public void AnimlDocumentValidatedCorrectly()
{
//// Create a new minimal AnIML document and add one sample
//// Using "1" as Id should result in a validation error b/c this name is not compliant with the
//// AnIML standard as xsd:ID does not allow numbers as first character
AnimlDocument animlDoc = new AnimlDocument()
{
SampleSet = new SampleSet()
};
animlDoc.SampleSet.Samples.Add(new Sample("TestSample", "1st sample")
{
Id = "1"
});
bool validationOutcome;
AnimlDocumentValidator validatorFail = AnimlDocumentValidator.CreateValidatorForAnimlDocument(animlDoc);
validationOutcome = validatorFail.Validate();
validationOutcome.Should().BeFalse();
validatorFail.ValidationMessages.Should().HaveCount(1);
//// Change the ID to a valid value and perform the validation once again.
animlDoc.SampleSet.Samples[0].Id = "ID-1";
AnimlDocumentValidator validatorSucceed = AnimlDocumentValidator.CreateValidatorForAnimlDocument(animlDoc);
validationOutcome = validatorSucceed.Validate();
validationOutcome.Should().BeTrue();
validatorSucceed.ValidationMessages.Should().BeEmpty();
}
private static void CreateAuditTrailEntries(ref AnimlDocument document)
{
document.AuditTrailEntrySet = new AuditTrailEntrySet();
Author author = new Author("John Doe", UserType.Human);
AuditTrailEntry auditTrailEntry = new AuditTrailEntry(DateTime.Now, author, Blobfish.Action.Created);
auditTrailEntry.Comment = "Creation of the AnIML document.";
document.AuditTrailEntrySet.AuditTrailEntries.Add(auditTrailEntry);
}
public void AnimlDocumentShouldHaveCorrectDeclarationAndNamespace()
{
XNamespace xNamespace = "urn:org:astm:animl:schema:core:draft:0.90";
AnimlDocument animlDocument = new AnimlDocument();
XDocument xDocument = animlDocument.ToXDocument();
xDocument.Declaration.Should().NotBeNull("XML declaration must not be null.");
xDocument.Declaration.Version.Should().NotBeNullOrEmpty().And.BeEquivalentTo("1.0", "XML document should be declated with version 1.0.");
xDocument.Declaration.Standalone.Should().NotBeNullOrEmpty().And.BeEquivalentTo("yes", "XML document should be declared as standalone.");
xDocument.Declaration.Encoding.Should().NotBeNullOrEmpty().And.BeEquivalentTo("utf-8", "XML document should be declared with encoding UTF-8.");
XName animlElementName = xNamespace + "AnIML";
xDocument.Should().HaveRoot(animlElementName, "AnIML document must have a root element named AnIML.");
xDocument.Element(animlElementName).Should().HaveAttribute("version", "0.90", "AnIML schema version must be 0.90.");
xDocument.Element(animlElementName).Name.NamespaceName.Should().Be(xNamespace.NamespaceName, $"Schema namespace of root AnIML must be {xNamespace}.");
}
public static void Main(string[] args)
{
List <double> values = GenerateValues(50, 0, 14);
AnimlDocumentBuilder documentBuilder = new AnimlDocumentBuilder()
.WithSampleSet(
new SampleSetBuilder()
.WithId("ID-SampleSet")
.WithSample(
new SampleBuilder("TestSample", "ID-TestSample")
.WithBarcode("B1234567890")
.WithComment("This is a test sample.")
.WithContainerInfo("CONT-123", ContainerType.Determinate, "A/1")
.WithDerived(false)
.WithId("S-1")
.WithSourceDataLocation("http://documentstore/B1234567890/data")
.Build())
.Build())
.WithExperimentStepSet(
new ExperimentStepSetBuilder()
.WithId("ID-ExperimentStepSet")
.WithExperimentStep(
new ExperimentStepBuilder("TestExperimentStep", "ID-ExperimentStep")
.WithComment("This is a test experiment step.")
.WithId("E-1")
.WithInfrastructure(
new InfrastructureBuilder()
.WithTimestamp(DateTime.Now)
.WithSampleReferenceSet(
new SampleReferenceSetBuilder()
.WithSampleReference(new SampleReference("ID-TestSample", "Test sample", SamplePurpose.Consumed))
.Build())
.Build())
.WithMethod(
new MethodBuilder()
.WithAuthor(
new AuthorBuilder("John Doe", UserType.Human)
.WithAffiliation("Black Mesa Corp.")
