上传文件到OSS 需要迁移

Uat_Study
hang 2023-11-23 12:15:17 +08:00
parent 3decef7693
commit abd5c8942d
7 changed files with 428 additions and 73 deletions

View File

@ -24,6 +24,7 @@ using Magicodes.ExporterAndImporter.Excel;
using MassTransit;
using MediatR;
using Microsoft.AspNetCore.Authorization;
using Microsoft.AspNetCore.Cors.Infrastructure;
using Microsoft.AspNetCore.Hosting;
using Microsoft.AspNetCore.Http;
using Microsoft.AspNetCore.Mvc;
@ -37,7 +38,7 @@ using Microsoft.Net.Http.Headers;
using MiniExcelLibs;
using Newtonsoft.Json;
using SharpCompress.Archives;
using SharpCompress.Common;
using SkiaSharp;
using System;
using System.Collections.Generic;
using System.Data;
@ -134,6 +135,32 @@ namespace IRaCIS.Core.API.Controllers
}
}
[Route("base")]
public virtual async Task FileUploadToOSSAsync(Func<string, Stream, Task<string>> toMemoryStreamFunc)
{
var boundary = HeaderUtilities.RemoveQuotes(MediaTypeHeaderValue.Parse(Request.ContentType).Boundary).Value;
var reader = new MultipartReader(boundary, HttpContext.Request.Body);
var section = await reader.ReadNextSectionAsync();
while (section != null)
{
var hasContentDispositionHeader = ContentDispositionHeaderValue.TryParse(section.ContentDisposition, out var contentDisposition);
if (hasContentDispositionHeader)
{
var fileName = contentDisposition.FileName.Value;
await toMemoryStreamFunc(fileName, section.Body);
}
section = await reader.ReadNextSectionAsync();
}
}
/// <summary> 流式上传 Dicom上传 </summary>
@ -280,9 +307,6 @@ namespace IRaCIS.Core.API.Controllers
if (!HttpContext.Request.HasFormContentType ||
!MediaTypeHeaderValue.TryParse(HttpContext.Request.ContentType, out var mediaTypeHeader) ||
string.IsNullOrEmpty(mediaTypeHeader.Boundary.Value))
@ -756,11 +780,13 @@ namespace IRaCIS.Core.API.Controllers
[HttpPost("QCOperation/UploadVisitCheckExcel/{trialId:guid}")]
[TypeFilter(typeof(TrialResourceFilter), Arguments = new object[] { "AfterStopCannNotOpt" })]
//[Authorize(Policy = IRaCISPolicy.PM_APM)]
public async Task<IResponseOutput> UploadVisitCheckExcel(Guid trialId)
public async Task<IResponseOutput> UploadVisitCheckExcel(Guid trialId, [FromServices] IOSSService oSSService)
{
var (serverFilePath, relativePath, fileName) = (string.Empty, string.Empty, string.Empty);
await FileUploadAsync(async (realFileName) =>
var fileName = string.Empty;
var templateFileStream = new MemoryStream();
await FileUploadToOSSAsync(async (realFileName, fileStream) =>
{
fileName = realFileName;
@ -770,19 +796,16 @@ namespace IRaCIS.Core.API.Controllers
throw new BusinessValidationFailedException(StaticData.International("UploadDownLoad_SupportedFormats"));
}
(serverFilePath, relativePath) = FileStoreHelper.GetTrialCheckFilePath(_hostEnvironment, fileName, trialId);
fileStream.CopyTo(templateFileStream);
templateFileStream.Seek(0, SeekOrigin.Begin);
await _repository.AddAsync(new UserUploadFile()
{
TrialId = trialId,
CreateTime = DateTime.Now,
FileName = fileName,
FilePath = relativePath,
RelativePath = relativePath,
CreateUserId = _userInfo.Id
});
return serverFilePath;
var ossRelativePath = oSSService.UploadToOSS(fileStream, "InspectionUpload/SiteSurvey", realFileName);
await _repository.AddAsync(new InspectionFile() { FileName = realFileName, RelativePath = ossRelativePath, TrialId = trialId });
return ossRelativePath;
});
@ -814,7 +837,7 @@ namespace IRaCIS.Core.API.Controllers
{
var Importer = new ExcelImporter();
var import = await Importer.Import<CheckViewModel>(System.IO.File.OpenRead(serverFilePath));
