public async Task ChemicalProcessing_ValidMol_GenerateExpectedSubstanceAggregate()
{
var recordId = Fixture.GetProcessedRecords(FileId).First();
var record = await Session.Get <Substance>(recordId);
record.Should().NotBeNull();
record.ShouldBeEquivalentTo(new
{
Id = recordId,
RecordType = RecordType.Structure,
Bucket = JohnId.ToString(),
OwnedBy = JohnId,
CreatedBy = JohnId,
CreatedDateTime = DateTimeOffset.UtcNow,
UpdatedBy = JohnId,
UpdatedDateTime = DateTimeOffset.UtcNow,
ParentId = FileId,
Status = RecordStatus.Processed,
Index = 0,
Issues = new List <Generic.Domain.ValueObjects.Issue>()
{
new Generic.Domain.ValueObjects.Issue {
Code = "Code", AuxInfo = "AuxInfo", Message = "Message", Severity = Severity.Information, Title = "Title"
}
}
}, options => options
.ExcludingMissingMembers()
);
record.Images.Should().NotBeNullOrEmpty();
record.Images.Should().ContainSingle();
record.Fields.Should().NotBeNullOrEmpty();
record.Fields.Should().HaveCount(3);
record.Properties.Should().NotBeNullOrEmpty();
record.Properties.Should().HaveCount(9);
record.BlobId.Should().NotBeEmpty();
}
public async Task ChemicalProcessing_ValidSdf_GenerateExpectedFileAggregate()
{
var blobInfo = await BlobStorage.GetFileInfo(BlobId, JohnId.ToString());
blobInfo.Should().NotBeNull();
var file = await Session.Get <RecordsFile.Domain.RecordsFile>(FileId);
file.Should().NotBeNull();
file.ShouldBeEquivalentTo(new
{
Id = FileId,
Type = FileType.Records,
Bucket = JohnId.ToString(),
BlobId = BlobId,
OwnedBy = JohnId,
CreatedBy = JohnId,
CreatedDateTime = DateTimeOffset.UtcNow,
UpdatedBy = JohnId,
UpdatedDateTime = DateTimeOffset.UtcNow,
ParentId = JohnId,
FileName = blobInfo.FileName,
Length = blobInfo.Length,
Md5 = blobInfo.MD5,
IsDeleted = false,
Status = FileStatus.Processed,
TotalRecords = 2,
Fields = new List <string>()
{
"StdInChI", "StdInChIKey", "SMILES"
}
}, options => options
.ExcludingMissingMembers()
);
file.Images.Should().NotBeNullOrEmpty();
file.Images.Count.Should().Be(1);
}
public async Task ChemicalProcessing_ValidCdx_GenerateExpectedFileEntity()
{
var blobInfo = await BlobStorage.GetFileInfo(BlobId, JohnId.ToString());
blobInfo.Should().NotBeNull();
var fileEntityResponse = await JohnApi.GetFileEntityById(FileId);
var fileEntity = JsonConvert.DeserializeObject <JObject>(await fileEntityResponse.Content.ReadAsStringAsync());
fileEntity.Should().NotBeNull();
fileEntity.Should().ContainsJson($@"
{{
'id': '{FileId}',
'blob': {{
'id': '{blobInfo.Id}',
'bucket': '{JohnId}',
'length': {blobInfo.Length},
'md5': '{blobInfo.MD5}'
}},
'subType': '{FileType.Records}',
'ownedBy': '{JohnId}',
'createdBy': '{JohnId}',
'createdDateTime': '{DateTime.UtcNow}',
'updatedBy': '{JohnId}',
'updatedDateTime': '{DateTime.UtcNow}',
'parentId': '{JohnId}',
'name': '{blobInfo.FileName}',
'status': '{FileStatus.Processed}',
'version': *EXIST*,
'totalRecords': 3,
'properties': *EXIST*
}}" );
fileEntity["images"].Should().NotBeNull();
fileEntity["images"].Should().HaveCount(1);
}
public async Task FileSharing_WithUnauthorizeUser_ReturnsExpectedFileNode()
{
var blobInfo = await BlobStorage.GetFileInfo(BlobId, JohnId.ToString());
