From 86375e9ce1c4a54a82816005fced123af39b4e77 Mon Sep 17 00:00:00 2001
From: zagganas <zagganas@athenarc.gr>
Date: Mon, 17 Jan 2022 19:17:59 +0000
Subject: [PATCH] Use TES for task execution

---
 components/RoCrateModal.php        |   8 +-
 components/RunFormWidget.php       |   3 +-
 controllers/SoftwareController.php | 422 ++++----------
 controllers/WorkflowController.php | 208 +------
 models/Software.php                | 885 ++++++++++++-----------------
 models/Workflow.php                |  57 +-
 scheduler_files/jobMonitor.py      | 262 ++++-----
 views/software/logs.php            |   5 +-
 views/software/run.php             |  39 +-
 web/js/software/logs.js            | 308 ++++------
 web/js/software/run-index.js       | 162 +-----
 11 files changed, 786 insertions(+), 1573 deletions(-)

diff --git a/components/RoCrateModal.php b/components/RoCrateModal.php
index 4387f68..0397c60 100644
--- a/components/RoCrateModal.php
+++ b/components/RoCrateModal.php
@@ -79,8 +79,8 @@ public static function addModal($jobid)
 			$fields=WorkflowInput::find()->where(['workflow_id'=>$software_id])->orderBy(['position'=> SORT_ASC])->all();
 			if (!empty($fields))
 			{
-				$fields=Workflow::getRerunFieldValues($jobid,$fields);
-				if ($fields==false)
+				$fields_tmp=Workflow::getRerunFieldValues($jobid,$fields);
+				if ($fields_tmp==false)
 				{
 					$fields=[];
 				}
@@ -90,7 +90,6 @@ public static function addModal($jobid)
 		
 		$model=RoCrate::find()->where(['jobid'=>$jobid])->one();
 
-		//print_r($history->jobid);
 		$disabled_fields=false;
 		if(!empty($model))
 		{
@@ -188,8 +187,7 @@ public static function addModal($jobid)
 		echo	'</div>';
 		echo "<div class='input-file-fields'>";
 		$i=0;
-		// print_r($history->jobid);
-		// exit(0);
+		
 		foreach ($fields as $field) 
 		{
 			
diff --git a/components/RunFormWidget.php b/components/RunFormWidget.php
index 197d255..c2472fc 100644
--- a/components/RunFormWidget.php
+++ b/components/RunFormWidget.php
@@ -61,13 +61,14 @@ public static function showOutputField($commandsDisabled,$outFolder,$username,$t
             $runType='workflow';
         }
         echo Html::hiddenInput('mountcaller',null ,['id'=>'mountcaller']);
+        $disabledBox=$commandsDisabled ? 'disabled-box' : '';
         ?>
         <div class="row">
                 <div class="col-md-12"> <h3>Output directory <i class="fa fa-question-circle question-symbol"  title="Select the folder where the output of the <?=$runType?> will be placed")> </i></h3> </div>
             </div>
             <div class="row">
                 <div class="col-md-12">     
-                    <?=Html::textInput('outFolder',$outFolder,['id' => 'outFolder','class'=>'mount-field','readonly'=>true,])?>
+                    <?=Html::textInput('outFolder',$outFolder,['id' => 'outFolder','class'=>"mount-field $disabledBox",'readonly'=>true,])?>
                     <?=Html::a("$select_icon Select",'javascript:void(0);',['class'=>'select-output-button btn btn-success btn-md','disabled'=>($commandsDisabled)])?>
                     <?=Html::a("$clear_icon Clear",'javascript:void(0);',['class'=>'clear-output-button btn btn-danger btn-md','disabled'=>($commandsDisabled)])?>
                 </div>
diff --git a/controllers/SoftwareController.php b/controllers/SoftwareController.php
index 5714c2a..29a6981 100644
--- a/controllers/SoftwareController.php
+++ b/controllers/SoftwareController.php
@@ -111,11 +111,6 @@ public function actions()
     public function actionIndex($selected_project='')
     {
     	
-    	 // $session = Yii::$app->session;
-   		 // $session->set('user_id', '1234');
-   		 // print_r($session['new_session']);
-   		 // exit(0);
-    	
         /**
          * If the user-data folder for the current user does not exist, 
          * create one
@@ -164,14 +159,6 @@ public function actionIndex($selected_project='')
                                       'images'=>$images, 'profiled'=>$profiled]);
     }
 
-    /* What the actual fuck is this???? */
-    // public function actionIsProfiled($name,$version)
-    // {
-    //     $profiled_value=Software::find()->select('profiled')->where(['name'=>$name])->andWhere(['version'=>$version])->scalar();
-    //     return $profiled_value;
-        
-    // }
-
     /**
      * Action to run a docker image uploaded in the system
      */
@@ -204,8 +191,7 @@ public function actionRun($name, $version)
 		}
 
         $software=Software::find()->where(['name'=>$name,'version'=>$version])->one();
-        $software_id=$software->id;
-        $software_instructions=$software->instructions;
+
         if (empty($software))
         {
             return $this->render('no_software',['name'=>$name,'version'=>$version]);
@@ -232,160 +218,39 @@ public function actionRun($name, $version)
          * or assign default values
          */
         $jobid=isset($_POST['jobid']) ? $_POST['jobid'] : '';
-        // $podid=isset($_POST['podid']) ? $_POST['podid'] : '';
-        $machineType=isset($_POST['machineType']) ? $_POST['machineType'] : '';
         $example=(isset($_POST['example']) && ($_POST['example']=="1")) ? true : false;
         $outFolder=(isset($_POST['outFolder'])) ? $_POST['outFolder'] : '';
 
-        /*
-         * contMount variables contain the mountpoints inside the container as specified during the addition process
-         * SystemMount variableσ contain the local path that will be mounted to the container.
-         */
-        // $containerMounts=$softwareModel::getContainerMountpoint($name,$version);
-        $icontMount=$software->imountpoint;
-        $ocontMount=$software->omountpoint;
-        $iocontMount='';
-        if ((!empty($icontMount)) && (!empty($ocontMount)))
-        {
-            if ($icontMount==$ocontMount)
-            {
-                $iocontMount=$icontMount;
-            }
-        }
-        // print_r($iocontMount);
-        // exit(0);
-
-        $isystemMountField=isset($_POST['isystemmount']) ? $_POST['isystemmount'] : '' ;
-        $osystemMountField=isset($_POST['osystemmount']) ? $_POST['osystemmount'] : '' ;
-        $iosystemMountField=isset($_POST['iosystemmount']) ? $_POST['iosystemmount'] : '' ;
-
-        if ($example)
-        {
-            $iosystemMountField='';
-            $isystemMountField='';
-            $osystemMountField='';
-            /*
-             * If iomount is empty, then see if imount and omount are filled
-             */
-            if (!empty($iocontMount))
-            {
-                $iosystemMountField='examples/' . $name . '/' . $version . '/io/';
-            }
-            else 
-            {
-                if (!empty($icontMount)) 
-                {
-                    $isystemMountField='examples/' . $name . '/' . $version . '/input/';
-                }
-                if (!empty($ocontMount)) 
-                {
-                    $osystemMountField='examples/' . $name . '/' . $version . '/output/';
-                }
-            }
-            
-        }
-
-
-        $iosystemMount='';
-        $isystemMount='';
-        $osystemMount='';
-        /*
-         * If iomount is empty, then see if imount and omount are fi
-         */
-        if (!empty($iocontMount))
-        {
-            $iosystemMount=Yii::$app->params['userDataPath'] . explode('@',$user)[0] . '/' . $iosystemMountField;
-        }
-        else 
-        {
-            if (!empty($icontMount)) 
-            {   
-                $isystemMount=Yii::$app->params['userDataPath'] . explode('@',$user)[0] . '/' . $isystemMountField;
-            }
-            if (!empty($ocontMount)) 
-            {
-                $osystemMount=Yii::$app->params['userDataPath'] . explode('@',$user)[0] . '/' . $osystemMountField;
-               
-            }
-        }
 
+        $username=User::getCurrentUser()['username'];
+        $homeFolder=Yii::$app->params['userDataPath'] . explode('@',$user)[0] . '/';
         
-        $mountpointExistError=false;
-        
-        
-        /*
-         * Check if i/o folders exist. If not, create them. Depends on whether there is one mountpoint for the 
-         */
-        
-        if (!empty($iocontMount))
+        if (!is_dir($homeFolder))
         {
-            if (!is_dir($iosystemMount))
-            {
-                Software::exec_log("mkdir -p $iosystemMount");
-                Software::exec_log("chmod 777 $iosystemMount");
-            }
-            else
-            {
-                Software::exec_log("chmod 777 $iosystemMount -R");
-            }
-
-        }
-        else
-        {
-            if (!empty($icontMount))
-            {
-                if (!is_dir($isystemMount))
-                {
-                    Software::exec_log("mkdir -p $isystemMount");
-                    Software::exec_log("chmod 777 $isystemMount");
-                }
-                else
-                {
-                    Software::exec_log("chmod 777 $isystemMount -R");
-                }
-            }
-            if (!empty($ocontMount))
-            {
-                // print_r($osystemMount);
-                // exit(0);
-                if (!is_dir($osystemMount))
-                {
-                    Software::exec_log("mkdir -p $osystemMount");
-                    Software::exec_log("chmod 777 $osystemMount");
-                }
-                else
-                {
-                    Software::exec_log("chmod 777 $osystemMount -R");
-                }
-            }
+            Software::exec_log("mkdir $homeFolder");
+            Software::exec_log("chmod 777 $homeFolder");
         }
+        $oSystemFolder=$outFolder;
+        $iSystemFolder='';
+
 
         if ($example)
         {
 
             $exampleFolder=Yii::$app->params['userDataPath']. 'examples/' . $name . '/' . $version . '/input';
-            if (!empty($iosystemMount))
-            {
-                $folder=$iosystemMount;
-            }
-            else
-            {
-                $folder=$isystemMount;
-            }
-            Software::exec_log("cp -r $exampleFolder/* $folder");
-            Software::exec_log("chmod 777 $folder");
+            $ifolder=$homeFolder . 'examples/' . $name . '/' . $version . '/input/';
+            $ofolder=$homeFolder . 'examples/' . $name . '/' . $version . '/output';
+            $iSystemFolder='examples/' . $name . '/' . $version . '/input/';
+            $oSystemFolder='examples/' . $name . '/' . $version . '/output/';
+            $outFolder=$oSystemFolder;
             
-        }
+            Software::exec_log("mkdir -p $ifolder $ofolder");
+            Software::exec_log("chmod 777 $ifolder");
+            Software::exec_log("chmod 777 $ofolder");
+            Software::exec_log("cp -r $exampleFolder/* $ifolder");
 
-        /*
-         * If pod is already running, get its ID
-         * by using the jobid and the name of the software
-         */
-
-        $podid=Software::runningPodIdByJob($name,$jobid);
-        // print_r($podid);
-        // exit(0);
-        
+            
+        }        
 
         /* 
          * Add parameters for the active form
@@ -408,8 +273,6 @@ public function actionRun($name, $version)
 
         $fields=SoftwareInput::find()->where(['softwareid'=>$software->id])->orderBy(['position'=> SORT_ASC])->all();
 
-         // print_r($fields);
-         // exit(0);
         /*
          * If the form has posted load the field values.
          * This was changed because it didn't work with checkboxes.
@@ -426,13 +289,11 @@ public function actionRun($name, $version)
 
         $superadmin=(User::hasRole("Admin", $superAdminAllowed = true)) ? 1 : 0;
 
-        $hasExample=$software->has_example;
-        $uploadedBy=$software->uploaded_by;
         /*
          * If the software uses the reference data stored in the shared folder
          * mount the shared folder to the pod
          */
-        $sharedFolder=($software->shared)? Yii::$app->params['sharedDataFolder']:'';
+        // $sharedFolder=($software->shared)? Yii::$app->params['sharedDataFolder']:'';
         /*
          * If the software uses gpus, pass the appropriate argument for execution
          * in the limits section
@@ -449,10 +310,17 @@ public function actionRun($name, $version)
             $field_count=0;
         }
 
+        /*
+         * $emptyFields is a variable that denotes whether all fields are empty.
+         */
         $emptyFields=true;
         
         for ($index=0; $index<$field_count; $index++)
         {
+            /*
+             * If the example is used, the fields values are not empty
+             * and values from the example are used
+             */
             if ($example)
             {
                 $emptyFields=false;
@@ -468,6 +336,13 @@ public function actionRun($name, $version)
             }
             else
             {
+                /*
+                 * If the field values are empty, assign 
+                 * empty values to each field. Boolean fields
+                 * get a false
+                 *
+                 * $emptyFields remains true
+                 */
                 if (empty($field_values))
                 {
                     if ($fields[$index]->field_type=='boolean')
@@ -480,13 +355,15 @@ public function actionRun($name, $version)
                     }
                     
                 }
+                /*
+                 * Add the value to each respective field.
+                 * For boolean values, strings are substituted
+                 */
                 else
                 {
                     $emptyFields=false;
                     if ($fields[$index]->field_type=='boolean')
                     {
-                        // print_r($field_values[$index]);
-                        // print_r("<br />");
                         $fields[$index]->value=($field_values[$index]=="0") ? false : true;
                     }
                     else
@@ -499,6 +376,10 @@ public function actionRun($name, $version)
 
         $container_command='';
         $errors=[];
+        /*
+         * If no inputs have been specified, 
+         * the script is run without additional arguments
+         */
         if (empty($fields))
         {
             /*
@@ -506,31 +387,29 @@ public function actionRun($name, $version)
              */
             if (Yii::$app->request->getIsPost())
             {
-                $script=$software->script;
-                $imountpoint=$icontMount;
-                $omountpoint=$ocontMount;
-                $iomountpoint=$iocontMount;
-                $container_command=$script;
+                $container_command=$software->script;
             }
         }
         else
         {
+            /*
+             * If values were provided for each field,
+             * create the command.
+             */
             if (!$emptyFields)
             {
                 $script=$software->script;
-                $imountpoint=$icontMount;
-                $omountpoint=$ocontMount;
-                $iomountpoint=$iocontMount;
-                $command_errors=Software::createCommand($script,$emptyFields,$fields,$imountpoint);
+                $ios=Software::getIOs($software,$fields,$iSystemFolder,$oSystemFolder);
+                $inputs=$ios[0];
+                $output=$ios[1];
+                $command_errors=Software::createCommand($software,$emptyFields,$fields);
                 $errors=$command_errors[0];
                 $container_command=$command_errors[1];
-                // print_r($container_command);
-                // exit(0);
             }
             else
             {
                 /*
-                 * Check if form has posted
+                 * Check if form has posted and post an error
                  */
                 if (Yii::$app->request->getIsPost())
                 {
@@ -544,8 +423,7 @@ public function actionRun($name, $version)
          * Get the user-data folder of the current user.
          * If it does not exist, then create it.
          */
-        $userFolder=Yii::$app->params['userDataPath'] . explode('@',User::getCurrentUser()['username'])[0];
-        $user=User::getCurrentUser()['username'];
+       
 
