/// <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)
{
string resultUri = _blastClient.GetJobResult(new Guid(requestIdentifier));
WebAccessor accessor = new WebAccessor();
WebAccessorResponse webAccessorResponse = null;
if (Configuration.UseBrowserProxy)
{
accessor.GetBrowserProxy();
}
webAccessorResponse = accessor.SubmitHttpRequest(
new Uri(resultUri),
false, // POST request
new Dictionary <string, string>());
if (!webAccessorResponse.IsSuccessful)
{
// failure
accessor.Close();
return(null);
}
accessor.Close();
return(webAccessorResponse.ResponseString);
}
static void Main(string[] args)
{
int newSeriesCount = 0;
int updatedSeriesCount = 0;
var jsonStorageProvider = new JsonFileStorageProvider();
using (var sqlStorageProvider = new SqlStorageProvider())
{
UserActivity userActivity;
Index index;
if (Config.Storage.ReadFromStorage)
{
userActivity = jsonStorageProvider.ReadUserActivity();
index = jsonStorageProvider.ReadIndex();
// index = new Index();
}
else
{
userActivity = new UserActivity();
index = new Index();
}
// high-level tasks
using (var webAccessor = new WebAccessor())
{
var taskRunner = new TaskRunner(webAccessor);
taskRunner.LogIn();
// newSeriesCount = taskRunner.AddSeriesToIndex(index);
// updatedSeriesCount = taskRunner.UpdatesSeriesToIndex(index);
// taskRunner.AddGenresToIndex(index);
taskRunner.UpdateUserActivity(userActivity);
taskRunner.AddUserActivityToIndex(userActivity, index);
}
if (Config.Storage.WriteToStorage)
{
jsonStorageProvider.WriteIndex(index);
jsonStorageProvider.WriteUserActivity(userActivity);
sqlStorageProvider.WriteIndex(index);
}
}
Console.WriteLine("Added {0} new series, updated {1}", newSeriesCount, updatedSeriesCount);
Console.WriteLine("Press [Spacebar] to exit.");
while (Console.ReadKey().Key != ConsoleKey.Spacebar)
{
}
;
}
/// <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)
{
string resultUri = _blastClient.GetJobResult(new Guid(requestIdentifier));
Stream responseStream = null;
string statusDescription = string.Empty;
WebAccessor accessor = new WebAccessor();
if (Configuration.UseBrowserProxy)
{
accessor.GetBrowserProxy();
}
if (!accessor.SubmitHttpRequest(
resultUri,
false, // POST request
new Dictionary <string, string>(),
out statusDescription,
out responseStream))
{
// failure
accessor.Close();
return(null);
}
string response = string.Empty;
using (StreamReader r = new StreamReader(responseStream))
{
response = r.ReadToEnd();
r.Close();
}
accessor.Close();
return(response);
}
/// <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>
/// Return the status of a submitted job.
/// </summary>
/// <param name="requestIdentifier">Identifier for the request of interest.</param>
/// <returns>The status of the request.</returns>
public ServiceRequestInformation GetRequestStatus(string requestIdentifier)
{
string information = string.Empty;
string errorInformation = string.Empty;
WebAccessor accessor = new WebAccessor();
WebAccessorResponse webAccessorResponse = null;
ServiceRequestInformation status = new ServiceRequestInformation();
Dictionary <string, string> settings = new Dictionary <string, string>();
settings.Add(PARAMETERCMD, "GET");
settings.Add(PARAMETERRID, System.Web.HttpUtility.UrlEncode(requestIdentifier));
if (Configuration.UseBrowserProxy)
{
accessor.GetBrowserProxy();
}
webAccessorResponse = accessor.SubmitHttpRequest(
ServiceUri,
true,
settings);
if (!webAccessorResponse.IsSuccessful)
{
// failure
accessor.Close();
status.Status = ServiceRequestStatus.Error;
status.StatusInformation = webAccessorResponse.StatusDescription;
return(status);
}
webAccessorResponse.StatusDescription = string.Empty;
