public override async Task <GNCloudFile> Insert(object entity)
{
LogUtil.LogMethod(logger, MethodBase.GetCurrentMethod());
GNCloudFile cloudFile = null;
try
{
cloudFile = (GNCloudFile)entity;
cloudFile.Id = Guid.NewGuid();
cloudFile.FolderPath = cloudFile.FileName.Replace(cloudFile.Description, "");
cloudFile.FileURL = GNCloudStorageService.GetObjectUrl(cloudFile.Volume, cloudFile.FileName);
cloudFile.CreateDateTime = DateTime.Now;
var tx = db.Database.BeginTransaction();
string sql = "INSERT INTO [gn].[GNCloudFiles] " +
"([Id],[FileURL],[Volume],[FileName],[FolderPath],[FileSize],[Description],[GNCloudFileCategoryId],[AWSRegionSystemName], " +
"[CreatedBy],[CreateDateTime]) " +
"VALUES " +
"(@Id, " +
"@FileURL, " +
"@Volume, " +
"@FileName, " +
"@FolderPath, " +
"@FileSize, " +
"@Description, " +
"@GNCloudFileCategoryId, " +
"@AWSRegionSystemName, " +
"@CreatedBy, " +
"@CreateDateTime)";
db.Database.ExecuteSqlCommand(sql,
new SqlParameter("@Id", cloudFile.Id),
new SqlParameter("@FileURL", cloudFile.FileURL),
new SqlParameter("@Volume", cloudFile.Volume),
new SqlParameter("@FileName", cloudFile.FileName),
new SqlParameter("@FolderPath", cloudFile.FolderPath),
new SqlParameter("@FileSize", cloudFile.FileSize),
new SqlParameter("@Description", cloudFile.Description),
new SqlParameter("@GNCloudFileCategoryId", cloudFile.GNCloudFileCategoryId),
new SqlParameter("@AWSRegionSystemName", cloudFile.AWSRegionSystemName),
new SqlParameter("@CreatedBy", cloudFile.CreatedBy),
new SqlParameter("@CreateDateTime", cloudFile.CreateDateTime.Value));
tx.Commit();
Guid sampleId = Guid.Empty;
Guid.TryParse(cloudFile.SampleId, out sampleId);
AssociateCloudFileToSample(cloudFile.Id, sampleId);
}
catch (Exception ex)
{
LogUtil.Error(logger, "Unable to insert Cloud File into Database.", ex);
}
return(cloudFile);
}
public void InitCloudServices(Guid AWSConfigId)
{
LogUtil.LogMethod(logger, MethodBase.GetCurrentMethod());
if (cloudStorageService == null)
{
cloudStorageService = new GNCloudStorageService();
cloudStorageService.AWSConfigId = AWSConfigId;
cloudStorageService.ConnectToCloudStorage();
}
}
public async Task <bool> ProcessQCMessage(NewSampleBatchStatus newSampleMessageStatus)
{
System.Console.WriteLine("QCQCQC " + newSampleMessageStatus.name);
try
{
GNCloudFileCategory fileCategory = db.GNCloudFileCategories.Where(a => a.Id == 1).FirstOrDefault();
string sampleName1 = newSampleMessageStatus.name;
string sampleName = sampleName1.Substring(0, sampleName1.IndexOf("_"));
//s3://sanford-fastq/151204_SN7001383_0164_AC7Y91ACXX/FASTQ/fastqc/AAA076960/AAA076960_S6_R2_001/
GNSample sample = db.GNSamples.Where(a => a.Name.Equals(sampleName) && a.IsReady == false).FirstOrDefault();
GNCloudStorageService st = new GNCloudStorageService();
string volume = "dev-gn-s3-01";
Guid fileId = Guid.NewGuid();
string folderPath = "fastq/" + sample.Id + "/" + fileId + "/";
string fastqFileName = folderPath + newSampleMessageStatus.name + ".fastq.gz";
string fileURL = "https://dev-gn-s3-01.s3.amazonaws.com/" + fastqFileName;
string originBucket = newSampleMessageStatus.filesBucket;
originBucket = originBucket.Replace("s3://", "");
originBucket = originBucket.Substring(0, originBucket.IndexOf("/")); //"sanford-fastq";
string QcOriginKey = newSampleMessageStatus.filesBucket;
QcOriginKey = QcOriginKey.Replace("s3://", "");
QcOriginKey = QcOriginKey.Substring(originBucket.Length + 1);
string FileDescription = newSampleMessageStatus.name + ".fastq.gz";
string fastqOriginKey = QcOriginKey.Substring(0, QcOriginKey.IndexOf("FASTQ/") + 5);
fastqOriginKey = fastqOriginKey + "/" + FileDescription;
QcOriginKey = QcOriginKey + "fastqc_report.html";
string destinationBucket = "dev-gn-s3-01/" + folderPath;
destinationBucket = "dev-gn-s3-01";
string QcFileName = folderPath + "fastqc_report.html";
string QcDestinationURL = "https://dev-gn-s3-01.s3.amazonaws.com/" + QcFileName;
st.CopyS3Object(originBucket, fastqOriginKey, destinationBucket, fastqFileName);
st.CopyS3Object(originBucket, QcOriginKey, destinationBucket, QcFileName);
GNCloudFile cloudFile = new GNCloudFile
{
Id = fileId,
GNCloudFileCategoryId = fileCategory.Id, //FASTQ
CloudFileCategory = fileCategory,
FileName = folderPath + fastqFileName,
FileURL = fileURL,
FolderPath = folderPath,
Volume = volume,
Description = fastqFileName,
FileSize = st.GetObjectSize(originBucket, fastqOriginKey),