         /**
          * Get the available jobs by getting the quota from eg-ci and counting the jobs
@@ -555,8 +433,7 @@ public function actionRun($name, $version)
         
 
         if(empty($quotas) && (Yii::$app->params['standalone']==false))
-        {
-            
+        {          
             return $this->render('project_error',['project'=>$project]);
         }
         $quotas=$quotas[0];
@@ -576,13 +453,7 @@ public function actionRun($name, $version)
             ->count();
 
 
-        if (!is_dir($userFolder))
-        {
-            Software::exec_log("mkdir $userFolder");
-            Software::exec_log("chmod 777 $userFolder");
-        }
-        $runError='';
-        $runPodId='';
+        $runErrors='';
 
         /**
          * Get the maximum value for memory an cpu from the project if:
@@ -598,63 +469,51 @@ public function actionRun($name, $version)
         /*
          * Check if the pod for the current job ID is already running
          */
-        $podRunning=Software::isAlreadyRunning($podid);
-
+        $jobAlreadyRunning=Software::isAlreadyRunning($jobid);
 
+        $limits=['gpu'=>$gpu, 'cpu'=>$maxCores,'ram'=>$maxMem,'gpu'=>$gpu];
         /*
          * If the form has posted, it is not empty and the pod is not already running,
          * run the command for the specific docker image.
          */
-        if ((empty($errors)) && (!empty($container_command)) && ($podRunning==false) )
+        if ( (empty($errors)) && (!empty($container_command)) && (!$jobAlreadyRunning) )
         {
-            // print_r($οsystemMount);
-            // exit(0);
             
-            $jobid=uniqid();
-            $result=Software::createAndRunJob($container_command, $fields, 
-                                                $name, $version, $jobid, $user, 
-                                                $podid, $machineType, 
-                                                $isystemMount, $isystemMountField,
-                                                $osystemMount, $osystemMountField,
-                                                $iosystemMount, $iosystemMountField,
-                                                $project,$maxMem,$maxCores,$sharedFolder,$gpu);
-
-            $runPodId=$result[0];
-            $runError=$result[1];
-            $machineType=$result[2];
+            $software->container_command=$container_command;
+            $software->limits=$limits;
+            $software->inputs=$inputs;
+            $software->outputs=$output;
+            $software->user=$user;
+            $software->project=$project;
+            $software->fields=$fields;
+            $software->outFolder=$outFolder;
+
+            /*
+             * Send the job to TES
+             */
+            $software->runJob();
+
+            $jobid=$software->jobid;
+            $runErrors=$software->errors;
         }
 
         /*
          * If pod started without errors, then send its ID to the form.
          */
 
-        if ($runPodId!='')
-
-        {
-            $podid=$runPodId;
-        }
-
-        
-        $type=1;
 
-        return $this->render('run', ['form_params'=>$form_params, 'name'=>$name, 
-            'version'=>$version,  'jobid'=>$jobid, 'software_id'=>$software_id, 'software_instructions'=>$software_instructions,
-            'errors'=>$errors, 'runErrors'=>$runError, 'podid'=>$podid, 'machineType'=>$machineType,
-            'fields'=>$fields,'isystemMount' => $isystemMountField, 'osystemMount' => $osystemMountField,
-            'iosystemMount' => $iosystemMountField, 'example' => '0', 'hasExample'=>$hasExample,
-            'username'=>$user,'icontMount'=>$icontMount,'ocontMount'=>$ocontMount,
-            'iocontMount'=>$iocontMount,'mountExistError'=>false,
-            'superadmin'=>$superadmin,'uploadedBy'=>$uploadedBy,'jobUsage'=>$jobUsage,'quotas'=>$quotas,
-            'maxMem'=>$maxMem, 'maxCores'=>$maxCores, 'project'=>$project, 'type'=>$type, 'outFolder'=>$outFolder]);
+        return $this->render('run', ['form_params'=>$form_params, 'software'=>$software, 'example' => '0',
+            'errors'=>$errors, 'runErrors'=>$runErrors, 
+            'fields'=>$fields,  'username'=>$username, 'superadmin'=>$superadmin,'quotas'=>$quotas,
+            'maxMem'=>$maxMem, 'maxCores'=>$maxCores, 'type'=>1, 'outFolder'=>$outFolder]);
     }
 
     /*
      * Get logs from the running pod to show on the webpage
      */
-    public function actionGetLogs($podid,$machineType,$jobid)
+    public function actionGetLogs($jobid)
     {
-
-        $results=Software::getLogs($podid);
+        $results=Software::getLogs($jobid);
         $logs=$results[1];
         $status=$results[0];
         $time=$results[2];
@@ -662,18 +521,14 @@ public function actionGetLogs($podid,$machineType,$jobid)
 
         
 
-        return $this->renderPartial('logs',['logs'=>$logs, 'status'=>$status, 'machineType'=>$machineType,'time'=>$time,'project'=>$history->project]);
+        return $this->renderPartial('logs',['logs'=>$logs, 'status'=>$status, 'time'=>$time,'project'=>$history->project]);
     }
-
     /*
-     * Clean up job and delete pod from the system
+     * Cancel job
      */
-    public function actionCleanUp($name,$jobid,$status)
+    public function actionCancelJob($jobid)
     {
-        $model=new Software;
-
-        $results=$model::cleanUp($name,$jobid,$status);
-
+        Software::cancelJob($jobid);
     }
 
     /*
@@ -807,7 +662,6 @@ public function actionUploadExisting()
             /*
              * Get the files and fields
              */
-            // $model->imageFile=UploadedFile::getInstance($model, 'imageFile');
             $model->cwlFile=UploadedFile::getInstance($model, 'cwlFile');
             $model->dois=implode('|',$dois);
             /*
@@ -1019,20 +873,9 @@ public function actionHistory($crate_id='')
          */
         $user=User::getCurrentUser()['username'];
 
-
-        // $inactiveJobs=Software::getInactiveJobs();
-        // print_r($inactiveJobs);
-        // exit(0);
-        
-        // foreach ($inactiveJobs as $job)
-        // {
-        //     Software::cleanUp($job[0],$job[1],'Complete');
-
-        // }
         $available=Software::getAvailableSoftware();
 
         $available_workflows=Workflow::getAvailableWorkflows();
-        // $results=Software::getUserHistory($user);
         $query=RunHistory::find()->where(['username'=>$user])
         ->andWhere(['mpi_proc'=>null])
         ->orderBy(['start'=>SORT_DESC]);
@@ -1068,20 +911,14 @@ public function actionRerun($jobid)
          * or assign default values
          */
 
-        $podid='';
-        $machineType='';
         $name=$history->softname;
         $version=$history->softversion;
         $project=$history->project;
-        $isystemMountField=$history->imountpoint;
-        $osystemMountField=$history->omountpoint;
-        $iosystemMountField=$history->iomountpoint;
+        $outFolder=$history->omountpoint;
         $maxMem=$history->max_ram;
         $maxCores=$history->max_cpu;
-        $commands='';
 
         $software=Software::find()->where(['name'=>$name,'version'=>$version])->one();
-        $software_instructions=$software->instructions;
         $uploadedBy=$software->uploaded_by;
 
         $fields=SoftwareInput::find()->where(['softwareid'=>$software->id])->orderBy(['position'=> SORT_ASC])->all();
@@ -1094,38 +931,6 @@ public function actionRerun($jobid)
         {
             return $this->render('cwl_changed');
         }
-
-
-        $icontMount=$software->imountpoint;
-        $ocontMount=$software->omountpoint;
-        $iocontMount='';
-        if ((!empty($icontMount)) && (!empty($ocontMount)))
-        {
-            if ($icontMount==$ocontMount)
-            {
-                $iocontMount=$icontMount;
-            }
-        }
-
-        $mountExistError=false;
-        if (!empty($iosystemMountField))
-        {
-            $folder=Yii::$app->params['userDataPath'] . explode('@',User::getCurrentUser()['username'])[0] . '/' .$iosystemMountField;
-            if (!is_dir($folder))
-            {
-                $mountExistError=true;
-            }
-        }
-        else
-        {
-            $ifolder=Yii::$app->params['userDataPath'] . explode('@',User::getCurrentUser()['username'])[0] . '/' .$isystemMountField;
-            $ofolder=Yii::$app->params['userDataPath'] . explode('@',User::getCurrentUser()['username'])[0] . '/' .$osystemMountField;
-
-            if ( (!is_dir($ifolder)) || (!is_dir($ofolder)) )
-            {
-                $mountExistError=true;
-            }
-        }
         
 
         /* 
@@ -1143,7 +948,6 @@ public function actionRerun($jobid)
         ];
         
 
-        $hasExample=$software->has_example;
         $username=User::getCurrentUser()['username'];
         $superadmin=(User::hasRole("Admin", $superAdminAllowed = true)) ? 1 : 0;
         $quotas=Software::getOndemandProjectQuotas($username,$project);
@@ -1169,22 +973,15 @@ public function actionRerun($jobid)
             ->count();
         $type=1;
 
-        return $this->render('run', ['form_params'=>$form_params, 'name'=>$name, 
-            'version'=>$version,  'jobid'=>'',
-            'errors'=>'', 'runErrors'=>'', 'podid'=>'', 'machineType'=>'',
-            'fields'=>$fields,'isystemMount' => $isystemMountField, 'osystemMount' => $osystemMountField,
-            'iosystemMount' => $iosystemMountField, 'example' => '0', 
-            'hasExample'=>$hasExample, 'superadmin'=>$superadmin,
-            'username'=>$username,'icontMount'=>$icontMount,'ocontMount'=>$ocontMount,
-            'iocontMount'=>$iocontMount,'mountExistError'=>$mountExistError,
-            'jobUsage'=>$jobUsage,'quotas'=>$quotas,
-            'maxMem'=>$maxMem, 'maxCores'=>$maxCores, 'project'=>$project, 'software_instructions'=>$software_instructions, 'type'=>$type, 'uploadedBy'=>$uploadedBy]);
+        return $this->render('run', ['form_params'=>$form_params, 'software'=>$software, 'example' => '0',
+            'errors'=>'', 'runErrors'=>'', 
+            'fields'=>$fields,  'username'=>$username, 'superadmin'=>$superadmin,'quotas'=>$quotas,
+            'maxMem'=>$maxMem, 'maxCores'=>$maxCores, 'type'=>1, 'outFolder'=>$outFolder]);
     }
 
     public function actionReattach($jobid)
     {
 
-    	// $result=$softwareModel::getRerunData($jobid);
         
         $history=RunHistory::find()->where(['jobid'=>$jobid])->one();
         if (empty($history))
@@ -1199,27 +996,10 @@ public function actionReattach($jobid)
         $version=$history->softversion;
         $maxMem=$history->max_ram;
         $maxCores=$history->max_cpu;
-        $isystemMountField=$history->imountpoint;
-        $osystemMountField=$history->omountpoint;
-        $iosystemMountField=$history->iomountpoint;
-        $software=Software::find()->where(['name'=>$name])->andWhere(['version'=>$version])->one();
-        $software_instructions=$software->instructions;
-        $uploadedBy=$software->uploaded_by;
-        
-
-        $podid=Software::runningPodIdByJob($name,$jobid);
+        $outFolder=$history->omountpoint;
         $software=Software::find()->where(['name'=>$name,'version'=>$version])->one();
-        $icontMount=$software->imountpoint;
-        $ocontMount=$software->omountpoint;
-        $iocontMount='';
-        if ((!empty($icontMount)) && (!empty($ocontMount)))
-        {
-            if ($icontMount==$ocontMount)
-            {
-                $iocontMount=$icontMount;
-            }
-        }
-        
+        $software->jobid=$jobid;
+        $uploadedBy=$software->uploaded_by;
 
         /* 
          * Add parameters for the active form
@@ -1241,7 +1021,6 @@ public function actionReattach($jobid)
          */
         $fields=Software::getRerunFieldValues($jobid,$fields);
 
-        $hasExample=$software->has_example;
         $username=User::getCurrentUser()['username'];
         $superadmin=(User::hasRole("Admin", $superAdminAllowed = true)) ? 1 : 0;
         
@@ -1268,17 +1047,10 @@ public function actionReattach($jobid)
             ->count();
 
         $type=1;
-        
-        return $this->render('run', ['form_params'=>$form_params, 'name'=>$name, 
-            'version'=>$version,  'jobid'=>$jobid,
-            'errors'=>'', 'runErrors'=>'', 'podid'=>$podid, 'machineType'=>$machineType,
-            'fields'=>$fields,'isystemMount' => $isystemMountField, 'osystemMount' => $osystemMountField,
-            'iosystemMount' => $iosystemMountField, 'example' => '0', 
-            'hasExample'=>$hasExample, 'superadmin'=>$superadmin,
-            'username'=>$username,'icontMount'=>$icontMount,'ocontMount'=>$ocontMount,'iocontMount'=>$iocontMount,
-            'mountExistError'=>false,
-            'jobUsage'=>$jobUsage,'quotas'=>$quotas,
-            'maxMem'=>$maxMem, 'maxCores'=>$maxCores, 'project'=>$project, 'software_instructions'=>$software_instructions,'type'=>$type, 'uploadedBy'=>$uploadedBy]);
+        return $this->render('run', ['form_params'=>$form_params, 'software'=>$software, 'example' => '0',
+            'errors'=>'', 'runErrors'=>'', 
+            'fields'=>$fields,  'username'=>$username, 'superadmin'=>$superadmin,'quotas'=>$quotas,
+            'maxMem'=>$maxMem, 'maxCores'=>$maxCores, 'type'=>1, 'outFolder'=>$outFolder]);
 
 
     }
diff --git a/controllers/WorkflowController.php b/controllers/WorkflowController.php
index 2209201..d096988 100644
--- a/controllers/WorkflowController.php
+++ b/controllers/WorkflowController.php
@@ -222,8 +222,6 @@ public function actionRun($name, $version, $project)
         $jobid=isset($_POST['jobid']) ? $_POST['jobid'] : '';
         $example=(isset($_POST['example']) && ($_POST['example']=="1")) ? true : false;
         $outFolder=(isset($_POST['outFolder'])) ? $_POST['outFolder'] : '';
-        // print_r($outFolder);
-        // exit(0);
 
 
         if ($example)
@@ -378,8 +376,6 @@ public function actionRun($name, $version, $project)
                             $fields[$index]->dropdownValues[$item]=$item;
                         }
                         $fields[$index]->dropdownSelected=$fields[$index]->default_value;
-                        // print_r($fields[$index]->dropdownValues);
-                        // exit(0);
                     }
                     else
                     {
@@ -392,13 +388,9 @@ public function actionRun($name, $version, $project)
                  */
                 else
                 {
-                    // print_r($field_values);
-                    // exit(0);
                     $emptyFields=false;
                     if ($fields[$index]->field_type=='boolean')
                     {
-                        // print_r($field_values[$index]);
-                        // print_r("<br />");
                         $fields[$index]->value=($field_values[$index]=="0") ? false : true;
                     }
                     else if ($fields[$index]->field_type=='enum')
@@ -500,17 +492,13 @@ public function actionRun($name, $version, $project)
         $maxMem=(!isset($_POST['memory'])) || (empty($_POST['memory'])) || floatval($_POST['memory'])<=0 || (floatval($_POST['memory']) > floatval($quotas['ram'])) ? floatval($quotas['ram']) : floatval($_POST['memory']);
         $maxCores=(!isset($_POST['cores'])) || (empty($_POST['cores'])) || floatval($_POST['cores'])<=0 || (floatval($_POST['cores']) > floatval($quotas['cores'])) ? floatval($quotas['cores']) : floatval($_POST['cores']);
 
