public GeneAnnotationProvider(IEnumerable <Stream> dbStreams)
{
Name = "Gene annotation provider";
_ngaReaders = new List <NgaReader>();
foreach (var dbStream in dbStreams)
{
_ngaReaders.Add(NgaReader.Read(dbStream));
}
}
public void ReadBackGeneAnnotations()
{
var writeStream = new MemoryStream();
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks);
var ngaWriter = new NgaWriter(writeStream, version, "mimo", SaCommon.SchemaVersion, true);
ngaWriter.Write(GetGeneAnnotations());
var readStream = new MemoryStream(writeStream.ToArray());
using (var ngaReader = new NgaReader(readStream))
{
Assert.Null(ngaReader.GetAnnotation("gene3"));
Assert.Equal("[{\"mimNumber\":123,\"geneName\":\"gene name 1 ('minibrain', Drosophila, homolog of)\",\"description\":\"describing gene 1\\n\\\"some citation\\\"\",\"phenotypes\":[{\"phenotype\":\"disease 1\",\"mapping\":\"mapping of the wildtype gene\",\"inheritances\":[\"autosomal recessive\"],\"comments\":\"unconfirmed or possibly spurious mapping\"}]}]", ngaReader.GetAnnotation("gene1"));
Assert.Equal("[{\"mimNumber\":124,\"geneName\":\"gene name 2\",\"phenotypes\":[{\"phenotype\":\"disease 2\",\"mapping\":\"chromosome deletion or duplication syndrome\",\"inheritances\":[\"whatever\",\"never-ever\"],\"comments\":\"nondiseases\"}]}]", ngaReader.GetAnnotation("gene2"));
}
ngaWriter.Dispose();
}
public void ReadBackGeneAnnotations()
{
NgaReader reader;
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks);
const string jsonKey = "mimo";
const bool isArray = true;
using (var ms = new MemoryStream())
{
using (var writer = new NgaWriter(ms, version, jsonKey, SaCommon.SchemaVersion, isArray, true))
{
writer.Write(GetGeneAnnotations());
}
ms.Position = 0;
reader = NgaReader.Read(ms);
}
Assert.NotNull(reader);
Assert.Null(reader.GetAnnotation("gene3"));
Assert.Equal("[{\"mimNumber\":123,\"geneName\":\"gene name 1 ('minibrain', Drosophila, homolog of)\",\"description\":\"describing gene 1\\n\\\"some citation\\\"\",\"phenotypes\":[{\"phenotype\":\"disease 1\",\"description\":\"This is disease 1\",\"mapping\":\"mapping of the wildtype gene\",\"inheritances\":[\"autosomal recessive\"],\"comments\":[\"unconfirmed or possibly spurious mapping\"]}]}]", reader.GetAnnotation("gene1"));
Assert.Equal("[{\"mimNumber\":124,\"geneName\":\"gene name 2\",\"phenotypes\":[{\"phenotype\":\"disease 2\",\"description\":\"COVID-19\",\"mapping\":\"chromosome deletion or duplication syndrome\",\"inheritances\":[\"whatever\",\"never-ever\"],\"comments\":[\"nondiseases\"]}]}]", reader.GetAnnotation("gene2"));
}
