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Fix posix issue #418

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merged 6 commits into from
Dec 18, 2023
Merged

Fix posix issue #418

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126273b
fix test failures on windows
jburel Dec 16, 2023
642fafb
use java.nio.file.Files instead of com.google.common.io.Files
jburel Dec 16, 2023
af27091
catch exception
jburel Dec 17, 2023
331e261
add option
jburel Dec 17, 2023
92d9d8c
convert to Path
jburel Dec 17, 2023
c5ec371
handle exception
jburel Dec 17, 2023
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32 changes: 16 additions & 16 deletions src/main/java/org/openmicroscopy/shoola/agents/fsimporter/view/ImporterModel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@

import java.io.File;
import java.text.SimpleDateFormat;
import java.nio.file.Files;
import java.util.Collection;
import java.util.Date;
import java.util.HashMap;
Expand Down Expand Up @@ -62,8 +63,6 @@
import org.openmicroscopy.shoola.util.CommonsLangUtils;
import org.openmicroscopy.shoola.util.roi.io.ROIReader;

import com.google.common.io.Files;

import omero.gateway.model.DataObject;
import omero.gateway.model.ExperimenterData;
import omero.gateway.model.FileAnnotationData;
Expand Down Expand Up @@ -731,22 +730,23 @@ component, ctx, new FileAnnotationData(f),
*/
private File createFile(String imageName)
{
File dir = Files.createTempDir();
String name;
String fileName = null;
if (object != null) {
fileName = object.getTableName();
}
if (CommonsLangUtils.isBlank(fileName)) {
name = "ImageJ-"+FilenameUtils.getBaseName(
try {
final String prefix = "ome_";
File dir = Files.createTempDirectory(prefix).toFile();
String name;
String fileName = null;
if (object != null) {
fileName = object.getTableName();
}
if (CommonsLangUtils.isBlank(fileName)) {
name = "ImageJ-"+FilenameUtils.getBaseName(
FilenameUtils.removeExtension(imageName))+"-Results-";
name += new SimpleDateFormat("yyyy-MM-dd").format(new Date());
} else {
name = FilenameUtils.removeExtension(fileName);
}
name += new SimpleDateFormat("yyyy-MM-dd").format(new Date());
} else {
name = FilenameUtils.removeExtension(fileName);
}

name += ".csv";
try {
name += ".csv";
File f = new File(dir, name);
//read data
ROIReader reader = new ROIReader();
Expand Down
12 changes: 7 additions & 5 deletions src/main/java/org/openmicroscopy/shoola/env/data/views/calls/ArchivedImageLoader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,9 @@
import java.util.List;
import java.util.Map;

import com.google.common.io.Files;
import java.nio.file.Files;
import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;

import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
Expand Down Expand Up @@ -158,8 +160,8 @@ public void doCall() throws Exception

File tmpFolder = null;
try {
if(zip)
tmpFolder = Files.createTempDir();
if (zip)
tmpFolder = Files.createTempDirectory("ome_").toFile();
else
tmpFolder = folder;

Expand All @@ -173,7 +175,7 @@ public void doCall() throws Exception

result = new HashMap<Boolean, List<File>>();

if(CollectionUtils.isEmpty(files))
if (CollectionUtils.isEmpty(files))
return;

if (zip) {
Expand All @@ -185,7 +187,7 @@ public void doCall() throws Exception
File to = new File(f.getParentFile(), baseName
+ "."
+ FilenameUtils.getExtension(f.getName()));
Files.move(f, to);
Files.move(f.toPath(), to.toPath(), REPLACE_EXISTING);
f = copyFile(to, folder.getParentFile());
((Map<Boolean, List<File>>)result).put(Boolean.TRUE, Arrays.asList(f));
}
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/openmicroscopy/shoola/env/data/views/calls/FileUploader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;

import com.google.common.io.Files;
import java.nio.file.Files;

