/*
* #%L
* ImageJ server for RESTful access to ImageJ.
* %%
* Copyright (C) 2013 - 2016 Board of Regents of the University of
* Wisconsin-Madison.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
package net.imagej.server.external;
import io.scif.io.IRandomAccess;
import io.scif.io.VirtualHandle;
import io.scif.services.LocationService;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.function.Function;
import java.util.stream.IntStream;
import org.scijava.Priority;
import org.scijava.io.AbstractIOPlugin;
import org.scijava.io.IOPlugin;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.table.DefaultGenericTable;
import org.scijava.table.GenericTable;
import org.scijava.util.FileUtils;
/**
* Plugin for reading/writing {@link GenericTable}s.
*
* @author Leon Yang
*/
@Plugin(type = IOPlugin.class, priority = Priority.LOW)
public class DefaultTableIOPlugin extends AbstractIOPlugin<GenericTable> {
@Parameter
private LocationService locationService;
/** Reads the first row of the input file as column headers. */
@Parameter(required = false)
private boolean readColHeaders = true;
/** Writes column headers to file if there exists at least one. */
@Parameter(required = false)
private boolean writeColHeaders = true;
/** Reads the first column of the input file as row headers. */
@Parameter(required = false)
private boolean readRowHeaders = false;
/** Writes row headers to file if there exists at least one. */
@Parameter(required = false)
private boolean writeRowHeaders = true;
/** Regex pattern that separates cells in each row of the table. */
@Parameter(required = false)
private char separator = ',';
/** End of line when writing to file. */
@Parameter(required = false)
private String eol = System.lineSeparator();
/**
* Quote character used for escaping separator and empty strings. Use two
* consecutive quotes to escape one.
*/
@Parameter(required = false)
private char quote = '"';
/**
* Text that appears at the top left corner when both column and row headers
* present.
*/
@Parameter(required = false)
private String cornerText = "\\";
/**
* Lambda function that converts the string of a cell to an appropriate value.
*/
@Parameter(required = false)
private Function<String, Object> parser = s -> s;
/** Lambda function that convert the cell content to a string. */
@Parameter(required = false)
private Function<Object, String> formatter = o -> o.toString();
// FIXME: The "txt" extension is extremely general and will conflict with
// other plugins. Consider another way to check supportsOpen/Close.
private static final Set<String> SUPPORTED_EXTENSIONS = Collections
.unmodifiableSet(new HashSet<>(Arrays.asList("csv", "txt", "prn", "dif",
"rtf")));
@Override
public Class<GenericTable> getDataType() {
return GenericTable.class;
}
@Override
public boolean supportsOpen(final String source) {
final String ext = FileUtils.getExtension(source).toLowerCase();
return SUPPORTED_EXTENSIONS.contains(ext);
}
@Override
public boolean supportsSave(final String source) {
return supportsOpen(source);
}
/**
* Process a given line into a list of tokens.
*/
private ArrayList<String> processRow(final String line) throws IOException {
final ArrayList<String> row = new ArrayList<>();
final StringBuilder sb = new StringBuilder();
int idx = 0;
int start = idx;
while (idx < line.length()) {
if (line.charAt(idx) == quote) {
sb.append(line.substring(start, idx));
boolean quoted = true;
idx++;
start = idx;
// find quoted string
while (idx < line.length()) {
if (line.charAt(idx) == quote) {
sb.append(line.substring(start, idx));
if (idx + 1 < line.length() && line.charAt(idx + 1) == quote) {
sb.append(quote);
idx += 2;
start = idx;
}
else {
idx++;
start = idx;
quoted = false;
break;
}
}
else {
idx++;
}
}
if (quoted) {
throw new IOException(String.format(
"Unbalanced quote at position %d: %s", idx, line));
}
}
else if (line.charAt(idx) == separator) {
sb.append(line.substring(start, idx));
row.add(sb.toString());
sb.setLength(0);
idx++;
start = idx;
}
else {
idx++;
}
}
sb.append(line.substring(start, idx));
row.add(sb.toString());
