public void AddGroupedObjectValues_TwoTimes()
{
var sb = StringBuilderCache.Acquire();
var json = new JsonObject(sb);
var descriptions = new[] { "test1", "test2" };
var descriptions2 = new[] { "test3" };
var points = new Point[2];
points[0] = new Point(1, 2);
points[1] = new Point(3, 4);
var points2 = new Point[1];
points2[0] = new Point(5, 6);
json.AddGroupedObjectValues("first", descriptions, points, points2);
json.AddGroupedObjectValues("second", descriptions2, points2);
const string expectedResult = "\"first\":{\"test1\":[{\"X\":1,\"Y\":2},{\"X\":3,\"Y\":4}],\"test2\":[{\"X\":5,\"Y\":6}]},\"second\":{\"test3\":[{\"X\":5,\"Y\":6}]}";
var observedResult = StringBuilderCache.GetStringAndRelease(sb);
Assert.Equal(expectedResult, observedResult);
}
public void AddGroupedObjectValues_MismatchedDescriptionCount()
{
Assert.Throws <ArgumentException>(delegate
{
var sb = StringBuilderCache.Acquire();
var json = new JsonObject(sb);
var descriptions = new[] { "test1", "test2" };
var points2 = new Point[1];
points2[0] = new Point(5, 6);
json.AddGroupedObjectValues("second", descriptions, points2);
});
}
public void AddGroupedObjectValues_NullDescriptions()
{
var sb = StringBuilderCache.Acquire();
var json = new JsonObject(sb);
var points2 = new Point[1];
points2[0] = new Point(5, 6);
json.AddGroupedObjectValues("second", null, points2);
var observedResult = StringBuilderCache.GetStringAndRelease(sb);
Assert.Equal(string.Empty, observedResult);
}
public void AddGroupedObjectValues_OneNullGroup()
{
var sb = StringBuilderCache.Acquire();
var json = new JsonObject(sb);
var descriptions = new[] { "test1", "test2" };
var points2 = new Point[1];
points2[0] = new Point(5, 6);
json.AddGroupedObjectValues("second", descriptions, points2, null as Point[]);
const string expectedResult = "\"second\":{\"test1\":[{\"X\":5,\"Y\":6}]}";
var observedResult = StringBuilderCache.GetStringAndRelease(sb);
Assert.Equal(expectedResult, observedResult);
}
public string GetJsonString(string originalChromName)
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
// data section
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("vid", Variant.VariantId);
jsonObject.AddStringValue("chromosome", originalChromName);
jsonObject.AddIntValue("begin", Variant.Start);
jsonObject.AddIntValue("end", Variant.End);
jsonObject.AddBoolValue("isReferenceMinorAllele", Variant.IsRefMinor);
if (!Variant.IsRefMinor)
{
jsonObject.AddStringValue("refAllele",
string.IsNullOrEmpty(Variant.RefAllele) ? "-" : Variant.RefAllele);
jsonObject.AddStringValue("altAllele",
string.IsNullOrEmpty(Variant.AltAllele) ? "-" : Variant.AltAllele);
}
else
{
jsonObject.AddStringValue("refAllele",
string.IsNullOrEmpty(Variant.AltAllele) ? "-" : Variant.AltAllele);
}
var variantType = GetVariantType(Variant.Type);
jsonObject.AddStringValue("variantType", variantType.ToString());
jsonObject.AddBoolValue("isDecomposedVariant", Variant.IsDecomposed);
if (variantType.ToString() != "SNV")
{
jsonObject.AddBoolValue("isRecomposedVariant", Variant.IsRecomposed);
}
jsonObject.AddStringValue("hgvsg", HgvsgNotation);
jsonObject.AddDoubleValue("phylopScore", PhylopScore);
if (RegulatoryRegions?.Count > 0)
{
jsonObject.AddObjectValues("regulatoryRegions", RegulatoryRegions);
}
if (SupplementaryAnnotations.Count > 0)
{
AddSAstoJsonObject(jsonObject);
}
foreach (var pluginData in PluginDataSet)
{
jsonObject.AddStringValue(pluginData.Name, pluginData.GetJsonString(), false);
}
if (OverlappingGenes.Count > 0)
{
jsonObject.AddStringValues("overlappingGenes", OverlappingGenes);
}
if (OverlappingTranscripts.Count > 0)
{
jsonObject.AddObjectValues("overlappingTranscripts", OverlappingTranscripts);
}
if (EnsemblTranscripts?.Count > 0 || RefSeqTranscripts?.Count > 0)
{
jsonObject.AddGroupedObjectValues("transcripts", TranscriptLabels, RefSeqTranscripts, EnsemblTranscripts);
}
sb.Append(JsonObject.CloseBrace);
return(StringBuilderCache.GetStringAndRelease(sb));
}