.WithEmail("*****@*****.**")
.WithLocation("New Mexico")
.WithPhone("+1 505 1234567")
.WithRole("Lab Technician")
.Build())
.WithDevice(
new DeviceBuilder("pH Meter")
.WithDeviceIdentifier("PH-11-1")
.WithFirmwareVersion("1.21a")
.WithManufacturer("pH Meter Manufacturing Corp.")
.WithSerialNumber("PHM0815")
.Build())
.WithId("M-1")
.WithName("pH Value")
.WithSoftware(
new SoftwareBuilder("pH Meter PC Software")
.WithManufacturer("pH Meter Manufacturing Corp.")
.WithOperatingSystem(Environment.OSVersion.ToString())
.WithVersion("2.08")
.Build())
.Build())
.WithResult(
new ResultBuilder("pH")
.WithSeriesSet(
new SeriesSetBuilder("pH Measurement", values.Count)
.WithSeries(
new SeriesBuilder("Time", "SER-PH-TIME", Dependency.Independent, SeriesType.Int32)
.WithId("SER-TIME")
.WithPlotScale(PlotScale.Linear)
.WithUnit(Units.Second)
.WithAutoIncrementedValueSet(0, 1)
.WithVisible(true)
.Build())
.WithSeries(
new SeriesBuilder("pH values", "SER-PH-VALS", Dependency.Dependent, SeriesType.Float64)
.WithId("SER-VALS")
.WithPlotScale(PlotScale.Linear)
.WithUnit(Units.Arbitrary)
.WithEncodedValueSet(values)
.WithVisible(true)
.Build())
.Build())
.Build())
.Build())
.Build());
AnimlDocument document = documentBuilder.Build();
string docString = documentBuilder.Build().ToXml();
//// Print the XML to the console
Console.WriteLine("Generated AnIML document using builders:");
Console.WriteLine("=========================");
Console.WriteLine(docString);
Console.WriteLine();
if (!string.IsNullOrEmpty(outputFilePath))
{
document.SaveAsFile(outputFilePath);
Console.WriteLine("Saved AnIML document to file:");
Console.WriteLine("=========================");
Console.WriteLine($"--> {outputFilePath}");
Console.WriteLine();
}
//// Validate the AnIML document against the AnIML core schema
Console.WriteLine("Validating document against the AnIML Core Schema:");
Console.WriteLine("==================================================");
AnimlDocumentValidator validator = AnimlDocumentValidator.CreateValidatorForAnimlDocumentString(docString);
if (!validator.Validate())
{
Console.WriteLine("Validation failed.");
validator.ValidationMessages.ForEach(Console.WriteLine);
}
else
{
Console.WriteLine("Validation succeeded.");
}
}
private static void CreateSamples(ref AnimlDocument document)
{
//// Initialize the SampleSet of the AnimlDocument
document.SampleSet = new SampleSet();
//// Create a sample with some dummy data
Sample sample = new Sample("SampleName", "S-1234")
{
Barcode = "B-1234",
Comment = "This is a comment",
ContainerId = "C-1234",
ContainerType = ContainerType.Simple,
Derived = false,
Id = "SampleId",
LocationInContainer = "A1",
SourceDataLocation = @"c:\test\1",
};
//// Initialize the TagSet for the Sample and add a Tag to it
sample.TagSet = new TagSet();
sample.TagSet.Tags.Add(new Tag("123", "456"));
//// Create a category and a sub-category
Category category = new Category("TestCategory")
{
Id = "CategoryId",
};
Category subCategory = new Category("SubCategory")
{
Id = "SubCategoryId",
};
//// Create a new Parameter with a double as value and assign it to the sub-categorys
Parameter parameter = new Parameter("Param X1", 123.05);
subCategory.Parameters.Add(parameter);
//// Create a SeriesSet with two IndividualValueSets
SeriesSet seriesSet = new SeriesSet("TestSeriesSetInd", 5);
Series xData = new Series("xData", "xS", Dependency.Independent, SeriesType.Int32);
IndividualValueSet xDataVals = new IndividualValueSet(new List <int>()
{
1, 2, 3, 4, 5
});
xData.ValueSets.Add(xDataVals);
Series yData = new Series("yData", "yS", Dependency.Dependent, SeriesType.Int32);
IndividualValueSet yDataVals = new IndividualValueSet(new List <int>()
{
2, 8, 9, 2, 0
});
yData.ValueSets.Add(yDataVals);
seriesSet.Series.Add(xData);
seriesSet.Series.Add(yData);
//// Create a SeriesSet with two EncodedValueSets
SeriesSet encSeriesSet = new SeriesSet("TestSeriesSetEnc", 4);
