edu.pitt.dbmi.data.reader.validation.tabular.TabularColumnFileValidation 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.tabular;
import edu.pitt.dbmi.data.reader.DataFileReader;
import edu.pitt.dbmi.data.reader.Delimiter;
import edu.pitt.dbmi.data.reader.tabular.AbstractTabularColumnFileReader;
import edu.pitt.dbmi.data.reader.util.Columns;
import edu.pitt.dbmi.data.reader.validation.MessageType;
import edu.pitt.dbmi.data.reader.validation.ValidationAttribute;
import edu.pitt.dbmi.data.reader.validation.ValidationCode;
import edu.pitt.dbmi.data.reader.validation.ValidationResult;
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.*;
/**
* Dec 12, 2018 3:28:26 PM
*
* @author Kevin V. Bui ([email protected])
* @version $Id: $Id
*/
public class TabularColumnFileValidation extends AbstractTabularColumnFileReader implements TabularColumnValidation {
private int maxNumOfMsg;
/**
* Constructor.
*
* @param dataFile The data file.
* @param delimiter The delimiter.
*/
public TabularColumnFileValidation(Path dataFile, Delimiter delimiter) {
super(dataFile, delimiter);
this.maxNumOfMsg = Integer.MAX_VALUE;
}
/**
* {@inheritDoc}
*
* Constructor.
*/
@Override
public List validate() {
return validate(Collections.EMPTY_SET);
}
/**
* {@inheritDoc}
*
* Validate the data file.
*/
@Override
public List validate(int[] excludedColumns) {
List results = new LinkedList<>();
try {
int numOfCols = countNumberOfColumns();
int[] excludedCols = Columns.sortNew(excludedColumns);
int[] validCols = Columns.extractValidColumnNumbers(numOfCols, excludedCols);
validateColumns(validCols, results);
} catch (IOException exception) {
if (results.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());
results.add(result);
}
}
return results;
}
/**
* {@inheritDoc}
*
* Validate the data file.
*/
@Override
public List validate(Set excludedColumns) {
List results = new LinkedList<>();
try {
if (excludedColumns == null || excludedColumns.isEmpty()) {
validateColumns(new int[0], results);
} else {
Set modifiedExcludedCols = new HashSet<>();
if (Character.isDefined(this.quoteCharacter)) {
excludedColumns.stream()
.map(String::trim)
.filter(e -> !e.isEmpty())
.forEach(e -> modifiedExcludedCols.add(stripCharacter(e, this.quoteCharacter)));
} else {
excludedColumns.stream()
.map(String::trim)
.filter(e -> !e.isEmpty())
.forEach(modifiedExcludedCols::add);
}
int[] excludedCols = toColumnNumbers(modifiedExcludedCols);
validateColumns(excludedCols, results);
}
} catch (IOException exception) {
if (results.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());
results.add(result);
}
}
return results;
}
private void validateColumns(int[] excludedColumns, 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();
byte prevChar = -1;
// comment marker check
byte[] comment = this.commentMarker.getBytes();
int cmntIndex = 0;
boolean checkForComment = comment.length > 0;
// excluded columns check
int numOfExCols = excludedColumns.length;
int exColsIndex = 0;
int colNum = 0;
int lineNum = 1;
StringBuilder dataBuilder = new StringBuilder();
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) {
finished = hasSeenNonblankChar && !skip;
if (finished) {
String value = dataBuilder.toString().trim();
dataBuilder.delete(0, dataBuilder.length());
colNum++;
if (numOfExCols == 0 || exColsIndex >= numOfExCols || colNum != excludedColumns[exColsIndex]) {
numOfVars++;
if (value.isEmpty()) {
String errMsg = String.format("Line %d, column %d: Missing variable name.", 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 {
dataBuilder.delete(0, dataBuilder.length());
}
lineNum++;
// 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);
} else {
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 (numOfExCols > 0 && (exColsIndex < numOfExCols && colNum == excludedColumns[exColsIndex])) {
exColsIndex++;
} else {
numOfVars++;
if (value.isEmpty()) {
String errMsg = String.format("Line %d, column %d: Missing variable name.", 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 {
dataBuilder.append((char) currChar);
}
}
}
}
prevChar = currChar;
}
}
finished = hasSeenNonblankChar && !skip;
if (finished) {
String value = dataBuilder.toString().trim();
dataBuilder.delete(0, dataBuilder.length());
colNum++;
if (numOfExCols == 0 || exColsIndex >= numOfExCols || colNum != excludedColumns[exColsIndex]) {
numOfVars++;
if (value.isEmpty()) {
String errMsg = String.format("Line %d, column %d: Missing variable name.", 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);
}
}
}
}
if (numOfVars <= 0) {
final String errMsg = "No variable was read in.";
ValidationResult result = new ValidationResult(ValidationCode.ERROR, MessageType.FILE_MISSING_VALUE, errMsg);
results.add(result);
}
String infoMsg = String.format("There are %d variables.", numOfVars);
ValidationResult result = new ValidationResult(ValidationCode.INFO, MessageType.FILE_SUMMARY, infoMsg);
results.add(result);
}
/**
* {@inheritDoc}
*
* Set the maximum number of messages.
*/
@Override
public void setMaximumNumberOfMessages(int maxNumOfMsg) {
this.maxNumOfMsg = maxNumOfMsg;
}
}