public void InvalidateNcbiWebServiceRequestStatusWithoutConfigPams()
{
// Gets the search query parameter and their values.
string alphabet = utilityObj.xmlUtil.GetTextValue(
Constants.EbiBlastResultsNode, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(
Constants.EbiBlastResultsNode, Constants.QuerySequency);
Sequence seq = new Sequence(Utility.GetAlphabet(alphabet), querySequence);
// Set Service confiruration parameters true.
NCBIBlastHandler service = new NCBIBlastHandler();
// Dispose Ncbi Blast Handler.
service.Dispose();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
service.Configuration = configParams;
BlastParameters searchParams = new BlastParameters();
// Get Request identifier from web service.
try
{
service.SubmitRequest(seq, searchParams);
Assert.Fail();
}
catch (Exception)
{
ApplicationLog.WriteLine(
"NcbiWebService P2 : Successfully validated the exception");
}
}
/// <summary>
/// Submits a blast query to a blast search provider.
/// This sample uses NCBI as the provider.
/// </summary>
/// <param name="sequence">Sequence to submit for searching.</param>
/// <returns>Job ID of the query. You can get the results using GetBlastResults after the job is completed.</returns>
public static string SubmitBlastQuery(ISequence sequence)
{
// Create the service provider
NCBIBlastHandler serviceProvider = new NCBIBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
serviceProvider.Configuration = configParams;
// create the request and return the job ID.
return serviceProvider.SubmitRequest(sequence, GetBlastSearchParams());
}
/// <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)
{
FastAParser fastaParser = new FastAParser();
fastaParser.Open(InputFile);
ISequence searchSequence = fastaParser.Parse().FirstOrDefault();
NCBIBlastHandler service = new NCBIBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
service.Configuration = configParams;
BlastParameters searchParams = new BlastParameters();
// fill in the BLAST settings:
searchParams.Add("Program", "blastn");
searchParams.Add("Database", "nr");
// higher Expect will return more results
searchParams.Add("Expect", "1e-10");
searchParams.Add("CompositionBasedStatistics", "0");
// create the request
string jobID = service.SubmitRequest(searchSequence, searchParams);
// query the status
ServiceRequestInformation info = service.GetRequestStatus(jobID);
if (info.Status != ServiceRequestStatus.Waiting &&
info.Status != ServiceRequestStatus.Ready)
{
// TODO: Add error handling here
}
// get async results, poll until ready
int maxAttempts = 10;
int attempt = 1;
while (attempt <= maxAttempts &&
info.Status != ServiceRequestStatus.Error &&
info.Status != ServiceRequestStatus.Ready)
{
++attempt;
info = service.GetRequestStatus(jobID);
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting || info.Status == ServiceRequestStatus.Queued
? 20000 * attempt : 0);
}
// Get blast result.
BlastXmlParser blastParser = new BlastXmlParser();
IList <BlastResult> results = blastParser.Parse(new StringReader(service.GetResult(jobID, searchParams)));
// Convert blast result to BlastCollator.
List <BlastResultCollator> blastResultCollator = new List <BlastResultCollator>();
foreach (BlastResult result in results)
{
foreach (BlastSearchRecord record in result.Records)
{
if (null != record.Hits &&
0 < record.Hits.Count)
{
foreach (Hit hit in record.Hits)
{
if (null != hit.Hsps &&
0 < hit.Hsps.Count)
{
foreach (Hsp hsp in hit.Hsps)
{
BlastResultCollator blast = new BlastResultCollator();
blast.Alignment = hsp.AlignmentLength;
blast.Bit = hsp.BitScore;
blast.EValue = hsp.EValue;
blast.Identity = hsp.IdentitiesCount;
blast.Length = hit.Length;
blast.QEnd = hsp.QueryEnd;
blast.QStart = hsp.QueryStart;
blast.QueryId = record.IterationQueryId;
blast.SEnd = hsp.HitEnd;
blast.SStart = hsp.HitStart;
blast.SubjectId = hit.Id;
blast.Positives = hsp.PositivesCount;
blast.QueryString = hsp.QuerySequence;
blast.SubjectString = hsp.HitSequence;
blast.Accession = hit.Accession;
blast.Description = hit.Def;
blastResultCollator.Add(blast);
}
}
}
}
}
}
BlastXmlSerializer serializer = new BlastXmlSerializer();
Stream stream = serializer.SerializeBlastOutput(blastResultCollator);
// set result to the output property.
BlastResult = GetSerializedData(stream);
return(ActivityExecutionStatus.Closed);
}
/// <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 SubmitSearchRequest method test cases
/// with the different parameters specified.
/// <param name="nodeName">xml node name.</param>
/// <param name="expectParameter">Expected parameter</param>
/// <param name="compositionBasedStaticParameter">Composition based static parameter</param>
/// </summary>
void ValidateSubmitSearchMethod(string nodeName,
string expectParameter, string compositionBasedStaticParameter)
{
// Gets the search query parameter and their values.