Series xDataEnc = new Series("xDataEnc", "xSE", Dependency.Independent, SeriesType.Int32);
EncodedValueSet xDataSetEnc = new EncodedValueSet(new List <int>()
{
0, 1, 2, 3, 4, 5
});
xDataEnc.ValueSets.Add(xDataSetEnc);
Series yDataEnc = new Series("yDataEnc", "ySE", Dependency.Dependent, SeriesType.Float32);
EncodedValueSet yDataSetEnc = new EncodedValueSet(new List <float>()
{
0.1f, 0.2f, 0.3f, 3f, 4f, 5f
});
yDataEnc.ValueSets.Add(yDataSetEnc);
encSeriesSet.Series.Add(xDataEnc);
encSeriesSet.Series.Add(yDataEnc);
//// Create a SeriesSet with two AutoIncrementedValueSets
SeriesSet aincSeriesSet = new SeriesSet("TestSeriesSetAInc", 4);
Series xDataAInc = new Series("xDataAInc", "xSAInc", Dependency.Independent, SeriesType.Int32);
AutoIncrementedValueSet xDataSetAInc = new AutoIncrementedValueSet(0, 1);
xDataAInc.ValueSets.Add(xDataSetAInc);
Series yDataAInc = new Series("yDataAInc", "ySAInc", Dependency.Dependent, SeriesType.Float32);
AutoIncrementedValueSet yDataSetAInc = new AutoIncrementedValueSet(0.0, 0.1);
yDataAInc.ValueSets.Add(yDataSetAInc);
aincSeriesSet.Series.Add(xDataAInc);
aincSeriesSet.Series.Add(yDataAInc);
//// Add the three ValueSets to the sub-categry
subCategory.SeriesSets.Add(seriesSet);
subCategory.SeriesSets.Add(encSeriesSet);
subCategory.SeriesSets.Add(aincSeriesSet);
//// Add the sub-categgory to the category
category.Categories.Add(subCategory);
/// Add the category to the sample
sample.Categories.Add(category);
//// Add the Sample to the SampleSet
document.SampleSet.Samples.Add(sample);
}
private static void CreateExperimentSteps(ref AnimlDocument document)
{
//// Create an ExperimentStepSet that contains all the experiment data.
ExperimentStepSet expStepSet = new ExperimentStepSet();
//// Create a first ExperimentStep. This ExperimentStep will reference the Sample.
ExperimentStep expStep1 = new ExperimentStep("FirstStep", "E-1");
expStep1.Comment = "This is the 1st experiment step";
//// Create the infrastructure that is needed to establish the reference between the ExperimentStep and the Sample.
expStep1.Infrastructure = new Infrastructure();
expStep1.Infrastructure.Timestamp = DateTime.Now;
expStep1.Infrastructure.SampleReferencetSet = new SampleReferenceSet();
expStep1.Infrastructure.SampleReferencetSet.SampleReferences.Add(new SampleReference(document.SampleSet.Samples[0].SampleId, "Sample under test.", SamplePurpose.Consumed));
//// Create the method information for the ExperimentStep
expStep1.Method = new Method();
expStep1.Method.Author = new Author("John Doe", UserType.Human)
{
Affiliation = "Black Mesa Corp.",
Email = "*****@*****.**",
Location = "New Mexico",
Phone = "+1 505 1234567",
Role = "Lab Technician",
};
expStep1.Method.Device = new Device("pH Meter")
{
DeviceIdentifier = "PH-11-1",
FirmwareVersion = "1.21a",
Manufacturer = "pH Meter Manufacturing Corp.",
SerialNumber = "PHM0815",
};
expStep1.Method.Software = new Software("pH Meter PC Software")
{
Manufacturer = "pH Meter Manufacturing Corp.",
OperatingSystem = Environment.OSVersion.ToString(),
Version = "2.08",
};
List <double> values = GenerateValues(50, 6, 3);
//// Create a Result for the 1st ExperimentStep
Result pHResult = new Result("pH");
pHResult.SeriesSet = new SeriesSet("pH Measurement", values.Count);
Series phTimeSeries = new Series("Time", "SER-PH-TIME", Dependency.Independent, SeriesType.Int32);
phTimeSeries.PlotScale = PlotScale.Linear;
phTimeSeries.ValueSets.Add(new AutoIncrementedValueSet(0, 1));
pHResult.SeriesSet.Series.Add(phTimeSeries);
Series phValueSeries = new Series("pH", "SER-PH-VALS", Dependency.Dependent, SeriesType.Float64);
phValueSeries.PlotScale = PlotScale.Linear;
phValueSeries.ValueSets.Add(new EncodedValueSet(values));
pHResult.SeriesSet.Series.Add(phValueSeries);
expStep1.Results.Add(pHResult);
//// Add the 1st ExperimentStep to the ExperimentStepSet.
expStepSet.ExperimentSteps.Add(expStep1);
//// Create a second ExperimentStep. This ExperimentStep will reference the first ExperimentStep.
