// Start is called before the first frame update
void Start()
{
ConfigParameters newConfigPrms = new ConfigParameters();
createJointGrid(newConfigPrms);
applyParamsToConfig(newConfigPrms);
/*
* Here are the public variables this script must address:
* public List<Vector3> Joints;
* public List<int> LoadIndices; //not necessary
* public List<int> LoadValues; // not necessary
* public List<int> PinIndices;
* public List<int> RollingJointIndices; //not necessary
* public List<int> MembersFirst;
* public List<int> MembersSecond;
* The following can still be modified directly in unity (not dependent on grid configuration):
* public GameObject VisualJoint;
* public GameObject VisualMember;
* public GameObject VisualPin;
* public GameObject VisualRolling;
* public float dt;
* public float speed;
*
*
*/
}
private static void UpdateHostConfig()
{
//Logger.Info("Enter");
AddRegisterEntriesInstaller.RegistryEditor regEditor = new AddRegisterEntriesInstaller.RegistryEditor();
if (ConfigHandler.Config.Policies.IsProxyEnabled)
{
if (PreviousConfig.Policies.IsProxyEnabled != ConfigHandler.Config.Policies.IsProxyEnabled)
{
regEditor.Start("enable");
}
regEditor.Start("recheck");
if (PreviousConfig.ByPassDetails.ByPassString != ConfigHandler.Config.ByPassDetails.ByPassString)
{
regEditor.Start("proxyoverride", ConfigHandler.Config.ByPassDetails.ByPassString);
}
}
else
{
if (PreviousConfig.Policies.IsProxyEnabled != ConfigHandler.Config.Policies.IsProxyEnabled)
{
regEditor.Start("disable");
}
}
PreviousConfig = ConfigHandler.Config;
//Logger.Info("Exit");
}
public static ConfigParameters ConfigLoad()
{
ConfigParameters config = null;
try
{
using (var stream = File.Open(configPath, FileMode.Open))
{
BinaryFormatter bFormatter = new BinaryFormatter();
try
{
config = (ConfigParameters)bFormatter.Deserialize(stream);
}
catch (SerializationException) //This must be a new client verion, reset config
{
config = null;
}
}
}
catch (DirectoryNotFoundException)
{
createDirectory();
}
catch (FileNotFoundException)
{
config = null; //We'll assign a new one.
}
return(config);
}
/// <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));
}
}
public void ValidateEbiWebServiceProperties()
{
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
IBlastServiceHandler service = null;
try
{
service = new EbiWuBlastHandler(configParams);
// Validate EBI Web Service properties.
Assert.AreEqual(Constants.EbiWebServiceDescription, service.Description);
Assert.AreEqual(Constants.EbiWebServiceName, service.Name);
ApplicationLog.WriteLine(
"EbiWebService : Successfully validated the Ebi WebService Properties");
Console.WriteLine(
"EbiWebService : Successfully validated the Ebi WebService Properties");
}
catch (Exception ex) { Assert.Fail(ex.Message); }
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
/// <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));
}
private static ConfigParameters GetConfigParameters(InterceptCallInfo info)
{
ConfigParameters cp = info.CallMethodInfo.LogParameters;
if (cp == null)
{
info.CallMethodInfo.LogParameters = cp = new ConfigParameters();
string[] ps = info.ConfigString.Split(';');
foreach (string p in ps)
{
string[] vs = p.Split('=');
if (vs.Length == 2)
{
switch (vs[0].ToLower().Trim())
{
case "filename": cp.FileName = vs[1].Trim(); break;
case "mincalltime": cp.MinCallTime = int. Parse(vs[1].Trim()); break;
case "logexceptions": cp.LogExceptions = bool.Parse(vs[1].Trim()); break;
case "logparameters": cp.LogParameters = bool.Parse(vs[1].Trim()); break;
}
}
}
}
return cp;
}
/// <summary>
/// Gets the hash code
/// </summary>
/// <returns>Hash code</returns>
public override int GetHashCode()
{
unchecked // Overflow is fine, just wrap
{
int hashCode = 41;
if (UID != null)
{
hashCode = hashCode * 59 + UID.GetHashCode();
}
if (Label != null)
{
hashCode = hashCode * 59 + Label.GetHashCode();