var import = await Importer.Import<CheckViewModel>(templateFileStream);
if (import.Exception != null) return ResponseOutput.NotOk(import.Exception.ToString());
@ -829,7 +852,7 @@ namespace IRaCIS.Core.API.Controllers
#region 临时方案 MiniExcel读取 然后保存为xlsx 再用 Magicodes验证数据
//因为csv 需要加配置文件 不然都是null
etcCheckList = MiniExcel.Query<CheckViewModel>(serverFilePath, null, configuration: new MiniExcelLibs.Csv.CsvConfiguration()
etcCheckList = MiniExcel.Query<CheckViewModel>(templateFileStream, null, configuration: new MiniExcelLibs.Csv.CsvConfiguration()
{
StreamReaderFunc = (stream) => new StreamReader(stream, Encoding.GetEncoding("gb2312"))
}).ToList();
@ -874,35 +897,35 @@ namespace IRaCIS.Core.API.Controllers
else
{
//为了支持 xls 引入新的组件库
using (var stream = System.IO.File.Open(serverFilePath, FileMode.Open, FileAccess.Read))
//using (var stream = System.IO.File.Open(templateFileStream, FileMode.Open, FileAccess.Read))
//{
// Auto-detect format, supports:
// - Binary Excel files (2.0-2003 format; *.xls)
// - OpenXml Excel files (2007 format; *.xlsx, *.xlsb)
using (var reader = ExcelReaderFactory.CreateReader(templateFileStream))
{
// Auto-detect format, supports:
// - Binary Excel files (2.0-2003 format; *.xls)
// - OpenXml Excel files (2007 format; *.xlsx, *.xlsb)
using (var reader = ExcelReaderFactory.CreateReader(stream))
// 2. Use the AsDataSet extension method
var dateset = reader.AsDataSet();
foreach (DataRow col in dateset.Tables[0].Rows)
{
// 2. Use the AsDataSet extension method
var dateset = reader.AsDataSet();
foreach (DataRow col in dateset.Tables[0].Rows)
etcCheckList.Add(new CheckViewModel()
{
etcCheckList.Add(new CheckViewModel()
{
SiteCode = col[0].ToString(),
SubjectCode = col[1].ToString(),
VisitName = col[2].ToString(),
StudyDate = col[3].ToString(),
Modality = col[4].ToString(),
});
}
etcCheckList.Remove(etcCheckList[0]);
// The result of each spreadsheet is in result.Tables
SiteCode = col[0].ToString(),
SubjectCode = col[1].ToString(),
VisitName = col[2].ToString(),
StudyDate = col[3].ToString(),
Modality = col[4].ToString(),
});
}
etcCheckList.Remove(etcCheckList[0]);
// The result of each spreadsheet is in result.Tables
}
}
if (etcCheckList == null || etcCheckList.Count == 0)
@ -940,6 +963,140 @@ namespace IRaCIS.Core.API.Controllers
return ResponseOutput.Ok();
}
}
#endregion
#region 医生文件上传下载
#region DTO
public class DoctorDownloadInfo
{
public Guid Id { get; set; }
public string Name { get; set; }
public string ReviewerCode { get; set; }
public List<DownloadFileInfo> FileList { get; set; }
}
public class DownloadFileInfo
{
public string FileName { get; set; }
public string Path { get; set; }
}
public class GetDoctorPathCommand
{
public int Language { get; set; }
public List<Guid> DoctorIdList { get; set; }
}
public class GetDoctoreAttachPathCommand
{
public Guid DoctorId { get; set; }
public List<Guid> AttachmentIdList { get; set; }
}
#endregion
/// <summary>医生文件上传下载</summary>
[ApiExplorerSettings(GroupName = "Common")]
[ApiController]
public class FileController : UploadBaseController
{
public IMapper _mapper { get; set; }
public IUserInfo _userInfo { get; set; }
private readonly IWebHostEnvironment _hostEnvironment;
private readonly IFileService _fileService;
public FileController(IMapper mapper, IUserInfo userInfo, IWebHostEnvironment hostEnvironment, IFileService fileService)
{
_fileService = fileService;
_hostEnvironment = hostEnvironment;
_mapper = mapper;
_userInfo = userInfo;
}
/// <summary>
