/// <summary>
/// Determines whether the specified ServiceRequestInformation is equal to the current instance.
/// </summary>
/// <param name="obj">The ServiceRequestInformation to compare with the current instance.</param>
/// <returns>Returns true is given ServiceRequestInformation is equal to current instance</returns>
public bool Equals(ServiceRequestInformation obj)
{
if (Status != obj.Status || StatusInformation != obj.StatusInformation)
{
return(false);
}
return(true);
}
/// <summary>
/// Fetch results asynchronous
/// </summary>
/// <param name="blastParameters">Blast Input config parameters</param>
/// <returns></returns>
private TestCaseOutput FetchResultsAsync(Dictionary <string, object> blastParameters)
{
// Get the input query string
string sequenceString = blastParameters[Constants.QuerySeqString] as string;
Sequence sequence = new Sequence(Alphabets.DNA, sequenceString);
// Set NCBIHandler configuration services
IBlastServiceHandler service = null;
object resultsObject = null;
try
{
service = new AzureBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
configParams.DefaultTimeout = 5;
configParams.Connection = new Uri(Constants.AzureUri);
service.Configuration = configParams;
BlastParameters blastSearchPams = blastParameters[Constants.BlastParmsConst]
as BlastParameters;
// Get Request identifier from web service.
string reqId = service.SubmitRequest(sequence, blastSearchPams);
// Get request information for first time.
ServiceRequestInformation info = service.GetRequestStatus(reqId);
// Ping service until request staus is ready.
int maxAttempts = 10;
int attempt = 1;
while (attempt <= maxAttempts && info.Status != ServiceRequestStatus.Ready &&
info.Status != ServiceRequestStatus.Error)
{
System.Threading.Thread.Sleep(2000);
++attempt;
info = service.GetRequestStatus(reqId);
}
IBlastParser blastXmlParser = new BlastXmlParser();
using (StringReader reader = new StringReader(service.GetResult(reqId, blastSearchPams)))
{
resultsObject = blastXmlParser.Parse(reader);
}
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
return(new TestCaseOutput(resultsObject, false));
}
/// <summary>
/// Validate general http request status by
/// differnt parameters for Azure web service..
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
void ValidateGeneralGetRequestStatusMethod(string nodeName)
{
// 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);
// Set Blast Parameters
BlastParameters queryParams = new BlastParameters();
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
Dictionary <string, object> testCaseParms = new Dictionary <string, object>();
testCaseParms.Add(Constants.BlastParmsConst, queryParams);
testCaseParms.Add(Constants.QuerySeqString, querySequence);
TestCaseParameters parameters = new TestCaseParameters(
Constants.AzureWebServiceRequestStatusForDnaTest, null,
GetRequestStatus, testCaseParms);
object resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
ServiceRequestInformation reqInfo = resultsObject as ServiceRequestInformation;
// Validate job status.
if (reqInfo.Status != ServiceRequestStatus.Waiting &&
reqInfo.Status != ServiceRequestStatus.Ready &&
reqInfo.Status != ServiceRequestStatus.Queued)
{
string error = ApplicationLog.WriteLine(string.Format(
null, "Unexpected error", reqInfo.Status));
Assert.Fail(error);
Console.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Unexpected error", reqInfo.Status));
}
else
{
Console.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Client Request status has been validated successfully."));
Console.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Request status {0} ", reqInfo.Status));
}
}
/// <summary>
/// Get the status of job using job id and control id after submitting the job
/// </summary>
/// <param name="parameters">job id, control id</param>
/// <returns>result with status of job</returns>
public MBF.Web.ServiceRequestInformation GetRequestStatus(ServiceParameters parameters)
{
string jobStatus = _baseClient.GetJobInfo(parameters.JobId, parameters.Parameters[CONTROLID].ToString());
string[] statusArray = jobStatus.Split('|');
ServiceRequestInformation info = new ServiceRequestInformation();
switch (statusArray[6])
{
case "FINISHED":
info.Status = ServiceRequestStatus.Ready;
break;
case "ERROR":
info.Status = ServiceRequestStatus.Error;
break;
default:
break;
}
return(info);
}
/// <summary>
/// Process the request. This method takes care of executing the rest of the steps
/// to complete the blast search request in a background thread. Which involves
/// 1. Submit the job to server
/// 2. Ping the service with the request identifier to get the status of request.
