/// <summary>
/// Method that extract data and save them a normalized CSV file
/// </summary>
public Dictionary <string, RawData> Extract()
{
var f = Directory.GetFiles(_repositoyFolder).ToList().OrderBy(x => x).LastOrDefault();
var data = new Dictionary <string, RawData>();
try
{
_logger.Debug($"Reading file: \"{f}\"");
using (var sr = File.OpenRead(f))
{
using (var xl = ExcelReaderFactory.CreateReader(sr, null))
{
var conf = new ExcelDataSetConfiguration
{
ConfigureDataTable = _ => new ExcelDataTableConfiguration
{
UseHeaderRow = true
}
};
var dataSet = xl.AsDataSet(conf);
var dataTable = dataSet.Tables[0];
var view = new DataView(dataTable)
{
Sort = "DateRep ASC"
};
var country = dataTable.Columns.IndexOf("CountryExp");
for (int i = 0; i < view.Count; i++)
{
var row = view[i];
var obj = new RawData()
{
DataProvider = "ECDC"
};
if (country == -1)
{
obj.Area = row.TryGetValue("countriesAndTerritories").Replace("UK", "United Kingdom").Replace("United_Kingdom", "United Kingdom");
obj.Date = new DateTime(Convert.ToInt32(row.TryGetValue("Year")), Convert.ToInt32(row.TryGetValue("Month")), Convert.ToInt32(row.TryGetValue("Day")));
obj.Confirmed = Convert.ToInt32(row.TryGetValue("Cases"));
obj.Death = Convert.ToInt32(row.TryGetValue("Deaths"));
}
else
{
obj.Area = row.TryGetValue("CountryExp");
obj.Date = Convert.ToDateTime(row.TryGetValue("DateRep"));
}
if (!data.ContainsKey(obj.ToString()))
{
data.Add(obj.ToString(), obj);
}
}
}
}
foreach (var area in data.Values.GroupBy(x => x.Area).OrderBy(x => x.Key))
{
_logger.Debug($"Processing {area.Key}");
var missingData = new List <RawData>();
var mindate = area.Min(x => x.Date);
var maxdate = area.Max(x => x.Date);
var nbDays = (maxdate - mindate).Days;
RawData previous = null;
RawData current = null;
// For some reason some days have no data. Must create missing day.
for (int i = 0; i <= nbDays; i++)
{
current = area.FirstOrDefault(x => x.Date == mindate.AddDays(i));
if (current == null)
{
current = new RawData {
DataProvider = "ECDC", Area = area.Key, Date = mindate.AddDays(i)
};
}
// Don't take the first day as previous day does not exist
if (i > 0)
{
// data is incremental, take previous day
previous = area.FirstOrDefault(x => x.Date == current.Date.AddDays(-1));
// If previous was missing then added to main data source, main source is not refreshed. Keep missing data in a list aside
if (previous == null)
{
previous = missingData.FirstOrDefault(x => x.Date == current.Date.AddDays(-1));
}
current.Confirmed += previous.Confirmed;
current.Death += previous.Death;
}
if (!data.ContainsKey(current.ToString()))
{
missingData.Add(current);
data.Add(current.ToString(), current);
}
}
if (missingData.Count > 0 && _logger.IsDebugEnabled)
{
_logger.Debug($"Missing day created for {area.Key}: \"{string.Join("\", \"", missingData.Select(x => $"{x.Date:yyyy-MM-dd}, c:{x.Confirmed}, d:{x.Death}"))}\"");
}
}
}
catch (Exception ex)
{
_logger.Error(ex.Message);
}
_logger.Info(string.Concat("Found ", data.Count, " records"));
using (var writer = new StreamWriter(this._outputFile))
{
using (var csv = new CsvWriter(writer, CultureInfo.GetCultureInfo("fr-fr")))
{
csv.WriteRecords(data.Values.OrderBy(x => x.Area).ThenBy(x => x.Date));
}
}
return(data);
}
/// <summary>
/// Method that extract data and save them a normalized CSV file
/// </summary>
public Dictionary <string, RawData> Extract()
{
var data = new Dictionary <string, RawData>();
var datesErrors = new HashSet <string>();
var missingFields = new HashSet <Tuple <string, string> >();
// Setting columns names aliases
var areaAlias = new string[] { "Country_Region", "Country/Region" };
var subareaAlias = new string[] { "Province_State", "Province/State" };
