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Fix tests on Windows
On Windows, files created during the tests could not be deleted, because of DataHandle objects not being closed. This commit fixes the issue by using try-with-resources to make sure the handles get closed after reading/writing.
1 parent 35c09a5 commit 5cb89a9

2 files changed

Lines changed: 131 additions & 111 deletions

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

Lines changed: 103 additions & 96 deletions
Original file line numberDiff line numberDiff line change
@@ -191,131 +191,138 @@ else if (line.charAt(idx) == separator) {
191191
public GenericTable open(final String source) throws IOException {
192192
// FIXME Assumes FileLocation
193193
final Location sourceLocation = new FileLocation(source);
194-
final DataHandle<? extends Location> handle = //
195-
dataHandleService.create(sourceLocation);
196-
if (!handle.exists()) {
197-
throw new IOException("Cannot open source");
198-
}
199-
long length = handle.length();
200-
201-
final byte[] buffer = new byte[(int) length];
202-
handle.read(buffer);
203-
final String text = new String(buffer);
204-
205194
final GenericTable table = new DefaultGenericTable();
206195

207-
// split by any line delimiter
208-
final String[] lines = text.split("\\R");
209-
if (lines.length == 0) return table;
210-
// process first line to get number of cols
196+
try (final DataHandle<? extends Location> handle = //
197+
dataHandleService.create(sourceLocation))
211198
{
212-
final ArrayList<String> tokens = processRow(lines[0]);
213-
if (readColHeaders) {
214-
final List<String> colHeaders;
215-
if (readRowHeaders) colHeaders = tokens.subList(1, tokens.size());
216-
else colHeaders = tokens;
217-
final String[] colHeadersArr = new String[colHeaders.size()];
218-
table.appendColumns(colHeaders.toArray(colHeadersArr));
199+
if (!handle.exists()) {
200+
throw new IOException("Cannot open source");
219201
}
220-
else {
202+
long length = handle.length();
203+
204+
final byte[] buffer = new byte[(int) length];
205+
handle.read(buffer);
206+
207+
final String text = new String(buffer);
208+
209+
210+
// split by any line delimiter
211+
final String[] lines = text.split("\\R");
212+
if (lines.length == 0) return table;
213+
// process first line to get number of cols
214+
{
215+
final ArrayList<String> tokens = processRow(lines[0]);
216+
if (readColHeaders) {
217+
final List<String> colHeaders;
218+
if (readRowHeaders) colHeaders = tokens.subList(1, tokens.size());
219+
else colHeaders = tokens;
220+
final String[] colHeadersArr = new String[colHeaders.size()];
221+
table.appendColumns(colHeaders.toArray(colHeadersArr));
222+
}
223+
else {
224+
final List<String> cols;
225+
if (readRowHeaders) {
226+
cols = tokens.subList(1, tokens.size());
227+
table.appendColumns(cols.size());
228+
table.appendRow(tokens.get(0));
229+
}
230+
else {
231+
cols = tokens;
232+
table.appendColumns(cols.size());
233+
table.appendRow();
234+
}
235+
for (int i = 0; i < cols.size(); i++) {
236+
table.set(i, 0, parser.apply(cols.get(i)));
237+
}
238+
}
239+
}
240+
for (int lineNum = 1; lineNum < lines.length; lineNum++) {
241+
final String line = lines[lineNum];
242+
final ArrayList<String> tokens = processRow(line);
221243
final List<String> cols;
222244
if (readRowHeaders) {
223245
cols = tokens.subList(1, tokens.size());
224-
table.appendColumns(cols.size());
225246
table.appendRow(tokens.get(0));
226247
}
227248
else {
228249
cols = tokens;
229-
table.appendColumns(cols.size());
230250
table.appendRow();
231251
}
252+
if (cols.size() != table.getColumnCount()) {
253+
throw new IOException("Line " + table.getRowCount() +
254+
" is not the same length as the first line.");
255+
}
232256
for (int i = 0; i < cols.size(); i++) {
233-
table.set(i, 0, parser.apply(cols.get(i)));
257+
table.set(i, lineNum - 1, parser.apply(cols.get(i)));
234258
}
235259
}
236260
}
237-
for (int lineNum = 1; lineNum < lines.length; lineNum++) {
238-
final String line = lines[lineNum];
239-
final ArrayList<String> tokens = processRow(line);
240-
final List<String> cols;
241-
if (readRowHeaders) {
242-
cols = tokens.subList(1, tokens.size());
243-
table.appendRow(tokens.get(0));
244-
}
245-
else {
246-
cols = tokens;
247-
table.appendRow();
248-
}
249-
if (cols.size() != table.getColumnCount()) {
250-
throw new IOException("Line " + table.getRowCount() +
251-
" is not the same length as the first line.");
252-
}
253-
for (int i = 0; i < cols.size(); i++) {
254-
table.set(i, lineNum - 1, parser.apply(cols.get(i)));
255-
}
256-
}
257261
return table;
258262
}
259263