blobInfo.Should().NotBeNull();
var fileEntityResponse = await UnauthorizedApi.GetNodeById(FileId);
fileEntityResponse.EnsureSuccessStatusCode();
fileEntityResponse.StatusCode.ShouldBeEquivalentTo(HttpStatusCode.OK);
var fileEntity = JsonConvert.DeserializeObject <JObject>(await fileEntityResponse.Content.ReadAsStringAsync());
fileEntity.Should().ContainsJson($@"
{{
'id': '{FileId}',
'blob': {{
'id': '{blobInfo.Id}',
'bucket': '{JohnId}',
'length': {blobInfo.Length},
'md5': '{blobInfo.MD5}'
}},
'subType': '{FileType.Records}',
'ownedBy': '{JohnId}',
'createdBy': '{JohnId}',
'createdDateTime': '{DateTime.UtcNow}',
'updatedBy': '{JohnId}',
'updatedDateTime': '{DateTime.UtcNow}',
'parentId': '{JohnId}',
'name': '{blobInfo.FileName}',
'status': '{FileStatus.Processed}',
'version': *EXIST*,
'totalRecords': 1,
'type': 'File'
}}" );
fileEntity["images"].Should().HaveCount(1);
}
protected async Task <Guid> TrainModel(string bucket, string fileName, IDictionary <string, object> metadata = null)
{
var blobId = await AddBlob(JohnId.ToString(), fileName, metadata);
Guid correlationId = NewId.NextGuid();
var modelFolderId = NewId.NextGuid();
if (metadata["case"].Equals("valid one model with success optimization") ||
metadata["case"].Equals("train model with failed optimization"))
{
await Harness.Bus.Publish <StartTraining>(new
{
Id = modelFolderId,
ParentId = modelFolderId,
SourceBlobId = blobId,
SourceBucket = bucket,
CorrelationId = correlationId,
UserId = JohnId,
SourceFileName = fileName,
Methods = new List <string>(new[]
{
"NaiveBayes"
}),
ClassName = "ClassName",
Optimize = true
});
}
else if (!metadata["case"].Equals("two valid models"))
{
await Harness.Bus.Publish <StartTraining>(new
{
Id = modelFolderId,
ParentId = modelFolderId,
SourceBlobId = blobId,
SourceBucket = bucket,
CorrelationId = correlationId,
UserId = JohnId,
SourceFileName = fileName,
Scaler = "Somebody knows what is Scaler???",
Methods = new List <string>(new[]
{
"NaiveBayes"
}),
ClassName = "ClassName",
SubSampleSize = (decimal)0.2,
TestDataSize = (decimal)0.2,
KFold = 4,
Fingerprints = new List <IDictionary <string, object> >()
{
new Dictionary <string, object>()
{
{ "radius", 3 },
{ "size", 1024 },
{ "type", FingerprintType.ecfp }
}
},
Optimize = false,
HyperParameters = new HyperParametersOptimization()
{
NumberOfIterations = 100, OptimizationMethod = "OptimizationMethod"
}
});
}
if (metadata["case"].Equals("two valid models"))
{
await Harness.Bus.Publish <StartTraining>(new
{
Id = modelFolderId,
ParentId = modelFolderId,
SourceBlobId = blobId,
SourceBucket = bucket,
CorrelationId = correlationId,
UserId = JohnId,
SourceFileName = fileName,
Scaler = "Somebody knows what is Scaler???",
Methods = new List <string>(new[]
{
"NaiveBayes",
"LogisticRegression"
}),
ClassName = "ClassName",
SubSampleSize = (decimal)0.2,
TestDataSize = (decimal)0.2,
KFold = 4,
Fingerprints = new List <IDictionary <string, object> >()
{
new Dictionary <string, object>()
{
{ "radius", 3 },
{ "size", 1024 },
{ "type", FingerprintType.ecfp }
}
},
Optimize = false
});
}
if (!Harness.Published.Select <TrainingFinished>(m => m.Context.Message.Id == modelFolderId).Any())