/// 3. Repeat step 1, at "RetryInterval" for "RetryCount" till a "success"/"failure"
/// status.
/// 4. If the status is a "failure" raise an completed event to notify the user
/// with appropriate details.
/// 5. If the status "success". Get the output of search from server in xml format.
/// 6. Parse the xml and the framework object model.
/// 7. Raise the completed event and notify user with the output.
/// </summary>
/// <param name="sender">Client request NCBI Blast search</param>
/// <param name="argument">Thread event argument</param>
private void ProcessRequestThread(object sender, DoWorkEventArgs argument)
{
BlastThreadParameter threadParameter = (BlastThreadParameter)argument.Argument;
string requestIdentifier = threadParameter.RequestIdentifier;
try
{
ServiceRequestInformation requestInfo = new ServiceRequestInformation();
requestInfo.Status = ServiceRequestStatus.Queued;
int retryCount = 0;
do
{
requestInfo = GetRequestStatus(requestIdentifier);
if (requestInfo.Status == ServiceRequestStatus.Ready ||
requestInfo.Status == ServiceRequestStatus.Error ||
workerThread.CancellationPending)
{
break;
}
retryCount++;
Thread.Sleep(RetryInterval * retryCount);
}while (retryCount < RetryCount);
if (workerThread.CancellationPending)
{
argument.Cancel = true;
}
else
{
BlastRequestCompletedEventArgs eventArgument = null;
string message;
if (requestInfo.Status == ServiceRequestStatus.Ready)
{
string output = GetResult(
requestIdentifier,
threadParameter.Parameters);
IList <BlastResult> result = Parser.Parse(new StringReader(output));
eventArgument = new BlastRequestCompletedEventArgs(
requestIdentifier,
true,
result,
null,
string.Empty,
workerThread.CancellationPending);
argument.Result = eventArgument;
}
else if (requestInfo.Status == ServiceRequestStatus.Error)
{
message = String.Format(CultureInfo.InvariantCulture,
Resources.BLASTREQUESTFAILED,
requestIdentifier,
requestInfo.Status,
requestInfo.StatusInformation);
eventArgument = new BlastRequestCompletedEventArgs(
requestIdentifier,
false,
null,
new Exception(message),
message,
workerThread.CancellationPending);
argument.Result = eventArgument;
}
else
{
message = String.Format(CultureInfo.InvariantCulture,
Resources.BLASTRETRIESEXCEEDED,
requestIdentifier,
requestInfo.Status,
requestInfo.StatusInformation);
eventArgument = new BlastRequestCompletedEventArgs(
requestIdentifier,
false,
null,
new TimeoutException(message),
message,
workerThread.CancellationPending);
argument.Result = eventArgument;
}
}
}
catch (Exception ex)
{
BlastRequestCompletedEventArgs eventArgument = new BlastRequestCompletedEventArgs(
string.Empty,
false,
null,
ex,
ex.Message,
workerThread.CancellationPending);
argument.Result = eventArgument;
}
}
/// <summary>
/// Return the status of a submitted job.
/// </summary>
/// <param name="requestIdentifier">Identifier for the request of interest.</param>
/// <returns>The status of the request.</returns>
public ServiceRequestInformation GetRequestStatus(string requestIdentifier)
{
string information = string.Empty;
string errorInformation = string.Empty;
WebAccessor accessor = new WebAccessor();
WebAccessorResponse webAccessorResponse = null;
ServiceRequestInformation status = new ServiceRequestInformation();
Dictionary <string, string> settings = new Dictionary <string, string>();
settings.Add(PARAMETERCMD, "GET");
settings.Add(PARAMETERRID, System.Web.HttpUtility.UrlEncode(requestIdentifier));
if (Configuration.UseBrowserProxy)
{
accessor.GetBrowserProxy();
}
webAccessorResponse = accessor.SubmitHttpRequest(
ServiceUri,
true,
settings);
if (!webAccessorResponse.IsSuccessful)
{
// failure
accessor.Close();
status.Status = ServiceRequestStatus.Error;
status.StatusInformation = webAccessorResponse.StatusDescription;
return(status);
}
webAccessorResponse.StatusDescription = string.Empty;
information = ExtractInfoSection(webAccessorResponse.ResponseString);
if (String.IsNullOrEmpty(information))
{
status.Status = ServiceRequestStatus.Error;
// see if we got an error message
errorInformation = ExtractBlastErrorSection(webAccessorResponse.ResponseString);
if (string.IsNullOrEmpty(errorInformation))
{
status.StatusInformation = "An unknown server error has occurred.";
}
else
{
status.StatusInformation = errorInformation;
}
return(status);
}
else
{
int statusStart = information.IndexOf("Status=", StringComparison.OrdinalIgnoreCase);
if (statusStart >= 0)
{
statusStart += "Status=".Length;
int statusEnd = information.IndexOf('\n', statusStart);
if (statusEnd >= 0)
{
webAccessorResponse.StatusDescription = information.Substring(statusStart, statusEnd - statusStart);
}
}
}
if (webAccessorResponse.StatusDescription == STATUSWAITING)
{
status.Status = ServiceRequestStatus.Waiting;
return(status);
}
else if (webAccessorResponse.StatusDescription == STATUSREADY)
{
status.Status = ServiceRequestStatus.Ready;
return(status);
}
status.Status = ServiceRequestStatus.Error;
status.StatusInformation = webAccessorResponse.StatusDescription;
return(status);
}
/// <summary>
/// Validate general http request status by
/// differnt parameters for Ebi web service..