information = ExtractInfoSection(webAccessorResponse.ResponseString);
if (String.IsNullOrEmpty(information))
{
status.Status = ServiceRequestStatus.Error;
// see if we got an error message
errorInformation = ExtractBlastErrorSection(webAccessorResponse.ResponseString);
if (string.IsNullOrEmpty(errorInformation))
{
status.StatusInformation = "An unknown server error has occurred.";
}
else
{
status.StatusInformation = errorInformation;
}
return(status);
}
else
{
int statusStart = information.IndexOf("Status=", StringComparison.OrdinalIgnoreCase);
if (statusStart >= 0)
{
statusStart += "Status=".Length;
int statusEnd = information.IndexOf('\n', statusStart);
if (statusEnd >= 0)
{
webAccessorResponse.StatusDescription = information.Substring(statusStart, statusEnd - statusStart);
}
}
}
if (webAccessorResponse.StatusDescription == STATUSWAITING)
{
status.Status = ServiceRequestStatus.Waiting;
return(status);
}
else if (webAccessorResponse.StatusDescription == STATUSREADY)
{
status.Status = ServiceRequestStatus.Ready;
return(status);
}
status.Status = ServiceRequestStatus.Error;
status.StatusInformation = webAccessorResponse.StatusDescription;
return(status);
}
/// <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>
/// 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();
}
}
public void BeginAsyncRequestTest()
{
BlastParameters searchParams = new BlastParameters();
// fill in the BLAST settings:
searchParams.Add("Command", "Put");
searchParams.Add("Program", "blastn");
searchParams.Add("Expect", "1e-10");
searchParams.Add("CompositionBasedStatistics", "0");
string badDbName = "ThisDatabaseDoesNotExist";
searchParams.Add("Database", badDbName);
// test parameters
string sequence = @"GACGCCGCCGCCACCACCGCCACCGCCGCAGCAGAAGCAGCGCACCGCAGGAGGGAAG" +
"ATGCCGGCGGGGCACGGGCTGCGGGCGCGGACGGCGACCTCTTCGCGCGGCCGTTCCGCAAGAAGGGTTA" +
"CATCCCGCTCACCACCTACCTGAGGACGTACAAGATCGGCGATTACGTNGACGTCAAGGTGAACGGTG";
searchParams.Add("Query", sequence);
AutoResetEvent requestSubmitWait = new AutoResetEvent(false);
AsyncWebMethodRequest input = new AsyncWebMethodRequest(
new Uri("http://www.ncbi.nlm.nih.gov/blast/Blast.cgi"),
CredentialCache.DefaultCredentials,
searchParams.Settings,
BuildQueryString(searchParams.Settings),
SubmitRequestCompleted,
requestSubmitWait);
WebAccessor target = new WebAccessor();
target.BeginAsyncRequest(input);
WaitHandle.WaitAny(new WaitHandle[] { requestSubmitWait });
Assert.IsFalse(string.IsNullOrEmpty(requestIdentifier));
// query the status
Dictionary <string, string> settings = new Dictionary <string, string>();
settings.Add("CMD", "GET");
settings.Add("RID", HttpUtility.UrlEncode(requestIdentifier));
AutoResetEvent requestStatusWait = new AutoResetEvent(false);
input = new AsyncWebMethodRequest(
new Uri("http://www.ncbi.nlm.nih.gov/blast/Blast.cgi"),
CredentialCache.DefaultCredentials,
settings,
BuildQueryString(settings),
RequestStatusCompleted,
requestStatusWait);
target.BeginAsyncRequest(input);
WaitHandle.WaitAny(new WaitHandle[] { requestStatusWait });
bool ok = false;
if (status.Status != ServiceRequestStatus.Waiting && status.Status != ServiceRequestStatus.Ready)
{
if (status.StatusInformation.Contains(badDbName) &&
status.StatusInformation.Contains("No alias or index file found for nucleotide database"))
{
ok = true;
}
}
if (!ok)
{
Assert.Fail("Failed to find server error message for bad request. Info: " + status.StatusInformation);
}
}
/// <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)
{
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);
}
public TaskRunner(WebAccessor webAccessor)
{
this.WebAccessor = webAccessor;
}
