624 lines
26 KiB
C#
624 lines
26 KiB
C#
using EasyCaching.Core;
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using FellowOakDicom;
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using IRaCIS.Core.Application.Contracts;
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using IRaCIS.Core.Application.Filter;
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using IRaCIS.Core.Application.Helper;
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using IRaCIS.Core.Application.Service.ImageAndDoc.DTO;
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using IRaCIS.Core.Domain.Share;
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using IRaCIS.Core.Infrastructure;
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using MassTransit;
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using MathNet.Numerics;
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using Medallion.Threading;
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using Microsoft.AspNetCore.Mvc;
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using System;
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using System.Collections.Generic;
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using System.IO.Compression;
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using System.Linq;
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using System.Text;
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using System.Threading.Tasks;
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namespace IRaCIS.Core.Application.Service.ImageAndDoc
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{
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public interface IDownloadAndUploadService
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{
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Task PackageAndAnonymizImage(Guid trialId, Guid subjectVisitId, bool isAnonymize = true);
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}
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[ApiExplorerSettings(GroupName = "Trial")]
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public class DownloadAndUploadService : BaseService, IDownloadAndUploadService
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{
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private readonly IEasyCachingProvider _provider;
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private readonly IRepository<SystemAnonymization> _systemAnonymizationRepository;
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private readonly IRepository<SubjectVisit> _subjectVisitRepository;
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private readonly IOSSService _oSSService;
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private readonly IRepository<StudyMonitor> _studyMonitorRepository;
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private readonly IDistributedLockProvider _distributedLockProvider;
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public DownloadAndUploadService(IEasyCachingProvider provider, IRepository<SystemAnonymization> systemAnonymizationRepository, IRepository<SubjectVisit> subjectVisitRepository, IOSSService oSSService,
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IRepository<StudyMonitor> studyMonitorRepository, IDistributedLockProvider distributedLockProvider)
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{
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_systemAnonymizationRepository = systemAnonymizationRepository;
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_subjectVisitRepository = subjectVisitRepository;
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_oSSService = oSSService;
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_studyMonitorRepository = studyMonitorRepository;
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_distributedLockProvider = distributedLockProvider;
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_provider = provider;
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}
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/// <summary>
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/// 获取该受试者任务上传列表（展示已上传情况）
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/// </summary>
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/// <param name="subjectId"></param>
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/// <returns></returns>
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public async Task<IResponseOutput<List<SubjectImageUploadDTO>>> GetSubjectImageUploadList(Guid subjectId)
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{
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var query = _repository.Where<VisitTask>(t => t.SubjectId == subjectId && t.SourceSubjectVisitId != null && t.DoctorUserId == _userInfo.Id)
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.Select(u => new SubjectImageUploadDTO()
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{
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VisitTaskId = u.Id,
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SubejctId = u.SubjectId,
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SiteId=u.Subject.SiteId,
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CriterionModalitys= u.TrialReadingCriterion.CriterionModalitys,
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SubjectCode = u.IsSelfAnalysis == true ? u.Subject.Code : u.BlindSubjectCode,
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TaskBlindName = u.TaskBlindName,
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TaskName = u.TaskName,
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SourceSubjectVisitId = u.SourceSubjectVisitId,
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PackState = u.SourceSubjectVisit.PackState,
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OrginalStudyList = u.SourceSubjectVisit.StudyList.Select(t => new StudyBasicInfo()
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{
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Id = t.Id,
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StudyInstanceUid = t.StudyInstanceUid,
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ModalityForEdit = t.ModalityForEdit,
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BodyPartExamined = t.BodyPartExamined,
