Merge pull request #3815 from sbesson/java_17

Java 17 support
ome · Jan 31, 2023 · f0017bd · f0017bd
2 parents ef03cc9 + f6d9c4b
commit f0017bd
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Showing 9 changed files with 91 additions and 56 deletions.
diff --git a/.github/workflows/ant.yml b/.github/workflows/ant.yml
@@ -7,7 +7,7 @@ jobs:
   build:
     strategy:
       matrix:
-        java: [1.8, 11]
+        java: [1.8, 11, 17]
         os: [ubuntu-latest, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:

diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -13,7 +13,7 @@ jobs:
   build:
     strategy:
       matrix:
-        java: [1.8, 11]
+        java: [1.8, 11, 17]
         os: [ubuntu-latest, windows-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     env:

diff --git a/components/formats-bsd/src/loci/formats/in/JPEGReader.java b/components/formats-bsd/src/loci/formats/in/JPEGReader.java
@@ -180,7 +180,7 @@ public void close(boolean fileOnly) throws IOException {
 
   // -- Helper reader --
 
-  static class DefaultJPEGReader extends ImageIOReader {
+  public static class DefaultJPEGReader extends ImageIOReader {
     public DefaultJPEGReader() {
       super("JPEG", new String[] {"jpg", "jpeg", "jpe"});
       suffixNecessary = false;

diff --git a/components/formats-gpl/src/loci/formats/in/CV7000Reader.java b/components/formats-gpl/src/loci/formats/in/CV7000Reader.java
@@ -79,7 +79,6 @@ public class CV7000Reader extends FormatReader {
   // -- Fields --
 
   private String[] allFiles;
-  private Location parent;
   private MinimalTiffReader reader;
   private String wppPath;
   private String detailPath;
@@ -239,7 +238,7 @@ protected void initFile(String id) throws FormatException, IOException {
     String wpiXML = readSanitizedXML(id);
     XMLTools.parseXML(wpiXML, plate);
 
-    parent = new Location(id).getAbsoluteFile().getParentFile();
+    Location parent = new Location(id).getAbsoluteFile().getParentFile();
     allFiles = parent.list(true);
     Arrays.sort(allFiles);
     for (int i=0; i<allFiles.length; i++) {

diff --git a/components/formats-gpl/src/loci/formats/in/CellVoyagerReader.java b/components/formats-gpl/src/loci/formats/in/CellVoyagerReader.java
@@ -111,18 +111,17 @@ public class CellVoyagerReader extends FormatReader
 
   private static final String SINGLE_TIFF_PATH_BUILDER = "W%dF%03dT%04dZ%02dC%d.tif";
 
-  private Location measurementFolder;
-  private Location imageFolder;
+  private String imageFolder;
 
   private List< ChannelInfo > channelInfos;
 
   private List< WellInfo > wells;
 
   private List< Integer > timePoints;
 
-  private Location measurementResultFile;
+  private String measurementResultFile;
 
-  private Location omeMeasurementFile;
+  private String omeMeasurementFile;
 
   public CellVoyagerReader()
   {
@@ -148,8 +147,6 @@ public byte[] openBytes( final int no, final byte[] buf, final int x, final int
     final AreaInfo area = well.areas.get( areaIndex );
     final MinimalTiffReader tiffReader = new MinimalTiffReader();
 
-    imageFolder = new Location(currentId).getAbsoluteFile().getParentFile();
-    imageFolder = new Location(imageFolder, "Image");
     for ( final FieldInfo field : area.fields )
     {
 
@@ -274,7 +271,7 @@ protected void initFile( final String id ) throws FormatException, IOException
   {
     super.initFile( id );
 
