public static void InitializeDatabase(GeneAnnotationDBContext context)
{
context.Database.Migrate();
InitializeConstants.Initialize(context);
var loadHugo = Environment.GetEnvironmentVariable("GA_DB_LOAD_HUGO");
if (loadHugo != null)
{
var hugoLoader = new HugoDataLoader(context, "hugo.csv.short");
hugoLoader.LoadData();
}
var loadUcsc = Environment.GetEnvironmentVariable("GA_DB_LOAD_UCSC");
if (loadUcsc != null)
{
var ucscLoader = new UcscDataLoader(context, "ucsc.csv.short");
ucscLoader.LoadData();
}
var loadLike = Environment.GetEnvironmentVariable("GA_DB_LOAD_LIKE");
if (loadLike != null)
{
var likeLoader = new LikeDataLoader(context, "like.csv.short");
likeLoader.LoadData();
}
}
public void LoadDataTest()
{
StaticLoggerFactory.LoggerFactory = new LoggerFactory();
StaticLoggerFactory.LoggerFactory.AddConsole();
StaticLoggerFactory.LoggerFactory.AddDebug();
var loadHugoData = new HugoDataLoader(Context, "hugo.csv.short");
loadHugoData.LoadData();
Assert.Equal(19, Context.Gene.Count());
}
public void AddLocationTest()
{
var loadHugoData = new HugoDataLoader(Context, "hugo.csv.short");
var loci = new[]
{
"6",
"12q24.31",
"X",
"Y",
"3p24.1-p22.1"
};
var cells = new List <string>();
for (var j = 0; j < loci.Length; j++)
{
var locus = loci[j];
Context.Gene.Add(GeneTestData.Genes[j]);
Context.SaveChanges();
var gene = Context.Gene.Find(j + 1);
for (var i = 0; i < HugoDataLoader.ColChromosome + 1; i++)
{
var cellValue = "";
if (i == HugoDataLoader.ColChromosome)
{
cellValue = locus;
}
cells.Insert(i, cellValue);
}
loadHugoData.SaveLocation(gene, cells);
Context.SaveChanges();
var geneLocation = gene
.GeneLocations
.Where(x => x.Locus == loci[j])
.Where(gl => gl.Gene == gene)
.Single(gl => gl.HgVersion == 19)
;
var match = _parseHugoChromosome(locus);
var chromosomeName = match.Groups[1].Value;
Assert.Equal(geneLocation.Locus, locus);
Assert.Equal(geneLocation.Chromosome.Name, chromosomeName);
}
}
public void AddGeneNamesTest()
{
var loadHugoData = new HugoDataLoader(Context, "hugo.csv.short");
Context.Gene.Add(GeneTestData.Genes[0]);
Context.GeneLocation.Add(GeneLocationTestData.GeneLocations[0]);
Context.GeneCoordinate.Add(GeneCoordinateTestData.GeneCoordinates[0]);
Context.SaveChanges();
var gene = Context.Gene.Find(1);
var names = new[]
{
"dat cool name",
"tripartite motif-containing 49-like",
"\"tripartite motif containing 49-like 1\"",
"\"tripartite motif containing 49D2, pseudogene\""
};
var cells = new[]
{
"",
"",
names[0],
"",
"",
"",
"",
string.Join(", ", names[1], names[2], names[3])
};
loadHugoData.SaveNames(gene, cells);
Context.SaveChanges();
/*
* var found = gene
* .GeneName
* .Sum(
* geneName => names
* .Select(name => name.Replace("\"", string.Empty))
* .Count(quotelessName => geneName.Name.Equals(quotelessName))
* );
*
* Assert.True(found == 4);
*/
}
