/// <summary>
/// Reads the input paths file
/// </summary>
/// <param name="path"></param>
/// <returns></returns>
public static InputAnalysisInfo ReadInputFile(string path)
{
var info = new InputAnalysisInfo();
var lines = File.ReadAllLines(path);
var readType = FileReadMode.None;
foreach (var line in lines)
{
var fixedLine = line.ToLower();
fixedLine = fixedLine.Trim();
var containsHeaderOpen = fixedLine.Contains("[");
var containsHeaderClose = fixedLine.Contains("]");
if (containsHeaderClose && containsHeaderOpen)
{
fixedLine = fixedLine.Replace(" ", "");
}
if (string.IsNullOrEmpty(fixedLine) || string.IsNullOrWhiteSpace(fixedLine))
{
continue;
}
// If wasModeChanged = true, then the current
// line is not data, but a tag to say change how read the next section.
var wasModeChanged = false;
switch (fixedLine)
{
case FILE_HEADER:
wasModeChanged = true;
readType = FileReadMode.Files;
break;
case DATABASE_HEADER:
wasModeChanged = true;
readType = FileReadMode.Database;
break;
case RAW_HEADER:
wasModeChanged = true;
readType = FileReadMode.RawFiles;
break;
case SCANS_HEADER:
wasModeChanged = true;
readType = FileReadMode.ScanFiles;
break;
case PEAKS_HEADER:
wasModeChanged = true;
readType = FileReadMode.Peaks;
break;
case SEQUENCE_HEADER:
wasModeChanged = true;
readType = FileReadMode.Sequence;
break;
default:
if (containsHeaderClose && containsHeaderOpen)
{
wasModeChanged = true;
readType = FileReadMode.Unknown;
throw new Exception(fixedLine + " is not a recognized data tag.");
}
wasModeChanged = false;
break;
}
if (!wasModeChanged)
{
switch (readType)
{
case FileReadMode.Files:
var baselineCheck = fixedLine.Split(BASELINE_INDICATOR);
if (baselineCheck.Length == 2 && !string.IsNullOrEmpty(baselineCheck[0]))
{
var newFile = new InputFile();
newFile.Path = baselineCheck[0];
newFile.FileType = InputFileType.Features;
info.BaselineFile = newFile;
info.Files.Add(newFile);
}
else if (!string.IsNullOrEmpty(baselineCheck[0]))
{
var newFile = new InputFile();
newFile.Path = baselineCheck[0];
newFile.FileType = InputFileType.Features;
info.Files.Add(newFile);
}
break;
case FileReadMode.Database:
var keys = fixedLine.Split('=');
if (keys.Length > 1)
{
keys[0] = keys[0].Replace('\t', ' ').Trim();
switch (keys[0].ToLower())
{
case "database":
info.Database.DatabaseFormat = MassTagDatabaseFormat.MassTagSystemSql;
info.Database.DatabaseName = keys[1];
break;
case "server":
info.Database.DatabaseFormat = MassTagDatabaseFormat.MassTagSystemSql;
info.Database.DatabaseServer = keys[1];
break;
case "sqlite":
info.Database.DatabaseFormat = MassTagDatabaseFormat.Sqlite;
info.Database.LocalPath = keys[1];
break;
case "metasample":
info.Database.DatabaseFormat = MassTagDatabaseFormat.DelimitedTextFile;
info.Database.LocalPath = keys[1];
break;
case "ims":
info.Database.DatabaseFormat = MassTagDatabaseFormat.SkipAlignment;
info.Database.LocalPath = keys[1];
break;
}
}
break;
case FileReadMode.RawFiles:
var rawFile = new InputFile();
rawFile.Path = fixedLine;
rawFile.FileType = InputFileType.Raw;
info.Files.Add(rawFile);
break;
case FileReadMode.ScanFiles:
var scanFile = new InputFile();
scanFile.Path = fixedLine;
scanFile.FileType = InputFileType.Scans;
info.Files.Add(scanFile);
break;
case FileReadMode.Unknown:
// do nothing!
break;
case FileReadMode.Sequence:
var sequenceFile = new InputFile();
sequenceFile.Path = fixedLine;
sequenceFile.FileType = InputFileType.Sequence;
info.Files.Add(sequenceFile);
break;
}
}
}
return(info);
}
/// <summary>
/// Loads factors from file or other.