-    measurementFolder = new Location( id ).getAbsoluteFile();
+    Location measurementFolder = new Location( id ).getAbsoluteFile();
     if ( !measurementFolder.exists() ) { throw new IOException( "File " + id + " does not exist." ); }
     if ( !measurementFolder.isDirectory() )
     {
@@ -283,22 +280,26 @@ protected void initFile( final String id ) throws FormatException, IOException
         measurementFolder = measurementFolder.getParentFile();
       }
     }
-    imageFolder = new Location(measurementFolder, "Image");
+    imageFolder = new Location(measurementFolder, "Image").getAbsolutePath();
 
-    measurementResultFile = new Location( measurementFolder, "MeasurementResult.xml" );
-    if ( !measurementResultFile.exists() ) { throw new IOException( "Could not find " + measurementResultFile + " in folder." ); }
+    Location measurementResult = new Location( measurementFolder, "MeasurementResult.xml" );
+    if ( !measurementResult.exists() ) { throw new IOException( "Could not find " + measurementResult + " in folder." ); }
+    else {
+      measurementResultFile = measurementResult.getAbsolutePath();
+    }
 
-    omeMeasurementFile = new Location( measurementFolder, "MeasurementResult.ome.xml" );
-    if ( !omeMeasurementFile.exists() ) { throw new IOException( "Could not find " + omeMeasurementFile + " in folder." ); }
+    Location omeMeasurement = new Location( measurementFolder, "MeasurementResult.ome.xml" );
+    if ( !omeMeasurement.exists() ) { throw new IOException( "Could not find " + omeMeasurement + " in folder." ); }
+    else {
+      omeMeasurementFile = omeMeasurement.getAbsolutePath();
+    }
 
     /*
      * Open MeasurementSettings file
      */
 
-    RandomAccessInputStream result =
-      new RandomAccessInputStream(measurementResultFile.getAbsolutePath());
     Document msDocument = null;
-    try {
+    try (RandomAccessInputStream result = new RandomAccessInputStream(measurementResultFile)) {
       msDocument = XMLTools.parseDOM(result);
     }
     catch (ParserConfigurationException e) {
@@ -307,9 +308,6 @@ protected void initFile( final String id ) throws FormatException, IOException
     catch (SAXException e) {
       throw new IOException(e);
     }
-    finally {
-      result.close();
-    }
 
     msDocument.getDocumentElement().normalize();
 
@@ -329,10 +327,9 @@ protected void initFile( final String id ) throws FormatException, IOException
      * Open OME metadata file
      */
 
-    RandomAccessInputStream measurement =
-      new RandomAccessInputStream(omeMeasurementFile.getAbsolutePath());
+
     Document omeDocument = null;
-    try {
+    try (RandomAccessInputStream measurement = new RandomAccessInputStream(omeMeasurementFile)) {
       omeDocument = XMLTools.parseDOM(measurement);
     }
     catch (ParserConfigurationException e) {
@@ -341,9 +338,6 @@ protected void initFile( final String id ) throws FormatException, IOException
     catch (SAXException e) {
       throw new IOException(e);
     }
-    finally {
-      measurement.close();
-    }
     omeDocument.getDocumentElement().normalize();
 
     /*
@@ -361,7 +355,7 @@ public String[] getSeriesUsedFiles( final boolean noPixels )
 
     if ( noPixels )
     {
-      return new String[] { measurementResultFile.getAbsolutePath(), omeMeasurementFile.getAbsolutePath() };
+      return new String[] { measurementResultFile, omeMeasurementFile };
     }
     else
     {
@@ -371,8 +365,8 @@ public String[] getSeriesUsedFiles( final boolean noPixels )
       final AreaInfo area = wells.get( wellIndex ).areas.get( areaIndex );
       final int nFields = area.fields.size();
       ArrayList<String> images = new ArrayList<String>();
-      images.add(measurementResultFile.getAbsolutePath());
-      images.add(omeMeasurementFile.getAbsolutePath());
+      images.add(measurementResultFile);
+      images.add(omeMeasurementFile);
 
       for ( final Integer timepoint : timePoints )
       {

diff --git a/components/formats-gpl/src/loci/formats/in/PrairieReader.java b/components/formats-gpl/src/loci/formats/in/PrairieReader.java
@@ -91,7 +91,7 @@ public class PrairieReader extends FormatReader {
   private TiffReader tiff;
 
