Merge remote-tracking branch 'origin/dev-jhdf5-1.10.11-dynamic-recomp…

…ilation'

# Conflicts:
#	src/main/java/ru/itmo/ctlab/hict/hict_library/chunkedfile/hdf5/HDF5LibraryInitializer.java
#	src/main/resources/libs/natives/linux_64/libh5blosc.so
#	src/main/resources/libs/natives/linux_64/libh5bshuf.so
#	src/main/resources/libs/natives/linux_64/libh5bz2.so
#	src/main/resources/libs/natives/linux_64/libh5jpeg.so
#	src/main/resources/libs/natives/linux_64/libh5lzf.so
#	src/main/resources/libs/natives/linux_64/libh5zfp.so
#	src/main/resources/libs/natives/linux_64/libh5zstd.so
#	src/main/resources/libs/natives/linux_64/libhdf5.so
#	src/main/resources/libs/natives/linux_64/libhdf5_java.so
#	src/main/resources/libs/natives/linux_64/libjhdf5.so
#	src/main/resources/libs/natives/linux_64/libnativedata.so
#	src/main/resources/libs/natives/linux_64/libunix.so
#	src/main/resources/libs/natives/windows_64/blosc.dll
#	src/main/resources/libs/natives/windows_64/hdf5.dll
#	src/main/resources/libs/natives/windows_64/hdf5_java.dll
#	src/main/resources/libs/natives/windows_64/hdf5_tools.dll
#	src/main/resources/libs/natives/windows_64/jhdf5.dll
#	src/main/resources/libs/natives/windows_64/libh5blosc.dll
#	src/main/resources/libs/natives/windows_64/libh5bshuf.dll
#	src/main/resources/libs/natives/windows_64/libh5bz2.dll
#	src/main/resources/libs/natives/windows_64/libh5lz4.dll
#	src/main/resources/libs/natives/windows_64/libh5lzf.dll
#	src/main/resources/libs/natives/windows_64/libh5zfp.dll
#	src/main/resources/libs/natives/windows_64/libh5zstd.dll
#	src/main/resources/libs/sis-jhdf5-19.04.1.jar
#	src/main/resources/natives/linux_64/libh5blosc.so
#	src/main/resources/natives/linux_64/libh5bshuf.so
#	src/main/resources/natives/linux_64/libh5bz2.so
#	src/main/resources/natives/linux_64/libh5jpeg.so
#	src/main/resources/natives/linux_64/libh5lzf.so
#	src/main/resources/natives/linux_64/libh5zfp.so
#	src/main/resources/natives/linux_64/libh5zstd.so
#	src/main/resources/natives/linux_64/libhdf5.so
#	src/main/resources/natives/linux_64/libhdf5_java.so
#	src/main/resources/natives/linux_64/libjhdf5.so
#	src/main/resources/natives/windows_64/blosc.dll
#	src/main/resources/natives/windows_64/hdf5.dll
#	src/main/resources/natives/windows_64/hdf5_java.dll
#	src/main/resources/natives/windows_64/jhdf5.dll
#	src/main/resources/natives/windows_64/libh5blosc.dll
#	src/main/resources/natives/windows_64/libh5bshuf.dll
#	src/main/resources/natives/windows_64/libh5bz2.dll
#	src/main/resources/natives/windows_64/libh5lz4.dll
#	src/main/resources/natives/windows_64/libh5lzf.dll
#	src/main/resources/natives/windows_64/libh5zfp.dll
#	src/main/resources/natives/windows_64/libh5zstd.dll
#	version.txt

.github/workflows/autobuild-release.yml

@@ -5,7 +5,7 @@ on:
     types:
       - created
   push:
-    branches: [ "master" ]
+    branches: [ "master", "dev*" ]
   pull_request:
     branches: [ "master", "dev*" ]
 
@@ -18,6 +18,10 @@ jobs:
       packages: write
 
     steps:
+      - name: Extract branch name
+        shell: bash
+        run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
+        id: extract_branch
       - uses: actions/checkout@v3
       - name: Setup Node.js environment
         uses: actions/setup-node@v3.8.1
@@ -44,8 +48,8 @@ jobs:
         uses: marvinpinto/action-automatic-releases@latest
         with:
           repo_token: ${{ secrets.GITHUB_TOKEN }}
-          automatic_release_tag: latest
+          automatic_release_tag: latest-${{ steps.extract_branch.outputs.branch }}
           prerelease: true
-          title: "Latest autogenerated build"
+          title: "Latest autogenerated build (branch ${{ steps.extract_branch.outputs.branch }})"
           files: |
             **/build/**/*hict*.jar

src/main/java/ru/itmo/ctlab/hict/hict_library/chunkedfile/hdf5/HDF5LibraryInitializer.java

