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stelfrichstelfrich
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Migrate implementations from imagej-server
This adds @lnyng's implementation of IOPlugin<GenericTable> as well as tests and a benchmark.
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‎pom.xml‎

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@@ -105,7 +105,13 @@ Institute of Molecular Cell Biology and Genetics.</license.copyrightOwners>
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<artifactId>commons-csv</artifactId>
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<version>1.3</version>
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</dependency>
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<!-- SCIFIO dependencies -->
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<dependency>
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<groupId>io.scif</groupId>
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<artifactId>scifio</artifactId>
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</dependency>
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<!-- Test scope dependencies -->
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<dependency>
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<groupId>junit</groupId>

‎src/main/java/net/imagej/table/DefaultTableIOPlugin.java‎

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

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