feat: Add comprehensive Java auto-detection#9
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quinnjr wants to merge 37 commits intoFIUBioRG:masterfrom
Open
feat: Add comprehensive Java auto-detection#9quinnjr wants to merge 37 commits intoFIUBioRG:masterfrom
quinnjr wants to merge 37 commits intoFIUBioRG:masterfrom
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…ubprocess exec functionality to project.
…into feature/plugin-dependency
… Modifying Dockerfile for better caching. Adding initial Java plugin support wrappers.
… dependency download fucntion to R language. Adding searching for Perl requirements.
…. Renaming source files properly.
Implement robust Java installation detection that works across platforms: - Add JavaConfig class to hold detection results - Add detect_java_config() function with multi-step detection: 1. Check JAVA_HOME environment variable 2. Find javac executable and derive JAVA_HOME 3. Search common installation directories by platform - Support Linux, macOS, and Windows installation paths - Properly configure JNI include paths (jni.h, jni_md.h) - Find and link libjvm shared library - Get Java version for logging RHEL/CentOS/AlmaLinux specific improvements: - Check /etc/alternatives/java_sdk symlink first (most reliable) - Handle java-X-openjdk-VERSION directory naming with arch suffix - Search for matching JDK when javac resolves to JRE - Detect RHEL-like systems and provide helpful error messages - Warn about missing -devel package when JNI headers not found Changes to SConstruct: - Change --without-java default to False (enable auto-detection) - Use detect_java_config() for robust detection - Only enable Java features if detection succeeds - Add proper imports for os and subprocess modules This enables Java plugin support to work out-of-the-box when a JDK is installed, without requiring manual JAVA_HOME configuration.
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Summary
Changes
New
detect_java_config()Function inbuild_support.pyMulti-step detection strategy:
JAVA_HOMEenvironment variablejavacexecutable and derive JAVA_HOME from it/usr/lib/jvm/*,/usr/java/*,/opt/java/*/Library/Java/JavaVirtualMachines/*, Homebrew locationsC:/Program Files/Java/*, Eclipse Adoptium, Microsoft JDKJavaConfigClassHolds detection results:
java_home: Path to JDK installationinclude_paths: JNI header directorieslib_paths: Library directorieslibjvm_path: Path to libjvm shared libraryis_valid: Whether detection succeededversion: Detected Java versionSConstruct Updates
--without-javadefault toFalse(enable auto-detection)detect_java_config()for robust detectionlibjvmTest plan