public CustomGene(string geneSymbol, List <string[]> values, SaJsonSchema jsonSchema, string inputLine)
{
GeneSymbol = geneSymbol;
_values = values;
_jsonSchema = jsonSchema;
_inputLine = inputLine;
}
public static Dictionary <string, List <ISuppGeneItem> > GetGeneToOmimEntriesAndSchema(IEnumerable <OmimItem> omimItems)
{
var geneToOmimEntries = new Dictionary <string, List <ISuppGeneItem> >();
SaJsonSchema jsonSchema = null;
foreach (var item in omimItems)
{
if (jsonSchema == null)
{
jsonSchema = item.JsonSchema;
}
if (item.GeneSymbol == null)
{
continue;
}
if (geneToOmimEntries.TryGetValue(item.GeneSymbol, out var mimList))
{
mimList.Add(item);
}
else
{
geneToOmimEntries[item.GeneSymbol] = new List <ISuppGeneItem> {
item
};
}
}
return(geneToOmimEntries);
}
public void CheckAndGetBoolFromString_InvalidValue_ThrowException()
{
Assert.Throws <UserErrorException>(() => SaJsonSchema.CheckAndGetBoolFromString("T"));
Assert.Throws <UserErrorException>(() => SaJsonSchema.CheckAndGetBoolFromString("F"));
Assert.Throws <UserErrorException>(() => SaJsonSchema.CheckAndGetBoolFromString("0"));
Assert.Throws <UserErrorException>(() => SaJsonSchema.CheckAndGetBoolFromString("-"));
}
public static OmimItem.Phenotype GetPhenotype(PhenotypeMap phenotypeMap, SaJsonSchema jsonSchema)
{
var phenotypeItem = phenotypeMap.phenotypeMap;
var(phenotype, comments) = ExtractPhenotypeAndComments(phenotypeItem.phenotype);
return(new OmimItem.Phenotype(phenotypeItem.phenotypeMimNumber, phenotype, (OmimItem.Mapping)phenotypeItem.phenotypeMappingKey, comments, ExtractInheritances(phenotypeItem.phenotypeInheritance), jsonSchema));
}
public static OmimItem.Phenotype GetPhenotype(PhenotypeMap phenotypeMap, SaJsonSchema jsonSchema)
{
var phenotypeItem = phenotypeMap.phenotypeMap;
var(phenotype, _) = ExtractPhenotypeAndComments(phenotypeItem.phenotype);
//Don't output any comments for now
return(new OmimItem.Phenotype(phenotypeItem.phenotypeMimNumber, phenotype, (OmimItem.Mapping)phenotypeItem.phenotypeMappingKey, OmimItem.Comments.unknown, ExtractInheritances(phenotypeItem.phenotypeInheritance), jsonSchema));
}
public OmimItem(string geneSymbol, string geneName, string description, int mimNumber, List <Phenotype> phenotypes, SaJsonSchema jsonSchema)
{
GeneSymbol = geneSymbol;
_geneName = geneName;
_description = description;
_mimNumber = mimNumber;
_phenotypes = phenotypes;
JsonSchema = jsonSchema;
}
public Phenotype(int mimNumber, string phenotype, Mapping mapping, Comment[] comments, HashSet <string> inheritance, SaJsonSchema schema)
{
_mimNumber = mimNumber;
_phenotype = phenotype;
_mapping = mapping;
_comments = comments;
_inheritance = inheritance;
_jsonSchema = schema;
}
public void OutputKeyAnnotation_AsExpected()
{
var sb = new StringBuilder();
var jsonSchema = new SaJsonSchema(sb);
jsonSchema.AddAnnotation("name", SaJsonKeyAnnotation.CreateFromProperties(SaJsonValueType.String, 0, null));
jsonSchema.OutputKeyAnnotation("name");
Assert.Equal("\"name\":{\"type\":\"string\"}", sb.ToString());
}
public void Create_InitialJsonObject_AsExpected()
{
var sb = new StringBuilder();
SaJsonSchema.Create(sb, "test", SaJsonValueType.ObjectArray, new List <string>());
const string expectedJsonString = "{\"$schema\":\"" + SchemaVersion + "\",\"type\":\"object\",\"properties\":{\"test\":{\"type\":\"array\",\"items\":{\"type\":\"object\",\"properties\":{";
Assert.Equal(expectedJsonString, sb.ToString());
}
public void CheckAndGetBoolFromString_AsExpected()
{
Assert.True(SaJsonSchema.CheckAndGetBoolFromString("true"));
