// constructor
public MapperUnit(ushort referenceIndex, int start, int end, MapperUnitType id)
: base(referenceIndex, start, end)
{
ID = id;
_hashCode = End.GetHashCode() ^
ID.GetHashCode() ^
ReferenceIndex.GetHashCode() ^
Start.GetHashCode();
}
public void GetMaxOffset_MissingAllOverlappingBins_ReturnMaxOffset()
{
const ulong expectedResults = ulong.MaxValue;
var idToChunks = new Dictionary <int, Interval[]>();
var refSeq = new ReferenceIndex(ChromosomeUtilities.Chr2, idToChunks, null);
ulong observedResults = SearchUtilities.GetMaxOffset(refSeq, 243171329);
Assert.Equal(expectedResults, observedResults);
}
public override int GetHashCode()
{
var hashCode = ReferenceIndex.GetHashCode() ^ Start.GetHashCode() ^ End.GetHashCode() ^
EntrezGeneId.GetHashCode() ^ EnsemblId.GetHashCode() ^ _hgncId.GetHashCode();
if (Symbol != null)
{
hashCode ^= Symbol.GetHashCode();
}
return(hashCode);
}
public Gene(ushort referenceIndex, int start, int end, string stableId, bool onReverseStrand)
: base(referenceIndex, start, end)
{
StableId = stableId;
_onReverseStrand = onReverseStrand;
_hashCode = End.GetHashCode() ^
_onReverseStrand.GetHashCode() ^
ReferenceIndex.GetHashCode() ^
StableId.GetHashCode() ^
Start.GetHashCode();
}
public void Test_FhirUri_Referance_IndexSetter_GoodFormat_NoMatchOnServiceRootUrl()
{
//Arrange
string ServiceRootUrlString = "http://SomeWhere.net.au/FhirApi/Patient";
string ReferanceUrlString = "http://SomeWhereElse.net.au/FhirApi/Encounter/10";
IFhirUri ReferanceFhirUri = Pyro.Common.CommonFactory.GetFhirUri(new Uri(ReferanceUrlString));
var FhirUri = new FhirUri();
FhirUri.Value = ReferanceUrlString;
//Mok the inbound Request Url, this contains the service root url from the db.
Mock <IDtoFhirRequestUri> MockIDtoFhirRequestUri = new Mock <IDtoFhirRequestUri>();
var ServiceRootUrl = new Uri(ServiceRootUrlString);
IFhirUri RequestFhirUri = Pyro.Common.CommonFactory.GetFhirUri(ServiceRootUrl);
MockIDtoFhirRequestUri.Setup(x => x.FhirUri).Returns(RequestFhirUri);
var ServiceDtoRootUrlStore = new Pyro.Common.BusinessEntities.Dto.DtoRootUrlStore();
ServiceDtoRootUrlStore.Id = 1;
ServiceDtoRootUrlStore.IsServersPrimaryUrlRoot = true;
ServiceDtoRootUrlStore.Url = ServiceRootUrlString;
MockIDtoFhirRequestUri.Setup(x => x.PrimaryRootUrlStore).Returns(ServiceDtoRootUrlStore);
//Mok the response from the db from the Common repository, this if request Url does not match service root url
Mock <Pyro.DataModel.Repository.Interfaces.ICommonRepository> MockICommonRepository = new Mock <Pyro.DataModel.Repository.Interfaces.ICommonRepository>();
var ReferanceRootUrlStore = new Pyro.DataModel.DatabaseModel.ServiceRootURL_Store();
ReferanceRootUrlStore.ServiceRootURL_StoreID = 0;
ReferanceRootUrlStore.IsServersPrimaryUrlRoot = false;
ReferanceRootUrlStore.RootUrl = ReferanceFhirUri.ServiceRootUrlForComparison;
MockICommonRepository.Setup(x => x.GetAndOrAddService_RootUrlStore(ReferanceFhirUri.ServiceRootUrlForComparison)).Returns(ReferanceRootUrlStore);
ReferenceIndex Index = new ReferenceIndex();
//Act
Index = IndexSetterFactory.Create(typeof(ReferenceIndex)).Set(FhirUri, Index, MockIDtoFhirRequestUri.Object, MockICommonRepository.Object) as ReferenceIndex;
//Assert
Assert.AreEqual(Index.FhirId, ReferanceFhirUri.Id);
Assert.AreEqual(Index.Type, ReferanceFhirUri.ResourseType);