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BodyPartForEdit = t.BodyPartForEdit,
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StudyCode = t.StudyCode,
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StudyTime = t.StudyTime,
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Description = t.Description,
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InstanceCount = t.InstanceCount,
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Modalities = t.Modalities,
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SeriesCount = t.SeriesCount,
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}).ToList(),
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UploadStudyList = u.TaskStudyList.Select(t => new StudyBasicInfo()
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{
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Id = t.Id,
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StudyInstanceUid = t.StudyInstanceUid,
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ModalityForEdit = t.ModalityForEdit,
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BodyPartExamined = t.BodyPartExamined,
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BodyPartForEdit = t.BodyPartForEdit,
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StudyCode = t.StudyCode,
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StudyTime = t.StudyTime,
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Description = t.Description,
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InstanceCount = t.InstanceCount,
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Modalities = t.Modalities,
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SeriesCount = t.SeriesCount,
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SopInstanceUidList = t.InstanceList.Select(t => t.SopInstanceUid).ToList(),
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}).ToList()
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})
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;
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var list = await query.ToListAsync();
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return ResponseOutput.Ok(list);
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}
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private void SpecialArchiveStudyDeal(TaskStudy study)
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{
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#region 特殊逻辑
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if (study.PatientBirthDate.Length == 8)
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{
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study.PatientBirthDate = $"{study.PatientBirthDate[0]}{study.PatientBirthDate[1]}{study.PatientBirthDate[2]}{study.PatientBirthDate[3]}-{study.PatientBirthDate[4]}{study.PatientBirthDate[5]}-{study.PatientBirthDate[6]}{study.PatientBirthDate[7]}";
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}
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var dicModalityList = _repository.Where<Dictionary>(t => t.Code == "Modality").SelectMany(t => t.ChildList.Select(c => c.Value)).ToList();
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var modality = study.Modalities;
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var modalityForEdit = dicModalityList.Contains(modality) ? modality : String.Empty;
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if (modality == "MR")
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{
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modalityForEdit = "MRI";
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}
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if (modality == "PT")
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{
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modalityForEdit = "PET";
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}
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if (modality == "PT、CT")
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{
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modalityForEdit = "PET-CT";
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}
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study.ModalityForEdit = modalityForEdit;
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#endregion
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}
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[TypeFilter(typeof(TrialResourceFilter), Arguments = new object[] { "AfterStopCannNotOpt" })]
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public async Task<IResponseOutput> PreArchiveDicomStudy(PriArchiveTaskStudyCommand preArchiveStudyCommand)
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{
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var studyMonitor = new StudyMonitor()
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{
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TrialId = preArchiveStudyCommand.TrialId,
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SubjectId = preArchiveStudyCommand.SubjectId,
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SubjectVisitId = preArchiveStudyCommand.SubjectVisitId,
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IsSuccess = false,
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UploadStartTime = DateTime.Now,
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IsDicom = true,
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IP = _userInfo.IP,
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IsDicomReUpload = preArchiveStudyCommand.IsDicomReUpload,
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FileSize = preArchiveStudyCommand.FileSize,
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FileCount = preArchiveStudyCommand.FileCount,
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};
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var addEntity = await _studyMonitorRepository.AddAsync(studyMonitor, true);
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return ResponseOutput.Ok(addEntity.Id);
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}
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[TypeFilter(typeof(TrialResourceFilter), Arguments = new object[] { "AfterStopCannNotOpt" })]
