public CreateOmimDatabase(string omimFile, string outputDirectory)
{
if (omimFile == null)
{
return;
}
_outputFile = Path.Combine(outputDirectory, OmimDatabaseCommon.OmimDatabaseFileName);
_omimReader = new OmimReader(new FileInfo(omimFile));
_dataVersion = AddSourceVersion(omimFile);
}
void TestOmimParser()
{
var expectedOmimEntries = new List <string>
{
"{\"mimNumber\":\"601405\",\"hgnc\":\"CTRC\",\"description\":\"Chymotrypsin\",\"phenotypes\":[{\"mimNumber\":\"167800\",\"phenotype\":\"Pancreatitis, chronic, susceptibility to\",\"mapping\":\"molecular basis of the disorder is known\",\"inheritances\":[\"Autosomal dominant\"],\"comments\":\"contribute to susceptibility to multifactorial disorders or to susceptibility to infection\"}]}",
"{\"mimNumber\":\"606928\",\"hgnc\":\"BMND3\",\"description\":\"Bone mineral density QTL 3\",\"phenotypes\":[{\"mimNumber\":\"606928\",\"phenotype\":\"Bone mineral density QTL 3\",\"mapping\":\"disease phenotype itself was mapped\",\"comments\":\"nondiseases\"}]}",
"{\"mimNumber\":\"103730\",\"hgnc\":\"ADH1C\",\"description\":\"Alcohol dehydrogenase IC (class I), gamma polypeptide\",\"phenotypes\":[{\"mimNumber\":\"103780\",\"phenotype\":\"Alcohol dependence, protection against\",\"mapping\":\"molecular basis of the disorder is known\",\"inheritances\":[\"Multifactorial\"],\"comments\":\"contribute to susceptibility to multifactorial disorders or to susceptibility to infection\"},{\"mimNumber\":\"168600\",\"phenotype\":\"Parkinson disease, susceptibility to\",\"mapping\":\"molecular basis of the disorder is known\",\"inheritances\":[\"Isolated cases\",\"Multifactorial\"],\"comments\":\"contribute to susceptibility to multifactorial disorders or to susceptibility to infection\"}]}",
"{\"mimNumber\":\"162230\",\"hgnc\":\"NEFH\",\"description\":\"Neurofilament, heavy polypeptide\",\"phenotypes\":[{\"mimNumber\":\"105400\",\"phenotype\":\"Amyotrophic lateral sclerosis, susceptibility to\",\"mapping\":\"molecular basis of the disorder is known\",\"inheritances\":[\"Autosomal recessive\",\"Autosomal dominant\"],\"comments\":\"unconfirmed or possibly spurious mapping\"},{\"mimNumber\":\"616924\",\"phenotype\":\"Charcot-Marie-Tooth disease, axonal, type 2CC\",\"mapping\":\"molecular basis of the disorder is known\",\"inheritances\":[\"Autosomal dominant\"]}]}",
"{\"mimNumber\":\"615410\",\"hgnc\":\"MRAP2\",\"description\":\"Melanocortin 2 receptor accessory protein 2\",\"phenotypes\":[{\"mimNumber\":\"615457\",\"phenotype\":\"Obesity, susceptibility to, BMIQ18\",\"mapping\":\"molecular basis of the disorder is known\",\"inheritances\":[\"Autosomal dominant\"],\"comments\":\"unconfirmed or possibly spurious mapping\"}]}",
"{\"mimNumber\":\"603517\",\"hgnc\":\"BCL10\",\"description\":\"B-cell leukemia/lymphoma 10\",\"phenotypes\":[{\"mimNumber\":\"616098\",\"phenotype\":\"Immunodeficiency 37\",\"mapping\":\"molecular basis of the disorder is known\",\"inheritances\":[\"Autosomal recessive\"],\"comments\":\"unconfirmed or possibly spurious mapping\"},{\"mimNumber\":\"137245\",\"phenotype\":\"Lymphoma, MALT, somatic\",\"mapping\":\"molecular basis of the disorder is known\"},{\"mimNumber\":\"605027\",\"phenotype\":\"Lymphoma, follicular, somatic\",\"mapping\":\"molecular basis of the disorder is known\",\"comments\":\"contribute to susceptibility to multifactorial disorders or to susceptibility to infection\"},{\"mimNumber\":\"273300\",\"phenotype\":\"Male germ cell tumor, somatic\",\"mapping\":\"molecular basis of the disorder is known\",\"comments\":\"contribute to susceptibility to multifactorial disorders or to susceptibility to infection\"},{\"mimNumber\":\"156240\",\"phenotype\":\"Mesothelioma, somatic\",\"mapping\":\"molecular basis of the disorder is known\",\"comments\":\"contribute to susceptibility to multifactorial disorders or to susceptibility to infection\"},{\"phenotype\":\"Sezary syndrome, somatic\",\"mapping\":\"molecular basis of the disorder is known\",\"comments\":\"contribute to susceptibility to multifactorial disorders or to susceptibility to infection\"}]}"
};
var omimFile = Resources.TopPath("testOmim.txt");
var omimReader = new OmimReader(new FileInfo(omimFile));
var observedOmimEntries = omimReader.ToList().Select(x => x.ToString()).ToList();
Assert.Equal(6, observedOmimEntries.Count);
Assert.True(expectedOmimEntries.SequenceEqual(observedOmimEntries));
}
void ReadAndWriteTests()
{
var omimFile = Resources.TopPath("testOmim.txt");
var randomPath = Path.GetTempPath();
var omimCreater = new CreateOmimDatabase(omimFile, randomPath);
omimCreater.Create();
var omimDataBaseFile = Path.Combine(randomPath, OmimDatabaseCommon.OmimDatabaseFileName);
var omimDatabaseReader = new OmimDatabaseReader(omimDataBaseFile);
var omimEntries = omimDatabaseReader.Read().ToList();
var omimReader = new OmimReader(new FileInfo(omimFile));
var expectedOmimEntries = omimReader.ToList();
Assert.Equal(6, expectedOmimEntries.Count);
Assert.Equal(expectedOmimEntries.Count, omimEntries.Count);
Assert.True(omimEntries.SequenceEqual(expectedOmimEntries));
}
