edu.pitt.dbmi.data.reader.tabular.TabularColumnFileReader 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.tabular;
import edu.pitt.dbmi.data.reader.DataColumn;
import edu.pitt.dbmi.data.reader.DataFileReader;
import edu.pitt.dbmi.data.reader.DataReaderException;
import edu.pitt.dbmi.data.reader.Delimiter;
import edu.pitt.dbmi.data.reader.util.Columns;
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.*;
/**
* Reads in columns of tabular data from file.
*
* Nov 7, 2018 2:24:23 PM
*
* @author Kevin V. Bui ([email protected])
* @version $Id: $Id
*/
public final class TabularColumnFileReader extends AbstractTabularColumnFileReader implements TabularColumnReader {
/**
* Constructor.
*
* @param dataFile The data file.
* @param delimiter The delimiter.
*/
public TabularColumnFileReader(Path dataFile, Delimiter delimiter) {
super(dataFile, delimiter);
}
/**
* {@inheritDoc}
*
* Reads in the data columns.
*/
@Override
public DataColumn[] readInDataColumns(boolean isDiscrete) throws IOException {
return readInDataColumns(Collections.EMPTY_SET, isDiscrete);
}
/**
* {@inheritDoc}
*
* Reads in the data columns.
*/
@Override
public DataColumn[] readInDataColumns(Set namesOfColumnsToExclude, boolean isDiscrete) throws IOException {
if (namesOfColumnsToExclude == null || namesOfColumnsToExclude.isEmpty()) {
return getColumns(new int[0], isDiscrete);
} else {
Set cleanedColumnNames = new HashSet<>();
if (Character.isDefined(this.quoteCharacter)) {
namesOfColumnsToExclude.stream()
.filter(Objects::nonNull)
.map(String::trim)
.filter(e -> !e.isEmpty())
.map(e -> stripCharacter(e, this.quoteCharacter))
.forEach(cleanedColumnNames::add);
} else {
namesOfColumnsToExclude.stream()
.filter(Objects::nonNull)
.map(String::trim)
.filter(e -> !e.isEmpty())
.forEach(cleanedColumnNames::add);
}
int[] columnsToExclude = toColumnNumbers(cleanedColumnNames);
return getColumns(columnsToExclude, isDiscrete);
}
}
/**
* {@inheritDoc}
*
* Reads in the data columns.
*/
@Override
public DataColumn[] readInDataColumns(int[] columnsToExclude, boolean isDiscrete) throws IOException {
int numOfCols = countNumberOfColumns();
int[] sortedColsToExclude = Columns.sortNew(columnsToExclude);
int[] validColsToExclude = Columns.extractValidColumnNumbers(numOfCols, sortedColsToExclude);
return getColumns(validColsToExclude, isDiscrete);
}
/**
* {@inheritDoc}
*
* Generates the data columns.
*/
@Override
public DataColumn[] generateColumns(int[] columnsToExclude, boolean isDiscrete) throws IOException {
List columns = new LinkedList<>();
int[] sortedColsToExclude = Columns.sortNew(columnsToExclude);
int numOfCols = countNumberOfColumns();
final String prefix = "C";
int index = 0;
for (int col = 1; col <= numOfCols && !Thread.currentThread().isInterrupted(); col++) {
if (index < sortedColsToExclude.length && col == sortedColsToExclude[index]) {
index++;
} else {
columns.add(new TabularDataColumn(prefix + col, col, false, isDiscrete));
}
}
return columns.toArray(new DataColumn[0]);
}
private DataColumn[] getColumns(int[] columnsToExclude, boolean isDiscrete) throws IOException {
List columns = new LinkedList<>();
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 = columnsToExclude.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 != columnsToExclude[exColsIndex]) {
if (value.isEmpty()) {
String errMsg = String.format("Missing variable name on line %d at column %d.", lineNum, colNum);
// TabularColumnFileReader.LOGGER.error(errMsg);
throw new DataReaderException(errMsg);
} else {
columns.add(new TabularDataColumn(value, colNum, false, isDiscrete));
}
}
} 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 == columnsToExclude[exColsIndex])) {
exColsIndex++;
} else {
if (value.isEmpty()) {
String errMsg = String.format("Missing variable name on line %d at column %d.", lineNum, colNum);
// TabularColumnFileReader.LOGGER.error(errMsg);
throw new DataReaderException(errMsg);
} else {
columns.add(new TabularDataColumn(value, colNum, false, isDiscrete));
}
}
} 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 != columnsToExclude[exColsIndex]) {
if (value.isEmpty()) {
String errMsg = String.format("Missing variable name on line %d at column %d.", lineNum, colNum);
// TabularColumnFileReader.LOGGER.error(errMsg);
throw new DataReaderException(errMsg);
} else {
columns.add(new TabularDataColumn(value, colNum, false, isDiscrete));
}
}
}
}
return columns.toArray(new DataColumn[0]);
}
}