public void Test_ToChar()
{
String s1 = "100";
String s2 = "10021";
String s3 = "201341";
String s4 = "201442";
String s5 = "3015";
String s6 = "400";
String s7 = "40021";
String s8 = "501341";
String s9 = "501442";
String s10 = "6015";
String s11 = "700";
String s12 = "70021";
String s13 = "801341";
String s14 = "801442";
String s15 = "9015";
String s16 = "9016";
String[] sorted = new String[16] {
s1, s2, s3, s4, s5, s6, s7, s8, s9, s10, s11, s12, s13, s14, s15, s16
};
String[] unsorted = new String[16] {
s8, s5, s9, s15, s3, s4, s13, s1, s11, s2, s7, s16, s10, s12, s14, s6
};
MostSignificantDigitFirstSort.Sort(unsorted, Alphabet.Decimal);
AssertUtilities.Sequence(sorted, unsorted);
}
public async Task TestGetAllAsync()
{
var expected = new CustomerGetAllResponse
{
Records = new List <CustomerGetAllRecordResponse>
{
new CustomerGetAllRecordResponse
{
Id = 1,
UserName = "******",
FirstName = "John",
LastName = "Smith",
CreatedDateTime = new DateTime(2019, 1, 1, 8, 20, 36),
ModifiedDateTime = new DateTime(2019, 1, 2, 9, 30, 42),
},
new CustomerGetAllRecordResponse
{
Id = 2,
UserName = "******",
FirstName = "Mary",
LastName = "McDonald",
CreatedDateTime = new DateTime(2018, 7, 4, 14, 40, 12),
ModifiedDateTime = new DateTime(2018, 9, 8, 18, 50, 18),
}
}
};
var actual = await Fixture.Customers.GetAllAsync();
Assert.Equal(HttpStatusCode.OK, actual.StatusCode);
AssertUtilities.Equal(expected, actual.Data);
}
public async Task RelistProduct_ValidRequest_ReturnsResponse()
{
var record = _productRecords.Where(e => !e.IsListed).First();
var id = record.Id;
var activateRequest = new RelistProductRequest
{
Id = id,
};
var activateResponse = await Fixture.Products.RelistProductAsync(activateRequest);
AssertUtilities.NotEmpty(activateResponse.Id);
Assert.Equal(record.Id, activateResponse.Id);
Assert.Equal(record.ProductCode, activateResponse.Code);
Assert.Equal(record.ProductName, activateResponse.Description);
Assert.Equal(record.ListPrice, activateResponse.UnitPrice);
Assert.True(activateResponse.IsListed);
var findRequest = new FindProductRequest {
Id = activateResponse.Id
};
var findResponse = await Fixture.Products.FindProductAsync(findRequest);
Assert.Equal(activateResponse.Id, findResponse.Id);
Assert.Equal(activateResponse.Code, findResponse.Code);
Assert.Equal(activateResponse.Description, findResponse.Description);
Assert.Equal(activateResponse.UnitPrice, findResponse.UnitPrice);
Assert.Equal(activateResponse.IsListed, findResponse.IsListed);
}
public async Task CreateProduct_ValidRequest_ReturnsResponse()
{
var createRequest = new CreateProductRequest
{
Code = "ABC",
Description = "My desc",
UnitPrice = 123.56m,
};
var createResponse = await Fixture.Products.CreateProductAsync(createRequest);
AssertUtilities.NotEmpty(createResponse.Id);
Assert.Equal(createRequest.Code, createResponse.Code);
Assert.Equal(createRequest.Description, createResponse.Description);
Assert.Equal(createRequest.UnitPrice, createResponse.UnitPrice);
Assert.True(createResponse.IsListed);
var findRequest = new FindProductRequest {
Id = createResponse.Id
};
var findResponse = await Fixture.Products.FindProductAsync(findRequest);
Assert.Equal(findRequest.Id, findResponse.Id);
Assert.Equal(createRequest.Code, findResponse.Code);
Assert.Equal(createRequest.Description, findResponse.Description);
Assert.Equal(createRequest.UnitPrice, findResponse.UnitPrice);
Assert.True(findResponse.IsListed);
}
public async Task UnlistProduct_ValidRequest_ReturnsResponse()
{
