
result.setAttribute(ValidationAttribute.EXPECTED_COUNT, rowNum);
result.setAttribute(ValidationAttribute.ACTUAL_COUNT, colNum);
results.add(result);
}
} else if (colNum < rowNum) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format(
"Line %d: Insufficient data. Expect %d value(s) but encounter %d.",
lineNum, rowNum, colNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_INSUFFICIENT_DATA, errMsg);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
result.setAttribute(ValidationAttribute.EXPECTED_COUNT, rowNum);
result.setAttribute(ValidationAttribute.ACTUAL_COUNT, colNum);
results.add(result);
}
} else {
if (value.isEmpty()) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format("Line %d, column %d: Missing value.", lineNum, colNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_MISSING_VALUE, errMsg);
result.setAttribute(ValidationAttribute.COLUMN_NUMBER, colNum);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
results.add(result);
}
} else {
try {
Double.parseDouble(value);
} catch (NumberFormatException exception) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format("Line %d, column %d: Invalid number %s.", lineNum, colNum, value);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_INVALID_NUMBER, errMsg);
result.setAttribute(ValidationAttribute.COLUMN_NUMBER, colNum);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
result.setAttribute(ValidationAttribute.VALUE, value);
results.add(result);
}
}
}
}
rowNum++;
}
lineDataNum++;
}
lineNum++;
// clear data
dataBuilder.delete(0, dataBuilder.length());
// reset states
skip = false;
hasSeenNonblankChar = false;
cmntIndex = 0;
colNum = 0;
checkForComment = comment.length > 0;
} else if (!skip) {
if (currChar > DataFileReader.SPACE_CHAR) {
hasSeenNonblankChar = true;
}
// skip blank chars at the begining of the line
if (currChar <= DataFileReader.SPACE_CHAR && !hasSeenNonblankChar) {
continue;
}
// check for comment marker to skip line
if (checkForComment) {
if (currChar == comment[cmntIndex]) {
cmntIndex++;
if (cmntIndex == comment.length) {
skip = true;
prevChar = currChar;
continue;
}
} else {
checkForComment = false;
}
}
if (lineDataNum >= 3) {
if (currChar == this.quoteCharacter) {
hasQuoteChar = !hasQuoteChar;
} else if (!hasQuoteChar) {
boolean isDelimiter;
if (this.delimiter == Delimiter.WHITESPACE) {
isDelimiter = (currChar <= DataFileReader.SPACE_CHAR) && (prevChar > DataFileReader.SPACE_CHAR);
} else {
isDelimiter = (currChar == delimChar);
}
if (isDelimiter) {
colNum++;
String value = dataBuilder.toString().trim();
dataBuilder.delete(0, dataBuilder.length());
if (colNum > rowNum) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format(
"Line %d: Excess data. Expect %d value(s) but encounter %d.",
lineNum, rowNum, colNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_EXCESS_DATA, errMsg);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
result.setAttribute(ValidationAttribute.EXPECTED_COUNT, rowNum);
result.setAttribute(ValidationAttribute.ACTUAL_COUNT, colNum);
results.add(result);
}
} else {
if (value.isEmpty()) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format("Line %d, column %d: Missing value.", lineNum, colNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_MISSING_VALUE, errMsg);
result.setAttribute(ValidationAttribute.COLUMN_NUMBER, colNum);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
results.add(result);
}
} else {
try {
Double.parseDouble(value);
} catch (NumberFormatException exception) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format("Line %d, column %d: Invalid number %s.", lineNum, colNum, value);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_INVALID_NUMBER, errMsg);
result.setAttribute(ValidationAttribute.COLUMN_NUMBER, colNum);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
result.setAttribute(ValidationAttribute.VALUE, value);
results.add(result);
}
}
}
}
} else {
dataBuilder.append((char) currChar);
}
}
}
}
prevChar = currChar;
}
}
if (hasSeenNonblankChar && !skip) {
if (lineDataNum >= 3) {
colNum++;
String value = dataBuilder.toString().trim();
if (colNum > rowNum) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format(
"Line %d: Excess data. Expect %d value(s) but encounter %d.",
lineNum, rowNum, colNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_EXCESS_DATA, errMsg);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
result.setAttribute(ValidationAttribute.EXPECTED_COUNT, rowNum);