}
if (Description != null)
{
hashCode = hashCode * 59 + Description.GetHashCode();
}
if (Category != null)
{
hashCode = hashCode * 59 + Category.GetHashCode();
}
if (Listed != null)
{
hashCode = hashCode * 59 + Listed.GetHashCode();
}
if (SupportedBridgeTypeUIDs != null)
{
hashCode = hashCode * 59 + SupportedBridgeTypeUIDs.GetHashCode();
}
if (Bridge != null)
{
hashCode = hashCode * 59 + Bridge.GetHashCode();
}
if (Channels != null)
{
hashCode = hashCode * 59 + Channels.GetHashCode();
}
if (ChannelGroups != null)
{
hashCode = hashCode * 59 + ChannelGroups.GetHashCode();
}
if (ConfigParameters != null)
{
hashCode = hashCode * 59 + ConfigParameters.GetHashCode();
}
if (ParameterGroups != null)
{
hashCode = hashCode * 59 + ParameterGroups.GetHashCode();
}
if (Properties != null)
{
hashCode = hashCode * 59 + Properties.GetHashCode();
}
if (ExtensibleChannelTypeIds != null)
{
hashCode = hashCode * 59 + ExtensibleChannelTypeIds.GetHashCode();
}
return(hashCode);
}
}
private static ConfigParameters GetConfigParameters(InterceptCallInfo info)
{
ConfigParameters cp = info.CallMethodInfo.CacheParameters;
if (cp == null)
{
info.CallMethodInfo.CacheParameters = cp = new ConfigParameters();
string[] ps = info.ConfigString.Split(';');
foreach (string p in ps)
{
string[] vs = p.Split('=');
if (vs.Length == 2)
{
switch (vs[0].ToLower().Trim())
{
case "maxcachetime": cp.MaxCacheTime = int.Parse(vs[1].Trim()); break;
case "isweak": cp.IsWeak = bool.Parse(vs[1].Trim()); break;
}
}
}
}
return(cp);
}
public void InvalidateBlastResultsUsingConstructorPams()
{
// create Ncbi Blast service object.
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
// Validate NcbiWebService ctor by passing null parser.
try
{
new NCBIBlastHandler(null, configParams);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"NcbiWebService P2 : Successfully validated the Argument null exception");
Console.WriteLine(
"NcbiWebService P2 : Successfully validated the Argument null exception");
}
// Validate NcbiWebService ctor by passing null config.
try
{
new NCBIBlastHandler(new BlastXmlParser(), null);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"NcbiWebService P2 : Successfully validated the Argument null exception");
Console.WriteLine(
"NcbiWebService P2 : Successfully validated the Argument null exception");
}
}
public void InvalidateBlastResultsUsingConstructorPam()
{
// create Ncbi Blast service object.
ConfigParameters configParams = null;
IBlastServiceHandler service = null;
// Validate NcbiWebService ctor by passing null parser.
try
{
service = new NCBIBlastHandler(configParams);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"NcbiWebService P2 : Successfully validated the Argument null exception");
Console.WriteLine(
"NcbiWebService P2 : Successfully validated the Argument null exception");
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
private static ConfigParameters GetConfigParameters(InterceptCallInfo info)
{
ConfigParameters cp = info.CallMethodInfo.LogParameters;
if (cp == null)
{
info.CallMethodInfo.LogParameters = cp = new ConfigParameters();
string[] ps = info.ConfigString.Split(';');
foreach (string p in ps)
{
string[] vs = p.Split('=');
if (vs.Length == 2)
{
switch (vs[0].ToLower().Trim())
{
case "filename": cp.FileName = vs[1].Trim(); break;
case "mincalltime": cp.MinCallTime = int.Parse(vs[1].Trim()); break;
case "logexceptions": cp.LogExceptions = bool.Parse(vs[1].Trim()); break;
case "logparameters": cp.LogParameters = bool.Parse(vs[1].Trim()); break;
}
}
}
}
return(cp);
}
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");
}
}
public void ValidateBioHPCBlastWebServiceProperties()
{
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
BioHPCBlastHandler service = null;
try
{
service = new BioHPCBlastHandler(configParams);
// Validate BioHPC Blast Web Service properties.