-        /*
-         * Check if the workflow for the current ID is already running
-         */
-        $workflowRunning=Software::isAlreadyRunning($jobid);
-
-
+        $workflowAlreadyRunning=Workflow::isAlreadyRunning($jobid);
+        
         /*
          * If the form has posted, it is not empty and the pod is not already running,
          * run the command for the specific docker image.
          */
-        if ((empty($errors)) && ($workflowRunning==false) &&  (!empty($workflowParams)))
+        if ((empty($errors)) && (!$workflowAlreadyRunning) && (!empty($workflowParams)))
         {
             /*
              * reset jobid because it might be filled from a previous submission
@@ -553,13 +541,8 @@ public function actionGetLogs($jobid)
         $time=$results[0];
         $history=RunHistory::find()->where(['jobid'=>$jobid])->one();
         $project=$history->project;
-        // print_r($history->project);
-        // exit(0);
-
-        //Workflow::checkStatus($status, $history)
 
         return $this->renderPartial('logs',['taskLogs'=>$taskLogs, 'status'=>$status, 'time'=>$time, 'project'=>$project]);
-        // return $this->render('logs',['taskLogs'=>$taskLogs, 'status'=>$status, 'time'=>$time]);
     }
 
     /*
@@ -607,10 +590,6 @@ public function actionCleanUp($name,$jobid,$status)
             return;
         }
 
-        $model=new Software;
-
-        $results=$model::cleanUp($name,$jobid,$status);
-
     }
 
     /*
@@ -1114,8 +1093,14 @@ public function actionReattach($jobid)
          * or assign default values
          */
 
+        $errors=[];
         $results=Workflow::getLogs($jobid);
-        Workflow::checkStatus($results[1], $history);
+        if (isset($results['error']))
+        {
+            $jobid=$results['jobid'];
+            $errors[]=$results['error'];
+        }
+        // Workflow::checkStatus($results[1], $history);
 
         $name=$history->softname;
         $version=$history->softversion;
@@ -1134,8 +1119,6 @@ public function actionReattach($jobid)
          */
         $fields=Workflow::getRerunFieldValues($jobid,$fields);            
 
-
-        // $mountExistError=false;
         if (!empty($outFolder))
         {
             $folder=Yii::$app->params['userDataPath'] . explode('@',User::getCurrentUser()['username'])[0] . '/' .$outFolder;
@@ -1149,9 +1132,6 @@ public function actionReattach($jobid)
                 Software::exec_log($command,$out,$ret);
             }
         }
-        
-        // print_r($outFolder);
-        // exit(0);
 
         /* 
          * Add parameters for the active form
@@ -1198,7 +1178,7 @@ public function actionReattach($jobid)
 
         return $this->render('run', ['form_params'=>$form_params, 'name'=>$name, 
             'version'=>$version,  'jobid'=>$jobid, 
-            'errors'=>'', 'runErrors'=>'','fields'=>$fields,
+            'errors'=>$errors, 'runErrors'=>'','fields'=>$fields,
             'example' => '0', 'hasExample'=>$hasExample,
             'username'=>$username,'superadmin'=>$superadmin,'uploadedBy'=>$uploadedBy,'jobUsage'=>$jobUsage,'quotas'=>$quotas,
             'maxMem'=>$maxMem, 'maxCores'=>$maxCores, 'project'=>$project,'outFolder' => $outFolder, 'workflow_instructions'=>$workflow_instructions, 'type'=>$type, 'visualize'=>$visualize]);
@@ -1213,10 +1193,6 @@ public function actionDownloadFiles($name,$version)
         $filepath=$workflow->original_file;
         $fileexploded=explode('/',$filepath);
         $filename=end($fileexploded);
-        // print_r($filename);
-        // print_r("<br />");
-        // print_r($filepath);
-        // exit(0);
 
         return Yii::$app->response->sendFile($filepath,$filename);
     }
@@ -1264,38 +1240,18 @@ public function actionAddExample($name,$version)
         $valueErrors=[];
         if (Yii::$app->request->getIsPost())
         {
-            // print_r($_FILES);
-            // exit(0);
             $folder=Yii::$app->params['userDataPath'] . '/workflow_examples/' . $name . '/' . $version . '/input/';
             $fieldPath='workflow_examples/' . $name . '/' . $version . '/input/';
-            // print_r($folder);
-            // exit(0);
+
             $command="mkdir -p $folder";
             Software::exec_log($command,$output,$ret);
 
             $command="chmod 777 $folder";
             Software::exec_log($command,$output,$ret);
 
-            // $i=0;
-            // $j=0;
-            // $k=0;
+
             $values=[];
 
-            // print_r($_FILES);
-            // print_r("<br />");
-            // print_r($_POST);
-            // exit(0);
-            // $fieldValues=isset($_POST['field_values']) ? $_POST['field_values'] : [];
-            // print_r($_FILES['field_values']);
-            // exit(0);
-            // $fileNames=$_FILES['field_values']['name'];
-            // $tmpFiles=$_FILES['field_values']['tmp_name'];
-            // print_r($_POST);
-            // exit(0);
-            // print_r($fileNames);
-            // print_r("<br />");
-            // print_r($tmpFiles);
-            // exit(0);
 
             if (!empty($fields))
             {
@@ -1430,144 +1386,6 @@ public function actionAddExample($name,$version)
         return $this->render('add_example',[ 'fields' => $fields, 'name'=>$name, 'version'=>$version, 'valueErrors'=>$valueErrors]);
     }
 
-
-
-
-    public function actionJobDetails($jobid)
-    {
-
-        // $softwareModel=new Software;
-        $result=Software::getJobDetails($jobid);
-        if (empty($result))
-        {
-            return $this->render('job_not_found',['jobid'=>$jobid]);
-        }
-
-        $machineType=$result['machinetype'];
-        $status=empty($result['status']) ? 'Running' : $result['status'];
-        $start=date("F j, Y, H:i:s",strtotime($result['start']));
-        $stop=empty($result['stop']) ? 'Not available yet' : date("F j, Y, H:i:s",strtotime($result['stop']));     
-        $isystemMountField=$result['imountpoint'];
-        $osystemMountField=$result['omountpoint'];
-        $iosystemMountField=$result['iomountpoint'];
-        if(empty($result['stop']))
-        {
-            $totalExecutionTime='Not available yet';  
-        }
-        else
-        {
-            $totalExecutionTime=date("H:i:s",(strtotime($stop)-strtotime($start)));
-        }
-
-        $maxRam=empty($result['ram']) ? 'Not available' : $result['ram'];
-        $maxCpu=empty($result['cpu']) ? 'Not available' : $result['cpu']/1000;
-
-       
-       // rint_r(strtotime($stop));
-       // print_r("");
-       // print_r(strtotime($start));
     
-             
-
-        // $rows=[
-        //     'Software name' => $result['softname'],
-        //     'Software version' => $result['softversion'],
-        //     'Status'=> $status,
-        //     'Started on'=>$start,
-        //     'Stopped on' => $stop,
-        //     'Total execution time' => $totalExecutionTime,
-        //     'Maximum memory footprint (GB)' => $maxRam,
-        //     'Maximum CPU load (cores)' => $maxCpu,
-        //     'Machine Type' => $machineType,
-        // ];
-
-        // if (!empty($iosystemMountField))
-        // {
-        //     $rows['I/O Mountpoint']=$iosystemMountField;
-        // }
-        // else
-        // {
-        //     if (!empty($isystemMountField))
-        //     {
-        //         $rows['Input Mountpoint']=$isystemMountField;
-        //     }
-
-        //     if (!empty($osystemMountField))
-        //     {
-        //         $rows['Output Mountpoint']=$osystemMountField;
-        //     }
-        // }
-
-        return $this->render('job_details',['name'=>$result['softname'],'version'=>$result['softversion'],
-                                            'status'=>$status, 'start'=>$start, 'stop'=>$stop, 'execTime'=>$totalExecutionTime,
-                                            'ram'=>$maxRam,'cpu'=>$maxCpu,'machineType' =>$machineType,
-                                            'iomount'=>$iosystemMountField, 'imount'=>$isystemMountField, 'omount'=>$osystemMountField,
-                                            'jobid'=>$jobid,
-                                            ]);
-
-
-    }
-
-
-    public function actionUserStatistics()
-    {
-
-        $softwareModel=new Software;
-        $user=User::getCurrentUser()['username'];
-        $projectTotals=$softwareModel::getUserStatistics($user);
-        $projectAggr=$softwareModel::getUserStatisticsPerProject($user);
-        $quotas=Software::getActiveProjectQuotas($user);
-      //  $tim=str_replace(":", "," , $result[2]);
-      //  $time=str_replace("," , "." , $result[2]);
-       
-        
-        
-
-         // print_r($result);
-         // exit(0);
-
-        // $rows=[
-        //     'Number of jobs'=>$result[0],
-        //     'Number of completed jobs'=>$result[1],
-        //     // 'Started on'=>$start,
-        //     // 'Stopped on' => $stop,
-        //     'Total execution time (in hours)' => $result[2],
-        //     'Average memory footprint (GB)' => $result[3],
-        //     'Average CPU load (cores)' => round($result[4])/1000,
-            
-        // ];
-
-      
-        
-        return $this->render('user_statistics',['projectTotals'=>$projectTotals,'projectAggr'=>$projectAggr, 'quotas'=>$quotas]);       
-              
-
-    }
-
-    public function actionImageDescription($name,$version)
-    {
-        $model=Software::find()->where(['name'=>$name, 'version'=>$version])->one();
-
-        return $this->renderAjax('image_description',['model'=>$model]);
-    }
-
-    public function actionDownloadLogs($jobid)
-    {
-        $filepath=Yii::$app->params['tmpFolderPath'] . $jobid . '/logs.txt';
-        $filename='logs.txt';
-        // print_r($filename);
-        // print_r("<br />");
-        // print_r($filepath);
-        // exit(0);
-        if (file_exists($filepath))
-        {
-            return Yii::$app->response->sendFile($filepath,$filename);
-        }
-        else
-        {
-            return false;
-        }
-        
-    }
     
 }
diff --git a/models/Software.php b/models/Software.php
index 204c0d2..72e6d62 100644
--- a/models/Software.php
+++ b/models/Software.php
@@ -54,7 +54,17 @@
 class Software extends \yii\db\ActiveRecord
 {
 
-    /**
+    public $container_command=[];
+    public $fields=[];
+    public $inputs=[];
+    public $outputs=[];
+    public $limits=[];
+    public $project='';
+    public $user='';
+    public $errors=[];
+    public $jobid='';
+    public $outFolder='';
+    /*
      * {@inheritdoc}
      */
     public static function tableName()
@@ -116,8 +126,6 @@ public static function getSoftwareNames($softUser)
             $query->where(['visibility'=>'public'])
                   ->orWhere(['and',['visibility'=>'private','uploaded_by'=>$softUser]]);
         }
-        // echo $query->createCommand()->getRawSql();
-        // exit(0);
 
         $rows=$query->all();
         $results=[];
@@ -148,16 +156,11 @@ public static function getSoftwareNames($softUser)
                 }
                     
             }
-            // $results[$name][$uploader][$version[0]]=$visibility;
         }
-        
-        // print_r($results);
-        // exit(0);
 
         
         return $results;
 
-        // return $rows;
     }
 
     
@@ -281,8 +284,8 @@ public static function getSoftwareDescriptions($softUser)
             $query->where(['visibility'=>'public'])
                   ->orWhere(['and',['visibility'=>'private','uploaded_by'=>$softUser]]);
         }
-        // echo $query->createCommand()->getRawSql();
-        // exit(0);
+        
+
 
         $rows=$query->all();
         $results=[];
@@ -292,16 +295,11 @@ public static function getSoftwareDescriptions($softUser)
             $version=$row['version'];
             $description=$row['description'];
             $results[]=['name'=>$name, 'version'=>$version, 'description'=>$description];
-            // $results[$name][$uploader][$version[0]]=$visibility;
         }
         
-        // print_r($results);
-        // exit(0);
-
         
         return $results;
 
-        // return $rows;
     }
 
     public static function getAvailableSoftware()
@@ -311,8 +309,6 @@ public static function getAvailableSoftware()
         $query->select('id,name,version,mpi')
               ->where(['mpi'=>false])
               ->from('software');
-        // echo $query->createCommand()->getRawSql();
-        // exit(0);
 
         $rows=$query->all();
         $results=[];
@@ -330,7 +326,6 @@ public static function getAvailableSoftware()
         }
         
         return $results;
-        // return $rows;
     }
 
     public static function getIndicators($softUser)
@@ -420,55 +415,48 @@ public static function getSoftwarePreviousCwl($name, $version)
    
 
 
-    public static function getContainerMountpoint($name, $version)
-    {
-        $query=new Query;
+    // public static function getContainerMountpoint($name, $version)
+    // {
+    //     $query=new Query;
 
-        $query->select(['imountpoint','omountpoint'])
-              ->from('software ')
-              ->where(['name'=>$name, 'version'=>$version]);
-        $rows=$query->one();
+    //     $query->select(['imountpoint','omountpoint'])
+    //           ->from('software ')
+    //           ->where(['name'=>$name, 'version'=>$version]);
+    //     $rows=$query->one();
         
-        $imount=$rows['imountpoint'];
-        $omount=$rows['omountpoint'];
+    //     $imount=$rows['imountpoint'];
+    //     $omount=$rows['omountpoint'];
 
-        $iomount='';
+    //     $iomount='';
         
-        if ((!empty($imount)) && (!empty($omount)))
-        {
-            if ($imount==$omount)
-            {
-                $iomount=$imount;
-            }
-        }
+    //     if ((!empty($imount)) && (!empty($omount)))
+    //     {
+    //         if ($imount==$omount)
+    //         {
+    //             $iomount=$imount;
+    //         }
+    //     }
 
-        // print_r($iomount);
-        // print_r("<br />");
-        // print_r($imount);
-        // print_r("<br />");
-        // print_r($omount);
-        // print_r("<br />");
-        // exit(0);
         
-        return [$imount, $omount, $iomount];
-    }
+    //     return [$imount, $omount, $iomount];
+    // }
 