260264
@Override
261-
public void save(final GenericTable table, final String source)
265+
public void save(final GenericTable table, final String destination)
262266
throws IOException
263267
{
264268
// FIXME Assumes FileLocation
265-
final Location sourceLocation = new FileLocation(source);
266-
final DataHandle<Location> handle = //
267-
dataHandleService.create(sourceLocation);
269+
final Location dstLocation = new FileLocation(destination);
268270

269-
final boolean writeRH = this.writeRowHeaders && table.getRowCount() > 0 &&
270-
IntStream.range(0, table.getRowCount()).allMatch(row -> table
271-
.getRowHeader(row) != null);
272-
final boolean writeCH = this.writeColHeaders && table
273-
.getColumnCount() > 0 && table.stream().allMatch(col -> col
274-
.getHeader() != null);
271+
try (final DataHandle<Location> handle = //
272+
dataHandleService.create(dstLocation))
273+
{
274+
final boolean writeRH = this.writeRowHeaders && table.getRowCount() > 0 &&
275+
IntStream.range(0, table.getRowCount()).allMatch(row -> table
276+
.getRowHeader(row) != null);
277+
final boolean writeCH = this.writeColHeaders && table
278+
.getColumnCount() > 0 && table.stream().allMatch(col -> col
279+
.getHeader() != null);
275280

276-
final StringBuilder sb = new StringBuilder();
277-
// write column headers
278-
if (writeCH) {
279-
if (writeRH) {
280-
sb.append(tryQuote(cornerText));
281-
if (table.getColumnCount() > 0) {
282-
sb.append(separator);
283-
sb.append(tryQuote(table.getColumnHeader(0)));
281+
final StringBuilder sb = new StringBuilder();
282+
// write column headers
283+
if (writeCH) {
284+
if (writeRH) {
285+
sb.append(tryQuote(cornerText));
286+
if (table.getColumnCount() > 0) {
287+
sb.append(separator);
288+
sb.append(tryQuote(table.getColumnHeader(0)));
289+
}
290+
}
291+
// avoid adding extra separator when there is 0 column
292+
else if (table.getColumnCount() > 0) {
293+
sb.append(tryQuote(table.getColumnHeader(0)));
294+
}
295+
for (int col = 1; col < table.getColumnCount(); col++) {
296+
sb.append(separator);
297+
sb.append(tryQuote(table.getColumnHeader(col)));
298+
}
299+
sb.append(eol);
300+
handle.writeBytes(sb.toString());
301+
sb.setLength(0);
284302
}
285-
}
286-
// avoid adding extra separator when there is 0 column
287-
else if (table.getColumnCount() > 0) {
288-
sb.append(tryQuote(table.getColumnHeader(0)));
289-
}
290-
for (int col = 1; col < table.getColumnCount(); col++) {
291-
sb.append(separator);
292-
sb.append(tryQuote(table.getColumnHeader(col)));
293-
}
294-
sb.append(eol);
295-
handle.writeBytes(sb.toString());
296-
sb.setLength(0);
297-
}
298-
// write each row
299-
for (int row = 0; row < table.getRowCount(); row++) {
300-
if (writeRH) {
301-
sb.append(tryQuote(table.getRowHeader(row)));
302-
if (table.getColumnCount() > 0) {
303-
sb.append(separator);
304-
sb.append(tryQuote(formatter.apply(table.get(0, row))));
303+
// write each row
304+
for (int row = 0; row < table.getRowCount(); row++) {
305+
if (writeRH) {
306+
sb.append(tryQuote(table.getRowHeader(row)));
307+
if (table.getColumnCount() > 0) {
308+
sb.append(separator);
309+
sb.append(tryQuote(formatter.apply(table.get(0, row))));
310+
}
311+
}
312+
// avoid adding extra separator when there is 0 column
313+
else if (table.getColumnCount() > 0) {
314+
sb.append(tryQuote(formatter.apply(table.get(0, row))));
315+
}
316+
for (int col = 1; col < table.getColumnCount(); col++) {
317+
sb.append(separator);
318+
sb.append(tryQuote(formatter.apply(table.get(col, row))));
319+
}
320+
sb.append(eol);
321+
handle.writeBytes(sb.toString());
322+
sb.setLength(0);
305323
}
306-
}
307-
// avoid adding extra separator when there is 0 column
308-
else if (table.getColumnCount() > 0) {
309-
sb.append(tryQuote(formatter.apply(table.get(0, row))));
310-
}
311-
for (int col = 1; col < table.getColumnCount(); col++) {
312-
sb.append(separator);
313-
sb.append(tryQuote(formatter.apply(table.get(col, row))));
314-
}
315-
sb.append(eol);
316-
handle.writeBytes(sb.toString());
317-
sb.setLength(0);
318324
}
325+
319326
}
320327

