/// <summary>
/// Gets the blast results from a given job ID.
/// If the job is not complete, this method will throw an exception.
/// </summary>
/// <param name="jobID">Job ID for which the blast results should be fetched.</param>
/// <returns>List of BlastResult.</returns>
public static IList<BlastResult> GetBlastResults(string jobID)
{
// Create the service provider
NCBIBlastHandler serviceProvider = new NCBIBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
serviceProvider.Configuration = configParams;
// Check the job status
ServiceRequestInformation info = serviceProvider.GetRequestStatus(jobID);
if (info.Status != ServiceRequestStatus.Ready)
{
throw new InvalidOperationException("Blast search results are not yet ready!");
}
// Get the results back and parse it.
IBlastParser blastXmlParser = new BlastXmlParser();
return blastXmlParser.Parse(new System.IO.StringReader(serviceProvider.GetResult(jobID, GetBlastSearchParams())));
}
/// <summary>
/// Validate general fetching results by passing
/// different parameters.
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="NcbiCtorPam">Ncbi constructor different parameters</param>
void GeneralMethodToValidateResults(string nodeName,
NcbiWebServiceCtorParameters NcbiCtorPam)
{
// Gets the search query parameter and their values.
string queryParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequencyparameter);
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName, 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);
object responseResults = null;
NCBIBlastHandler service;
IBlastParser blastXmlParser = new BlastXmlParser();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
switch (NcbiCtorPam)
{
case NcbiWebServiceCtorParameters.ConfigPams:
service = new NCBIBlastHandler(configParams);
break;
case NcbiWebServiceCtorParameters.ParserAndConfigPams:
service = new NCBIBlastHandler(blastXmlParser, configParams);
break;
default:
service = new NCBIBlastHandler();
break;
}
ISequence sequence = new Sequence(Utility.GetAlphabet("DNA"), "ATCGCC");
BlastParameters searchParams = new BlastParameters();
searchParams.Add(queryParameter, querySequence);
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
// Careate a request without passing sequence.
string reqId = service.SubmitRequest(sequence, searchParams);
// validate request identifier.
Assert.IsNotNull(reqId);
// submit request identifier and get 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 = 10;
int attempt = 1;
while (attempt <= maxAttempts
&& info.Status != ServiceRequestStatus.Error
&& info.Status != ServiceRequestStatus.Ready)
{
Thread.Sleep(info.Status == ServiceRequestStatus.Waiting ? 40000 : 0);
info = service.GetRequestStatus(reqId);
++attempt;
}
responseResults = blastXmlParser.Parse(
new StringReader(service.GetResult(reqId, searchParams)));
// Validate blast results.
Assert.IsNotNull(responseResults);
List<BlastResult> blastResults = responseResults as List<BlastResult>;
Assert.IsNotNull(blastResults);
BlastSearchRecord record = blastResults[0].Records[0];
Hit hit = null;
if (record.Hits.Count > 0)
{
hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null), expectedHitId);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast BVT: Hits count '{0}'.", blastResults.Count));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast BVT: Accession '{0}'.", hit.Accession));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast BVT: Hit Id '{0}'.", hit.Id));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast BVT: Hits Count '{0}'.", hit.Hsps.Count));
}
}
/// <summary>
/// Validate general fetching results.by passing
/// differnt parameters.
/// <param name="nodeName">xml node name.</param>
/// <param name="expectParameter">expectparameter name</param>
/// <param name="compositionBasedStaticParameter">compositionBasedStaticParameter name</param>
/// <param name="isFetchSynchronous">Is Fetch Synchronous?</param>
/// </summary>
void ValidateGeneralFetchResults(
string nodeName, string expectParameter,
string compositionBasedStaticParameter,
bool isFetchSynchronous)
{
// Gets the search query parameter and their values.
string queryParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequencyparameter);
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string optionalExpectParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastExpectParameter);
string optionalExpectValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastExpectparameterValue);
string optionalCBSParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastCompositionBasedStaticsParameter);
string optionalCBSParameterValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastCompositionBasedStaticsValue);
string expectedHitId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitID);
string expectedAccession = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitAccession);
object responseResults = null;
NCBIBlastHandler service = new NCBIBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
service.Configuration = configParams;
ISequence sequence = new Sequence(Alphabets.DNA, "ATCGGGGCCC");
BlastParameters searchParams = new BlastParameters();
// Set mandatory parameters only if optional parameters are null
if ((0 == string.Compare(expectParameter, null, true,
CultureInfo.CurrentCulture))
&& (0 == string.Compare(compositionBasedStaticParameter, null, true,
CultureInfo.CurrentCulture)))
{
searchParams.Add(queryParameter, querySequence);
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
}
else
{
searchParams.Add(queryParameter, querySequence);
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(optionalExpectParameter, optionalExpectValue);
searchParams.Add(optionalCBSParameter, optionalCBSParameterValue);
}
// Careate a request without passing sequence.
string reqId = service.SubmitRequest(sequence, searchParams);
// validate request identifier.
Assert.IsNotNull(reqId);
// submit request identifier and get 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 = 10;
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 ? 30000 : 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> blastResults = responseResults as List<BlastResult>;
Assert.IsNotNull(blastResults);
BlastSearchRecord record = blastResults[0].Records[0];
if (record.Hits.Count > 0)
{
Hit hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null), expectedHitId);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast BVT: Hits count '{0}'.", blastResults.Count));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast BVT: Accession '{0}'.", hit.Accession));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast BVT: Hit Id '{0}'.", hit.Id));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"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 != blastResults[0].Records[0].Hits
&& 0 < blastResults[0].Records[0].Hits.Count
&& null != blastResults[0].Records[0].Hits[0].Hsps
&& 0 < blastResults[0].Records[0].Hits[0].Hsps.Count)
{
Assert.AreEqual(blastResults[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.");
}
}
}
/// <summary>
/// Validate general Parse() method by passing
/// differnt XML node name
/// <param name="nodeName">xml node name.</param>
/// <param name="textReader">true to validate Parse(text-reader)
/// method else parse(file-name)</param>
/// </summary>
void ValidateParseXmlGeneralTestCases(string nodeName, bool textReader)
{
// Gets the Blast Xml file
string blastFilePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastResultfilePath);
string expectedBitScore = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BitScore);
string expectedDatabselength = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseLength);
string expectedParameterMatrix = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ParameterMatrix);
string expectedGapCost = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ParameterGap);
string expectedHitSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitSequence);
string expectedAccession = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitAccession);
string expectedAlignmentLength = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlignmentLength);
string expectedResultCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ResultsCount);
string expectedHitsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitsCount);
// Validate if Xml file exists in the mentioned path.
Assert.IsTrue(File.Exists(blastFilePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast P1: File Exists in the Path '{0}'.", blastFilePath));
// Parse a Blast xml file.
BlastXmlParser parser = new BlastXmlParser();
IList<BlastResult> blastResults = null;
if (textReader)
{
using (StreamReader reader = File.OpenText(blastFilePath))
{
blastResults = parser.Parse(reader);
}
}
else
{
blastResults = parser.Parse(blastFilePath);
}
blastResults = parser.Parse(blastFilePath);
// Validate Meta data
BlastXmlMetadata meta = blastResults[0].Metadata;
Assert.AreEqual(meta.ParameterGapOpen.ToString((IFormatProvider)null),
expectedGapCost);
Assert.AreEqual(meta.ParameterMatrix.ToString((IFormatProvider)null),
expectedParameterMatrix);
// Validate blast records.
BlastSearchRecord record = blastResults[4].Records[0];
Assert.AreEqual(expectedResultCount,
blastResults.Count.ToString((IFormatProvider)null));
Assert.AreEqual(expectedDatabselength,
record.Statistics.DatabaseLength.ToString((IFormatProvider)null));
Assert.AreEqual(expectedHitsCount,
record.Hits.Count.ToString((IFormatProvider)null));
Assert.AreEqual(expectedAccession,
record.Hits[0].Accession.ToString((IFormatProvider)null));
Assert.AreEqual(expectedHitsCount,
record.Hits[0].Hsps.Count.ToString((IFormatProvider)null));
// Validate bit score.
