...
String[] cmdArgs = {"Rscript", medreportPath, "-i", destFilePath1, "-o", webRptPath + "/" + runID};

//        String command = "Rscript " + medreportPath + " -i " + destFilePath1 + " -o " + webRptPath + "/" + runID;

        try {

            Process process = Runtime.getRuntime().exec(cmdArgs);   // 调动外部程序

            BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream(), StandardCharsets.UTF_8));  // 获取标准输出

            String line;

            while ((line = br.readLine()) != null) {

                System.out.println(line + "\n");

            }

            BufferedReader brError = new BufferedReader(new InputStreamReader(process.getErrorStream(), StandardCharsets.UTF_8));  // 获取标准错误输出

            String lineError;

            while((lineError = brError.readLine()) != null) {

                System.out.println(lineError + "\n");

            }

            process.waitFor();

        } catch (Exception e) {

            e.printStackTrace();

        }
...

public class Runtime extends Object // Runtime 直接继承 Object

public static Runtime getRunTime()  // 获取 Runtime 实例的 static 方法

public Process exec(...) throws IOException  // 执行外部程序，exec()有多个重载方法 

package java_python;

import java.io.BufferedReader;

import java.io.InputStream;

import java.io.InputStreamReader;

/*

 *  直接使用 Runtime 调用外部程序

 *  在Java中通过Runtime调用Python程序与直接执行Python程序的效果是一样的，可以在Python中读取传递的参数，也可以在Java中读取到Python的执行结果。

 *  需要注意的是，不能在Python中通过return语句返回结果，只能将返回值写入到标准输出流中，然后在Java中通过标准输入流读取Python的输出值。

 */

public class RunPythonByRuntime {

    public static void main(String[] args) {

        String exe = "python";  // 使用python3   依赖biopython

        String command = "C:\\Users\\mail.simcere.com\\eclipse-workspace\\python_test\\test\\test01.py";  // python 脚本路径

        String term = "meningitis";  // 参数

        String[] cmdArr = new String[] {exe, command, term};

        Process process;

        try {

            process = Runtime.getRuntime().exec(cmdArr);  // 执行python程序

            InputStream inputStream = process.getInputStream();  // 获取python程序的标准输出

            BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(inputStream));  // 转换为BufferedReader对象实例

            String line = null;

            while((line = bufferedReader.readLine()) != null) {  // 逐行读入python程序的输出结果

                System.out.println(line);

            }

            process.waitFor();

        } catch (Exception e) {

            e.printStackTrace();

        }

    }

}

#coding=utf-8

import sys

from Bio import Entrez

from Bio import Medline

term = sys.argv[1]  # 需要外界传入 meningitis

retmax = 5  # 控制返回的文献数目

Entrez.email = "771966294@qq.com"

handle = Entrez.esearch(db="pubmed", term=term, retmax=retmax)

record = Entrez.read(handle)

handle = Entrez.efetch(db="pubmed", id=record["IdList"], rettype="medline", retmode="text")

records = Medline.parse(handle)

records = list(records)

handle.close()

rst = ""

for record in records:  # record 是一个字典

    rst += ">\nPMID:" + record.get("PMID", "?") \

         + "\nTitle:" + record.get("TI", "?") \

         + "\nAuthors:" + ";".join(record.get("AU", "?")) \

         + "\nAbstract:" + record.get("AB", "?") \

         + "\nKeywords:" + ";".join(record.get("OT", "?")) \

         + "\nMesh Terms:" + ";".join(record.get("MH", "?")) \

         + "\nJournal:" + record.get("TA", "?") \

         + "\nDate of Publication:" + record.get("DP", "?") \

         + "\ndoi:" + record.get("SO", "?") \

         + "\n"

print(rst)