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public async Task<IResponseOutput> AddOrUpdateArchiveTaskStudy(TaskArchiveStudyCommand incommand)
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{
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#region 获取该subject 已生成任务的访视的检查
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var queryStudy = _repository.Where<VisitTask>(t => t.SubjectId == incommand.SubjectId && t.SourceSubjectVisitId != null && t.DoctorUserId == _userInfo.Id).Select(u => new
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{
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VisitTaskId = u.Id,
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SourceSubjectVisitId = u.SourceSubjectVisitId,
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OrginalStudyList = u.SourceSubjectVisit.StudyList.Select(t => new StudyBasicInfo()
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{
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Id = t.Id,
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StudyInstanceUid = t.StudyInstanceUid
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}).ToList(),
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});
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var studyList = await queryStudy.ToListAsync();
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var findOriginStudy = studyList.FirstOrDefault(c => c.OrginalStudyList.Any(t => t.StudyInstanceUid == incommand.Study.StudyInstanceUid));
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if (findOriginStudy == null)
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{
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return ResponseOutput.NotOk("该检查不属于该受试者，请核查");
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}
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#endregion
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var modalitys = string.Empty;
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try
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{
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var trialId = incommand.TrialId;
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var studyMonitor = await _studyMonitorRepository.FirstOrDefaultAsync(t => t.Id == incommand.StudyMonitorId);
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studyMonitor.UploadFinishedTime = DateTime.Now;
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studyMonitor.ArchiveFinishedTime = DateTime.Now;
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studyMonitor.FailedFileCount = incommand.FailedFileCount;
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studyMonitor.IsSuccess = incommand.FailedFileCount == 0;
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studyMonitor.RecordPath = incommand.RecordPath;
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//上传
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if (studyMonitor.IsDicomReUpload == false)
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{
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var study = _mapper.Map<TaskStudy>(incommand.Study);
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var @lock = _distributedLockProvider.CreateLock($"StudyCode");
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using (await @lock.AcquireAsync())
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{
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//查询数据库获取最大的Code 没有记录则为0
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var dbStudyCodeIntMax = _repository.Where<TaskStudy>(s => s.TrialId == trialId).Select(t => t.Code).DefaultIfEmpty().Max();
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//获取缓存中的值 并发的时候，需要记录，已被占用的值 这样其他线程在此占用的最大的值上递增
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var cacheMaxCodeInt = _provider.Get<int>($"{trialId}_{StaticData.CacheKey.StudyMaxCode}").Value;
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int currentNextCodeInt = cacheMaxCodeInt > dbStudyCodeIntMax ? cacheMaxCodeInt + 1 : dbStudyCodeIntMax + 1;
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study.Code = currentNextCodeInt;
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study.StudyCode = AppSettings.GetCodeStr(currentNextCodeInt, nameof(DicomStudy));
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_provider.Set<int>($"{trialId}_{StaticData.CacheKey.StudyMaxCode}", study.Code, TimeSpan.FromMinutes(30));
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}
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study.Id = IdentifierHelper.CreateGuid(incommand.Study.StudyInstanceUid, incommand.TrialId.ToString(), findOriginStudy.VisitTaskId.ToString());
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study.TrialId = incommand.TrialId;
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//study.SiteId = incommand.SiteId;
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study.SubjectId = incommand.SubjectId;
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study.VisitTaskId = findOriginStudy.VisitTaskId;
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//study.SubjectVisitId = incommand.SubjectVisitId;
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//特殊处理逻辑
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study.Modalities = string.Join("、", incommand.Study.SeriesList.Select(t => t.Modality).Distinct());
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SpecialArchiveStudyDeal(study);
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modalitys = study.Modalities;
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await _repository.AddAsync(study);
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studyMonitor.StudyId = study.Id;
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studyMonitor.StudyCode = study.StudyCode;
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foreach (var seriesItem in incommand.Study.SeriesList)
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{
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var series = _mapper.Map<TaskSeries>(seriesItem);
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series.Id = IdentifierHelper.CreateGuid(seriesItem.StudyInstanceUid, seriesItem.SeriesInstanceUid, incommand.TrialId.ToString(), findOriginStudy.VisitTaskId.ToString());
