/// <summary>
/// Writes the reads to StandardOutput.
/// </summary>
/// <param name="reads">Reads to write.</param>
private static void WriteOutput(IEnumerable <ISequence> reads)
{
foreach (ISequence seq in reads)
{
Console.WriteLine(FastAFormatter.FormatString(seq));
}
}
/// <summary>
/// Get the blast service request object with all the request parameter set
/// </summary>
/// <param name="sequence">Input sequece</param>
/// <param name="parameters">Blast parameters</param>
/// <returns>Blast service request object</returns>
private static BlastSerivceRequest GetRequestParameter(
ISequence sequence,
BlastParameters parameters)
{
BlastSerivceRequest blastParameter = new BlastSerivceRequest();
// Sets the format of output expected from Azure Blast service
blastParameter.OptionM = OPTIONMVALUE;
// Sets the name of Job owner
blastParameter.Owner = Resources.OWNERVALUE;
blastParameter.ParitionNumber = PARTITIONVALUE;
// Convert string to byte
string inputContent = FastAFormatter.FormatString(sequence);
ASCIIEncoding asciiEncoding = new ASCIIEncoding();
blastParameter.InputContent = asciiEncoding.GetBytes(inputContent);
// Other parameters
// Set the Title of Job
blastParameter.Title = sequence.ID;
// Name of the database to be searched in
blastParameter.DatabaseName = parameters.Settings[PARAMETERDATABASE];
// Type of search program to be executed
blastParameter.ProgramName = parameters.Settings[PARAMETERPROGRAM];
return(blastParameter);
}
/// <summary>
/// CreateJob() to get job id and control id and Submit job
/// using input sequence with job id and control id
/// </summary>
/// <param name="sequence">input sequences</param>
/// <param name="parameters">input params</param>
/// <returns>result params with job id and control id</returns>
public ServiceParameters SubmitRequest(IList <ISequence> sequence, ClustalWParameters parameters)
{
ServiceParameters result = new ServiceParameters();
if (null == sequence)
{
throw new ArgumentNullException("Sequence");
}
if (null == parameters)
{
throw new ArgumentNullException("Parameters");
}
// ClusterOption = biosim cbsum1 cbsum2k8 cbsusrv05 cbsum2 or Auto
string[] output = _baseClient.CreateJob(tAppId.P_CLUSTALW, "test_BioHPC_Job", "1", parameters.Values[ClustalWParameters.Email].ToString(),
string.Empty, parameters.Values[ClustalWParameters.ClusterOption].ToString());
if (!output[0].Contains(ERROR))
{
result.JobId = output[1];
result.Parameters.Add(CONTROLID, output[2]);
AppInputData inputData = _baseClient.InitializeApplicationParams(tAppId.P_CLUSTALW, "test_BioHPC_Job");
StringBuilder inputSequence = new StringBuilder();
foreach (ISequence seq in sequence)
{
inputSequence.AppendLine(FastAFormatter.FormatString(seq));
}
inputData.clustalw.inputsource = QuerySrcType.paste;
inputData.clustalw.inputstring = inputSequence.ToString();
inputData.clustalw.isDNA = false;
inputData.clustalw.action = (ClwActions)Enum.Parse(typeof(ClwActions),
parameters.Values[ClustalWParameters.ActionAlign].ToString());
inputData.clustalw.email_notify = true;
_baseClient.SubmitJob(result.JobId, result.Parameters[CONTROLID].ToString(), inputData);
result.Parameters.Add(SUBMISSONRESULT, SUCCESS);
// Only if the event is registered, invoke the thread
if (null != RequestCompleted)
{
// 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(result);
}
}
else
{
result.Parameters.Add(SUBMISSONRESULT, output[0]);
}
return(result);
}
/// <summary>
/// Writes delta for query sequences.
/// </summary>
/// <param name="delta">The Deltas.</param>
private void WriteDelta(
IList<List<IEnumerable<DeltaAlignment>>> delta)
{
TextWriter textWriterConsoleOutSave = Console.Out;
if (!string.IsNullOrEmpty(this.OutputFile))
{
FileStream fileStreamConsoleOut = new FileStream(this.OutputFile, FileMode.Create);
StreamWriter streamWriterConsoleOut = new StreamWriter(fileStreamConsoleOut);
Console.SetOut(streamWriterConsoleOut);
streamWriterConsoleOut.AutoFlush = true;
}
foreach (var alignment in delta)
{
foreach (IEnumerable<DeltaAlignment> align in alignment)
{
foreach (DeltaAlignment deltaAlignment in align)
{
Console.WriteLine(
">" +
deltaAlignment.ReferenceSequenceId);
if (deltaAlignment.QuerySequence != null)
{
Console.WriteLine(FastAFormatter.FormatString(deltaAlignment.QuerySequence).Substring(1));
}
else
{
//To provide empty lines in place of query sequence id and query sequence
Console.WriteLine();
Console.WriteLine();
}
Console.WriteLine(
deltaAlignment.FirstSequenceStart + " " +
deltaAlignment.FirstSequenceEnd + " " +
deltaAlignment.SecondSequenceStart + " " +
deltaAlignment.SecondSequenceEnd + " " +
deltaAlignment.Errors + " " +
deltaAlignment.SimilarityErrors + " " +
deltaAlignment.NonAlphas);
foreach (long deltas in deltaAlignment.Deltas)
{
Console.WriteLine(deltas);
}
Console.WriteLine("*");
}
Console.WriteLine("--");
}
}
Console.SetOut(textWriterConsoleOutSave);
}
public void FastAFormatterInvalidateFormatString()
{
ISequence iSeq = null;
try
{
string formattedString = FastAFormatter.FormatString(iSeq);
Assert.Fail();
}
catch (ArgumentNullException ex)
{
ApplicationLog.Write("Fasta P2 : ArgumentNullException caught successfully. " + ex.Message);
}
}
/// <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.
/// 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);
}