/// <summary>
/// Submit the search request with the user supplied configuration parameters
/// and sequence. Implementation should make use of the Bio.IO formatters
/// to convert the sequence into the web interface compliant sequence format.
/// This method performs parameter validation and throw Exception on invalid input.
/// </summary>
/// <remarks>An exception is thrown if the request does not succeed.</remarks>
/// <param name="sequence">The sequence to search with</param>
/// <param name="parameters">Blast input parameters</param>
/// <returns>Request Identifier</returns>
public string SubmitRequest(ISequence sequence, BlastParameters parameters)
{
if (null == sequence)
{
throw new ArgumentNullException("sequence");
}
if (null == parameters)
{
throw new ArgumentNullException("parameters");
}
string requestIdentifier;
// Create blast client object if not created already or if connection string has changed.
if (blastClient == null || blastClient.Endpoint.Address.Uri != configuration.Connection)
{
InitializeBlastClient();
}
// Validate the Parameter
ParameterValidationResult valid = ValidateParameters(parameters);
if (!valid.IsValid)
{
throw new Exception(valid.ValidationErrors);
}
// Submit the job to server
BlastSerivceRequest blastRequest = GetRequestParameter(
sequence,
parameters);
try
{
requestIdentifier = blastClient.SubmitJob(blastRequest).ToString();
}
catch (FaultException <BlastFault> fault)
{
throw new Exception(fault.Message);
}
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
BlastThreadParameter threadParameter = new BlastThreadParameter(
requestIdentifier,
sequence,
parameters);
// Start the BackGroundThread to check the status of job
workerThread = new BackgroundWorker();
workerThread.WorkerSupportsCancellation = true;
workerThread.DoWork += new DoWorkEventHandler(ProcessRequestThread);
workerThread.RunWorkerCompleted += new RunWorkerCompletedEventHandler(CompletedRequestThread);
workerThread.RunWorkerAsync(threadParameter);
}
return(requestIdentifier);
}
/// <summary>
/// Process the request. This method takes care of executing the rest of the steps
/// to complete the blast search request in a background thread. Which involves
/// 1. Submit the job to server
/// 2. Ping the service with the request identifier to get the status of request.
/// 3. Repeat step 1, at "RetryInterval" for "RetryCount" till a "success"/"failure"
/// status.
/// 4. If the status is a "failure" raise an completed event to notify the user
/// with appropriate details.
/// 5. If the status "success". Get the output of search from server in xml format.
/// 6. Parse the xml and the framework object model.
/// 7. Raise the completed event and notify user with the output.
/// </summary>
/// <param name="sender">Client request NCBI Blast search</param>
/// <param name="argument">Thread event argument</param>
private void ProcessRequestThread(object sender, DoWorkEventArgs argument)
{
BlastThreadParameter threadParameter = (BlastThreadParameter)argument.Argument;
string requestIdentifier = threadParameter.RequestIdentifier;
try
{
ServiceRequestInformation requestInfo = new ServiceRequestInformation();
requestInfo.Status = ServiceRequestStatus.Queued;
int retryCount = 0;
do
{
requestInfo = GetRequestStatus(requestIdentifier);
if (requestInfo.Status == ServiceRequestStatus.Ready ||
requestInfo.Status == ServiceRequestStatus.Error ||
workerThread.CancellationPending)
{
break;
}
retryCount++;
Thread.Sleep(RetryInterval * retryCount);
}while (retryCount < RetryCount);
if (workerThread.CancellationPending)
{
argument.Cancel = true;
}
else
{
BlastRequestCompletedEventArgs eventArgument = null;
string message;
if (requestInfo.Status == ServiceRequestStatus.Ready)
{
string output = GetResult(
requestIdentifier,
threadParameter.Parameters);
IList <BlastResult> result = Parser.Parse(new StringReader(output));
eventArgument = new BlastRequestCompletedEventArgs(
requestIdentifier,
true,
result,
null,
string.Empty,
workerThread.CancellationPending);
argument.Result = eventArgument;
}
