ROCrates for workflows

athenarc · Feb 4, 2021 · c26056e · c26056e
1 parent 8f1a3c2
commit c26056e
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Showing 9 changed files with 393 additions and 52 deletions.
diff --git a/components/RoCrateModal.php b/components/RoCrateModal.php
@@ -11,6 +11,7 @@
 use app\models\SoftwareMpi;
 use app\models\Workflow;
 use app\models\SoftwareInput;
+use app\models\WorkflowInput;
 use app\models\RoCrate;
 use yii\widgets\ActiveForm; 
 
@@ -25,18 +26,40 @@ public static function addModal($jobid)
 		$download_icon='<i class="fas fa-question-circle" title="Download a local copy of the RO-Crate object to be produced"></i>';
 		$edit_icon='<i class="fas fa-pencil-alt"></i>';
 		$download_icon='<i class="fas fa-download"></i>';
-
 		$required='<span style="color:red">*</span>';
+
 		$history=RunHistory::find()->where(['jobid'=>$jobid])->one();
 		$software_id=$history->software_id;
-		$software=Software::find()->where(['id'=>$software_id])->one();
+
+		$public_url='';
+		$image_url='';
+
+		if($history->type=='job')
+		{
+			$software=Software::find()->where(['id'=>$software_id])->one();
+			$soft_type='Software';
+			$fields=SoftwareInput::find()->where(['softwareid'=>$software_id])->orderBy(['position'=> SORT_ASC])->all();
+			$fields=Software::getRerunFieldValues($jobid,$fields);
+		}
+		elseif ($history->type=='workflow')
+		{
+			$workflow=Workflow::find()->where(['id'=>$software_id])->one();
+			$soft_type='Workflow';
+			$fields=WorkflowInput::find()->where(['workflow_id'=>$software_id])->orderBy(['position'=> SORT_ASC])->all();
+			$fields=Workflow::getRerunFieldValues($jobid,$fields);
+
+		}
+
+
 		$model=RoCrate::find()->where(['jobid'=>$jobid])->one();
+
+		//print_r($history->jobid);
 		$disabled_fields=false;
 		if(!empty($model))
 		{
 			$disabled_fields=true;
 		}
-		$image_url='';
+
 		$disabled=false;
 		if ((!empty($software)) && (empty($model->software_url)))
 		{
@@ -46,16 +69,19 @@ public static function addModal($jobid)
         		$disabled=true;
             	$image=$software->original_image;
             	$image_url='https://hub.docker.com/r/'.$image;
+
+
         	}
 
 		}
-		elseif ((!empty($software)) && (!empty($model->software_url)))
+		elseif ((!empty($software) || (!empty($workflow))) && (!empty($model->software_url)))
      	{
          		$image_url=$model->software_url;
         }
 
-		$fields=SoftwareInput::find()->where(['softwareid'=>$software_id])->orderBy(['position'=> SORT_ASC])->all();
-		$fields=Software::getRerunFieldValues($jobid,$fields);
+
+
+
 
 		$field_to_url=[];
         if(empty($model))
@@ -92,19 +118,32 @@ public static function addModal($jobid)
 
