public void InvalidateEbiWebServiceRequestStatusWithoutConfigPams()
{
// Gets the search query parameter and their values.
string alphabet = utilityObj.xmlUtil.GetTextValue(
Constants.EbiBlastResultsNode, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(
Constants.EbiBlastResultsNode, Constants.QuerySequency);
Sequence seq = new Sequence(Utility.GetAlphabet(alphabet),
querySequence);
// Set Service confiruration parameters true.
EbiWuBlastHandler service = new EbiWuBlastHandler();
// Dispose Ebi Blast Handler.
service.Dispose();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
service.Configuration = configParams;
BlastParameters searchParams = new BlastParameters();
// Get Request identifier from web service.
try
{
service.SubmitRequest(seq, searchParams);
Assert.Fail();
}
catch (Exception)
{
ApplicationLog.WriteLine(
"EbiWebService P2 : Successfully validated the exception");
}
}
/// <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>
/// 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);
}
else
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT: Client Request status has been validated successfully."));
ApplicationLog.WriteLine(string.Concat(
"Azure Blast BVT: Request status ", reqInfo.Status));
}
}
/// <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;
}
}
/// <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>
/// Initializes a new instance of the ThreadParameter class.
/// </summary>
/// <param name="requestIdentifier">Job identifier</param>
/// <param name="sequence">Sequence Object</param>
/// <param name="parameter">Blast Parameters</param>
public BlastThreadParameter(
string requestIdentifier,
ISequence sequence,
BlastParameters parameter)
{
_requestIdentifier = requestIdentifier;
_sequence = sequence;
_parameter = parameter;
}
/// <summary>
/// Initializes a new instance of the WebServiceInputEventArgs class
/// </summary>
/// <param name="parameters">the selected service parameters</param>
/// <param name="webserviceName">Name of the webservice used.</param>
/// <param name="configuration">Configuration of service</param>
public WebServiceInputEventArgs(
BlastParameters parameters,
string webServiceName,
ConfigParameters configuration)
{
this.serviceParam = parameters;
this.webServiceName = webServiceName;
this.configuration = configuration;
}
/// <summary>
/// Validate Cancel submitted job by passing job id.
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
static void ValidateCancelSubmittedJob(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 emailParameter = Utility._xmlUtil.GetTextValue(
nodeName, Constants.Emailparameter);
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);
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);
// Cancel subitted job.
bool result = service.CancelRequest(reqId);
// validate the cancelled job.
Assert.IsTrue(result);
Console.WriteLine(string.Format(null,
"EBI Blast P1 : Submitted job cancelled was successfully.",
queryProgramValue));
}
else
{
Assert.Ignore("The test case ignored due to connection failure");
}
}
/// <summary>
/// Validates general Add method test cases with the xml node name specified.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="methodName">Name of the Add method</param>
void ValidateAddGeneralTescases(string nodeName, string methodName)
{
// Gets the search query parameter and their values.
string querySequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = _utilityObj._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.DatabaseValue);
string queryProgramValue = _utilityObj._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.ProgramValue);
string querySequenceParameter = _utilityObj._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.QuerySequencyparameter);
string queryDatabaseParameter = _utilityObj._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.DatabaseParameter);
string queryProgramParameter = _utilityObj._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.ProgramParameter);
// Set Service confiruration parameters true.
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
// Create search parameters object.
BlastParameters queryParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
if (0 == string.Compare(methodName, "Add", true, CultureInfo.CurrentCulture))
{
queryParams.Add(querySequenceParameter, querySequence);
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
}
else
{
queryParams.AddIfAbsent(querySequenceParameter, querySequence);
queryParams.AddIfAbsent(queryDatabaseParameter, queryDatabaseValue);
queryParams.AddIfAbsent(queryProgramParameter, queryProgramValue);
}
// Validate search query parameters.
Assert.IsTrue(queryParams.Settings.ContainsValue(querySequence));
Assert.IsTrue(queryParams.Settings.ContainsValue(queryDatabaseValue));
Assert.IsTrue(queryParams.Settings.ContainsValue(queryProgramValue));
Assert.AreEqual(queryParams.Settings.Count, 3);
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT : Query Sequence{0} is as expected.",
querySequence));
Console.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT : DataBase Value{0} is as expected.",
queryDatabaseValue));
Console.WriteLine(string.Format((IFormatProvider)null,
"Azure Blast BVT : Program Value {0} is as expected.",
queryProgramValue));
}
/// <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
/// Disabling this test case till web service is up.
public void ValidateCancelSubmittedJob()
{
if (_IsWebServiceAvailable)
{
// 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 reqId = string.Empty;
bool result = false;
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);
// Cancel subitted job.
result = service.CancelRequest(reqId);
// validate the cancelled job.
Assert.IsTrue(result);
Console.WriteLine(string.Format(null,
"Azure Blast BVT : Submitted job cancelled was successfully.",
queryProgramValue));
}
else
{
Assert.Ignore("The test case ignored due to connection failure");
}
}
public void ValidateEBIWuBlastManadatoryParams()
{
// Gets the search query parameter and their values.
string querySequence = Utility._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.QuerySequency);
string queryDatabaseValue = Utility._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.DatabaseValue);
string queryProgramValue = Utility._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.ProgramValue);
string queryDatabaseParameter = Utility._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.DatabaseParameter);
string queryProgramParameter = Utility._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.ProgramParameter);
string emailParameter = Utility._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.Emailparameter);
string email = Utility._xmlUtil.GetTextValue(
Constants.BlastParametersNode, Constants.EmailAdress);
// Set Service confiruration parameters true.
IBlastServiceHandler 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(null,
"Ebi Blast BVT: Query Sequence{0} is as expected.", querySequence));
Console.WriteLine(string.Format(null,
"Ebi Blast BVT: DataBase Value{0} is as expected.", queryDatabaseValue));
Console.WriteLine(string.Format(null,
"Ebi Blast BVT: Program Value {0} is as expected.", queryProgramValue));
}
/// <summary>
/// Create sample blast parameters.