Assert.True(SaJsonSchema.CheckAndGetBoolFromString("TRUE"));
Assert.False(SaJsonSchema.CheckAndGetBoolFromString("false"));
Assert.False(SaJsonSchema.CheckAndGetBoolFromString("False"));
Assert.False(SaJsonSchema.CheckAndGetBoolFromString(""));
Assert.False(SaJsonSchema.CheckAndGetBoolFromString("."));
}
/// <summary>
/// constructor
/// </summary>
public CustomInterval(IChromosome chromosome, int start, int end, List <string[]> values, SaJsonSchema jsonSchema, string inputLine)
{
Chromosome = chromosome;
Start = start;
End = end;
VariantType = VariantType.structural_alteration;
_values = values;
_jsonSchema = jsonSchema;
_inputLine = inputLine;
}
public CustomItem(IChromosome chromosome, int start, string refAllele, string altAllele, string[][] values, SaJsonSchema jsonSchema, string inputLine)
{
Chromosome = chromosome;
Position = start;
RefAllele = refAllele;
AltAllele = altAllele;
_values = values;
_jsonSchema = jsonSchema;
_inputLine = inputLine;
}
public OmimParser(GeneSymbolUpdater geneSymbolUpdater, SaJsonSchema jsonSchema, string apiKey, string dumpFilePath)
{
_geneSymbolUpdater = geneSymbolUpdater;
_jsonSchema = jsonSchema;
if (dumpFilePath != null)
{
_zipFileStream = new FileStream(dumpFilePath, FileMode.Create);
_zipArchive = new ZipArchive(_zipFileStream, ZipArchiveMode.Create);
}
_httpClient = new HttpClient();
_httpClient.DefaultRequestHeaders.Add("ApiKey", apiKey);
}
public static SaJsonSchema Get()
{
var jsonSchema = SaJsonSchema.Create(new StringBuilder(), SaCommon.ClinvarTag, PrimaryValueType, JsonKeys);
jsonSchema.SetNonSaKeys(new [] { "isAlleleSpecific" });
foreach ((string key, var valueType) in JsonKeys.Zip(ValueTypes, (a, b) => (a, b)))
{
jsonSchema.AddAnnotation(key, SaJsonKeyAnnotation.CreateFromProperties(valueType, 0, null));
}
return(jsonSchema);
}
public void GetJsonString_AsExpected()
{
var jsonSchema = SaJsonSchema.Create(new StringBuilder(), "test", SaJsonValueType.ObjectArray, new List <string> {
"name", "phone", "employed"
});
jsonSchema.AddAnnotation("name", SaJsonKeyAnnotation.CreateFromProperties(SaJsonValueType.String, 0, null));
jsonSchema.AddAnnotation("phone", SaJsonKeyAnnotation.CreateFromProperties(SaJsonValueType.Number, 0, "phone number"));
jsonSchema.AddAnnotation("employed", SaJsonKeyAnnotation.CreateFromProperties(SaJsonValueType.Bool, 0, null));
var jsonString = jsonSchema.GetJsonString(new List <string[]> {
new[] { "Ada" }, new[] { "123456" }, new[] { "true" }
});
Assert.Equal("\"name\":\"Ada\",\"phone\":123456,\"employed\":true", jsonString);
}
public void GetJsonString_DoubleValueHandling_AsExpected()
{
var jsonSchema = SaJsonSchema.Create(new StringBuilder(), "test", SaJsonValueType.ObjectArray, new List <string> {
"allAf", "doubleValue1", "doubleValue2"
});
jsonSchema.AddAnnotation("allAf", SaJsonKeyAnnotation.CreateFromProperties(SaJsonValueType.Number, CustomAnnotationCategories.AlleleFrequency, null));
jsonSchema.AddAnnotation("doubleValue1", SaJsonKeyAnnotation.CreateFromProperties(SaJsonValueType.Number, 0, "A double value"));
jsonSchema.AddAnnotation("doubleValue2", SaJsonKeyAnnotation.CreateFromProperties(SaJsonValueType.Number, 0, "Another double value"));
var jsonString = jsonSchema.GetJsonString(new List <string[]> {
new[] { "0.12345678" }, new[] { "0.12" }, new[] { "0.12345678" }
});
Assert.Equal("\"allAf\":0.123457,\"doubleValue1\":0.12,\"doubleValue2\":0.12345678", jsonString);
}
public ClinVarItem(IChromosome chromosome,
int position,
int stop,
string refAllele,
string altAllele,
SaJsonSchema jsonSchema,
IEnumerable <string> alleleOrigins,
