public bool ReadLastAcquiredFileDate(IAutoQCLogger logger, IProcessControl processControl)
{
logger.Log("Getting the acquisition date on the newest file imported into the Skyline document.", 1, 0);
var exeDir = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
if (exeDir == null)
{
logger.LogError("Cound not get path to the Skyline report file");
return(false);
}
var skyrFile = Path.Combine(exeDir, "FileAcquisitionTime.skyr");
var reportFile = Path.Combine(SkylineFileDir, "AcquisitionTimes.csv");
// Export a report from the given Skyline file
var args =
string.Format(
@" --in=""{0}"" --report-conflict-resolution=overwrite --report-add=""{1}"" --report-name=""{2}"" --report-file=""{3}""",
SkylineFilePath, skyrFile, "AcquisitionTimes", reportFile);
var procInfo = new ProcessInfo(AutoQCForm.SkylineRunnerPath, AutoQCForm.SKYLINE_RUNNER, args, args);
if (!processControl.RunProcess(procInfo))
{
logger.LogError("Error getting the last acquired file date from the Skyline document.");
return(false);
}
// Read the exported report to get the last AcquiredTime for imported results in the Skyline doucment.
if (!File.Exists(reportFile))
{
logger.LogError("Could not find report outout {0}", reportFile);
return(false);
}
try
{
LastAcquiredFileDate = GetLastAcquiredFileDate(reportFile, logger);
if (!LastAcquiredFileDate.Equals(DateTime.MinValue))
{
logger.Log("The most recent acquisition date in the Skyline document is {0}", LastAcquiredFileDate);
}
else
{
logger.Log("The Skyline document does not have any imported results.");
}
}
catch (IOException e)
{
logger.LogError("Exception reading file {0}. Exception details are: ", reportFile);
logger.LogException(e);
return(false);
}
return(true);
}
public bool IsIntegrateAllChecked(IAutoQCLogger logger)
{
try
{
using (var stream = new FileStream(SkylineFilePath, FileMode.Open))
{
using (XmlReader reader = XmlReader.Create(stream))
{
reader.MoveToContent();
var done = false;
while (reader.Read() && !done)
{
switch (reader.NodeType)
{
case XmlNodeType.Element:
if (reader.Name == "transition_integration")
{
if (reader.MoveToAttribute("integrate_all"))
{
bool integrateAll;
Boolean.TryParse(reader.Value, out integrateAll);
return(integrateAll);
}
done = true;
}
break;
case XmlNodeType.EndElement:
if (reader.Name.Equals("transition_settings")) // We have come too far
{
done = true;
}
break;
}
}
}
}
}
catch (Exception e)
{
logger.LogError("Exception reading file {0}. Exception details are: ", SkylineFilePath);
logger.LogException(e);
return(false);
}
logger.LogError("Skyline documents with QC results should have the\"Integrate all\" setting, under the \"Settings\" menu, checked. Please save the Skyline document with \"Integrate all\" checked and restart AutoQC.");
return(false);
}
private bool ImportFile(DoWorkEventArgs e, ImportContext importContext, bool addToReimportQueueOnFailure = true)
{
var filePath = importContext.GetCurrentFile();
try
{
_fileWatcher.WaitForFileReady(filePath);
}
catch (FileStatusException fse)
{
if (!FileStatusException.DOES_NOT_EXIST.Equals(fse.Message))
{
_logger.LogError("File does not exist: {0}.", filePath);
}
else
{
_logger.LogException(fse);
}
// Put the file in the re-import queue
if (addToReimportQueueOnFailure)
{
_logger.Log("Adding file to re-import queue: {0}", filePath);
_fileWatcher.AddToReimportQueue(filePath);
}
return(false);
}
if (_worker.CancellationPending)
{
e.Result = CANCELLED;
return(false);
}
if (!ProcessOneFile(importContext))
{
if (addToReimportQueueOnFailure)
{
_logger.Log("Adding file to re-import queue: {0}", filePath);
_fileWatcher.AddToReimportQueue(filePath);
}
return(false);
}
return(true);
}
private static DateTime GetLastAcquiredFileDate(string reportFile, IAutoQCLogger logger)
{
var lastAcq = new DateTime();
using (var reader = new StreamReader(reportFile))
{
string line; // Read the column headers
var first = true;
while ((line = reader.ReadLine()) != null)
{
if (first)
{
first = false;
continue;
}
var values = line.Split(',');
if (values.Length == 3)
{
DateTime acqDate = new DateTime();
try
{
acqDate = DateTime.Parse(values[2]);
}
catch (Exception e)
{
logger.LogError("Error parsing acquired time from Skyline report: {0}", reportFile);
logger.LogException(e);
}
if (acqDate.CompareTo(lastAcq) == 1)
{
lastAcq = acqDate;
}
}
}
}
return(lastAcq);
}
public void PingPanoramaServer()
{
var panoramaServerUri = _panoramaSettingsTab.PanoramaServerUri;
if (_panoramaSettingsTab.IsSelected() && panoramaServerUri != null)
{