/// </summary>
/// <returns>BlastParameters object.</returns>
static BlastParameters GetBlastSearchParams()
{
BlastParameters searchParams = new BlastParameters();
searchParams.Add("Program", "blastn");
searchParams.Add("Database", "nr");
// higher Expect will return more results
searchParams.Add("Expect", "1e-10");
searchParams.Add("CompositionBasedStatistics", "0");
return searchParams;
}
/// <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>
/// Validate a Azure Blast Service Request status for invalid Sequence.
/// Input : Invalid sequence.
/// Output : Valdiate request status for invalid sequence.
/// </summary>
public void InvalidateAzureWebServiceRequestStatusForInvalidConfigPams()
{
// Gets the search query parameter and their values.
string alphabet = _utilityObj._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.AlphabetNameNode);
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);
Sequence seq = new Sequence(Utility.GetAlphabet(alphabet), querySequence);
// Set Service confiruration parameters true.
AzureBlastHandler service = new AzureBlastHandler();
// Dispose Azure Blast Handler.
service.Dispose();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
configParams.DefaultTimeout = 10;
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.
try
{
service.SubmitRequest(seq, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"AzureWebService P2 : Successfully validated the exception");
Console.WriteLine(
"AzureWebService P2 : Successfully validated the exception");
}
}
/// <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>
/// This event is fired on click of the submit button on the dialog,
/// this would validate the parameters accordingly and on success would initiate adding
/// of the parameters to the given service parameters
/// </summary>
/// <param name="sender">submit button</param>
/// <param name="e">Event Data</param>
private void OnBtnSubmitClick(object sender, RoutedEventArgs e)
{
BlastParameters serviceParam = new BlastParameters();
bool valid = this.AddServiceParams(ref serviceParam, this.firstStk);
if (valid)
{
valid = this.AddServiceParams(ref serviceParam, this.secondStk);
}
if (valid)
{
valid = this.AddServiceParams(ref serviceParam, this.thirdColumnParams);
}
if (valid)
{
valid = this.AddServiceParams(ref serviceParam, this.commonParamsStk);
}
if (valid && this.serviceParams.Visibility == Visibility.Visible)
{
valid = this.AddServiceParams(ref serviceParam, this.serviceParams);
}
if (valid)
{
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = (bool)this.chkUseBrowerProxy.IsChecked;
configParams.DefaultTimeout = 1;
valid = this.AddConfigurationParameter(configParams, this.stkConfigurationParams);
WebServiceInputEventArgs args = new WebServiceInputEventArgs(serviceParam, this.serviceName, configParams);
this.WebServiceInputArgs = args;
if (this.ExecuteSearch != null && valid)
{
this.ExecuteSearch.Invoke(this, args);
this.Close();
}
}
if (valid)
{
this.Close();
}
}
/// <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 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>
/// This method validates the gap cost input
/// and on success adds the gap cost to the service parameters
/// </summary>
/// <param name="serviceParam">service param to add the param</param>
/// <returns>whether the gap cost was valid and added or not</returns>
private bool CheckNAddGapCostField(ref BlastParameters serviceParam)
{
int number;
if (!Int32.TryParse(this.gapOpenTxt.Text, out number) && number != 0)
{
MessageDialogBox.Show(Resource.INVALID_TEXT + GAPCOSTS + Resource.VALUE_TEXT, Properties.Resource.CAPTION, MessageDialogButton.OK);
return(false);
}
if (!Int32.TryParse(this.gapOpenTxt.Text, out number) && number != 0)
{
MessageDialogBox.Show(Resource.INVALID_TEXT + GAPCOSTS + Resource.VALUE_TEXT, Properties.Resource.CAPTION, MessageDialogButton.OK);
return(false);
}
serviceParam.Add(GAPCOSTS, this.gapOpenTxt.Text + " " + this.gapExtendedTxt.Text);
return(true);
}
/// <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>
/// This method would validate and add the params to the service
/// parameters for the requested search
/// </summary>
/// <param name="serviceParam">Service parameter</param>
/// <param name="paramName">Param name</param>
/// <param name="paramValue">Param value</param>
/// <returns>whether the parameter was valid</returns>
private static bool AddValidServiceParams(ref BlastParameters serviceParam, string paramName, string paramValue)
{
RequestParameter param = BlastParameters.Parameters[paramName];
if (string.IsNullOrEmpty(paramValue))
{
return(true);
}
else if (param.DataType == PARAMTYPEINT && param.Validator == null)
{
int number;
// Validate the int and double values which doesnot have validators.
if (!Int32.TryParse(paramValue, out number))
{
MessageBox.Show(Properties.Resources.INVALID_TEXT + paramName + Properties.Resources.VALUE_TEXT, Properties.Resources.CAPTION, MessageBoxButton.OK, MessageBoxImage.Error);
return(false);
}
}
else if (param.DataType == PARAMTYPEDOUBLE && param.Validator == null)
{
double number;
if (!Double.TryParse(paramValue, out number))
{
MessageBox.Show(Properties.Resources.INVALID_TEXT + paramName + Properties.Resources.VALUE_TEXT, Properties.Resources.CAPTION, MessageBoxButton.OK, MessageBoxImage.Error);
return(false);
}
}
if (param.IsValid(paramValue))
{
serviceParam.Add(paramName, paramValue);
return(true);
}
else
{
MessageBox.Show(Properties.Resources.INVALID_TEXT + paramName + Properties.Resources.VALUE_TEXT, Properties.Resources.CAPTION, MessageBoxButton.OK, MessageBoxImage.Error);
return(false);
}
}
/// <summary>
/// This method would validate and add the params to the service
/// parameters for the requested search
/// </summary>
/// <param name="serviceParam">Service parameter</param>
/// <param name="paramName">Param name</param>
/// <param name="paramValue">Param value</param>
/// <returns>whether the parameter was valid</returns>
private static bool CheckNAddServiceParams(ref BlastParameters serviceParam, string paramName, string paramValue)
{
RequestParameter param = BlastParameters.Parameters[paramName];
if (string.IsNullOrEmpty(paramValue))
{
return(true);
}
else if (param.DataType == "int" && param.Validator == null)
{
int number;
// Validate the int and double values which doesnot have validators.