var record = _productRecords.Where(e => e.IsListed).First();
var id = record.Id;
var dectivateRequest = new UnlistProductRequest
{
Id = id,
};
var deactivateResponse = await Fixture.Products.UnlistProductAsync(dectivateRequest);
AssertUtilities.NotEmpty(deactivateResponse.Id);
Assert.Equal(record.Id, deactivateResponse.Id);
Assert.Equal(record.ProductCode, deactivateResponse.Code);
Assert.Equal(record.ProductName, deactivateResponse.Description);
Assert.Equal(record.ListPrice, deactivateResponse.UnitPrice);
Assert.False(deactivateResponse.IsActive);
var findRequest = new FindProductRequest {
Id = deactivateResponse.Id
};
var findResponse = await Fixture.Products.FindProductAsync(findRequest);
Assert.Equal(deactivateResponse.Id, findResponse.Id);
Assert.Equal(deactivateResponse.Code, findResponse.Code);
Assert.Equal(deactivateResponse.Description, findResponse.Description);
Assert.Equal(deactivateResponse.UnitPrice, findResponse.UnitPrice);
Assert.Equal(deactivateResponse.IsActive, findResponse.IsListed);
}
public async Task TestGetCollectionAsync()
{
var actual = await JsonPlaceholderClient.Posts.GetAsync();
Assert.Equal(HttpStatusCode.OK, actual.StatusCode);
var expectedCount = 100;
var actualCount = actual.Data.Count();
Assert.Equal(expectedCount, actualCount);
var expectedFirst = new PostDto
{
Id = 1,
UserId = 1,
Title = "sunt aut facere repellat provident occaecati excepturi optio reprehenderit",
Body = "quia et suscipit\nsuscipit recusandae consequuntur expedita et cum\nreprehenderit molestiae ut ut quas totam\nnostrum rerum est autem sunt rem eveniet architecto",
};
var actualFirst = actual.Data.First();
AssertUtilities.Equal(expectedFirst, actualFirst);
var expectedLast = new PostDto
{
Id = 100,
UserId = 10,
Title = "at nam consequatur ea labore ea harum",
Body = "cupiditate quo est a modi nesciunt soluta\nipsa voluptas error itaque dicta in\nautem qui minus magnam et distinctio eum\naccusamus ratione error aut",
};
var actualLast = actual.Data.Last();
AssertUtilities.Equal(expectedLast, actualLast);
}
public void ShouldReturnAccessableWritableLeaves(List <string> writableFolders, List <string> readableFolders, List <string> resultShouldContain)
{
var result = FolderStructureUtilities.GetWritableFolderStructure(readableFolders, writableFolders);
var resultFolders = result.GetLeafFolders();
AssertUtilities.CollectionContainsSubcollection(resultFolders, resultShouldContain);
}
public void ShouldNotReturnReadOnlyLeaves(List <string> writableFolders, List <string> readableFolders, List <string> resultShouldNotContain)
{
var result = FolderStructureUtilities.GetWritableFolderStructure(readableFolders, writableFolders);
var resultFolders = result.GetLeafFolders();
AssertUtilities.CollectionDoesNotContainSubcollection(resultFolders, resultShouldNotContain);
}
public void IntergenicVariant()
{
var sa = new SupplementaryAnnotationPosition(47960)
{
IsRefMinorAllele = true,
GlobalMajorAllele = "A",
GlobalMajorAlleleFrequency = "0.9239"
};
var saReader = new MockSupplementaryAnnotationReader(sa);
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000518655_chr1_Ensembl84"), saReader,
"chr1 47960 . T . 1242.00 PASS SNVSB=-87.0;SNVHPOL=3");
Assert.NotNull(annotatedVariant);
Assert.Contains("\"isReferenceMinorAllele\":true", annotatedVariant.ToString());
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.FirstOrDefault();
Assert.NotNull(altAllele);
// intergenic variant are not exposed in the JSON file
AssertUtilities.CheckEnsemblTranscriptCount(0, altAllele);