/// New 医生首页 多选 获取多个医生信息+文件路径列表 医生压缩包名称 doctorCode + "_" + doctorName _(时间戳或者随机的Guid)
/// </summary>
/// <returns></returns>
[HttpPost, Route("file/GetOfficialResume")]
public async Task<IResponseOutput<List<DoctorDownloadInfo>>> GetOfficialResume(GetDoctorPathCommand command,
[FromServices] IRepository<Attachment> _attachmentrepository)
{
var list = await _attachmentrepository.Where(t => command.DoctorIdList.Contains(t.DoctorId) && command.Language==t.Language).GroupBy(t => new { Name = t.Doctor.FirstName + "_" + t.Doctor.LastName, ReviewerCode = t.Doctor.ReviewerCode, t.DoctorId })
.Select(g => new DoctorDownloadInfo()
{
Id = g.Key.DoctorId,
Name = g.Key.Name,
ReviewerCode = g.Key.ReviewerCode,
FileList = g.Select(t => new DownloadFileInfo() { FileName = t.FileName, Path = t.Path }).ToList()
}).ToListAsync();
return ResponseOutput.Ok(list);
}
/// <summary>
/// New 项目入组 勾选获取简历路径
/// </summary>
/// <param name="command"></param>
/// <param name="_doctorService"></param>
/// <param name="_attachmentrepository"></param>
/// <returns></returns>
[HttpPost,Route("file/GetTrialDoctorOfficialResume")]
public async Task<IResponseOutput<List<DoctorDownloadInfo>>> GetTrialDoctorOfficialResume(GetDoctorPathCommand command,
[FromServices] IDoctorService _doctorService,
[FromServices] IRepository<Attachment> _attachmentrepository)
{
var list = await _attachmentrepository.Where(t => command.DoctorIdList.Contains(t.DoctorId) && command.Language == t.Language && t.IsOfficial && t.Type.Equals("Resume")).GroupBy(t => new { Name = t.Doctor.FirstName + "_" + t.Doctor.LastName, ReviewerCode = t.Doctor.ReviewerCode, t.DoctorId })
.Select(g => new DoctorDownloadInfo()
{
Id = g.Key.DoctorId,
Name = g.Key.Name,
ReviewerCode = g.Key.ReviewerCode,
FileList = g.Select(t => new DownloadFileInfo() { FileName = t.FileName, Path = t.Path }).ToList()
}).ToListAsync();
return ResponseOutput.Ok(list);
}
/// <summary>
/// new 医生详情 勾选或者下载文件路径
/// </summary>
/// <param name="command"></param>
/// <param name="_doctorService"></param>
/// <param name="_attachmentrepository"></param>
/// <returns></returns>
[HttpPost, Route("file/GetDoctorAttachment")]
public async Task<IResponseOutput<DoctorDownloadInfo>> GetDoctorAttachment(GetDoctoreAttachPathCommand command,
[FromServices] IDoctorService _doctorService,
[FromServices] IRepository<Attachment> _attachmentrepository)
{
var find = await _attachmentrepository.Where(t => command.DoctorId==t.DoctorId && command.AttachmentIdList.Contains(t.Id)).GroupBy(t => new { Name = t.Doctor.FirstName + "_" + t.Doctor.LastName, ReviewerCode = t.Doctor.ReviewerCode, t.DoctorId })
.Select(g => new DoctorDownloadInfo()
{
Id = g.Key.DoctorId,
Name = g.Key.Name,
ReviewerCode = g.Key.ReviewerCode,
FileList = g.Select(t => new DownloadFileInfo() { FileName = t.FileName, Path = t.Path }).ToList()
}).FirstOrDefaultAsync();
return ResponseOutput.Ok(find);
}
}
@ -980,30 +1137,36 @@ namespace IRaCIS.Core.API.Controllers
[DisableFormValueModelBinding]
[UnitOfWork]
public async Task<IResponseOutput> UploadTrialSiteSurveyUser(Guid trialId, string baseUrl, string routeUrl,
[FromServices] IRepository<TrialSite> _trialSiteRepository,
[FromServices] IRepository<UserType> _usertypeRepository,
[FromServices] ITrialSiteSurveyService _trialSiteSurveyService)
[FromServices] IRepository<TrialSite> _trialSiteRepository,
[FromServices] IRepository<UserType> _usertypeRepository,
[FromServices] ITrialSiteSurveyService _trialSiteSurveyService)
{
