public void GffFormatterValidateStreams()
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(Constants.SimpleGffNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
IList <ISequence> seqs = null;
Sequence originalSequence = null;
using (GffParser parserObj = new GffParser(filePath))
{
seqs = parserObj.Parse().ToList();
originalSequence = (Sequence)seqs[0];
}
// Use the formatter to write the original sequences to a temp file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Gff Formatter BVT: Creating the Temp file '{0}'.",
Constants.GffTempFileName));
using (StreamWriter writer = new StreamWriter(Constants.GffTempFileName))
{
using (GffFormatter formatter = new GffFormatter())
{
formatter.ShouldWriteSequenceData = true;
formatter.Open(writer);
formatter.Write(originalSequence);
}
}
// Read the new file, then compare the sequences
IList <ISequence> seqsNew = null;
using (GffParser newParser = new GffParser(Constants.GffTempFileName))
{
seqsNew = newParser.Parse().ToList();
}
Assert.IsNotNull(seqsNew);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Gff Formatter BVT: New Sequence is '{0}'.",
seqsNew[0].ToString()));
bool val = ValidateFeatures(seqsNew[0], Constants.SimpleGffNodeName);
Assert.IsTrue(val);
ApplicationLog.WriteLine(
"GFF Formatter BVT : All the features validated successfully.");
// Now compare the sequences.
int countNew = seqsNew.Count();
int expectedCount = 1;
Assert.AreEqual(expectedCount, countNew);
ApplicationLog.WriteLine("The Number of sequences are matching.");
Assert.AreEqual(originalSequence.ID, seqsNew[0].ID);
ISequence newSeq = seqsNew.FirstOrDefault();
Assert.AreEqual(new string(originalSequence.Select(x => (char)x).ToArray()),
new string(newSeq.Select(x => (char)x).ToArray()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Gff Formatter BVT: The Gff sequences '{0}' are matching with Write() method.",
seqsNew[0].ToString()));
// Passed all the tests, delete the tmp file. If we failed an Assert,
// the tmp file will still be there in case we need it for debugging.
if (File.Exists(Constants.GffTempFileName))
{
File.Delete(Constants.GffTempFileName);
}
ApplicationLog.WriteLine("Deleted the temp file created.");
}
/// <summary>
/// Validates the Format() method in Gff Formatter based on the parameters.
/// </summary>
/// <param name="nodeName">Xml Node name to be read.</param>
/// <param name="isFilePath">Is file path passed as parameter?</param>
/// <param name="isSequenceList">Is sequence list passed as parameter?</param>
void ValidateFormatGeneralTestCases(string nodeName,
bool isFilePath, bool isSequenceList)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
IList <ISequence> seqs = null;
GffParser parserObj = new GffParser(filePath);
seqs = parserObj.Parse().ToList();
Sequence originalSequence = (Sequence)seqs[0];
// Use the formatter to write the original sequences to a temp file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Gff Formatter BVT: Creating the Temp file '{0}'.",
Constants.GffTempFileName));
GffFormatter formatter = new GffFormatter(Constants.GffTempFileName);
formatter.ShouldWriteSequenceData = true;
if (isFilePath)
{
if (isSequenceList)
{
formatter.Write(seqs);
}
else
{
formatter.Write(originalSequence);
}
}
else
{
if (isSequenceList)
{
formatter.Write(seqs);
}
else
{
formatter.Write(originalSequence);
}
}
// Read the new file, then compare the sequences
IList <ISequence> seqsNew = null;
using (GffParser newParser = new GffParser(Constants.GffTempFileName))
{
seqsNew = newParser.Parse().ToList();
}
Assert.IsNotNull(seqsNew);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Gff Formatter BVT: New Sequence is '{0}'.",
seqsNew[0].ToString()));
bool val = ValidateFeatures(seqsNew[0], nodeName);
Assert.IsTrue(val);
ApplicationLog.WriteLine(
"GFF Formatter BVT : All the features validated successfully.");
Console.WriteLine(
"GFF Formatter BVT : All the features validated successfully.");
// Now compare the sequences.
int countNew = seqsNew.Count();
int expectedCount = 1;
Assert.AreEqual(expectedCount, countNew);
ApplicationLog.WriteLine("The Number of sequences are matching.");
Assert.AreEqual(originalSequence.ID, seqsNew[0].ID);
byte[] TempSeqData = new byte[originalSequence.Count];
for (int i = 0; i < originalSequence.Count; i++)
{
TempSeqData[i] = originalSequence[i];
}
string orgSeq = ASCIIEncoding.ASCII.GetString(TempSeqData);
ISequence newSeq = seqsNew.FirstOrDefault();
byte[] TempSeqData1 = new byte[newSeq.Count];
for (int i = 0; i < newSeq.Count; i++)
{
TempSeqData1[i] = newSeq[i];
}
string newSeqString = ASCIIEncoding.ASCII.GetString(TempSeqData1);
Assert.AreEqual(orgSeq, newSeqString);
Console.WriteLine(string.Format((IFormatProvider)null,
"Gff Formatter BVT: The Gff sequences '{0}' are matching with Format() method and is as expected.",
seqsNew[0].ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Gff Formatter BVT: The Gff sequences '{0}' are matching with Format() method.",
seqsNew[0].ToString()));
// Passed all the tests, delete the tmp file. If we failed an Assert,
// the tmp file will still be there in case we need it for debugging.
if (File.Exists(Constants.GffTempFileName))
{
File.Delete(Constants.GffTempFileName);
}
ApplicationLog.WriteLine("Deleted the temp file created.");
}
/// <summary>
/// General method to invalidate Argument Null exceptions generated from different methods.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="method">Gff Parse method parameters</param>
void InvalidateGffWriteMethod(ArgumentNullExceptions method)
{
ISequence sequence = null;
List <ISequence> collection = new List <ISequence>();
string sequenceData = null;
GffFormatter gffFormatter = null;
try
{
switch (method)
{
case ArgumentNullExceptions.writeWithEmptyFile:
sequenceData = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGffDnaNodeName, Constants.ExpectedSequenceNode);
using (gffFormatter = new GffFormatter())
{
gffFormatter.Write(new Sequence(DnaAlphabet.Instance, sequenceData));
}
break;
case ArgumentNullExceptions.writeWithEmptySequence:
using (gffFormatter = new GffFormatter())
{
gffFormatter.Write(sequence);
}
break;
case ArgumentNullExceptions.FormatString:
using (gffFormatter = new GffFormatter())
{
gffFormatter.FormatString(sequence);
}
break;
case ArgumentNullExceptions.writeCollectionWithEmptyFile:
sequenceData = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleGffDnaNodeName, Constants.ExpectedSequenceNode);
collection.Add(new Sequence(DnaAlphabet.Instance, sequenceData));
using (gffFormatter = new GffFormatter())
{
gffFormatter.Write(collection);
}
break;
case ArgumentNullExceptions.writeCollectionWithEmptySequence:
using (gffFormatter = new GffFormatter())
{
gffFormatter.Write(collection);
}
break;
default:
break;
}
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"GFF P2 : Exception is validated successfully.");
}
}
