Revert "Another attempt to use re-compiled SiS jHDF5 library with re-…

…compiled HDF5 1.10.11 library from sources with plugin support enabled. Currently only for Windows and Linux."

This reverts commit 7d4adf9.

build.gradle.kts

@@ -42,10 +42,10 @@ application {
 }
 
 dependencies {
-  implementation(fileTree("src/main/resources/libs"))
-  runtimeOnly(fileTree("src/main/resources/libs/natives"))
+//  implementation(fileTree("src/main/resources/libs"))
+//  runtimeOnly(fileTree("src/main/resources/libs/natives"))
 
-//  implementation("cisd:jhdf5:19.04.1")
+  implementation("cisd:jhdf5:19.04.1")
 
 
   // https://mvnrepository.com/artifact/cisd/base

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

@@ -27,38 +27,24 @@ public class HDF5LibraryInitializer {
   private static final PathCollectingJNIExtractor jniExtractor = new PathCollectingJNIExtractor(defaultJNIExtractor);
 
   static {
-    // 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)");
-    // SiS-modified jni/ folder source linked to libhdf5.a on Linux, SiS-modified version of hdf5_java.dll on Windows
+    libraryNames.put("hdf5", "HDF5");
     libraryNames.put("jhdf5", "jHDF5");
-    // 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("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("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)");
-    // 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)");
 
     initializeHDF5Library();
   }
@@ -74,12 +60,11 @@ public static synchronized void initializeHDF5Library() {
       final var name = e.getValue();
       log.info("Loading " + name + " library");
       try {
-        if (!NativeLibraryUtil.loadNativeLibrary(jniExtractor, lib, "resources/", "resources/libs/", "resources/libs/natives/", "/resources/", "/resources/libs/", "/resources/libs/natives/")) {
+        if (!NativeLibraryUtil.loadNativeLibrary(jniExtractor, lib)) {
           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");
@@ -91,6 +76,14 @@ public static synchronized void initializeHDF5Library() {
       }
     }
 
+    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");
@@ -102,16 +95,6 @@ public static synchronized void initializeHDF5Library() {
       }
     }
 
-    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);
-    }
-
-
-
-
     hdf5LibraryInitialized.set(true);
   }
 

version.txt

@@ -1 +1 @@
-1.0.30-72a7298-webui_cc7ffbd
+1.0.29-aed9a29-webui_d454f01