protected override void LoadFromFile(string path)
{
var separator = _csvSeparatorSelector.GetCsvSeparator(path);
//if separator selection dialog was cancelled, abort
if (!(separator is char separatorCharacter))
{
return;
}
//we keep a copy of the already loaded sheets, in case the reading fails
var alreadyLoadedDataSheets = DataSheets.Clone();
DataSheets.Clear();
try
{
using (var reader = new CsvReaderDisposer(path, separatorCharacter))
{
var csv = reader.Csv;
var headers = csv.GetFieldHeaders();
var rows = new List <List <string> >(headers.Length);
var dataSheet = new DataSheet
{
SheetName = ""
};
for (var i = 0; i < headers.Length; i++)
{
dataSheet.AddColumn(headers[i], i);
}
var currentRow = new string[csv.FieldCount];
while (csv.ReadNextRecord())
{
csv.CopyCurrentRecordTo(currentRow);
var rowList = currentRow.ToList();
var levels = getMeasurementLevels(rowList);
dataSheet.CalculateColumnDescription(levels);
dataSheet.AddRow(rowList);
}
dataSheet.RemoveEmptyColumns();
dataSheet.RemoveEmptyRows();
DataSheets.AddSheet(dataSheet);
}
}
catch (Exception e)
{
DataSheets.CopySheetsFrom(alreadyLoadedDataSheets);
_logger.AddError(e.Message);
throw new InvalidObservedDataFileException(e.Message);
}
}
protected override void LoadFromFile(string path)
{
//we keep a copy of the already loaded sheets, in case the reading fails
var alreadyLoadedDataSheets = DataSheets.Clone();
DataSheets.Clear();
try
{
var reader = new ExcelReader(path);
while (reader.MoveToNextSheet())
{
if (!reader.MoveToNextRow())
{
continue;
}
var rawSheetData = new DataSheet
{
SheetName = reader.CurrentSheet.SheetName
};
var headers = reader.CurrentRow;
for (var j = 0; j < headers.Count; j++)
{
rawSheetData.AddColumn(headers[j], j);
}
while (reader.MoveToNextRow())
{
//the first two could even be done only once
var levels = reader.GetMeasurementLevels(headers.Count);
rawSheetData.CalculateColumnDescription(levels);
rawSheetData.AddRow(reader.CurrentRow);
}
rawSheetData.RemoveEmptyColumns();
rawSheetData.RemoveEmptyRows();
DataSheets.AddSheet(rawSheetData);
}
}
catch (Exception ex)
{
DataSheets.CopySheetsFrom(alreadyLoadedDataSheets);
_logger.AddError(ex.Message);
throw new InvalidObservedDataFileException(ex.Message);
}
}
public override void GlobalContext()
{
base.GlobalContext();
_dataSourceFile = A.Fake <IDataSourceFile>();
_importer = A.Fake <IImporter>();
_view = A.Fake <IImporterDataView>();
_dataSheet = new DataSheet {
SheetName = "sheet1"
};
_dataSheet.AddColumn("test_column", 0);
_dataSheet.AddRow(new List <string>()
{
"1"
});
_dataSheet2 = new DataSheet {
SheetName = "sheet2"
};
_dataSheet2.AddColumn("test_column", 0);
_dataSheet2.AddRow(new List <string>()
{
"1"
});
_dataSheet3 = new DataSheet {
SheetName = "sheet3"
};
_dataSheet3.AddColumn("test_column", 0);
_dataSheet3.AddRow(new List <string>()
{
"1"
});
_sheetsCollection = new DataSheetCollection();
_sheetsCollection.AddSheet(_dataSheet);
_sheetsCollection.AddSheet(_dataSheet2);
_sheetsCollection.AddSheet(_dataSheet3);
A.CallTo(() => _importer.LoadFile(A <ColumnInfoCache> ._, A <string> ._, A <IReadOnlyList <MetaDataCategory> > ._)).Returns(_dataSourceFile);
A.CallTo(() => _view.GetActiveFilterCriteria()).Returns("active_filter_criteria");
A.CallTo(() => _dataSourceFile.DataSheets).Returns(_sheetsCollection);
}
protected override void Context()
{
_columnInfos = new ColumnInfoCache
{
new ColumnInfo()
{
DisplayName = "Time", IsMandatory = true
},
new ColumnInfo()
{
DisplayName = "Concentration", IsMandatory = true
},
new ColumnInfo()
{
DisplayName = "Error", IsMandatory = false
}
};
_metaDataCategories = new List <MetaDataCategory>()
{
new MetaDataCategory()
{
Name = "Organ"
},
new MetaDataCategory()
{
Name = "Compartment"
},
new MetaDataCategory()
{
Name = "Species"
},
new MetaDataCategory()
{
Name = "Dose"
},
new MetaDataCategory()
{
Name = "Molecule"
},
new MetaDataCategory()
{
Name = "Route"
}
};
sut = new DataFormatNonmem();
_headersCache = new Cache <string, ColumnDescription>()
{
{
"Organ",
new ColumnDescription(0, new List <string>()
{
"PeripheralVenousBlood"
}, ColumnDescription.MeasurementLevel.Discrete)
},
{
"Compartment",
new ColumnDescription(1, new List <string>()
{
"Arterialized"
}, ColumnDescription.MeasurementLevel.Discrete)
},
{
"Species",
new ColumnDescription(2, new List <string>()
{
"Human"
}, ColumnDescription.MeasurementLevel.Discrete)
},
{
"Dose",
new ColumnDescription(3, new List <string>()
{
"75 [g] glucose"
}, ColumnDescription.MeasurementLevel.Discrete)
},
{
"Molecule",
new ColumnDescription(4, new List <string>()
{
"GLP-1_7-36 total", "Glucose", "Insuline", "GIP_total", "Glucagon"
}, ColumnDescription.MeasurementLevel.Discrete)
},
{
"Time",
new ColumnDescription(5, null, ColumnDescription.MeasurementLevel.Numeric)
},
{
"Concentration",
new ColumnDescription(6, null, ColumnDescription.MeasurementLevel.Numeric)
},
{
"Error",
new ColumnDescription(7, null, ColumnDescription.MeasurementLevel.Numeric)
},
{
"Route",
new ColumnDescription(8, new List <string>()
{
"po"
}, ColumnDescription.MeasurementLevel.Discrete)
},
{
"Groupe Id",
new ColumnDescription(9, new List <string>()
{
"H", "T2DM"
}, ColumnDescription.MeasurementLevel.Discrete)
},
{
"Time_unit",
new ColumnDescription(10, new List <string>()
{
"min"
}, ColumnDescription.MeasurementLevel.Discrete)
},
{
"Concentration_unit",
new ColumnDescription(11, new List <string>()
{
"pmol/l"
}, ColumnDescription.MeasurementLevel.Discrete)
},
{
"Error_unit",
new ColumnDescription(12, new List <string>()
{
"pmol/l"
}, ColumnDescription.MeasurementLevel.Discrete)
},
{
"Concentration_lloq",
new ColumnDescription(13)
{
Level = ColumnDescription.MeasurementLevel.Numeric
}
}
};
_basicFormat = new TestDataSheet(_headersCache);
foreach (var molecule in _molecules)
{
foreach (var groupId in _groupIds)
{
for (var time = 0; time < 10; time++)
{
_basicFormat.AddRow(new List <string>()
{
"PeripheralVenousBlood",
"Arterialized",
"Human",
"75 [g] glucose",
molecule,
$"time",
"0",
"0",
"po",
groupId,
"min",
"pmol/l",
"pmol/l",
$"{0.01}"
});
}
}
}
}