AssertUtilities.CheckRefSeqTranscriptCount(0, altAllele);
}
public void Test_ToChar()
{
String s1 = "100";
String s2 = "10021";
String s3 = "201341";
String s4 = "201442";
String s5 = "3015";
String s6 = "400";
String s7 = "40021";
String s8 = "501341";
String s9 = "501442";
String s10 = "6015";
String s11 = "700";
String s12 = "70021";
String s13 = "801341";
String s14 = "801442";
String s15 = "9015";
String s16 = "9016";
String[] sorted = new String[16] {
s1, s2, s3, s4, s5, s6, s7, s8, s9, s10, s11, s12, s13, s14, s15, s16
};
String[] unsorted = new String[16] {
s8, s5, s9, s15, s3, s4, s13, s1, s11, s2, s7, s16, s10, s12, s14, s6
};
QuickSort3WaySort.Sort(unsorted);
AssertUtilities.Sequence(sorted, unsorted);
}
public async Task ListProducts_Valid_OK()
{
var listRequest = new ListProductRequest {
};
var actual = await Fixture.Api.Products.ListProductsAsync(listRequest);
Assert.Equal(HttpStatusCode.OK, actual.StatusCode);
var actualContent = actual.Data;
Assert.Equal(2, actualContent.Records.Count);
var expectedFirst = _productRecords[0];
var actualFirst = actualContent.Records[0];
AssertUtilities.NotEmpty(actualFirst.Id);
Assert.Equal($"{expectedFirst.ProductCode} - {expectedFirst.ProductName}", actualFirst.Name);
var expectedSecond = _productRecords[1];
var actualSecond = actualContent.Records[1];
AssertUtilities.NotEmpty(actualSecond.Id);
Assert.Equal($"{expectedSecond.ProductCode} - {expectedSecond.ProductName}", actualSecond.Name);
}
public async Task ListCustomers_OK()
{
var listRequest = new ListCustomersRequest {
};
var actual = await Fixture.Api.Customers.ListCustomersAsync(listRequest);
Assert.Equal(HttpStatusCode.OK, actual.StatusCode);
var actualContent = actual.Data;
Assert.Equal(2, actualContent.Records.Count);
var expectedFirst = _customerRecords[0];
var actualFirst = actualContent.Records[0];
AssertUtilities.NotEmpty(actualFirst.Id);
Assert.Equal(expectedFirst.FirstName + " " + expectedFirst.LastName, actualFirst.Name);
var expectedSecond = _customerRecords[1];
var actualSecond = actualContent.Records[1];
AssertUtilities.NotEmpty(actualSecond.Id);
Assert.Equal(expectedSecond.FirstName + " " + expectedSecond.LastName, actualSecond.Name);
}
public async Task TestGetExportsCsvAsync()
{
var csvSerializationService = new CsvSerializer();
var expectedDtos = new List <CustomerExportGetCollectionResponse>
{
new CustomerExportGetCollectionResponse
{
Id = 1,
UserName = "******",
FirstName = "John",
LastName = "Smith",
},
new CustomerExportGetCollectionResponse
{
Id = 2,
UserName = "******",
FirstName = "Mary",
LastName = "McDonald",
}
};
var expected = csvSerializationService.Serialize(expectedDtos);
var actual = await Fixture.Customers.GetCsvExportsAsync();
Assert.Equal(HttpStatusCode.OK, actual.StatusCode);
AssertUtilities.Equal(expected, actual.ContentString);
}
public async Task CreateCustomer_Valid_Created()
{
var createRequest = new CreateCustomerRequest
{
FirstName = "First name 1",
LastName = "Last name 1",
};
var createResponse = await Fixture.Api.Customers.CreateCustomerAsync(createRequest);
Assert.Equal(HttpStatusCode.Created, createResponse.StatusCode);
var createResponseContent = createResponse.Data;
AssertUtilities.NotEmpty(createResponseContent.Id);
Assert.Equal(createRequest.FirstName, createResponseContent.FirstName);
Assert.Equal(createRequest.LastName, createResponseContent.LastName);
var findRequest = new FindCustomerRequest {
Id = createResponseContent.Id
};
var findResponse = await Fixture.Api.Customers.FindCustomerAsync(findRequest);