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
void ValidateEbiGeneralGetRequestStatusMethod(string nodeName,
string alphabet)
{
// 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 emailParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Emailparameter);
string email = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
string reqId = string.Empty;
// Create a sequence.
Sequence seq = new Sequence(Utility.GetAlphabet(alphabet),
querySequence);
// Set Service confiruration parameters true.
IBlastServiceHandler ebiBlastService = new EbiWuBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
ebiBlastService.Configuration = configParameters;
// Create search parameters object.
BlastParameters queryParams = new BlastParameters();
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
queryParams.Add(emailParameter, email);
queryParams.Add("SequenceType", alphabet.ToLower(CultureInfo.CurrentCulture).Replace("ambiguous", ""));
// Create a request
reqId = ebiBlastService.SubmitRequest(seq, queryParams);
// validate request identifier.
Assert.IsNotNull(reqId);
// submit request identifier and get the status
ServiceRequestInformation reqInfo = ebiBlastService.GetRequestStatus(reqId);
// Validate job status.
if (reqInfo.Status != ServiceRequestStatus.Waiting &&
reqInfo.Status != ServiceRequestStatus.Ready)
{
string error = ApplicationLog.WriteLine(
string.Concat("Unexpected error", reqInfo.Status));
Assert.Fail(error);
Console.WriteLine(string.Concat(
"Unexpected error ", reqInfo.Status));
}
else
{
Console.WriteLine(string.Concat(
"Request status ", reqInfo.Status));
}
}
/// <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.");
}
}
}
public void ValidateProcessRequestThread()
{
// Gets the search query parameter and their values.
string alphabetName = utilityObj.xmlUtil.GetTextValue(
Constants.EbiSynchronousResults, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(
Constants.EbiSynchronousResults, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
Constants.EbiSynchronousResults, Constants.DatabaseValue);
string emailParameter = utilityObj.xmlUtil.GetTextValue(
Constants.EbiSynchronousResults, Constants.Emailparameter);
string email = utilityObj.xmlUtil.GetTextValue(
Constants.EbiSynchronousResults, Constants.EmailAdress);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
Constants.EbiSynchronousResults, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
Constants.EbiSynchronousResults, Constants.ProgramParameter);
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
// create Ebi Blast service object.
EbiWuBlastHandler service = new EbiWuBlastHandler();
try
{
service.RequestCompleted += new EventHandler <BlastRequestCompletedEventArgs>(ebiBlastService_RequestCompleted);
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);
}
}
catch (Exception ex) { Assert.Fail(ex.Message); }
finally
{
if (service != null)
{
service.Dispose();
}
}
}
/// <summary>
/// Validate general http request status by
/// differnt parameters for Ebi web service..
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
static void ValidateEbiGeneralGetRequestStatusMethod(string nodeName)
{
if (_IsWebServiceAvailable)
{
// Gets the search query parameter and their values.
string alphabetName = Utility._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = Utility._xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = Utility._xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string queryProgramValue = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = Utility._xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string emailParameter = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Emailparameter);
string email = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
string reqId = string.Empty;
// Create a sequence.
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
// Set Service confiruration parameters true.
