/// <summary>
/// The execution method for the activity.
/// </summary>
/// <param name="executionContext">The execution context.</param>
/// <returns>The execution status.</returns>
protected override ActivityExecutionStatus Execute(ActivityExecutionContext executionContext)
{
GenBankFormatter formatter = new GenBankFormatter();
formatter.Open(OutputFile);
if ((Sequence == null) && (SequenceList != null))
{
foreach (ISequence sequence in SequenceList)
{
formatter.Write(sequence);
}
}
else if ((Sequence != null) && (SequenceList == null))
{
formatter.Write(Sequence);
}
else if ((Sequence != null) && (SequenceList != null))
{
foreach (ISequence sequence in SequenceList)
{
formatter.Write(sequence);
}
formatter.Write(Sequence);
}
formatter.Close();
return(ActivityExecutionStatus.Closed);
}
public void GenBankFormatterValidateWriteUsingStream()
{
InitializeXmlVariables();
// Create a Sequence with all attributes.
// Parse and update the properties instead of parsing entire file.
using (ISequenceParser parser1 = new GenBankParser(FilePath))
{
IEnumerable <ISequence> seqList1 = parser1.Parse();
string tempFileName = System.IO.Path.GetTempFileName();
GenBankMetadata metadata = null;
ISequence seq = null;
string expectedUpdatedSequence =
ExpectedSequence.Replace("\r", "").Replace("\n", "").Replace(" ", "");
Sequence orgSeq =
new Sequence(Utility.GetAlphabet(AlphabetName), expectedUpdatedSequence);
orgSeq.Metadata.Add("GenBank",
(GenBankMetadata)seqList1.ElementAt(0).Metadata["GenBank"]);
orgSeq.ID = seqList1.ElementAt(0).ID;
using (ISequenceFormatter formatter = new GenBankFormatter())
{
using (StreamWriter writer = new StreamWriter(tempFileName))
{
formatter.Open(writer);
formatter.Write(orgSeq);
}
}
using (GenBankParser parserObj = new GenBankParser(tempFileName))
{
IEnumerable <ISequence> seqList = parserObj.Parse();
seq = seqList.ElementAt(0);
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID");
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
metadata = (GenBankMetadata)seq.Metadata["GenBank"];
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandType, metadata.Locus.Strand.ToString());
}
}
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture), metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture));
Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse(SequenceDate, null), metadata.Locus.Date);
Assert.AreEqual(Version, metadata.Version.Version.ToString((IFormatProvider)null));
Assert.AreEqual(PrimaryId, metadata.Version.GiNumber);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, new string(seq.Select(a => (char)a).ToArray()));
ApplicationLog.WriteLine("GenBank Formatter BVT: Successfully validated the Sequence");
Console.WriteLine(string.Format((IFormatProvider)null, "GenBank Formatter BVT: Successfully validated the Sequence '{0}'", ExpectedSequence));
File.Delete(tempFileName);
}
}
public void GenBankFormatterWithParseValidateWriteFilePath()
{
InitializeXmlVariables();
// parse
using (ISequenceParser parserObj = new GenBankParser(FilePath))
{
IEnumerable <ISequence> seqList = parserObj.Parse();
ISequence seq = seqList.ElementAt(0);
string tempFileName = System.IO.Path.GetTempFileName();
using (ISequenceFormatter formatter = new GenBankFormatter(tempFileName))
{
formatter.Write(seq);
formatter.Close();
// parse
ISequenceParser parserObjFromFile = new GenBankParser(tempFileName);
seqList = parserObjFromFile.Parse();
seq = seqList.ElementAt(0);
Assert.AreEqual(Utility.GetAlphabet(AlphabetName), seq.Alphabet);
Assert.AreEqual(SeqId, seq.ID);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the Alphabet, Molecular type, Sequence ID and Display ID");
// test the metadata that is tricky to parse, and will not be tested implicitly by
// testing the formatting
GenBankMetadata metadata =
(GenBankMetadata)seq.Metadata["GenBank"];
if (metadata.Locus.Strand != SequenceStrandType.None)
{
Assert.AreEqual(StrandType,
metadata.Locus.Strand.ToString());
}
Assert.AreEqual(StrandTopology.ToUpper(CultureInfo.CurrentCulture),
metadata.Locus.StrandTopology.ToString().ToUpper(CultureInfo.CurrentCulture));
Assert.AreEqual(Div, metadata.Locus.DivisionCode.ToString());
Assert.AreEqual(DateTime.Parse(SequenceDate, null),
metadata.Locus.Date);
Assert.AreEqual(Version, metadata.Version.Version.ToString((IFormatProvider)null));
Assert.AreEqual(PrimaryId, metadata.Version.GiNumber);
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the StrandType, StrandTopology, Division, Date, Version, PrimaryID Properties");
// test the sequence string
Assert.AreEqual(ExpectedSequence, new string(seq.Select(a => (char)a).ToArray()));
ApplicationLog.WriteLine(
"GenBank Formatter BVT: Successfully validated the Sequence");
Console.WriteLine(string.Format((IFormatProvider)null,
"GenBank Formatter BVT: Successfully validated the Sequence '{0}'",
ExpectedSequence));
parserObjFromFile.Close();
parserObjFromFile.Dispose();
File.Delete(tempFileName);
}
}
}