 		echo Html::hiddenInput('softname',$history->softname);
 		echo Html::hiddenInput('softversion',$history->softversion);
-
+
+
 		echo "<div class='modal fade' tabindex='-1' role='dialog' id='experiment-modal-$jobid' aria-labelledby='experiment-modal' aria-hidden='true'>";
 		echo '<div class="modal-dialog modal-dialog-centered modal-lg modal-size" role="document">';
 		echo '<div class="modal-content" >';
 		echo '<div class="modal-header">';
-		echo "<div class='modal-title text-center size' id='exampleModalLongTitle'>RO-Crate object details</div>";
+		echo "<div class='modal-title text-center size' id='exampleModalLongTitle'>RO-Crate object details  &nbsp; &nbsp;" 
+				. Html::img('@web/img/ro-crate.svg', ['width'=>'15%'])."</div>";
 		echo '</div>';
+		echo '<div class="rocrate-description">RO-Crate is a community effort to establish a lightweight approach to packaging research data with their metadata. For more details please visit the official '. Html::a('RO-Crate webpage','http://www.researchobject.org/ro-crate/', ['target'=>'_blank']).'.</div>';
 		echo '<div class="inputs">';
 		echo '<div class="modal-body modal-size">';
 		echo  '<div class="row body-row">';
-		echo     "<span class='col-md-7 field-row'>Software public URL $required $software_icon  : </span>";
+		echo     "<span class='col-md-7 field-row'>$soft_type public URL $required $software_icon  : </span>";
 		echo		 '<span class="col-md-5" >'.$form->field($model,'software_url')->label("")->textInput(['value'=>$image_url, 'disabled'=>$disabled, 'disabled'=>$disabled_fields]).'</span>
 				</div>';
+		echo  '<div class="row body-row">
+					<span class="col-md-7 field-row"> Public URL of the output dataset:</span> 
+					<span class="col-md-5">'. $form->field($model,'output')->label("")
+					->textInput(['value'=>$model->output, 'disabled'=>$disabled_fields]).'</span>';
+		echo	'</div>';
+		echo  "<div class='row body-row'>
+					<span class='col-md-7 field-row'> Publication DOI $publication_icon :</span> 
+					<span class='col-md-5'>". $form->field($model,'publication')->label("")
+					->textInput(['value'=>$model->publication, 'disabled'=>$disabled_fields])."</span>
+				</div>";
 		echo "<div class='input-file-fields'>";
 		$i=0;
 
@@ -125,16 +164,6 @@ public static function addModal($jobid)
 			}
 		}
 		echo "</div>";
-		echo  '<div class="row body-row">
-					<span class="col-md-7 field-row"> Public URL of the output dataset:</span> 
-					<span class="col-md-5">'. $form->field($model,'output')->label("")
-					->textInput(['value'=>$model->output, 'disabled'=>$disabled_fields]).'</span>';
-		echo	'</div>';
-		echo  "<div class='row body-row'>
-					<span class='col-md-7 field-row'> Publication DOI $publication_icon :</span> 
-					<span class='col-md-5'>". $form->field($model,'publication')->label("")
-					->textInput(['value'=>$model->publication, 'disabled'=>$disabled_fields])."</span>
-				</div>";
 		echo '</div>';
 		echo '</div>';
 		echo '<div class="modal-footer">';

diff --git a/controllers/SoftwareController.php b/controllers/SoftwareController.php
@@ -28,6 +28,7 @@
 use webvimark\modules\UserManagement\models\User;
 use app\models\RunHistory;
 use app\models\SoftwareInput;
+use app\models\WorkflowInput;
 use app\models\Workflow;
 use yii\data\Pagination;
 
@@ -1653,10 +1654,21 @@ public function actionCreateExperiment($jobid)
 
         $model=new RoCrate();
         $history=RunHistory::find()->where(['jobid'=>$jobid])->one();
-        $software_id=$history->software_id;
-        $software=Software::find()->where(['id'=>$software_id])->one();
-        $fields=SoftwareInput::find()->where(['softwareid'=>$software_id])->orderBy(['position'=> SORT_ASC])->all();
-        $fields=Software::getRerunFieldValues($jobid,$fields);
+        if($history->type=='job')
+        {
+            $software_id=$history->software_id;
+            $software=Software::find()->where(['id'=>$software_id])->one();
+            $fields=SoftwareInput::find()->where(['softwareid'=>$software_id])->orderBy(['position'=> SORT_ASC])->all();
+            $fields=Software::getRerunFieldValues($jobid,$fields);
+        }
+        else
+        {
+            $workflow_id=$history->software_id;
+            $software=Workflow::find()->where(['id'=>$workflow_id])->one();
+            $fields=WorkflowInput::find()->where(['workflow_id'=>$workflow_id])->orderBy(['position'=> SORT_ASC])->all();
+            $fields=Workflow::getRerunFieldValues($jobid,$fields);
+
+        }
 