   /** The associated XML files. */
-  private Location xmlFile, cfgFile, envFile;
+  private String xmlFile, cfgFile, envFile;
 
   /** Format-specific metadata. */
   private PrairieMetadata meta;
@@ -215,9 +215,9 @@ public String[] getSeriesUsedFiles(boolean noPixels) {
 
     // add metadata files to the used files list
     final ArrayList<String> usedFiles = new ArrayList<String>();
-    if (xmlFile != null) usedFiles.add(xmlFile.getAbsolutePath());
-    if (cfgFile != null) usedFiles.add(cfgFile.getAbsolutePath());
-    if (envFile != null) usedFiles.add(envFile.getAbsolutePath());
+    if (xmlFile != null) usedFiles.add(xmlFile);
+    if (cfgFile != null) usedFiles.add(cfgFile);
+    if (envFile != null) usedFiles.add(envFile);
 
     if (!noPixels) {
       // add TIFF files to the used files list
@@ -319,15 +319,15 @@ protected void initFile(String id) throws FormatException, IOException {
     tiff = new TiffReader();
 
     if (checkSuffix(id, XML_SUFFIX)) {
-      xmlFile = new Location(id);
+      xmlFile = new Location(id).getAbsolutePath();
       findMetadataFiles();
     }
     else if (checkSuffix(id, CFG_SUFFIX)) {
-      cfgFile = new Location(id);
+      cfgFile = new Location(id).getAbsolutePath();
       findMetadataFiles();
     }
     else if (checkSuffix(id, ENV_SUFFIX)) {
-      envFile = new Location(id);
+      envFile = new Location(id).getAbsolutePath();
       findMetadataFiles();
     }
     else {
@@ -344,7 +344,7 @@ else if (checkSuffix(id, ENV_SUFFIX)) {
       }
     }
 
-    currentId = xmlFile.getAbsolutePath();
+    currentId = xmlFile;
 
     parsePrairieMetadata();
     populateCoreMetadata();
@@ -356,9 +356,24 @@ else if (checkSuffix(id, ENV_SUFFIX)) {
 
   private void findMetadataFiles() {
     LOGGER.info("Finding metadata files");
-    if (xmlFile == null) xmlFile = find(XML_SUFFIX);
-    if (cfgFile == null) cfgFile = find(CFG_SUFFIX);
-    if (envFile == null) envFile = find(ENV_SUFFIX);
+    if (xmlFile == null) {
+      Location xml = find(XML_SUFFIX);
+      if (xml != null) {
+        xmlFile = xml.getAbsolutePath();
+      }
+    }
+    if (cfgFile == null) {
+      Location cfg = find(CFG_SUFFIX);
+      if (cfg != null) {
+        cfgFile = cfg.getAbsolutePath();
+      }
+    }
+    if (envFile == null) {
+      Location env = find(ENV_SUFFIX);
+      if (env != null) {
+        envFile = env.getAbsolutePath();
+      }
+    }
   }
 
   /**
@@ -368,11 +383,19 @@ private void findMetadataFiles() {
   private void parsePrairieMetadata() throws FormatException, IOException {
     LOGGER.info("Parsing Prairie metadata");
 
-    final Document xml, cfg, env;
+    Document xml = null;
+    Document cfg = null;
+    Document env = null;
     try {
-      xml = parseDOM(xmlFile);
-      cfg = parseDOM(cfgFile);
-      env = parseDOM(envFile);
+      if (xmlFile != null) {
+        xml = parseDOM(new Location(xmlFile));
+      }
+      if (cfgFile != null) {
+        cfg = parseDOM(new Location(cfgFile));
+      }
+      if (envFile != null) {
+        env = parseDOM(new Location(envFile));
+      }
     }
     catch (ParserConfigurationException exc) {
       throw new FormatException(exc);
@@ -725,7 +748,7 @@ private void warnFilename(final Sequence sequence, final int index,
 