/// </summary>
private void ConstructFactorInformation(InputAnalysisInfo analysisSetupInformation,
ObservableCollection<DatasetInformation> datasets, FeatureDataAccessProviders providers)
{
var mage = new MAGEFactorAdapter();
if (analysisSetupInformation.FactorFile == null)
{
Logger.PrintMessage("Loading Factor Information from DMS");
mage.LoadFactorsFromDMS(datasets, providers);
}
else
{
Logger.PrintMessage("Loading Factor Information from file: " + analysisSetupInformation.FactorFile);
mage.LoadFactorsFromFile(analysisSetupInformation.FactorFile, datasets, providers);
}
}
private void ImportFactors(AnalysisConfig config, bool databaseExists)
{
Logger.PrintMessage("Updating factors");
if (!databaseExists)
{
Logger.PrintMessage("The database you specified to extract data from does not exist.");
return;
}
// Create access to data.
var providers = SetupDataProviders(false);
if (providers == null)
{
Logger.PrintMessage("Could not create connection to database.");
return;
}
// Find all the datasets
var datasetsFactors = providers.DatasetCache.FindAll();
if (datasetsFactors == null || datasetsFactors.Count == 0)
{
Logger.PrintMessage("There are no datasets present in the current database.");
CleanupDataProviders();
return;
}
var info = new InputAnalysisInfo();
if (config.options.ContainsKey("-factors"))
{
Logger.PrintMessage("Factor file specified.");
var factorFile = config.options["-factors"][0];
info.FactorFile = factorFile;
}
ConstructFactorInformation(info, datasetsFactors.ToObservableCollection(), providers);
CleanupDataProviders();
}
/// <summary>
/// Constructs dataset infromation from the input analysis information.
/// </summary>
private void ConstructDatasetInformation(InputAnalysisInfo analysisSetupInformation, MultiAlignAnalysis analysis,
bool insertIntoDatabase)
{
// Create dataset information.
Logger.PrintMessage("Creating dataset and other input information.");
var datasets = DatasetInformation.CreateDatasetsFromInputFile(analysisSetupInformation.Files);
analysis.MetaData.Datasets.AddRange(datasets);
if (insertIntoDatabase)
{
m_config.Analysis.DataProviders.DatasetCache.AddAll(datasets);
}
}
/// <summary>
/// Constructs the baseline databases.
/// </summary>
private bool ConstructBaselines(InputAnalysisInfo analysisSetupInformation, AnalysisMetaData analysisMetaData,
bool useMtdb)
{
Logger.PrintMessage("Confirming baseline selections.");
if (useMtdb)
{
switch (analysisSetupInformation.Database.DatabaseFormat)
{
case MassTagDatabaseFormat.MassTagSystemSql:
Logger.PrintMessage("Using Mass Tag Database:");
Logger.PrintMessage(string.Format("\tServer: {0}",
analysisSetupInformation.Database.DatabaseServer));
Logger.PrintMessage(string.Format("\tDatabase Name: {0}",
analysisSetupInformation.Database.DatabaseName));
m_config.Analysis.MetaData.Database = analysisSetupInformation.Database;
break;
case MassTagDatabaseFormat.Sqlite:
Logger.PrintMessage("Using local Sqlite Mass Tag Database at location: ");
Logger.PrintMessage(string.Format("\tFull Path: {0}",
analysisSetupInformation.Database.LocalPath));
Logger.PrintMessage(string.Format("\tDatabase Name: {0}",
Path.GetFileName(analysisSetupInformation.Database.LocalPath)));
m_config.Analysis.MetaData.Database = analysisSetupInformation.Database;
break;
case MassTagDatabaseFormat.DelimitedTextFile:
Logger.PrintMessage("Using local MetaSample Mass Tag Database at location: ");
Logger.PrintMessage(string.Format("\tFull Path: {0}",
analysisSetupInformation.Database.LocalPath));
