/// <summary>
/// Gets the search results for the pertinent request identifier.
/// Implementation should have dedicated parsers to format the received results into Bio
/// </summary>
/// <remarks>An exception is thrown if the request does not succeed.</remarks>
/// <param name="requestIdentifier">Identifier for the request of interest.</param>
/// <param name="parameters">Blast input parameters</param>
/// <returns>The search results</returns>
public string GetResult(
string requestIdentifier,
BlastParameters parameters)
{
if (parameters == null)
{
throw new ArgumentNullException("parameters");
}
string status = string.Empty;
string information = string.Empty;
WebAccessor accessor = new WebAccessor();
WebAccessorResponse webAccessorResponse = null;
parameters.Add(PARAMETERCOMMAND, COMMANDGET);
parameters.Add(PARAMETERJOBID, requestIdentifier);
parameters.Add(PARAMETERFORMAT, FORMATXML);
if (Configuration.UseBrowserProxy)
{
accessor.GetBrowserProxy();
}
webAccessorResponse = accessor.SubmitHttpRequest(
ServiceUri,
true, // POST request
parameters.Settings);
if (!webAccessorResponse.IsSuccessful)
{
// failure
accessor.Close();
return(null);
}
accessor.Close();
information = ExtractInfoSection(webAccessorResponse.ResponseString);
if (!String.IsNullOrEmpty(information))
{
int statusStart = information.IndexOf("Status=", StringComparison.OrdinalIgnoreCase);
if (statusStart >= 0)
{
statusStart += "Status=".Length;
int statusEnd = information.IndexOf('\n', statusStart);
if (statusEnd >= 0)
{
status = information.Substring(statusStart, statusEnd - statusStart);
}
}
}
if (!string.IsNullOrEmpty(status))
{
if (status == STATUSWAITING)
{
return(null);
}
else
{
string message = String.Format(CultureInfo.InvariantCulture,
Resources.INVALIDNCBISTATUS,
status);
throw new Exception(message);
}
}
return(webAccessorResponse.ResponseString);
}
/// <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. 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)
{
parameters.Add("Query", sequence.ToString());
}
if (null == parameters)
{
throw new ArgumentNullException("parameters");
}
string requestIdentifier = string.Empty;
// Validate the Parameter
ParameterValidationResult valid = ValidateParameters(parameters);
if (!valid.IsValid)
{
throw new Exception(valid.ValidationErrors);
}
parameters.Add(PARAMETERCOMMAND, COMMANDPUT);
Stream responseStream = null;
string statusDescription = string.Empty;
WebAccessor accessor = new WebAccessor();
if (Configuration.UseBrowserProxy)
{
accessor.GetBrowserProxy();
}
if (!accessor.SubmitHttpRequest(
ServiceUri,
true, // do POST
parameters.Settings, // request parameters
out statusDescription,
out responseStream))
{
// failed
accessor.Close();
throw new Exception(String.Format(
Resource.HTTPSUBMITFAILED,
statusDescription));
}
string response = string.Empty;
using (StreamReader r = new StreamReader(responseStream))
{
response = r.ReadToEnd();
string info = ExtractInfoSection(response);
if (!String.IsNullOrEmpty(info))
{
int ridStart = info.IndexOf("RID = ");
if (ridStart >= 0)
{
ridStart += "RID = ".Length;
int ridEnd = info.IndexOf('\n', ridStart);
if (ridEnd >= 0)
{
requestIdentifier = info.Substring(ridStart, ridEnd - ridStart);
}
}
}
r.Close();
}
accessor.Close();
if (string.IsNullOrEmpty(requestIdentifier))
{
string message = String.Format(
Resource.RIDEXTRACTFAILED,
ExtractError(response));
throw new Exception(message);
}
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
ThreadParameter threadParameter = new ThreadParameter(
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>
/// Gets the search results for the pertinent request identifier.
/// Implementation should have dedicated parsers to format the received results into MBF
/// </summary>
/// <remarks>An exception is thrown if the request does not succeed.</remarks>
/// <param name="requestIdentifier">Identifier for the request of interest.</param>
/// <param name="parameters">Blast input parameters</param>
/// <returns>The search results</returns>
public string GetResult(
string requestIdentifier,
BlastParameters parameters)
{
Stream responseStream = null;
string status = string.Empty;
string response = string.Empty;
string information = string.Empty;
string statusDescription = string.Empty;
WebAccessor accessor = new WebAccessor();
parameters.Add(PARAMETERCOMMAND, COMMANDGET);
parameters.Add(PARAMETERJOBID, requestIdentifier);
parameters.Add(PARAMETERFORMAT, FORMATXML);
if (Configuration.UseBrowserProxy)
{
accessor.GetBrowserProxy();
}
if (!accessor.SubmitHttpRequest(
ServiceUri,
true, // POST request
parameters.Settings,
out statusDescription,
out responseStream))
{
// failure
accessor.Close();
return(null);
}
using (StreamReader r = new StreamReader(responseStream))
{
response = r.ReadToEnd();
r.Close();
}
accessor.Close();
information = ExtractInfoSection(response);
if (!String.IsNullOrEmpty(information))
{
int statusStart = information.IndexOf("Status=");
if (statusStart >= 0)
{
statusStart += "Status=".Length;
int statusEnd = information.IndexOf('\n', statusStart);
if (statusEnd >= 0)
{
status = information.Substring(statusStart, statusEnd - statusStart);
}
}
}
if (status != string.Empty)
{
if (status == STATUSWAITING)
{
return(null);
}
else
{
string message = String.Format(
Resource.INVALIDNCBISTATUS,
status);
throw new Exception(message);
}
}
return(response);
}
/// <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);
}