var (serverFilePath, relativePath, fileName) = (string.Empty, string.Empty, string.Empty);
await FileUploadAsync(async (realFileName) =>
{
fileName = realFileName;
var templateFileStream = new MemoryStream();
if (!fileName.EndsWith(".xlsx", StringComparison.OrdinalIgnoreCase))
await FileUploadToOSSAsync(async (realFileName, fileStream) =>
{
await fileStream.CopyToAsync(templateFileStream);
templateFileStream.Seek(0, SeekOrigin.Begin);
if (!realFileName.EndsWith(".xlsx", StringComparison.OrdinalIgnoreCase))
{
// 请用提供格式的模板excel上传需要处理的数据
throw new BusinessValidationFailedException(StaticData.International("UploadDownLoad_TemplateUploadData"));
}
(serverFilePath, relativePath) = FileStoreHelper.GetOtherFileUploadPath(_hostEnvironment, StaticData.Folder.TempFile, fileName);
var ossRelativePath = oSSService.UploadToOSS(fileStream, "InspectionUpload/SiteSurvey", realFileName);
//FileStoreHelper.UploadOOS(serverFilePath, "testc/test", true);
await _inspectionFileRepository.AddAsync(new InspectionFile() { FileName = realFileName, RelativePath = ossRelativePath, TrialId = trialId });
return ossRelativePath;
return serverFilePath;
});
//去掉空白行
var excelList = MiniExcel.Query<SiteSurveyUserImportDto>(serverFilePath).ToList()
var excelList = MiniExcel.Query<SiteSurveyUserImportDto>(templateFileStream,excelType:ExcelType.XLSX).ToList()
.Where(t => !(string.IsNullOrWhiteSpace(t.TrialSiteCode) && string.IsNullOrWhiteSpace(t.FirstName) && string.IsNullOrWhiteSpace(t.LastName) && string.IsNullOrWhiteSpace(t.Email)
&& string.IsNullOrWhiteSpace(t.Phone) && string.IsNullOrWhiteSpace(t.UserTypeStr) && string.IsNullOrWhiteSpace(t.OrganizationName))).ToList();
@ -1033,7 +1196,7 @@ namespace IRaCIS.Core.API.Controllers
//有邮箱不符合邮箱格式,请核查Excel数据
throw new BusinessValidationFailedException(StaticData.International("UploadDownLoad_InvalidEmail"));
}
var generateUserTypeList = new List<string>() { "CRC", "SR", "CRA" };
var generateUserTypeList = new List<string>() { "CRC", "CRA" };
if (excelList.Any(t => !generateUserTypeList.Contains(t.UserTypeStr.ToUpper())))
{
@ -1045,7 +1208,7 @@ namespace IRaCIS.Core.API.Controllers
throw new BusinessValidationFailedException(StaticData.International("UploadDownLoad_NoValiddata"));
}
//处理好 用户类型 和用户类型枚举
var sysUserTypeList = _usertypeRepository.Where(t => t.UserTypeEnum == UserTypeEnum.CRA || t.UserTypeEnum == UserTypeEnum.ClinicalResearchCoordinator || t.UserTypeEnum == UserTypeEnum.SR).Select(t => new { UserTypeId = t.Id, t.UserTypeEnum }).ToList();
var sysUserTypeList = _usertypeRepository.Where(t => t.UserTypeEnum == UserTypeEnum.CRA || t.UserTypeEnum == UserTypeEnum.ClinicalResearchCoordinator ).Select(t => new { UserTypeId = t.Id, t.UserTypeEnum }).ToList();
var siteList = _trialSiteRepository.Where(t => t.TrialId == trialId && siteCodeList.Contains(t.TrialSiteCode)).Select(t => new { t.TrialSiteCode, t.SiteId }).ToList();
foreach (var item in excelList)
@ -1063,10 +1226,7 @@ namespace IRaCIS.Core.API.Controllers
item.UserTypeEnum = UserTypeEnum.CRA;
break;
case "SR":
item.UserTypeId = sysUserTypeList.FirstOrDefault(t => t.UserTypeEnum == UserTypeEnum.SR).UserTypeId;
item.UserTypeEnum = UserTypeEnum.SR;
break;
}

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@ -219,7 +219,7 @@
<param name="_noneDicomStudyRepository"></param>
<returns></returns>
</member>
<member name="M:IRaCIS.Core.API.Controllers.StudyController.UploadVisitCheckExcel(System.Guid)">
<member name="M:IRaCIS.Core.API.Controllers.StudyController.UploadVisitCheckExcel(System.Guid,IRaCIS.Core.Application.Helper.IOSSService)">