Logger.PrintMessage(string.Format("\tDatabase Name: {0}",
Path.GetFileName(analysisSetupInformation.Database.LocalPath)));
m_config.Analysis.MetaData.Database = analysisSetupInformation.Database;
break;
}
// Validate the baseline
if (analysisSetupInformation.BaselineFile == null)
{
m_config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB = true;
Logger.PrintMessage(string.Format("Using mass tag database {0} as the alignment baseline.",
analysisSetupInformation.Database.DatabaseName));
}
else
{
m_config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB = false;
m_config.Analysis.MetaData.BaselineDataset = null;
foreach (var info in analysisMetaData.Datasets)
{
if (info.Features.Path == analysisSetupInformation.BaselineFile.Path)
{
m_config.Analysis.MetaData.BaselineDataset = info;
info.IsBaseline = true;
m_config.Analysis.DataProviders.DatasetCache.Update(info);
}
}
Logger.PrintMessage(string.Format("Using dataset {0} as the alignment baseline.",
m_config.Analysis.MetaData.BaselineDataset));
}
}
else
{
m_config.Analysis.MetaData.Database = analysisSetupInformation.Database;
m_config.Analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB = false;
if (analysisSetupInformation.BaselineFile == null)
{
Logger.PrintMessage("No baseline dataset or database was selected.");
return false;
}
m_config.Analysis.MetaData.BaselineDataset = null;
foreach (var info in analysisMetaData.Datasets)
{
if (info.Features.Path == analysisSetupInformation.BaselineFile.Path)
{
info.IsBaseline = true;
m_config.Analysis.MetaData.BaselineDataset = info;
m_config.Analysis.DataProviders.DatasetCache.Update(info);
}
}
Logger.PrintMessage(string.Format("Using dataset {0} as the alignment baseline.",
m_config.Analysis.MetaData.BaselineDataset));
}
return true;
}
private MultiAlignAnalysis ConstructAnalysisObject(InputAnalysisInfo analysisSetupInformation)
{
Logger.PrintMessage("Creating Analysis Objects.");
var analysis = new MultiAlignAnalysis
{
MetaData = { AnalysisPath = m_config.AnalysisPath, AnalysisName = m_config.AnalysisName }
};
analysis.Options.AlignmentOptions.IsAlignmentBaselineAMasstagDB = true;
analysis.MetaData.ParameterFile = m_config.ParameterFile;
analysis.MetaData.InputFileDefinition = m_config.InputPaths;
analysis.MetaData.AnalysisSetupInfo = analysisSetupInformation;
return analysis;
}
private bool ReadInputDefinitionFile(out InputAnalysisInfo analysisSetupInformation, out bool useMtdb)
{
// Read the input datasets.
if (!File.Exists(m_config.InputPaths))
{
Logger.PrintMessage(string.Format("The input file {0} does not exist.", m_config.InputPaths));
}
else
{
Logger.PrintMessage("Copying input file to output directory.");
try
{
var dateSuffix = AnalysisPathUtils.BuildDateSuffix();
var newPath = Path.GetFileNameWithoutExtension(m_config.InputPaths);
newPath = newPath + "_" + dateSuffix + ".txt";
File.Copy(m_config.InputPaths, Path.Combine(m_config.AnalysisPath, newPath));
}
catch (Exception ex)
{
Logger.PrintMessage("Could not copy the input file to the output directory. " + ex.Message);
}
}
Logger.PrintMessage("Parsing Input Filenames and Databases.");
useMtdb = false;
analysisSetupInformation = null;
try
{
analysisSetupInformation = MultiAlignFileInputReader.ReadInputFile(m_config.InputPaths);
}
catch (Exception ex)
{
Logger.PrintMessage("The input file had some bad lines in it. " + ex.Message);
return false;
}
Logger.PrintMessage("Found " + analysisSetupInformation.Files.Count + " files.");
// Validate the mass tag database settings.