Assert.IsNotNull(Index.Url);
Assert.AreEqual(Index.Url.ServiceRootURL_StoreID, 0);
Assert.IsFalse(Index.Url.IsServersPrimaryUrlRoot);
Assert.AreEqual(Index.Url.RootUrl, ReferanceFhirUri.ServiceRootUrlForComparison);
Assert.IsNull(Index.VersionId);
Assert.IsNull(Index.ServiceRootURL_StoreID);
//Test GetAndOrAddPyro_RootUrlStore called once to add or get the Url from / to the db
Assert.DoesNotThrow(() => MockICommonRepository.Verify(x => x.GetAndOrAddService_RootUrlStore(ReferanceFhirUri.ServiceRootUrlForComparison), Times.Once));
}
public Exon(ushort referenceIndex, int start, int end, string stableId, bool onReverseStrand, byte?phase)
: base(referenceIndex, start, end)
{
_stableId = stableId;
OnReverseStrand = onReverseStrand;
Phase = phase;
_hashCode = End.GetHashCode() ^
OnReverseStrand.GetHashCode() ^
ReferenceIndex.GetHashCode() ^
_stableId.GetHashCode() ^
Start.GetHashCode();
}
public void GetMaxOffset_Nominal()
{
const ulong expectedResults = 3591443312067;
var idToChunks = new Dictionary <int, Interval[]>
{
[6311] = new[] { new Interval(3591443312067, 3592132724129) }
};
var refSeq = new ReferenceIndex(ChromosomeUtilities.Chr2, idToChunks, null);
ulong observedResults = SearchUtilities.GetMaxOffset(refSeq, 26699126);
Assert.Equal(expectedResults, observedResults);
}
public void GetMaxOffset_MissingBin()
{
const ulong expectedResults = 3724057593420;
var idToChunks = new Dictionary <int, Interval[]>
{
[6878] = new[] { new Interval(3724057593420, 3724057615020) }
};
var refSeq = new ReferenceIndex(ChromosomeUtilities.Chr2, idToChunks, null);
ulong observedResults = SearchUtilities.GetMaxOffset(refSeq, 35962881);
Assert.Equal(expectedResults, observedResults);
}
public void GetMaxOffset_MissingFirstBin()
{
const ulong expectedResults = 3724908138137;
var idToChunks = new Dictionary <int, Interval[]>
{
[860] = new[] { new Interval(3724908138137, 3724908155075) }
};
var refSeq = new ReferenceIndex(ChromosomeUtilities.Chr2, idToChunks, null);
ulong observedResults = SearchUtilities.GetMaxOffset(refSeq, 36028417);
Assert.Equal(expectedResults, observedResults);
}
public void Test_ResourceReference_Referance_IndexSetter_GoodFormat_MatchesServiceRootUrl()
{
//Arrange
string ServiceRootUrl = "http://somewhere.net.au/FhirApi/Patient";
string ReferanceUrl = "http://somewhere.net.au/FhirApi/Encounter/10";
IFhirUri ReferanceFhirUri = Common.CommonFactory.GetFhirUri(new Uri(ReferanceUrl));
var ResourceReference = new ResourceReference();
ResourceReference.Reference = ReferanceUrl;
//Mok the inbound Request Url, this contains the service root url from the db.
Mock <IDtoFhirRequestUri> MockIDtoFhirRequestUri = new Mock <IDtoFhirRequestUri>();
var RootUrl = new Uri(ServiceRootUrl);
IFhirUri RequestFhirUri = Common.CommonFactory.GetFhirUri(RootUrl);
MockIDtoFhirRequestUri.Setup(x => x.FhirUri).Returns(RequestFhirUri);
var DtoRootUrlStore = new Pyro.Common.BusinessEntities.Dto.DtoRootUrlStore();
DtoRootUrlStore.Id = 1;
DtoRootUrlStore.IsServersPrimaryUrlRoot = true;
DtoRootUrlStore.Url = ServiceRootUrl;
MockIDtoFhirRequestUri.Setup(x => x.PrimaryRootUrlStore).Returns(DtoRootUrlStore);
//Mok the response from the db from the Common repository, this if request Url does not match service root url
Mock <Pyro.DataModel.Repository.Interfaces.ICommonRepository> MockICommonRepository = new Mock <Pyro.DataModel.Repository.Interfaces.ICommonRepository>();