if (!Int32.TryParse(paramValue, out number))
{
MessageDialogBox.Show(Resource.INVALID_TEXT + paramName + Resource.VALUE_TEXT, Properties.Resource.CAPTION, MessageDialogButton.OK);
return(false);
}
}
else if (param.DataType == "double" && param.Validator == null)
{
double number;
if (!Double.TryParse(paramValue, out number))
{
MessageDialogBox.Show(Resource.INVALID_TEXT + paramName + Resource.VALUE_TEXT, Properties.Resource.CAPTION, MessageDialogButton.OK);
return(false);
}
}
if (param.IsValid(paramValue))
{
serviceParam.Add(paramName, paramValue);
return(true);
}
else
{
MessageDialogBox.Show(Resource.INVALID_TEXT + paramName + Resource.VALUE_TEXT, Properties.Resource.CAPTION, MessageDialogButton.OK);
return(false);
}
}
/// <summary>
/// Validate a Azure Blast Service Request without setting any config parameters.
/// Input : Invalid config parameters.
/// Output : Invalidate request status.
/// </summary>
public void InvalidateAzureWebServiceRequestStatusWithoutConfigPams()
{
// Gets the search query parameter and their values.
string alphabet = _utilityObj._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.AlphabetNameNode);
string querySequence = _utilityObj._xmlUtil.GetTextValue(
Constants.AzureBlastResultsNode, Constants.QuerySequency);
Sequence seq = new Sequence(Utility.GetAlphabet(alphabet), querySequence);
string reqId = string.Empty;
// Set Service confiruration parameters true.
AzureBlastHandler service = new AzureBlastHandler();
// Dispose Azure Blast Handler.
service.Dispose();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
configParams.DefaultTimeout = 1;
configParams.Connection = new Uri(Constants.AzureUri);
service.Configuration = configParams;
BlastParameters searchParams = new BlastParameters();
// Get Request identifier from web service.
try
{
reqId = service.SubmitRequest(seq, searchParams);
Assert.IsTrue(string.IsNullOrEmpty(reqId));
Assert.Fail();
}
catch (WebException)
{
ApplicationLog.WriteLine("AzureWebService P2 : Successfully validated the exception");
Console.WriteLine("AzureWebService P2 : Successfully validated the exception");
}
}
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();
}
}
}
/// <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));
}
}
public void ValidateProcessRequestThread()
{
// 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 = Constants.EmailForWS;
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
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
BioHPCBlastHandler service = new BioHPCBlastHandler();
try
{
ConfigParameters configParameters = new ConfigParameters();
configParameters.EmailAddress = email;
configParameters.Password = String.Empty;
configParameters.UseBrowserProxy = true;
service.Configuration = configParameters;
service.RequestCompleted += new EventHandler<BlastRequestCompletedEventArgs>(service_RequestCompleted);
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);
string reqId = String.Empty;
// Waiting for the any previous request to get completed.
Thread.Sleep(150000);
// Create a request without passing sequence.
reqId = service.SubmitRequest(seq, searchParams);
// Cancel subitted job.
bool result = service.CancelRequest(reqId);
// validate the cancelled job.
Assert.IsTrue(result);
}
finally
{
if (service != null)
service.Dispose();
}
}
/// <summary>
/// Validate Cancel submitted job by passing job id.
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
void ValidateCancelSubmittedJob(
string nodeName,
RequestType type)
{
// Gets the search query parameter and their values.
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string email = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
string queryProgramValue = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string 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();
IBlastServiceHandler 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);
TestCaseParameters parameters = null;
object resultsObject = null;
// Create a request without passing sequence.
switch (type)
{
case RequestType.DnaStrSubmit:
parameters = new TestCaseParameters(
Constants.BioHPCCancelRequestUsingDnaSeq,
null, GetRequestIdentifier, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
break;
case RequestType.ProteinStrSubmit:
parameters = new TestCaseParameters(
Constants.BioHPCRequestIdentifierForProteinSeqTest,
null, GetRequestIdentifier, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
break;
case RequestType.DnalstSubmit:
parameters = new TestCaseParameters(
Constants.BioHPCRequestIdentifierForDnaSeqTest,
null, GetRequestIdentifierUsingSeqList, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
break;
case RequestType.ProteinlstSubmit:
parameters = new TestCaseParameters(
Constants.BioHPCCancelRequestUsingProteinSeq,
null, GetRequestIdentifierUsingSeqList, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
break;
}
// Cancel subitted job.
bool result = service.CancelRequest(resultsObject as string);
// validate the cancelled job.
Assert.IsTrue(result);
Console.WriteLine(string.Concat(
"BioHPC Blast Bvt : Submitted job cancelled was successfully. ",
queryProgramValue));
}
/// <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>
/// Validate general SubmitHttpRequest() method by passing
/// differnt XML node name
/// <param name="nodeName">xml node name.</param>
/// </summary>
void ValidateSubmitHttpRequestMethod(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);
string queryParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequencyparameter);
string webUri = utilityObj.xmlUtil.GetTextValue(
Constants.BlastRequestParametersNode, Constants.BlastWebServiceUri);
WebAccessorResponse requestResult = null;
// Set Service confiruration parameters true.
IBlastServiceHandler blastService = null;
try
{
blastService = new NCBIBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
blastService.Configuration = configParameters;
// Create search parameters object.
