/// <summary>
/// This method is called when the user wants to run BLAST on a sequence
/// </summary>
private void OnBlastSequence()
{
// Get the full sequence, or the selected fragment
ISequence sequence = !string.IsNullOrEmpty(SelectedSequenceFragment)
? new Sequence(SelectedSequence.RawSequence.Alphabet, SelectedSequenceFragment)
: SelectedSequence.RawSequence;
IBlastServiceHandler blastServiceHandler = SelectedBlastAlgorithm;
BlastParameters bp = new BlastParameters();
bp.Add("Program", "blastn");
bp.Add("Database", "nr");
bp.Add("Expect", "10.0");
blastServiceHandler.RequestCompleted += new EventHandler <BlastRequestCompletedEventArgs>(BlastServiceHandlerRequestCompleted);
try
{
IsRunning = blastServiceHandler.SubmitRequest(sequence, bp);
if (string.IsNullOrEmpty(IsRunning))
{
ShowError("Failed to execute Blast", "No results returned", null);
}
}
catch (Exception ex)
{
ShowError("Failed to execute Blast", "Error occurred", ex);
ResultHits = null;
}
}
public void ValidateEbiWebServiceProperties()
{
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
IBlastServiceHandler service = null;
try
{
service = new EbiWuBlastHandler(configParams);
// Validate EBI Web Service properties.
Assert.AreEqual(Constants.EbiWebServiceDescription, service.Description);
Assert.AreEqual(Constants.EbiWebServiceName, service.Name);
ApplicationLog.WriteLine(
"EbiWebService : Successfully validated the Ebi WebService Properties");
Console.WriteLine(
"EbiWebService : Successfully validated the Ebi WebService Properties");
}
catch (Exception ex) { Assert.Fail(ex.Message); }
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
public void InvalidateNcbiCancelRequest()
{
IBlastServiceHandler service = null;
// Validate ServiceMeta ctor by passing null config.
try
{
service = new NCBIBlastHandler();
service.CancelRequest(null);
Assert.Fail();
}
catch (Exception)
{
ApplicationLog.WriteLine(
"NcbiWebService P2 : Successfully validated the exception");
Console.WriteLine(
"NcbiWebService P2 : Successfully validated the exception");
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
public void InvalidateBlastResultsUsingConstructorPam()
{
// create Ncbi Blast service object.
ConfigParameters configParams = null;
IBlastServiceHandler service = null;
// Validate NcbiWebService ctor by passing null parser.
try
{
service = new NCBIBlastHandler(configParams);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"NcbiWebService P2 : Successfully validated the Argument null exception");
Console.WriteLine(
"NcbiWebService P2 : Successfully validated the Argument null exception");
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
/// <summary>
/// Get Request identifier for submitted job.
/// </summary>
/// <param name="blastParameters">Blast Input config parameters</param>
/// <returns></returns>
private TestCaseOutput GetRequestIdentifier(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 reqId = 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.
reqId = service.SubmitRequest(sequence, blastSearchPams);
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
return(new TestCaseOutput(reqId, false));
}
/// <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>
/// This method renders the single line report for BLAST hits.
/// </summary>
/// <param name="results">BLAST hits</param>
private void RenderSingleLineReport(IList <BlastResult> results, IBlastServiceHandler blastService, string databaseName)
{
this.lstSingleLineReport.ItemsSource = null;
this.lstSingleLineReport.Items.Clear();
this.blastResultCollator.Clear();
this.Focus();
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.Uri = BlastHitUrlResolver.ResolveUrl(hit.Id, blastService, databaseName);
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;
blast.Gaps = hsp.Gaps;
this.blastResultCollator.Add(blast);
}
}
}
}
}
}
this.lstSingleLineReport.ItemsSource = this.blastResultCollator;
// Invoke the Silvermap
if (this.blastResultCollator.Count > 0 || this.webServiceReportTab.SelectedIndex == 1)
{
this.silverMapControl.InvokeSilverMap(this.blastResultCollator);
}
}
/// <summary>
/// Validate a Azure Blast Service constructor with invalid parameters.
