Ejemplo n.º 1
0
        /// <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()");
        }
Ejemplo n.º 2
0
        /// <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;

            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);
                Console.WriteLine(string.Concat("JobId:", svcparams.JobId));
                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()));
                    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");
        }
Ejemplo n.º 3
0
        /// <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();
            }
        }
Ejemplo n.º 4
0
        /// <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()");
        }