{
throw new TimeoutException();
}
return(modelFolderId);
}
public async Task ChemicalProcessing_ValidCdxWithThreeRecords_GenerateExpectedRecordsEntityAndRecordsNode()
{
var records = Fixture.GetProcessedRecords(FileId);
records.Should().HaveCount(3);
foreach (var recordId in records)
{
var recordView = Records.Find(new BsonDocument("_id", recordId)).FirstOrDefault() as IDictionary <string, object>;
recordView.Should().NotBeNull();
var recordBlob = recordView["Blob"];
recordBlob.Should().NotBeNull();
recordBlob.Should().BeAssignableTo <IDictionary <string, object> >();
var recordBlobId = (recordBlob as IDictionary <string, object>)["_id"];
recordBlobId.Should().NotBeNull();
recordBlobId.Should().BeOfType <Guid>();
var index = Convert.ToInt32(recordView["Index"]);
index.Should().BeGreaterOrEqualTo(0);
var record = await Session.Get <Substance>((Guid)recordId);
record.Should().NotBeNull();
record.ShouldBeEquivalentTo(new
{
Id = recordId,
RecordType = RecordType.Structure,
Bucket = JohnId.ToString(),
BlobId = recordBlobId,
OwnedBy = JohnId,
CreatedBy = JohnId,
CreatedDateTime = DateTimeOffset.UtcNow,
UpdatedBy = JohnId,
UpdatedDateTime = DateTimeOffset.UtcNow,
ParentId = FileId,
Status = RecordStatus.Processed,
Index = index,
Issues = new List <Generic.Domain.ValueObjects.Issue>()
{
new Generic.Domain.ValueObjects.Issue {
Code = "Code", AuxInfo = "AuxInfo", Message = "Message", Severity = Generic.Domain.ValueObjects.Severity.Information, Title = "Title"
}
}
}, options => options
.ExcludingMissingMembers()
);
record.Images.Should().NotBeNullOrEmpty();
record.Images.Should().ContainSingle();
record.Fields.Should().BeEmpty();
record.Properties.Should().NotBeNullOrEmpty();
record.Properties.Should().HaveCount(9);
recordView.Should().EntityShouldBeEquivalentTo(record);
var recordNode = Nodes.Find(new BsonDocument("_id", (Guid)recordId)).FirstOrDefault() as IDictionary <string, object>;
recordNode.Should().NotBeNull();
recordNode.Should().NodeShouldBeEquivalentTo(record);
}
}
public async Task CategoryTree_UpdateExistantCategoryTree_BuiltExpectedDocument()
{
var contentRequest = await JohnApi.GetData($"/api/categorytrees/tree/{CategoryId}");
var jsonCategory = await contentRequest.Content.ReadAsJObjectAsync();
jsonCategory.Should().HaveElement("id");
jsonCategory["id"].Value <string>().Should().Be(CategoryId.ToString());
jsonCategory.Should().HaveElement("createdBy");
jsonCategory["createdBy"].Value <string>().Should().Be(JohnId.ToString());
jsonCategory.Should().HaveElement("createdDateTime")
.And.HaveElement("createdDateTime")
.And.HaveElement("updatedDateTime");
jsonCategory.Should().HaveElement("version");
jsonCategory["version"].Value <int>().Should().Be(2);
jsonCategory.Should().HaveElement("nodes");
var treeNodes = jsonCategory["nodes"].Value <JArray>();
treeNodes.Should().HaveCount(6);
treeNodes.Select(i => i.Should().HaveElement("id"));
var titles = treeNodes.Select(i => i["title"].Value <string>());
titles.Should().Contain(new List <string> {
"Level 0: Main Node 1", "NoNameNode", "1", "2", "3", "4"
});