Assert.AreEqual(Constants.BioHPCWebServiceDescription,
service.Description);
Assert.AreEqual(Constants.BioHPCWebServiceName,
service.Name);
Assert.IsNotNull(service.Configuration);
Assert.IsNotNull(service.Parser);
ApplicationLog.WriteLine(
"BioHPC Blast Bvt : Successfully validated the BioHPC Blast WebService Properties");
Console.WriteLine(
"BioHPC Blast Bvt : Successfully validated the BioHPC Blast WebService Properties");
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
/// <summary>
/// Validate Submit Job and Fetch ResultSync() using multiple input sequences
/// </summary>
/// <param name="nodeName">xml node name</param>
void ValidateFetchResultSync(string nodeName)
{
// Read input from config file
string filepath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string emailId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailIDNode);
string clusterOption = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ClusterOptionNode);
string actionAlign = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ActionAlignNode);
// Initialize with parser and config params
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler =
new TestIClustalWServiceHandler(clustalparser, configparams);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
IEnumerable <ISequence> sequence = null;
// Get the input sequences
using (FastAParser parser = new FastAParser(filepath))
{
sequence = parser.Parse();
// Submit job and validate it returned valid job id and control id
ServiceParameters svcparameters =
handler.SubmitRequest(sequence.ToList(), parameters);
Assert.IsFalse(string.IsNullOrEmpty(svcparameters.JobId));
ApplicationLog.WriteLine(string.Concat("JobId", svcparameters.JobId));
foreach (string key in svcparameters.Parameters.Keys)
{
Assert.IsFalse(string.IsNullOrEmpty(svcparameters.Parameters[key].ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "{0}:{1}",
key, svcparameters.Parameters[key].ToString()));
}
// Get the results and validate it is not null.
ClustalWResult result = handler.FetchResultsSync(svcparameters);
Assert.IsNotNull(result);
Assert.IsNotNull(result.SequenceAlignment);
foreach (IAlignedSequence alignSeq in result.SequenceAlignment.AlignedSequences)
{
ApplicationLog.WriteLine("Aligned Sequence Sequences :");
foreach (ISequence seq in alignSeq.Sequences)
{
ApplicationLog.WriteLine(string.Concat("Sequence:", seq.ToString()));
}
}
}
ApplicationLog.WriteLine(@"ClustalWServiceHandler BVT : Submit job and Get Results is successfully completed using FetchResultSync()");
}
/// <summary>
/// Validate if the connection is successful
/// </summary>
/// <returns>True, if connection is successful</returns>
static bool ValidateWebServiceConnection()
{
// Read input from config file
string filepath = Utility._xmlUtil.GetTextValue(
Constants.DefaultOptionNode, Constants.FilePathNode);
string emailId = Utility._xmlUtil.GetTextValue(
Constants.DefaultOptionNode, Constants.EmailIDNode);
string clusterOption = Utility._xmlUtil.GetTextValue(
Constants.DefaultOptionNode, Constants.ClusterOptionNode);
string actionAlign = Utility._xmlUtil.GetTextValue(
Constants.DefaultOptionNode, Constants.ActionAlignNode);
// Initialize with parser and config params
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler =
new TestIClustalWServiceHandler(clustalparser, configparams);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
// Get the input sequences
FastaParser parser = new FastaParser();
IList <ISequence> sequence = parser.Parse(filepath);