AWSRegionSystemName = db.AWSRegions.FirstOrDefault().AWSRegionSystemName,
CreateDateTime = DateTime.Now,
CreatedBy = Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784"),
SampleId = sample.Id.ToString(),
PassedQC = (newSampleMessageStatus.isError.Equals("false")),
QcReportLocation = QcDestinationURL
};
db.GNCloudFiles.Add(cloudFile);
sample.CloudFiles.Add(cloudFile);
if (sample.CloudFiles.Count() == 2 && sample.CloudFiles.Where(a => a.PassedQC == false).Count() == 0)
{
sample.IsReady = true;
if (sample.GNNewSampleBatchSample.GNNewSampleBatch.AutoStartAnalysis)
{
GNAnalysisRequest analysis = sample.GNAnalysisRequestGNSamples.FirstOrDefault().GNAnalysisRequest;
AnalysisRequestService analysisService = new AnalysisRequestService(db);
GNContact userContact = db.GNContacts.Find(Guid.Parse("0750f896-e7d6-48d4-a1b9-007059f62784"));
await analysisService.StartAnalysis(userContact, analysis.Id);
}
}
db.SaveChanges();
}
catch (Exception e)
{
System.Console.WriteLine("***Unable to Update QC-COMPLETED status. " + e.Message + e.StackTrace + " **********************************");
Exception e2 = new Exception("Unable to Update QC-COMPLETED status.", e);
LogUtil.Warn(logger, e2.Message, e2);
return(false);
}
return(true);
}
public override GNAnalysisRequest DetailsOnLoad(GNAnalysisRequest analysisRequest)
{
EvalActionPrivileges(analysisRequest);
GNCloudStorageService st = new GNCloudStorageService();
// bool res = ((AnalysisRequestService)entityService).tempPersistStatus(analysisRequest);
auditResult = audit.LogEvent(UserContact, analysisRequest.Id, this.ENTITY, this.Request.UserHostAddress, EVENT_LOAD_DETAILS_UI);
//In case during the creation of result files all where left as type=6, review and update to the corredct types.
try
{
if (analysisRequest.AnalysisResult != null && analysisRequest.AnalysisResult.ResultFiles != null)
{
if (analysisRequest.AnalysisResult.ResultFiles.Where(a => a.GNCloudFileCategoryId == 6).Count() > 0)
{
((AnalysisRequestService)entityService).UpdateFileExtensions(analysisRequest.AnalysisResult);
}
}
}
catch (Exception e)
{
}
//Breadcrumbs Info
ViewBag.CurrentAnalysisRequest = analysisRequest;
GNProject Project = db.GNProjects.Where(a => a.Id.Equals(analysisRequest.GNProjectId)).FirstOrDefault();
ViewBag.CurrentProject = Project;
Guid TeamId = Project.Teams.FirstOrDefault().Id;
GNTeam Team = db.GNTeams.Where(a => a.Id.Equals(TeamId)).FirstOrDefault();
ViewBag.CurrentTeam = Team;
ViewBag.DateVCFSentToCartagenia = "NO";
try
{
string stsCartagenia = "CARTAGENIA";
GNAnalysisStatus statusCartagenia = db.GNAnalysisStatus.Where(a => a.GNAnalysisRequestId == analysisRequest.Id && a.Status == stsCartagenia).FirstOrDefault();
if (statusCartagenia != null)
{
ViewBag.DateVCFSentToCartagenia = TimeZoneInfo.ConvertTime((DateTime)statusCartagenia.CreateDateTime, analysisRequest.Project.Teams.FirstOrDefault().Organization.OrgTimeZoneInfo).ToString();
}
}
catch (Exception notFound)
{
ViewBag.DateVCFSentToCartagenia = "NO";
}
GNSettingsTemplate Template = db.GNOrganizations.Where(a => a.Id.Equals(Team.OrganizationId)).FirstOrDefault().GNSettingsTemplate;
ViewBag.TemplateConfigTertiaryFrequency = (Double.Parse(Template.GNSettingsTemplateConfigs.Where(a => a.GNSettingsTemplateField.Id.Equals("TERTIARY_FREQUENCY")).FirstOrDefault().Value) * 100);
ViewBag.TemplateConfigTertiarySplicingTreshold = Template.GNSettingsTemplateConfigs.Where(a => a.GNSettingsTemplateField.Id.Equals("TERTIARY_SPLICING_THRESHOLD")).FirstOrDefault().Value;
//2016.02.04 if the last status was error due to a corrupted file, attach the name of the file to the short status
ViewBag.CorruptFilenameFound = "NA";
if (analysisRequest.CurrentStatusShort.Equals("ERROR"))
{
string lastStatusReported = analysisRequest.AnalysisStatus.LastOrDefault().Message;
if (lastStatusReported.Contains("corrupt file"))
{
string corruptFileName = lastStatusReported.Substring(lastStatusReported.LastIndexOf('/') + 1);
ViewBag.CorruptFilenameFound = analysisRequest.CurrentStatusShort + ": corrupt file found " + corruptFileName;
}
}
if (Request["sampleId"] != null)
{
Guid sampleId = Guid.Parse(Request["sampleId"]);
GNSample Sample = db.GNSamples.Where(a => a.Id.Equals(sampleId)).FirstOrDefault();
ViewBag.CurrentSample = Sample;
}
return(base.DetailsOnLoad(analysisRequest));
}
public S3FileUploadController()
{
//instantiate services
CloudStorageService = new GNCloudStorageService();
}
