text: /**
   * The MIT License (MIT)
   * Copyright (c) 2016-2017 Intel Corporation
   * Copyright (c) 2020 Omics Data Automation, Inc.
   *
   * Permission is hereby granted, free of charge, to any person obtaining a copy of 
   * this software and associated documentation files (the "Software"), to deal in 
   * the Software without restriction, including without limitation the rights to 
   * use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of 
   * the Software, and to permit persons to whom the Software is furnished to do so, 
   * subject to the following conditions:
   *
   * The above copyright notice and this permission notice shall be included in all 
   * copies or substantial portions of the Software.
   *
   * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS 
   * FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR 
   * COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER 
   * IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN 
   * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
  
  #include "jni_mpi_init.h"
  #include "genomicsdb_GenomicsDBLibLoader.h"
  
  JNIMpiInit g_jni_mpi_init;
  
  std::string get_system_property(JNIEnv* env, const std::string& name ) {
    jclass java_system_class = env->FindClass("java/lang/System");
    jmethodID java_property_method = env->GetStaticMethodID(java_system_class, "getProperty", "(Ljava/lang/String;)Ljava/lang/String;");
    jstring java_property_name = env->NewStringUTF(name.c_str());
    jstring java_property_value = static_cast<jstring>(env->CallStaticObjectMethod(java_system_class, java_property_method, java_property_name ));
    if (java_property_value) {
      const char* property = env->GetStringUTFChars(java_property_value, 0);
      std::string property_string = property?std::string(property):"";
      env->ReleaseStringUTFChars(java_property_value, property);
      return property_string;
    }
    return "";
  }
  
  JNIEXPORT jint JNICALL Java_org_genomicsdb_GenomicsDBLibLoader_jniGenomicsDBOneTimeInitialize
    (JNIEnv * env, jclass obj)
  {
    std::string gatk_stacktrace_on_user_exception = get_system_property(env, "GATK_STACKTRACE_ON_USER_EXCEPTION");
    if (!gatk_stacktrace_on_user_exception.empty()) {
      setenv("GENOMICSDB_PRINT_STACKTRACE", gatk_stacktrace_on_user_exception.c_str(), 1);
    }
    g_jni_mpi_init.initialize();
    return 0;
  }
  