var firstNode = treeNodes.Where(i => i.Value <string>("title") == "Level 0: Main Node 1").SingleOrDefault();
firstNode.Should().NotBeNull();
firstNode.Should().HaveElement("title");
var insideNodes = firstNode["children"].Value <JArray>();
insideNodes.Should().HaveCount(2);
var insideTitles = insideNodes.Select(i => i["title"].Value <string>());
insideTitles.Should().Contain(new List <string> {
"Level 1: Node 1", "Level 1: Node 2"
});
insideNodes.Select(i => i.Should().HaveElement("id"));
var lastNode = treeNodes.Where(i => i.Value <string>("title") == "4").SingleOrDefault();
lastNode.Should().NotBeNull();
var lastNodeInsideNodes = lastNode["children"].Value <JArray>();
lastNodeInsideNodes.Should().HaveCount(2);
var lastNodeInsideTitles = lastNodeInsideNodes.Select(i => i["title"].Value <string>());
lastNodeInsideTitles.Should().Contain(new List <string> {
"4-1", "4-2"
});
lastNodeInsideNodes.Select(i => i.Should().HaveElement("id"));
var lastNodeSubnode = lastNodeInsideNodes.Where(i => i.Value <string>("title") == "4-2").SingleOrDefault();
lastNodeSubnode.Should().NotBeNull();
var lastSubnodeChildren = lastNodeSubnode["children"].Value <JArray>();
lastSubnodeChildren.Should().HaveCount(1);
lastSubnodeChildren.Single().Should().HaveElement("id");
}
public async Task ChemicalProcessing_ValidSdf_GenerateExpectedFileEntity()
{
var blobInfo = await BlobStorage.GetFileInfo(BlobId, JohnId.ToString());
blobInfo.Should().NotBeNull();
var fileEntityResponse = await JohnApi.GetFileEntityById(FileId);
var fileEntity = JsonConvert.DeserializeObject <JObject>(await fileEntityResponse.Content.ReadAsStringAsync());
fileEntity.Should().NotBeNull();
fileEntity.Should().ContainsJson($@"
{{
'id': '{FileId}',
'blob': {{
'id': '{blobInfo.Id}',
'bucket': '{JohnId}',
'length': {blobInfo.Length},
'md5': '{blobInfo.MD5}'
}},
'subType': '{FileType.Records}',
'ownedBy': '{JohnId}',
'createdBy': '{JohnId}',
'createdDateTime': *EXIST*,
'updatedBy': '{JohnId}',
'updatedDateTime': *EXIST*,
'parentId': '{JohnId}',
'name': '{blobInfo.FileName}',
'status': '{FileStatus.Processed}',
'version': 8,
'totalRecords': 10,
'properties': {{
'fields': [
'DATABASE_ID',
'DATABASE_NAME',
'SMILES',
'INCHI_IDENTIFIER',
'INCHI_KEY',
'FORMULA',
'MOLECULAR_WEIGHT',
'EXACT_MASS',
'JCHEM_ACCEPTOR_COUNT',
'JCHEM_AVERAGE_POLARIZABILITY',
'JCHEM_BIOAVAILABILITY',
'JCHEM_DONOR_COUNT',
'JCHEM_FORMAL_CHARGE',
'JCHEM_GHOSE_FILTER',
'JCHEM_IUPAC',
'ALOGPS_LOGP',
'JCHEM_LOGP',
'ALOGPS_LOGS',
'JCHEM_MDDR_LIKE_RULE',
'JCHEM_NUMBER_OF_RINGS',
'JCHEM_PHYSIOLOGICAL_CHARGE',
'JCHEM_PKA',
'JCHEM_PKA_STRONGEST_ACIDIC',
'JCHEM_PKA_STRONGEST_BASIC',
'JCHEM_POLAR_SURFACE_AREA',
'JCHEM_REFRACTIVITY',
'JCHEM_ROTATABLE_BOND_COUNT',
'JCHEM_RULE_OF_FIVE',
'ALOGPS_SOLUBILITY',
'JCHEM_TRADITIONAL_IUPAC',
'JCHEM_VEBER_RULE',
'DRUGBANK_ID',
'SECONDARY_ACCESSION_NUMBERS',
'DRUG_GROUPS',
'GENERIC_NAME',
'PRODUCTS',
'SALTS',
'SYNONYMS',
'INTERNATIONAL_BRANDS',
'JCHEM_ATOM_COUNT'
],
'chemicalProperties': [
'MOST_ABUNDANT_MASS',
'MONOISOTOPIC_MASS',
'MOLECULAR_WEIGHT',
'MOLECULAR_FORMULA',
'SMILES',
'InChIKey',
'InChI'
]
}}
}}" );
fileEntity["images"].Should().NotBeNull();
fileEntity["images"].Should().HaveCount(1);
}