Hsp highScoreSgment = record.Hits[0].Hsps[0];
Assert.AreEqual(expectedAlignmentLength,
highScoreSgment.AlignmentLength.ToString((IFormatProvider)null));
Assert.AreEqual(expectedBitScore, highScoreSgment.BitScore.ToString((
IFormatProvider)null));
Assert.AreEqual(expectedHitSequence, highScoreSgment.HitSequence.ToString(
(IFormatProvider)null));
// Log results to VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast P1: Bit Sequence '{0}'.",
highScoreSgment.HitSequence.ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast P1: Bit Score '{0}'.",
highScoreSgment.BitScore));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast P1: Bit Alignment '{0}'.",
highScoreSgment.AlignmentLength));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast P1: Hits Count '{0}'.",
record.Hits[0].Hsps.Count));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast P1: Results Count '{0}'.",
blastResults.Count));
}
/// <summary>
/// Validate general fetching results.by passing
/// differnt parameters for BioHPC Blast web service.
/// <param name="nodeName">xml node name.</param>
/// <param name="isFetchSynchronous">Is Fetch Synchronous?</param>
/// </summary>
void ValidateBioHPCBlastResultsFetch(
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 email = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName,
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);
int maxAttempts = int.Parse(utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.MaxAttemptsNode), (IFormatProvider)null);
int waitingTime = int.Parse(utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.WaitTimeNode), (IFormatProvider)null);
string expect = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Expectparameter);
string emailNotify = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyParameterNode);
string jobName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.JobNameParameterNode);
string expectValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectNode);
string emailNotifyValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyNode);
string jobNameValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.JobNameNode);
object responseResults = null;
Sequence seq = new Sequence(
Utility.GetAlphabet(alphabetName),
querySequence);
// create BioHPC Blast Web Service object.
IBlastServiceHandler service = new BioHPCBlastHandler();
ConfigParameters configPams = new ConfigParameters();
configPams.EmailAddress = email;
configPams.Password = String.Empty;
configPams.UseBrowserProxy = true;
service.Configuration = configPams;
BlastParameters searchParams = new BlastParameters();
// Set Request parameters.
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(expect, expectValue);
searchParams.Add(emailNotify, emailNotifyValue);
searchParams.Add(jobName, jobNameValue);
// Create a request without passing sequence.
string reqId = service.SubmitRequest(seq, searchParams);
// validate request identifier.
Assert.IsNotNull(reqId);
ServiceRequestInformation info = service.GetRequestStatus(reqId);
if (info.Status != ServiceRequestStatus.Waiting
&& info.Status != ServiceRequestStatus.Ready
&& info.Status != ServiceRequestStatus.Queued)
{
string err =
ApplicationLog.WriteLine("Unexpected status: '{0}'",
info.Status);
Assert.Fail(err);
}
// get async results, poll until ready
int attempt = 1;
while (attempt <= maxAttempts
&& info.Status != ServiceRequestStatus.Error
&& info.Status != ServiceRequestStatus.Ready)
{
++attempt;
if (isFetchSynchronous)
{
info = service.GetRequestStatus(reqId);
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting
|| info.Status == ServiceRequestStatus.Queued
? waitingTime * attempt : 0);
}
else
{
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting
|| info.Status == ServiceRequestStatus.Queued ?
waitingTime * attempt : 0);
info = service.GetRequestStatus(reqId);
}
}
IBlastParser blastXmlParser = new BlastXmlParser();
responseResults = blastXmlParser.Parse(
new StringReader(service.GetResult(reqId, searchParams)));
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,
"BioHPC Blast BVT : Hits count '{0}'.", eBlastResults.Count));
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Accession '{0}'.", hit.Accession));
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Hit Id '{0}'.", hit.Id));
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC 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.");
}
}
}