try
{
useMtdb = analysisSetupInformation.Database.ValidateDatabaseType();
}
catch (AnalysisMTDBSetupException ex)
{
Logger.PrintMessage("There was a problem with the mass tag database specification. " + ex.Message);
return false;
}
return true;
}
/// <summary>
/// Reads the input paths file
/// </summary>
/// <param name="path"></param>
/// <returns></returns>
public static InputAnalysisInfo ReadInputFile(string path)
{
var info = new InputAnalysisInfo();
var lines = File.ReadAllLines(path);
var readType = FileReadMode.None;
foreach (var line in lines)
{
var fixedLine = line.ToLower();
fixedLine = fixedLine.Trim();
var containsHeaderOpen = fixedLine.Contains("[");
var containsHeaderClose = fixedLine.Contains("]");
if (containsHeaderClose && containsHeaderOpen)
{
fixedLine = fixedLine.Replace(" ", "");
}
if (string.IsNullOrEmpty(fixedLine) || string.IsNullOrWhiteSpace(fixedLine))
{
continue;
}
// If wasModeChanged = true, then the current
// line is not data, but a tag to say change how read the next section.
var wasModeChanged = false;
switch (fixedLine)
{
case FILE_HEADER:
wasModeChanged = true;
readType = FileReadMode.Files;
break;
case DATABASE_HEADER:
wasModeChanged = true;
readType = FileReadMode.Database;
break;
case RAW_HEADER:
wasModeChanged = true;
readType = FileReadMode.RawFiles;
break;
case SCANS_HEADER:
wasModeChanged = true;
readType = FileReadMode.ScanFiles;
break;
case PEAKS_HEADER:
wasModeChanged = true;
readType = FileReadMode.Peaks;
break;
case SEQUENCE_HEADER:
wasModeChanged = true;
readType = FileReadMode.Sequence;
break;
default:
if (containsHeaderClose && containsHeaderOpen)
{
wasModeChanged = true;
readType = FileReadMode.Unknown;
throw new Exception(fixedLine + " is not a recognized data tag.");
}
wasModeChanged = false;
break;
}
if (!wasModeChanged)
{
switch (readType)
{
case FileReadMode.Files:
var baselineCheck = fixedLine.Split(BASELINE_INDICATOR);
if (baselineCheck.Length == 2 && !string.IsNullOrEmpty(baselineCheck[0]))
{
var newFile = new InputFile();
newFile.Path = baselineCheck[0];
newFile.FileType = InputFileType.Features;
info.BaselineFile = newFile;
info.Files.Add(newFile);
}
else if (!string.IsNullOrEmpty(baselineCheck[0]))
{
var newFile = new InputFile();
newFile.Path = baselineCheck[0];
newFile.FileType = InputFileType.Features;
info.Files.Add(newFile);
}
break;
case FileReadMode.Database:
var keys = fixedLine.Split('=');
if (keys.Length > 1)
{
keys[0] = keys[0].Replace('\t', ' ').Trim();
switch (keys[0].ToLower())
{
case "database":
info.Database.DatabaseFormat = MassTagDatabaseFormat.MassTagSystemSql;
info.Database.DatabaseName = keys[1];
break;
case "server":
info.Database.DatabaseFormat = MassTagDatabaseFormat.MassTagSystemSql;
info.Database.DatabaseServer = keys[1];
break;
case "sqlite":
info.Database.DatabaseFormat = MassTagDatabaseFormat.Sqlite;
info.Database.LocalPath = keys[1];
break;
case "metasample":
info.Database.DatabaseFormat = MassTagDatabaseFormat.DelimitedTextFile;
info.Database.LocalPath = keys[1];
break;
case "ims":
info.Database.DatabaseFormat = MassTagDatabaseFormat.SkipAlignment;
info.Database.LocalPath = keys[1];
break;
}
}
break;
case FileReadMode.RawFiles:
var rawFile = new InputFile();
rawFile.Path = fixedLine;
rawFile.FileType = InputFileType.Raw;
info.Files.Add(rawFile);
break;
case FileReadMode.ScanFiles:
var scanFile = new InputFile();
scanFile.Path = fixedLine;
scanFile.FileType = InputFileType.Scans;
info.Files.Add(scanFile);
break;
case FileReadMode.Unknown:
// do nothing!
break;
case FileReadMode.Sequence:
var sequenceFile = new InputFile();
sequenceFile.Path = fixedLine;
sequenceFile.FileType = InputFileType.Sequence;
info.Files.Add(sequenceFile);
break;
}
}
}
return info;
}