BlastParameters queryParams = new BlastParameters();
// Add mandatory parameter values to search query parameters.
queryParams.Add(queryParameter, querySequence);
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
//Submit Http request
WebAccessor webAccessor = new WebAccessor();
webAccessor.GetBrowserProxy();
requestResult = webAccessor.SubmitHttpRequest(new Uri(webUri), true,
queryParams.Settings);
// Validate the Submitted request.
Assert.IsTrue(requestResult.IsSuccessful);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Http Request was submitted successfully"));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast P1: DataBase Value {0} is as expected.",
queryDatabaseValue));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast P1: Program Value {0} is as expected.",
queryProgramValue));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast P1: Query sequence {0} is as expected.",
querySequence));
webAccessor.Close();
}
finally
{
if (blastService != null)
((IDisposable)blastService).Dispose();
}
}
/// <summary>
/// Validate general AddIfAbsent() method by passing
/// differnt XML node name
/// <param name="nodeName">xml node name.</param>
/// </summary>
void ValidateAddIfAbsentMethod(string nodeName)
{
// Gets the search query parameter and their values.
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string querySequenceParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequencyparameter);
// Set Service confiruration parameters true.
IBlastServiceHandler blastService = null;
try
{
blastService = new NCBIBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
blastService.Configuration = configParameters;
// Create search parameters object.
BlastParameters queryParams = new BlastParameters();
// Add mandatory sequence as query paramter
queryParams.AddIfAbsent(querySequenceParameter, querySequence);
// Validate added sequence to request setting configuration.
Assert.IsTrue(queryParams.Settings.ContainsValue(querySequence));
// Logs to the VSTest GUI (ApplicationLog.Out) window
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast P1: Validation of Add method was completed successfully."));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast P1: Query Sequence{0} is as expected.", querySequence));
}
finally
{
if (blastService != null)
((IDisposable)blastService).Dispose();
}
}
/// <summary>
/// Validate general SubmitSearchRequest method test cases
/// with the different parameters specified.
/// <param name="nodeName">xml node name.</param>
/// <param name="expectParameter">Expected parameter</param>
/// <param name="compositionBasedStaticParameter">Composition based static parameter</param>
/// </summary>
void ValidateSubmitSearchMethod(string nodeName,
string expectParameter, string compositionBasedStaticParameter)
{
// Gets the search query parameter and their values.
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string optionalExpectParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastExpectParameter);
string optionalExpectValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastExpectparameterValue);
string optionalCBSParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastCompositionBasedStaticsParameter);
string optionalCBSParameterValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastCompositionBasedStaticsValue);
string reqId = string.Empty;
// Create a sequence.
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
// Set Service confiruration parameters true.
IBlastServiceHandler blastService = null;
try
{
blastService = new NCBIBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
blastService.Configuration = configParameters;
// Create search parameters object.
BlastParameters queryParams = new BlastParameters();
// Add parameter values to search query parameters.
if ((0 == string.Compare(expectParameter, null, true,
CultureInfo.CurrentCulture))
&& (0 == string.Compare(compositionBasedStaticParameter, null, true,
CultureInfo.CurrentCulture)))
{
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
}
else
{
queryParams.Add(queryDatabaseParameter, queryDatabaseValue);
queryParams.Add(queryProgramParameter, queryProgramValue);
queryParams.Add(optionalExpectParameter, optionalExpectValue);
queryParams.Add(optionalCBSParameter, optionalCBSParameterValue);
}
// Submit search request with valid parameter.
reqId = blastService.SubmitRequest(seq, queryParams);
// Validate request identifier returned by web service.
Assert.IsNotNull(reqId);
// Logs to the VSTest GUI (ApplicationLog.Out) window
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast P1: Validation of SubmitSearchRequest() method was completed successfully."));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast P1: Request Id {0} is as expected.", reqId));
}
finally
{
if (blastService != null)
((IDisposable)blastService).Dispose();
}
}
public void ValidateNcbiSubmitSearchRequestForQueryList()
{
string nodeName = Constants.EmRelDatabaseParametersNode;
// Gets the search query parameter and their values.
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
// Create a sequence.
IList<ISequence> seqList = new List<ISequence>();
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName), querySequence);
seqList.Add(seq);
// Set Service confiruration parameters true.
IBlastServiceHandler NcbiBlastService = null;
try
{
NcbiBlastService = new NCBIBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
NcbiBlastService.Configuration = configParameters;
// Create search parameters object.
BlastParameters NcbiParams = new BlastParameters();
// Add parameter values to search query parameters.
NcbiParams.Add(queryDatabaseParameter, queryDatabaseValue);
NcbiParams.Add(queryProgramParameter, queryProgramValue);
// Get Request identifier from web service for SeqList.
// Automated this case to hit the Code.
NcbiBlastService.SubmitRequest(seqList, NcbiParams);
}
catch (NotImplementedException)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Ncbi Blast P1 : Validated the exception successfully."));
}
finally
{
if (NcbiBlastService != null)
((IDisposable)NcbiBlastService).Dispose();
}
}
/// <summary>
/// Validate Cancel submitted job by passing job id.
/// <param name="nodeName">different alphabet node name</param>
/// </summary>
void ValidateCancelSubmittedJob(
string nodeName,
RequestType type)
{
// Gets the search query parameter and their values.
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string email = Constants.EmailForWS; ;
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 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
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
IBlastServiceHandler service = new BioHPCBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.EmailAddress = email;
configParameters.Password = String.Empty;
configParameters.UseBrowserProxy = true;
service.Configuration = configParameters;
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);
string reqId = String.Empty;
// Waiting for the any previous request to get completed.
