// Test wiggle fixed step
private static WiggleAnnotation TestParserFixedStep(string filename)
{
WiggleParser p = new WiggleParser();
WiggleAnnotation an = p.Parse(filename).First();
Assert.IsTrue(an.Chromosome == "chr19");
Assert.IsTrue(an.BasePosition == 59307401);
Assert.IsTrue(an.Step == 300);
Assert.IsTrue(an.Span == 200);
Assert.IsTrue(an.Metadata["type"] == "wiggle_0");
Assert.IsTrue(an.Metadata["name"] == "ArrayExpt1");
Assert.IsTrue(an.Metadata["description"] == "20 degrees, 2 hr");
float[] values = an.GetValueArray(0, 3);
Assert.IsTrue(values[0] == 1000);
Assert.IsTrue(values[1] == 900);
Assert.IsTrue(values[2] == 800);
values = an.GetValueArray(7, 3);
Assert.IsTrue(values[0] == 300);
Assert.IsTrue(values[1] == 200);
Assert.IsTrue(values[2] == 100);
return(an);
}
// Test wiggle variable step
private static WiggleAnnotation TestParserVariableStep(string filename)
{
WiggleParser p = new WiggleParser();
WiggleAnnotation an = p.Parse(filename).First();
Assert.IsTrue(an.Chromosome == "chr19");
Assert.IsTrue(an.Step == 0);
Assert.IsTrue(an.BasePosition == 0);
Assert.IsTrue(an.Span == 150);
Assert.IsTrue(an.Metadata["type"] == "wiggle_0");
Assert.IsTrue(an.Metadata["name"] == "ArrayExpt1");
Assert.IsTrue(an.Metadata["description"] == "20 degrees, 2 hr");
var x = an.GetEnumerator();
x.MoveNext();
Assert.IsTrue(x.Current.Key == 59304701); Assert.IsTrue(x.Current.Value == 10.0);
x.MoveNext();
Assert.IsTrue(x.Current.Key == 59304901); Assert.IsTrue(x.Current.Value == 12.5);
x.MoveNext();
Assert.IsTrue(x.Current.Key == 59305401); Assert.IsTrue(x.Current.Value == 15.0);
x.MoveNext(); x.MoveNext(); x.MoveNext(); x.MoveNext(); x.MoveNext(); x.MoveNext();
Assert.IsTrue(x.Current.Key == 59307871); Assert.IsTrue(x.Current.Value == 10.0);
return(an);
}
public void ValidateWiggleParserPublicProperties()
{
// Gets the filepath from the Xml
string filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Wiggle Parser BVT: File Exists in the Path '{0}'.", filePath));
//Get the expected values from configuration file.
string expectedDescription = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.ParserDescriptionNode);
string expectedName = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.NameNode);
string expectedFileType = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.FileTypesNode);
WiggleParser parser = new WiggleParser();
//Parse the file
var annotation = parser.Parse(filePath);
Assert.IsNotNull(annotation);
Assert.AreEqual(expectedDescription, parser.Description);
Assert.AreEqual(expectedName, parser.Name);
Assert.AreEqual(expectedFileType, parser.SupportedFileTypes);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Wiggle Parser BVT: Validation of all public properties is successful"));
}
public void TestWiggleFormatter()
{
string filepathTmp = Path.GetTempFileName();
using (WiggleFormatter formatter = new WiggleFormatter(filepathTmp))
{
formatter.Write(CreateDummyAnnotation());
}
WiggleParser parser = new WiggleParser();
VerifyDummyAnnotation(parser.Parse(filepathTmp));
}
public void TestWiggleFormatter()
{
string filepathTmp = Path.GetTempFileName();
WiggleFormatter formatter = new WiggleFormatter();
using (formatter.Open(filepathTmp))
{
formatter.Format(CreateDummyAnnotation());
}
WiggleParser parser = new WiggleParser();
VerifyDummyAnnotation(parser.Parse(filepathTmp).First());
}
// Test wiggle variable step
private static WiggleAnnotation TestParserVariableStep(string filename)
{
WiggleParser p = new WiggleParser();
WiggleAnnotation an = p.Parse(filename).First();
Assert.IsTrue(an.Chromosome == "chr19");
Assert.IsTrue(an.Step == 0);
Assert.IsTrue(an.BasePosition == 0);
Assert.IsTrue(an.Span == 150);
Assert.IsTrue(an.Metadata["type"] == "wiggle_0");