Assert.Equal(HttpStatusCode.OK, findResponse.StatusCode);
var findResponseContent = findResponse.Data;
Assert.Equal(createResponseContent.Id, findResponseContent.Id);
Assert.Equal(createRequest.FirstName, findResponseContent.FirstName);
Assert.Equal(createRequest.LastName, findResponseContent.LastName);
}
public void MultiAlleleProteinAlteringVariant()
{
// GGGACTGGA|protein_altering_variant|MODIFIER||91544|Transcript|NM_183008.2|protein_coding|16/16||NM_183008.2:c.1501_1533delinsTCCAGTCCC|NP_892120.2:p.Pro501_Pro509delinsSer|1774-1806|1501-1533|501-511|PSPGPGPGPSP/SSP|CCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCC/TCCAGTCCC|||-1|||YES||NP_892120.2|rseq_mrna_match&rseq_ens_match_cds||||||||
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("NM_183008_chr1_RefSeq84"),
"chr1\t26608819\t.\tAGGGACTGGGGCCGGGACCGGGACCGGGACTGGG\tAGGGACTGGG,AGGGACTGGA\t60\tPASS\tCIGAR=1M24D9M,9M25D1I;RU=.,.;REFREP=3,.;IDREP=2,.;GMAF=A|0.3934;cosmic=COSM3749046;CSQT=1|CEP85|NM_022778.3|downstream_gene_variant,2|CEP85|NM_022778.3|downstream_gene_variant,1|SH3BGRL3|NM_031286.3|downstream_gene_variant,2|SH3BGRL3|NM_031286.3|downstream_gene_variant,1|UBXN11|NM_183008.2|inframe_deletion,2|UBXN11|NM_183008.2|\tGT:GQ:GQX:DPI:AD\t1/2:143:119:23:0,3,3");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckAlleleCount(2, annotatedVariant);
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.ElementAt(1);
Assert.NotNull(altAllele);
AssertUtilities.CheckRefSeqTranscriptCount(1, altAllele);
var transcript = altAllele.RefSeqTranscripts.FirstOrDefault();
Assert.NotNull(transcript);
// ReSharper disable once PossibleNullReferenceException
var observedConsequence = string.Join("&", transcript.Consequence);
const string expectedConsequence = "protein_altering_variant";
Assert.Equal(expectedConsequence, observedConsequence);
}
public void MantaInsertionRsId()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnotGRCh38("chr1_186774064_186774065.nsa"),
"chr1 186774064 MantaINS:338:0:0:0:0:0 C CTATATATATACTTTATATATACTGTATGTGTATATATAAAGTATATATATAGTG 101 MinGQ END=186774064;SVTYPE=INS;SVLEN=54;CIGAR=1M54I;CIPOS=0,8;HOMLEN=8;HOMSEQ=TATATATA GT:FT:GQ:PL:PR:SR 0/0:MinGQ:4:48,3,0:0,0:0,1 0/0:MinGQ:3:50,3,0:0,0:0,1 1/1:MinGQ:7:148,9,0:0,0:0,3");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains("rs57376790", annotatedVariant);
}
public void Test_Path_Iteration()
{
BreadthFirstSearch bfs = this.CreateBFS();
AssertUtilities.Sequence(new Int32[2] {
5, 3
}, bfs.PathFromSourceTo(3));
}
public void BreakEnd()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, null,
"chr2 13394888 MantaBND:543:0:1:0:0:0:0 G G]chr15:20404341] 114 MaxDepth SVTYPE=BND;MATEID=MantaBND:543:0:1:0:0:0:1;CIPOS=0,3;HOMLEN=3;HOMSEQ=AGT;BND_DEPTH=10;MATE_BND_DEPTH=7 GT:FT:GQ:PL:PR:SR 0/1:PASS:83:133,0,93:2,0:1,3 0/1:PASS:30:80,0,68:3,2:0,3 0/0:MinGQ:11:40,0,153:2,0:2,1");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains("\"altAlleles\":[\"G]chr15:20404341]\"]", annotatedVariant);
}
public void IndelVariantType()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, null,
"chr1 23259022 MantaDEL:58:0:1:0:0:0 GAGGATCACTTGAGCCCAGGAGTTCCAGACCAGCCCGGGCAACATGGTGAAACCCCACCTCTACAAAAAATACAAAAGTTACCCAGGCATGGTGGCACATGCCTATAGTCCCAGCTGCTGGGAGGGTTGAGGTGGGAGGATCACTTGAGCCAGGGAGGTGGAGACTGCAGTGAGCCATGATCACACCACTGCATTCAAGCCTAGGCTGCAACCTCGAGATTTTTTTTTTTTTTGAGATCCTGTCTCAAAAAAAATTTTTTTTGGCCAGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGC GT 95 PASS END=23259340;SVTYPE=DEL;SVLEN=-318;CIGAR=1M1I318D GT:FT:GQ:PL:PR:SR 0/0:PASS:50:0,1,2:1,0:0,0 1/1:MinGQ:7:147,9,0:0,0:1,3 0/0:PASS:53:0,3,59:0,0:1,0");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains("\"variantType\":\"indel\"", annotatedVariant);
