Install IJAVA Java kernel in jupyterlab

xp1632 commented 11 months ago

	Java	Jupyterlab	Jupyter Notebook
Components V
IJAVA Java Kernel	9+	until 2019	until 2019
Fiji	8(?)

xp1632 commented 11 months ago

IJAVA is still broadly used for a lot of other projects until 2023 April https://github.com/oracle/tribuo/issues/332
IJAVA kernel is also developed based on Jshell, and support windows system

xp1632 commented 11 months ago

3.7.1 Install Ijava: ref of the book: ( https://subscription.packtpub.com/book/data/9781789137408/5)

Install from source (https://github.com/SpencerPark/IJava#install-from-source)
[x] Install JAVA and test through java --version
[x] Find jdk shell throughjava --list-modules | findstr "jdk.jshell", shoudl output jdk.jshell@ followed by your java version.
[x] Install Jupyter environment
[x] Clone IJAVA from (https://github.com/SpencerPark/IJava) to local (E:\IJava)

3.7.2 Error of Gradlew and JAVA version

[ ] Try installation with gradlew installKernel in Windows system

E:\IJava>gradlew installKernel

FAILURE: Build failed with an exception.

* What went wrong:
Could not create service of type ScriptPluginFactory using BuildScopeServices.createScriptPluginFactory().
> Could not create service of type PluginResolutionStrategyInternal using BuildScopeServices.createPluginResolutionStrategy().

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 0s

And while check the issue of IJAVA, that is caused by the gradlew in IJAVA is too old for new JAVA version:
- https://github.com/SpencerPark/IJava/issues/129
- Java 17 is supported only by gradle versions 7.3+.
One solution is to update gradle as in
- https://github.com/SpencerPark/IJava/pull/134
- https://github.com/SpencerPark/Jupyter-kernel-installer-gradle/pull/14

xp1632 commented 11 months ago

The solution of update branch is : https://github.com/saalfeldlab/IJava

3.7.3 IJAVA branch that has JAVA 17 compatible gradle setup

ref : (https://github.com/saalfeldlab/IJava)
we clone this branch in E:/IJava17/
and in the directory, we run gradlew installKernel --prefix=/path/to/installation/prefix
it download the gradlew of version 7.5.1, original we have 4.8.1 which is too old
Gradle 7.5.1 support JAVA 18, now we are at JAVA 21
we get error :


Welcome to Gradle 7.5.1!

Here are the highlights of this release:
 - Support for Java 18
 - Support for building with Groovy 4
 - Much more responsive continuous builds
 - Improved diagnostics for dependency resolution

For more details see https://docs.gradle.org/7.5.1/release-notes.html

Starting a Gradle Daemon (subsequent builds will be faster)

FAILURE: Build failed with an exception.

* What went wrong:
Could not open cp_settings generic class cache for settings file 'E:\IJava17\settings.gradle' (C:\Users\59803\.gradle\caches\7.5.1\scripts\9bimkwnf2r5z14vz759vkfnnb).
> BUG! exception in phase 'semantic analysis' in source unit '_BuildScript_' Unsupported class file major version 65

* Try:
> Run with --stacktrace option to get the stack trace.
> Run with --info or --debug option to get more log output.
> Run with --scan to get full insights.

* Get more help at https://help.gradle.org

3.7.4 Trying if java 17 works,

we installed Java 17 in C:\Program Files\Java\jdk-17

ref: https://blog.csdn.net/wq6ylg08/article/details/91352199

And we also need to change the environment variable of java from version 21 to current 17
which is change JAVA_HOME : C:\Program Files\Java\jdk-xx xx is our current 17
and change PATH: C:\Program Files\Java\jdk-xx\bin
and test java -version:

now we have

java version "17.0.8" 2023-07-18 LTS
Java(TM) SE Runtime Environment (build 17.0.8+9-LTS-211)
Java HotSpot(TM) 64-Bit Server VM (build 17.0.8+9-LTS-211, mixed mode, sharing)

remember you need to reopen cmd to see the change

3.7.5 with JAVA 17 and the fixed IJAVA, build successfully

E:\IJava17>gradlew installKernel --prefix=/path/to/installation/prefix
Starting a Gradle Daemon, 1 incompatible Daemon could not be reused, use --status for details