<summary>
一致性核查 excel上传 支持三种格式
</summary>

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@ -0,0 +1,194 @@
using Aliyun.OSS;
using IRaCIS.Core.Application.Contracts;
using IRaCIS.Core.Infrastructure;
using Microsoft.Extensions.Hosting;
using Microsoft.Extensions.Options;
using NPOI.HPSF;
using SharpCompress.Common;
using System;
using System.Collections.Generic;
using System.Drawing;
using System.IO;
using System.Linq;
using System.Security.AccessControl;
using System.Text;
using System.Threading.Tasks;
namespace IRaCIS.Core.Application.Helper
{
public class MinIOOptions
{
public string Endpoint { get; set; }
public string Port { get; set; }
public bool UseSSL { get; set; }
public string AccessKey { get; set; }
public string SecretKey { get; set; }
public string BucketName { get; set; }
}
public class AliyunOSSOptions
{
public string RegionId { get; set; }
public string AccessKeyId { get; set; }
public string AccessKeySecret { get; set; }
public string EndPoint { get; set; }
public string BucketName { get; set; }
public string RoleArn { get; set; }
public string Region { get; set; }
public string ViewEndpoint { get; set; }
}
public class ObjectStoreServiceOptions
{
public string ObjectStoreUse { get; set; }
public AliyunOSSOptions AliyunOSS { get; set; }
public MinIOOptions MinIO { get; set; }
}
public class ObjectStoreDTO
{
public string ObjectStoreUse { get; set; }
public AliyunOSSTempToken AliyunOSS { get; set; }
public MinIOOptions MinIO { get; set; }
}
public class AliyunOSSTempToken
{
public string AccessKeyId { get; set; }
public string AccessKeySecret { get; set; }
public string SecurityToken { get; set; }
public string Expiration { get; set; }
public string Region { get; set; }
public string BucketName { get; set; }
public string ViewEndpoint { get; set; }
}
public enum ObjectStoreUse
{
AliyunOSS = 0,
MinIO = 1,
AWS = 2,
}
public interface IOSSService
{
public string UploadToOSS(Stream fileStream, string oosFolderPath, string fileRealName);
public string UploadToOSS(string localFilePath, string oosFolderPath);
public void DownLoadFromOSS(string ossRelativePath, string localFilePath);
}
public class OSSService : IOSSService
{
public AliyunOSSOptions _OSSConfig { get; set; }
public OssClient _ossClient { get; set; }
public OSSService(IOptionsMonitor<AliyunOSSOptions> options)
{
var ossOptions = options.CurrentValue;
_OSSConfig = ossOptions;
_ossClient = new OssClient(_OSSConfig.EndPoint, _OSSConfig.AccessKeyId, _OSSConfig.AccessKeySecret);
}
public string UploadToOSS(Stream fileStream, string oosFolderPath,string fileRealName)
{
var ossRelativePath = oosFolderPath + "/" + fileRealName;
try
{
using (var memoryStream = new MemoryStream())
{
fileStream.Seek(0, SeekOrigin.Begin);
fileStream.CopyTo(memoryStream);
memoryStream.Seek(0, SeekOrigin.Begin);
// 上传文件
var result = _ossClient.PutObject(_OSSConfig.BucketName, ossRelativePath, memoryStream);
}
return ossRelativePath;
}
catch (Exception ex)
{
throw new BusinessValidationFailedException("oss上传失败" + ex.Message);
}
}
public string UploadToOSS(string localFilePath, string oosFolderPath)
{
var localFileName = Path.GetFileName(localFilePath);
var ossRelativePath = oosFolderPath + "/" + localFileName;
try
{
// 上传文件
var result = _ossClient.PutObject(_OSSConfig.BucketName, ossRelativePath, localFilePath);
return ossRelativePath;
}
catch (Exception ex)
{
throw new BusinessValidationFailedException("oss上传失败" + ex.Message);
}
}