IBlastServiceHandler ebiBlastService = new EbiWuBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
ebiBlastService.Configuration = configParameters;
// Create search parameters object.
BlastParameters queryParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
queryParams.Add(emailParameter, email);
// Create a request
reqId = ebiBlastService.SubmitRequest(seq, queryParams);
// validate request identifier.
Assert.IsNotNull(reqId);
// submit request identifier and get the status
ServiceRequestInformation reqInfo = ebiBlastService.GetRequestStatus(reqId);
// Validate job status.
if (reqInfo.Status != ServiceRequestStatus.Waiting &&
reqInfo.Status != ServiceRequestStatus.Ready)
{
string error = ApplicationLog.WriteLine(string.Format(
null, "Unexpected error", reqInfo.Status));
Assert.Fail(error);
Console.WriteLine(string.Format(null,
"Unexpected error", reqInfo.Status));
}
else
{
Console.WriteLine(string.Format(null,
"Request status {0} ", reqInfo.Status));
}
}
else
{
Assert.Ignore("The test case ignored due to connection failure");
}
}
/// <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>
static void ValidateBioHPCBlastResultsFetch(
string nodeName,
bool isFetchSynchronous)
{
if (_IsWebServiceAvailable)
{
// Gets the search query parameter and their values.
string alphabetName = Utility._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = Utility._xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = Utility._xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string email = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
string queryProgramValue = Utility._xmlUtil.GetTextValue(
nodeName,
Constants.ProgramValue);
string queryDatabaseParameter = Utility._xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string expectedHitId = Utility._xmlUtil.GetTextValue(
nodeName, Constants.HitID);
string expectedAccession = Utility._xmlUtil.GetTextValue(
nodeName, Constants.HitAccession);
string expectedResultCount = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ResultsCount);
string expectedHitsCount = Utility._xmlUtil.GetTextValue(
nodeName, Constants.HitsCount);
string expectedEntropyStatistics =
Utility._xmlUtil.GetTextValue(
nodeName, Constants.EntropyStatistics);
string expectedKappaStatistics = Utility._xmlUtil.GetTextValue(
nodeName, Constants.KappaStatistics);
string expectedLambdaStatistics = Utility._xmlUtil.GetTextValue(
nodeName, Constants.LambdaStatistics);
string expectedLength = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Length);
int maxAttempts = int.Parse(Utility._xmlUtil.GetTextValue(
nodeName, Constants.MaxAttemptsNode));
int waitingTime = int.Parse(Utility._xmlUtil.GetTextValue(
nodeName, Constants.WaitingTimeNode));
string expect = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Expectparameter);
string emailNotify = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyParameterNode);
string jobName = Utility._xmlUtil.GetTextValue(
nodeName, Constants.JobNameParameterNode);
string expectValue = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ExpectNode);
string emailNotifyValue = Utility._xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyNode);
string jobNameValue = Utility._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)));
// 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(), expectedLength);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null),
expectedHitId);
Assert.AreEqual(hit.Hsps.Count.ToString((IFormatProvider)null),
expectedResultCount);
Console.WriteLine(string.Format(null,
"BioHPC Blast BVT : Hits count '{0}'.", eBlastResults.Count));
Console.WriteLine(string.Format(null,
"BioHPC Blast BVT : Accession '{0}'.", hit.Accession));
Console.WriteLine(string.Format(null,
"BioHPC Blast BVT : Hit Id '{0}'.", hit.Id));
Console.WriteLine(string.Format(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.");
}
}
}
else
{
Assert.Ignore(
"The test case ignored due to connection failure");
}
}
/// <summary>
/// Fetch Asynchronous results
/// </summary>
/// <param name="blastParameters">Blast config parameters</param>
/// <returns>BioHPC Web service results</returns>
private TestCaseOutput FetchResultsASyncTest(Dictionary <string, object> blastParameters)
{
// Get the input query string
string sequenceString = blastParameters[Constants.QuerySeqString] as string;
string alphabetName = blastParameters[Constants.AlphabetString] as string;