Thread.Sleep(150000);
// Create a request without passing sequence.
switch (type)
{
case RequestType.StrSubmit:
reqId = service.SubmitRequest(seq, searchParams);
break;
case RequestType.LstSubmit:
IList<ISequence> lstSeq = new List<ISequence>();
lstSeq.Add(seq);
reqId = service.SubmitRequest(lstSeq, searchParams);
break;
}
// Cancel subitted job.
bool result = service.CancelRequest(reqId);
// validate the cancelled job.
Assert.IsTrue(result);
Console.WriteLine(string.Concat(
"BioHPC Blast Bvt : Submitted job cancelled was successfully. ",
queryProgramValue));
}
/// <summary>
/// Validate general fetching results.by passing
/// differnt parameters for BioHPC Blast web service.
/// <param name="nodeName">xml node name.</param>
/// <param name="isFetchSynchronous">Is Fetch Synchronous?</param>
/// </summary>
void ValidateBioHPCBlastResultsFetch(
string nodeName,
RequestType reqType)
{
// Gets the search query parameter and their values.
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string email = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
string queryProgramValue = _utilityObj._xmlUtil.GetTextValue(
nodeName,
Constants.ProgramValue);
string queryDatabaseParameter = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string expectedHitId = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.HitID);
string expectedAccession = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.HitAccession);
string expectedResultCount = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ResultsCount);
string expectedHitsCount = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.HitsCount);
string expectedEntropyStatistics =
_utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.EntropyStatistics);
string expectedKappaStatistics = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.KappaStatistics);
string expectedLambdaStatistics = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.LambdaStatistics);
string expectedLength = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.Length);
int maxAttempts = int.Parse(_utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.MaxAttemptsNode), (IFormatProvider)null);
int waitingTime = int.Parse(_utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.WaitTimeNode), (IFormatProvider)null);
string expect = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.Expectparameter);
string emailNotify = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyParameterNode);
string jobName = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.JobNameParameterNode);
string expectValue = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectNode);
string emailNotifyValue = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyNode);
string jobNameValue = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.JobNameNode);
// 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);
testCaseParms.Add(Constants.MaxAttemptString, maxAttempts.ToString((IFormatProvider)null));
testCaseParms.Add(Constants.WaitTimeString, waitingTime);
TestCaseParameters parameters = null;
object resultsObject = null;
switch (reqType)
{
case RequestType.FetchSyncUsingDnaSeq:
parameters = new TestCaseParameters(
Constants.BioHPCFetchResultsSyncTest,
null, FetchResultsSyncTest, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
break;
case RequestType.FetchASyncUsingDnaSeq:
parameters = new TestCaseParameters(
Constants.BioHPCFetchResultsASyncTest,
null, FetchResultsASyncTest, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
break;
case RequestType.FetchSyncUsingProteinSeq:
parameters = new TestCaseParameters(
Constants.FetchResultsSyncUsingProteinSeq,
null, FetchResultsSyncTest, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
break;
case RequestType.FetchASyncUsingProteinSeq:
parameters = new TestCaseParameters(
Constants.FetchResultsUsingProteinSeq,
null, FetchResultsASyncTest, testCaseParms);
resultsObject = _TestCaseSimulator.Simulate(parameters).Result;
break;
}
// Validate blast results.
Assert.IsNotNull(resultsObject);
List <BlastResult> bioHPCResults = resultsObject as List <BlastResult>;
Assert.IsNotNull(bioHPCResults);
Assert.AreEqual(bioHPCResults.Count.ToString(
(IFormatProvider)null), expectedResultCount);
Assert.AreEqual(bioHPCResults[0].Records.Count.ToString((
IFormatProvider)null), expectedResultCount);
BlastSearchRecord record = bioHPCResults[0].Records[0];
Assert.AreEqual(record.Statistics.Kappa.ToString(
(IFormatProvider)null), expectedKappaStatistics);
Assert.AreEqual(record.Statistics.Lambda.ToString(
(IFormatProvider)null), expectedLambdaStatistics);
Assert.AreEqual(record.Statistics.Entropy.ToString(
(IFormatProvider)null), expectedEntropyStatistics);
Assert.AreEqual(record.Hits.Count.ToString(
(IFormatProvider)null), expectedHitsCount);
Hit hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Length.ToString((IFormatProvider)null),
expectedLength);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null),
expectedHitId);
Assert.AreEqual(hit.Hsps.Count.ToString((IFormatProvider)null),
expectedResultCount);
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Hits count '{0}'.", bioHPCResults.Count));
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Accession '{0}'.", hit.Accession));
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Hit Id '{0}'.", hit.Id));
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Hits Count '{0}'.", hit.Hsps.Count));
}
/// <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));
}
}
/// <summary>
/// A helper method for the BLAST task. Submits a job to BLAST.
/// </summary>
/// <param name="qp"></param>
/// <returns></returns>
private BlastJob submit(QueueSequence qp)
{
// Configure BLAST service
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = Up.BlastUseBrowserProxy;
BlastParameters searchParams = new BlastParameters();
string query = ">" + qp.Sequence.DisplayID + "\n" + qp.Sequence.ToString();
searchParams.Add("Program", Up.BlastProgram);
searchParams.Add("Database", Up.BlastDatabase);
searchParams.Add("GeneticCode", Up.BlastGeneticCode);
searchParams.Add("Expect", "10");
searchParams.Add("Query", query);
// Create BLAST service
NCBIBlastHandler blastService = new NCBIBlastHandler();
blastService.Configuration = configParams;
// Submit BLAST Job
string jobId;
try
{
jobId = blastService.SubmitRequest(qp.Sequence, searchParams);
}
catch(Exception eee)
{
if (eee.Message.Contains("WebException"))
{
ToggleProxy();
}
BlastJob blastJob2 = new BlastJob();
blastJob2.JobStatus = BlastJob.FAILED;
blastJob2.Query = qp.Sequence;
blastJob2.Position = qp.Position;
return blastJob2;
}
// Make sure job was submitted successfully
ServiceRequestInformation info = blastService.GetRequestStatus(jobId);
if (info.Status != ServiceRequestStatus.Waiting
&& info.Status != ServiceRequestStatus.Ready
&& info.Status != ServiceRequestStatus.Queued)
{
//Console.WriteLine("\tError Submitting Job: " + info.Status);
BlastJob blastJob2 = new BlastJob();
blastJob2.JobStatus = BlastJob.FAILED;
blastJob2.Query = qp.Sequence;
blastJob2.Position = qp.Position;
return blastJob2;
}
Thread.Sleep(BlastQueue.SubmitDelay);
//Console.WriteLine("\tSuccessfully submitted jobId: " + jobId);
// Return a BlastJob, set jobStatus to BUSY
BlastJob blastJob = new BlastJob()
{
JobId = jobId,
SearchParams = searchParams,
ConfigParams = configParams,
BlastService = blastService,
JobStatus = BlastJob.BUSY,
Query = qp.Sequence,
Position = qp.Position
};
return blastJob;
}
public void ValidateAddMethodForDifferentDatabaseValue()
{
// Gets the search query parameter and their values.