 
         $input_data=[];
@@ -1682,18 +1694,32 @@ public function actionCreateExperiment($jobid)
             $software_name=$_POST['softname'];
             $software_version=$_POST['softversion'];
             $software_url=$model->software_url;
-            foreach ($model->input as $input_name=>$input_url) 
+
+            if($model->input)
             {
-               $input_data[$input_name]['url']=$input_url;
-
+                foreach ($model->input as $input_name=>$input_url) 
+                {
+                   $input_data[$input_name]['url']=$input_url;
+
+                }
             }
 
 
             $output_data=$model->output;
             $publication=$model->publication;
-
-            $result=ROCrate::CreateROObject($jobid, $software_name,$software_version,$software_url,$input_data,$output_data,$publication);
-            $software=$result[0];
+            if($history->type=='job')
+            {
+                $result=ROCrate::CreateROObjectSoftware($jobid, $software_name,$software_version,$software_url,$input_data,$output_data,$publication);
+            }
+            else
+            {
+                $result=ROCrate::CreateROObjectWorkflow($jobid, $software_name,$software_version,$software_url,$input_data,$output_data,$publication);
+            }
+
+            //$workflow=$result[0];
+
+            // print_r($workflow);
+            // exit(0);
 
             Yii::$app->session->setFlash('success', "$result[1]");
         }

diff --git a/models/RoCrate.php b/models/RoCrate.php
@@ -4,6 +4,7 @@
 
 use Yii;
 use yii\helpers\Html;
+use yii\helpers\Url;
 use webvimark\modules\UserManagement\models\User;
 use app\models\SoftwareInput;
 use app\models\Software;
@@ -60,20 +61,14 @@ public function attributeLabels()
         ];
     }
 
-    public function CreateROObject($jobid, $software_name,$software_version,$software_url,$input_data,$output_data,$publication)
+    public function CreateROObjectSoftware($jobid, $software_name,$software_version,$software_url,$input_data,$output_data,$publication)
     {
 
         $software=Software::find()->where(['name'=>$software_name])->andWhere(['version'=>$software_version])->one();
         $software_id=$software->id;
         $docker=$software->docker_or_local;
-        if(empty($software))
-        {
-            $software=Workflow::find()->where(['name'=>$software_name])->andWhere(['version'=>$software_version])->one();
-
-        }
-
         $software_description=$software->description;
-        $location=empty($software->location)?"$software->cwl_path":"$software->location";
+        $location=$software->cwl_path;
 		$creator=explode('@',$software->uploaded_by)[0];
 
 
@@ -142,8 +137,97 @@ public function CreateROObject($jobid, $software_name,$software_version,$softwar
         Html::a('here', ['software/download-rocrate', 'jobid'=>$jobid]). ".";
 
         exec($command,$out,$ret);
+
+        // print_r($out);
+        // exit(0);
 
 		return [$software, $success];
 