else if (requestInfo.Status == ServiceRequestStatus.Error)
{
message = String.Format(CultureInfo.InvariantCulture,
Resources.BLASTREQUESTFAILED,
requestIdentifier,
requestInfo.Status,
requestInfo.StatusInformation);
eventArgument = new BlastRequestCompletedEventArgs(
requestIdentifier,
false,
null,
new Exception(message),
message,
workerThread.CancellationPending);
argument.Result = eventArgument;
}
else
{
message = String.Format(CultureInfo.InvariantCulture,
Resources.BLASTRETRIESEXCEEDED,
requestIdentifier,
requestInfo.Status,
requestInfo.StatusInformation);
eventArgument = new BlastRequestCompletedEventArgs(
requestIdentifier,
false,
null,
new TimeoutException(message),
message,
workerThread.CancellationPending);
argument.Result = eventArgument;
}
}
}
catch (Exception ex)
{
BlastRequestCompletedEventArgs eventArgument = new BlastRequestCompletedEventArgs(
string.Empty,
false,
null,
ex,
ex.Message,
workerThread.CancellationPending);
argument.Result = eventArgument;
}
}
/// <summary>
/// Submit the search request with the user supplied configuration parameters and sequence
/// Implementation should make use of the Bio.IO formatters to convert the sequence into
/// the web interface compliant sequence format
/// </summary>
/// <remarks>An exception is thrown if the request does not succeed.</remarks>
/// <param name="sequences">List of sequence to search with</param>
/// <param name="parameters">Blast input parameters</param>
/// <returns>Request Identifier</returns>
public string SubmitRequest(IList <ISequence> sequences, BlastParameters parameters)
{
if (null == parameters)
{
throw new ArgumentNullException("parameters");
}
if (null != sequences)
{
StringBuilder sb = new StringBuilder();
foreach (ISequence seq in sequences)
{
sb.Append(FastAFormatter.FormatString(seq));
sb.Append("\n");
}
parameters.Add("Query", sb.ToString());
}
if (!string.IsNullOrEmpty(Configuration.EmailAddress))
{
if (!parameters.Settings.ContainsKey(PARAMETEREMAIL))
{
parameters.Add(PARAMETEREMAIL, Configuration.EmailAddress);
}
}
string requestIdentifier = string.Empty;
// Validate the Parameter
ParameterValidationResult valid = ValidateParameters(parameters);
if (!valid.IsValid)
{
throw new Exception(valid.ValidationErrors);
}
parameters.Add(PARAMETERCOMMAND, COMMANDPUT);
WebAccessor accessor = new WebAccessor();
WebAccessorResponse webAccessorResponse;
if (Configuration.UseBrowserProxy)
{
accessor.GetBrowserProxy();
}
webAccessorResponse = accessor.SubmitHttpRequest(
ServiceUri,
true, // do POST
parameters.Settings); // request parameters
if (!webAccessorResponse.IsSuccessful)
{
// failed
accessor.Close();
throw new Exception(String.Format(CultureInfo.InvariantCulture,
Resources.HTTPSUBMITFAILED,
webAccessorResponse.StatusDescription));
}
string info = ExtractInfoSection(webAccessorResponse.ResponseString);
if (!String.IsNullOrEmpty(info))
{
int ridStart = info.IndexOf("RID = ", StringComparison.OrdinalIgnoreCase);
if (ridStart >= 0)
{
ridStart += "RID = ".Length;
int ridEnd = info.IndexOf('\n', ridStart);
if (ridEnd >= 0)
{
requestIdentifier = info.Substring(ridStart, ridEnd - ridStart);
}
}
}
accessor.Close();
if (string.IsNullOrEmpty(requestIdentifier))
{
string message = String.Format(CultureInfo.InvariantCulture,
Resources.RIDEXTRACTFAILED,
ExtractError(webAccessorResponse.ResponseString));
throw new Exception(message);
}
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
BlastThreadParameter threadParameter = new BlastThreadParameter(
requestIdentifier,
null, // Sequence parameter is not used any where, hence passing null.
parameters);
// Start the BackGroundThread to check the status of job
workerThread = new BackgroundWorker();
workerThread.WorkerSupportsCancellation = true;
workerThread.DoWork += new DoWorkEventHandler(ProcessRequestThread);
workerThread.RunWorkerCompleted += new RunWorkerCompletedEventHandler(CompletedRequestThread);
workerThread.RunWorkerAsync(threadParameter);
}
return(requestIdentifier);
}
/// <summary>
/// Submit the search request with the user supplied configuration parameters and sequence list.