var panoramaClient = new WebPanoramaClient(panoramaServerUri);
try
{
var success = panoramaClient.PingPanorama(_panoramaSettingsTab.Settings.PanoramaFolder,
_panoramaSettingsTab.Settings.PanoramaUserEmail,
_panoramaSettingsTab.DecryptPassword(_panoramaSettingsTab.Settings.PanoramaPassword
));
if (success && _status != 1)
{
_logger.Log("Successfully pinged Panorama server.");
_status = 1;
}
if (!success && _status != 2)
{
_logger.LogErrorToFile("Error pinging Panorama server. Please confirm that " + panoramaServerUri +
" is running LabKey Server 16.1 or higher.");
_status = 2;
}
}
catch (Exception ex)
{
if (_status != 2)
{
_logger.LogError("Error pinging Panorama server " + panoramaServerUri);
_logger.LogException(ex);
_status = 2;
}
}
}
}
void OnFileWatcherError(ErrorEventArgs e)
{
_logger.LogError("There was an error watching the folder. {0}", e.GetException().Message);
_folderAvailable = false;
}
private static DateTime GetLastAcquiredFileDate(string reportFile, IAutoQCLogger logger)
{
var lastAcq = new DateTime();
using (var reader = new StreamReader(reportFile))
{
string line; // Read the column headers
var first = true;
while ((line = reader.ReadLine()) != null)
{
if (first)
{
first = false;
continue;
}
var values = line.Split(',');
if (values.Length == 3)
{
DateTime acqDate = new DateTime();
try
{
acqDate = DateTime.Parse(values[2]);
}
catch (Exception e)
{
logger.LogError("Error parsing acquired time from Skyline report: {0}", reportFile);
logger.LogException(e);
}
if (acqDate.CompareTo(lastAcq) == 1)
{
lastAcq = acqDate;
}
}
}
}
return lastAcq;
}
public bool ReadLastAcquiredFileDate(IAutoQCLogger logger, IProcessControl processControl)
{
logger.Log("Getting the acquisition date on the newest file imported into the Skyline document.", 1, 0);
var exeDir = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
if (exeDir == null)
{
logger.LogError("Cound not get path to the Skyline report file");
return false;
}
var skyrFile = Path.Combine(exeDir, "FileAcquisitionTime.skyr");
var reportFile = Path.Combine(SkylineFileDir, "AcquisitionTimes.csv");
// Export a report from the given Skyline file
var args =
string.Format(
@" --in=""{0}"" --report-conflict-resolution=overwrite --report-add=""{1}"" --report-name=""{2}"" --report-file=""{3}""",
SkylineFilePath, skyrFile, "AcquisitionTimes", reportFile);
var procInfo = new ProcessInfo(AutoQCForm.SkylineRunnerPath, AutoQCForm.SKYLINE_RUNNER, args, args);
if (!processControl.RunProcess(procInfo))
{
logger.LogError("Error getting the last acquired file date from the Skyline document.");
return false;
}
// Read the exported report to get the last AcquiredTime for imported results in the Skyline doucment.
if (!File.Exists(reportFile))
{
logger.LogError("Could not find report outout {0}", reportFile);
return false;
}
try
{
LastAcquiredFileDate = GetLastAcquiredFileDate(reportFile, logger);
if (!LastAcquiredFileDate.Equals(DateTime.MinValue))
{
logger.Log("The most recent acquisition date in the Skyline document is {0}", LastAcquiredFileDate);
}
else
{
logger.Log("The Skyline document does not have any imported results.");
}
}
catch (IOException e)
{
logger.LogError("Exception reading file {0}. Exception details are: ", reportFile);
logger.LogException(e);
return false;
}
return true;
}
public bool IsIntegrateAllChecked(IAutoQCLogger logger)
{
try
{
using (var stream = new FileStream(SkylineFilePath, FileMode.Open))
{
using (XmlReader reader = XmlReader.Create(stream))
{
reader.MoveToContent();
var done = false;
while (reader.Read() && !done)
{
switch (reader.NodeType)
{
case XmlNodeType.Element:
if (reader.Name == "transition_integration")
{
if (reader.MoveToAttribute("integrate_all"))
{
bool integrateAll;
Boolean.TryParse(reader.Value, out integrateAll);
return integrateAll;
}
done = true;
}
break;
case XmlNodeType.EndElement:
if (reader.Name.Equals("transition_settings")) // We have come too far
{
done = true;
}
break;
}
}
}
}
}
catch (Exception e)
{
logger.LogError("Exception reading file {0}. Exception details are: ", SkylineFilePath);
logger.LogException(e);
return false;
}
logger.LogError("Skyline documents with QC results should have the\"Integrate all\" setting, under the \"Settings\" menu, checked. Please save the Skyline document with \"Integrate all\" checked and restart AutoQC.");
return false;
}
public void LogError(string message, params Object[] args)
{
Logger.LogError(message, args);
}
private void LogError(string message, params Object[] args)
{
_logger.LogError(message, 1, 1, args);
}
