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