/// Input : Invalid service config parameters.
/// Output : Invalidate Azure web service constructor.
/// </summary>
public void InvalidateAzureWebHandlerCtor()
{
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
configParams.DefaultTimeout = 10;
configParams.Connection = new Uri(Constants.AzureUri);
BlastXmlParser parser = new BlastXmlParser();
// Validate AzureWebService ctor by passing null parser.
IBlastServiceHandler service = null;
try
{
service = new AzureBlastHandler(null, configParams);
Assert.IsNotNull(service);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"AzureWebService P2 : Successfully validated the Argument null exception");
Console.WriteLine(
"AzureWebService P2 : Successfully validated the Argument null exception");
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
// Validate AzureWebService ctor by passing null configuration parameters.
try
{
service = new AzureBlastHandler(parser, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"AzureWebService P2 : Successfully validated the Argument null exception");
Console.WriteLine(
"AzureWebService P2 : Successfully validated the Argument null exception");
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
/// <summary>
/// Validate Cancelling submitted Job.
/// Input Data :Valid search query, Database value and program value.
/// Output Data : Validation of Cancelling submitted Job.
/// </summary>
/// Invalidated the test case for the Bug 115
public void ValidateCancelSubmittedJob()
{
// Gets the search query parameter and their values.
string querySequence = _utilityObj._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.QuerySequency);
string queryDatabaseValue = _utilityObj._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.DatabaseValue);
string queryProgramValue = _utilityObj._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.ProgramValue);
string queryDatabaseParameter = _utilityObj._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.DatabaseParameter);
string queryProgramParameter = _utilityObj._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.ProgramParameter);
// Set Blast Parameters
IBlastServiceHandler service = null;
try
{
service = new AzureBlastHandler();
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);
// Get request identifier
TestCaseParameters parameters = new TestCaseParameters(
Constants.AzureWebServiceCancelSubmitRequestTest, null,
GetRequestIdentifier, testCaseParms);
object resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
// Cancel subitted job.
bool result = service.CancelRequest(resultsObject as string);
// validate the cancelled job.
Assert.IsTrue(result);
Console.WriteLine(string.Format(null,
"Azure Blast BVT : Submitted job cancelled was successfully.",
queryProgramValue));
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
/// <summary>
/// This method displays BLAST hits on the UI.
/// </summary>
/// <param name="results">BLAST hits</param>
public void DisplayWebServiceOutput(IList <BlastResult> results, IBlastServiceHandler blastService, string databaseName)
{
if (results != null && results.Count >= 1)
{
this.RenderSingleLineReport(results, blastService, databaseName);
this.blastResult = results[0];
this.txtDate.Text = DateTime.Now.Date.ToString(CultureInfo.CurrentCulture);
this.txtDataBaseName.Text = this.blastResult.Metadata.Database;
this.txtVersion.Text = this.blastResult.Metadata.Version;
}
}
/// <summary>
/// This method is called when the user wants to run BLAST on a sequence
/// </summary>
private void OnBlastSequence()
{
// Get the full sequence, or the selected fragment
ISequence sequence = !string.IsNullOrEmpty(SelectedSequenceFragment)
? new Sequence(SelectedSequence.RawSequence.Alphabet, SelectedSequenceFragment)
: SelectedSequence.RawSequence;
IBlastServiceHandler blastServiceHandler = SelectedBlastAlgorithm;
BlastParameters bp = new BlastParameters();
bp.Add("Program", "blastn");
bp.Add("Database", "nr");
bp.Add("Expect", "10.0");
try
{
string resultKey = blastServiceHandler.SubmitRequest(sequence, bp);
if (string.IsNullOrEmpty(resultKey))