     }
+
+    public function CreateROObjectWorkflow($jobid, $software_name,$software_version,$software_url,$input_data,$output_data,$publication)
+    {
+
+        $workflow=Workflow::find()->where(['name'=>$software_name])->andWhere(['version'=>$software_version])->one();
+        $workflow_id=$workflow->id;
+
+
+        $workflow_description=$workflow->description;
+        $location=$workflow->original_file;
+        $creator=explode('@',$workflow->uploaded_by)[0];
+        $url = Url::base('https');
+        $image=$url. "/img/workflows/$workflow->visualize";
+
+
+
+        $ROCratesFolder=Yii::$app->params['ROCratesFolder'];
+
+        if (!is_dir($ROCratesFolder))
+        {
+            exec("mkdir $ROCratesFolder");
+        }
+        exec("chmod 777 $ROCratesFolder -R 2>&1",$out,$ret);
+
+        $fields=WorkflowInput::find()->where(['workflow_id'=>$workflow_id])->orderBy(['position'=> SORT_ASC])->all();
+        $fields=Workflow::getRerunFieldValues($jobid,$fields);
+        $field_names=[];
+        foreach ($fields as $field) 
+        {
+           $field_names[]=$field->name;
+        }
+
+        $arguments=['software_name'=>$software_name, 
+                    'software_version'=>$software_version,
+                    'software_description'=>$workflow_description, 
+                    'software_url'=>$software_url,
+                    'output_data'=>['id'=>uniqid(), 'data'=>$output_data], 
+                    'publication'=>$publication, 
+                    'ROCratesFolder'=>$ROCratesFolder, 
+                    'location'=>$location,
+                    'creator'=>$creator, 
+                    'jobid'=>$jobid,
+                    'input_data'=>$input_data, 
+                    'number_of_inputs'=>count($input_data),
+                    'field_names'=>$field_names,
+                    'image'=>$image
+
+
+        ];
+
+
+        $username=User::getCurrentUser()['username'];
+
+        $query=Yii::$app->db->createCommand()->delete('ro_crate',["jobid" => $jobid])->execute();
+
+        $query=Yii::$app->db->createCommand()->insert('ro_crate',
+        [
+            "username"=>$username,
+            "jobid" => $jobid,
+            'date'=>'NOW()',
+            'output'=>$output_data,
+            'input'=>json_encode($input_data),
+            'publication'=>$publication,
+            'software_url'=>$software_url,
+        ]
+        )->execute();
+
+
+        $filepath=Yii::$app->params['ROCratesFolder']. 'arguments.json';
+        $arguments_file = fopen($filepath, "w");
+        fwrite($arguments_file, json_encode($arguments));
+        fclose($arguments_file);
+
+        $command="sudo -u ". Yii::$app->params['systemUser'] . " " . Yii::$app->params['scriptsFolder'] . 
+        "ro-crate.py ";
+        $command.= "2>&1";       
+
+        $success="ROCrate object has been created. You can download the ROCrate object by clicking ". 
+        Html::a('here', ['software/download-rocrate', 'jobid'=>$jobid]). ".";
+
+        exec($command,$out,$ret);
+
+
+        return [$workflow, $success];
+
+    }
 }
diff --git a/scheduler_files/ro-crate.py b/scheduler_files/ro-crate.py
@@ -25,12 +25,8 @@
   data = json.load(f)
 
 
-# inputs=data['input_data']['0']
-# print(data['input_data']['0'])
 
 
-# print(data['software_description'])
-
 wf_path = data['location']
 files_list = []
 
@@ -43,6 +39,8 @@
 wf_crate.name = data['software_name']
 wf_crate.description=data['software_description']
 wf_crate.creator=data['creator']
+print(data['image'])
+wf_crate.image = data['image']
 
 main_entity = entity.Entity(wf_crate, data['software_url'],
             properties={
@@ -52,7 +50,7 @@
                 "@type": ["File", "SoftwareSourceCode"],
                 "input": [ "{@id: #" + data['input_data']["%s"%x]['id']+"}" for x in data['field_names']],
                 "output": [{"@id": "#" + data['output_data']['id']}],
-                "version": data['version']
+                "version": data['software_version']
                 },
                  )
 

diff --git a/views/layouts/main.php b/views/layouts/main.php
@@ -172,7 +172,9 @@
 <footer class="footer bg-light">
     <div class="container">
         <p class="pull-left">&copy; Athena RC <?= date('Y') ?></p>
-        <p class="col-md-offset-4 col-md-3"><?=$footerImageLink?></p>
+        <p class="powered col-md-2">Powered by  <?= Html::a('Schema', 'https://github.com/athenarc/schema', 
+        ['target'=>'_blank'])?></p>
+        <p class="col-md-offset-2 col-md-3"><?=$footerImageLink?></p>
         <p class="col-md-offset-1 col-md-2"><?=Html::a('Privacy & cookie policy','https://egci-beta.imsi.athenarc.gr/index.php?r=site/privacy')?></p>
         <p class="pull-right"><?=$twitter_link?>&nbsp;<?=$youtube_link?></p>
     </div>