@@ -27,25 +27,45 @@ public class HDF5LibraryInitializer {
   private static final PathCollectingJNIExtractor jniExtractor = new PathCollectingJNIExtractor(defaultJNIExtractor);
 
   static {
-    libraryNames.put("hdf5", "HDF5");
-    libraryNames.put("jhdf5", "jHDF5");
-    libraryNames.put("hdf5_tools", "HDF5_tools");
-    libraryNames.put("hdf5_java", "HDF5_java");
-    libraryNames.put("libh5blosc", "HDF5 BLOSC filter plugin (Linux-style naming)");
-    libraryNames.put("h5blosc", "HDF5 BLOSC filter plugin (Windows-style naming)");
+    //libraryNames.put("jhdf5", "jHDF5");
+    // SiS JHDF5 dependencies:
+    // libraryNames.put("libnativedata", "NativeData (Linux-style naming)");
+    // libraryNames.put("nativedata", "NativeData (Windows-style naming)");
+    // libraryNames.put("libunix", "libunix.so (Linux-style naming), not needed on Windows");
+    // libraryNames.put("unix", "libunix.so (Windows-style naming), not needed on Windows");
+    // Main HDF5 library, rebuilt from sources:
+//    libraryNames.put("libhdf5", "HDF5 (Linux-style naming)");
+//    libraryNames.put("hdf5", "HDF5 (Windows-style naming)");
+    // HDF5_java library (from source on Linux, from SiS-modified jni/ folder JHDF5 source on Windows):
+    // libraryNames.put("libhdf5_java", "HDF5 (Linux-style naming)");
+    // libraryNames.put("hdf5_java", "HDF5 (Windows-style naming)");
+    // This library might be in dependencies:
+    // libraryNames.put("hdf5_tools", "HDF5_tools");
+    // The most important HDF5 filter plugins for HiCT (bitshuffle and LZF compression):
     libraryNames.put("libh5bshuf", "HDF5 Shuffle filter plugin (Linux-style naming)");
     libraryNames.put("h5bshuf", "HDF5 Shuffle filter plugin (Windows-style naming)");
+    libraryNames.put("h5lzf", "HDF5 LZ4 filter plugin (Windows-style naming)");
+    libraryNames.put("libh5lzf", "HDF5 LZF filter plugin (Linux-style naming)");
+    // SiS-modified jni/ folder source linked to libhdf5.a on Linux, SiS-modified version of hdf5_java.dll on Windows
+    // libraryNames.put("jhdf5", "jHDF5");
+    // Other general compression plugins:
     libraryNames.put("libh5bz2", "HDF5 BZ2 filter plugin (Linux-style naming)");
     libraryNames.put("h5bz2", "HDF5 BZ2 filter plugin (Windows-style naming)");
     libraryNames.put("libh5lz4", "HDF5 LZ4 filter plugin (Linux-style naming)");
     libraryNames.put("h5lz4", "HDF5 LZ4 filter plugin (Windows-style naming)");
-    libraryNames.put("libh5lzf", "HDF5 LZF filter plugin (Linux-style naming)");
-    libraryNames.put("h5lzf", "HDF5 LZF filter plugin (Windows-style naming)");
     libraryNames.put("libh5zfp", "HDF5 ZFP filter plugin (Linux-style naming)");
     libraryNames.put("h5zfp", "HDF5 ZFP filter plugin (Windows-style naming)");
     libraryNames.put("libh5zstd", "HDF5 zSTD filter plugin (Linux-style naming)");
     libraryNames.put("h5zstd", "HDF5 zSTD filter plugin (Windows-style naming)");
-
+    // Lossy compression plugins currently not used by HiCT:
+//    libraryNames.put("libh5blosc", "HDF5 BLOSC filter plugin (Linux-style naming)");
+//    libraryNames.put("h5blosc", "HDF5 BLOSC filter plugin (Windows-style naming)");
+    /*
+    libraryNames.put("hdf5", "HDF5 (Windows-style naming)");
+    libraryNames.put("h5bshuf", "HDF5 Shuffle filter plugin (Windows-style naming)");
+    libraryNames.put("h5lzf", "HDF5 LZF filter plugin (Windows-style naming)");
+    libraryNames.put("jhdf5", "jHDF5");
+    */
     initializeHDF5Library();
   }
 