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series.StudyId = study.Id;
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series.TrialId = incommand.TrialId;
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//series.SiteId = incommand.SiteId;
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series.SubjectId = incommand.SubjectId;
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//series.SubjectVisitId = incommand.SubjectVisitId;
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series.VisitTaskId = findOriginStudy.VisitTaskId;
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//前端传递的数量不准，上传的时候，把失败的也加进来了，以实际数组的数字为准
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series.InstanceCount = seriesItem.InstanceList.Count;
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await _repository.AddAsync(series);
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foreach (var instanceItem in seriesItem.InstanceList)
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{
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var isntance = _mapper.Map<TaskInstance>(instanceItem);
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Guid instanceId = IdentifierHelper.CreateGuid(study.StudyInstanceUid, series.SeriesInstanceUid, isntance.SopInstanceUid, study.TrialId.ToString(), findOriginStudy.VisitTaskId.ToString());
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isntance.Id = instanceId;
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isntance.StudyId = study.Id;
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isntance.SeriesId = series.Id;
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isntance.TrialId = incommand.TrialId;
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//isntance.SiteId = incommand.SiteId;
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isntance.SubjectId = incommand.SubjectId;
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//isntance.SubjectVisitId = incommand.SubjectVisitId;
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isntance.VisitTaskId = findOriginStudy.VisitTaskId;
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await _repository.AddAsync(isntance);
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}
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}
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}
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else
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{
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var studyId = IdentifierHelper.CreateGuid(incommand.Study.StudyInstanceUid, incommand.TrialId.ToString()); ;
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var study = await _repository.Where<TaskStudy>().FirstOrDefaultAsync(t => t.Id == studyId);
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//重传的时候也要赋值检查Id
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studyMonitor.StudyId = study.Id;
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studyMonitor.StudyCode = study.StudyCode;
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//特殊处理逻辑
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study.Modalities = string.Join("、", incommand.Study.SeriesList.Select(t => t.Modality).Union(study.Modalities.Split("、", StringSplitOptions.RemoveEmptyEntries)).Distinct());
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SpecialArchiveStudyDeal(study);
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modalitys = study.Modalities;
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// 少了整个序列
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//某个序列下少了instance
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foreach (var seriesItem in incommand.Study.SeriesList)
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{
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var seriesId = IdentifierHelper.CreateGuid(seriesItem.StudyInstanceUid, seriesItem.SeriesInstanceUid, trialId.ToString(), findOriginStudy.VisitTaskId.ToString());
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TaskSeries dicomSeries = await _repository.FirstOrDefaultAsync<TaskSeries>(t => t.Id == seriesId);
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//判断重复
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if (dicomSeries == null)
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{
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var series = _mapper.Map<TaskSeries>(seriesItem);
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series.Id = seriesId;
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series.StudyId = study.Id;
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series.TrialId = incommand.TrialId;
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//series.SiteId = incommand.SiteId;
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series.SubjectId = incommand.SubjectId;
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//series.SubjectVisitId = incommand.SubjectVisitId;
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dicomSeries = await _repository.AddAsync(series);
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//新的序列 那么 检查的序列数量+1
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study.SeriesCount += 1;
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}
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else
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{
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//该序列掉了instance
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dicomSeries.InstanceCount += seriesItem.InstanceList.Count;
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}
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foreach (var instanceItem in seriesItem.InstanceList)
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{
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var insntance = _mapper.Map<TaskInstance>(instanceItem);
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insntance.Id = IdentifierHelper.CreateGuid(insntance.StudyInstanceUid, insntance.SeriesInstanceUid, insntance.SopInstanceUid, trialId.ToString(), findOriginStudy.VisitTaskId.ToString());
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insntance.StudyId = study.Id;
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insntance.SeriesId = dicomSeries.Id;
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insntance.TrialId = incommand.TrialId;