ExperimentStep expStep2 = new ExperimentStep("SecondStep", "E-2");
expStep2.Comment = "This is the 2nd experiment step";
//// Create the infrastructure that is needed to establish the reference between the 1st and the 2nd ExperimentStep.
expStep2.Infrastructure = new Infrastructure();
expStep2.Infrastructure.Timestamp = DateTime.Now;
expStep2.Infrastructure.ExperimentDataReferenceSet = new ExperimentDataReferenceSet();
expStep2.Infrastructure.ExperimentDataReferenceSet.ExperimentDataReferences.Add(new ExperimentDataReference("E-1", "Data source", ExperimentDataPurpose.Consumed));
//// Create a Result for the 2nd ExperimentStep
Result calcResult = new Result("Calc");
calcResult.SeriesSet = new SeriesSet("Calculated Results", 3);
Series resultNamesSeries = new Series("ResultName", "SER-CALC-NAMES", Dependency.Independent, SeriesType.String);
resultNamesSeries.PlotScale = PlotScale.None;
resultNamesSeries.ValueSets.Add(new IndividualValueSet(new List <string>()
{
"Min", "Max", "Average"
}));
calcResult.SeriesSet.Series.Add(resultNamesSeries);
Series resultValuesSeries = new Series("ResultValue", "SER-CALC-VALUES", Dependency.Dependent, SeriesType.Float64);
resultValuesSeries.PlotScale = PlotScale.None;
resultValuesSeries.ValueSets.Add(new IndividualValueSet(new List <double>()
{
values.Min(), values.Max(), values.Average()
}));
calcResult.SeriesSet.Series.Add(resultValuesSeries);
expStep2.Results.Add(calcResult);
//// Add the 2nd ExperimentStep to the ExperimentStepSet.
expStepSet.ExperimentSteps.Add(expStep2);
document.ExperimentStepSet = expStepSet;
}
static void Main(string[] args)
{
//// Create a new AnimlDocument
AnimlDocument document = new AnimlDocument();
//// Create Sample(s) in the AnimlDocument
CreateSamples(ref document);
//// Create ExperimentStep(s) in the AnimlDocument
CreateExperimentSteps(ref document);
////Create AuditTrailEntry(s) in the AnimlDocument
CreateAuditTrailEntries(ref document);
//// Generate the AnIML document XML from the AnimlDocument object
string docString = document.ToXml();
//// Print the XML to the console
Console.WriteLine("Generated AnIML document:");
Console.WriteLine("=========================");
Console.WriteLine(docString);
Console.WriteLine();
if (!string.IsNullOrEmpty(outputFilePath))
{
document.SaveAsFile(outputFilePath);
Console.WriteLine("Saved AnIML document to file:");
Console.WriteLine("=========================");
Console.WriteLine($"--> {outputFilePath}");
Console.WriteLine();
}
//// Create a new document from the generated XML (to test importing XML)
AnimlDocument document2 = AnimlDocument.ReadFromString(docString);
string docString2 = document2.ToXml();
Console.WriteLine("AnIML document from import:");
Console.WriteLine("=========================");
Console.WriteLine(docString2);
Console.WriteLine();
//// Compare the initial XML with the one after reading from the XML
Console.WriteLine("AnIML documents are equal:");
Console.WriteLine("==========================");
Console.WriteLine(docString.Equals(docString2, StringComparison.Ordinal) ? "YES" : "NO");
Console.WriteLine();
//// Validate the AnIML document against the AnIML core schema
Console.WriteLine("Validating document against the AnIML Core Schema:");
Console.WriteLine("==================================================");
AnimlDocumentValidator validator = AnimlDocumentValidator.CreateValidatorForAnimlDocumentString(docString);
if (!validator.Validate())
{
Console.WriteLine("Validation failed.");
validator.ValidationMessages.ForEach(Console.WriteLine);
}
else
{
Console.WriteLine("Validation succeeded.");
}
}
public AnimlDocumentBuilder()
{
this.animlDocument = new AnimlDocument();
}