public void DownLoadFromOSS(string ossRelativePath, string localFilePath)
{
try
{
var result = _ossClient.GetObject(_OSSConfig.BucketName, ossRelativePath);
// 将下载的文件流保存到本地文件
using (var fs = File.OpenWrite(localFilePath))
{
result.Content.CopyTo(fs);
fs.Close();
}
}
catch (Exception ex)
{
throw new BusinessValidationFailedException("oss下载失败!" + ex.Message);
}
}
}
}

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@ -19,7 +19,7 @@ namespace IRaCIS.Core.Application.Image.QA
private readonly IRepository<ClinicalDataTrialSet> _clinicalDataTrialSet;
private readonly IRepository<TrialQCQuestionAnswer> _trialQCQuestionAnswerRepository;
private readonly IRepository<TrialQCQuestion> _trialQCQuestionRepository;
private readonly IRepository<UserUploadFile> _UserUploadFileRepository;
private readonly IRepository<InspectionFile> _consistencyCheckFileRepository;
private IReadingImageTaskService _IReadingImageTaskService;
@ -30,7 +30,7 @@ namespace IRaCIS.Core.Application.Image.QA
IRepository<TrialQCQuestionAnswer> trialQCQuestionAnswerRepository,
IRepository<TrialQCQuestion> trialQCQuestionRepository,
IReadingImageTaskService IReadingImageTaskService,
IRepository<UserUploadFile> UserUploadFileRepository
IRepository<InspectionFile> consistencyCheckFileRepository
)
{
this._IReadingImageTaskService = IReadingImageTaskService;
@ -851,8 +851,8 @@ namespace IRaCIS.Core.Application.Image.QA
[HttpPost]
public async Task<PageOutput<GetUserUploadFileDto>> GetUserUploadFile(GetUserUploadFileInDto indto)
{
var query = _repository.Where<UserUploadFile>(t => t.TrialId == indto.TrialId)
.ProjectTo<GetUserUploadFileDto>(_mapper.ConfigurationProvider);
var query = _repository.Where<InspectionFile>(t => t.TrialId == indto.TrialId)
.ProjectTo<GetConsistencyCheckFileDto>(_mapper.ConfigurationProvider);
return await query.ToPagedListAsync(indto.PageIndex, indto.PageSize, "CreateTime", false);
}

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@ -494,7 +494,7 @@ namespace IRaCIS.Core.Application.Service
;
// 一致性核查文件
CreateMap<UserUploadFile, GetUserUploadFileDto>()
CreateMap<InspectionFile, GetConsistencyCheckFileDto>()
.ForMember(d => d.CreateUserName, u => u.MapFrom(t => t.User.FirstName + "/" + t.User.LastName));

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@ -311,6 +311,10 @@ namespace IRaCIS.Application.Services
await _repository.BatchDeleteAsync<CriterionNidusTrial>(o => o.TrialReadingCriterion.TrialId == trialId);
await _repository.BatchDeleteAsync<CheckChallengeDialog>(o => o.SubjectVisit.TrialId == trialId);
await _repository.BatchDeleteAsync<ClinicalDataTrialSet>(o => o.TrialId == trialId);
await _repository.BatchDeleteAsync<InspectionFile>(o => o.TrialId == trialId);
await _repository.BatchDeleteAsync<CriterionNidusSystem>(o => o.TrialReadingCriterion.TrialId == trialId);
await _repository.BatchDeleteAsync<DataInspection>(o => o.TrialId == trialId);
await _repository.BatchDeleteAsync<DicomStudy>(t => t.TrialId == trialId);
await _repository.BatchDeleteAsync<StudyMonitor>(t => t.TrialId == trialId);

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@ -7,18 +7,15 @@ namespace IRaCIS.Core.Domain.Models
///<summary>
/// 一致性核查文件
///</summary>
[Table("UserUploadFile")]
public class UserUploadFile : Entity, IAuditAdd
[Table("InspectionFile")]
public class InspectionFile : Entity, IAuditAdd
{
/// <summary>
/// 文件名称
/// </summary>
public string FileName { get; set; }
/// <summary>
/// 文件路径
/// </summary>
public string FilePath { get; set; }
/// <summary>
/// 相对路径