/// <summary>
/// Validate general fetching results.by passing
/// differnt parameters for Ebi web service..
/// <param name="nodeName">xml node name.</param>
/// <param name="isFetchSynchronous">Is Fetch Synchronous?</param>
/// </summary>
void ValidateEBIWuBlastResultsFetch(
string nodeName,
bool isFetchSynchronous)
{
// Gets the search query parameter and their values.
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string emailParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Emailparameter);
string email = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string expectedHitId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitID);
string expectedAccession = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitAccession);
string expectedResultCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ResultsCount);
string expectedHitsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitsCount);
string expectedEntropyStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EntropyStatistics);
string expectedKappaStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.KappaStatistics);
string expectedLambdaStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LambdaStatistics);
string expectedLength = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Length);
object responseResults = null;
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
// create Ebi Blast service object.
IBlastServiceHandler service = new EbiWuBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
service.Configuration = configParams;
BlastParameters searchParams = new BlastParameters();
// Set Request parameters.
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(emailParameter, email);
searchParams.Add("SequenceType",
alphabetName.ToLower(CultureInfo.CurrentCulture).Replace("ambiguous", ""));
// Create a request without passing sequence.
string reqId = service.SubmitRequest(seq, searchParams);
// validate request identifier.
Assert.IsNotNull(reqId);
// query the status
ServiceRequestInformation info = service.GetRequestStatus(reqId);
if (info.Status != ServiceRequestStatus.Waiting &&
info.Status != ServiceRequestStatus.Ready)
{
string err =
ApplicationLog.WriteLine("Unexpected status: '{0}'", info.Status);
Assert.Fail(err);
}
// get async results, poll until ready
int maxAttempts = 20;
int attempt = 1;
while (attempt <= maxAttempts &&
info.Status != ServiceRequestStatus.Error &&
info.Status != ServiceRequestStatus.Ready)
{
if (isFetchSynchronous)
{
info = service.GetRequestStatus(reqId);
Thread.Sleep(info.Status == ServiceRequestStatus.Waiting ||
info.Status == ServiceRequestStatus.Queued
? 20000 * attempt : 0);
}
else
{
Thread.Sleep(info.Status == ServiceRequestStatus.Waiting ? 20000 : 0);
info = service.GetRequestStatus(reqId);
}
++attempt;
}
IBlastParser blastXmlParser = new BlastXmlParser();
responseResults = blastXmlParser.Parse(
new StringReader(service.GetResult(reqId, searchParams)));
// Validate blast results.
Assert.IsNotNull(responseResults);
List <BlastResult> eBlastResults = responseResults as List <BlastResult>;
Assert.IsNotNull(eBlastResults);
Assert.AreEqual(eBlastResults.Count.ToString(
(IFormatProvider)null), expectedResultCount);
Assert.AreEqual(eBlastResults[0].Records.Count.ToString((
IFormatProvider)null), expectedResultCount);
BlastSearchRecord record = eBlastResults[0].Records[0];
Assert.AreEqual(record.Statistics.Kappa.ToString(
(IFormatProvider)null), expectedKappaStatistics);
Assert.AreEqual(record.Statistics.Lambda.ToString(
(IFormatProvider)null), expectedLambdaStatistics);
Assert.AreEqual(record.Statistics.Entropy.ToString(
(IFormatProvider)null), expectedEntropyStatistics);
Assert.AreEqual(record.Hits.Count.ToString(
(IFormatProvider)null), expectedHitsCount);
Hit hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Length.ToString((IFormatProvider)null), expectedLength);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null), expectedHitId);
Assert.AreEqual(hit.Hsps.Count.ToString((IFormatProvider)null),
expectedResultCount);
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: Hits count '{0}'.", eBlastResults.Count));
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: Accession '{0}'.", hit.Accession));
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: Hit Id '{0}'.", hit.Id));
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: Hits Count '{0}'.", hit.Hsps.Count));
// Validate the results Synchronously with the results got earlier.
if (isFetchSynchronous)
{
IList <BlastResult> syncBlastResults =
service.FetchResultsSync(reqId, searchParams) as List <BlastResult>;
Assert.IsNotNull(syncBlastResults);
if (null != eBlastResults[0].Records[0].Hits &&
0 < eBlastResults[0].Records[0].Hits.Count &&
null != eBlastResults[0].Records[0].Hits[0].Hsps &&
0 < eBlastResults[0].Records[0].Hits[0].Hsps.Count)
{
Assert.AreEqual(eBlastResults[0].Records[0].Hits[0].Hsps[0].QuerySequence,
syncBlastResults[0].Records[0].Hits[0].Hsps[0].QuerySequence);
}
else
{
ApplicationLog.WriteLine(
"No significant hits found with the these parameters.");
Console.WriteLine("No significant hits found with the these parameters.");
}
}
}
/// <summary>
/// Validate Fetch results Asynchronous.
/// </summary>
/// <param name="blastParameters">Ebi blast service config parameters</param>
/// <returns></returns>
private TestCaseOutput FetchResultsSync(Dictionary <string, object> blastParameters)
{
// Get the input query string
string sequenceString = blastParameters[Constants.QuerySeqString] as string;
string alphabetName = blastParameters[Constants.AlphabetString] as string;
Sequence sequence = new Sequence(Utility.GetAlphabet(alphabetName),
sequenceString);
// create Ebi Blast service object.
IBlastServiceHandler service = null;
IList <BlastResult> syncBlastResults = null;
try
{
service = new EbiWuBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
service.Configuration = configParams;
BlastParameters blastSearchPams = blastParameters[Constants.BlastParmsConst]
as BlastParameters;
// Create a request without passing sequence.
string reqId = service.SubmitRequest(sequence, blastSearchPams);
// validate request identifier.
Assert.IsNotNull(reqId);
// query the status
ServiceRequestInformation info = service.GetRequestStatus(reqId);
if (info.Status != ServiceRequestStatus.Waiting &&
info.Status != ServiceRequestStatus.Ready)
{
string err =
ApplicationLog.WriteLine("Unexpected status: '{0}'", info.Status);
Assert.Fail(err);
}
// get async results, poll until ready
int maxAttempts = 3;
int attempt = 1;
while (attempt <= maxAttempts &&
info.Status != ServiceRequestStatus.Error &&
info.Status != ServiceRequestStatus.Ready)
{
info = service.GetRequestStatus(reqId);
Thread.Sleep(info.Status == ServiceRequestStatus.Waiting ||
info.Status == ServiceRequestStatus.Queued
? 20000 * attempt : 0);
++attempt;
}
syncBlastResults =
service.FetchResultsSync(reqId, blastSearchPams) as List <BlastResult>;
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
return(new TestCaseOutput(syncBlastResults, false));
}