string databaseParameter = utilityObj.xmlUtil.GetTextValue(
Constants.BlastDataBaseNode, Constants.DatabaseParameter);
string swissprotDBValue = utilityObj.xmlUtil.GetTextValue(
Constants.BlastDataBaseNode, Constants.SwissprotDBValue);
string expectedParametersCount = utilityObj.xmlUtil.GetTextValue(
Constants.BlastProgramNode, Constants.expectedParameterCount);
// Set Service confiruration parameters true.
IBlastServiceHandler blastService = null;
try
{
blastService = new NCBIBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
blastService.Configuration = configParameters;
// Create search parameters object.
BlastParameters queryParams = new BlastParameters();
// Add a swissprot database parameter
queryParams.Add(databaseParameter, swissprotDBValue);
// Validate swissprot database parameter
Assert.IsTrue(queryParams.Settings.ContainsValue(swissprotDBValue));
Assert.AreEqual(queryParams.Settings.Count.ToString(
(IFormatProvider)null), expectedParametersCount);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast P1: Validation of Swissprot database parameter was completed successfully."));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast P1: Default database {0} is as expected.", swissprotDBValue));
}
finally
{
if (blastService != null)
((IDisposable)blastService).Dispose();
}
}
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);
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName),
querySequence);
// create BioHPC Blast Web Service object.
IBlastServiceHandler service = new BioHPCBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.EmailAddress = email;
configParams.Password = string.Empty;
//configParams.UseBrowserProxy = true;
service.Configuration = configParams;
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);
try
{
// Create a request without passing sequence.
string reqId = service.SubmitRequest(seq, searchParams);
Assert.IsNotNull(reqId);
}
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();
}
}
/// <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 general fetching results.by passing
/// differnt parameters.
/// <param name="nodeName">xml node name.</param>
/// <param name="expectParameter">expectparameter name</param>
/// <param name="compositionBasedStaticParameter">compositionBasedStaticParameter name</param>
/// <param name="isFetchSynchronous">Is Fetch Synchronous?</param>
/// </summary>
void ValidateGeneralFetchResults(
string nodeName, string expectParameter,
string compositionBasedStaticParameter,
bool isFetchSynchronous)
{
// Gets the search query parameter and their values.
string queryParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequencyparameter);
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string optionalExpectParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastExpectParameter);
string optionalExpectValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastExpectparameterValue);
string optionalCBSParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastCompositionBasedStaticsParameter);
string optionalCBSParameterValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.BlastCompositionBasedStaticsValue);
string expectedHitId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitID);
string expectedAccession = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitAccession);
object responseResults = null;
NCBIBlastHandler service = new NCBIBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
service.Configuration = configParams;
ISequence sequence = new Sequence(Alphabets.DNA, "ATCGGGGCCC");
BlastParameters searchParams = new BlastParameters();
// Set mandatory parameters only if optional parameters are null
if ((0 == string.Compare(expectParameter, null, true,
CultureInfo.CurrentCulture))
&& (0 == string.Compare(compositionBasedStaticParameter, null, true,
CultureInfo.CurrentCulture)))
{
searchParams.Add(queryParameter, querySequence);
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
}
else
{
searchParams.Add(queryParameter, querySequence);
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(optionalExpectParameter, optionalExpectValue);
searchParams.Add(optionalCBSParameter, optionalCBSParameterValue);
}
// Careate a request without passing sequence.
string reqId = service.SubmitRequest(sequence, searchParams);
// validate request identifier.
Assert.IsNotNull(reqId);
// submit request identifier and get the status
ServiceRequestInformation info = service.GetRequestStatus(reqId);
if (info.Status != ServiceRequestStatus.Waiting &&
info.Status != ServiceRequestStatus.Ready)
{
string err = ApplicationLog.WriteLine("Unexpected status: '{0}'", info.Status);
Assert.Fail(err);
}
// get async results, poll until ready
int maxAttempts = 10;
int attempt = 1;
while (attempt <= maxAttempts
&& info.Status != ServiceRequestStatus.Error
&& info.Status != ServiceRequestStatus.Ready)
{
if (isFetchSynchronous)
{
info = service.GetRequestStatus(reqId);
Thread.Sleep(info.Status == ServiceRequestStatus.Waiting
|| info.Status == ServiceRequestStatus.Queued
? 20000 * attempt : 0);
}
else
{
Thread.Sleep(info.Status == ServiceRequestStatus.Waiting ? 30000 : 0);
info = service.GetRequestStatus(reqId);
}
++attempt;
}
IBlastParser blastXmlParser = new BlastXmlParser();
responseResults = blastXmlParser.Parse(
new StringReader(service.GetResult(reqId, searchParams)));
// Validate blast results.