result.setAttribute(ValidationAttribute.ACTUAL_COUNT, colNum);
results.add(result);
}
} else if (colNum < rowNum) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format(
"Line %d: Insufficient data. Expect %d value(s) but encounter %d.",
lineNum, rowNum, colNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_INSUFFICIENT_DATA, errMsg);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
result.setAttribute(ValidationAttribute.EXPECTED_COUNT, rowNum);
result.setAttribute(ValidationAttribute.ACTUAL_COUNT, colNum);
results.add(result);
}
} else {
if (value.isEmpty()) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format("Line %d, column %d: Missing value.", lineNum, colNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_MISSING_VALUE, errMsg);
result.setAttribute(ValidationAttribute.COLUMN_NUMBER, colNum);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
results.add(result);
}
} else {
try {
Double.parseDouble(value);
} catch (NumberFormatException exception) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format("Line %d, column %d: Invalid number %s.", lineNum, colNum, value);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_INVALID_NUMBER, errMsg);
result.setAttribute(ValidationAttribute.COLUMN_NUMBER, colNum);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
result.setAttribute(ValidationAttribute.VALUE, value);
results.add(result);
}
}
}
}
rowNum++;
}
}
rowNum--; // minus the extra count for possibly the next line
if (rowNum > numOfVars) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format(
"Excess data. Expect %d row(s) but encounter %d.",
numOfVars, rowNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_EXCESS_DATA, errMsg);
result.setAttribute(ValidationAttribute.EXPECTED_COUNT, numOfVars);
result.setAttribute(ValidationAttribute.ACTUAL_COUNT, rowNum);
results.add(result);
}
} else if (rowNum < numOfVars) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format(
"Insufficient data. Expect %d row(s) but encounter %d.",
numOfVars, rowNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_EXCESS_DATA, errMsg);
result.setAttribute(ValidationAttribute.EXPECTED_COUNT, numOfVars);
result.setAttribute(ValidationAttribute.ACTUAL_COUNT, rowNum);
results.add(result);
}
}
}
}
private int validateVariables(List results) throws IOException {
int numOfVars = 0;
try (InputStream in = Files.newInputStream(this.dataFile, StandardOpenOption.READ)) {
boolean skip = false;
boolean hasSeenNonblankChar = false;
boolean hasQuoteChar = false;
boolean finished = false;
byte delimChar = this.delimiter.getByteValue();
// comment marker check
byte[] comment = this.commentMarker.getBytes();
int cmntIndex = 0;
boolean checkForComment = comment.length > 0;
int lineDataNum = 1;
int colNum = 0;
int lineNum = 1;
StringBuilder dataBuilder = new StringBuilder();
byte prevChar = -1;
byte[] buffer = new byte[DataFileReader.BUFFER_SIZE];
int len;
while ((len = in.read(buffer)) != -1 && !finished && !Thread.currentThread().isInterrupted()) {
for (int i = 0; i < len && !finished && !Thread.currentThread().isInterrupted(); i++) {
byte currChar = buffer[i];
if (currChar == DataFileReader.CARRIAGE_RETURN || currChar == DataFileReader.LINE_FEED) {
if (currChar == DataFileReader.LINE_FEED && prevChar == DataFileReader.CARRIAGE_RETURN) {
prevChar = DataFileReader.LINE_FEED;
continue;
}
if (hasSeenNonblankChar && !skip) {
if (lineDataNum == 2) {
String value = dataBuilder.toString().trim();
colNum++;
if (value.isEmpty()) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format("Line %d, column %d: Missing value.", lineNum, colNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_MISSING_VALUE, errMsg);
result.setAttribute(ValidationAttribute.COLUMN_NUMBER, colNum);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
results.add(result);
}
}
numOfVars++;
finished = true;
}
lineDataNum++;
}
lineNum++;
// clear data
dataBuilder.delete(0, dataBuilder.length());
// reset states
skip = false;
hasSeenNonblankChar = false;
cmntIndex = 0;
checkForComment = comment.length > 0;
} else if (!skip) {
if (currChar > DataFileReader.SPACE_CHAR) {
hasSeenNonblankChar = true;
}
// skip blank chars at the begining of the line
if (currChar <= DataFileReader.SPACE_CHAR && !hasSeenNonblankChar) {
continue;
}
// check for comment marker to skip line
if (checkForComment) {
if (currChar == comment[cmntIndex]) {
cmntIndex++;
if (cmntIndex == comment.length) {