var latAlias = new string[] { "Latitude", "Lat" };
var lngAlias = new string[] { "Longitude", "Long_" };
var files = Directory.GetFiles(_repositoryFolder, "*.csv", SearchOption.AllDirectories).ToList().OrderBy(x => x);
foreach (var f in files)
#region EXTRACT DATA FROM FILES
{
int counter = 0;
int addedLines = 0;
using (var sr = new StreamReader(f))
{
using (var csv = new CustomCsvReader(sr, CultureInfo.InvariantCulture))
{
csv.Configuration.MissingFieldFound = delegate(string[] tab, int count, ReadingContext ctxt)
{
var miss = new Tuple <string, string>(Path.GetFileName(f), string.Join(", ", tab));
if (!missingFields.Contains(miss))
{
missingFields.Add(miss);
}
};
csv.Read();
csv.ReadHeader();
#region FETCH COLUMNS INDEX
var idxArea = csv.GetFieldIndex(areaAlias);
var idxSub = csv.GetFieldIndex(subareaAlias);
var idxAdmin2 = csv.GetFieldIndex("Admin2");
var idxConf = csv.GetFieldIndex("Confirmed");
var idxDeath = csv.GetFieldIndex("Deaths");
var idxLat = csv.GetFieldIndex(latAlias);
var idxLng = csv.GetFieldIndex(lngAlias);
#endregion
while (csv.Read())
{
#region PROCESSING A LINE
counter++;
try
{
var date = Path.GetFileNameWithoutExtension(f);
if (DateTime.TryParseExact(date, _dateFormats, CultureInfo.GetCultureInfo("fr-fr"), DateTimeStyles.AdjustToUniversal, out DateTime lastUpdate))
{
string area = csv.GetField(idxArea).Replace("Mainland China", "China").Replace("UK", "United Kingdom").Replace("United_Kingdom", "United Kingdom");
string subarea = csv.GetField(idxSub);
if (!string.IsNullOrEmpty(area))
{
var obj = new RawData();
obj.DataProvider = "JohnsHopkins";
obj.Area = area;
obj.SubArea = subarea;
obj.Admin2 = csv.GetField(idxAdmin2)?.Replace("Unassigned", string.Empty);
obj.Date = lastUpdate;
obj.Confirmed = csv.GetFieldAsInt(idxConf, _us);
obj.Death = csv.GetFieldAsInt(idxDeath, _us);
obj.Latitude = csv.GetFieldAsDouble(idxLat, _us);
obj.Longitude = csv.GetFieldAsDouble(idxLng, _us);
if (!data.ContainsKey(obj.ToString()))
{
data.Add(obj.ToString(), obj);
addedLines++;
}
}
}
else
{
if (!datesErrors.Contains(date))
{
datesErrors.Add(string.Concat(csv.Context.Row.ToString().PadLeft(6, '0'), " \"", f, "\": ", date));
}
}
}
catch (Exception ex)
{
_logger.Error(string.Concat("\"", f, "\"", ": ", ex.Message));
_logger.Debug(string.Join(" ; ", csv.Context.HeaderRecord));
_logger.Debug(string.Join(" ; ", csv.Context.Record));
throw ex;
}
#endregion
}
}
}
var copyFile = Path.Combine(_copyRepositoryFolder, Path.GetFileName(f));
if (!File.Exists(copyFile))
{
// Make a copy
File.Copy(f, copyFile);
}
_logger.Debug($"Processing file \"{Path.GetFileName(f)}\", number of lines added/processed: {addedLines}/{counter}");
};
#endregion
#region LOGGING ERRORS
if (missingFields.Count > 0)
{
_logger.Warn($"There are {missingFields.GroupBy(x => x.Item1).Count()} files in which some columns could not be found: \"{string.Join(", ", missingFields.GroupBy(x => x.Item2).Select(x => x.Key))}\"");
if (_logger.IsDebugEnabled)
{
_logger.Debug(string.Concat("Following fields could not be found:\n", string.Join("\n", missingFields.GroupBy(x => x.Item1).Select(x => $"{x.Key}: \"{string.Join("\", \"", x.Select(y => y.Item2))}\""))));
}
}
if (datesErrors.Count > 0)
{
_logger.Warn($"There are {datesErrors.Count} dates not correctly formated");
if (_logger.IsDebugEnabled)
{
_logger.Debug(string.Concat("Following dates are not in correct format:\n", string.Join("\n", datesErrors)));
}
}
#endregion
_logger.Info(string.Concat("Found ", data.Count, " records"));
// Writing output file
using (var writer = new StreamWriter(_outputFile))
{
using (var csv = new CsvWriter(writer, CultureInfo.GetCultureInfo("fr-fr")))
{
csv.WriteRecords(data.Select(x => x.Value));
}
}
return(data);
}