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 alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
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 reqId = string.Empty;
// Create a sequence.
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
// Set Service confiruration parameters true.
IBlastServiceHandler blastService = null;
try
{
blastService = new NCBIBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
blastService.Configuration = configParameters;
// Create search parameters object.
BlastParameters queryParams = new BlastParameters();
// Add parameter values to search query parameters.
if ((0 == string.Compare(expectParameter, null, true,
CultureInfo.CurrentCulture))
&& (0 == string.Compare(compositionBasedStaticParameter, null, true,
CultureInfo.CurrentCulture)))
{
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
}
else
{
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
queryParams.Add(optionalExpectParameter, optionalExpectValue);
queryParams.Add(optionalCBSParameter, optionalCBSParameterValue);
}
// Submit search request with valid parameter.
reqId = blastService.SubmitRequest(seq, queryParams);
// Validate request identifier returned by web service.
Assert.IsNotNull(reqId);
// Logs to the VSTest GUI (ApplicationLog.Out) window
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast P1: Validation of SubmitSearchRequest() method was completed successfully."));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast P1: Request Id {0} is as expected.", reqId));
}
finally
{
if (blastService != null)
((IDisposable)blastService).Dispose();
}
}
public void ValidateNcbiSubmitSearchRequestForQueryList()
{
string nodeName = Constants.EmRelDatabaseParametersNode;
// Gets the search query parameter and their values.
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 alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
// Create a sequence.
IList<ISequence> seqList = new List<ISequence>();
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName), querySequence);
seqList.Add(seq);
// Set Service confiruration parameters true.
IBlastServiceHandler NcbiBlastService = null;
try
{
NcbiBlastService = new NCBIBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
NcbiBlastService.Configuration = configParameters;
// Create search parameters object.
BlastParameters NcbiParams = new BlastParameters();
// Add parameter values to search query parameters.
NcbiParams.Add(queryDatabaseParameter, queryDatabaseValue);
NcbiParams.Add(queryProgramParameter, queryProgramValue);
// Get Request identifier from web service for SeqList.
// Automated this case to hit the Code.
NcbiBlastService.SubmitRequest(seqList, NcbiParams);
}
catch (NotImplementedException)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Ncbi Blast P1 : Validated the exception successfully."));
}
finally
{
if (NcbiBlastService != null)
((IDisposable)NcbiBlastService).Dispose();
}
}
/// <summary>
/// A helper method for the BLAST task. Submits a job to BLAST.
/// </summary>
/// <param name="qp"></param>
/// <returns></returns>
private BlastJob submit(QueueSequence qp)
{
// Configure BLAST service
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = Up.BlastUseBrowserProxy;
BlastParameters searchParams = new BlastParameters();
string query = ">" + qp.Sequence.DisplayID + "\n" + qp.Sequence.ToString();
searchParams.Add("Program", Up.BlastProgram);
searchParams.Add("Database", Up.BlastDatabase);
searchParams.Add("GeneticCode", Up.BlastGeneticCode);
searchParams.Add("Expect", "10");
searchParams.Add("Query", query);
// Create BLAST service
NCBIBlastHandler blastService = new NCBIBlastHandler();
blastService.Configuration = configParams;
// Submit BLAST Job
string jobId;
try
{
jobId = blastService.SubmitRequest(qp.Sequence, searchParams);
}
catch(Exception eee)
{
if (eee.Message.Contains("WebException"))
{
ToggleProxy();
}
BlastJob blastJob2 = new BlastJob();
blastJob2.JobStatus = BlastJob.FAILED;
blastJob2.Query = qp.Sequence;
blastJob2.Position = qp.Position;
return blastJob2;
}
// Make sure job was submitted successfully
ServiceRequestInformation info = blastService.GetRequestStatus(jobId);
if (info.Status != ServiceRequestStatus.Waiting
&& info.Status != ServiceRequestStatus.Ready
&& info.Status != ServiceRequestStatus.Queued)
{
//Console.WriteLine("\tError Submitting Job: " + info.Status);
BlastJob blastJob2 = new BlastJob();
blastJob2.JobStatus = BlastJob.FAILED;
blastJob2.Query = qp.Sequence;
blastJob2.Position = qp.Position;
return blastJob2;
}
Thread.Sleep(BlastQueue.SubmitDelay);
//Console.WriteLine("\tSuccessfully submitted jobId: " + jobId);
// Return a BlastJob, set jobStatus to BUSY
BlastJob blastJob = new BlastJob()
{
JobId = jobId,
SearchParams = searchParams,
ConfigParams = configParams,
BlastService = blastService,
JobStatus = BlastJob.BUSY,
Query = qp.Sequence,
Position = qp.Position
};
return blastJob;
}