public void ClustalWParse()
{
string filepath = @"TestUtils\ClustalW\AlignmentData.aln";
Assert.IsTrue(File.Exists(filepath));
IList<Dictionary<string, string>> expectedOutput = new List<Dictionary<string, string>>();
Dictionary<string, string> expectedAlignment = new Dictionary<string, string>();
expectedAlignment["CYS1_DICDI"] = "-----MKVILLFVLAVFTVFVSS---------------RGIPPEEQ------------SQ"
+ "FLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE"
+ "FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG-AVTPVKNQGQCGSCWSFS"
+ "TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG"
+ "GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KNETVMAGYIVSTGPLAIAADAV"
+ "E-WQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQG"
+ "YIYLRRGKNTCGVSNFVSTSII--";
expectedAlignment["ALEU_HORVU"] = "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALR"
+ "FARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTN----RKGLPYRLGINRFSDMSWEE"
+ "FQATRL-GAAQTCSATLAGNHLMRDA--AALPETKDWREDG-IVSPVKNQAHCGSCWTFS"
+ "TTGALEAAYTQATGKNISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYIKYNG"
+ "GIDTEESYPYKGVNGV-CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVI"
+ "DGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGV-----PYWLIKNSWGADWGDNG"
+ "YFKMEMGKNMCAIATCASYPVVAA";
expectedAlignment["CATH_HUMAN"] = "------MWATLPLLCAGAWLLGV--------PVCGAAELSVNSLEK------------FH"
+ "FKSWMSKHRKTY-STEEYHHRLQTFASNWRKINAHN----NGNHTFKMALNQFSDMSFAE"
+ "IKHKYLWSEPQNCSAT--KSNYLRGT--GPYPPSVDWRKKGNFVSPVKNQGACGSCWTFS"
+ "TTGALESAIAIATGKMLSLAEQQLVDCAQDFNNY--------GCQGGLPSQAFEYILYNK"
+ "GIMGEDTYPYQGKDGY-CKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVT"
+ "QDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNGI-----PYWIVKNSWGPQWGMNG"
+ "YFLIERGKNMCGLAACASYPIPLV";
expectedOutput.Add(expectedAlignment);
IList<ISequenceAlignment> actualOutput = null;
ISequenceAlignmentParser parser = new ClustalWParser();
using (parser.Open(filepath))
{
actualOutput = parser.Parse().ToList();
}
CompareOutput(actualOutput, expectedOutput);
}
/// <summary>
/// Parsers the ClustalW file for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
private void ParserGeneralTestCases(string nodeName, AdditionalParameters addParam)
{
// Gets the Filename
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
Assert.IsFalse(string.IsNullOrEmpty(filePath));
ApplicationLog.WriteLine(string.Format("ClustalW Parser BVT: Reading the File from location '{0}'", filePath));
// Get the range list after parsing.
var parserObj = new ClustalWParser();
IEnumerable<ISequenceAlignment> sequenceAlignmentList = null;
ISequenceAlignment sequenceAlignment = null;
// Gets the SequenceAlignment list based on the parameters.
switch (addParam)
{
case AdditionalParameters.Parse:
sequenceAlignmentList = parserObj.Parse(filePath).ToList();
break;
case AdditionalParameters.ParseOne:
sequenceAlignment = parserObj.ParseOne(filePath);
break;
case AdditionalParameters.ParseTextReader:
using (var strRdrObj = File.OpenRead(filePath))
{
sequenceAlignmentList = parserObj.Parse(strRdrObj).ToList();
}
break;
case AdditionalParameters.ParseOneTextReader:
using (var strRdrObj = File.OpenRead(filePath))
{
sequenceAlignment = parserObj.ParseOne(strRdrObj);
}
break;
default:
break;
}
// Gets all the expected values from xml.