/// Implementation should make use of the Bio.IO formatters to convert the sequence into
/// the web interface compliant sequence format
/// </summary>
/// <remarks>An exception is thrown if the request does not succeed.</remarks>
/// <param name="sequences">List of sequence to search with</param>
/// <param name="parameters">Blast input parameters</param>
/// <returns>Unique Search ID generated by Bio</returns>
public string SubmitRequest(IList <ISequence> sequences, BlastParameters parameters)
{
if (sequences == null)
{
throw new Exception(Resources.BIOHPCNOSEQUENCE);
}
if (parameters == null)
{
throw new ArgumentNullException("parameters");
}
string requestIdentifier;
// Start of BioHPC-specific code
// we are submitting BLAST and give the job a name
tAppId appID = tAppId.P_BLAST;
string jobname = BlastParameters.Parameters["JobName"].DefaultValue;
if (parameters.Settings.ContainsKey(PARAMETERJOBNAME))
{
if (!String.IsNullOrEmpty(parameters.Settings[PARAMETERJOBNAME]))
{
jobname = parameters.Settings[PARAMETERJOBNAME];
}
}
if (parameters.Settings.ContainsKey(PARAMETEREMAIL))
{
if (string.IsNullOrEmpty(Configuration.EmailAddress))
{
Configuration.EmailAddress = parameters.Settings[PARAMETEREMAIL];
}
}
// initialize input parameters with defaults
AppInputData pars = blastClient.InitializeApplicationParams(appID, jobname);
// Retrieve database names for easy access by parameter validator
dnaDatabases = GetServiceMetadata(MetadataDatabasesDna);
protDatabases = GetServiceMetadata(MetadataDatabasesProt);
// Validate the parameter
ParameterValidationResult valid = ValidateParameters(parameters, pars);
if (!valid.IsValid)
{
throw new Exception(valid.ValidationErrors);
}
// ValidateParameters updated some of the entries in pars and put them
// into its ParametersObject - we need to fetch the updated pars
pars = valid.ParametersObject as AppInputData;
// Set some remaining parameters...
pars.blast.querysource = QuerySrcType.paste;
// We request XML as format, since this is what we can parse...
pars.blast.options.format = OutputFormat.XML;
// Query sequence should be in full Fasta format.
// We concatenate all the sequences from the list into a single string.
pars.blast.query = String.Empty;
foreach (ISequence auxseq in sequences)
{
pars.blast.query += FastAFormatter.FormatString(auxseq) + "\n";
}
pars.blast.query = pars.blast.query.Substring(0, pars.blast.query.Length - 1); // remobe trailing newline...
// Run parameters and query string are ready. Submit the job to server:
// Create a new BLAST job.
string jobid = String.Empty;
string cntrl = String.Empty;
try
{
string[] outtab = blastClient.CreateJob(appID, jobname, "1", Configuration.EmailAddress, Configuration.Password, "Auto");
if (outtab[0].IndexOf(MsgError, StringComparison.Ordinal) != -1)
{
throw new Exception(String.Format(CultureInfo.InvariantCulture, Resources.BIOHPCJOBNOTCREATED, outtab[0]));
}
jobid = outtab[1];
cntrl = outtab[2];
requestIdentifier = jobid + "_" + cntrl;
}
catch
{
throw new Exception(Resources.BIOHPCSERVERABSENT);
}
// Finally, we can submit the job
try
{
string result = blastClient.SubmitJob(jobid, cntrl, pars);
if (result.IndexOf(MsgError, StringComparison.Ordinal) != -1)
{
throw new Exception(String.Format(CultureInfo.InvariantCulture, Resources.BIOHPCJOBNOTSUBMITTED, jobid, result));
}
}
catch
{
throw new Exception(Resources.BIOHPCSERVERABSENT);
}
// end of BioHPC-specific code
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
// ThreadParameter wants a single sequence - nor sure what this is for.