 
-    public static function getUserHistory($softUser)
-    {
-        $query=new Query;
+    // public static function getUserHistory($softUser)
+    // {
+    //     $query=new Query;
 
-        $query->select(['start','stop','command','status','softname', 'softversion','jobid', 'ram', 'cpu', 'machinetype', 'project','software_id'])
-              ->from('run_history')
-              ->where(['username'=>$softUser]);
+    //     $query->select(['start','stop','command','status','softname', 'softversion','jobid', 'ram', 'cpu', 'machinetype', 'project','software_id'])
+    //           ->from('run_history')
+    //           ->where(['username'=>$softUser]);
 
-        $pages = new Pagination(['totalCount' => $query->count()]);
-        $pages->setPageSize(10);
+    //     $pages = new Pagination(['totalCount' => $query->count()]);
+    //     $pages->setPageSize(10);
         
-        $results = $query->orderBy('start DESC')->offset($pages->offset)->limit($pages->limit)->all();
+    //     $results = $query->orderBy('start DESC')->offset($pages->offset)->limit($pages->limit)->all();
 
-        return [$pages,$results];
-    }
+    //     return [$pages,$results];
+    // }
 
     
 
@@ -476,62 +464,113 @@ public static function getUserHistory($softUser)
      * If the user has uploaded a CWL file, 
      * then get the custom form fields.
      */
-    public static function getSoftwareFields($name,$version)
-    {
-        $query=new Query;
-
-        $query->select('si.name, si.position, si.field_type, si.prefix, si.default_value, si.optional, si.separate si.example') 
-              ->from('software sf')
-              ->join('INNER JOIN', 'software_inputs si', 'si.softwareid=sf.id')
-              ->where(['sf.name'=>$name, 'sf.version'=>$version])
-              ->orderBY(['si.position'=>SORT_ASC]);
-        $rows=$query->all();
-
-        return $rows;
-    }
+    // public static function getSoftwareFields($name,$version)
+    // {
+    //     $query=new Query;
+
+    //     $query->select('si.name, si.position, si.field_type, si.prefix, si.default_value, si.optional, si.separate si.example') 
+    //           ->from('software sf')
+    //           ->join('INNER JOIN', 'software_inputs si', 'si.softwareid=sf.id')
+    //           ->where(['sf.name'=>$name, 'sf.version'=>$version])
+    //           ->orderBY(['si.position'=>SORT_ASC]);
+    //     $rows=$query->all();
+
+    //     return $rows;
+    // }
     /*
      * If the user has uploaded a CWL file, 
      * then get the docker image script name.
      */
-    public static function getScript($name,$version)
+    // public static function getScript($name,$version)
+    // {
+    //     $query=new Query;
+
+    //     $query->select('script, imountpoint,omountpoint')
+    //           ->from('software')
+    //           ->where(['name'=>$name, 'version'=>$version]);
+    //     $path=$query->one();
+
+    //     $imount=$path['imountpoint'];
+    //     $omount=$path['omountpoint'];
+    //     $iomount='';
+    //     if ((!empty($imount)) || (empty($omount)))
+    //     {
+    //         if ($imount==$omount)
+    //         {
+    //             $iomount=$imount;
+    //         }
+    //     }
+
+    //     return [$path['script'],$imount,$omount,$iomount];
+    // }
+    public static function getIOs($software,$fields,$iSystemFolder,$oSystemFolder)
     {
-        $query=new Query;
+        $userFolder=Yii::$app->params['userDataPath'] . explode('@',User::getCurrentUser()['username'])[0];
+        $ofolder=$userFolder . '/' . $oSystemFolder;
+        if (!is_dir($ofolder))
+        {
+            self::exec_log("mkdir -p $ofolder");
+            self::exec_log("chmod 777 $ofolder");
+        }
+        /*
+         * We installed schema on a server instead of deploying with helm
+         * and our FTP is jailed, with the root being the user-data folder.
+         * Change does not affect helm deployments, because the parameter does not exist.
+         */
+        if (isset(Yii::$app->params['ftpJailPath']) and (!empty(Yii::$app->params['ftpJailPath'])))
+        {
+            $userFolder=str_replace(Yii::$app->params['ftpJailPath'],'',$userFolder);
+        }
 
-        $query->select('script, imountpoint,omountpoint')
-              ->from('software')
-              ->where(['name'=>$name, 'version'=>$version]);
-        $path=$query->one();
+        /*
+         * Prepare output directory location.
+         */
 
-        $imount=$path['imountpoint'];
-        $omount=$path['omountpoint'];
-        $iomount='';
-        if ((!empty($imount)) || (empty($omount)))
+        $url= "ftp://" . Yii::$app->params['ftpIp'] . '//' . $userFolder . '/' . $oSystemFolder;
+        $outputs=[['type'=>'DIRECTORY','path'=>$software->omountpoint,'url'=>$url]];
+        $inputs=[];
+        foreach ($fields as $field)
         {
-            if ($imount==$omount)
+            if (($field->field_type!='Directory') && ($field->field_type!='File'))
             {
-                $iomount=$imount;
+                continue;
+            }
+            $input=[];
+            if ($field->field_type=='Directory')
+            {
+                $url="ftp://" . Yii::$app->params['ftpIp'] . '//' . $userFolder . '/' . $iSystemFolder . $field->value;
+                $path=$software->imountpoint;
+                $type='DIRECTORY';
             }
+            else
+            {
+                $url="ftp://" . Yii::$app->params['ftpIp'] . '//' . $userFolder . '/'  . $iSystemFolder . $field->value;
+                $filename=explode('/',$field->value);
+                $filename=end($filename);
+                $path=$software->imountpoint . '/' . $filename;
+                $type='FILE';
+            }
+            $inputs[]=['type'=>$type,'path'=>$path,'url'=>$url];
         }
 
-        return [$path['script'],$imount,$omount,$iomount];
+        return [$inputs,$outputs];
     }
 
-
     /*
      * Check if the commands posted are empty.
      */
-    public static function createCommand($script,$emptyFields,$fields,$mountpoint)
+    public static function createCommand($software,$emptyFields,$fields)
     {   
 
         $errors=[];
         /**
          * Return one command with the mountpoint attached and one without it
          */
-        $command=$script;
+        $command=$software->script;
 
         if ( (!$emptyFields))
         {
-            // print_r(3);
+            
             foreach ($fields as $field)
             {
                 if ($field->field_type=='boolean')
@@ -575,7 +614,7 @@ public static function createCommand($script,$emptyFields,$fields,$mountpoint)
                             {
                                 if (($field->field_type=='File') || ($field->field_type=='Directory'))
                                 {
-                                    $command.= ' ' . $field->prefix . $field_gap . $mountpoint . '/' . $field->value;
+                                    $command.= ' ' . $field->prefix . $field_gap . $software->imountpoint . '/' . $field->value;
                                 }
                                 else
                                 {
@@ -590,7 +629,7 @@ public static function createCommand($script,$emptyFields,$fields,$mountpoint)
                             {
                                 if (($field->field_type=='File') || ($field->field_type=='Directory'))
                                 {
-                                    $command.= ' ' . $field->prefix . $field_gap . $mountpoint . '/' . $field->value;
+                                    $command.= ' ' . $field->prefix . $field_gap . $software->imountpoint . '/' . $field->value;
                                 }
                                 else
                                 {
@@ -643,7 +682,7 @@ public static function createCommand($script,$emptyFields,$fields,$mountpoint)
                                     {
                                         if (($field->field_type=='File') || ($field->field_type=='Directory'))
                                         {
-                                            $finalValue.= ' ' . $field->prefix . $field_gap . $mountpoint . '/' . $val;
+                                            $finalValue.= ' ' . $field->prefix . $field_gap . $software->imountpoint . '/' . $val;
                                         }
                                         else
                                         {
@@ -686,7 +725,7 @@ public static function createCommand($script,$emptyFields,$fields,$mountpoint)
                                     {
                                         if (($field->field_type=='File') || ($field->field_type=='Directory'))
                                         {
-                                            $finalValue.= $mountpoint . '/' . $val . $separator;
+                                            $finalValue.= $software->imountpoint . '/' . $val . $separator;
                                         }
                                         else
                                         {
@@ -731,7 +770,7 @@ public static function createCommand($script,$emptyFields,$fields,$mountpoint)
                                 {
                                     if (($field->field_type=='File') || ($field->field_type=='Directory'))
                                     {
-                                        $finalValue.= ' ' . $field->prefix . $field_gap . $mountpoint . '/' . $field->value;
+                                        $finalValue.= ' ' . $field->prefix . $field_gap . $software->imountpoint . '/' . $field->value;
                                     }
                                     else
                                     {
@@ -774,7 +813,7 @@ public static function createCommand($script,$emptyFields,$fields,$mountpoint)
                                 {
                                     if (($field->field_type=='File') || ($field->field_type=='Directory'))
                                     {
-                                        $finalValue.= $mountpoint . '/' . $field->value . $separator;
+                                        $finalValue.= $software->imountpoint . '/' . $field->value . $separator;
                                     }
                                     else
                                     {
@@ -797,59 +836,83 @@ public static function createCommand($script,$emptyFields,$fields,$mountpoint)
     /*
      * This function creates the job YAML file and sends it to Kubernetes
      */
-    public static function createAndRunJob($commands, $fields,
-                                    $name, $version, $jobid, $user, 
-                                    $podid, $machineType, 
-                                    $isystemMount, $isystemMountField,
-                                    $osystemMount, $osystemMountField,
-                                    $iosystemMount, $iosystemMountField, 
-                                    $project,$maxMem,$maxCores,$sharedFolder,$gpu)
+    public function runJob()
     {
-        
+        $data=[];
         /*
-         * Scheduler (python) script physical location
+         * Create job name. Leftover from the old method, but it works.
          */
-        $scheduler=self::sudoWrap(Yii::$app->params['scriptsFolder'] . "scheduler.py");
-        $stats=self::sudoWrap(Yii::$app->params['scriptsFolder'] . "jobMonitor.py");
-        
-        /* 
-         * Get image repository location from the DB
+        $taskName=str_replace('_','-',$this->name);
+        $taskName=str_replace(' ','-',$taskName);
+        $taskName=str_replace("\t",'-',$taskName);
+        $taskName.= '-' . $this->version;
+
+        /*
+         * Get container command and eliminate empty strings
          */
-        $software=Software::find()->where(['name'=>$name, 'version'=>$version])->one();
-        $image=$software->image;
-        $workingdir=$software->workingdir;
-        $imountpoint=$software->imountpoint;
-        $omountpoint=$software->omountpoint;
-        $softwareId=$software->id;
-        
-        $iomountpoint='';
-        if ((!empty($imountpoint)) || (empty($omountpoint)))
+        $command_str=$this->container_command;
+        $tmp=explode(' ',$this->container_command);
+        $this->container_command=[];
+        foreach ($tmp as $token)
         {
-            if ($imountpoint==$omountpoint)
+            if ($token=='')
             {
-                $iomountpoint=$imountpoint;
+                continue;
             }
+            $this->container_command[]=$token;
+        }
+
+        /*
+         * Get data to be sent to TES
+         */
+        $data['name']=$taskName;
+        $data['inputs']=$this->inputs;
+        $data['outputs']=$this->outputs;
+
+        /* 
+         * Get resources or limits depending on the type of TES
+         */
+        if (isset(Yii::$app->params['schemaTes']) && (!empty(Yii::$app->params['schemaTes'])))
+        {
+            $resources=['cpu_cores'=>$this->limits['cpu'], 'ram_gb'=>$this->limits['ram'],'gpu'=>$this->limits['gpu']];
+            $data['limits']=$resources;
+            $data['resources']=$resources;
+        }
+        else
+        {
+            $resources=['cpu_cores'=>$this->limits['cpu'], 'ram_gb'=>$this->limits['ram'],'disk_gb'=>'30'];
+            $data['resources']=$resources;
+        }
+
+        /*
+         * Create TES executor
+         */
+        $executor=[];
+        $executor['image']=$this->image;
+        $executor['command']=$this->container_command;
+        $executor['workdir']=$this->omountpoint;
+        $data['executors']=[$executor];
+        $url=self::getTesUrl();
+        $client=new Client();
+        $response = $client->createRequest()
+                    ->setFormat(Client::FORMAT_JSON)
+                    ->setData($data)
+                    ->setMethod('POST')
+                    ->setUrl($url)
+                    ->send();
+
+        if (!$response->getIsOk())
+        {
+            $this->errors=['There was an error sending the job to TESK. <br />Please contact an administrator'];
+            return;
         }
-        // $nameNoQuotes=$name;
-        $softName=$name;
-        $nameNoQuotes=str_replace('_','-',$name);
-        $versionNoQuotes=$version;
-        $name=self::enclose($name);
-        $version=self::enclose($version);
-        $iomountpoint=self::enclose($iomountpoint);
-        $imountpoint=self::enclose($imountpoint);
-        $omountpoint=self::enclose($omountpoint);
-        $iosystemMount=self::enclose($iosystemMount);
-        $isystemMount=self::enclose($isystemMount);
-        $osystemMount=self::enclose($osystemMount);
-        $workingdir=self::enclose($workingdir);
-        $sharedFolder=self::enclose($sharedFolder);
-        $gpu=self::enclose($gpu);
+
+        $this->jobid=$response->data['id'];
 
         /*
-         * Create the tmp folder to store the YAML file
+         * Create the tmp folder to store the aux files
          */
-        $folder=Yii::$app->params['tmpFolderPath'] . "$jobid/";
+        $folder=Yii::$app->params['tmpFolderPath'] . "$this->jobid/";
 
         if (file_exists($folder))
         {
@@ -865,361 +928,210 @@ public static function createAndRunJob($commands, $fields,
          * Store inputs in a file in the tmp directory
          */
         $fieldValues=[];
-        foreach($fields as $field)
+        foreach($this->fields as $field)
         {
                 $fieldValues[$field->name]=$field->value;
             
         }
 
-        $fieldValues=json_encode($fieldValues,JSON_UNESCAPED_SLASHES);
-
-        $machineType=SoftwareProfiler::getMachineType($fields,$software,$folder,$isystemMount,$iosystemMount,$maxMem);
+        $fieldValues=json_encode($fieldValues,JSON_UNESCAPED_SLASHES|JSON_PRETTY_PRINT);
 
-        $filename=$folder . 'fields.txt';
+        $filename=$folder . 'fields.json';
         file_put_contents($filename, $fieldValues);
 
         /*
-         * Store the commands in a file in the tmp directory
+         * Store the json call in a file in the tmp directory
          */
-        $filename=$folder . 'commands.txt';
-
-        file_put_contents($filename, $commands);
+        $filename=$folder . 'tesCall.json';
+        $tesCall=json_encode($data,JSON_UNESCAPED_SLASHES|JSON_PRETTY_PRINT);
+        file_put_contents($filename, $tesCall);
 
 
 
         Software::exec_log("chmod 777 $folder -R",$out,$ret);
 
