/// <summary>Will add GSMs from db to the given Experiment</summary>
/// <param name="experiment">Experiment to have its GSMs property updated</param>
public static void AddExperimentGSMToExperimentFromDb(Experiment experiment, SQLiteDataReader reader)
{
ExperimentGSM gsm = new ExperimentGSM(reader["gsm_id"].ToString(), reader["gsm_value"].ToString());
gsm.Id = Convert.ToInt32(reader["id"].ToString());
gsm.ExperimentId = reader["experiment_id"].ToString();
experiment.GSMs.Add(gsm);
}
/// <summary>Sets an Experiment property from given data</summary>
/// <remarks>Method will figure out which property exactly to update</remarks>
/// <param name="experiment">Experiment to be updated</param>
/// <param name="lineFromCsvFile">Data from CSV containing the value to be set</param>
public static void SetExperimentPropertyFromCsvLine(Experiment experiment, string lineFromCsvFile)
{
string[] data;
if (lineFromCsvFile.Contains("="))
{
data = lineFromCsvFile.Split('=');
data = Normalise(data);
switch (data[0])
{
case "^DATABASE":
experiment.Database = data[1];
break;
case "!Database_name":
experiment.DatabaseName = data[1];
break;
case "!Database_institute":
experiment.DatabaseInstitute = data[1];
break;
case "!Database_web_link":
experiment.DatabaseWebLink = data[1];
break;
case "!Database_email":
experiment.DatabaseEmail = data[1];
break;
case "!Database_ref":
experiment.DatabaseRef = data[1];
break;
case "^DATASET":
experiment.Dataset = RemoveCommas(data[1]);
break;
case "!dataset_title":
experiment.DatasetTitle = data[1];
break;
case "!dataset_description":
experiment.DatasetDescription = data[1];
break;
case "!dataset_type":
experiment.DatasetType = data[1];
break;
case "!dataset_pubmed_id":
experiment.DatasetPubmedId = data[1];
break;
case "!dataset_platform":
experiment.DatasetPlatform = data[1];
break;
case "!dataset_platform_organism":
experiment.DatasetPlatformOrganism = data[1];
break;
case "!dataset_platform_technology_type":
experiment.DatasetPlatformTechnologyType = data[1];
break;
case "!dataset_feature_count":
experiment.DatasetFeatureCount = data[1];
break;
case "!dataset_sample_organism":
experiment.DatasetSampleOrganism = data[1];
break;
case "!dataset_sample_type":
experiment.DatasetSampleType = data[1];
break;
case "!dataset_reference_series":
experiment.DatasetReferenceSeries = data[1];
break;
case "!dataset_update_date":
experiment.DatasetUpdateDate = data[1];
break;
}
if (data[0].StartsWith("#GSM"))
{
ExperimentGSM gsm = new ExperimentGSM(data[0], data[1]);
experiment.GSMs.Add(gsm);
}
}
else
{
lineFromCsvFile = FixInvalidDatasetTableIdentifiers(lineFromCsvFile);
data = lineFromCsvFile.Split(',');
if (data[0].EndsWith("_at"))
{
StringBuilder datasetValue = new StringBuilder();
for (int i = 2; i < data.Length; i++)
{
try
{
datasetValue.Append(data[i]);
datasetValue.Append(";");
}
catch (ArgumentOutOfRangeException)
{
MessageBox.Show("Dataset table rows cannot contain double quotes and should be comma-separated. Row ID_REF: " + data[0], "Dataset table invalid row", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
datasetValue.Remove(datasetValue.Length - 1, 1); // remove last ';' separator
DatasetTableRow datasetRow = new DatasetTableRow(data[0], data[1], datasetValue.ToString());
experiment.DatasetTable.Add(datasetRow);
}
}
}