Fixed but with existing image upload (missing instructions)

controllers/SoftwareController.php

@@ -883,7 +883,6 @@ public function actionEditSoftware($name, $version)
                 'public'=>'Everyone',
                 'private' => 'Only me',];
 
-
         $model->dois=array_filter(explode('|', $model->dois));
 
         if ($model->load(Yii::$app->request->post()) && $model->validate()) 

models/SoftwareUploadExisting.php

@@ -123,6 +123,7 @@ public function upload()
         $original=$this->quotes($original);
         $this->covid19=($this->covid19=='1') ? "'t'" : "'f'";
         $this->biotools=$this->quotes($this->biotools);
+        $this->instructions=$this->quotes($this->instructions);
 
         //add dois string in a file and pass it on to python
         $dataFolder=Yii::$app->params['tmpImagePath'] . $username . '/' . str_replace(' ','-',$this->name) . '/' . str_replace(' ','-',$this->version) . '/';
@@ -167,9 +168,10 @@ public function upload()
         $mpi=($this->mpi=='1') ? $this->quotes('t') : $this->quotes('f');
         $username=$this->quotes($username);
 
-        $arguments=[$this->name, $this->version, $this->image, $cwlFileName, 
-                    $username, $this->visibility, $this->imountpoint, $this->omountpoint, $this->commandRetrieval,
-                    $this->description, $this->biotools, $doiFile, $mpi, $workingdir,$original,$dockerhub,$this->covid19 ];
+        $arguments=[
+            $this->name, $this->version, $this->image, $cwlFileName, 
+            $username, $this->visibility, $this->imountpoint, $this->omountpoint, $this->commandRetrieval,
+            $this->description, $this->biotools, $doiFile, $mpi, $workingdir,$original,$dockerhub,$this->covid19, $this->instructions];
 
         // $command="sudo -u user /data/www/schema_test/scheduler_files/imageUploader.py ";
         $command="sudo -u ". Yii::$app->params['systemUser'] . " " . Yii::$app->params['scriptsFolder'] . "existingImageUploader.py ";

scheduler_files/existingImageUploader.py

@@ -24,6 +24,7 @@
 original=sys.argv[15]
 docker_or_local=sys.argv[16]
 covid19=sys.argv[17]
+instructions=sys.argv[18]
 
 def quoteEnclose(string):
     return "'" + string + "'"
@@ -56,7 +57,7 @@ def quoteEnclose(string):
     workingDir='/'
 
 uf.imageStoreAndClassify(softName,softVersion, image,script,user,visibility,
-    workingDir,imountPoint,omountPoint,description,cwlPath,biotools,doiFile,mpi,original,docker_or_local,covid19)
+    workingDir,imountPoint,omountPoint,description,cwlPath,biotools,doiFile,mpi,original,docker_or_local,covid19,instructions)
 
 if 'inputs' not in cwlContent:
     cwlContent['inputs']=[];

views/software/software_upload.php

@@ -92,7 +92,7 @@
                      'options' => ['rows' => 4],
                      'preset' => 'basic'
                 ]);
-                ?>
+        ?>
         <br /><br />
         <div class="form-group">
             <?= Html::submitButton("$submit_icon Submit", ['class' => 'btn btn-primary']) ?>