-
         /*
-         * Classify software, create YAML job configuration file,
-         * send the file to Kubernetes to run and get the machine type.
+         * Insert to DB
          */
-        $arguments=[
-            $name,$version,$image,
-            $jobid,$folder, $workingdir, 
-            $imountpoint, $isystemMount,
-            $omountpoint, $osystemMount,
-            $iomountpoint, $iosystemMount,
-            $maxMem,$maxCores*1000, Yii::$app->params['nfsIp'],
-            $machineType,$sharedFolder,$gpu];
-
-        $schedulerCommand=$scheduler . ' ' . implode(' ',$arguments) . " 2>&1";
-
-        // print_r($schedulerCommand);
-        // exit(0);
-        Software::exec_log($schedulerCommand,$output,$ret);
+        $history=new RunHistory();
+        $history->username=User::getCurrentUser()['username'];
+        $history->jobid=$this->jobid;
+        $history->command=$command_str;
+        $history->omountpoint=$this->outFolder;
+        $history->start='NOW()';
+        $history->softname=$this->name;
+        $history->softversion=$this->version;
+        $history->project=$this->project;
+        $history->max_ram=$this->limits['cpu'];
+        $history->max_cpu=$this->limits['ram'];
+        $history->software_id=$this->id;
+        $history->type='job';
+        $history->save(false);
 
-        // print_r($output);
-        // exit(0);
-        $jobName=strtolower($nameNoQuotes) . '-' . $jobid;
         /*
-         * This replacements are performed in configFileCreator.py too.
-         * Anything changed here should be changed there.
-         * Job cancelling is also affected.
+         * Run the monitor script in the background
          */
-        $jobName=str_replace('_','-',$jobName);
-        $jobName=str_replace(' ','-',$jobName);
-        $jobName=str_replace("\t",'-',$jobName);
-        $arguments=[$jobName, $jobid, $folder];
-        $statsCommand=$stats . ' ' . implode(' ', $arguments);
+        $monitor=self::sudoWrap(Yii::$app->params['scriptsFolder'] . "jobMonitor.py");
+        $jobid=self::enclose($this->jobid);
+        $enfolder=self::enclose($folder);
+        $tesEndpoint=self::enclose(Yii::$app->params['teskEndpoint']);
+        $schemaTes=(isset(Yii::$app->params['schemaTes']) && (!empty(Yii::$app->params['schemaTes'])))?"'1'":"'0'";
+        $arguments=[$jobid, $folder,$tesEndpoint,$schemaTes];
+        $monitorCommand=$monitor . ' ' . implode(' ', $arguments);
         $monitorLog=$folder . 'monitorLog.txt';
         /*
          * Uncomment the following line and comment the other one to debug the monitor
          */
-        // shell_exec(sprintf("%s > $monitorLog 2>&1 &", $statsCommand));
-        shell_exec(sprintf("%s > /dev/null 2>&1 &", $statsCommand));
-
-        
-        /*
-         * Read the output and check if the pod was created.
-         * If not, add error message.
-         */
-        if (!preg_match("/job\.batch\/[a-z0-9:space:]+/",$output[0]))
-        {   
-            $error="";
-            foreach ($output as $out)
-            {
-                $error.=$out . "<br />";
-            }
-            $error.="Please contact the system administrator.";
-            return [$podid, $error, $machineType];  
-        }
-
-        /*
-         * Get the pod ID by using the job name.
-         */
-        
-
-        $query=Yii::$app->db->createCommand()->insert('run_history',
-                [
-
-                    "username"=>User::getCurrentUser()['username'],
-                    "jobid" => $jobid,
-                    "command" => $commands,
-                    "imountpoint" => $isystemMountField,
-                    "omountpoint" => $osystemMountField,
-                    "iomountpoint" => $iosystemMountField,
-                    "start" => 'NOW()',
-                    "softname" => $softName,
-                    "softversion"=> $versionNoQuotes,
-                    "machinetype"=> $machineType,
-                    "project"=>$project,
-                    "max_ram"=> $maxMem,
-                    "max_cpu" => $maxCores,
-                    'software_id' => $softwareId,
-                    'type'=>'job',
-
-                ]
-            )->execute();
-
-        // print_r($statsCommand);
-        // exit(0);
+        shell_exec(sprintf("%s > $monitorLog 2>&1 &", $monitorCommand));
+        // shell_exec(sprintf("%s > /dev/null 2>&1 &", $monitorCommand));
 
-        unset($output);
-
-        
-        if (isset(Yii::$app->params['namespaces']['jobs']))
-        {
-            $namespace=Yii::$app->params['namespaces']['jobs'];
-            $command=self::sudoWrap("kubectl get pods --no-headers -n $namespace 2>&1") . " | grep $jobName | tr -s ' ' ";
-
-            Software::exec_log($command,$output,$ret);
-        }
-        else
-        {
-            $command=self::sudoWrap("kubectl get pods --no-headers 2>&1") . " | grep $jobName | tr -s ' ' ";
-            Software::exec_log($command,$output,$ret);
-        }
         
-
-        $podString='';
-        foreach ($output as $out)
-        {   
-            // print_r($out);
-            // print_r("<br />");
-            if (strpos($out,$jobName)!== false)
-            {
-                $podString=explode(' ', $out)[0];
-                break;
-            }
-
-        }
-
-        if (empty($podString))
-        {
-            $error="There was an error submitting the job to Kubernetes.<br />Please reload the page and try again or contact an administrator.";
-            return [$podid, $error, $machineType];
-        }
-        return [$podString,'', $machineType];
+        return;
 
     }
 
     /*
      * Get pod logs by using the pod ID
      */
-    public static function getLogs($podid)
+    public static function getLogs($jobid)
     {
-        if (isset(Yii::$app->params['namespaces']['jobs']))
+        $url=self::getTesUrl();
+        if (isset(Yii::$app->params['schemaTes']) && (!empty(Yii::$app->params['schemaTes'])))
         {
-            $namespace=Yii::$app->params['namespaces']['jobs'];
-            $logsCommand=self::sudoWrap("kubectl logs $podid -n $namespace 2>&1");
-            $command=self::sudoWrap("kubectl get pods --no-headers $podid -n $namespace 2>&1");   
+            $urlArray=[$url, 'jobid'=>$jobid, 'view'=>'FULL'];
         }
         else
         {
-            $logsCommand=self::sudoWrap("kubectl logs $podid 2>&1");
-            $command=self::sudoWrap("kubectl get pods --no-headers $podid 2>&1");
+            $urlArray=[$url . "/$jobid", 'view'=>'FULL'];
         }
-        Software::exec_log($logsCommand,$logs,$ret);
+        $client=new Client();
+        $response = $client->createRequest()
+                    ->setFormat(Client::FORMAT_JSON)
+                    ->setMethod('GET')
+                    ->setUrl($urlArray)
+                    ->send();
 
-        Software::exec_log($command,$output,$ret);
-        $splt=preg_split('/[\s]+/', $output[0]);
-        $status=$splt[2];
-        $time=$splt[4];
-        if ($status=='server')
+        if (!$response->getIsOk())
         {
-            $status='Completed';
-            $time='N/A';
+            return['COMPLETE',['Job logs unavailable. Please visit the "Job History" page to download the logs.'],"N/A"];
         }
-        
-
-        return [$status,$logs,$time];
-    }
 
-    /*
-     * Erase job after it is completed or terminated.
-     */
-    public static function cleanUp($name,$jobid,$status)
-    {
-        $folder=$userFolder=Yii::$app->params['tmpFolderPath'] . "/$jobid/";
-
-        #Clear job
-        $jobName=strtolower($name). '-' . $jobid;
-        $jobName=str_replace('_','-',$jobName);
-        $jobName=str_replace(' ','-',$jobName);
-        $jobName=str_replace("\t",'-',$jobName);
-        $yaml=$folder . $jobName . '.yaml';
-
-        if ($status=='Completed')
-        {       
+        $status=$response->data['state'];
+        try
+        {
+            $logs=$response->data['logs'][0]['logs'][0]['stdout'];
+        }
+        catch (\Exception $e)
+        {
+            $logs="";
+        }
         
-            $command=self::sudoWrap("kubectl describe job $jobName 2>&1");
-            Software::exec_log($command, $output, $ret);
-            // print_r($output);
-            // exit(0);
-            $start='';
-            $stop='';
-            foreach ($output as $line)
+        $logs=explode("\n",$logs);
+        try
+        {
+            $start=$response->data['logs'][0]['logs'][0]['start_time'];
+            $start=str_replace('T',' ',$start);
+            $start=str_replace('Z',' ',$start);
+            $startdate=new \DateTime($start);
+            $enddate=new \DateTime('NOW');
+            $diff=$enddate->diff($startdate);
+            
+            $timestr=$diff->s . "s";
+            if ($diff->i>0)
             {
-                $startStr="Start Time:";
-                $startlen=strlen($startStr);
-                $stopStr="Completed At:";
-                $stoplen=strlen($stopStr);
-                // $cancelStr="Canceled At:";
-                // $cancellen=strlen($cancelStr);
-        
-                if (substr($line,0,$startlen)==$startStr)
-                {
-                    $tokens=explode(',', $line)[1];
-                    $tokens=explode('+', $tokens)[0];
-                    $datetime=strtotime($tokens);
-                    $start=date("Y-m-d H:i:s", $datetime);
-                }
-        
-                if (substr($line,0,$stoplen)==$stopStr)
-                {
-                    $tokens=explode(',', $line)[1];
-                    $tokens=explode('+', $tokens)[0];
-                    $datetime=strtotime($tokens);
-                    $stop=date("Y-m-d H:i:s", $datetime);
-                }
-        
-                    // if (substr($line,0,$cancellen)==$cancelStr)
-                    // {
-                    //     $tokens=explode(',', $line)[1];
-                    //     $tokens=explode('+', $tokens)[0];
-                    //     $datetime=strtotime($tokens);
-                    //     $stop=date("Y-m-d H:i:s", $datetime);
-                    // }
-        
+                $timestr=$diff->i . 'm ' . $timestr;
+            }
+            if ($diff->h>0)
+            {
+                $timestr=$diff->h . 'h ' . $timestr;
+            }
+            if ($diff->d>0)
+            {
+                $timestr=$diff->d . 'd, ' . $timestr;
+            }
+            if ($diff->m>0)
+            {
+                $timestr=$diff->m . 'm ' . $timestr;
+            }
+            if ($diff->y>0)
+            {
+                $timestr=$diff->y . 'y ' . $timestr;
             }
-            Yii::$app->db->createCommand()->update('run_history',
-                [
-                    'start' => $start,
-                    'stop' => $stop,
-                    'status' => $status,
-                ],
-                "jobid='$jobid'"
-            )->execute();
-                // print_r($start);
-                // print_r("<br />");
-                // print_r($stop);
-                // exit(0);
         }
-        else
+        catch (\Exception $e)
         {
-            Yii::$app->db->createCommand()->update('run_history',
-                [
-                    'stop' => 'NOW()',
-                    'status' => $status,
-                ],
-                "jobid='$jobid'"
-            )->execute();
-        }
+            $timestr="N/A";
 
-        
-                // print_r( Yii::$app->db->createCommand()->update('run_history',
-                //     [
-                //         'start' => $start,
-                //         'stop' => $stop,
-                //         'status' => $status,
-                //     ],
-                //     "softname='$name' AND username='$user' AND jobid='$jobid'"
-                // )->getRawSql());
-
-        $podid=self::runningPodIdByJob($name,$jobid);
-        $command=self::sudoWrap("kubectl logs $podid 2>&1");
-        Software::exec_log($command,$logs,$ret);
-        file_put_contents($folder . 'logs.txt', implode("\n",$logs));
-
-        $command=self::sudoWrap("kubectl delete -f $yaml");
-        Software::exec_log($command,$out,$ret);
+        }        
 
+            
+        
+        return [$status,$logs,$timestr];
     }
 
-    /*
-     * Check is podid is running
-     */
-    public static function isAlreadyRunning($podid)
+    public static function isAlreadyRunning($jobid)
     {
-        if ($podid=='')
-        {
-            return false;
-        }
-
         /*
-         * The following could have been implemented by using the "--no-headers"
-         * flag and checking whether the output is empty instead of count($output)==1.
+         * If jobid is empty, the page is loaded for the first time.
+         * If not, ask TES whether the job exists in the system.
+         * If the job results in 404 error, then it has run and deleted
+         * or not has not run at all.
          */
-        $command=self::sudoWrap("kubectl get pods $podid 2>&1");
-        Software::exec_log($command,$output,$ret);
-        if (count($output)==1)
+        if (empty($jobid))
         {
             return false;
         }
+        $url=self::getTesUrl();
+        if (isset(Yii::$app->params['schemaTes']) && (!empty(Yii::$app->params['schemaTes'])))
+        {
+            $urlArray=[$url, 'jobid'=>$jobid];
+        }
         else
+        {
+            $urlArray=[$url . "/$jobid"];
+        }
+        $client=new Client();
+        $response = $client->createRequest()
+                    ->setFormat(Client::FORMAT_JSON)
+                    ->setMethod('GET')
+                    ->setUrl($urlArray)
+                    ->send();
+
+        if ($response->getIsOk())
         {
             return true;
         }
+        return false;
     }
 
-    /*
-     * Use name and job ID to get the pod ID.
-     */
-    public static function runningPodIdByJob($name,$jobid)
+    public static function cancelJob($jobid)
     {
-        $podid='';
-        if (isset(Yii::$app->params['namespaces']['jobs']))
+        /*
+         * Cancel job by making the appropriate call 
+         * to the TES api.
+         */
+        $url=self::getTesUrl();
+        if (isset(Yii::$app->params['schemaTes']) && (!empty(Yii::$app->params['schemaTes'])))
         {
-            $namespace=Yii::$app->params['namespaces']['jobs'];
-            $command=self::sudoWrap("kubectl get pods -n $namespace --no-headers 2>&1");
+            $urlArray=[$url . '/cancel', 'jobid'=>$jobid];
         }
         else
         {
-            $command=self::sudoWrap("kubectl get pods --no-headers 2>&1");
-        }
-       
-
-        Software::exec_log($command,$out,$ret);
-
-        foreach ($out as $row)
-        {
-            $podTokens=preg_split('/[\s]+/', $row);
-
-            $podString=$podTokens[0];
-            $podStatus=$podTokens[2];
-            $tokens=explode('-',$podString);
-            if ((strtolower($name)==$tokens[0]) && ($jobid==$tokens[1]))
-            {
-                $podid=$podString;
-                break;
-            }
+            $urlArray=[$url . "/$jobid:cancel"];
         }
-        if ($podStatus=='Terminating')
-        {
-            $podid='';
-        }
-        return $podid;
-
+        $client=new Client();
+        $response = $client->createRequest()
+                    ->setFormat(Client::FORMAT_JSON)
+                    ->setMethod('POST')
+                    ->setUrl($urlArray)
+                    ->send();
     }
 