{
ShowError("Failed to execute Blast", "No results returned", null);
}
else
{
IList <BlastResult> results =
blastServiceHandler.FetchResultsSync(resultKey, bp);
if (results == null || results.Count == 0)
{
MessageBox.Show("No Results returned.");
ResultHits = null;
}
else
{
ResultHits = results[0].Records[0].Hits;
}
}
}
catch (Exception ex)
{
ShowError("Failed to execute Blast", "Error occurred", ex);
ResultHits = null;
}
}
/// <summary>
/// Get the url for a blast hit
/// </summary>
/// <param name="hitID">Blast hit id</param>
/// <param name="blastService">Instance of the blast service</param>
/// <param name="databaseName">Database name used in the blast query</param>
/// <returns>A url if resolved, else null</returns>
public static string ResolveUrl(string hitID, IBlastServiceHandler blastService, string databaseName)
{
// NCBI
if (blastService.Name == WebServices.NcbiBlast.Name)
{
string[] idSplit = hitID.Split('|');
if (idSplit.Length < 2)
{
return(null);
}
string id = idSplit[1];
return(string.Format("http://www.ncbi.nlm.nih.gov/protein/{0}", id));
}
// EBI
else if (blastService.Name == WebServices.EbiBlast.Name)
{
string[] idSplit = hitID.Split(':', ';');
if (idSplit.Length < 2)
{
return(null);
}
string id = idSplit[1];
switch (databaseName)
{
case "em_rel":
return(string.Format("http://www.ebi.ac.uk/ena/data/view/{0}", id));
case "uniprot":
return(string.Format("http://www.uniprot.org/uniprot/{0}.html", id));
default:
return(null);
}
}
// Return null if url was not resolved
return(null);
}
/// <summary>
/// Get BioHPC web service request status.
/// </summary>
/// <param name="blastParameters">Blast config parameters</param>
/// <returns>BioHPC webservice request status</returns>
private TestCaseOutput GetRequestStatus(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);
//Set BioHPC web service config parameters
IBlastServiceHandler service = null;
object serviceInfo = 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);
// Get service request status.
serviceInfo = service.GetRequestStatus(reqId);
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
return(new TestCaseOutput(serviceInfo, false));
}
/// <summary>
/// This method is called when the user wants to run BLAST on a sequence
/// </summary>
private void OnBlastSequence()
{
// Get the full sequence, or the selected fragment
ISequence sequence = !string.IsNullOrEmpty(SelectedSequenceFragment)
? new Sequence(SelectedSequence.RawSequence.Alphabet, SelectedSequenceFragment)
: SelectedSequence.RawSequence;
IBlastServiceHandler blastServiceHandler = SelectedBlastAlgorithm;
BlastParameters bp = new BlastParameters();
foreach (var item in BlastParameters.Where(kv => !string.IsNullOrEmpty(kv.Value)))
{
bp.Add(item.Key, item.Value);
}
if (!string.IsNullOrEmpty(Url))
{
blastServiceHandler.Configuration.Connection = new Uri(Url);
if (Url.StartsWith("https"))
{
blastServiceHandler.Configuration.UseHttps = true;
}
}
blastServiceHandler.Configuration.UseBrowserProxy = UseBrowserProxy;
blastServiceHandler.RequestCompleted += new EventHandler <BlastRequestCompletedEventArgs>(BlastServiceHandlerRequestCompleted);
try
{
IsRunning = blastServiceHandler.SubmitRequest(sequence, bp);
if (string.IsNullOrEmpty(IsRunning))
{
ShowError("Failed to execute Blast", "No results returned", null);
}
}
catch (Exception ex)
{
ShowError("Failed to execute Blast", "Error occurred", ex);
ResultHits = null;
}
}
/// <summary>
/// Validate Request status of the submited request.
/// </summary>
/// <param name="blastParameters">Ebi blast service config parameters</param>
/// <returns></returns>
private TestCaseOutput GetRequestStatusTest(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;
object reqInfoObject = 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
reqInfoObject = service.GetRequestStatus(reqId);
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
return(new TestCaseOutput(reqInfoObject, false));
}
/// <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));
}
public void ValidateBioHPCCtor()
{
// Gets the search query parameter and their values.
