public List<aim_dotnet.Annotation> getAnnotationOfAnnotationInfoList(AIMQueryParameters queryParameters)
{
var annoStr = getAnnotationOfAnnotationInfo(queryParameters);
if (annoStr == null)
return null;
var annotations = new List<aim_dotnet.Annotation>();
var xmlModel = new aim_dotnet.XmlModel();
foreach (var str in annoStr)
{
var annoAnnotation = xmlModel.ReadAnnotationFromXmlString(str) as aim_dotnet.AnnotationOfAnnotation;
if (annoAnnotation != null)
annotations.Add(annoAnnotation);
}
return annotations;
}
public List <aim_dotnet.Annotation> getAnnotationOfAnnotationInfoList(AIMQueryParameters queryParameters)
{
var annoStr = getAnnotationOfAnnotationInfo(queryParameters);
if (annoStr == null)
{
return(null);
}
var annotations = new List <aim_dotnet.Annotation>();
var xmlModel = new aim_dotnet.XmlModel();
foreach (var str in annoStr)
{
var annoAnnotation = xmlModel.ReadAnnotationFromXmlString(str) as aim_dotnet.AnnotationOfAnnotation;
if (annoAnnotation != null)
{
annotations.Add(annoAnnotation);
}
}
return(annotations);
}
private int SendAnnotationsInFolderToDataService(string folderName, string dataServiceUrl)
{
if (string.IsNullOrEmpty(folderName) || string.IsNullOrEmpty(dataServiceUrl))
{
Platform.Log(LogLevel.Error, "Trying to send queued annotations from an invalid folder ({0}) or to an invalid data service ({1})", folderName, dataServiceUrl);
return 0;
}
var folderPath = System.IO.Path.Combine(AimSettings.Default.AnnotationQueuesFolder, folderName);
if (!System.IO.Directory.Exists(folderPath))
return 0;
var sentCounter = 0;
try
{
var annotationFiles = System.IO.Directory.GetFiles(folderPath, "*.xml", System.IO.SearchOption.TopDirectoryOnly);
const int fileCountToSendAtOnce = 10;
for (var i = 0; i < (annotationFiles.Length + fileCountToSendAtOnce) / fileCountToSendAtOnce; i++)
{
var xmlAnnotations = new Dictionary<string, string>();
var readAnnotationFiles = new List<string>();
using (var xmlModel = new aim_dotnet.XmlModel())
{
var nextBatchMax = Math.Min((i + 1)*fileCountToSendAtOnce, annotationFiles.Length);
for (var j = i*fileCountToSendAtOnce; j < nextBatchMax; j++)
{
var annotationPathName = System.IO.Path.Combine(folderPath, annotationFiles[j]);
try
{
var annotations = xmlModel.ReadAnnotationsFromFile(annotationPathName);
try
{
foreach (var annotation in annotations)
{
xmlAnnotations.Add(annotation.UniqueIdentifier, xmlModel.WriteAnnotationToXmlString(annotation));
}
readAnnotationFiles.Add(annotationPathName);
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Failed to convert annotation to XML string. File: {0}", annotationPathName);
xmlAnnotations.Clear();
}
finally
{
annotations.Clear();
}
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Failed to read annotation file from queue: {0}", annotationPathName);
}
}
}
if (xmlAnnotations.Count > 0)
{
try
{
AIMTCGAService.AIMTCGASubmit.sendAIMTCGAAnnotation(new List<string>(xmlAnnotations.Values).ToArray());
sentCounter += xmlAnnotations.Count;
Debug.Assert(readAnnotationFiles.Count <= xmlAnnotations.Count, "There are more files to delete than read annoations");
xmlAnnotations.Clear();
foreach (var readAnnotationFile in readAnnotationFiles)
{
try
{
System.IO.File.Delete(readAnnotationFile);
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Failed to delete sent annoation file ({0}). The file will be send again.", readAnnotationFile);
}
}
readAnnotationFiles.Clear();
}
catch (Exception ex)
{
Platform.Log(LogLevel.Debug, ex, "Failed to send annotations to the AIM Data Serice ({0}).", dataServiceUrl);
break;
}
}
}
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Failed to send files from {0} to server {1}", folderPath, dataServiceUrl);
}
return sentCounter;
}
public static bool WriteXmlAnnotationToFile(aim_dotnet.Annotation annotation, string filePathName)
{
var xmlModel = new aim_dotnet.XmlModel();
try
{
xmlModel.WriteAnnotationToFile(annotation, filePathName);
return true;
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Failed to save annotation to file \"{0}\"", filePathName);
}
finally
{
xmlModel = null;
}
return false;
}
public static string[] WriteXmlAnnotationsToFolder(List<aim_dotnet.Annotation> annotations, string folderPath)
{
var savedFileNames = new List<string>();
var xmlModel = new aim_dotnet.XmlModel();
