/// <summary>
/// General method to invalidate Phylip parser
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="method">Phylip Parser method parameters</param>
void InvalidatePhylipParserTestCases(
string nodeName,
ParserTestAttributes method)
{
try
{
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName,
Constants.FilePathNode);
PhylipParser parser = new PhylipParser();
switch (method)
{
case ParserTestAttributes.Parse:
parser.Parse(filePath);
break;
case ParserTestAttributes.ParseOne:
parser.ParseOne(filePath);
break;
default:
break;
}
Assert.Fail();
}
catch (InvalidDataException)
{
ApplicationLog.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
Console.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
}
catch (FormatException)
{
ApplicationLog.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
Console.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
}
}
/// <summary>
/// Parsers the Phylip file for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
static void ParserGeneralTestCases(string nodeName,
ParserTestAttributes addParam)
{
// Gets the Filename
string filePath = Utility._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
Assert.IsNotEmpty(filePath);
ApplicationLog.WriteLine(string.Format(
"Phylip Parser BVT: Reading the File from location '{0}'", filePath));
Console.WriteLine(string.Format(
"Phylip Parser BVT: Reading the File from location '{0}'", filePath));
// Get the rangelist after parsing.
PhylipParser parserObj = new PhylipParser();
IList <ISequenceAlignment> sequenceAlignmentList = null;
ISequenceAlignment sequenceAlignment = null;
// Gets the SequenceAlignment list based on the parameters.
switch (addParam)
{
case ParserTestAttributes.Parse:
sequenceAlignmentList = parserObj.Parse(filePath);
break;
case ParserTestAttributes.ParseOne:
sequenceAlignment = parserObj.ParseOne(filePath);
break;
case ParserTestAttributes.ParseTextReader:
sequenceAlignmentList = parserObj.Parse(
new StreamReader(filePath));
break;
case ParserTestAttributes.ParseOneTextReader:
sequenceAlignment = parserObj.ParseOne(
new StreamReader(filePath));
break;
case ParserTestAttributes.ParseOneTextReaderReadOnly:
sequenceAlignment = parserObj.ParseOne(
new StreamReader(filePath), false);
break;
case ParserTestAttributes.ParseTextReaderReadOnly:
sequenceAlignmentList = parserObj.Parse(
new StreamReader(filePath), false);
break;
case ParserTestAttributes.ParseReadOnly:
sequenceAlignmentList = parserObj.Parse(filePath,
false);
break;
case ParserTestAttributes.ParseOneReadOnly:
sequenceAlignment = parserObj.ParseOne(filePath,
false);
break;
case ParserTestAttributes.ParseEncoding:
PhylipParser parser =
new PhylipParser(Encodings.Ncbi4NA);
sequenceAlignmentList = parser.Parse(
new StreamReader(filePath), false);
break;
default:
break;
}
// Gets all the expected values from xml.
IList <Dictionary <string, string> > expectedAlignmentList =
new List <Dictionary <string, string> >();
Dictionary <string, string> expectedAlignmentObj =
new Dictionary <string, string>();
XmlNode expectedAlignmentNodes = Utility._xmlUtil.GetNode(
nodeName, Constants.ExpectedAlignmentNode);
XmlNodeList alignNodes = expectedAlignmentNodes.ChildNodes;
// Create a ISequenceAlignment List
switch (addParam)
{
case ParserTestAttributes.ParseOne:
case ParserTestAttributes.ParseOneTextReader:
case ParserTestAttributes.ParseOneTextReaderReadOnly:
case ParserTestAttributes.ParseOneReadOnly:
sequenceAlignmentList = new List <ISequenceAlignment>();
sequenceAlignmentList.Add(sequenceAlignment);
break;
default:
break;
}
foreach (XmlNode expectedAlignment in alignNodes)
{
expectedAlignmentObj[expectedAlignment.Name] =
expectedAlignment.InnerText;
}
expectedAlignmentList.Add(expectedAlignmentObj);
Assert.IsTrue(CompareOutput(sequenceAlignmentList,
expectedAlignmentList));
ApplicationLog.WriteLine(
"Phylip Parser BVT: Successfully validated all the Alignment Sequences");
Console.WriteLine(
"Phylip Parser BVT: Successfully validated all the Alignment Sequences");
}
/// <summary>
/// Parsers the Phylip file for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
void ParserGeneralTestCases(string nodeName, ParserTestAttributes addParam)
{
// Gets the Filename
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
Assert.IsFalse(string.IsNullOrEmpty(filePath));
ApplicationLog.WriteLine(string.Format("Phylip Parser BVT: Reading the File from location '{0}'", filePath));
// Get the range list after parsing.