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode,
Constants.AlphabetNameNode);
string querySequence = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode,
Constants.QuerySequency);
string queryDatabaseValue = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode,
Constants.DatabaseValue);
string email = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode,
Constants.EmailAdress);
string queryProgramValue = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode,
Constants.ProgramValue);
string queryDatabaseParameter = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode,
Constants.DatabaseParameter);
string queryProgramParameter = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode,
Constants.ProgramParameter);
string expect = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.Expectparameter);
string emailNotify = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.EmailNotifyParameterNode);
string jobName = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.JobNameParameterNode);
string expectValue = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.ExpectNode);
string emailNotifyValue = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.EmailNotifyNode);
string jobNameValue = _utilityObj._xmlUtil.GetTextValue(
Constants.BioHPCAsynchronousResultsNode, Constants.JobNameNode);
// Set Blast Parameters
BlastParameters queryParams = new BlastParameters();
IBlastServiceHandler service = null;
object resultsObject = null;
try
{
service = new BioHPCBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.EmailAddress = email;
configParameters.Password = String.Empty;
configParameters.UseBrowserProxy = true;
service.Configuration = configParameters;
// 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);
// Get request Identifier
TestCaseParameters parameters = new TestCaseParameters(
Constants.BioHPCRequestIdentifierForDnaSeqTest,
null, GetRequestIdentifier, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
Assert.IsNotNull(resultsObject as string);
}
catch (WebException ex)
{
Assert.Fail();
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast Bvt : Connection not successful with error '{0}'",
ex.Message));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast Bvt : Connection not successful with error '{0}'",
ex.Message));
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
public void ValidateEBIWuBlastManadatoryParams()
{
// Gets the search query parameter and their values.
string querySequence = _utilityObj._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.QuerySequency);
string queryDatabaseValue = _utilityObj._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.DatabaseValue);
string queryProgramValue = _utilityObj._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.ProgramValue);
string queryDatabaseParameter = _utilityObj._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.DatabaseParameter);
string queryProgramParameter = _utilityObj._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.ProgramParameter);
string emailParameter = _utilityObj._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.Emailparameter);
string email = _utilityObj._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.EmailAdress);
// Set Service confiruration parameters true.
IBlastServiceHandler service = null;
try
{
service = new EbiWuBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
service.Configuration = configParameters;
// Create search parameters object.
BlastParameters ebiParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
//ebiParams.Add(querySequenceParameter, querySequence);
ebiParams.Add(queryDatabaseParameter, queryDatabaseValue);
ebiParams.Add(queryProgramParameter, queryProgramValue);
ebiParams.Add(emailParameter, email);
// Validate search query parameters.
ParameterValidationResult validateParameters =
EbiWuBlastHandler.ValidateParameters(ebiParams);
bool result = validateParameters.IsValid;
Assert.IsTrue(result);
// Assert.IsTrue(ebiParams.Settings.ContainsValue(querySequence));
Assert.IsTrue(ebiParams.Settings.ContainsValue(queryDatabaseValue));
Assert.IsTrue(ebiParams.Settings.ContainsValue(queryProgramValue));
Assert.IsTrue(ebiParams.Settings.ContainsValue(email));
Assert.AreEqual(ebiParams.Settings.Count, 3);
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: Query Sequence{0} is as expected.", querySequence));
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: DataBase Value{0} is as expected.", queryDatabaseValue));
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: Program Value {0} is as expected.", queryProgramValue));
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
/// <summary>
/// Validate Cancel submitted job by passing job id.
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
void ValidateCancelSubmittedJob(string nodeName)
{
// 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(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
// create Ebi Blast service object.
IBlastServiceHandler service = null;
try
{
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);
// Cancel subitted job.
bool result = service.CancelRequest(reqId);
// validate the cancelled job.