+
     public static function listDirectories($directory)
     {
-        // $files = array_filter(scandir($directory),'is_dir');
         $files = scandir($directory);
         $results=[];
-        // print_r($files);
-        // exit(0);
         
         foreach($files as $key => $value)
         {
@@ -1247,15 +1159,10 @@ public static function softwareRemove($name,$version)
         $success='';
         $error='';
         
-        // print_r($command);
-        // print_r("<br /><br />");
-        // exit(0);
         session_write_close();
         Software::exec_log($command,$out,$ret);
         session_start();
-        // print_r($out);
-        // print_r($ret);
-        // exit(0);
+       
         if ($ret==0)
         {
             $success="Successfully deleted image $name v.$version!";
@@ -1288,7 +1195,7 @@ public static function getRerunFieldValues($jobid,$fields)
     {
         $folder=Yii::$app->params['tmpFolderPath'] . '/' . $jobid . '/';
 
-        $file=$folder . 'fields.txt';
+        $file=$folder . 'fields.json';
 
         if (file_exists($file))
         {  
@@ -1296,9 +1203,23 @@ public static function getRerunFieldValues($jobid,$fields)
         }
         else
         {
-            return $fields;
+            /*
+             * try fields.txt for backward compatibility
+             */
+            $file=$folder . 'fields.txt';
+            $content=file_get_contents($file);
+            if (file_exists($file))
+            {  
+                $content=file_get_contents($file);
+            }
+            else
+            {
+                return $fields;
+            }
+
+            
         }
-        // print_r($file);
+        
         $json=json_decode($content,true);
 
         if (empty($json))
@@ -1328,19 +1249,26 @@ public static function getRerunFieldValues($jobid,$fields)
                     $fields[$i]->value=trim($field_values[$i]);
                 }
             }
-            // print_r($fields[--$i]->value?'true':'false');
-            // exit(0);
         
         }
         else
         {
-            foreach ($fields as $field)
+            if (!empty($fields))
+            {
+                $fieldCount=count($fields);
+            }
+            else
             {
-                if (!array_key_exists($field->name,$json))
+                $fieldCount=0;
+            }
+
+            for ($i=0; $i<$fieldCount; $i++)
+            {
+                if (!array_key_exists($fields[$i]->name,$json))
                 {
-                    return false;
+                    continue;
                 }
-                $field->value=$json[$field->name];
+                $fields[$i]->value=$json[$fields[$i]->name];
             }
         }
         return $fields;
@@ -1382,92 +1310,11 @@ public static function updateExampleFields($name,$version,$values)
         
     }
 
-    public static function hasExample($name,$version)
-    {
-        $query=new Query;
-        $result=$query->select(['has_example'])
-              ->from('software')
-              ->where(['name'=>$name, 'version'=>$version])
-              ->one();
-
-        return $result['has_example'];
-
-    }
-    public static function uploadedBy($name,$version)
-    {
-        $query=new Query;
-        $result=$query->select(['uploaded_by'])
-              ->from('software')
-              ->where(['name'=>$name, 'version'=>$version])
-              ->one();
-
-        return $result['uploaded_by'];
-
-    }
-
-    public static function getInactiveJobs()
-    {
-
-        $command=self::sudoWrap('kubectl get jobs --no-headers 2>&1');
-        
-        Software::exec_log($command,$output,$ret);
-
-        // print_r($output);
-        // exit(0);
-        if (trim($output[0])=="No resources found in default namespace.")
-        {
-            return [];
-        }
-        if (trim($output[0])=="No resources found.")
-        {
-            return [];
-        }
-
-        $inactive=[];
-        $active=[];
-        
-        foreach ($output as $line)
-        {
-            $tokens_tmp=explode(' ',$line);
-            $tokens=[];
-            foreach ($tokens_tmp as $token)
-            {
-                if (!empty($token))
-                    $tokens[]=$token;
-            }
-            // print_r($tokens);
-            // exit(0);
-            $completed_tokens=explode('/',$tokens[1]);
-            $completed=intval($completed_tokens[0]);
-            $total=intval($completed_tokens[1]);
-            // var_dump($total);
-            // var_dump($completed);
-            // exit(0);
-            if ($completed!=$total)
-                continue;
-            // $status='Completed';
-            $job=$tokens[0];
-            // if ($status=='Completed')
-            // {
-            $job=explode('-',$job);
-            $inactive[]=$job;
-            // }
-        
-
-        }
-        // print_r($inactive);
-        // exit(0);
-        return $inactive;
-
-
-    }
 
 
     public static function getActiveProjects()
     {
         $username=User::getCurrentUser()['username']; 
-        // print_r("https://egci-beta.imsi.athenarc.gr/index.php?r=api/active-ondemand-quotas&username=$username");
-        // exit(0);  
         $client = new Client();
         $response = $client->createRequest()
                 ->setMethod('GET')
@@ -1475,8 +1322,6 @@ public static function getActiveProjects()
                 ->send();
 
         $projects=$response->data;
-        // print_r($projects);
-        // exit(0);
         
         $projectNames=[];
         $projectJobs=[];
@@ -1503,8 +1348,6 @@ public static function getActiveProjects()
                             ])
                             ->groupBy('project') //->createCommand()->getRawSql();
                             ->all();
-        // print_r($projectUsage);
-        // exit(0);
         $projectsDB=[];
         foreach($projectUsage as $project) 
         {
@@ -1530,7 +1373,7 @@ public static function getActiveProjects()
     
 
 
-     public static function getUserStatistics($softUser)
+    public static function getUserStatistics($softUser)
     {
         $query=new Query;
 
@@ -1717,4 +1560,18 @@ public static function exec_log($command, array &$out=null, int &$ret=null)
             error_log(implode(" ", $out));
         }
     }
+
+    public static function getTesUrl()
+    {
+        if (isset(Yii::$app->params['schemaTes']) && (!empty(Yii::$app->params['schemaTes'])))
+        {
+            return Yii::$app->params['teskEndpoint'] . "/v1/tasks";
+        }
+        else
+        {
+            return Yii::$app->params['teskEndpoint'] . "/v1/tasks";
+        }
+    }
+
+
 }
diff --git a/models/Workflow.php b/models/Workflow.php
index 3e29c82..e7db2b9 100644
--- a/models/Workflow.php
+++ b/models/Workflow.php
@@ -189,18 +189,6 @@ public static function getParameters($fields)
         return [json_encode($params,JSON_UNESCAPED_SLASHES),$errors];
     }
 
-    /*
-     * If the job did not submit, then return false
-     */
-    public static function isAlreadyRunning($jobid)
-    {
-        if ($jobid=='')
-        {
-            return false;
-        }
-        
-    }
-
     /*
      * Returns a list of folders to be used in the 
      * select folder popup
@@ -598,7 +586,6 @@ public static function runWorkflow($workflow, $newLocation, $tmpWorkflowFolder,
                     ->setMethod('POST')
                     ->setUrl($url)
                     ->send();
-                // ->toString();
         }
         catch (Exception $e)
         {
@@ -645,8 +632,6 @@ public static function runWorkflow($workflow, $newLocation, $tmpWorkflowFolder,
         $data=$response->data;
         
         $jobid=$data['run_id'];
-        // print_r($data);
-        // exit(0);
 
         $query=Yii::$app->db->createCommand()->insert('run_history',
                 [
@@ -717,6 +702,37 @@ public static function runWorkflow($workflow, $newLocation, $tmpWorkflowFolder,
 
     }
 
+    public static function isAlreadyRunning($jobid)
+    {
+        $stopStates=['COMPLETE'=>false,'EXECUTOR_ERROR'=>false,'SYSTEM_ERROR'=>false,'CANCELED'=>false,'CANCELING'=>false,];
+        if (empty($jobid))
+        {
+            return false;
+        }
+        $url=Yii::$app->params['wesEndpoint'] . '/ga4gh/wes/v1/runs/' . $jobid;
+        $client = new Client();
+        $response = $client->createRequest()
+                ->addHeaders(['Content-Type'=>'application/json','Accept'=>'application/json'])
+                ->setMethod('GET')
+                ->setUrl($url)
+                ->send();
+        if ($response->getIsOk())
+        {
+            $state=$response->data['state'];
+            if (isset($stopStates[$state]))
+            {
+                return false;
+            }
+            else
+            {
+                return true;
+            }
+        }
+
+        return false;
+
+    }
+
     public static function getLogs($jobid)
     {
         $url=Yii::$app->params['wesEndpoint'] . '/ga4gh/wes/v1/runs/' . $jobid;
@@ -727,6 +743,7 @@ public static function getLogs($jobid)
                 ->setUrl($url)
                 ->send();
         $statusCode=$response->getStatusCode();
+        
         if ($statusCode==400)
         {
             $error='Malformed request. Please contact an administrator';
@@ -742,6 +759,11 @@ public static function getLogs($jobid)
             $error='Requester not authorized to perform this action. Please contact an administrator';
             return ['jobid'=>'','error'=>$error];
         }
+        else if ($statusCode==404)
+        {
+            $error='Job not found in the workflows system. Please contact an administrator';
+            return ['jobid'=>'','error'=>$error];
+        }
         else if ($statusCode==500)
         {
             $error='An unexpected error occurred. Please contact an administrator';
@@ -807,12 +829,9 @@ public static function getLogs($jobid)
         
         $logs=[];
         $i=1;
-        // print_r($taskLogs);
-        // exit(0);
+        
         foreach ($taskLogs as $index=>$log)
         {
-            // print_r($status);
-            // exit(0);
             if (!empty($log))
             {
                 $value=[
diff --git a/scheduler_files/jobMonitor.py b/scheduler_files/jobMonitor.py
index e099832..c75fef4 100755
--- a/scheduler_files/jobMonitor.py
+++ b/scheduler_files/jobMonitor.py
@@ -24,13 +24,15 @@
 import sys
 import subprocess
 import time
+import requests
 import psycopg2 as psg
 import json
 from datetime import datetime
 
-jobName=sys.argv[1]
-jobid=sys.argv[2]
-folder=sys.argv[3]
+jobid=sys.argv[1]
+folder=sys.argv[2]
+endpoint=sys.argv[3]
+tesType=sys.argv[4]
 
 configFileName=os.path.dirname(os.path.abspath(__file__)) + '/configuration.json'
 configFile=open(configFileName,'r')
@@ -41,189 +43,119 @@
 dbuser=db['username']
 passwd=db['password']
 dbname=db['database']
-namespaces=config.get('namespaces',None)
-jobNamespace=None
-if namespaces is not None:
-    jobNamespace=namespaces.get('jobs',None)
 
-if jobNamespace is not None:
-    command="kubectl get pods -n " + jobNamespace + " --no-headers -l job-name=" + jobName + " | tr -s ' '"
-else:
-    command="kubectl get pods --no-headers -l job-name=" + jobName + " | tr -s ' '"
-try:
-    out=subprocess.check_output(command,stderr=subprocess.STDOUT,shell=True, encoding='utf-8')
-except subprocess.CalledProcessError as exc:
-    print(exc.output)
-
-podid=''
-out=out.split(' ')
-podid=out[0]
-status=out[2]
-status_code=0
 cpu=0
 memory=0
 
-stopStatuses=set(['Completed','Error','StartError','ErrImagePullBackOff', "ContainerCannotRun","RunContainerError","OOMKilled", 'OutOfcpu'])
-while status not in stopStatuses:
-    
-    code=0
-    if jobNamespace is not None:
-        command="kubectl top pod --use-protocol-buffers --no-headers " + podid + ' -n ' + jobNamespace
-    else:
-        command="kubectl top pod --use-protocol-buffers --no-headers " + podid 
-    try:
-        out=subprocess.check_output(command,stderr=subprocess.STDOUT,shell=True, encoding='utf-8')
-    except subprocess.CalledProcessError as exc:
-        code=exc.returncode            
+if tesType=='1':
+    taskUrl=endpoint + '/v1/tasks?id=' + jobid + '&view=FULL'
+else:
+    taskUrl=endpoint + '/v1/tasks/' + jobid + '?view=FULL'
 
-    if code==0:
-        command='echo  "'+ out + "\" | tr -s ' ' " 
+headers={'Accept':'application/json', 'Content-Type': 'application/json'}
+response = requests.get(taskUrl,headers=headers)
+if not response.ok:
+    print(2,'Job not found.')
+    exit(2)
+try:
+    content=json.loads(response.content)
+except Exception as e:
+    print(3,e)
+    exit(3)
+
+state=content['state']
+states=['UNKNOWN','QUEUED','INITIALIZING','RUNNING','PAUSED','COMPLETE','EXECUTOR_ERROR','SYSTEM_ERROR','CANCELED']
+stopStates=['COMPLETE','CANCELED'];
+errorStatues=['EXECUTOR_ERROR','SYSTEM_ERROR']
+sqlStates={'COMPLETE':'Complete','EXECUTOR_ERROR':'Error','SYSTEM_ERROR':'Error','CANCELED':'Canceled'}
+
+toleration=0;
+while state not in stopStates:
+    if tesType=='1':
         try:
-            out=subprocess.check_output(command,stderr=subprocess.STDOUT,shell=True, encoding='utf-8')
-        except subprocess.CalledProcessError as exc:
-            code=exc.returncode
-        tokens=out.split(' ')
-        topmem=float(tokens[2][:-2])
-
-        memmeasure=tokens[2][-2:]
-
-        if memmeasure=='Mi':
-            topmem/=1024.0
-        elif memmeasure=='Ki':
-            topmem/=(1024.0*1024)
-        
-        if memory<topmem:
-            memory=topmem
-        topcpu=int(tokens[1][:-1])
-        if cpu<topcpu:
-            cpu=topcpu
-    
-    time.sleep(1)
-
-    if jobNamespace is not None:
-        command="kubectl get pod --no-headers " + podid + " -n " + jobNamespace +  " | tr -s ' '"
-    else:
-        command="kubectl get pod --no-headers " + podid + " | tr -s ' '"
-    try:
-        out=subprocess.check_output(command,stderr=subprocess.STDOUT,shell=True, encoding='utf-8')
-    except subprocess.CalledProcessError as exc:
-        print(exc.output)
-    #Job was canceled
-    if "No" in out:
-        status='Canceled'
-        break
-    #If it is running, get the status
-    out=out.strip().split('\n')
-    if len(out)>1:
-        for line in out:
-            line=line.split(' ')
-            status=line[2]
-            print(out)
-            if status=='OOMKilled':
-                break
-    else:
-        out=out[0]
-        out=out.split(' ')
-        status=out[2]
-
-if status!='Canceled':
-    #Get start and end times
-    if jobNamespace is not None:
-        command="kubectl get job " + jobName + " -o=jsonpath='{.status.completionTime}' -n " + jobNamespace
+            resources=content['current_resources']
+            tmp_cpu=resources['cpu_cores']
+            tmp_memory=resources['ram_gb']
+            if memory<tmp_memory:
+                memory=tmp_memory
+            if cpu<tmp_cpu:
+                cpu=tmp_cpu
+        except:
+            pass
     else:
-        command="kubectl get job " + jobName + " -o=jsonpath='{.status.completionTime}'"
+        resources=content['resources']
+        cpu=resources['cpu_cores']
+        memory=resources['ram_gb']
 