skip = true;
prevChar = currChar;
continue;
}
} else {
checkForComment = false;
}
}
if (lineDataNum == 2) {
if (currChar == this.quoteCharacter) {
hasQuoteChar = !hasQuoteChar;
} else if (!hasQuoteChar) {
boolean isDelimiter;
if (this.delimiter == Delimiter.WHITESPACE) {
isDelimiter = (currChar <= DataFileReader.SPACE_CHAR) && (prevChar > DataFileReader.SPACE_CHAR);
} else {
isDelimiter = (currChar == delimChar);
}
if (isDelimiter) {
String value = dataBuilder.toString().trim();
dataBuilder.delete(0, dataBuilder.length());
colNum++;
if (value.isEmpty()) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format("Line %d, column %d: Missing value.", lineNum, colNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_MISSING_VALUE, errMsg);
result.setAttribute(ValidationAttribute.COLUMN_NUMBER, colNum);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
results.add(result);
}
}
numOfVars++;
} else {
dataBuilder.append((char) currChar);
}
}
}
}
prevChar = currChar;
}
}
if (hasSeenNonblankChar && !skip) {
if (lineDataNum == 2) {
String value = dataBuilder.toString().trim();
dataBuilder.delete(0, dataBuilder.length());
colNum++;
if (value.isEmpty()) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format("Line %d, column %d: Missing value.", lineNum, colNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_MISSING_VALUE, errMsg);
result.setAttribute(ValidationAttribute.COLUMN_NUMBER, colNum);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
results.add(result);
}
}
numOfVars++;
}
}
}
if (numOfVars == 0) {
if (results.size() <= this.maxNumOfMsg) {
final String errMsg = "Covariance file does not contain variable names.";
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_MISSING_VALUE, errMsg);
results.add(result);
}
}
return numOfVars;
}
private int validateNumberOfCases(List results) throws IOException {
int count = 0;
try (InputStream in = Files.newInputStream(this.dataFile, StandardOpenOption.READ)) {
boolean skip = false;
boolean hasSeenNonblankChar = false;
boolean hasQuoteChar = false;
boolean finished = false;
// comment marker check
byte[] comment = this.commentMarker.getBytes();
int cmntIndex = 0;
boolean checkForComment = comment.length > 0;
int lineNum = 1;
StringBuilder dataBuilder = new StringBuilder();
byte prevChar = -1;
byte[] buffer = new byte[DataFileReader.BUFFER_SIZE];
int len;
while ((len = in.read(buffer)) != -1 && !finished && !Thread.currentThread().isInterrupted()) {
for (int i = 0; i < len && !finished && !Thread.currentThread().isInterrupted(); i++) {
byte currChar = buffer[i];
if (currChar == DataFileReader.CARRIAGE_RETURN || currChar == DataFileReader.LINE_FEED) {
if (currChar == DataFileReader.LINE_FEED && prevChar == DataFileReader.CARRIAGE_RETURN) {
prevChar = DataFileReader.LINE_FEED;
continue;
}
finished = hasSeenNonblankChar && !skip;
if (!finished) {
lineNum++;
// clear data
dataBuilder.delete(0, dataBuilder.length());
// reset states
skip = false;
hasSeenNonblankChar = false;
cmntIndex = 0;
checkForComment = comment.length > 0;
}
} else if (!skip) {
if (currChar > DataFileReader.SPACE_CHAR) {
hasSeenNonblankChar = true;
}
// skip blank chars at the begining of the line
if (currChar <= DataFileReader.SPACE_CHAR && !hasSeenNonblankChar) {
continue;
}
// check for comment marker to skip line
if (checkForComment) {
if (currChar == comment[cmntIndex]) {
cmntIndex++;
if (cmntIndex == comment.length) {
skip = true;
prevChar = currChar;
continue;
}
} else {
checkForComment = false;
}
}
if (currChar == this.quoteCharacter) {
hasQuoteChar = !hasQuoteChar;
} else if (!hasQuoteChar) {
dataBuilder.append((char) currChar);
}
}
prevChar = currChar;
}
}
String value = dataBuilder.toString().trim();
if (value.isEmpty()) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format("Line %d: Missing number of cases.", lineNum);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_MISSING_VALUE, errMsg);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
results.add(result);
}
} else {
try {
count += Integer.parseInt(value);
} catch (NumberFormatException exception) {
if (results.size() <= this.maxNumOfMsg) {
String errMsg = String.format("Line %d: Invalid number %s.", lineNum, value);
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_INVALID_NUMBER, errMsg);
result.setAttribute(ValidationAttribute.LINE_NUMBER, lineNum);
result.setAttribute(ValidationAttribute.VALUE, value);
results.add(result);
}
}
}
}
return count;
}
}