foreach (var annotation in annotations)
{
string xmlFileName = null;
var fileName = string.IsNullOrEmpty(annotation.UniqueIdentifier) ? System.IO.Path.GetRandomFileName() : annotation.UniqueIdentifier;
try
{
xmlFileName = System.IO.Path.ChangeExtension(System.IO.Path.Combine(folderPath, fileName), "xml");
xmlModel.WriteAnnotationToFile(annotation, xmlFileName);
savedFileNames.Add(xmlFileName);
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Failed to save annotation to file \"{0}\"", xmlFileName);
try
{
if (!string.IsNullOrEmpty(xmlFileName))
System.IO.File.Delete(xmlFileName);
}
catch (Exception)
{
}
}
}
xmlModel = null;
return savedFileNames.ToArray();
}
private int SendAnnotationsInFolderToDataService(string folderName, string dataServiceUrl)
{
if (string.IsNullOrEmpty(folderName) || string.IsNullOrEmpty(dataServiceUrl))
{
Platform.Log(LogLevel.Error, "Trying to send queued annotations from an invalid folder ({0}) or to an invalid data service ({1})", folderName, dataServiceUrl);
return(0);
}
var folderPath = System.IO.Path.Combine(AimSettings.Default.AnnotationQueuesFolder, folderName);
if (!System.IO.Directory.Exists(folderPath))
{
return(0);
}
var sentCounter = 0;
try
{
var annotationFiles = System.IO.Directory.GetFiles(folderPath, "*.xml", System.IO.SearchOption.TopDirectoryOnly);
const int fileCountToSendAtOnce = 10;
for (var i = 0; i < (annotationFiles.Length + fileCountToSendAtOnce) / fileCountToSendAtOnce; i++)
{
var xmlAnnotations = new Dictionary <string, string>();
var readAnnotationFiles = new List <string>();
using (var xmlModel = new aim_dotnet.XmlModel())
{
var nextBatchMax = Math.Min((i + 1) * fileCountToSendAtOnce, annotationFiles.Length);
for (var j = i * fileCountToSendAtOnce; j < nextBatchMax; j++)
{
var annotationPathName = System.IO.Path.Combine(folderPath, annotationFiles[j]);
try
{
var annotations = xmlModel.ReadAnnotationsFromFile(annotationPathName);
try
{
foreach (var annotation in annotations)
{
xmlAnnotations.Add(annotation.UniqueIdentifier, xmlModel.WriteAnnotationToXmlString(annotation));
}
readAnnotationFiles.Add(annotationPathName);
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Failed to convert annotation to XML string. File: {0}", annotationPathName);
xmlAnnotations.Clear();
}
finally
{
annotations.Clear();
}
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Failed to read annotation file from queue: {0}", annotationPathName);
}
}
}
if (xmlAnnotations.Count > 0)
{
try
{
AIMTCGAService.AIMTCGASubmit.sendAIMTCGAAnnotation(new List <string>(xmlAnnotations.Values).ToArray());
sentCounter += xmlAnnotations.Count;
Debug.Assert(readAnnotationFiles.Count <= xmlAnnotations.Count, "There are more files to delete than read annoations");
xmlAnnotations.Clear();
foreach (var readAnnotationFile in readAnnotationFiles)
{
try
{
System.IO.File.Delete(readAnnotationFile);
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Failed to delete sent annoation file ({0}). The file will be send again.", readAnnotationFile);
}
}
readAnnotationFiles.Clear();
}
catch (Exception ex)
{
Platform.Log(LogLevel.Debug, ex, "Failed to send annotations to the AIM Data Serice ({0}).", dataServiceUrl);
break;
}
}
}
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Failed to send files from {0} to server {1}", folderPath, dataServiceUrl);
}
return(sentCounter);
}
// Writes all annotations to a given folder. Returns number of annotations written.
public static int WriteXmlAnnotationsToFolder(List<aim_dotnet.Annotation> annotations, string folderPath)
{
int cnt = 0;
aim_dotnet.XmlModel xmlModel = new aim_dotnet.XmlModel();
foreach (aim_dotnet.Annotation annotation in annotations)
{
string tempFileNameXml = null;
string fileName = string.IsNullOrEmpty(annotation.UniqueIdentifier) ? System.IO.Path.GetRandomFileName() : annotation.UniqueIdentifier;
try
{
tempFileNameXml = System.IO.Path.ChangeExtension(System.IO.Path.Combine(folderPath, fileName), "xml");
xmlModel.WriteAnnotationToFile(annotation, tempFileNameXml);
cnt++;
}
catch (Exception ex)
{
Platform.Log(LogLevel.Error, ex, "Failed to save annotation to file \"{0}\"", tempFileNameXml);
try
{
if (!string.IsNullOrEmpty(tempFileNameXml))
System.IO.File.Delete(tempFileNameXml);
}
catch (Exception)
{
}
}
}
xmlModel = null;
return cnt;
}