Assert.IsTrue(an.Metadata["name"] == "ArrayExpt1");
Assert.IsTrue(an.Metadata["description"] == "20 degrees, 2 hr");
var x = an.GetEnumerator();
x.MoveNext();
Assert.IsTrue(x.Current.Key == 59304701); Assert.IsTrue(x.Current.Value == 10.0);
x.MoveNext();
Assert.IsTrue(x.Current.Key == 59304901); Assert.IsTrue(x.Current.Value == 12.5);
x.MoveNext();
Assert.IsTrue(x.Current.Key == 59305401); Assert.IsTrue(x.Current.Value == 15.0);
x.MoveNext(); x.MoveNext(); x.MoveNext(); x.MoveNext(); x.MoveNext(); x.MoveNext();
Assert.IsTrue(x.Current.Key == 59307871); Assert.IsTrue(x.Current.Value == 10.0);
return an;
}
// Test wiggle fixed step
private static WiggleAnnotation TestParserFixedStep(string filename)
{
WiggleParser p = new WiggleParser();
WiggleAnnotation an = p.Parse(filename).First();
Assert.IsTrue(an.Chromosome == "chr19");
Assert.IsTrue(an.BasePosition == 59307401);
Assert.IsTrue(an.Step == 300);
Assert.IsTrue(an.Span == 200);
Assert.IsTrue(an.Metadata["type"] == "wiggle_0");
Assert.IsTrue(an.Metadata["name"] == "ArrayExpt1");
Assert.IsTrue(an.Metadata["description"] == "20 degrees, 2 hr");
float[] values = an.GetValueArray(0, 3);
Assert.IsTrue(values[0] == 1000);
Assert.IsTrue(values[1] == 900);
Assert.IsTrue(values[2] == 800);
values = an.GetValueArray(7, 3);
Assert.IsTrue(values[0] == 300);
Assert.IsTrue(values[1] == 200);
Assert.IsTrue(values[2] == 100);
return an;
}
/// <summary>
/// Validate Exceptions from Wiggle Parser with invalid metadata.
/// </summary>
/// <param name="nodeName">Node containing the invalid file name.</param>
public void ValidateFormatException(string nodeName)
{
// Gets the filepath.
String filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.
InValidFileNamesNode, nodeName);
Assert.IsTrue(File.Exists(filePath));
WiggleParser parser=new WiggleParser();
try
{
parser.Parse(filePath);
}
catch (FormatException exception)
{
ApplicationLog.WriteLine(
"Wiggle P2 test cases : Successfully validated Format exception:", exception.Message);
}
}
/// <summary>
/// Validate Exceptions from Wiggle Parser and Formatter for General test cases.
/// </summary>
/// <param name="exceptionType"></param>
public void ValidateArgumentNullException(ExceptionType exceptionType)
{
// Gets the filepath.
String filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
WiggleAnnotation annotation =null;
try
{
switch (exceptionType)
{
case ExceptionType.NullFormatter:
WiggleFormatter formatter = new WiggleFormatter();
formatter.Format(null, annotation);
break;
case ExceptionType.NullParser:
WiggleParser parser = new WiggleParser();
string valueForParse = null;
parser.ParseOne(valueForParse);
break;
case ExceptionType.NullAnnotationWithData:
annotation = new WiggleAnnotation(null, Constants.StringByteArray);
break;
case ExceptionType.NullAnnotationWithChromosomeName:
float[] data = new float[2] { 1.0F, 2.0F };
annotation = new WiggleAnnotation(data, null,0,0);
break;
}
}
catch (ArgumentNullException exception)
{
ApplicationLog.WriteLine(
"Wiggle P2 test cases : Successfully validated the exception:", exception.Message);
}
}
/// <summary>
/// Validate Wiggle Formatter for fixed and variable steps.
/// </summary>
/// <param name="nodeName">Nodename</param>
/// <param name="formatType">Write using a stream/File Name.</param>
private void ValidateWiggleFormatter(string nodeName, FormatType formatType)
{
// Gets the filepath.
String filePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
WiggleAnnotation annotation = null, annotationNew = null;
string[] expectedValues = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedValuesNode).Split(',');
string[] expectedPoints = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedKeysNode).Split(',');
//Parse the file.