string variantType,
string id,
string variationId,
ClinVarCommon.ReviewStatus reviewStatus,
IEnumerable <string> medGenIds,
IEnumerable <string> omimIds,
IEnumerable <string> orphanetIds,
IEnumerable <string> phenotypes,
string[] significances,
IEnumerable <long> pubmedIds = null,
long lastUpdatedDate = long.MinValue
)
{
Chromosome = chromosome;
Position = position;
Stop = stop;
AlleleOrigins = alleleOrigins;
AltAllele = altAllele;
JsonSchema = jsonSchema;
VariantType = variantType;
Id = id;
VariationId = variationId;
MedGenIds = medGenIds;
OmimIds = omimIds;
OrphanetIds = orphanetIds;
Phenotypes = phenotypes;
RefAllele = refAllele;
Significances = significances;
PubmedIds = pubmedIds;
LastUpdatedDate = lastUpdatedDate;
IsAlleleSpecific = null;
ReviewStatus = reviewStatus;
}
public void ToString_AsExpected()
{
var jsonSchema = SaJsonSchema.Create(new StringBuilder(), "test", SaJsonValueType.ObjectArray, new List <string> {
"name", "phone", "employed"
});
jsonSchema.AddAnnotation("name", SaJsonKeyAnnotation.CreateFromProperties(SaJsonValueType.String, 0, null));
jsonSchema.AddAnnotation("phone", SaJsonKeyAnnotation.CreateFromProperties(SaJsonValueType.Number, 0, "phone number"));
jsonSchema.AddAnnotation("employed", SaJsonKeyAnnotation.CreateFromProperties(SaJsonValueType.Bool, 0, null));
jsonSchema.TotalItems = 100;
jsonSchema.KeyCounts["name"] = 100;
jsonSchema.KeyCounts["phone"] = 50;
jsonSchema.KeyCounts["employed"] = 0;
const string expectedJsonSchemaString = "{\"$schema\":\"" + SchemaVersion + "\",\"type\":\"object\",\"properties\":{\"test\":{\"type\":\"array\",\"items\":{\"type\":\"object\",\"properties\":{"
+ "\"name\":{\"type\":\"string\"},\"phone\":{\"type\":\"number\",\"description\":\"phone number\"}},"
+ "\"required\":[\"name\"],\"additionalProperties\":false}}}}";
Assert.Equal(expectedJsonSchemaString, jsonSchema.ToString());
// make sure the returned string is the same when ToString method is called more than once
Assert.Equal(expectedJsonSchemaString, jsonSchema.ToString());
}
public void CheckAndGetNullableDoubleFromString_GetNull_AsExpected()
{
Assert.Null(SaJsonSchema.CheckAndGetNullableDoubleFromString(""));
Assert.Null(SaJsonSchema.CheckAndGetNullableDoubleFromString("."));
}
public void CheckAndGetNullableDoubleFromString_NotANum_ThrowException()
{
Assert.Throws <UserErrorException>(() => SaJsonSchema.CheckAndGetNullableDoubleFromString("Bob"));
Assert.Throws <UserErrorException>(() => SaJsonSchema.CheckAndGetNullableDoubleFromString("1+1"));
Assert.Throws <UserErrorException>(() => SaJsonSchema.CheckAndGetNullableDoubleFromString("bool"));
}
public OmimParser(string mimToGeneSymbolFile, string omimJsonFile, SaJsonSchema jsonSchema)
{
_mimToGeneSymbolFile = mimToGeneSymbolFile;
_omimJsonFile = omimJsonFile;
_jsonSchema = jsonSchema;
}
public static OmimItem.Phenotype GetPhenotype(PhenotypeMap phenotypeMap,
IDictionary <int, string> phenotypeDescriptions, SaJsonSchema jsonSchema)
{
var phenotypeItem = phenotypeMap.phenotypeMap;
var mimNumber = phenotypeItem.phenotypeMimNumber;
phenotypeDescriptions.TryGetValue(mimNumber, out var description);
var(phenotype, comments) = ExtractPhenotypeAndComments(phenotypeItem.phenotype);
return(new OmimItem.Phenotype(mimNumber, phenotype, description, (OmimItem.Mapping)phenotypeItem.phenotypeMappingKey, comments, ExtractInheritances(phenotypeItem.phenotypeInheritance), jsonSchema));
}
private void InitiateSchema()
{
JsonSchema = SaJsonSchema.Create(new StringBuilder(), JsonTag, SaJsonValueType.Object, JsonKeys);
}