@@ -55,16 +75,63 @@ public static synchronized void initializeHDF5Library() {
       return;
     }
 
+    NativeLibraryUtil.loadNativeLibrary(jniExtractor, "hdf5", "resources/", "resources/libs/", "resources/libs/natives/", "/resources/", "/resources/libs/", "/resources/libs/natives/");
+    log.info("Loaded HDF5");
+//    NativeLibraryUtil.loadNativeLibrary(jniExtractor, "jhdf5", "resources/", "resources/libs/", "resources/libs/natives/", "/resources/", "/resources/libs/", "/resources/libs/natives/");
+//    log.info("Loaded JHDF5");
+
+    for (int i = H5.H5PLsize() - 1; i >= 0; --i) {
+      final String path;
+      try {
+        path = H5.H5PLget(i);
+      } catch (final HDF5LibraryException e) {
+        log.error("Failed to get plugin path with index " + i);
+        continue;
+      }
+
+      try {
+        H5.H5PLremove(i);
+        log.info("Removed pre-existing path with index " + i + " that was " + path);
+      } catch (final HDF5LibraryException e) {
+        log.error("Failed to remove plugin path with index " + i + " that is " + path);
+        continue;
+      }
+    }
+
+//    for (final var libPath : jniExtractor.getFullPathsCollection()) {
+//      try {
+//        log.info("Prepending " + libPath + " to the plugin path registry of H5 library");
+//        H5.H5PLprepend(libPath);
+//        log.info("Appending " + libPath + " to the plugin path registry of H5 library");
+//        H5.H5PLappend(libPath);
+//      } catch (final HDF5LibraryException e) {
+//        log.error("Failed to append " + libPath + " to the plugin registry", e);
+//      }
+//    }
+
+//    for (final var libPath : jniExtractor.getAbsolutePathsCollection()) {
+//      try {
+//        log.info("Prepending " + libPath + " to the plugin path registry of H5 library");
+//        H5.H5PLprepend(libPath);
+//        log.info("Appending " + libPath + " to the plugin path registry of H5 library");
+//        H5.H5PLappend(libPath);
+//      } catch (final HDF5LibraryException e) {
+//        log.error("Failed to append " + libPath + " to the plugin registry", e);
+//      }
+//    }
+
+
     for (final var e : libraryNames.entrySet()) {
       final var lib = e.getKey();
       final var name = e.getValue();
       log.info("Loading " + name + " library");
       try {
-        if (!NativeLibraryUtil.loadNativeLibrary(jniExtractor, lib)) {
+        if (!NativeLibraryUtil.loadNativeLibrary(jniExtractor, lib, "resources/", "resources/libs/", "resources/libs/natives/", "/resources/", "/resources/libs/", "/resources/libs/natives/")) {
           log.warn("Failed to load library " + lib + " with custom JNI Extractor, will try fallback method.");
           NativeLoader.loadLibrary(lib);
           log.warn("Fallback method succeeded but the library path won't be added to the H5 plugins search registry.");
         }
+        log.info("Successfully loaded library " + lib + " using NativeLoader");
       } catch (final IOException err) {
         log.warn("Failed to load native library " + name + " by NativeLoader due to IOException", err);
 //        log.warn("Failed to load native library due to IOException");
@@ -76,14 +143,54 @@ public static synchronized void initializeHDF5Library() {
       }
     }
 