}
public void Test_Pre()
{
DepthFirstOrder order = new DepthFirstOrder(this.CreateDigraph());
AssertUtilities.Sequence(new Int32[6] {
0, 3, 4, 5, 1, 2
}, order.Pre());
}
public void Test_Post()
{
DepthFirstOrder order = new DepthFirstOrder(this.CreateDigraph());
AssertUtilities.Sequence(new Int32[6] {
5, 4, 3, 2, 1, 0
}, order.Post());
}
public void Test_ReversePost()
{
DepthFirstOrder order = new DepthFirstOrder(this.CreateDigraph());
AssertUtilities.Sequence(new Int32[6] {
0, 1, 2, 3, 4, 5
}, order.ReversePost());
}
public void Test_ToIndices()
{
Alphabet alphabet = Alphabet.Decimal;
AssertUtilities.Sequence(new Int32[3] {
7, 8, 9
}, alphabet.ToIndices("789"));
}
public void SuppIntervalCnv()
{
var annotatedVariant = DataUtilities.GetSuppIntervalVariant(Resources.MiniSuppAnnot("chr1_713035_713060.nsa"),
"chr1 713045 . T <CN1> . LowGQX;HighDPFRatio END=718045;SVTYPE=CNV;BLOCKAVG_min30p3a GT:GQX:DP:DPF .:.:0:1");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckIntervalCount(28, annotatedVariant);
AssertUtilities.CheckJsonContains("variantType\":\"copy_number_variation\"", annotatedVariant);
}
public void RefNameMismatch()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr1_672000_672092.nsa"),
"chr1 672000 . C <DEL> 0.1 LowQ SVTYPE=DEL;END=672092;ALTDEDUP=1;ALTDUP=0;REFDEDUP=0;REFDUP=0;INTERGENIC=False . .");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains("dgv1n111", annotatedVariant);
}
public void GatkGenomeVcf()
{
const bool isGatkGenomeVcf = true;
var vcfVariant = VcfUtilities.GetVcfVariant("1 10360 . C <NON_REF> . PASS END=10362 GT:DP:GQ:MIN_DP:PL 0/0:198:99:196:0,120,1800", isGatkGenomeVcf);
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000483270_chr1_Ensembl84"), vcfVariant);
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckAlleleCount(0, annotatedVariant);
}
public void Test_ToChars()
{
Alphabet alphabet = Alphabet.Decimal;
AssertUtilities.Sequence(new Char[3] {
'7', '8', '9'
}, alphabet.ToChars(new Int32[3] {
7, 8, 9
}));
}
public void SvDelPartiallyOverlappingGene()
{
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000546909_chr14_Ensembl84"),
"14 19443800 . G <DEL> . PASS SVTYPE=DEL;END=19452000");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains("\"overlappingGenes\":[\"RP11-536C10.15\"]", annotatedVariant);
AssertUtilities.CheckJsonContains("ENST00000546909", annotatedVariant);
}
public void NextToGene()
{
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000546909_chr14_Ensembl84"),
"14 19443847 14_19462000 G <CNV> . PASS SVTYPE=CNV;END=19462000;CN=0;CNscore=13.41;LOH=0;ensembl_gene_id=ENSG00000257990,ENSG00000257558");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonDoesNotContain("\"overlappingGenes\":[\"RP11-536C10.15\"]", annotatedVariant);
AssertUtilities.CheckJsonDoesNotContain("ENST00000546909", annotatedVariant);
}
public void InsertionReciprocalOverlap()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr1_756265_756269.nsa"),
"1 756267 . T <INS> . PASS SVTYPE=INS;END=756267");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonDoesNotContain("\"reciprocalOverlap\":NaN", annotatedVariant);
AssertUtilities.CheckJsonContains("esv1032937", annotatedVariant);
AssertUtilities.CheckJsonDoesNotContain("\"reciprocalOverlap\"", annotatedVariant);
}