> Task :installer:compileKotlin
'compileJava' task (current target is 17) and 'compileKotlin' task (current target is 1.8) jvm target compatibility should be set to the same Java version.
w: Runtime JAR files in the classpath should have the same version. These files were found in the classpath:
    C:/Users/59803/.gradle/wrapper/dists/gradle-7.5.1-all/1ehga6e77gqps5uk2kc5kf1vc/gradle-7.5.1/lib/kotlin-stdlib-1.6.21.jar (version 1.6)
    C:/Users/59803/.gradle/wrapper/dists/gradle-7.5.1-all/1ehga6e77gqps5uk2kc5kf1vc/gradle-7.5.1/lib/kotlin-stdlib-common-1.6.21.jar (version 1.6)
    C:/Users/59803/.gradle/wrapper/dists/gradle-7.5.1-all/1ehga6e77gqps5uk2kc5kf1vc/gradle-7.5.1/lib/kotlin-stdlib-jdk7-1.6.21.jar (version 1.6)
    C:/Users/59803/.gradle/wrapper/dists/gradle-7.5.1-all/1ehga6e77gqps5uk2kc5kf1vc/gradle-7.5.1/lib/kotlin-stdlib-jdk8-1.6.21.jar (version 1.6)
    C:/Users/59803/.gradle/wrapper/dists/gradle-7.5.1-all/1ehga6e77gqps5uk2kc5kf1vc/gradle-7.5.1/lib/kotlin-reflect-1.6.21.jar (version 1.6)
    C:/Users/59803/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-stdlib-jdk8/1.5.31/ff5d99aecd328872494e8921b72bf6e3af97af3e/kotlin-stdlib-jdk8-1.5.31.jar (version 1.5)
    C:/Users/59803/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-stdlib-jdk7/1.5.31/77e0f2568912e45d26c31fd417a332458508acdf/kotlin-stdlib-jdk7-1.5.31.jar (version 1.5)
    C:/Users/59803/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-stdlib/1.5.31/6628d61d0f5603568e72d2d5915d2c034b4f1c55/kotlin-stdlib-1.5.31.jar (version 1.5)
    C:/Users/59803/.gradle/caches/modules-2/files-2.1/org.jetbrains.kotlin/kotlin-stdlib-common/1.5.31/43331609c7de811fed085e0dfd150874b157c32/kotlin-stdlib-common-1.5.31.jar (version 1.5)
w: Some runtime JAR files in the classpath have an incompatible version. Consider removing them from the classpath
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\InstallKernelTask.kt: (45, 24): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\InstallKernelTask.kt: (64, 9): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\InstallKernelTask.kt: (69, 9): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\KernelExtension.kt: (39, 24): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\KernelExtension.kt: (78, 9): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\KernelParameterSpecContainer.kt: (32, 24): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\KernelParameterSpecContainer.kt: (42, 182): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\KernelParameterSpecContainer.kt: (46, 182): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\KernelParameterSpecContainer.kt: (50, 178): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\KernelParameterSpecContainer.kt: (54, 180): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\ZipKernelTask.kt: (43, 24): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\ZipKernelTask.kt: (184, 9): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\ZipKernelTask.kt: (198, 9): 'ConfigureUtil' is deprecated. Deprecated in Java
w: E:\IJava17\installer\src\main\kotlin\io\github\spencerpark\jupyter\gradle\ZipKernelTask.kt: (230, 9): 'ConfigureUtil' is deprecated. Deprecated in Java

> Task :compileJava
Note: E:\IJava17\src\main\java\io\github\spencerpark\ijava\magics\dependencies\Maven.java uses or overrides a deprecated API.
Note: Recompile with -Xlint:deprecation for details.

Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.

You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.

See https://docs.gradle.org/7.5.1/userguide/command_line_interface.html#sec:command_line_warnings

BUILD SUCCESSFUL in 58s
12 actionable tasks: 12 executed

we can see we build it successfully

xp1632 commented 11 months ago

3.7.6 No kernel found

however we can not find the kernel
and by reading the first several lines, we suspect the java 8 we installed before is interrupting
thus we uninstalled java 8 and build again, we didn't see the version differences warning this time
but jupyter kernelspec list we still didn't find the kernel

3.7.7 we try the pre-built libnary installation:

ref:(https://github.com/SpencerPark/IJava#install-pre-built-binary)

not sure if there's future version conflict
however, by downloading ijava release
unzip it to a temp folder
in temp folder directory,(for me I also activate my conda base env) run python install.py --sys-prefix,

this time the kernel is installed:


(base) C:\Users\59803\Downloads\ijava-1.3.0>python install.py --sys-prefix
C:\Users\59803\Downloads\ijava-1.3.0\install.py:164: DeprecationWarning: replace is ignored. Installing a kernelspec always replaces an existing installation
install_dest = KernelSpecManager().install_kernel_spec(
Installed java kernel into "E:\Users\59803\anaconda3\share\jupyter\kernels\java"

(base) C:\Users\59803\Downloads\ijava-1.3.0>jupyter kernelspec list Available kernels: python3 C:\Users\59803\AppData\Roaming\Python\share\jupyter\kernels\python3 java E:\Users\59803\anaconda3\share\jupyter\kernels\java

xp1632 commented 11 months ago

By using released version of IJava, Java 12 is the current release.
I am not sure the extent that we need of using this java kernel, but for now, the java code is running in jupyter lab

xp1632 / VPE_IP

Install IJAVA Java kernel in jupyterlab #17

remember you need to reopen `cmd` to see the change

xp1632 / VPE_IP

Install IJAVA Java kernel in jupyterlab #17

remember you need to reopen cmd to see the change

remember you need to reopen `cmd` to see the change