PhylipParser parserObj = new PhylipParser();
IEnumerable<ISequenceAlignment> sequenceAlignmentList = null;
ISequenceAlignment sequenceAlignment = null;
// Gets the SequenceAlignment list based on the parameters.
switch (addParam)
{
case ParserTestAttributes.Parse:
sequenceAlignmentList = parserObj.Parse(filePath);
break;
case ParserTestAttributes.ParseOne:
sequenceAlignment = parserObj.ParseOne(filePath);
break;
case ParserTestAttributes.ParseTextReader:
using (var rdrObj = File.OpenRead(filePath))
{
sequenceAlignmentList = parserObj.Parse(rdrObj).ToList();
}
break;
case ParserTestAttributes.ParseOneTextReader:
using (var rdrObj = File.OpenRead(filePath))
{
sequenceAlignment = parserObj.ParseOne(rdrObj);
}
break;
default:
break;
}
// Gets all the expected values from xml.
var expectedAlignmentList = new List<Dictionary<string, string>>();
var expectedAlignmentObj = new Dictionary<string, string>();
XElement expectedAlignmentNodes = utilityObj.xmlUtil.GetNode(nodeName, Constants.ExpectedAlignmentNode);
IList<XNode> nodes = expectedAlignmentNodes.Nodes().ToList();
//Get all the values from the elements in the node.
foreach (XElement node in nodes)
expectedAlignmentObj[node.Name.ToString()] = node.Value;
// Create a ISequenceAlignment List
switch (addParam)
{
case ParserTestAttributes.ParseOne:
case ParserTestAttributes.ParseOneTextReader:
sequenceAlignmentList = new List<ISequenceAlignment> { sequenceAlignment };
break;
default:
break;
}
expectedAlignmentList.Add(expectedAlignmentObj);
Assert.IsTrue(CompareOutput(sequenceAlignmentList.ToList(), expectedAlignmentList));
ApplicationLog.WriteLine("Phylip Parser BVT: Successfully validated all the Alignment Sequences");
}
/// <summary>
/// Parsers the Phylip file for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
void ParserGeneralTestCases(string nodeName, ParserTestAttributes addParam)
{
// Gets the Filename
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode).TestDir();
Assert.IsFalse(string.IsNullOrEmpty(filePath));
ApplicationLog.WriteLine($"Phylip Parser BVT: Reading the File from location '{filePath}'");
// Get the range list after parsing.
PhylipParser parserObj = new PhylipParser();
IEnumerable <ISequenceAlignment> sequenceAlignmentList = null;
ISequenceAlignment sequenceAlignment = null;
// Gets the SequenceAlignment list based on the parameters.
switch (addParam)
{
case ParserTestAttributes.Parse:
sequenceAlignmentList = parserObj.Parse(filePath);
break;
case ParserTestAttributes.ParseOne:
sequenceAlignment = parserObj.ParseOne(filePath);
break;
case ParserTestAttributes.ParseTextReader:
using (var rdrObj = File.OpenRead(filePath))
{
sequenceAlignmentList = parserObj.Parse(rdrObj).ToList();
}
break;
case ParserTestAttributes.ParseOneTextReader:
using (var rdrObj = File.OpenRead(filePath))
{
sequenceAlignment = parserObj.ParseOne(rdrObj);
}
break;
default:
break;
}
// Gets all the expected values from xml.
var expectedAlignmentList = new List <Dictionary <string, string> >();
var expectedAlignmentObj = new Dictionary <string, string>();
XElement expectedAlignmentNodes = utilityObj.xmlUtil.GetNode(nodeName, Constants.ExpectedAlignmentNode);
IList <XNode> nodes = expectedAlignmentNodes.Nodes().ToList();
//Get all the values from the elements in the node.
foreach (XElement node in nodes)
{
expectedAlignmentObj[node.Name.ToString()] = node.Value;
}
// Create a ISequenceAlignment List
switch (addParam)
{
case ParserTestAttributes.ParseOne:
case ParserTestAttributes.ParseOneTextReader:
sequenceAlignmentList = new List <ISequenceAlignment> {
sequenceAlignment
};
break;
default:
break;
}
expectedAlignmentList.Add(expectedAlignmentObj);
Assert.IsTrue(CompareOutput(sequenceAlignmentList.ToList(), expectedAlignmentList));
ApplicationLog.WriteLine("Phylip Parser BVT: Successfully validated all the Alignment Sequences");
}
/// <summary>
/// General method to invalidate Phylip parser
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="method">Phylip Parser method parameters</param>
void InvalidatePhylipParserTestCases(
string nodeName,
ParserTestAttributes method)
{
try
{
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName,
Constants.FilePathNode);
PhylipParser parser = new PhylipParser();
switch (method)
{
case ParserTestAttributes.Parse:
parser.Parse(filePath).First();
break;
case ParserTestAttributes.ParseOne:
parser.ParseOne(filePath);
break;
default:
break;
}
Assert.Fail();
}
catch (InvalidDataException)
{
ApplicationLog.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
}
catch (Exception)
{
ApplicationLog.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
}
}