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//insntance.SiteId = incommand.SiteId;
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insntance.SubjectId = incommand.SubjectId;
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insntance.VisitTaskId = findOriginStudy.VisitTaskId;
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await _repository.AddAsync(insntance);
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}
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// 不管是新的序列 还是 该序列 掉了Instance 重传的时候 检查的instance 数量都会增加
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study.InstanceCount += seriesItem.InstanceList.Count;
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}
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}
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var @lock2 = _distributedLockProvider.CreateLock($"StudyCommit");
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using (await @lock2.AcquireAsync())
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{
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await _repository.SaveChangesAsync();
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}
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}
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catch (Exception ex)
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{
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return ResponseOutput.NotOk(ex.Message);
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}
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finally
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{
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_provider.Remove($"StudyUid_{incommand.TrialId}_{incommand.Study.StudyInstanceUid}");
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}
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return ResponseOutput.Ok(modalitys);
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}
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[HttpDelete]
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public async Task<IResponseOutput> DeleteTaskStudy(Guid visitTaskId)
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{
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await _repository.BatchDeleteAsync<TaskStudy>(t => t.VisitTaskId == visitTaskId);
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await _repository.BatchDeleteAsync<TaskSeries>(t => t.VisitTaskId == visitTaskId);
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await _repository.BatchDeleteAsync<TaskInstance>(t => t.VisitTaskId == visitTaskId);
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return ResponseOutput.Ok();
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}
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/// <summary>
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/// 打包和匿名化影像 默认是匿名化打包，也可以不匿名化打包
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/// </summary>
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/// <param name="trialId"></param>
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/// <param name="subjectVisitId"></param>
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/// <param name="isAnonymize"></param>
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/// <returns></returns>
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public async Task<IResponseOutput> RequestPackageAndAnonymizImage(Guid trialId, Guid subjectVisitId, bool isAnonymize = true)
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{
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var subjectVisit = await _subjectVisitRepository.FirstOrDefaultAsync(t => t.Id == subjectVisitId);
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if (subjectVisit.PackState == PackState.WaitPack)
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{
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HangfireJobHelper.NotImmediatelyOnceOnlyJob<IDownloadAndUploadService>(t => t.PackageAndAnonymizImage(trialId, subjectVisitId, isAnonymize), TimeSpan.FromSeconds(1));
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subjectVisit.PackState = PackState.Packing;
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await _subjectVisitRepository.SaveChangesAsync();
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}
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return ResponseOutput.Ok(subjectVisit.VisitImageZipPath);
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}
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/// <summary>
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/// 后台任务调用，前端忽略该接口
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/// </summary>
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/// <param name="trialId"></param>
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/// <param name="subjectVisitId"></param>
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/// <param name="isAnonymize"></param>
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/// <returns></returns>
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public async Task PackageAndAnonymizImage(Guid trialId, Guid subjectVisitId, bool isAnonymize = true)
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{
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var subjectVisit = await _subjectVisitRepository.FirstOrDefaultAsync(t => t.Id == subjectVisitId);
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try
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{
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var addOrUpdateFixedFieldList = new List<SystemAnonymization>();
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var ircFieldList = new List<SystemAnonymization>();
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if (isAnonymize)
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{
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var systemAnonymizationList = _systemAnonymizationRepository.Where(t => t.IsEnable).ToList();
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addOrUpdateFixedFieldList = systemAnonymizationList.Where(t => t.IsFixed).ToList();
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ircFieldList = systemAnonymizationList.Where(t => t.IsFixed == false).ToList();