import org.openmicroscopy.shoola.env.LookupNames;
import org.openmicroscopy.shoola.env.data.OmeroMetadataService;
Expand Down Expand Up @@ -126,7 +126,7 @@ private void uploadFile(ImportErrorObject object)
}
}
if (b || id > 0) {
directory = Files.createTempDir();
directory = Files.createTempDirectory("ome_").toFile();
//Add the file to the directory.
if (f != null) {
directory = new File(directory.getParentFile(),
Expand Down
23 changes: 12 additions & 11 deletions src/main/java/org/openmicroscopy/shoola/env/data/views/calls/ResultsSaver.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
import ij.ImagePlus;

import java.io.File;
import java.nio.file.Files;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.Iterator;
Expand All @@ -41,7 +42,7 @@
import org.openmicroscopy.shoola.util.CommonsLangUtils;
import org.openmicroscopy.shoola.util.roi.io.ROIReader;

import com.google.common.io.Files;


import omero.gateway.model.ExperimenterData;
import omero.gateway.model.FileAnnotationData;
Expand Down Expand Up @@ -83,17 +84,17 @@ public class ResultsSaver
*/
private File createFile(ImagePlus img, String fileName)
{
File dir = Files.createTempDir();
String name;
if (CommonsLangUtils.isBlank(fileName)) {
name = "ImageJ-"+FilenameUtils.getBaseName(
FilenameUtils.removeExtension(img.getTitle()))+"-Results-";
name += new SimpleDateFormat("yyyy-MM-dd").format(new Date());
} else {
name = FilenameUtils.removeExtension(fileName);
}
name += ".csv";
try {
File dir = Files.createTempDirectory("ome_").toFile();
String name;
if (CommonsLangUtils.isBlank(fileName)) {
name = "ImageJ-"+FilenameUtils.getBaseName(
FilenameUtils.removeExtension(img.getTitle()))+"-Results-";
name += new SimpleDateFormat("yyyy-MM-dd").format(new Date());
} else {
name = FilenameUtils.removeExtension(fileName);
}
name += ".csv";
File f = new File(dir, name);
//read data
ROIReader reader = new ROIReader();
Expand Down
15 changes: 8 additions & 7 deletions src/test/java/org/openmicroscopy/shoola/util/file/TestIOUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
import java.io.FileOutputStream;
import java.io.IOException;

import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.zip.ZipEntry;
Expand All @@ -34,8 +35,6 @@
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;

import com.google.common.io.Files;

import junit.framework.TestCase;


Expand Down Expand Up @@ -136,11 +135,12 @@ private void clean(File f)
public void testZipDirectory()
{
try {
File dir = Files.createTempDir();
final String prefix = "test_ome";
File dir = Files.createTempDirectory(prefix).toFile();
File f = File.createTempFile("testZipDirectory", ".tmp", dir);
File zip = IOUtil.zipDirectory(dir);
assertEquals(FilenameUtils.getExtension(zip.getName()), "zip");
File destDir = Files.createTempDir();
File destDir = Files.createTempDirectory(prefix).toFile();
boolean b = unzip(zip, destDir);
assertEquals(true, b);
File[] files = destDir.listFiles();
Expand All @@ -159,15 +159,16 @@ public void testZipDirectory()
public void testZipDirectoryWithSubfolder()
{
try {
File dir = Files.createTempDir();
final String prefix = "test_ome";
File dir = Files.createTempDirectory(prefix).toFile();
File f = File.createTempFile("testZipDirectoryWithSubfolder", ".tmp", dir);
File subfolder = Files.createTempDir();
File subfolder = Files.createTempDirectory(prefix).toFile();
File f1 = File.createTempFile("sub_testZipDirectoryWithSubfolder", ".tmp", subfolder);

FileUtils.moveDirectoryToDirectory(subfolder, dir, false);

File zip = IOUtil.zipDirectory(dir);
File destDir = Files.createTempDir();
File destDir = Files.createTempDirectory(prefix).toFile();
boolean b = unzip(zip, destDir);
assertEquals(true, b);
File[] files = destDir.listFiles();
Expand Down