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v2.1

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yurui 2023-06-14 00:02:28 +08:00
父節點 d0734ef962
當前提交 3a73df1ef9
共有 9 個檔案被更改，包括 55 行新增 和 25 行删除
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21
src/main/java/com/weilab/biology/controller/JobController.java
查看文件

@ -17,8 +17,8 @@ import com.weilab.biology.core.validation.EnumValidation;
import com.weilab.biology.mapper.JobMapper;
import com.weilab.biology.service.AppConfigService;
import com.weilab.biology.service.JobService;
import com.weilab.biology.util.JobIdUtil;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.PostMapping;
@ -43,12 +43,9 @@ public class JobController {
@Autowired
private JobMapper jobMapper;
@Value("${biology.request-path}")
private String requestPath;
@PostMapping("/submit")
public Result submit(@RequestParam String appName,
@RequestParam(required = false) Long jobId,
@RequestParam(required = false) String jobId,
@RequestParam(required = false) String dataStr,
@RequestParam(required = false) MultipartFile dataFile,
@RequestParam String param,
@ -64,7 +61,7 @@ public class JobController {
}
Job job = null;
if (jobId != null) {
if (StrUtil.isNotBlank(jobId)) {
// jobId不为空，从数据库获取已创建的任务
job = jobMapper.selectById(jobId);
if (job == null) {
@ -72,18 +69,23 @@ public class JobController {
}
} else {
job = new Job();
job.setJobId(JobIdUtil.newId());
}
// 解析param字符串为map对象
JSONObject reqParamMap = null;
try {
reqParamMap = JSON.parseObject(param);
reqParamMap.put("type", type);
} catch (Exception e) {
return Result.getResult(CommonError.PARAM_WRONG);
}
// 将reqParam覆盖添加到原有job的param中
JSONObject params = JSON.parseObject(job.getParam());
if (params == null) {
params = new JSONObject();
}
params.putAll(reqParamMap);
job.setParam(JSON.toJSONString(params));
job.setAppId(appConfig.getAppId());
@ -103,6 +105,7 @@ public class JobController {
}
Job job = new Job();
job.setJobId(JobIdUtil.newId());
job.setAppId(appConfig.getAppId());
job.setParam("{}");
job.setStatus(JobStatusEnum.CREATING.getKey());
@ -115,7 +118,7 @@ public class JobController {
* 上传文件接口，将文件地址保存至本地，并将路径放入参数中
*/
@PostMapping("/file/upload")
public Result uploadFile(@RequestParam Long jobId,
public Result uploadFile(@RequestParam String jobId,
@RequestParam String fileKey,
@RequestParam MultipartFile file) {
Job job = jobMapper.selectById(jobId);
@ -145,7 +148,7 @@ public class JobController {
}
@PostMapping("/status/update")
public Result updateJobStatus(@RequestParam Integer jobId,
public Result updateJobStatus(@RequestParam String jobId,
@EnumValidation(clazz = JobStatusEnum.class, message = "没有此状态") @RequestParam Integer status,
@RequestParam(required = false) String result) {
if (status.equals(JobStatusEnum.WAITING.getKey())) {
@ -167,7 +170,7 @@ public class JobController {
}
@GetMapping("/info/{jobId}")
public Result getJobInfo(@PathVariable Integer jobId) {
public Result getJobInfo(@PathVariable String jobId) {
return jobService.getJobInfo(jobId);
}

2
src/main/java/com/weilab/biology/core/data/dto/JobDto.java
查看文件

@ -22,7 +22,7 @@ public class JobDto implements Serializable {
/**
* jobId
*/
private Integer jobId;
private String jobId;
/**
* 任务状态

2
src/main/java/com/weilab/biology/core/data/dto/JobLessDto.java
查看文件

@ -21,7 +21,7 @@ public class JobLessDto {
/**
* jobId
*/
private Integer jobId;
private String jobId;
/**
* 任务状态

4
src/main/java/com/weilab/biology/core/data/po/Job.java
查看文件

@ -23,8 +23,8 @@ public class Job implements Serializable {
/**
* jobId
*/
@TableId(value = "job_id", type = IdType.AUTO)
private Integer jobId;
@TableId(value = "job_id", type = IdType.INPUT)
private String jobId;
/**
* 应用ID

2
src/main/java/com/weilab/biology/mapper/AppConfigMapper.java
查看文件

@ -2,6 +2,7 @@ package com.weilab.biology.mapper;
import com.weilab.biology.core.data.po.AppConfig;
import com.baomidou.mybatisplus.core.mapper.BaseMapper;
import org.apache.ibatis.annotations.Mapper;
import org.apache.ibatis.annotations.Param;
/**
@ -12,6 +13,7 @@ import org.apache.ibatis.annotations.Param;
* @author
* @since 2023-05-05
*/
@Mapper
public interface AppConfigMapper extends BaseMapper<AppConfig> {
AppConfig getAppConfigByAppName(@Param("appName") String appName);