Assert.IsNotNull(responseResults);
List<BlastResult> blastResults = responseResults as List<BlastResult>;
Assert.IsNotNull(blastResults);
BlastSearchRecord record = blastResults[0].Records[0];
if (record.Hits.Count > 0)
{
Hit hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null), expectedHitId);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast BVT: Hits count '{0}'.", blastResults.Count));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast BVT: Accession '{0}'.", hit.Accession));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast BVT: Hit Id '{0}'.", hit.Id));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast BVT: Hits Count '{0}'.", hit.Hsps.Count));
}
// Validate the results Synchronously with the results got earlier.
if (isFetchSynchronous)
{
IList<BlastResult> syncBlastResults =
service.FetchResultsSync(reqId, searchParams) as List<BlastResult>;
Assert.IsNotNull(syncBlastResults);
if (null != blastResults[0].Records[0].Hits
&& 0 < blastResults[0].Records[0].Hits.Count
&& null != blastResults[0].Records[0].Hits[0].Hsps
&& 0 < blastResults[0].Records[0].Hits[0].Hsps.Count)
{
Assert.AreEqual(blastResults[0].Records[0].Hits[0].Hsps[0].QuerySequence,
syncBlastResults[0].Records[0].Hits[0].Hsps[0].QuerySequence);
}
else
{
ApplicationLog.WriteLine("No significant hits found with the these parameters.");
}
}
}
/// <summary>
/// Validate general fetching results by passing
/// different parameters.
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="NcbiCtorPam">Ncbi constructor different parameters</param>
void GeneralMethodToValidateResults(string nodeName,
NcbiWebServiceCtorParameters NcbiCtorPam)
{
// Gets the search query parameter and their values.
string queryParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequencyparameter);
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string expectedHitId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitID);
string expectedAccession = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitAccession);
object responseResults = null;
NCBIBlastHandler service;
IBlastParser blastXmlParser = new BlastXmlParser();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
switch (NcbiCtorPam)
{
case NcbiWebServiceCtorParameters.ConfigPams:
service = new NCBIBlastHandler(configParams);
break;
case NcbiWebServiceCtorParameters.ParserAndConfigPams:
service = new NCBIBlastHandler(blastXmlParser, configParams);
break;
default:
service = new NCBIBlastHandler();
break;
}
ISequence sequence = new Sequence(Utility.GetAlphabet("DNA"), "ATCGCC");
BlastParameters searchParams = new BlastParameters();
searchParams.Add(queryParameter, querySequence);
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
// Careate a request without passing sequence.
string reqId = service.SubmitRequest(sequence, searchParams);
// validate request identifier.
Assert.IsNotNull(reqId);
// submit request identifier and get the status
ServiceRequestInformation info = service.GetRequestStatus(reqId);
if (info.Status != ServiceRequestStatus.Waiting
&& info.Status != ServiceRequestStatus.Ready)
{
string err = ApplicationLog.WriteLine("Unexpected status: '{0}'", info.Status);
Assert.Fail(err);
}
// get async results, poll until ready
int maxAttempts = 10;
int attempt = 1;
while (attempt <= maxAttempts
&& info.Status != ServiceRequestStatus.Error
&& info.Status != ServiceRequestStatus.Ready)
{
Thread.Sleep(info.Status == ServiceRequestStatus.Waiting ? 40000 : 0);
info = service.GetRequestStatus(reqId);
++attempt;
}
responseResults = blastXmlParser.Parse(
new StringReader(service.GetResult(reqId, searchParams)));
// Validate blast results.
Assert.IsNotNull(responseResults);
List<BlastResult> blastResults = responseResults as List<BlastResult>;
Assert.IsNotNull(blastResults);
BlastSearchRecord record = blastResults[0].Records[0];
Hit hit = null;
if (record.Hits.Count > 0)
{
hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null), expectedHitId);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast BVT: Hits count '{0}'.", blastResults.Count));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast BVT: Accession '{0}'.", hit.Accession));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast BVT: Hit Id '{0}'.", hit.Id));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "Blast BVT: Hits Count '{0}'.", hit.Hsps.Count));
}
}
public void ValidateAddIfAbsentForOptionalQuerySearchValues()
{
// Gets the search query parameter and their values.
string optionalParameter = utilityObj.xmlUtil.GetTextValue(
Constants.BlastProgramNode, Constants.Expectparameter);
string optionalParameterValue = utilityObj.xmlUtil.GetTextValue(
Constants.BlastProgramNode, Constants.optionalValue);
string expectedParametersCount = utilityObj.xmlUtil.GetTextValue(
Constants.BlastProgramNode, Constants.expectedParameterCount);
// Set Service confiruration parameters true.
IBlastServiceHandler blastService = null;
try
{
blastService = new NCBIBlastHandler();
ConfigParameters configParameters = new ConfigParameters();
configParameters.UseBrowserProxy = true;
blastService.Configuration = configParameters;
// Create search parameters object.
BlastParameters queryParams = new BlastParameters();
// Add a threshold parameter value.
queryParams.AddIfAbsent(optionalParameter, optionalParameterValue);
// Validate threshold parameter value.
Assert.IsTrue(queryParams.Settings.ContainsValue(optionalParameterValue));
Assert.AreEqual(queryParams.Settings.Count.ToString((
IFormatProvider)null), expectedParametersCount);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast P1: Validation of expect parameter was completed successfully."));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Blast P1: expect value parameter {0} is as expected.", optionalParameterValue));
}
finally
{
if (blastService != null)
((IDisposable)blastService).Dispose();
}
}
/// <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");
}
}
/// <summary>
/// Validate general fetching results.by passing
/// differnt parameters for BioHPC Blast web service.