+    time.sleep(1)
+    #
+    # Get latest state
+    #
+    headers={'Accept':'application/json', 'Content-Type': 'application/json'}
+    response = requests.get(taskUrl,headers=headers)
+    if not response.ok:
+        print(4,'Job not found by loop.')
+        exit(4)
     try:
-        endOut=subprocess.check_output(command,stderr=subprocess.STDOUT,shell=True, encoding='utf-8')
-    except subprocess.CalledProcessError as exc:
-        print(exc.output)
-    end=endOut.replace('T',' ').replace('Z',' ').strip()
-    
-    if jobNamespace is not None:
-        command="kubectl get job " + jobName + " -o=jsonpath='{.status.startTime}' -n " + jobNamespace
-    else:
-        command="kubectl get job " + jobName + " -o=jsonpath='{.status.startTime}'"
+        content=json.loads(response.content)
+    except Exception as e:
+        print(5,e)
+        exit(5)
+    state=content['state']
+    if state in errorStatues:
+        if toleration>2:
+            break
+        toleration+=1
+
+k8sformat="%Y-%m-%dT%H:%M:%S.%fZ"
+sqlformat="%Y-%m-%d %H:%M:%S"
+while 'end_time' not in content['logs'][0]:
+    headers={'Accept':'application/json', 'Content-Type': 'application/json'}
+    response = requests.get(taskUrl,headers=headers)
+    if not response.ok:
+        print(6,'Job not found by loop.')
+        exit(6)
     try:
-        out=subprocess.check_output(command,stderr=subprocess.STDOUT,shell=True, encoding='utf-8')
-    except subprocess.CalledProcessError as exc:
-        print(exc.output)
-    start=out.replace('T',' ').replace('Z',' ').strip()
+        content=json.loads(response.content)
+    except Exception as e:
+        print(7,e)
+        exit(7)
+    time.sleep(1)
 
-    if status=='Completed':
-        status='Complete'
-    
+endTime=content['logs'][0]['end_time']
+startTime=content['logs'][0]['start_time']
+endobj=datetime.strptime(endTime,k8sformat)
+startobj=datetime.strptime(startTime,k8sformat)
+status=sqlStates[state]
 
 conn=psg.connect(host=host, user=dbuser, password=passwd, dbname=dbname)
 cur=conn.cursor()
-sql="SELECT status FROM run_history WHERE jobid='" + jobid + "'"
-cur.execute(sql)
-result=cur.fetchone()
-if result[0]=='Canceled':
-    status='Canceled'
-
-if status=='Canceled':
-    #everything is done with PHP on the interface
-    pass
-elif status=='Complete':
-    query="UPDATE run_history SET ram=" + str(memory) + ", cpu=" + str(cpu) + ", start='" + start +"', stop='" + str(end) + "', status='" + status +"' WHERE jobid='" + jobid + "'"
-    status_code=0
-    cur.execute(query)
-    conn.commit()
-
-elif status=='OOMKilled':
-    query="UPDATE run_history SET stop='NOW()', status='Out_of_RAM', remote_status_code=-10 WHERE jobid='" + jobid + "'"
-    status_code=-10
-    cur.execute(query)
-    conn.commit()
-elif status=='OutOfcpu':
-    query="UPDATE run_history SET stop='NOW()', status='Out_οf_CPU', remote_status_code=-10 WHERE jobid='" + jobid + "'"
-    status_code=-11
-    cur.execute(query)
-    conn.commit()
-else:
-    query="UPDATE run_history SET stop='NOW()', status='Error', remote_status_code=-9 WHERE jobid='" + jobid + "'"
-    status_code=-2
-    cur.execute(query)
-    conn.commit()
-
-
+query="UPDATE run_history SET ram=" + str(memory) + ", cpu=" + str(cpu) + ", start='" + startobj.strftime(sqlformat) +"', stop='" + endobj.strftime(sqlformat) + "', status='" + status +"' WHERE jobid='" + jobid + "'"
+cur.execute(query)
+conn.commit()
 conn.close()
+try:
+    logs=content['logs'][0]['logs'][0]['stdout']
+except:
+    logs=""
 
-if (status!='Canceled'):
-    #Get logs
-    if jobNamespace is not None:
-        command="kubectl get pods -n " + jobNamespace + " --no-headers -l job-name=" + jobName + " | tr -s ' '"
-    else:
-        command="kubectl get pods --no-headers -l job-name=" + jobName + " | tr -s ' '"
-    try:
-        out=subprocess.check_output(command,stderr=subprocess.STDOUT,shell=True, encoding='utf-8')
-    except subprocess.CalledProcessError as exc:
-        print(exc.output)
+logFile=folder + '/logs.txt'
+g=open(logFile,'w')
+g.write(logs)
+g.close()
 
-    podid=''
-    out=out.split(' ')
-    podid=out[0]
+if config['cleanTeskJobs']:
+    namespaces=config.get('namespaces',None)
+    jobNamespace=None
+    if namespaces is not None:
+        jobNamespace=namespaces.get('tesk',None)
 
     if jobNamespace is not None:
-        command="kubectl logs " + podid + " -n " + jobNamespace + " 2>&1"
+        command="for j in $(kubectl get jobs -n " + jobNamespace + " --no-headers | grep '" + jobid +  "' | tr -s ' ' | cut -d ' ' -f 1); do kubectl delete jobs -n " + jobNamespace + " $j; done"
     else:
-        command="kubectl logs " + podid + " 2>&1"
-
+        command="kubectl get jobs --no-headers -l | grep '" + jobid +  "' | tr -s ' '| cut -d ' ' -f 1); do kubectl delete jobs $j; done "
     try:
-        logs=subprocess.check_output(command,stderr=subprocess.STDOUT,shell=True, encoding='utf-8')
+        out=subprocess.check_output(command,stderr=subprocess.STDOUT,shell=True, encoding='utf-8')
     except subprocess.CalledProcessError as exc:
-        logs=''
         print(exc.output)
-    except UnicodeDecodeError as exc:
-        logs=''
-        print(exc)
-
-    logFile=folder + '/logs.txt'
-    g=open(logFile,'w')
-    g.write(logs)
-    g.close()
-
-#Clean job
-yamlFile=folder + '/' + jobName + '.yaml'
-returnCode=subprocess.call(['kubectl','delete','-f',yamlFile])
 
diff --git a/views/software/logs.php b/views/software/logs.php
index 52656d4..0eedc04 100644
--- a/views/software/logs.php
+++ b/views/software/logs.php
@@ -45,14 +45,13 @@
 <?php	
 }
 ?>
-<div><b>Type of machine:</b> <?=$machineType?></div>
 <div class="status-div col-md-3>">
 	<div class="status-label"><b>Status:</b></div>
-	<div id="status-value" class="<?= ($status=="Completed") ? "status-completed" : "status-running" ?> "><?=$status?></div>
+	<div id="status-value" class="<?= ($status=="COMPLETE") ? "status-completed" : "status-running" ?> "><?=$status?></div>
 </div>
 <div class="status-div col-md-3>">
 	<div class="status-label"><b>Running time:</b></div>
-	<div id="exec-time-value" class="<?= ($status=="Completed") ? "status-completed" : "status-running" ?> "><?=$time?></div>
+	<div id="exec-time-value" class="<?= ($status=="COMPLETE") ? "status-completed" : "status-running" ?> "><?=$time?></div>
 </div>
 
 
diff --git a/views/software/run.php b/views/software/run.php
index 64a98a6..e01f3bc 100644
--- a/views/software/run.php
+++ b/views/software/run.php
@@ -37,9 +37,9 @@
 echo Html::CssFile('@web/css/software/run.css');
 $this->registerJsFile('@web/js/software/run-index.js', ['depends' => [\yii\web\JqueryAsset::className()]]);
 
-$this->title = "New job ($name v.$version) ";
+$this->title = "New job ($software->name v.$software->version) ";
 
-$commandsDisabled= ($jobid!='') ? true : false;
+$commandsDisabled= ($software->jobid!='') ? true : false;
 if($commandsDisabled)
 {
 $commandBoxClass= 'disabled-box';
@@ -49,7 +49,7 @@
 $commandBoxClass='';
 }
 
-if ($hasExample)
+if ($software->has_example)
 {
 $exampleBtnLink='javascript:void(0);';
 }
@@ -91,31 +91,28 @@
 
             <?php           
             RunFormWidget::showOutputField($commandsDisabled,$outFolder,$username,$type);
-            RunFormWidget::showHiddenFields($jobid,$name,$version,$example, $hasExample);
+            RunFormWidget::showHiddenFields($software->jobid,$software->name,$software->version,$example, $software->has_example);
             RunFormWidget::showArguments($fields,$type,$commandBoxClass,$commandsDisabled);
             RunFormWidget::showResources($quotas,$maxCores,$maxMem,$commandsDisabled,$commandBoxClass);
-            RunFormWidget::showRunButtons($superadmin,$username,$uploadedBy,$hasExample,$commandsDisabled,$type,$name,$version,$software_instructions);
+            RunFormWidget::showRunButtons($superadmin,$username,$software->uploaded_by,$software->has_example,$commandsDisabled,$type,$software->name,$software->version,$software->instructions);
 
             ?>
-        </div>
-    </div>
 <?php
 ActiveForm::end();
 ?>
-    
-    <?=RunFormWidget::showErrors($errors, $runErrors)?>
-	   
-    <div id="pod-logs"></div>
-        <?php
-        if ($commandsDisabled)
-        {
-            echo "<div id='initial-status'>";
-        	echo "<h3>Runtime Info:</h3>";
-        	echo "<b>Status:</b> <div class='status-init'>QUEUED</div><br />";
-            echo $this->registerJsFile('@web/js/software/logs.js', ['depends' => [\yii\web\JqueryAsset::className()]] );
-            
-        }?>
-    <br />
+            <?=RunFormWidget::showErrors($errors, $runErrors)?>
+            <div id="pod-logs"></div>
+                <?php
+                if ($commandsDisabled)
+                {
+                    echo "<div id='initial-status'>";
+                	echo "<h3>Runtime Info:</h3>";
+                	echo "<b>Status:</b> <div class='status-init'>INITIALIZING</div><br />";
+                    echo $this->registerJsFile('@web/js/software/logs.js', ['depends' => [\yii\web\JqueryAsset::className()]] );
+                    
+                }?>
+            </div>
+        </div>
     </div>
 </div> <!-- site-software-->
 
diff --git a/web/js/software/logs.js b/web/js/software/logs.js
index e7405b6..2e1b1dc 100644
--- a/web/js/software/logs.js
+++ b/web/js/software/logs.js
@@ -27,179 +27,11 @@ $(document).ready(function()
 
     $(".cancel-button-container").css('display','inline-block');
 