XElement expectedAlignmentNodes = utilityObj.xmlUtil.GetNode(nodeName, Constants.ExpectedAlignmentNode);
IList<XNode> nodes = expectedAlignmentNodes.Nodes().ToList();
//Get all the values from the elements in the node.
var expectedAlignmentObj = new Dictionary<string, string>();
foreach (XElement node in nodes)
{
expectedAlignmentObj[node.Name.ToString()] = node.Value;
}
//Create a ISequenceAlignment List
switch (addParam)
{
case AdditionalParameters.ParseOne:
case AdditionalParameters.ParseOneTextReader:
sequenceAlignmentList = new List<ISequenceAlignment>() { sequenceAlignment };
break;
default:
break;
}
var expectedAlignmentList = new List<Dictionary<string, string>> { expectedAlignmentObj };
Assert.IsTrue(CompareOutput(sequenceAlignmentList.ToList(), expectedAlignmentList));
ApplicationLog.WriteLine("ClustalW Parser BVT: Successfully validated all the Alignment Sequences");
}
public void ClustalWParserValidatePublicProperties()
{
string description = utilityObj.xmlUtil.GetTextValue(
Constants.ClustalWDescriptionsNode, Constants.DescriptionNode);
string name = utilityObj.xmlUtil.GetTextValue(
Constants.ClustalWDescriptionsNode, Constants.NameNode);
string supportedFileTypes = utilityObj.xmlUtil.GetTextValue(
Constants.ClustalWDescriptionsNode, Constants.SupportedFileTypesNode);
// Get the rangelist after parsing.
var parserObj = new ClustalWParser();
//Validate Description for ClustalW Parser.
Assert.AreEqual(description, parserObj.Description);
ApplicationLog.WriteLine(string.Format(null,
"ClustalW Parser BVT: Successfully validated description"));
//Validate Name for Clustal W parser.
Assert.AreEqual(name, parserObj.Name);
ApplicationLog.WriteLine(string.Format(null,
"ClustalW Parser BVT: Successfully validated Name"));
//Validate supported file types for Clustal W parser.
Assert.AreEqual(supportedFileTypes, parserObj.SupportedFileTypes);
ApplicationLog.WriteLine(string.Format(null,
"ClustalW Parser BVT: Successfully validated Supported File types."));
}
void ValidateCancelRequest(string nodeName)
{
// Read input from config file
string filepath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string emailId = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.EmailIDNode);
string clusterOption = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ClusterOptionNode);
string actionAlign = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ActionAlignNode);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
IEnumerable<ISequence> sequence = null;
// Get the input sequences
using (FastAParser parser = new FastAParser(filepath))
{
sequence = parser.Parse();
// Submit job and cancel job
// Validate cancel job is working as expected
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler =
new TestIClustalWServiceHandler(clustalparser, configparams);
ServiceParameters svcparams = handler.SubmitRequest(sequence.ToList(), parameters);
bool result = handler.CancelRequest(svcparams);
Assert.IsTrue(result);
ApplicationLog.WriteLine(string.Concat("JobId:", svcparams.JobId));
Assert.IsFalse(string.IsNullOrEmpty(svcparams.JobId));
foreach (string key in svcparams.Parameters.Keys)
{
Assert.IsFalse(string.IsNullOrEmpty(svcparams.Parameters[key].ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "{0} : {1}",
key, svcparams.Parameters[key].ToString()));
}
}
ApplicationLog.WriteLine(
"ClustalWServiceHandler BVT : Cancel job is submitted as expected");
}
/// <summary>
/// Validate submit job and Get Results using event handler
/// </summary>
/// <param name="nodeName">xml node name</param>
void ValidateFetchResultsUsingEvent(string nodeName)
{
// Read input from config file
string filepath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string emailId = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.EmailIDNode);
string clusterOption = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ClusterOptionNode);
string actionAlign = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ActionAlignNode);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
IEnumerable<ISequence> sequence = null;
// Get the input sequences
using (FastAParser parser = new FastAParser(filepath))
{
sequence = parser.Parse();
// Register event and submit request
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler =
new TestIClustalWServiceHandler(clustalparser, configparams);
handler.RequestCompleted +=
new EventHandler<ClustalWCompletedEventArgs>(handler_RequestCompleted);
ServiceParameters svcparams = handler.SubmitRequest(sequence.ToList(), parameters);
WaitHandle[] aryHandler = new WaitHandle[1];
aryHandler[0] = _resetEvent;
WaitHandle.WaitAny(aryHandler);
// Validate the submit job results
Assert.IsFalse(string.IsNullOrEmpty(svcparams.JobId));
foreach (string key in svcparams.Parameters.Keys)
{
Assert.IsFalse(string.IsNullOrEmpty(svcparams.Parameters[key].ToString()));
}
_resetEvent.Close();
_resetEvent.Dispose();
}
}
/// <summary>
/// Validate submit job and FetchResultAsync() using multiple input sequences
/// </summary>
/// <param name="nodeName">xml node name</param>
void ValidateFetchResultAsync(string nodeName)
{
// Read input from config file
string filepath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string emailId = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.EmailIDNode);
string clusterOption = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClusterOptionNode);
string actionAlign = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ActionAlignNode);
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler = new TestIClustalWServiceHandler(clustalparser, configparams);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
// Get input sequences
using (FastAParser parser = new FastAParser(filepath))
{
IEnumerable<ISequence> sequence = parser.Parse();
// Submit job and validate it returned valid job id and control id
ServiceParameters svcparameters = handler.SubmitRequest(sequence.ToList(), parameters);
Assert.IsFalse(string.IsNullOrEmpty(svcparameters.JobId));
foreach (string key in svcparameters.Parameters.Keys)
{
Assert.IsFalse(string.IsNullOrEmpty(svcparameters.Parameters[key].ToString()));
}
// Get the results and validate it is not null.
