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 AddLocation()
{
var likeLoader = new LikeDataLoader(Context, "like.csv.short");
const int start = 2112;
const int end = 4224;
likeLoader.CurrentRow = new[]
{
"stuffz",
"ch13",
start.ToString(),
end.ToString(),
"priest of syrinx"
};
likeLoader.CurrentGene = _insertedGeneWithOutSymbol;
likeLoader.AddLocation();
Assert.Equal(
1,
likeLoader
.CurrentGene
.GeneLocations.Single(gl => gl.HgVersion == 19)
.GeneCoordinates
.Count(gc => gc.Start == start && gc.End == end)
);
Assert.Equal(
likeLoader.CurrentRow[LikeDataLoader.ColLocus],
likeLoader
.CurrentGene
.GeneLocations.Single(gl => gl.HgVersion == 19)
.Locus
);
}
public void AddKnownFunctionTest()
{
var likeLoader = new LikeDataLoader(Context, "like.csv.short");
likeLoader.CurrentRow = new[]
{
"stuffz",
"ch13",
"1",
"2",
"priest of syrinx",
"",
"",
"",
"",
"God Of Balance"
};
likeLoader.CurrentGene = _insertedGeneWithOutKnowFunction;
likeLoader.AddKnownFunction();
Assert.Equal(
likeLoader.CurrentRow[LikeDataLoader.ColKnownFunction],
likeLoader
.CurrentGene
.KnownFunction
);
}
public void LoadFileTest()
{
var likeLoader = new LikeDataLoader(Context, "like.csv.short");
var ex = Record.Exception(
() => { likeLoader.LoadFile(); }
);
Assert.Null(ex);
}
public void FindOrCreateNewGene()
{
var likeLoader = new LikeDataLoader(Context, "like.csv.short");
likeLoader.CurrentRow = new[]
{
"bla",
"ch1",
"100",
"200",
"Bobs your ungle"
};
likeLoader.FindOrCreateGene();
Assert.True(likeLoader.CurrentGene.Id > 0);
}
public void FindOrCreateExistingGene()
{
var likeLoader = new LikeDataLoader(Context, "like.csv.short");
likeLoader.CurrentRow = new[]
{
SymbolTestData.Symbols[0].Name,
"ch1",
"100",
"200",
"locus",
};
likeLoader.FindOrCreateGene();
Assert.True(
likeLoader.CurrentGene.Symbol.SingleOrDefault(s => s.Name == SymbolTestData.Symbols[0].Name) != null
);
}