try
{
// Submit job and validate it returned valid job id and control id
ServiceParameters svcparameters =
handler.SubmitRequest(sequence, parameters);
if (string.IsNullOrEmpty(svcparameters.JobId))
{
Console.WriteLine(
"ClustalW BVT : Connection not successful with no Job ID");
ApplicationLog.WriteLine(
"ClustalW BVT : Connection not successful with no Job ID");
return(false);
}
handler.FetchResultsSync(svcparameters);
}
catch (Exception ex)
{
Console.WriteLine(string.Format(
"ClustalW BVT : Connection not successful with error '{0}'", ex.Message));
ApplicationLog.WriteLine(string.Format(
"ClustalW BVT : Connection not successful with error '{0}'", ex.Message));
return(false);
}
Console.WriteLine("ClustalW BVT : Connection Successful");
return(true);
}
void applyParamsToConfig(ConfigParameters theseParams)
{
BeamConfiguration thisConfig = GetComponent <BeamConfiguration>();
thisConfig.MembersFirst = theseParams.MembersFirst;
thisConfig.MembersSecond = theseParams.MembersSecond;
thisConfig.Joints = theseParams.Joints;
thisConfig.PinIndices = theseParams.PinIndices;
}
/// <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 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");
}
}
/// <summary>
/// Validate the CancelRequest()
/// </summary>
/// <param name="nodeName">xml node name</param>
void ValidateCancelRequest(string nodeName)
{
// Read input from config file
string filepath = _utilityObj._xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string emailId = _utilityObj._xmlUtil.GetTextValue(nodeName,
Constants.EmailIDNode);
string clusterOption = _utilityObj._xmlUtil.GetTextValue(nodeName,
Constants.ClusterOptionNode);
string actionAlign = _utilityObj._xmlUtil.GetTextValue(nodeName,
Constants.ActionAlignNode);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
IList <ISequence> sequence = null;
// Get the input sequences
using (FastaParser parser = new FastaParser())
{
sequence = parser.Parse(filepath);
}
// Submit job and cancel job
// Validate cancel job is working as expected
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler =
new TestIClustalWServiceHandler(clustalparser, configparams);
ServiceParameters svcparams = handler.SubmitRequest(sequence, parameters);
bool result = handler.CancelRequest(svcparams);
Assert.IsTrue(result);
Console.WriteLine(string.Concat("JobId:", svcparams.JobId));
ApplicationLog.WriteLine(string.Concat("JobId:", svcparams.JobId));
Assert.IsTrue(string.IsNullOrEmpty(svcparams.JobId));
foreach (string key in svcparams.Parameters.Keys)
{
Assert.IsTrue(string.IsNullOrEmpty(svcparams.Parameters[key].ToString()));
Console.WriteLine(string.Format((IFormatProvider)null, "{0} : {1}",
key, svcparams.Parameters[key].ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "{0} : {1}",
key, svcparams.Parameters[key].ToString()));
}
Console.WriteLine(
"ClustalWServiceHandler BVT : Cancel job is submitted as expected");
ApplicationLog.WriteLine(
"ClustalWServiceHandler BVT : Cancel job is submitted as expected");
}
/// <summary>
/// Validate a Azure Blast Service constructor with invalid parameters.
/// Input : Invalid service config parameters.
/// Output : Invalidate Azure web service constructor.
/// </summary>
public void InvalidateAzureWebHandlerCtor()
{
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
configParams.DefaultTimeout = 10;
configParams.Connection = new Uri(Constants.AzureUri);
BlastXmlParser parser = new BlastXmlParser();
// Validate AzureWebService ctor by passing null parser.