-    function cleanUp()
+    function enableForm()
     {
-    	var jobid=$("#hidden_jobid_input").val();
-      	var name=$("#hidden_name_input").val();
-    	// $.ajax({
-     //        url: "index.php?r=software/clean-up",
-     //        type: "GET",
-     //        data: { "jobid": jobid, "name": name, 'status': 'Complete'},
-     //        dataType: "html",
-            // success: function (data) 
-            // {
-            //   $("#initial-status").hide();
-            //   $('#pod-logs').html(data); 
-              
-            //   status=$("#status-value").text(); 
-            //   if (status == "Completed") 
-            //     {
-            //       clearInterval(refreshId);
-            //     }
-            // },
-            // retries: 2,
-            // complete: function() 
-            // {
-            // // Schedule the next request when the current one's complete
-            //   setInterval(sendRequest, 5000); // The interval set to 5 seconds
-            // },
-        // });
-    }
-    function cancelClean()
-    {
-      var jobid=$("#hidden_jobid_input").val();
-      var name=$("#hidden_name_input").val();
-      $.ajax({
-            url: "index.php?r=software/clean-up",
-            type: "GET",
-            data: { "jobid": jobid, "name": name, "status": "Canceled"},
-            dataType: "html",
-            success: function (data) 
-            {
-                clearInterval(refreshId);
-                $("#status-value").html("Canceled");
-                $(".job-output").hide();
-                $(".running-logo").hide();
-                $("#command-text-box").removeClass('disabled-box');
-                $("#command-text-box").prop('readonly',false);
-                $(".cancel-button-container").css('display','none');
-                $(".select-mount-button").removeAttr('disabled');
-                $(".clear-mount-button").removeAttr('disabled');
-                $("#software-start-run-button").removeAttr('disabled');
-            }
-            //   $("#initial-status").hide();
-            //   $('#pod-logs').html(data); 
-              
-            //   status=$("#status-value").text(); 
-            //   if (status == "Completed") 
-            //     {
-            //       clearInterval(refreshId);
-            //     }
-            // },
-            // retries: 2,
-            // complete: function() 
-            // {
-            // // Schedule the next request when the current one's complete
-            //   setInterval(sendRequest, 5000); // The interval set to 5 seconds
-            // },
-        });
-    }
-    function sendRequest(refId)
-    {
-      var podid=$("#hidden_podid_input").val();
-      var machineType=$("#hidden_machineType_input").val();
-      var jobid=$("#hidden_jobid_input").val();
-      // window.alert(jobid);
-        $.ajax({
-                url: "index.php?r=software/get-logs",
-                type: "GET",
-                data: { "podid": podid, "machineType": machineType, "jobid" : jobid },
-                dataType: "html",
-                success: function (data) 
-                {
-                    $("#initial-status").hide();
-                    $('#pod-logs').html(data);
-                    $('.container-logs').scrollTop($('.container-logs').prop('scrollHeight')); 
-              
-              
-                    status=$("#status-value").text(); 
-                    if ( (status == "Completed") || (status == "Error") || (status == "ImagePullBackOff") || (status == "Terminating") || (status == "Canceled") || (status=="OOMKilled"))
-                    {
-                        clearInterval(refId);
-                        setTimeout(cleanUp(),2000);
-                        totalFields=Number($("#hidden_fieldsNum").val());
-                        var i=0;
-                        for (i=0; i<totalFields; i++)
-                        {
-                            var fieldID="#field-" + i;
-                            var field=$(fieldID);
-                            field.removeClass('disabled-box');
-                            if ( (!field.hasClass('file_field')) && (!field.hasClass('folder_field')) && (!field.hasClass('array_field')) )
-                            {
-                                field.prop('readonly',false);
-                                // window.alert(field.prop('readonly'));
-                            } 
-                            
-                        }
-                        if ((status!='Error') && (status!="ImagePullBackOff"))
-                        {
-                            // $(".job-output").hide();
-                            $(".run-gif-img").hide();
-
-                        }
-                        else
-                        {
-                            $(".run-gif-img").hide();
-                        }
-                        
-                        $("#systemmount").removeClass('disabled-box');
-                        $("#systemmount").prop('readonly',false);
-                        $("#memory").removeClass('disabled-box');
-                        $("#cores").removeClass('disabled-box');
-                        $("#systemmount").prop('readonly',false);
-                        $("#memory").prop('readonly',false);
-                        $("#cores").prop('readonly',false);
-                        $(".cancel-button-container").css('display','none');
-                        $("#select-active-form-btn").removeClass('disabled-btn');
-                        $("#select-non-active-form-btn").removeClass('disabled-btn');
-                        $(".select-mount-button").removeAttr('disabled');
-                        $(".clear-mount-button").removeAttr('disabled');
-                        $("#software-start-run-button").removeAttr('disabled');
-                        $(".clear-file-btn").each(function(){
-                            $(this).removeAttr('disabled');
-                        });
-                        $(".select-file-btn").each(function(){
-                            $(this).removeAttr('disabled');
-                        });
-                        $(".clear-folder-btn").each(function(){
-                            $(this).removeAttr('disabled');
-                        });
-                        $(".select-folder-btn").each(function(){
-                            $(this).removeAttr('disabled');
-                        });
-                        $(".btn-default-values").each(function(){
-                            $(this).removeAttr('disabled');
-                        });
-                        if ($("#has_example").length)
-                        {
-                            $("#software-run-example-button").removeAttr('disabled');
-                        }
-                        else
-                        {
-                            if ($(".add-example-link").length)
-                            {
-                                $(".add-example-link").show();
-                            }
-                        }
-                    }
-
-                },
-                retries: 2,
-            // complete: function() 
-            // {
-            // // Schedule the next request when the current one's complete
-            //   setInterval(sendRequest, 5000); // The interval set to 5 seconds
-            // },
-            });
-    }
-
-    $("#software-cancel-button").click(function(){
-
-
-        clearInterval(refreshId);
-        cancelClean();
         totalFields=Number($("#hidden_fieldsNum").val());
-        for (i=0; i<=totalFields; i++)
+        var i=0;
+        for (i=0; i<totalFields; i++)
         {
             var fieldID="#field-" + i;
             var field=$(fieldID);
@@ -207,20 +39,23 @@ $(document).ready(function()
             if ( (!field.hasClass('file_field')) && (!field.hasClass('folder_field')) && (!field.hasClass('array_field')) )
             {
                 field.prop('readonly',false);
-            } 
+            }
+            
         }
-        $(".job-output").hide()
-        $("#isystemmount").removeClass('disabled-box');
-        $("#iosystemmount").removeClass('disabled-box');
-        $("#osystemmount").removeClass('disabled-box');
-        $(".select-mount-button").removeAttr('disabled');
-        $(".clear-mount-button").removeAttr('disabled');
+        $(".run-gif-img").hide();
+        
+        $("#outFolder").removeClass('disabled-box');
+        $("#outFolder").prop('readonly',false);
         $("#memory").removeClass('disabled-box');
         $("#cores").removeClass('disabled-box');
         $("#systemmount").prop('readonly',false);
         $("#memory").prop('readonly',false);
         $("#cores").prop('readonly',false);
-        // $("#command-text-box").removeClass('disabled-box');
+        $(".cancel-button-container").css('display','none');
+        $(".select-output-button").removeAttr('disabled');
+        $(".clear-output-button").removeAttr('disabled');
+        $("#software-start-run-button").removeAttr('disabled');
+        $("#software-cancel-button").hide();
         $(".clear-file-btn").each(function(){
             $(this).removeAttr('disabled');
         });
@@ -236,9 +71,6 @@ $(document).ready(function()
         $(".btn-default-values").each(function(){
             $(this).removeAttr('disabled');
         });
-        // $("#command-text-box").prop('readonly',false);
-        $("#select-active-form-btn").removeClass('disabled-btn');
-        $("#select-non-active-form-btn").removeClass('disabled-btn');
         if ($("#has_example").length)
         {
             $("#software-run-example-button").removeAttr('disabled');
@@ -250,13 +82,123 @@ $(document).ready(function()
                 $(".add-example-link").show();
             }
         }
+    }
+    function sendRequest(refId)
+    {
+        var jobid=$("#hidden_jobid_input").val();
+        $.ajax({
+                url: "index.php?r=software/get-logs",
+                type: "GET",
+                data: {"jobid" : jobid },
+                dataType: "html",
+                success: function (data) 
+                {
+                    $("#initial-status").hide();
+                    $('#pod-logs').html(data);
+                    $('.container-logs').scrollTop($('.container-logs').prop('scrollHeight')); 
+              
+              
+                    status=$("#status-value").text(); 
+                    if ( (status == "COMPLETE") || (status == "SYSTEM_ERROR") || (status == "EXECUTOR_ERROR") || (status == "CANCELED") )
+                    {
+                        clearInterval(refId);
+                        setTimeout(enableForm(),2000);
+                    }
+                        
+
+                },
+                retries: 2,
+            });
+    }
+
+    $("#software-cancel-button").click(function(){
+
+        var jobid=$("#hidden_jobid_input").val();
+        $.ajax({
+            url: "index.php?r=software/cancel-job",
+            type: "GET",
+            data: { "jobid": jobid,},
+            dataType: "html",
+            success: function (data) 
+            {
+                // clearInterval(refreshId);
+                // setTimeout(enableForm(),2000);
+                // $(".job-output").hide();
+                // $(".running-logo").hide();
+                // $("#command-text-box").removeClass('disabled-box');
+                // $("#command-text-box").prop('readonly',false);
+                // $(".cancel-button-container").css('display','none');
+                // $(".select-mount-button").removeAttr('disabled');
+                // $(".clear-mount-button").removeAttr('disabled');
+                // $("#software-start-run-button").removeAttr('disabled');
+            }
+        });
+
+        // clearInterval(refreshId);
+        // cancelClean();
+        // totalFields=Number($("#hidden_fieldsNum").val());
+        // for (i=0; i<=totalFields; i++)
+        // {
+        //     var fieldID="#field-" + i;
+        //     var field=$(fieldID);
+        //     field.removeClass('disabled-box');
+        //     if ( (!field.hasClass('file_field')) && (!field.hasClass('folder_field')) && (!field.hasClass('array_field')) )
+        //     {
+        //         field.prop('readonly',false);
+        //     } 
+        // }
+        // $(".job-output").hide()
+        // $("#isystemmount").removeClass('disabled-box');
+        // $("#iosystemmount").removeClass('disabled-box');
+        // $("#osystemmount").removeClass('disabled-box');
+        // $(".select-mount-button").removeAttr('disabled');
+        // $(".clear-mount-button").removeAttr('disabled');
+        // $("#memory").removeClass('disabled-box');
+        // $("#cores").removeClass('disabled-box');
+        // $("#systemmount").prop('readonly',false);
+        // $("#memory").prop('readonly',false);
+        // $("#cores").prop('readonly',false);
+        // // $("#command-text-box").removeClass('disabled-box');
+        // $(".clear-file-btn").each(function(){
+        //     $(this).removeAttr('disabled');
+        // });
+        // $(".select-file-btn").each(function(){
+        //     $(this).removeAttr('disabled');
+        // });
+        // $(".clear-folder-btn").each(function(){
+        //     $(this).removeAttr('disabled');
+        // });
+        // $(".select-folder-btn").each(function(){
+        //     $(this).removeAttr('disabled');
+        // });
+        // $(".btn-default-values").each(function(){
+        //     $(this).removeAttr('disabled');
+        // });
+        // // $("#command-text-box").prop('readonly',false);
+        // $("#select-active-form-btn").removeClass('disabled-btn');
+        // $("#select-non-active-form-btn").removeClass('disabled-btn');
+        // if ($("#has_example").length)
+        // {
+        //     $("#software-run-example-button").removeAttr('disabled');
+        // }
+        // else
+        // {
+        //     if ($(".add-example-link").length)
+        //     {
+        //         $(".add-example-link").show();
+        //     }
+        // }
+        enableForm();
 
     
     });
 
+    /*
+     * This part is executed once the view file is rendered.
+     * and starts the ajax calls for the logs.
+     */
     var refreshId = setInterval(function() 
     {
-      
       sendRequest(refreshId);
       
     }, 2000);
diff --git a/web/js/software/run-index.js b/web/js/software/run-index.js
index ad7e214..684ce8a 100644
--- a/web/js/software/run-index.js
+++ b/web/js/software/run-index.js
@@ -35,14 +35,12 @@ $(document).ready(function() {
 	            field.addClass('disabled-box');
 	            field.prop('readonly',true);
 	        }
-	        $("#systemmount").addClass('disabled-box');
+	        $("#outFolder").addClass('disabled-box');
 	        $("#memory").addClass('disabled-box');
 	        $("#cores").addClass('disabled-box');
-	        $("#systemmount").prop('readonly',true);
+	        $("#outFolder").prop('readonly',true);
 	        $("#memory").prop('readonly',true);
 	        $("#cores").prop('readonly',true);
-			$("#command-text-box").prop('readonly',true)
-			$("#command-text-box").addClass('disabled-box');
 			$(".add-example-link").hide();
 			$("#software_commands_form").submit();
 		}
@@ -50,143 +48,6 @@ $(document).ready(function() {
 	
 	});
 
-	//if the example button is pressed make the command box active
-	// $(".software-example-button").click(function(){
-	// 	$("#active-run-form").show();
-	// 	$("#select-active-form-btn").addClass('active-tab');
-	// 	$("#non-active-run-form").hide();
-	// 	$("#select-non-active-form-btn").removeClass('active-tab');
-		
-	// 	var commands=$("#hidden_example_input").val();
-	// 	$("#command-text-box").val(commands);
-	// 	$("#command-text-box").prop('readonly',true)
-	// 	$("#command-text-box").addClass('disabled-box');
-	// 	$("#software_commands_form").submit();
-	
-	// });
-
-	//on submit show command box
-	// if ($("#command-text-box").prop('readonly')==true)
-	// {
-	// 	$("#command-text-box").addClass('disabled-box');
-	// 	$("#active-run-form").show();
-	// 	$("#non-active-run-form").hide();
-	// 	// $("#select-active-form-btn").addClass('disabled-btn');
-	// 	// $("#select-non-active-form-btn").addClass('disabled-btn');
-	// }
-
-	// $("#select-active-form-btn").click(function(){
-	// 	if ($("#select-active-form-btn").hasClass('disabled-btn')==false)
-	// 	{
-	// 		$("#active-run-form").show();
-	// 		$("#select-active-form-btn").addClass('active-tab');
-	// 		$("#non-active-run-form").hide();
-	// 		$("#select-non-active-form-btn").removeClass('active-tab');
-			
-	// 	}
-
-	// });
-
-	// $("#select-non-active-form-btn").click(function(){
-	// 	if ($("#select-non-active-form-btn").hasClass('disabled-btn')==false)
-	// 	{
-	// 		// var command=$("#command-text-box").val();
-	// 		// var tokens=command.split(" ");
-	// 		// var total=tokens.length;
-	// 		// var i;
-
-	// 		// for (i=0; i<=total; i++)
-	// 		// {
-	// 		// 	$("#field-" + i).val(tokens[i]);
-	// 		// }
-	// 		$("#active-run-form").hide();
-	// 		$("#select-active-form-btn").removeClass('active-tab');
-	// 		$("#non-active-run-form").show();
-	// 		$("#select-non-active-form-btn").addClass('active-tab');
-	// 	}
-
-	// });
-
-	$(".select-mount-button").click(function(){
-		var disabled = $(this).attr('disabled');
-		if (!disabled)
-		{
-			var caller=$(this).parent().children('.mount-field').attr('id');
-			$("#mountcaller").val("#" + caller);
-			// window.alert(caller);
-			var link = $("#selectmounturl").val();
-			window.open(link, "Ratting",
-				"height=500,width=800,left=100,top=100,resizable=yes,scrollbars=yes,toolbar=no,menubar=no,location=no,directories=no, status=no");
-		}
-	});
-
-	$(".clear-mount-button").click(function(){
-		var mountf=$(this).parent().children('.mount-field');
-		mountf.val('');
-		mountf.trigger("change");
-	});
-
-	$("#isystemmount").change(function(){
-		if ($(".mount-exist-error").length)
-		{
-			$(".mount-exist-error").hide();
-			$("#software-start-run-button").removeClass('hidden-element');
-		}
-
-		totalFields=Number($("#hidden_fieldsNum").val());
-		for (i=0; i<totalFields; i++)
-        {
-        	var fieldID="#field-" + i;
-            var field=$(fieldID);
-            hiddenInput=field.parent().children('.hidden_select_file_url');
-            if (hiddenInput.length)
-            {
-            	field.val('');
-            }
-            hiddenInput=field.parent().children('.hidden_select_folder_url');
-            if (hiddenInput.length)
-            {
-            	field.val('');
-            }
-        }
-
-	});
-
-	$("#osystemmount").change(function(){
-		if ($(".mount-exist-error").length)
-		{
-			$(".mount-exist-error").hide();
-			$("#software-start-run-button").removeClass('hidden-element');
-		}
-
-	});
-
-	$("#iosystemmount").change(function(){
-		if ($(".mount-exist-error").length)
-		{
-			$(".mount-exist-error").hide();
-			$("#software-start-run-button").removeClass('hidden-element');
-		}
-
-		totalFields=Number($("#hidden_fieldsNum").val());
-		// window.alert(totalFields);
-		totalFields=Number($("#hidden_fieldsNum").val());
-		for (i=0; i<totalFields; i++)
-        {
-        	var fieldID="#field-" + i;
-            var field=$(fieldID);
-            hiddenInput=field.parent().children('.hidden_select_file_url');
-            if (hiddenInput.length)
-            {
-            	field.val('');
-            }
-            hiddenInput=field.parent().children('.hidden_select_folder_url');
-            if (hiddenInput.length)
-            {
-            	field.val('');
-            }
-        }
-	});
 
 	$(".btn-default-values").click(function(){
 		var disabled = $("#software-start-run-button").attr('disabled');
@@ -309,6 +170,23 @@ $(document).ready(function() {
 			$(".required").addClass('hidden');
 			$(".non-required").removeClass('hidden');
 		}
-		});
+	});
 
+	$(".select-output-button").click(function(){
+		var disabled = $(this).attr('disabled');
+		if (!disabled)
+		{
+			var caller=$(this).parent().children('.mount-field').attr('id');
+			$("#mountcaller").val("#" + caller);
+			// window.alert(caller);
+			var link = $("#selectoutputurl").val();
+			window.open(link, "Ratting",
+				"height=500,width=800,left=100,top=100,resizable=yes,scrollbars=yes,toolbar=no,menubar=no,location=no,directories=no, status=no");
+		}
+	});
+	$(".clear-output-button").click(function(){
+		var mountf=$(this).parent().children('.mount-field');
+		mountf.val('');
+		mountf.trigger("change");
+	});
 });
\ No newline at end of file