string email = blastParameters[Constants.EmailString] as string;
Sequence sequence = new Sequence(Utility.GetAlphabet(alphabetName),
sequenceString);
string maxAttempts = blastParameters[Constants.MaxAttemptString] as string;
string waitTime = blastParameters[Constants.WaitTimeString] as string;
//Set BioHPC web service config parameters
IBlastServiceHandler service = null;
object responseResults = null;
try
{
service = new BioHPCBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.EmailAddress = email;
configParameters.Password = String.Empty;
configParameters.UseBrowserProxy = true;
service.Configuration = configParameters;
BlastParameters blastSearchPams = blastParameters[Constants.BlastParmsConst]
as BlastParameters;
// Submit request and get request identifier
string reqId = service.SubmitRequest(sequence, blastSearchPams);
// 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 <= Int32.Parse(maxAttempts, (IFormatProvider)null) &&
info.Status != ServiceRequestStatus.Error &&
info.Status != ServiceRequestStatus.Ready)
{
++attempt;
info = service.GetRequestStatus(reqId);
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting ||
info.Status == ServiceRequestStatus.Queued
? Int32.Parse(waitTime, (IFormatProvider)null) * attempt : 0);
}
IBlastParser blastXmlParser = new BlastXmlParser();
using (StringReader reader = new StringReader(service.GetResult(reqId, blastSearchPams)))
{
responseResults = blastXmlParser.Parse(reader);
}
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
return(new TestCaseOutput(responseResults, false));
}
/// <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);
}
public void BeginAsyncRequestTest()
{
status = new ServiceRequestInformation();
BlastParameters searchParams = new BlastParameters();
// fill in the BLAST settings:
searchParams.Add("Command", "Put");
searchParams.Add("Program", "blastn");
searchParams.Add("Expect", "1e-10");
searchParams.Add("CompositionBasedStatistics", "0");
string badDbName = "ThisDatabaseDoesNotExist";
searchParams.Add("Database", badDbName);
// test parameters
string sequence = @"GACGCCGCCGCCACCACCGCCACCGCCGCAGCAGAAGCAGCGCACCGCAGGAGGGAAG" +
"ATGCCGGCGGGGCACGGGCTGCGGGCGCGGACGGCGACCTCTTCGCGCGGCCGTTCCGCAAGAAGGGTTA" +
"CATCCCGCTCACCACCTACCTGAGGACGTACAAGATCGGCGATTACGTNGACGTCAAGGTGAACGGTG";
searchParams.Add("Query", sequence);
AutoResetEvent requestSubmitWait = new AutoResetEvent(false);
AsyncWebMethodRequest input = new AsyncWebMethodRequest(
new Uri("http://www.ncbi.nlm.nih.gov/blast/Blast.cgi"),
CredentialCache.DefaultCredentials,
searchParams.Settings,
BuildQueryString(searchParams.Settings),
SubmitRequestCompleted,
requestSubmitWait);
WebAccessor target = new WebAccessor();
target.GetBrowserProxy();
target.BeginAsyncRequest(input);
WaitHandle.WaitAny(new WaitHandle[] { requestSubmitWait });
Assert.IsFalse(string.IsNullOrEmpty(requestIdentifier));
// query the status
Dictionary <string, string> settings = new Dictionary <string, string>();
settings.Add("CMD", "GET");
settings.Add("RID", HttpUtility.UrlEncode(requestIdentifier));
AutoResetEvent requestStatusWait = new AutoResetEvent(false);
input = new AsyncWebMethodRequest(
new Uri("http://www.ncbi.nlm.nih.gov/blast/Blast.cgi"),
CredentialCache.DefaultCredentials,
settings,
BuildQueryString(settings),
RequestStatusCompleted,
requestStatusWait);
target.BeginAsyncRequest(input);
WaitHandle.WaitAny(new WaitHandle[] { requestStatusWait });
bool ok = false;
if (status.Status != ServiceRequestStatus.Waiting && status.Status != ServiceRequestStatus.Ready)
{
if (status.StatusInformation.Contains(badDbName) &&
status.StatusInformation.Contains("No alias or index file found for nucleotide database"))
{
ok = true;
}
}
if (!ok)
{
Assert.Fail("Failed to find server error message for bad request. Info: " + status.StatusInformation);
}
}
/// <summary>
/// Validate general http request status by
/// differnt parameters for BioHPC Blast Web Service.
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
void ValidateBioHPCGeneralGetRequestStatusMethod(string nodeName,
string moleculeType)
{
// 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 queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string email = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
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);
// Create a sequence.
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
// Set Service confiruration parameters true.