IBlastServiceHandler service = null;
try
{
service = new AzureBlastHandler(null, configParams);
Assert.IsNotNull(service);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"AzureWebService P2 : Successfully validated the Argument null exception");
Console.WriteLine(
"AzureWebService P2 : Successfully validated the Argument null exception");
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
// Validate AzureWebService ctor by passing null configuration parameters.
try
{
service = new AzureBlastHandler(parser, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"AzureWebService P2 : Successfully validated the Argument null exception");
Console.WriteLine(
"AzureWebService P2 : Successfully validated the Argument null exception");
}
finally
{
if (service != null)
{
((IDisposable)service).Dispose();
}
}
}
public void SetParameters(ConfigParameters parameters)
{
if (parameters == null) {
throw new ArgumentNullException(nameof(parameters));
}
long min;
if (parameters.TryGet("size", out min)) {
minSize = min * 1024 * 1024;
}
}
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>
/// Submits a blast query to a blast search provider.
/// This sample uses NCBI as the provider.
/// </summary>
/// <param name="sequence">Sequence to submit for searching.</param>
/// <returns>Job ID of the query. You can get the results using GetBlastResults after the job is completed.</returns>
public static string SubmitBlastQuery(ISequence sequence)
{
// Create the service provider
NCBIBlastHandler serviceProvider = new NCBIBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
serviceProvider.Configuration = configParams;
// create the request and return the job ID.
return serviceProvider.SubmitRequest(sequence, GetBlastSearchParams());
}
/// <summary>
/// Validate submit job and Get Results using event handler
/// </summary>
/// <param name="nodeName">xml node name</param>
void ValidateFetchResultsUsingEvent(string nodeName)
{
// Read input from config file
string filepath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string emailId = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.EmailIDNode);
string clusterOption = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ClusterOptionNode);
string actionAlign = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ActionAlignNode);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
IEnumerable <ISequence> sequence = null;
// Get the input sequences
using (FastAParser parser = new FastAParser(filepath))
{
sequence = parser.Parse();
// Register event and submit request
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler =
new TestIClustalWServiceHandler(clustalparser, configparams);
handler.RequestCompleted +=
new EventHandler <ClustalWCompletedEventArgs>(handler_RequestCompleted);
ServiceParameters svcparams = handler.SubmitRequest(sequence.ToList(), parameters);
WaitHandle[] aryHandler = new WaitHandle[1];
aryHandler[0] = _resetEvent;
WaitHandle.WaitAny(aryHandler);
// Validate the submit job results
Assert.IsFalse(string.IsNullOrEmpty(svcparams.JobId));
Console.WriteLine("JobId:" + svcparams.JobId);
foreach (string key in svcparams.Parameters.Keys)
{
Assert.IsFalse(string.IsNullOrEmpty(svcparams.Parameters[key].ToString()));
Console.WriteLine(string.Format((IFormatProvider)null, "{0} : {1}",
key, svcparams.Parameters[key].ToString()));
}
aryHandler = null;
_resetEvent.Close();
_resetEvent.Dispose();
}
}
public static void Start()
{
//Logger.Info("Enter");
PreviousConfig = ConfigHandler.Config;
while (true)
{
//while (!ThreadPool.UnsafeQueueUserWorkItem(new WaitCallback(SearchConfigurationChange), null)) ;
SearchConfigurationChange(null);
UpdateHostConfig();