Assert.IsTrue(result);
Console.WriteLine(string.Concat(
"EBI Blast P1 : Submitted job cancelled was successfully.",
queryProgramValue));
}
catch (Exception ex) { Assert.Fail(ex.Message); }
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
/// <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 the Azure Blast Service Request status Queued.
/// Input : Invalid request parameters.
/// Output : Invalidate request status.
/// </summary>
public void InvalidateAzureWebServiceRequestStatus()
{
// Gets the search query parameter and their values.
string queryProgramValue = _utilityObj._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.ProgramValue);
string queryDatabaseParameter = _utilityObj._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.DatabaseParameter);
string queryDatabaseValue = _utilityObj._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.DatabaseValue);
string queryProgramParameter = _utilityObj._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.ProgramParameter);
string reqId = string.Empty;
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
configParams.DefaultTimeout = 1;
configParams.RetryInterval = 10;
configParams.RetryCount = 1;
configParams.Connection = new Uri(Constants.AzureUri);
// Create search parameters object.
BlastParameters searchParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
IBlastServiceHandler service = null;
try
{
service = new AzureBlastHandler(configParams);
// Set Service confiruration parameters true.
service.Configuration = configParams;
// Get Request identifier from web service.
//reqId = service.SubmitRequest(seq, searchParams);
}
catch (WebException ex)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"AzureWebService P2 : Connection Failed with the error '{0}'", ex.Message));
Console.WriteLine(string.Format((IFormatProvider)null,
"AzureWebService P2 : Connection Failed with the error '{0}'", ex.Message));
Assert.Inconclusive("Test case ignored due to connection failure");
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
try
{
object responseResults = service.FetchResultsSync(reqId, searchParams);
Assert.IsNotNull(responseResults);
Assert.Fail();
}
catch (WebException)
{
ApplicationLog.WriteLine("AzureWebService P2 : Successfully validated the exception");
Console.WriteLine("AzureWebService P2 : Successfully validated the exception");
}
}
public void ValidateEBIWuBlastManadatoryParams()
{
// Gets the search query parameter and their values.
string querySequence = utilityObj.xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.DatabaseValue);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.ProgramParameter);
string emailParameter = utilityObj.xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.Emailparameter);
string email = utilityObj.xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.EmailAdress);
string alphabetName = utilityObj.xmlUtil.GetTextValue(
Constants.EbiAsynchronousResultsNode, Constants.AlphabetNameNode);
// Set Service confiruration parameters true.
IBlastServiceHandler service = null;
try
{
service = new EbiWuBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
service.Configuration = configParameters;
// Create search parameters object.
BlastParameters ebiParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
//ebiParams.Add(querySequenceParameter, querySequence);
ebiParams.Add(queryDatabaseParameter, queryDatabaseValue);
ebiParams.Add(queryProgramParameter, queryProgramValue);
ebiParams.Add(emailParameter, email);
ebiParams.Add("SequenceType",
alphabetName.ToLower(CultureInfo.CurrentCulture).Replace("ambiguous", ""));
// Validate search query parameters.
ParameterValidationResult validateParameters =
EbiWuBlastHandler.ValidateParameters(ebiParams);
bool result = validateParameters.IsValid;
Assert.IsTrue(result);
// Assert.IsTrue(ebiParams.Settings.ContainsValue(querySequence));
Assert.IsTrue(ebiParams.Settings.ContainsValue(queryDatabaseValue));
Assert.IsTrue(ebiParams.Settings.ContainsValue(queryProgramValue));
Assert.IsTrue(ebiParams.Settings.ContainsValue(email));
Assert.AreEqual(ebiParams.Settings.Count, 4);
// Logs to the VSTest GUI (Console.Out) window
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: Query Sequence{0} is as expected.", querySequence));
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: DataBase Value{0} is as expected.", queryDatabaseValue));
Console.WriteLine(string.Format((IFormatProvider)null,
"Ebi Blast BVT: Program Value {0} is as expected.", queryProgramValue));
}
catch (Exception ex) { Assert.Fail(ex.Message); }
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