IBlastServiceHandler service = new BioHPCBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.EmailAddress = email;
configParameters.Password = String.Empty;
configParameters.UseBrowserProxy = true;
service.Configuration = configParameters;
// Create search parameters object.
BlastParameters queryParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
queryParams.Add(expect, expectValue);
queryParams.Add(emailNotify, emailNotifyValue);
queryParams.Add(jobName, jobNameValue);
// Create a request
// Waiting for the any previous request to get completed.
Thread.Sleep(150000);
string reqId = service.SubmitRequest(seq, queryParams);
// validate request identifier.
Assert.IsNotNull(reqId);
// submit request identifier and get the status
ServiceRequestInformation reqInfo =
service.GetRequestStatus(reqId);
// Validate job status.
if (reqInfo.Status != ServiceRequestStatus.Waiting &&
reqInfo.Status != ServiceRequestStatus.Ready &&
reqInfo.Status != ServiceRequestStatus.Queued)
{
string error = ApplicationLog.WriteLine(string.Concat(
"Unexpected error ", reqInfo.Status));
Assert.Fail(error);
Console.WriteLine(string.Concat(
"Unexpected error ", reqInfo.Status));
}
else
{
Console.WriteLine(string.Concat(
"Request status ", reqInfo.Status));
}
}
/// <summary>
/// Validate general http request status by
/// differnt parameters for Azure web service..
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
void ValidateGeneralGetRequestStatusMethod(string nodeName)
{
// Gets the search query parameter and their values.
string alphabet = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
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 reqId = string.Empty;
Sequence seq = new Sequence(Utility.GetAlphabet(alphabet), querySequence);
// Set Service confiruration parameters true.
IBlastServiceHandler service = new AzureBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
configParams.DefaultTimeout = 5;
configParams.Connection = new Uri(Constants.AzureUri);
service.Configuration = configParams;
// Create search parameters object.
BlastParameters searchParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
// Get Request identifier from web service.
reqId = service.SubmitRequest(seq, searchParams);
// Get request information for first time.
ServiceRequestInformation reqInfo = service.GetRequestStatus(reqId);
// Validate job status.
if (reqInfo.Status != ServiceRequestStatus.Waiting &&
reqInfo.Status != ServiceRequestStatus.Ready &&
reqInfo.Status != ServiceRequestStatus.Queued)
{
string error = ApplicationLog.WriteLine(string.Concat(
"Unexpected error", reqInfo.Status));
Assert.Fail(error);
Console.WriteLine(string.Concat(
"Azure Blast BVT: Unexpected error ", reqInfo.Status));
}
else
{
Console.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Client Request status has been validated successfully."));
Console.WriteLine(string.Concat(
"Azure Blast BVT: Request status ", reqInfo.Status));
}
}
/// <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));
}
/// <summary>
/// Validate general http request status by
/// differnt parameters for Ebi web service..
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
void ValidateEbiGeneralGetRequestStatusMethod(string nodeName,
string alphabet)
{
// 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 queryProgramValue = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string emailParameter = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.Emailparameter);
string email = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
// Set Blast Parameters
BlastParameters queryParams = new BlastParameters();
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
queryParams.Add(emailParameter, email);
Dictionary <string, object> testCaseParms = new Dictionary <string, object>();
testCaseParms.Add(Constants.BlastParmsConst, queryParams);
testCaseParms.Add(Constants.QuerySeqString, querySequence);
testCaseParms.Add(Constants.AlphabetString, alphabetName);
TestCaseParameters parameters = null;
object resultsObject = null;
if (alphabet == "Protein")
{
parameters = parameters = new TestCaseParameters(Constants.EbiGetRequestStatusInfoForProteinSeqTest,
null, GetRequestStatusTest, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
}
else
{
parameters = parameters = new TestCaseParameters(
Constants.EbiGetRequestStatusInfoForDnaSeqNode, null,
GetRequestStatusTest, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
}
// submit request identifier and get the status
ServiceRequestInformation reqInfo = resultsObject as ServiceRequestInformation;
// Validate job status.
if (reqInfo.Status != ServiceRequestStatus.Waiting &&
reqInfo.Status != ServiceRequestStatus.Ready)
{
string error = ApplicationLog.WriteLine(string.Format(
null, "Unexpected error", reqInfo.Status));
Assert.Fail(error);
Console.WriteLine(string.Format((IFormatProvider)null,
"Unexpected error", reqInfo.Status));
}
else
{
Console.WriteLine(string.Format((IFormatProvider)null,
"Request status {0} ", reqInfo.Status));
}
}
/// <summary>
/// Validate general http request status by
/// differnt parameters for BioHPC Blast Web Service.