Thread.Sleep(ConfigHandler.Config.Policies.HeartBeatInterval);
}
}
public void SetParameters(ConfigParameters parameters)
{
if (parameters == null) {
throw new ArgumentNullException(nameof(parameters));
}
min = parameters.MaybeGet<uint>("min");
max = parameters.MaybeGet<uint>("max");
minWidth = parameters.MaybeGet<uint>("minwidth");
maxWidth = parameters.MaybeGet<uint>("maxwidth");
minHeight = parameters.MaybeGet<uint>("minheight");
maxHeight = parameters.MaybeGet<uint>("maxheight");
}
void createJointGrid(ConfigParameters thisConfig)
{
thisConfig.initialize();
for (int i = 0; i < length; i++)
{
for (int j = 0; j < width; j++)
{
thisConfig.Joints.Add(new Vector3(i * spacing, height, j * spacing));
//0,0, 0,width (last in row )length,0 (first in last row) length,width (last in last row)
}
}
for (int i = 0; i < length * width; i++)
{
//i % length -
//i / length == width:
if (((i) / width != length - 1))
{
thisConfig.MembersFirst.Add(i);
thisConfig.MembersSecond.Add(i + width);
}
if (i % width != (width - 1))
{
thisConfig.MembersFirst.Add(i);
thisConfig.MembersSecond.Add(i + 1);
}
}
for (int i = 0; i < length * width; i++)
{
//i % length -
//i / length == width:
switch (thisStyle)
{
case pinStyle.noPins:
break;
case pinStyle.pinPerimeter:
if (i % width == (width - 1) || i % width == 0 || ((i) / width == length - 1) || ((i) / width == 0))
{
thisConfig.PinIndices.Add(i);
}
break;
case pinStyle.pinCorners:
if (i % width == (width - 1) && ((i) / width == length - 1) || i % width == 0 && ((i) / width == 0))
{
thisConfig.PinIndices.Add(i);
}
break;
}
}
}
/// <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");
}
}
public void SetParameters(ConfigParameters parameters)
{
if (parameters == null)
{
throw new ArgumentNullException(nameof(parameters));
}
min = parameters.MaybeGet <uint>("min");
max = parameters.MaybeGet <uint>("max");
minWidth = parameters.MaybeGet <uint>("minwidth");
maxWidth = parameters.MaybeGet <uint>("maxwidth");
minHeight = parameters.MaybeGet <uint>("minheight");
maxHeight = parameters.MaybeGet <uint>("maxheight");
}
public void SetParameters(ConfigParameters parameters)
{
if (parameters == null) {
throw new ArgumentNullException(nameof(parameters));
}
foreach (var v in parameters.GetValuesForKey("date")) {
DateTime min;
if (DateTime.TryParse(v, out min)) {
minDate = min;
}
}
}
public void SetParameters(ConfigParameters parameters)
{
if (parameters == null)
{
throw new ArgumentNullException(nameof(parameters));
}
long min;
if (parameters.TryGet("size", out min))
{
minSize = min * 1024 * 1024;
}
}
public void SetParameters(ConfigParameters parameters)
{
if (parameters == null) {
throw new ArgumentNullException(nameof(parameters));
}
var filters = from f in parameters.Keys
let e = Escape(f)
select e;
filter = new Regex(
string.Join("|", filters),
RegexOptions.Compiled | RegexOptions.IgnoreCase
);
NoticeFormat("Using filter {0}", filter.ToString());
}
/// <summary>
/// Gets the blast results from a given job ID.
/// If the job is not complete, this method will throw an exception.
/// </summary>
/// <param name="jobID">Job ID for which the blast results should be fetched.</param>
/// <returns>List of BlastResult.</returns>
public static IList<BlastResult> GetBlastResults(string jobID)
{
// Create the service provider
NCBIBlastHandler serviceProvider = new NCBIBlastHandler();
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
serviceProvider.Configuration = configParams;
// Check the job status
ServiceRequestInformation info = serviceProvider.GetRequestStatus(jobID);
if (info.Status != ServiceRequestStatus.Ready)
{
throw new InvalidOperationException("Blast search results are not yet ready!");
}
// Get the results back and parse it.
