/// <summary>
/// Read supplementary files according to file paths and data types.
/// </summary>
/// <param name="suppFiles"></param>
/// <param name="supplDataTypes"></param>
/// <param name="processInfo"></param>
/// <returns></returns>
/// <exception cref="NotImplementedException"></exception>
public static IData[] ReadSupplementaryData(string[] suppFiles, DataType[] supplDataTypes, ProcessInfo processInfo)
{
var numSupplTables = suppFiles.Length;
IData[] supplData = new IData[numSupplTables];
for (int i = 0; i < numSupplTables; i++)
{
switch (supplDataTypes[i])
{
case DataType.Matrix:
var mdata = PerseusFactory.CreateMatrixData();
PerseusUtils.ReadMatrixFromFile(mdata, processInfo, suppFiles[i], '\t');
supplData[i] = mdata;
break;
case DataType.Network:
var ndata = PerseusFactory.CreateNetworkData();
FolderFormat.Read(ndata, suppFiles[i], processInfo);
supplData[i] = ndata;
break;
default:
throw new NotImplementedException($"Data type {supplDataTypes[i]} not supported!");
}
}
return(supplData);
}
public void LoadData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables, ref IDocumentData[] documents,
ProcessInfo processInfo)
{
var remoteExe = GetExectuable(param);
var paramFile = Path.GetTempFileName();
param.ToFile(paramFile);
var outFile = Path.GetTempFileName();
if (!TryGetCodeFile(param, out string codeFile))
{
processInfo.ErrString = $"Code file '{codeFile}' was not found";
return;
}
;
if (supplTables == null)
{
supplTables = Enumerable.Range(0, NumSupplTables).Select(i => PerseusFactory.CreateMatrixData()).ToArray();
}
var suppFiles = supplTables.Select(i => Path.GetTempFileName()).ToArray();
var args = $"{codeFile} {paramFile} {outFile} {string.Join(" ", suppFiles)}";
Debug.WriteLine($"executing > {remoteExe} {args}");
if (Utils.RunProcess(remoteExe, args, processInfo.Status, out string processInfoErrString) != 0)
{
processInfo.ErrString = processInfoErrString;
return;
}
;
PerseusUtils.ReadMatrixFromFile(mdata, processInfo, outFile, '\t');
for (int i = 0; i < NumSupplTables; i++)
{
PerseusUtils.ReadMatrixFromFile(supplTables[i], processInfo, suppFiles[i], '\t');
}
}
private static void ReadMatrixDataInto(IDataWithAnnotationColumns data, string file, ProcessInfo processInfo)
{
var mdata = PerseusFactory.CreateMatrixData();
PerseusUtils.ReadMatrixFromFile(mdata, processInfo, file, '\t');
data.CopyAnnotationColumnsFrom(mdata);
}
public void LoadData(IMatrixData mdata, Parameters parameters, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
PerseusLoadMatrixParam par = (PerseusLoadMatrixParam)parameters.GetParam("File");
string filename = par.Filename;
if (string.IsNullOrEmpty(filename))
{
processInfo.ErrString = "Please specify a filename";
return;
}
PerseusUtils.ReadMatrixFromFile(mdata, processInfo, filename, par.MainColumnIndices, par.NumericalColumnIndices,
par.CategoryColumnIndices, par.TextColumnIndices, par.MultiNumericalColumnIndices, par.MainFilterParameters,
par.NumericalFilterParameters, par.ShortenExpressionColumnNames);
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables, ref IDocumentData[] documents,
ProcessInfo processInfo)
{
var remoteExe = param.GetParam <string>(InterpreterLabel).Value;
if (string.IsNullOrWhiteSpace(remoteExe))
{
processInfo.ErrString = Resources.RemoteExeNotSpecified;
return;
}
var inFile = Path.GetTempFileName();
PerseusUtils.WriteMatrixToFile(mdata, inFile, AdditionalMatrices);
var outFile = Path.GetTempFileName();
if (!TryGetCodeFile(param, out string codeFile))
{
processInfo.ErrString = $"Code file '{codeFile}' was not found";
return;
}
;
if (supplTables == null)
{
supplTables = Enumerable.Range(0, NumSupplTables).Select(i => PerseusFactory.CreateMatrixData()).ToArray();
}
var suppFiles = supplTables.Select(i => Path.GetTempFileName()).ToArray();
var commandLineArguments = GetCommandLineArguments(param);
var args = $"{codeFile} {commandLineArguments} {inFile} {outFile} {string.Join(" ", suppFiles)}";
Debug.WriteLine($"executing > {remoteExe} {args}");
if (Utils.RunProcess(remoteExe, args, processInfo.Status, out string processInfoErrString) != 0)
{
processInfo.ErrString = processInfoErrString;
return;
}
;
mdata.Clear();
PerseusUtils.ReadMatrixFromFile(mdata, processInfo, outFile, '\t');
for (int i = 0; i < NumSupplTables; i++)
{
PerseusUtils.ReadMatrixFromFile(supplTables[i], processInfo, suppFiles[i], '\t');
}
}
public void LoadData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables, ref IDocumentData[] documents,
ProcessInfo processInfo)
{
var remoteExe = GetExectuable(param);
var paramFile = Path.GetTempFileName();
param.ToFile(paramFile);
var outFile = Path.GetTempFileName();
var codeFile = GetCodeFile(param);
var args = $"{codeFile} {paramFile} {outFile}";
Debug.WriteLine($"executing > {remoteExe} {args}");
if (Utils.RunProcess(remoteExe, args, processInfo.Status, out string processInfoErrString) != 0)
{
processInfo.ErrString = processInfoErrString;
return;
}
;
PerseusUtils.ReadMatrixFromFile(mdata, processInfo, outFile, '\t');
}