WiggleParser parser = new WiggleParser();
annotation = parser.ParseOne(filePath);
WiggleFormatter formatter = null;
//Write to a new file.
switch (formatType)
{
case FormatType.Stream:
using (var writer = File.Create(Constants.WiggleTempFileName))
{
formatter = new WiggleFormatter();
formatter.Format(writer, annotation);
formatter.Close();
}
break;
default:
formatter = new WiggleFormatter();
formatter.Format(annotation, Constants.WiggleTempFileName);
formatter.Close();
break;
}
//Read the new file and then compare the annotations.
WiggleParser parserNew = new WiggleParser();
annotationNew = parserNew.ParseOne(Constants.WiggleTempFileName);
int index = 0;
//Validate keys and values of the parsed file.
foreach (KeyValuePair<long, float> keyvaluePair in annotationNew)
{
Assert.AreEqual(long.Parse(expectedPoints[index],
CultureInfo.InvariantCulture), keyvaluePair.Key);
Assert.AreEqual(float.Parse(expectedValues[index],
CultureInfo.InvariantCulture), keyvaluePair.Value);
index++;
}
File.Delete(Constants.WiggleTempFileName);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Wiggle Formatter BVT: Successfully validated the written file"));
}
/// <summary>
/// Validate Wiggle Parser for fixed and variable steps.
/// </summary>
/// <param name="nodeName">Nodename</param>
/// <param name="parseType">Read using a stream/File Name.</param>
private void ValidateWiggleParser(string nodeName, ParseType parseType)
{
// Gets the filepath.
String filePath = this.utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
int index = 0;
WiggleAnnotation annotation = null;
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Wiggle Parser BVT: File Exists in the Path '{0}'.", filePath));
string[] expectedValues = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedValuesNode).Split(',');
string[] expectedPoints = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ExpectedKeysNode).Split(',');
WiggleParser parser = new WiggleParser();
switch (parseType)
{
case ParseType.Stream:
using (var stream = File.OpenRead(filePath))
{
annotation = parser.ParseOne(stream);
}
break;
default:
annotation = parser.ParseOne(filePath);
break;
}
//Validate keys and values of the parsed file.
foreach (KeyValuePair<long, float> keyvaluePair in annotation)
{
Assert.AreEqual(long.Parse(expectedPoints[index],
CultureInfo.InvariantCulture), keyvaluePair.Key);
Assert.AreEqual(float.Parse(expectedValues[index],
CultureInfo.InvariantCulture), keyvaluePair.Value);
index++;
}
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Wiggle Parser BVT: Successfully validated the parsed file"));
}
public void ValidateAnnotationPublicProperties()
{
WiggleAnnotation annotation = null;
// Gets the filepath from the Xml
string filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Wiggle Parser BVT: File Exists in the Path '{0}'.", filePath));
string expectedbasePosition = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.BasePositionNode);
string expectedchromosome = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.ChromosomeNode);
string expectedannotationCount = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.AnnotationCountNode);
string expectedSpan = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.ExpectedSpanNode);
string expectedStep = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.ExpectedStepNode);
string annotationTypeNode = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.AnnotationTypeNode);
string[] annotationKeys = this.utilityObj.xmlUtil.GetTextValues(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.AnnotationMetadataNode);
string[] values = annotationKeys[0].Split(',');
string[] keys = annotationKeys[1].Split(',');
WiggleParser parser = new WiggleParser();
//Parse the file
annotation = parser.ParseOne(filePath);
Assert.AreEqual(long.Parse(expectedbasePosition, CultureInfo.InvariantCulture)
, annotation.BasePosition);
Assert.AreEqual(expectedchromosome, annotation.Chromosome);
Assert.AreEqual(long.Parse(expectedannotationCount, CultureInfo.InvariantCulture)
, annotation.Count);
Assert.AreEqual(int.Parse(expectedSpan,
CultureInfo.InvariantCulture), annotation.Span);
Assert.AreEqual(int.Parse(expectedStep,
CultureInfo.InvariantCulture), annotation.Step);
Assert.AreEqual(annotationTypeNode, annotation.AnnotationType.ToString());
Dictionary<string, string> annotationMetadata = annotation.Metadata;
//Validate Annotation Metadata.
for (int i = 0; i < annotationMetadata.Count; i++)
{
Assert.AreEqual(keys[i], annotationMetadata.ElementAt(i).Key);
Assert.AreEqual(values[i], annotationMetadata.ElementAt(i).Value);
}
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Wiggle Parser BVT: Validation of Annotation public properties is successfull"));
}
