OpenSlide Java

This is a Java binding to OpenSlide.

Build requirements

• JDK
• Apache Ant
• OpenSlide >= 3.4.0

Building on Linux or Mac OS X

Install

1. autoconf
2. autoconf-archive
3. automake

Optional: set the <property name="target" value="11"/> value in build.xml to the Java compile target version.

# set JAVA_HOME and JDK_HOME to the respective paths, then run
autoreconf -i && ./configure && make && make install

This will install the openslide.jar and libopenslide-jni.{ dylib | so } to /usr/local/lib/openslide-java/,

Caution: this build contains a hard-coded path to the OpenSlide library! The bindings expect the OpenSlide lib to be installed on the target system.

Building OSX native lib

NB: Following the invaluable addition to packaging OpenSlide Java by quath.

Build the library

# install python 3 and macpack
brew install python3
pip3 install macpack

# create build dirs
mkdir -p packaging/osx-java-default/libs
cd packaging/osx-java-default
cp /usr/local/lib/openslide-java/openslide.jar ./openslide-java-default.jar
cp /usr/local/lib/openslide-java/libopenslide-jni.jnilib ./libs

macpack ./libs/libopenslide-jni.jnilib -d .
zip -d ./openslide-java-default.jar resources/openslide.properties
jar cf ./openslide-natives-osx.jar -C ./libs .

TODO: we need to load the openslide-jni from the jar when using from maven repository.

Deploying bindings and natives to a Maven repository

Prerequisites:

1. mvn command installed
2. Access to $MAVEN_REPO_URL and the $MVN_REPO_ID is configured in your local .m2/settings.xml
3. Deploy using the helper script in the build-compat folder

cd build-compat
sh ./mvn-deploy-file.sh default osx MVN_REPO_ID MVN_REPO_ID

Building portable Java 8/11 in Docker (for Linux)

NB: Following the invaluable addition to packaging OpenSlide Java by quath.

Build the latest version against the default Java 1.6 target with the latest OpenSlide binaries:

docker build -t local/openslide-java:6-git --build-arg ENV_JAVA_COMPILE_TARGET=6 -f build-compat/Dockerfile .

You need to explicitly enable the patching / dependency bundling step using --build-arg BUNDLE=1 to build the dependencies as JAR and patch the openslide.jar file.

docker run --rm -v $PWD/packaging/linux-java-6:/exchange local/openslide-java:6-git /bin/bash -c "cp /artifacts/openslide*.jar /exchange"

Compatibility builds for Java 8 and Java 11 are located in /build-compat/java-*:

docker build -t local/openslide-java:8-git --build-arg ENV_JAVA_COMPILE_TARGET=8 -f build-compat/Dockerfile .
# then
docker run --rm -v $PWD/packaging/linux-java-8:/exchange local/openslide-java:8-git /bin/bash -c "cp /artifacts/openslide*.jar /exchange"

docker build -t local/openslide-java:11-git --build-arg ENV_JAVA_COMPILE_TARGET=11 -f build-compat/Dockerfile .
# then
docker run --rm -v $PWD/packaging/linux-java-11:/exchange local/openslide-java:11-git /bin/bash -c "cp /artifacts/openslide*.jar /exchange"

Deploying dependencies and natives to a Maven repository

Prerequisites:

1. mvn command installed
2. Access to $MAVEN_REPO_URL and the $MVN_REPO_ID is configured in your local .m2/settings.xml
3. Deploy using the helper script in the build-compat folder

cd build-compat
# USAGE: sh ./mvn-deploy-file.sh JAVA_TARGET OS_TARGET MVN_REPO_ID MVN_REPO_ID
# e.g.
sh ./mvn-deploy-file.sh 11 linux MVN_REPO_ID MVN_REPO_ID

TODO: we need to load the openslide-jni from the jar when using from maven repository.

Cross-compiling for Windows with MinGW-w64

PKG_CONFIG=pkg-config \
	PKG_CONFIG_PATH=/path/to/cross/compiled/openslide/lib/pkgconfig \
	./configure --host=i686-w64-mingw32 --build=$(build-aux/config.guess)
make
make install

For a 64-bit JRE, substitute --host=x86_64-w64-mingw32.

Building on Windows

Ensure that the path to the openslide-java source tree does not contain whitespace.

Install Cygwin, selecting these additional packages:

• make
• pkg-config
• mingw64-i686-gcc-core and/or mingw64-x86_64-gcc-core

(Cygwin is only needed for the build environment; the resulting binaries do not require Cygwin.)

Also install a JDK and Apache Ant.

Then:

./configure --prefix=/path/to/install/dir \
	--host=i686-w64-mingw32 --build=$(build-aux/config.guess) \
	PKG_CONFIG_PATH="/path/to/openslide/lib/pkgconfig" \
	JAVA_HOME="$(cygpath c:/Program\ Files/Java/jdk*)" \
	ANT_HOME="/path/to/ant/directory"
make
make install

For a 64-bit JRE, substitute --host=x86_64-w64-mingw32.