return row;
}
@Override
public GenericTable open(final String source) throws IOException {
final IRandomAccess handle = locationService.getHandle(source);
if (handle instanceof VirtualHandle) {
throw new IOException("Cannot open source");
}
handle.seek(0);
final byte[] buffer = new byte[(int) handle.length()];
handle.read(buffer);
final String text = new String(buffer);
final GenericTable table = new DefaultGenericTable();
// split by any line delimiter
final String[] lines = text.split("\\R");
if (lines.length == 0) return table;
// process first line to get number of cols
{
final ArrayList<String> tokens = processRow(lines[0]);
if (readColHeaders) {
final List<String> colHeaders;
if (readRowHeaders) colHeaders = tokens.subList(1, tokens.size());
else colHeaders = tokens;
final String[] colHeadersArr = new String[colHeaders.size()];
table.appendColumns(colHeaders.toArray(colHeadersArr));
}
else {
final List<String> cols;
if (readRowHeaders) {
cols = tokens.subList(1, tokens.size());
table.appendColumns(cols.size());
table.appendRow(tokens.get(0));
}
else {
cols = tokens;
table.appendColumns(cols.size());
table.appendRow();
}
for (int i = 0; i < cols.size(); i++) {
table.set(i, 0, parser.apply(cols.get(i)));
}
}
}
for (int lineNum = 1; lineNum < lines.length; lineNum++) {
final String line = lines[lineNum];
final ArrayList<String> tokens = processRow(line);
final List<String> cols;
if (readRowHeaders) {
cols = tokens.subList(1, tokens.size());
table.appendRow(tokens.get(0));
}
else {
cols = tokens;
table.appendRow();
}
if (cols.size() != table.getColumnCount()) {
throw new IOException("Line " + table.getRowCount() +
" is not the same length as the first line.");
}
for (int i = 0; i < cols.size(); i++) {
table.set(i, lineNum - 1, parser.apply(cols.get(i)));
}
}
return table;
}
@Override
public void save(final GenericTable table, final String source)
throws IOException
{
final IRandomAccess handle = locationService.getHandle(source, true);
if (handle instanceof VirtualHandle) {
throw new IOException("Cannot open source");
}
handle.seek(0);
final boolean writeRH = this.writeRowHeaders && table.getRowCount() > 0 &&
IntStream.range(0, table.getRowCount()).allMatch(row -> table
.getRowHeader(row) != null);
final boolean writeCH = this.writeColHeaders && table
.getColumnCount() > 0 && table.stream().allMatch(col -> col
.getHeader() != null);
final StringBuilder sb = new StringBuilder();
// write column headers
if (writeCH) {
if (writeRH) {
sb.append(tryQuote(cornerText));
if (table.getColumnCount() > 0) {
sb.append(separator);
sb.append(tryQuote(table.getColumnHeader(0)));
}
}
// avoid adding extra separator when there is 0 column
else if (table.getColumnCount() > 0) {
sb.append(tryQuote(table.getColumnHeader(0)));
}
for (int col = 1; col < table.getColumnCount(); col++) {
sb.append(separator);
sb.append(tryQuote(table.getColumnHeader(col)));
}
sb.append(eol);
handle.writeBytes(sb.toString());
sb.setLength(0);
}
// write each row
for (int row = 0; row < table.getRowCount(); row++) {
if (writeRH) {
sb.append(tryQuote(table.getRowHeader(row)));
if (table.getColumnCount() > 0) {
sb.append(separator);
sb.append(tryQuote(formatter.apply(table.get(0, row))));
}
}
// avoid adding extra separator when there is 0 column
else if (table.getColumnCount() > 0) {
sb.append(tryQuote(formatter.apply(table.get(0, row))));
}
for (int col = 1; col < table.getColumnCount(); col++) {
sb.append(separator);
sb.append(tryQuote(formatter.apply(table.get(col, row))));
}
sb.append(eol);
handle.writeBytes(sb.toString());
sb.setLength(0);
}
}
/**
* Try to quote a string if:
* <li>it is null or empty</li>
* <li>it has quotes inside</li>
* <li>it has separators or EOL inside</li>
*
* @param str string to quote
* @return string, possibly quoted
*/
private String tryQuote(final String str) {
if (str == null || str.length() == 0) return "" + quote + quote;
if (str.indexOf(quote) != -1) return quote + str.replace("" + quote, "" +
quote + quote) + quote;
if (str.indexOf(separator) != -1) return quote + str + quote;
return str;
}
}