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
void ValidateBioHPCGeneralGetRequestStatusMethod(string nodeName,
string moleculeType)
{
// 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 queryProgramValue = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string email = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
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);
// Set Blast Parameters
BlastParameters queryParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
queryParams.Add(expect, expectValue);
queryParams.Add(emailNotify, emailNotifyValue);
queryParams.Add(jobName, jobNameValue);
Dictionary <string, object> testCaseParms = new Dictionary <string, object>();
testCaseParms.Add(Constants.BlastParmsConst, queryParams);
testCaseParms.Add(Constants.QuerySeqString, querySequence);
testCaseParms.Add(Constants.AlphabetString, alphabetName);
testCaseParms.Add(Constants.EmailString, email);
TestCaseParameters parameters = null;
object resultsObject = null;
if ("Dna" == moleculeType)
{
parameters = new TestCaseParameters(
Constants.BioHPCGetRequestStatusInfoForDnaSeqTest,
null, GetRequestStatus, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
}
else
{
parameters = new TestCaseParameters(
Constants.BioHPCGetRequestStatusInfoForProteinSeqTest,
null, GetRequestStatus, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
}
// Get service request status information.
ServiceRequestInformation reqInfo = resultsObject as ServiceRequestInformation;
// Validate job status.
if (reqInfo.Status != ServiceRequestStatus.Waiting &&
reqInfo.Status != ServiceRequestStatus.Ready &&
reqInfo.Status != ServiceRequestStatus.Queued)
{
string error = ApplicationLog.WriteLine(string.Concat(
"Unexpected error ", reqInfo.Status));
Assert.Fail(error);
Console.WriteLine(string.Concat(
"Unexpected error ", reqInfo.Status));
}
else
{
Console.WriteLine(string.Concat(
"Request status ", reqInfo.Status));
}
}
public void EBIWuBlastResultsWithQueryParams()
{
// Gets the search query parameter and their values.
string alphabetName = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.AlphabetNameNode);
string querySequence = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.QuerySequency);
string queryDatabaseValue = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.DatabaseValue);
string emailParameter = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.Emailparameter);
string email = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.EmailAdress);
string queryProgramValue = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.ProgramValue);
string queryDatabaseParameter = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.DatabaseParameter);
string queryProgramParameter = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.ProgramParameter);
string expectedHitId = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.HitID);
string expectedAccession = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.HitAccession);
string expectedResultCount = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.ResultsCount);
string expectedHitsCount = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.HitsCount);
string expectedEntropyStatistics = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.EntropyStatistics);
string expectedKappaStatistics = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.KappaStatistics);
string expectedLambdaStatistics = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.LambdaStatistics);
string expectedLength = Utility._xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, 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);
// 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 = 15;
int attempt = 1;
while (attempt <= maxAttempts &&
info.Status != ServiceRequestStatus.Error &&
info.Status != ServiceRequestStatus.Ready)
{
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(), expectedLength);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null), expectedHitId);
Assert.AreEqual(hit.Hsps.Count.ToString((IFormatProvider)null), expectedResultCount);
Console.WriteLine(string.Format(null,
"Ebi Blast BVT: Hits count '{0}'.", eBlastResults.Count));
Console.WriteLine(string.Format(null,
"Ebi Blast BVT: Accession '{0}'.", hit.Accession));
Console.WriteLine(string.Format(null,
"Ebi Blast BVT: Hit Id '{0}'.", hit.Id));
Console.WriteLine(string.Format(null,
"Ebi Blast BVT: Hits Count '{0}'.", hit.Hsps.Count));
Console.WriteLine(string.Format(null,
"Ebi Blast BVT: Hits Length '{0}'.", hit.Length));
}
/// <summary>
/// Validates general Add method test cases with the xml node name specified.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="isSyncFetch">True for Synchronous fetch</param>
void GeneralMethodToValidateResults(string nodeName, bool isSyncFetch)
{
// Gets the search query parameter and their values.
string alphabet = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
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);
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 expectedHspHitsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HspHitsCount);
string expectedSleepTime = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SleepTime);
string reqId = string.Empty;
object responseResults = null;
int maxAttempts = 20;
int attempt = 1;
Sequence seq = new Sequence(Utility.GetAlphabet(alphabet), querySequence);
// Set Service confiruration parameters true.
