feat: The first version of Java library that contains GDAL 3.5.3 and …

…all required native libraries

.gitattributes

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+*.jar filter=lfs diff=lfs merge=lfs -text
+src/main/resources/native/linux-x86-64/* filter=lfs diff=lfs merge=lfs -text
+*.gpkg filter=lfs diff=lfs merge=lfs -text

.gitignore

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+build
+out
+.idea
+.gradle

README.md

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+gdal-jni-with-native
+======
+This project builds GDAL, extract native libraries and makes it available as Java library. At the moment it only supports GDAL on Ubuntu x64  (Linux)
+
+### Build
+In order to build the project the following should happen:
+1. Build GDAL docker image, [build_gdal.sh](scripts.build_gdal.sh) is responsible for that
+2. Build [lddtopo-rs](https://github.com/REASY/lddtopo-rs), [build_lddtopo.sh](scripts/build_lddtopo.sh) is responsible for that
+3. Analyze the dependencies of /usr/share/java/libgdalalljni.so by building DAG and running topological sort on it
+4. Copy all required native modules to src/main/resources/native
+5. Generate src/main/resources/native/modules.txt that contains new line separated list of modules to be loaded. The order comes from topological sort!
+
+All of this is done in a script [generate_native_modules.sh](scripts/generate_native_modules.sh), just run it from root folder of the repo to get the final JAR
+```bash
+./scripts/generate_native_modules.sh
+```

build.gradle

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+group = 'gdal-jni-with-native'
+version = '3.5.3.0'
+
+buildscript {
+    repositories {
+        jcenter()
+        mavenLocal()
+        mavenCentral()
+        maven { url "https://plugins.gradle.org/m2/" }
+    }
+}
+
+apply plugin: 'maven'
+apply plugin: 'java'
+apply plugin: 'idea'
+
+sourceCompatibility = 1.8
+targetCompatibility = 1.8
+
+sourceSets {
+    main {
+        resources {
+            srcDir "src/main/resources"
+        }
+    }
+    test {
+        resources {
+            srcDir "src/test/resources"
+        }
+    }
+}
+
+repositories {
+    mavenLocal()
+    mavenCentral()
+    jcenter()
+}
+
+dependencies {
+    implementation group: 'net.java.dev.jna', name: 'jna', version: '5.13.0'
+    implementation files("libs/gdal-3.5.3.jar",
+            "libs/gdal-3.5.3-javadoc.jar",
+            "libs/gdal-3.5.3-sources.jar"
+    )
+}
+
+jar {
+    from {
+        configurations.compile.collect { it.isDirectory() ? it : zipTree(it) }
+        configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
+    }
+}
+
+task sourcesJar(type: Jar, dependsOn: classes) {
+    classifier = 'sources'
+    from sourceSets.main.allSource
+}
+
+task javadocJar(type: Jar, dependsOn: javadoc) {
+    classifier = 'javadoc'
+    from javadoc.destinationDir
+}
+
+artifacts {
+    archives sourcesJar
+    archives javadocJar
+}
+
+install {
+    repositories.mavenInstaller {
+        pom.project {
+            licenses {
+                license {
+                    name 'The Apache Software License, Version 2.0'
+                    url 'http://www.apache.org/licenses/LICENSE-2.0.txt'
+                    distribution 'repo'
+                }
+            }
+        }
+    }
+}

docker/README.md

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+Docker images
+=====
+
+# GDAL image with native libraries
+[gdal-ubuntu-small.dockerfile](gdal-ubuntu-small.dockerfile) is based on the one provided by GDAL team, [Small: osgeo/gdal:ubuntu-small-latest](https://github.com/OSGeo/gdal/tree/release/3.5/docker#small-osgeogdalubuntu-small-latest) with two modifications:
+- Added swig and Java to be able to generate JNI
+- [Removed the load of native library in gdal](https://github.com/OSGeo/gdal/blob/release/3.5/swig/include/java/gdal_java.i#L18). Proper load of all required native all libraries is the reason why this library exists. 
+
+# lddtopo
+[lddtopo.dockerfile](lddtopo.dockerfile) is built on top of gdal-ubuntu-small.dockerfile. It uses https://github.com/REASY/lddtopo-rs to build the dependency graph of a provided library and run topological sort to get the order in which they should be loaded. 

docker/bh-set-envvars.sh

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+#!/bin/sh
+set -eu
+
+if test "${TARGET_ARCH:-}" != ""; then
+  if test "${TARGET_ARCH}" = "arm64"; then
+      export GCC_ARCH=aarch64
+  else
+      echo "Unhandled architecture: ${TARGET_ARCH}"
+      exit 0
+  fi
+  export APT_ARCH_SUFFIX=":${TARGET_ARCH}"
+  export CC=${GCC_ARCH}-linux-gnu-gcc-9
+  export CXX=${GCC_ARCH}-linux-gnu-g++-9
+  export WITH_HOST="--host=${GCC_ARCH}-linux-gnu"
+else
+  export APT_ARCH_SUFFIX=""
+  export WITH_HOST=""
+  GCC_ARCH="$(uname -m)"
+  export GCC_ARCH
+fi

docker/extract_native.sh

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+#!/usr/bin/env bash
+
+set -e
+
+if [[ -z "$1" || -z "$2" ]]
+  then
+    echo "Missing mandatory arguments: path_shared_library, path_where_to_copy"
+    exit 1
+fi
+
+path_shared_library=$1
+copy_path=$2
+path_to_json="/tmp/topo_sorted.json"
+
+RUST_LOG=info /opt/lddtopo-rs/target/release/lddtopo-rs --shared-library-path $path_shared_library --output-file $path_to_json
+
+# Skipping libmfhdfalt due to /tmp/xxxx.7669203887046987097/libmfhdfalt_5076252650710112250.so: undefined symbol: error_top
+# Skip libproj.so.15
+modules_to_ignore=("ld-linux-x86-64" "libc.so" "libm.so" "libpthread"  "libstdc" "libmfhdfalt" "libproj.so.15")
+os_name="linux"
+arch_type="x86-64"
+
+dest_folder="$copy_path/native/${os_name}-${arch_type}"
+mkdir -p $dest_folder
+
+path_native_modules_to_load="${copy_path}/native/${os_name}-${arch_type}.txt"
+rm -rf "$path_native_modules_to_load"
+
+for OUTPUT in $(jq -r '.topo_sorted_libs[] |  .name + ":" + .path' $path_to_json)
+do
+  lib=$(echo $OUTPUT | cut -d ":" -f 1)
+  found=false
+  for i in "${modules_to_ignore[@]}"; do
+      if grep -q "$i" <<< "$lib"; then
+          #echo "Found $i in $lib, ignoring...";
+          found=true;
+          break;
+      fi
+  done
+
+  if $found; then
+    continue;
+  fi
+
+  path=$(echo $OUTPUT | cut -d ":" -f 2)
+  dest_path="${dest_folder}/$lib"
+  #echo $dest_path
+
+  cp $path $dest_path
+  echo "Copied $lib to $dest_path"
+
+  # Write native module to the list of modules
+  echo $lib >> $path_native_modules_to_load
+done
+