/// <param name="nodeName">xml node name.</param>
/// <param name="isFetchSynchronous">Is Fetch Synchronous?</param>
/// </summary>
void ValidateBioHPCBlastResultsFetch(
string nodeName, bool isFetchSynchronous)
{
// Gets the search query parameter and their values.
string alphabetName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlphabetNameNode);
string querySequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.QuerySequency);
string queryDatabaseValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseValue);
string email = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailAdress);
string queryProgramValue = utilityObj.xmlUtil.GetTextValue(
nodeName,
Constants.ProgramValue);
string queryDatabaseParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DatabaseParameter);
string queryProgramParameter = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ProgramParameter);
string expectedHitId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitID);
string expectedAccession = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitAccession);
string expectedResultCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ResultsCount);
string expectedHitsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.HitsCount);
string expectedEntropyStatistics =
utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EntropyStatistics);
string expectedKappaStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.KappaStatistics);
string expectedLambdaStatistics = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LambdaStatistics);
string expectedLength = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Length);
int maxAttempts = int.Parse(utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.MaxAttemptsNode), (IFormatProvider)null);
int waitingTime = int.Parse(utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.WaitTimeNode), (IFormatProvider)null);
string expect = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.Expectparameter);
string emailNotify = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyParameterNode);
string jobName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.JobNameParameterNode);
string expectValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectNode);
string emailNotifyValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailNotifyNode);
string jobNameValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.JobNameNode);
object responseResults = null;
Sequence seq = new Sequence(
Utility.GetAlphabet(alphabetName),
querySequence);
// create BioHPC Blast Web Service object.
IBlastServiceHandler service = new BioHPCBlastHandler();
ConfigParameters configPams = new ConfigParameters();
configPams.EmailAddress = email;
configPams.Password = String.Empty;
configPams.UseBrowserProxy = true;
service.Configuration = configPams;
BlastParameters searchParams = new BlastParameters();
// Set Request parameters.
searchParams.Add(queryDatabaseParameter, queryDatabaseValue);
searchParams.Add(queryProgramParameter, queryProgramValue);
searchParams.Add(expect, expectValue);
searchParams.Add(emailNotify, emailNotifyValue);
searchParams.Add(jobName, jobNameValue);
// Create a request without passing sequence.
string reqId = service.SubmitRequest(seq, searchParams);
// validate request identifier.
Assert.IsNotNull(reqId);
ServiceRequestInformation info = service.GetRequestStatus(reqId);
if (info.Status != ServiceRequestStatus.Waiting
&& info.Status != ServiceRequestStatus.Ready
&& info.Status != ServiceRequestStatus.Queued)
{
string err =
ApplicationLog.WriteLine("Unexpected status: '{0}'",
info.Status);
Assert.Fail(err);
}
// get async results, poll until ready
int attempt = 1;
while (attempt <= maxAttempts
&& info.Status != ServiceRequestStatus.Error
&& info.Status != ServiceRequestStatus.Ready)
{
++attempt;
if (isFetchSynchronous)
{
info = service.GetRequestStatus(reqId);
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting
|| info.Status == ServiceRequestStatus.Queued
? waitingTime * attempt : 0);
}
else
{
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting
|| info.Status == ServiceRequestStatus.Queued ?
waitingTime * attempt : 0);
info = service.GetRequestStatus(reqId);
}
}
IBlastParser blastXmlParser = new BlastXmlParser();
responseResults = blastXmlParser.Parse(
new StringReader(service.GetResult(reqId, searchParams)));
Assert.IsNotNull(responseResults);
List<BlastResult> eBlastResults =
responseResults as List<BlastResult>;
Assert.IsNotNull(eBlastResults);
Assert.AreEqual(eBlastResults.Count.ToString(
(IFormatProvider)null), expectedResultCount);
Assert.AreEqual(eBlastResults[0].Records.Count.ToString((
IFormatProvider)null), expectedResultCount);
BlastSearchRecord record = eBlastResults[0].Records[0];
Assert.AreEqual(record.Statistics.Kappa.ToString(
(IFormatProvider)null), expectedKappaStatistics);
Assert.AreEqual(record.Statistics.Lambda.ToString(
(IFormatProvider)null), expectedLambdaStatistics);
Assert.AreEqual(record.Statistics.Entropy.ToString(
(IFormatProvider)null), expectedEntropyStatistics);
Assert.AreEqual(record.Hits.Count.ToString(
(IFormatProvider)null), expectedHitsCount);
Hit hit = record.Hits[0];
Assert.AreEqual(hit.Accession, expectedAccession);
Assert.AreEqual(hit.Length.ToString((IFormatProvider)null),
expectedLength);
Assert.AreEqual(hit.Id.ToString((IFormatProvider)null),
expectedHitId);
Assert.AreEqual(hit.Hsps.Count.ToString((IFormatProvider)null),
expectedResultCount);
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Hits count '{0}'.", eBlastResults.Count));
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Accession '{0}'.", hit.Accession));
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Hit Id '{0}'.", hit.Id));
Console.WriteLine(string.Format((IFormatProvider)null,
"BioHPC Blast BVT : Hits Count '{0}'.", hit.Hsps.Count));
// Validate the results Synchronously with the results got earlier.
if (isFetchSynchronous)
{
IList<BlastResult> syncBlastResults =
service.FetchResultsSync(reqId, searchParams) as List<BlastResult>;
Assert.IsNotNull(syncBlastResults);
if (null != eBlastResults[0].Records[0].Hits
&& 0 < eBlastResults[0].Records[0].Hits.Count
&& null != eBlastResults[0].Records[0].Hits[0].Hsps
&& 0 < eBlastResults[0].Records[0].Hits[0].Hsps.Count)
{
Assert.AreEqual(
eBlastResults[0].Records[0].Hits[0].Hsps[0].QuerySequence,
syncBlastResults[0].Records[0].Hits[0].Hsps[0].QuerySequence);
}
else
{
ApplicationLog.WriteLine(
"No significant hits found with the these parameters.");
Console.WriteLine(
"No significant hits found with the these parameters.");
}
}
}