10
src/main/java/com/weilab/biology/service/AppConfigService.java
查看文件

@ -4,7 +4,7 @@ import com.baomidou.mybatisplus.extension.service.impl.ServiceImpl;
import com.weilab.biology.core.data.dto.AppConfigDto;
import com.weilab.biology.core.data.po.AppConfig;
import com.weilab.biology.mapper.AppConfigMapper;
import org.apache.ibatis.annotations.Mapper;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
/**
@ -18,18 +18,18 @@ import org.springframework.stereotype.Service;
@Service
public class AppConfigService extends ServiceImpl<AppConfigMapper, AppConfig> {
@Mapper
@Autowired
private AppConfigMapper appConfigMapper;
/**
* 通过appName获取应用配置
*
* @param appName 唯一应用名
* @return AppConfigDto
*/
public AppConfigDto getAppConfig( String appName) {
return AppConfigDto.parse(appConfigMapper.getAppConfigByAppName(appName));
public AppConfigDto getAppConfig(String appName) {
return AppConfigDto.parse(appConfigMapper.getAppConfigByAppName(appName));
}
}

17
src/main/java/com/weilab/biology/service/JobService.java
查看文件

@ -58,7 +58,7 @@ public class JobService extends ServiceImpl<JobMapper, Job> {
try {
// dataStr和dataFile均为蛋白质序列，两者含义相同只保留其一，dataFile的优先级大于dataStr
// 若dataFile为空，则将dataStr写入本地文件，之后向python传递文件路径参数
String dataPath = String.format(appConfig.getRequestPath() + "job-%d-dataStr.txt", job.getJobId());
String dataPath = String.format(appConfig.getRequestPath() + "job-%s-dataStr.txt", job.getJobId());
if (dataFile != null) {
FileUtil.writeFromStream(dataFile.getInputStream(), dataPath);
} else if (!StrUtil.isBlank(dataStr)) {
@ -82,7 +82,7 @@ public class JobService extends ServiceImpl<JobMapper, Job> {
return getJobInfo(job.getJobId());
}
public Result getJobInfo(Integer jobId) {
public Result getJobInfo(String jobId) {
Job job = jobMapper.selectById(jobId);
if (job == null) {
return Result.getResult(CommonError.CONTENT_NOT_FOUND);
@ -160,6 +160,7 @@ public class JobService extends ServiceImpl<JobMapper, Job> {
private void runJob(AppConfigDto appConfig, Job job) {
try {
FileUtil.mkdir(appConfig.getLogPath());
String logFilePath = String.format(appConfig.getLogPath() + "task-log-%s.txt", job.getJobId());
String cmd = String.format("%s -setting '%s' >> %s 2>&1", appConfig.getCmd(), job.getParam(), logFilePath);
String[] cmds = new String[]{"/bin/sh", "-c", cmd};
@ -180,7 +181,7 @@ public class JobService extends ServiceImpl<JobMapper, Job> {
/**
* 开启异步定时任务，校验超时任务
*/
private void asyncScheduleTask(AppConfigDto appConfig, Integer jobId) {
private void asyncScheduleTask(AppConfigDto appConfig, String jobId) {
//等待120秒，检查是否已运行
taskExecutorUtil.schedule(() -> {
Job job = jobMapper.selectById(jobId);
@ -205,8 +206,8 @@ public class JobService extends ServiceImpl<JobMapper, Job> {
}
// 多个参数
String param1 = job.getRequestTime().format(DateTimeFormatter.ofPattern("yyyyMMdd")) + job.getJobId();
String param2 = param1;
String jobId = job.getJobId();
String time = LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss"));
String content = appConfig.getEmailTemplate().getString(status.getRemark());
String subject = appConfig.getEmailTemplate().getString("subject");
@ -214,7 +215,11 @@ public class JobService extends ServiceImpl<JobMapper, Job> {
return;
}
mailUtil.send(mail, String.format(subject, param1), String.format(content, param1, param2));
// 格式化填充参数
content = content.replaceAll("%jobId%", jobId).replaceAll("%time%", time);
subject = subject.replaceAll("%jobId%", jobId).replaceAll("%time%", time);
mailUtil.send(mail, subject, content);
}
}

20
src/main/java/com/weilab/biology/util/JobIdUtil.java Normal file
查看文件

@ -0,0 +1,20 @@
package com.weilab.biology.util;
import cn.hutool.core.util.IdUtil;
import java.time.LocalDate;
import java.time.LocalDateTime;
import java.time.format.DateTimeFormatter;
/**
* @author yurui
* @date 2023/6/13
*/
public class JobIdUtil {
public static String newId() {
return LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyyMMddHHmmss"))
+ IdUtil.fastUUID().substring(0, 8);
}
}

2
src/main/resources/mapper/JobMapper.xml
查看文件

@ -2,7 +2,7 @@
<!DOCTYPE mapper PUBLIC "-//mybatis.org//DTD Mapper 3.0//EN" "http://mybatis.org/dtd/mybatis-3-mapper.dtd">
<mapper namespace="com.weilab.biology.mapper.JobMapper">
<resultMap id="BaseResultMap" type="com.weilab.biology.core.data.po.Job">
<id column="job_id" jdbcType="INTEGER" property="jobId"/>
<id column="job_id" jdbcType="VARCHAR" property="jobId"/>
<result column="param" jdbcType="VARCHAR" property="param"/>
<result column="mail" jdbcType="VARCHAR" property="mail"/>
<result column="result" jdbcType="LONGVARCHAR" property="result"/>