public Boolean cargarArchivo()
{
logger.EscribirLog("Cargamos la información de Metada de PharmaGKB", Logger.Tipo.Informativo, false);
logger.EscribirLog("Chequeamos si existe el archivo " + filePath, Logger.Tipo.Informativo, false);
if (!File.Exists(filePath))
{
logger.EscribirLog("No existe el archivo " + filePath, Logger.Tipo.Informativo, false);
return(false);
}
foreach (string CMAMetadata in File.ReadAllLines(filePath))
{
string[] varsa = CMAMetadata.Split('\t');
int ClinicalAnnotationID = 0;
if (int.TryParse(varsa[0], out ClinicalAnnotationID))
{
CAMetaData cAMeta = new CAMetaData();
cAMeta.ClinicalAnnotationID = ClinicalAnnotationID;
String[] location = varsa[1].Split(',');
foreach (String s in location)
{
if (s.Contains("\""))
{
cAMeta.Location.Add(s.Split('"')[1]);
}
else
{
cAMeta.Location.Add(s);
}
}
String[] GenId = varsa[2].Split(',');
foreach (String s in GenId)
{
if (s.Contains("\""))
{
string genid = s;
if (s.Contains("("))
{
genid = s.Split('"')[1].Split('(')[1].Split(')')[0];
}
cAMeta.GeneId.Add(genid);
cAMeta.Gen.Add(GenController.Instance.getByID(genid));
}
else
{
string genid = s;
if (s.Contains("("))
{
genid = s.Split('(')[1].Split(')')[0];
}
cAMeta.GeneId.Add(genid);
cAMeta.Gen.Add(GenController.Instance.getByID(genid));
}
}
cAMeta.LevelofEvidence = varsa[3];
cAMeta.ClinicalAnnotationTypes = varsa[4];
String[] GenotipoID = varsa[5].Split(',');
foreach (String s in GenotipoID)
{
if (s.Contains("\""))
{
cAMeta.GenotypePhenotypeIDs.Add(int.Parse(s.Split('"')[1]));
Genotipo genotipo = GenotipoController.Instance.getById(int.Parse(s.Split('"')[1]));
if (genotipo != null)
{
cAMeta.Genotipos.Add(genotipo);
}
Phenotype phenotype = PhenotypesController.Instance.getById(s.Split('"')[1]);
if (phenotype != null)
{
cAMeta.Phenotypes.Add(phenotype);
}
}
else
{
cAMeta.GenotypePhenotypeIDs.Add(int.Parse(s));
Genotipo genotipo = GenotipoController.Instance.getById(int.Parse(s));
if (genotipo != null)
{
cAMeta.Genotipos.Add(genotipo);
}
Phenotype phenotype = PhenotypesController.Instance.getById(s);
if (phenotype != null)
{
cAMeta.Phenotypes.Add(phenotype);
}
}
}
cAMeta.AnnotationText = varsa[6];
String[] Anotaciones = varsa[7].Split(',');
foreach (String s in Anotaciones)
{
if (s.Contains("\""))
{
cAMeta.VariantAnnotationsIDs.Add(int.Parse(s.Split('"')[1]));
cAMeta.Anotaciones.Add(AnotacionesController.Instance.getById(int.Parse(s.Split('"')[1])));
}
else
{
cAMeta.GeneId.Add(s);
cAMeta.Gen.Add(GenController.Instance.getByID(s));
}
}
cAMeta.VariantAnnotations = varsa[8];
String[] pmids = varsa[9].Split(';');
foreach (String s in pmids)
{
if (s.Contains("\""))
{
cAMeta.PMIDs.Add(int.Parse(s.Split(',')[1]));
}
else
{
cAMeta.PMIDs.Add(int.Parse(s));
}
}
cAMeta.EvidenceCount = int.Parse(varsa[10]);
string[] relatedchemicals = varsa[11].Split(',');
foreach (string s in relatedchemicals)
{
if (s != "")
{
if (s.Contains("\""))
{
cAMeta.RelatedChemicalsId.Add(s.Split('"')[1]);
cAMeta.chemicals.Add(ChemicalsController.Instance.getById(s.Split('"')[1]));
}
else
{
cAMeta.RelatedChemicalsId.Add(s);
cAMeta.chemicals.Add(ChemicalsController.Instance.getById(s));
}
}
}
string[] relatedDiseases = varsa[12].Split('"');
foreach (string s in relatedDiseases)
{
if (s != "" && s != ",")
{
if (s.Contains("\""))
{
if (s.Contains("("))
{
string PhenotypeID = s.Split('"')[0].Split('(')[1].Split(')')[0];
cAMeta.RelatedDiseasesId.Add(PhenotypeID);
cAMeta.Phenotypes.Add(PhenotypesController.Instance.getById(PhenotypeID));
}
else
{
cAMeta.Phenotypes.Add(PhenotypesController.Instance.getById(s.Split('"')[1]));
}
}
else
{
string PhenotypeID = string.Empty;
string[] lista = s.Split('(');
foreach (string auxs in lista)
{
if (auxs.StartsWith("PA"))
{
PhenotypeID = auxs.Split(')')[0];
}
}
cAMeta.RelatedDiseasesId.Add(PhenotypeID);
Phenotype ph = PhenotypesController.Instance.getById(PhenotypeID);
if (ph != null)
{
cAMeta.Phenotypes.Add(ph);
}
else
{
Console.WriteLine("Tuvimos problemas con {0}" + s);
}
}
}
}
cAMeta.BiogeographicalGroups = varsa[13];
cAMeta.Chromosome = varsa[14];
CAMetaDatas.Add(cAMeta);
}
}
logger.EscribirLog("Cargamos " + CAMetaDatas.Count + " Metadatas", Logger.Tipo.Informativo, true);
return(true);
}