IBlastParser blastXmlParser = new BlastXmlParser();
return blastXmlParser.Parse(new System.IO.StringReader(serviceProvider.GetResult(jobID, GetBlastSearchParams())));
}
public void SetParameters(ConfigParameters parameters)
{
cascade = !parameters.Has("no-cascade") && parameters.Get("cascade", cascade);
}
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 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));
}
private static ConfigParameters GetConfigParameters(InterceptCallInfo info)
{
ConfigParameters cp = info.CallMethodInfo.CacheParameters;
if (cp == null)
{
info.CallMethodInfo.CacheParameters = cp = new ConfigParameters();
string[] ps = info.ConfigString.Split(';');
foreach (string p in ps)
{
string[] vs = p.Split('=');
if (vs.Length == 2)
{
switch (vs[0].ToLower().Trim())
{
case "maxcachetime": cp.MaxCacheTime = int. Parse(vs[1].Trim()); break;
case "isweak": cp.IsWeak = bool.Parse(vs[1].Trim()); break;
}
}
}
}
return cp;
}
/// <summary>
/// Validate Submit Job and Fetch ResultSync() using multiple input sequences
/// </summary>
/// <param name="nodeName">xml node name</param>
void ValidateFetchResultSync(string nodeName)
{
// Read input from config file
string filepath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string emailId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailIDNode);
string clusterOption = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ClusterOptionNode);
string actionAlign = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ActionAlignNode);
// Initialize with parser and config params
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler =
new TestIClustalWServiceHandler(clustalparser, configparams);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
IEnumerable<ISequence> sequence = null;
// Get the input sequences
using (FastAParser parser = new FastAParser(filepath))
{
sequence = parser.Parse();
// Submit job and validate it returned valid job id and control id
ServiceParameters svcparameters =
handler.SubmitRequest(sequence.ToList(), parameters);
Assert.IsFalse(string.IsNullOrEmpty(svcparameters.JobId));
ApplicationLog.WriteLine(string.Concat("JobId", svcparameters.JobId));
foreach (string key in svcparameters.Parameters.Keys)
{
Assert.IsFalse(string.IsNullOrEmpty(svcparameters.Parameters[key].ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "{0}:{1}",
key, svcparameters.Parameters[key].ToString()));
}
// Get the results and validate it is not null.
ClustalWResult result = handler.FetchResultsSync(svcparameters);
Assert.IsNotNull(result);
Assert.IsNotNull(result.SequenceAlignment);
foreach (IAlignedSequence alignSeq in result.SequenceAlignment.AlignedSequences)
{
ApplicationLog.WriteLine("Aligned Sequence Sequences :");
foreach (ISequence seq in alignSeq.Sequences)
{
ApplicationLog.WriteLine(string.Concat("Sequence:", seq.ToString()));
}
}
}
ApplicationLog.WriteLine(@"ClustalWServiceHandler BVT : Submit job and Get Results is successfully completed using FetchResultSync()");
}
/// <summary>
/// Validate submit job and Get Results using event handler
/// </summary>
/// <param name="nodeName">xml node name</param>
void ValidateFetchResultsUsingEvent(string nodeName)
{
// Read input from config file
string filepath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string emailId = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.EmailIDNode);
string clusterOption = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ClusterOptionNode);
string actionAlign = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ActionAlignNode);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
IEnumerable<ISequence> sequence = null;
// Get the input sequences
using (FastAParser parser = new FastAParser(filepath))
{
sequence = parser.Parse();
// Register event and submit request
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler =
new TestIClustalWServiceHandler(clustalparser, configparams);
handler.RequestCompleted +=
new EventHandler<ClustalWCompletedEventArgs>(handler_RequestCompleted);
ServiceParameters svcparams = handler.SubmitRequest(sequence.ToList(), parameters);
WaitHandle[] aryHandler = new WaitHandle[1];
aryHandler[0] = _resetEvent;
WaitHandle.WaitAny(aryHandler);
// Validate the submit job results
Assert.IsFalse(string.IsNullOrEmpty(svcparams.JobId));
foreach (string key in svcparams.Parameters.Keys)
{
Assert.IsFalse(string.IsNullOrEmpty(svcparams.Parameters[key].ToString()));
}
_resetEvent.Close();
_resetEvent.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();
}
}
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 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.");
}
}
}
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();
}
}