int retrycount = 0;
ServiceRequestInformation info;
do
{
info = handler.GetRequestStatus(svcparameters);
if (info.Status == ServiceRequestStatus.Ready)
{
break;
}
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting
|| info.Status == ServiceRequestStatus.Queued ?
Constants.ClusterRetryInterval * retrycount : 0);
retrycount++;
}
while (retrycount < 10);
ClustalWResult result = null;
if (info.Status == ServiceRequestStatus.Ready)
{
result = handler.FetchResultsAsync(svcparameters);
}
Assert.IsNotNull(result, "Failed to retrieve results from submitted task, Server may be offline or slow.");
Assert.IsNotNull(result.SequenceAlignment);
foreach (IAlignedSequence alignSeq in result.SequenceAlignment.AlignedSequences)
{
ApplicationLog.WriteLine("Aligned Sequence Sequences : ");
foreach (ISequence seq in alignSeq.Sequences)
{
ApplicationLog.WriteLine(string.Concat("Sequence:", seq.ToString()));
}
}
}
ApplicationLog.WriteLine(@"ClustalWServiceHandler BVT : Submit job and Get Results is successfully completed using FetchResultAsync()");
}
/// <summary>
/// Validate Submit Job and Fetch ResultSync() using multiple input sequences
/// </summary>
/// <param name="nodeName">xml node name</param>
void ValidateFetchResultSync(string nodeName)
{
// Read input from config file
string filepath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string emailId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailIDNode);
string clusterOption = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ClusterOptionNode);
string actionAlign = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ActionAlignNode);
// Initialize with parser and config params
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler =
new TestIClustalWServiceHandler(clustalparser, configparams);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
IEnumerable<ISequence> sequence = null;
// Get the input sequences
using (FastAParser parser = new FastAParser(filepath))
{
sequence = parser.Parse();
// Submit job and validate it returned valid job id and control id
ServiceParameters svcparameters =
handler.SubmitRequest(sequence.ToList(), parameters);
Assert.IsFalse(string.IsNullOrEmpty(svcparameters.JobId));
ApplicationLog.WriteLine(string.Concat("JobId", svcparameters.JobId));
foreach (string key in svcparameters.Parameters.Keys)
{
Assert.IsFalse(string.IsNullOrEmpty(svcparameters.Parameters[key].ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "{0}:{1}",
key, svcparameters.Parameters[key].ToString()));
}
// Get the results and validate it is not null.
ClustalWResult result = handler.FetchResultsSync(svcparameters);
Assert.IsNotNull(result);
Assert.IsNotNull(result.SequenceAlignment);
foreach (IAlignedSequence alignSeq in result.SequenceAlignment.AlignedSequences)
{
ApplicationLog.WriteLine("Aligned Sequence Sequences :");
foreach (ISequence seq in alignSeq.Sequences)
{
ApplicationLog.WriteLine(string.Concat("Sequence:", seq.ToString()));
}
}
}
ApplicationLog.WriteLine(@"ClustalWServiceHandler BVT : Submit job and Get Results is successfully completed using FetchResultSync()");
}