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}
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var subjectAndVisitInfo = _subjectVisitRepository.Where(t => t.Id == subjectVisitId).Select(t => new { SubjectCode = t.Subject.Code, t.Trial.TrialCode, t.VisitNum }).FirstOrDefault();
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var query = from sv in _subjectVisitRepository.Where(t => t.Id == subjectVisitId)
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select new
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{
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SubjectCode = sv.Subject.Code,
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VisitName = sv.VisitName,
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StudyList = sv.StudyList.Select(u => new
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{
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u.PatientId,
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u.StudyTime,
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u.StudyCode,
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SeriesList = u.SeriesList.Select(z => new
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{
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z.Modality,
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InstancePathList = z.DicomInstanceList.Select(k => new
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{
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k.Path
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})
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})
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})
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};
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var info = query.FirstOrDefault();
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if (info != null)
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{
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// 创建一个临时文件夹来存放文件
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string tempFolderPath = Path.Combine(Directory.GetCurrentDirectory(), $"DownloadTemp_{NewId.NextGuid()}");
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Directory.CreateDirectory(tempFolderPath);
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|
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// 遍历查询结果
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foreach (var studyInfo in info.StudyList)
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{
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|
// 遍历 Series
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|
foreach (var seriesInfo in studyInfo.SeriesList)
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|
{
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string studyFolderPath = Path.Combine(tempFolderPath, $"{info.SubjectCode}_{info.VisitName}", $"{studyInfo.StudyCode}_{studyInfo.StudyTime?.ToString("yyyy-MM-dd")}_{seriesInfo.Modality}");
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// 创建 影像 文件夹
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Directory.CreateDirectory(studyFolderPath);
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|
|
|
// 遍历 InstancePathList
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|
foreach (var instanceInfo in seriesInfo.InstancePathList)
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|
{
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|
// 复制文件到相应的文件夹
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|
string destinationPath = Path.Combine(studyFolderPath, Path.GetFileName(instanceInfo.Path));
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|
|
|
//下载到当前目录
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|
await _oSSService.DownLoadFromOSSAsync(instanceInfo.Path, destinationPath);
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|
|
|
#region 匿名化逻辑
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|
|
|
|
|
if (isAnonymize)
|
|
{
|
|
DicomFile dicomFile = await DicomFile.OpenAsync(destinationPath, Encoding.Default);
|
|
|
|
DicomDataset dataset = dicomFile.Dataset;
|
|
|
|
foreach (var item in addOrUpdateFixedFieldList)
|
|
{
|
|
|
|
var dicomTag = new DicomTag(Convert.ToUInt16(item.Group, 16), Convert.ToUInt16(item.Element, 16));
|
|
|
|
dataset.AddOrUpdate(dicomTag, item.ReplaceValue);
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|
}
|
|
|
|
foreach (var item in ircFieldList)
|
|
{
|
|
|
|
var dicomTag = new DicomTag(Convert.ToUInt16(item.Group, 16), Convert.ToUInt16(item.Element, 16));
|
|
|
|
if (dicomTag == DicomTag.ClinicalTrialProtocolID)
|
|
{
|
|
dataset.AddOrUpdate(dicomTag, subjectAndVisitInfo.TrialCode);
|
|
|
|
}
|
|
if (dicomTag == DicomTag.ClinicalTrialSiteID)
|
|
{
|
|
//dataset.AddOrUpdate(dicomTag, subjectAndVisitInfo.TrialSiteCode);
|
|
|
|
}
|
|
if (dicomTag == DicomTag.ClinicalTrialSubjectID)
|
|
{
|
|
dataset.AddOrUpdate(dicomTag, subjectAndVisitInfo.SubjectCode);
|
|
|
|
}
|
|
if (dicomTag == DicomTag.ClinicalTrialTimePointID)
|
|
{
|
|
dataset.AddOrUpdate(dicomTag, subjectAndVisitInfo.VisitNum.ToString());
|
|
|
|
}
|
|
if (dicomTag == DicomTag.PatientID)
|
|
{
|
|
dataset.AddOrUpdate(dicomTag, subjectAndVisitInfo.TrialCode + "_" + subjectAndVisitInfo.SubjectCode);
|
|
|
|
}
|
|
|
|
}
|
|
}
|
|
#endregion
|
|
}
|
|
}
|
|
}
|
|
|
|
var zipPath = Path.Combine(Directory.GetCurrentDirectory(), $"{info.SubjectCode}_{info.VisitName}_ImageStudy.zip");
|
|
|
|
ZipFile.CreateFromDirectory(tempFolderPath, zipPath);
|
|
|
|
//上传到Oss
|
|
var relativePath = await _oSSService.UploadToOSSAsync(zipPath, $"download_zip", false);
|
|
|
|
|
|
//subjectVisit.PackState = PackState.Packed;
|
|
//subjectVisit.VisitImageZipPath = relativePath;
|
|
//await _subjectVisitRepository.SaveChangesAsync();
|
|
await _subjectVisitRepository.BatchUpdateNoTrackingAsync(t => t.Id == subjectVisitId, u => new SubjectVisit() { PackState = PackState.Packed, VisitImageZipPath = relativePath });
|
|
|
|
|
|
//清理文件夹
|
|
Directory.Delete(tempFolderPath, true);
|
|
File.Delete(zipPath);
|
|
|
|
}
|
|
}
|
|
catch (Exception ex)
|
|
{
|
|
await _subjectVisitRepository.BatchUpdateNoTrackingAsync(t => t.Id == subjectVisitId, u => new SubjectVisit() { PackState = PackState.WaitPack });
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
}
|
|
|
|
}
|
|
}
|