+//
+//    for (int i = H5.H5PLsize() - 1; i >= 0; --i) {
+//      final String path;
+//      try {
+//        path = H5.H5PLget(i);
+//      } catch (final HDF5LibraryException e) {
+//        log.error("Failed to get plugin path with index " + i);
+//        continue;
+//      }
+//
+//      try {
+//        H5.H5PLremove(i);
+//        log.info("Removed pre-existing path with index " + i + " that was " + path);
+//      } catch (final HDF5LibraryException e) {
+//        log.error("Failed to remove plugin path with index " + i + " that is " + path);
+//        continue;
+//      }
+//    }
+//
+//    for (final var libPath : jniExtractor.getFullPathsCollection()) {
+//      try {
+//        log.info("Prepending " + libPath + " to the plugin path registry of H5 library");
+//        H5.H5PLprepend(libPath);
+//        log.info("Appending " + libPath + " to the plugin path registry of H5 library");
+//        H5.H5PLappend(libPath);
+//      } catch (final HDF5LibraryException e) {
+//        log.error("Failed to append " + libPath + " to the plugin registry", e);
+//      }
+//    }
+
+    for (final var libPath : jniExtractor.getAbsolutePathsCollection()) {
+      try {
+        log.info("Prepending " + libPath + " to the plugin path registry of H5 library");
+        H5.H5PLprepend(libPath);
+        log.info("Appending " + libPath + " to the plugin path registry of H5 library");
+        H5.H5PLappend(libPath);
+      } catch (final HDF5LibraryException e) {
+        log.error("Failed to append " + libPath + " to the plugin registry", e);
+      }
+    }
+
     try {
       H5.loadH5Lib();
       log.info("Loaded HDF5 library");
     } catch (final Throwable uoe) {
       log.error("Caught an Unsupported Operation Exception while initializing HDF5 Library, if it complains about library version, you can simply ignore that", uoe);
     }
 
-
     for (final var libPath : jniExtractor.getAbsolutePathsCollection()) {
       try {
         log.info("Prepending " + libPath + " to the plugin path registry of H5 library");

src/main/java/ru/itmo/ctlab/hict/hict_server/dto/symmetric/visualization/SimpleLinearGradientDTO.java

@@ -9,6 +9,7 @@
 import ru.itmo.ctlab.hict.hict_library.visualization.colormap.gradient.SimpleLinearGradient;
 
 import java.awt.*;
+import java.util.Locale;
 import java.util.regex.Pattern;
 
 @Getter(AccessLevel.PUBLIC)
@@ -33,8 +34,8 @@ public SimpleLinearGradientDTO(String startColorHEX, String endColorHEX, double
 //    final String endHEX = String.format("#%02x%02x%02x%02x", cmap.getEndColor().getRed(), cmap.getEndColor().getGreen(), cmap.getEndColor().getBlue(), cmap.getEndColor().getAlpha());
 
     return new SimpleLinearGradientDTO(
-      String.format("rgba(%d,%d,%d,%f)", cmap.getStartColor().getRed(), cmap.getStartColor().getGreen(), cmap.getStartColor().getBlue(), ((double) cmap.getStartColor().getAlpha() / 255.0d)),
-      String.format("rgba(%d,%d,%d,%f)", cmap.getEndColor().getRed(), cmap.getEndColor().getGreen(), cmap.getEndColor().getBlue(), ((double) cmap.getEndColor().getAlpha() / 255.0d)),
+      String.format(Locale.US, "rgba(%d,%d,%d,%f)", cmap.getStartColor().getRed(), cmap.getStartColor().getGreen(), cmap.getStartColor().getBlue(), ((double) cmap.getStartColor().getAlpha() / 255.0d)),
+      String.format(Locale.US, "rgba(%d,%d,%d,%f)", cmap.getEndColor().getRed(), cmap.getEndColor().getGreen(), cmap.getEndColor().getBlue(), ((double) cmap.getEndColor().getAlpha() / 255.0d)),
       cmap.getMinSignal(),
       cmap.getMaxSignal()
     );

src/main/java/ru/itmo/ctlab/hict/hict_server/handlers/files/FSHandlersHolder.java

@@ -31,7 +31,7 @@ public void addHandlersToRouter(final @NotNull Router router) {
 
       final List<?> files;
       try (final var fileStream = Files.walk(dataDirectory)) {
-        files = fileStream.filter(Files::isRegularFile).map(dataDirectory::relativize).map(Object::toString).filter(p -> p.endsWith(".hict.hdf5")).collect(Collectors.toList());
+        files = fileStream.filter(Files::isRegularFile).map(dataDirectory::relativize).map(Object::toString).collect(Collectors.toList());
       } catch (final IOException e) {
         throw new RuntimeException(e);
       }

version.txt

@@ -1 +1 @@
-1.0.29-aed9a29-webui_d454f01
+1.0.34-677dc4a-webui_8060ecf