var RootUrlStore = new Pyro.DataModel.DatabaseModel.ServiceRootURL_Store();
RootUrlStore.ServiceRootURL_StoreID = 0;
RootUrlStore.IsServersPrimaryUrlRoot = false;
RootUrlStore.RootUrl = ReferanceFhirUri.ServiceRootUrlForComparison;
MockICommonRepository.Setup(x => x.GetAndOrAddService_RootUrlStore(ReferanceFhirUri.ServiceRootUrlForComparison)).Returns(RootUrlStore);
ReferenceIndex Index = new ReferenceIndex();
//Act
Index = IndexSetterFactory.Create(typeof(ReferenceIndex)).Set(ResourceReference, Index, MockIDtoFhirRequestUri.Object, MockICommonRepository.Object) as ReferenceIndex;
//Assert
Assert.AreEqual(Index.FhirId, ReferanceFhirUri.Id);
Assert.AreEqual(Index.Type, ReferanceFhirUri.ResourseType);
Assert.AreEqual(Index.ServiceRootURL_StoreID, 1);
Assert.IsNull(Index.Url);
Assert.IsNull(Index.VersionId);
//Test GetAndOrAddPyro_RootUrlStore not called because Reference url root matches server root url
Assert.DoesNotThrow(() => MockICommonRepository.Verify(x => x.GetAndOrAddService_RootUrlStore(ReferanceFhirUri.ServiceRootUrlForComparison), Times.Never()));
}
public void GetMinOffset_MissingBin()
{
const ulong expectedResults = 3723191187417;
var linearFileOffsets = new ulong[2196];
linearFileOffsets[2195] = expectedResults;
var idToChunks = new Dictionary <int, Interval[]>
{
[6876] = new[] { new Interval(1, 1) }
};
var refSeq = new ReferenceIndex(ChromosomeUtilities.Chr2, idToChunks, linearFileOffsets);
ulong observedResults = SearchUtilities.GetMinOffset(refSeq, 35979265);
Assert.Equal(expectedResults, observedResults);
}
public void GetMinOffset_Nominal()
{
const ulong expectedResults = 3591443256775;
var linearFileOffsets = new ulong[1630];
linearFileOffsets[1629] = expectedResults;
var idToChunks = new Dictionary <int, Interval[]>
{
[6310] = new[] { new Interval(1, 1) }
};
var refSeq = new ReferenceIndex(ChromosomeUtilities.Chr2, idToChunks, linearFileOffsets);
ulong observedResults = SearchUtilities.GetMinOffset(refSeq, 26699125);
Assert.Equal(expectedResults, observedResults);
}
public void GetOffset_Nominal()
{
var linearFileOffsets = new ulong[1630];
linearFileOffsets[1629] = 3591443256775;
var idToChunks = GetIdToChunks();
var refSeqs = new ReferenceIndex[2];
refSeqs[1] = new ReferenceIndex(ChromosomeUtilities.Chr2, idToChunks, linearFileOffsets);
var index = new Index(Constants.VcfFormat, 0, 0, 0, '#', 0, refSeqs, _refNameToTabixIndex);
long observedResult = index.GetOffset("chr2", 26699126);
Assert.Equal(3591443256857, observedResult);
}
public void Test_FhirUri_Referance_IndexSetter_Uri_Is_RelativeUri()
{
//Info: This is a Uri that is not a Fhir resource reference, it is actually a GUID expressed as a Uri.
//In this case as it is not a FhirUriReferance we want to return null as it is not searchable as a
//Search parameter type of Reference.
//Arrange
string ServiceRootUrlString = "http://SomeWhere.net.au/FhirApi/Patient";
string ReferanceUrlString = "Encounter/10";
IFhirUri ReferanceFhirUri = Common.CommonFactory.GetFhirUri(ReferanceUrlString);
//IFhirUri ReferanceFhirUri = new Pyro.Common.BusinessEntities.UriSupport.DtoFhirUri(ReferanceUrlString);
FhirUri FhirUri = new FhirUri();
FhirUri.Value = ReferanceUrlString;
//Mok the inbound Request Url, this contains the service root url from the db.