IBlastServiceHandler service = new AzureBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
configParams.DefaultTimeout = 5;
configParams.Connection = new Uri(Constants.AzureUri);
service.Configuration = configParams;
// Create search parameters object.
BlastParameters searchParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
// Get Request identifier from web service.
reqId = service.SubmitRequest(seq, searchParams);
// Get request information for first time.
ServiceRequestInformation info = service.GetRequestStatus(reqId);
// Ping service until request staus is ready.
while (attempt <= maxAttempts && info.Status != ServiceRequestStatus.Ready &&
info.Status != ServiceRequestStatus.Error)
{
System.Threading.Thread.Sleep(Convert.ToInt32(expectedSleepTime, (IFormatProvider)null));
++attempt;
info = service.GetRequestStatus(reqId);
}
// Get results.
if (isSyncFetch)
{
responseResults = service.FetchResultsSync(reqId, searchParams);
}
else
{
responseResults = service.GetResult(reqId, searchParams);
}
Assert.IsNotNull(responseResults);
if (!isSyncFetch)
{
//Parse and validate results
BlastXmlParser parser = new BlastXmlParser();
IList <BlastResult> blastResults =
parser.Parse(new StringReader(responseResults.ToString()));
Assert.AreEqual(blastResults.Count.ToString(
(IFormatProvider)null), expectedHitsCount);
Assert.AreEqual(blastResults[0].Records.Count.ToString(
(IFormatProvider)null), expectedHitsCount);
BlastSearchRecord record = blastResults[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), expectedResultCount);
Hit hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null), expectedHitId);
Assert.AreEqual(hit.Hsps.Count.ToString((IFormatProvider)null), expectedHspHitsCount);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Hits Count '{0}'.", hit.Hsps.Count));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Hits Count '{0}'.", hit.Hsps.Count));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Hits count '{0}'.", blastResults.Count));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Accession '{0}'.", hit.Accession));
}
}
/// <summary>
/// Validate if the connection is successful
/// </summary>
/// <returns>True, if connection is successful</returns>
static bool ValidateWebServiceConnection()
{
// Gets the search query parameter and their values.
string alphabet = Utility._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.AlphabetNameNode);
string querySequence = Utility._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.QuerySequency);
string queryDatabaseValue = Utility._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.DatabaseValue);
string queryProgramValue = Utility._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.ProgramValue);
string queryDatabaseParameter = Utility._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.DatabaseParameter);
string queryProgramParameter = Utility._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.ProgramParameter);
string expectedSleepTime = Utility._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.SleepTime);
string reqId = string.Empty;
object responseResults = null;
int maxAttempts = 20;
int attempt = 1;
Sequence seq = new Sequence(Utility.GetAlphabet(alphabet), querySequence);
// Set Service confiruration parameters true.
IBlastServiceHandler service = new AzureBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
configParams.DefaultTimeout = 5;
configParams.Connection = new Uri(Constants.AzureUri);
service.Configuration = configParams;
// Create search parameters object.
BlastParameters searchParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
try
{
// Get Request identifier from web service.
reqId = service.SubmitRequest(seq, searchParams);
// Get request information for first time.
ServiceRequestInformation info = service.GetRequestStatus(reqId);
// Ping service until request staus is ready.
while (attempt <= maxAttempts && info.Status != ServiceRequestStatus.Ready &&
info.Status != ServiceRequestStatus.Error)
{
System.Threading.Thread.Sleep(Convert.ToInt32(expectedSleepTime));
++attempt;
info = service.GetRequestStatus(reqId);
}
responseResults = service.GetResult(reqId, searchParams);
if (null == responseResults)
{
Console.WriteLine(
"Azure BVT : Connection not successful with no Response result");
ApplicationLog.WriteLine(
"Azure BVT : Connection not successful with no Response result");
return(false);
}
}
catch (Exception ex)
{
Console.WriteLine(string.Format(
"Azure BVT : Connection not successful with error '{0}'", ex.Message));
ApplicationLog.WriteLine(string.Format(
"Azure BVT : Connection not successful with error '{0}'", ex.Message));
return(false);
}
Console.WriteLine("Azure BVT : Connection Successful");
return(true);
}