321328
/**

‎src/test/java/net/imagej/table/DefaultTableIOPluginTest.java‎

Lines changed: 28 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -31,11 +31,13 @@
3131
package net.imagej.table;
3232

3333
import static org.junit.Assert.assertEquals;
34+
import static org.junit.Assert.assertTrue;
3435
import static org.junit.Assert.fail;
3536

3637
import java.io.File;
3738
import java.io.IOException;
3839
import java.lang.reflect.Field;
40+
import java.util.ArrayList;
3941
import java.util.HashMap;
4042
import java.util.List;
4143
import java.util.function.Function;
@@ -44,11 +46,11 @@
4446
import org.junit.Before;
4547
import org.junit.Test;
4648
import org.scijava.Context;
49+
import org.scijava.io.IOPlugin;
50+
import org.scijava.io.IOService;
4751
import org.scijava.io.handle.DataHandle;
4852
import org.scijava.io.handle.DataHandleService;
4953
import org.scijava.io.location.FileLocation;
50-
import org.scijava.io.IOPlugin;
51-
import org.scijava.io.IOService;
5254
import org.scijava.io.location.Location;
5355
import org.scijava.plugin.Parameter;
5456
import org.scijava.util.ClassUtils;
@@ -61,14 +63,17 @@
6163
public class DefaultTableIOPluginTest {
6264

6365
private static final Context ctx = new Context();
66+
67+
private List<File> tempFiles = new ArrayList<>();
6468

6569
@Before
6670
@After
6771
public void removeTempFiles() {
68-
Location source = new FileLocation("table.txt");
69-
new File(source.getURI()).delete();
70-
source = new FileLocation("fake.csv");
72+
Location source = new FileLocation("fake.csv");
7173
new File(source.getURI()).delete();
74+
for (File f : tempFiles) {
75+
assertTrue(f.delete());
76+
}
7277
}
7378

7479
/**
@@ -263,21 +268,29 @@ private void assertTableEquals(final String[] colHeaders,
263268
private GenericTable openTable(final String tableSource,
264269
final IOPlugin<GenericTable> tableIO) throws IOException
265270
{
266-
final Location dest = new FileLocation("table.txt");
267-
final DataHandle<? extends Location> destHandle = ctx.service(DataHandleService.class).create(dest);
268-
destHandle.write(tableSource.getBytes());
269-
return tableIO.open("table.txt");
271+
final DataHandleService dataHandleService = ctx.service(DataHandleService.class);
272+
GenericTable result;
273+
File tempFile = File.createTempFile("openTest", ".txt");
274+
tempFiles.add(tempFile);
275+
try (DataHandle<Location> destHandle = dataHandleService.create(new FileLocation(tempFile))) {
276+
destHandle.write(tableSource.getBytes());
277+
result = tableIO.open(tempFile.getAbsolutePath());
278+
}
279+
return result;
270280
}
271281

272282
private String saveTable(final GenericTable table,
273283
final IOPlugin<GenericTable> tableIO) throws IOException
274284
{
275-
final Location source = new FileLocation("table.txt");
276-
// Remove file during tests
277-
new File(source.getURI()).delete();
278-
final DataHandle<? extends Location> sourceHandle = ctx.service(DataHandleService.class).create(source);
279-
tableIO.save(table, "table.txt");
280-
return sourceHandle.readString(Integer.MAX_VALUE);
285+
final DataHandleService dataHandleService = ctx.service(DataHandleService.class);
286+
String result;
287+
File tempFile = File.createTempFile("saveTest", ".txt");
288+
tempFiles.add(tempFile);
289+
try (DataHandle<Location> sourceHandle = dataHandleService.create(new FileLocation(tempFile))) {
290+
tableIO.save(table, tempFile.getAbsolutePath());
291+
result = sourceHandle.readString(Integer.MAX_VALUE);
292+
}
293+
return result;
281294
}
282295

283296
private void setValues(final Object instance, final String[] fieldNames,

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