Mock <IDtoFhirRequestUri> MockIDtoFhirRequestUri = new Mock <IDtoFhirRequestUri>();
var ServiceRootUrl = new Uri(ServiceRootUrlString);
IFhirUri RequestFhirUri = Pyro.Common.CommonFactory.GetFhirUri(ServiceRootUrl);
MockIDtoFhirRequestUri.Setup(x => x.FhirUri).Returns(RequestFhirUri);
var ServiceDtoRootUrlStore = new Pyro.Common.BusinessEntities.Dto.DtoRootUrlStore();
ServiceDtoRootUrlStore.Id = 1;
ServiceDtoRootUrlStore.IsServersPrimaryUrlRoot = true;
ServiceDtoRootUrlStore.Url = ServiceRootUrlString;
MockIDtoFhirRequestUri.Setup(x => x.PrimaryRootUrlStore).Returns(ServiceDtoRootUrlStore);
//Mok the response from the db from the Common repository, this if request Url does not match service root url
Mock <Pyro.DataModel.Repository.Interfaces.ICommonRepository> MockICommonRepository = new Mock <Pyro.DataModel.Repository.Interfaces.ICommonRepository>();
ReferenceIndex Index = new ReferenceIndex();
//Act
Index = IndexSetterFactory.Create(typeof(ReferenceIndex)).Set(FhirUri, Index, MockIDtoFhirRequestUri.Object, MockICommonRepository.Object) as ReferenceIndex;
//Assert
Assert.AreEqual(Index.FhirId, ReferanceFhirUri.Id);
Assert.AreEqual(Index.Type, ReferanceFhirUri.ResourseType);
Assert.IsNull(Index.Url);
Assert.IsNull(Index.VersionId);
Assert.AreEqual(Index.ServiceRootURL_StoreID, 1);
Assert.DoesNotThrow(() => MockICommonRepository.Verify(x => x.GetAndOrAddService_RootUrlStore(ReferanceFhirUri.ServiceRootUrlForComparison), Times.Never));
}
public void GetMinOffset_MissingFirstBin()
{
const ulong expectedResults = 4351134646660;
var linearFileOffsets = new ulong[5353];
linearFileOffsets[5352] = expectedResults;
var idToChunks = new Dictionary <int, Interval[]>
{
[1254] = new[] { new Interval(1, 1) }
};
var refSeq = new ReferenceIndex(ChromosomeUtilities.Chr2, idToChunks, linearFileOffsets);
ulong observedResults = SearchUtilities.GetMinOffset(refSeq, 87687168);
Assert.Equal(expectedResults, observedResults);
}
public void GetTabixReferenceSequence_Nominal()
{
var linearFileOffsets = new ulong[1630];
linearFileOffsets[1629] = 3591443256775;
var idToChunks = GetIdToChunks();
var refSeqs = new ReferenceIndex[2];
refSeqs[1] = new ReferenceIndex(ChromosomeUtilities.Chr2, idToChunks, linearFileOffsets);
var index = new Index(Constants.VcfFormat, 0, 0, 0, '#', 0, refSeqs, _refNameToTabixIndex);
var refSeq = index.GetTabixReferenceSequence("chr2");
Assert.Equal("chr2", refSeq.Chromosome.UcscName);
}
public void GetOffset_NoOverlappingBins_UseLinearIndex_WithTruncatedIndex_ReturnMinusOne()
{
var linearFileOffsets = new ulong[1];
linearFileOffsets[0] = 11418;
var idToChunks = new Dictionary <int, Interval[]>();
var refSeqs = new ReferenceIndex[2];
refSeqs[0] = new ReferenceIndex(ChromosomeUtilities.Chr1, idToChunks, linearFileOffsets);
var index = new Index(Constants.VcfFormat, 0, 0, 0, '#', 0, refSeqs, _refNameToTabixIndex);
long observedResult = index.GetOffset("chr1", 100_000);
Assert.Equal(-1, observedResult);
}
public Slice(ushort referenceIndex, int start, int end, bool onReverseStrand, bool isCircular, bool isTopLevel, CoordSystem coordSystem,
int sequenceRegionLen, string sequenceRegionName)
: base(referenceIndex, start, end)
{
_onReverseStrand = onReverseStrand;
_isCircular = isCircular;
_isTopLevel = isTopLevel;
CoordinateSystem = coordSystem;
_sequenceRegionLen = sequenceRegionLen;
_sequenceRegionName = sequenceRegionName;
_hashCode = End.GetHashCode() ^
_isCircular.GetHashCode() ^
_isTopLevel.GetHashCode() ^
_onReverseStrand.GetHashCode() ^
ReferenceIndex.GetHashCode() ^
_sequenceRegionLen.GetHashCode() ^
_sequenceRegionName.GetHashCode() ^
Start.GetHashCode();
}
/// <summary>
/// generates the hash code
/// </summary>
private void GenerateHashCode()
{
_hashCode = BioType.GetHashCode() ^
CompDnaCodingEnd.GetHashCode() ^
CompDnaCodingStart.GetHashCode() ^
End.GetHashCode() ^
IsCanonical.GetHashCode() ^
OnReverseStrand.GetHashCode() ^
ReferenceIndex.GetHashCode() ^
Start.GetHashCode();
if (CcdsId != null) _hashCode ^= CcdsId.GetHashCode();
if (DatabaseId != null) _hashCode ^= DatabaseId.GetHashCode();
if (ProteinId != null) _hashCode ^= ProteinId.GetHashCode();
if (RefSeqId != null) _hashCode ^= RefSeqId.GetHashCode();
if (GeneStableId != null) _hashCode ^= GeneStableId.GetHashCode();
if (StableId != null) _hashCode ^= StableId.GetHashCode();
if (Gene != null) _hashCode ^= Gene.GetHashCode();
if (Slice != null) _hashCode ^= Slice.GetHashCode();
}
public void Test_ResourceReference_Referance_IndexSetter_Uri_Is_Not_A_Fhir_Referance_Uri()
{
//Info: This is a Uri that is not a Fhir resource reference, it is actually a GUID expressed as a Uri.