   /** Gets the absolute path to the filename of the given {@link PFile}. */
   private String getPath(final PFile file) {
-    final Location f = new Location(xmlFile.getParent(), file.getFilename());
+    final Location f = new Location(new Location(xmlFile).getParent(), file.getFilename());
     return f.getAbsolutePath();
   }
 

diff --git a/components/formats-gpl/src/loci/formats/in/VolocityReader.java b/components/formats-gpl/src/loci/formats/in/VolocityReader.java
@@ -69,7 +69,7 @@ public class VolocityReader extends FormatReader {
   private ArrayList<Stack> stacks;
   private ArrayList<String> extraFiles;
   private Object[][] sampleTable, stringTable;
-  private Location dir = null;
+  private String dir = null;
 
   private ArrayList<Double[]> timestamps = new ArrayList<Double[]>();
 
@@ -258,13 +258,14 @@ protected void initFile(String id) throws FormatException, IOException {
     extraFiles.add(file.getAbsolutePath());
 
     Location parentDir = file.getParentFile();
-    dir = new Location(parentDir, DATA_DIR);
+    Location dataDir = new Location(parentDir, DATA_DIR);
+    dir = dataDir.getAbsolutePath();
 
-    if (dir.exists()) {
-      String[] files = dir.list(true);
+    if (dataDir.exists()) {
+      String[] files = dataDir.list(true);
       for (String f : files) {
         if (!checkSuffix(f, "aisf") && !checkSuffix(f, "atsf")) {
-          extraFiles.add(new Location(dir, f).getAbsolutePath());
+          extraFiles.add(new Location(dataDir, f).getAbsolutePath());
         }
       }
     }
@@ -851,7 +852,7 @@ private RandomAccessInputStream getStream(int row) throws IOException {
     return data;
   }
 
-  private String getFile(Integer parent, Location dir) {
+  private String getFile(Integer parent, String dir) {
     for (int row=0; row<sampleTable.length; row++) {
       if (parent.equals(sampleTable[row][0])) {
         Object o = sampleTable[row][14];

diff --git a/components/test-suite/pom.xml b/components/test-suite/pom.xml
@@ -91,7 +91,7 @@
     <dependency>
       <groupId>org.kohsuke</groupId>
       <artifactId>file-leak-detector</artifactId>
-      <version>1.13</version>
+      <version>1.15</version>
       <!-- the regular jar does not specify a main class -->
       <classifier>jar-with-dependencies</classifier>
       <exclusions>
@@ -165,4 +165,22 @@
       <timezone>-6</timezone>
     </developer>
   </developers>
+
+  <repositories>
+    <repository>
+      <id>central</id>
+      <name>Central Repository</name>
+      <url>https://repo.maven.apache.org/maven2</url>
+    </repository>
+    <repository>
+      <id>ome</id>
+      <name>OME Artifactory</name>
+      <url>https://artifacts.openmicroscopy.org/artifactory/maven/</url>
+    </repository>
+    <repository>
+      <id>imagej.public</id>
+      <name>Jenkins repository</name>
+      <url>https://repo.jenkins-ci.org/releases/</url>
+    </repository>
+  </repositories>
 </project>
diff --git a/pom.xml b/pom.xml
@@ -55,7 +55,7 @@
     <ome-poi.version>5.3.7</ome-poi.version>
     <ome-mdbtools.version>5.3.2</ome-mdbtools.version>
     <ome-jai.version>0.1.3</ome-jai.version>
-    <ome-codecs.version>0.4.1</ome-codecs.version>
+    <ome-codecs.version>0.4.2</ome-codecs.version>
     <jxrlib.version>0.2.4</jxrlib.version>
     <xalan.version>2.7.2</xalan.version>
     <sqlite.version>3.28.0</sqlite.version>