// We'll give it the first sequence from the list, i.e., sequence[0]
BlastThreadParameter threadParameter = new BlastThreadParameter(
requestIdentifier,
sequences[0],
parameters);
// Start the BackGroundThread to check the status of job
workerThread = new BackgroundWorker();
workerThread.WorkerSupportsCancellation = true;
workerThread.DoWork += new DoWorkEventHandler(ProcessRequestThread);
workerThread.RunWorkerCompleted += new RunWorkerCompletedEventHandler(CompletedRequestThread);
workerThread.RunWorkerAsync(threadParameter);
}
return(requestIdentifier);
}
/// <summary>
/// Submit the search request with the user supplied configuration parameters and sequence
/// Implementation should make use of the Bio.IO formatters to convert the sequence into
/// the web interface compliant sequence format
/// </summary>
/// <remarks>An exception is thrown if the request does not succeed.</remarks>
/// <param name="sequences">List of sequence to search with</param>
/// <param name="parameters">Blast input parameters</param>
/// <returns>Request Identifier</returns>
public string SubmitRequest(IList <ISequence> sequences, BlastParameters parameters)
{
string emailAddress = string.Empty;
if (null == sequences)
{
throw new ArgumentNullException("sequences");
}
if (null == parameters)
{
throw new ArgumentNullException("parameters");
}
string tempEmail;
if (parameters.Settings.TryGetValue(ParameterEmail, out tempEmail) &&
!string.IsNullOrEmpty(tempEmail))
{
emailAddress = tempEmail;
}
string requestIdentifier = string.Empty;
// Validate the Parameter
ParameterValidationResult valid = ValidateParameters(parameters);
if (!valid.IsValid)
{
throw new Exception(valid.ValidationErrors);
}
// Submit the job to server
InputParameters blastRequest = GetRequestParameter(parameters);
StringBuilder seqBuilder = new StringBuilder();
foreach (ISequence sequence in sequences)
{
byte[] buffer = new byte[80];
int bufferIndex = 0, maxLineSize = 80;
seqBuilder.AppendLine(">" + sequence.ID);
for (long index = 0; index < sequence.Count; index += maxLineSize)
{
for (bufferIndex = 0; bufferIndex < maxLineSize && index + bufferIndex < sequence.Count; bufferIndex++)
{
buffer[bufferIndex] = sequence[index + bufferIndex];
}
string line = ASCIIEncoding.ASCII.GetString(buffer, 0, bufferIndex);
seqBuilder.AppendLine(line);
}
}
blastRequest.sequence = seqBuilder.ToString();
requestIdentifier = blastClient.run(emailAddress, string.Empty, blastRequest);
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
BlastThreadParameter threadParameter = new BlastThreadParameter(
requestIdentifier,
null,
parameters);
// Start the BackGroundThread to check the status of job
workerThread = new BackgroundWorker();
workerThread.WorkerSupportsCancellation = true;
workerThread.DoWork += new DoWorkEventHandler(ProcessRequestThread);
workerThread.RunWorkerCompleted += new RunWorkerCompletedEventHandler(CompletedRequestThread);
workerThread.RunWorkerAsync(threadParameter);
}
return(requestIdentifier);
}
/// <summary>
/// Submit the search request with the user supplied configuration parameters
/// and sequence. Implementation should make use of the Bio.IO formatters
/// to convert the sequence into the web interface compliant sequence format.
/// This method performs parameter validation and throw Exception on invalid input.
/// </summary>
/// <remarks>An exception is thrown if the request does not succeed.</remarks>
/// <param name="sequence">The sequence to search with</param>
/// <param name="parameters">Blast input parameters</param>
/// <returns>Request Identifier</returns>
public string SubmitRequest(ISequence sequence, BlastParameters parameters)
{
if (null == sequence)
{
throw new ArgumentNullException("sequence");
}
if (null == parameters)
{
throw new ArgumentNullException("parameters");
}
if (!string.IsNullOrEmpty(Configuration.EmailAddress))
{
if (!parameters.Settings.ContainsKey(ParameterEmail))
{
parameters.Add(ParameterEmail, Configuration.EmailAddress);
}
}
string requestIdentifier = string.Empty;
// Validate the Parameter
ParameterValidationResult valid = ValidateParameters(parameters);
if (!valid.IsValid)
{
throw new Exception(valid.ValidationErrors);
}
// Submit the job to server
inputParams blastRequest = GetRequestParameter(parameters);
blastRequest.appxml = AppXmlYes;
blastRequest.async = true;
data[] mydata = new data[1];
mydata[0] = new data();
mydata[0].type = SequenceType;
mydata[0].content = FastAFormatter.FormatString(sequence);
requestIdentifier = blastClient.runWUBlast(blastRequest, mydata);
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
BlastThreadParameter threadParameter = new BlastThreadParameter(
requestIdentifier,
sequence,
parameters);
// Start the BackGroundThread to check the status of job
workerThread = new BackgroundWorker();
workerThread.WorkerSupportsCancellation = true;
workerThread.DoWork += new DoWorkEventHandler(ProcessRequestThread);
workerThread.RunWorkerCompleted += new RunWorkerCompletedEventHandler(CompletedRequestThread);
workerThread.RunWorkerAsync(threadParameter);
}
return(requestIdentifier);
}