void ValidateCancelRequest(string nodeName)
{
// Read input from config file
string filepath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string emailId = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.EmailIDNode);
string clusterOption = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ClusterOptionNode);
string actionAlign = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.ActionAlignNode);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
IEnumerable<ISequence> sequence = null;
// Get the input sequences
using (FastAParser parser = new FastAParser(filepath))
{
sequence = parser.Parse();
// Submit job and cancel job
// Validate cancel job is working as expected
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler =
new TestIClustalWServiceHandler(clustalparser, configparams);
ServiceParameters svcparams = handler.SubmitRequest(sequence.ToList(), parameters);
bool result = handler.CancelRequest(svcparams);
Assert.IsTrue(result);
ApplicationLog.WriteLine(string.Concat("JobId:", svcparams.JobId));
Assert.IsFalse(string.IsNullOrEmpty(svcparams.JobId));
foreach (string key in svcparams.Parameters.Keys)
{
Assert.IsFalse(string.IsNullOrEmpty(svcparams.Parameters[key].ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "{0} : {1}",
key, svcparams.Parameters[key].ToString()));
}
}
ApplicationLog.WriteLine(
"ClustalWServiceHandler BVT : Cancel job is submitted as expected");
}
/// <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 submit job and FetchResultAsync() using multiple input sequences
/// </summary>
/// <param name="nodeName">xml node name</param>
void ValidateFetchResultAsync(string nodeName)
{
// Read input from config file
string filepath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string emailId = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.EmailIDNode);
string clusterOption = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ClusterOptionNode);
string actionAlign = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ActionAlignNode);
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler = new TestIClustalWServiceHandler(clustalparser, configparams);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
// Get input sequences
using (FastAParser parser = new FastAParser(filepath))
{
IEnumerable<ISequence> sequence = parser.Parse();
// Submit job and validate it returned valid job id and control id
ServiceParameters svcparameters = handler.SubmitRequest(sequence.ToList(), parameters);
Assert.IsFalse(string.IsNullOrEmpty(svcparameters.JobId));
foreach (string key in svcparameters.Parameters.Keys)
{
Assert.IsFalse(string.IsNullOrEmpty(svcparameters.Parameters[key].ToString()));
}
// Get the results and validate it is not null.
int retrycount = 0;
ServiceRequestInformation info;
do
{
info = handler.GetRequestStatus(svcparameters);
if (info.Status == ServiceRequestStatus.Ready)
{
break;
}
Thread.Sleep(
info.Status == ServiceRequestStatus.Waiting
|| info.Status == ServiceRequestStatus.Queued ?
Constants.ClusterRetryInterval * retrycount : 0);
retrycount++;
}
while (retrycount < 10);
ClustalWResult result = null;
if (info.Status == ServiceRequestStatus.Ready)
{
result = handler.FetchResultsAsync(svcparameters);
}
Assert.IsNotNull(result, "Failed to retrieve results from submitted task, Server may be offline or slow.");
Assert.IsNotNull(result.SequenceAlignment);
foreach (IAlignedSequence alignSeq in result.SequenceAlignment.AlignedSequences)
{
ApplicationLog.WriteLine("Aligned Sequence Sequences : ");
foreach (ISequence seq in alignSeq.Sequences)
{
ApplicationLog.WriteLine(string.Concat("Sequence:", seq.ToString()));
}
}
}
ApplicationLog.WriteLine(@"ClustalWServiceHandler BVT : Submit job and Get Results is successfully completed using FetchResultAsync()");
}
/// <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>
/// 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();
}
}
/// <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 ValidateBioHPCBlastWebServiceProperties()
{
ConfigParameters configParams = new ConfigParameters();
configParams.UseBrowserProxy = true;
BioHPCBlastHandler service = null;
try
{
service = new BioHPCBlastHandler(configParams);
// Validate BioHPC Blast Web Service properties.
Assert.AreEqual(Constants.BioHPCWebServiceDescription,
service.Description);
Assert.AreEqual(Constants.BioHPCWebServiceName,
service.Name);
Assert.IsNotNull(service.Configuration);
Assert.IsNotNull(service.Parser);
ApplicationLog.WriteLine(
"BioHPC Blast Bvt : Successfully validated the BioHPC Blast WebService Properties");
Console.WriteLine(
"BioHPC Blast Bvt : Successfully validated the BioHPC Blast WebService Properties");
}
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));
}
}