//In this case as it is not a FhirUriReferance we want to return null as it is not searchable as a
//Search parameter type of Reference.
//Arrange
string ServiceRootUrlString = "http://SomeWhere.net.au/FhirApi/Patient";
string ReferanceUrlString = "urn:uuid:53fefa32-fcbb-4ff8-8a92-55ee120877b7";
var ResourceReference = new ResourceReference();
ResourceReference.Reference = ReferanceUrlString;
//Mok the inbound Request Url, this contains the service root url from the db.
Mock <IDtoFhirRequestUri> MockIDtoFhirRequestUri = new Mock <IDtoFhirRequestUri>();
var ServiceRootUrl = new Uri(ServiceRootUrlString);
IFhirUri RequestFhirUri = Common.CommonFactory.GetFhirUri(ServiceRootUrl);
MockIDtoFhirRequestUri.Setup(x => x.FhirUri).Returns(RequestFhirUri);
var ServiceDtoRootUrlStore = new Pyro.Common.BusinessEntities.Dto.DtoRootUrlStore();
ServiceDtoRootUrlStore.Id = 1;
ServiceDtoRootUrlStore.IsServersPrimaryUrlRoot = true;
ServiceDtoRootUrlStore.Url = ServiceRootUrlString;
MockIDtoFhirRequestUri.Setup(x => x.PrimaryRootUrlStore).Returns(ServiceDtoRootUrlStore);
//Mok the response from the db from the Common repository, this if request Url does not match service root url
Mock <Pyro.DataModel.Repository.Interfaces.ICommonRepository> MockICommonRepository = new Mock <Pyro.DataModel.Repository.Interfaces.ICommonRepository>();
ReferenceIndex Index = new ReferenceIndex();
//Act
Index = IndexSetterFactory.Create(typeof(ReferenceIndex)).Set(ResourceReference, Index, MockIDtoFhirRequestUri.Object, MockICommonRepository.Object) as ReferenceIndex;
//Assert
Assert.IsNull(Index);
Assert.DoesNotThrow(() => MockICommonRepository.Verify(x => x.GetAndOrAddService_RootUrlStore(ReferanceUrlString), Times.Never));
}
public void GetOffset_FixNegativeBeginCoordinate()
{
var linearFileOffsets = new ulong[1];
linearFileOffsets[0] = 3213608733669;
var idToChunks = new Dictionary <int, Interval[]>
{
[585] = new[] { new Interval(3213608740412, 3213608740487) },
[4681] = new[] { new Interval(3213608733669, 3213608740412) },
[4682] = new[] { new Interval(3213608740487, 3214303562687) }
};
var refSeqs = new ReferenceIndex[2];
refSeqs[1] = new ReferenceIndex(ChromosomeUtilities.Chr2, idToChunks, linearFileOffsets);
var index = new Index(Constants.VcfFormat, 0, 0, 0, '#', 0, refSeqs, _refNameToTabixIndex);
long observedResult = index.GetOffset("chr2", 0);
Assert.Equal(3213608733669, observedResult);
}
public void GetOffset_HandleDiff_TabixIndex_And_RefIndex()
{
var linearFileOffsets = new ulong[1630];
linearFileOffsets[1629] = 3591443256775;
var idToChunks = GetIdToChunks();
// tabix index 10 = chr2 = ref index 1
var refSeqs = new ReferenceIndex[11];
refSeqs[10] = new ReferenceIndex(ChromosomeUtilities.Chr2, idToChunks, linearFileOffsets);
var refNameToTabixIndex = new Dictionary <string, ushort> {
["chr2"] = 10
};
var index = new Index(Constants.VcfFormat, 0, 0, 0, '#', 0, refSeqs, refNameToTabixIndex);
long observedResult = index.GetOffset("chr2", 26699126);
Assert.Equal(3591443256857, observedResult);
}
