OG-609 orthologs to purple form

app/assets/js/gene.js

@@ -177,12 +177,79 @@ $(document).on('click', '#experiments-form .js-experiment-short', function() {
 
 $(document).on('click', '#experiments-form .js-lifespan-experiment-short', function() {
     let modelId = $(this).attr('model-id')
-    let container =  $(this).closest('.js-short-form-container')
+    let container = $(this).closest('.js-short-form-container')
     $.get('/gene/load-widget-form?modelName=LifespanExperiment&widgetName=GeneralLifespanExperimentWidget&id='
-        +modelId
-        +'&modelParams[gene_id]='+$(this).attr('gene-id')
-        +'&modelParams[type]=experiment'
-        +'&geneId='+$(this).attr('gene-id'), function (data) {
+        + modelId
+        + '&modelParams[gene_id]=' + $(this).attr('gene-id')
+        + '&modelParams[type]=experiment'
+        + '&geneId=' + $(this).attr('gene-id'), function (data) {
         container.html(data);
+    })
+})
+
+//ортологи в эксперименты
+$(document).on('change', '#experiments-form .js-lifespan-experiment-block [id$="model_organism_id"]', function() {
+    let t = $(this);
+    let model_organism_id = t.val();
+    let gene_id = $('.js-lifespan-experiment-block [name$="[currentGeneId]"]').val();
+    $.get('/gene/get-orthologs?modelOrganismId='+model_organism_id+'&geneId='+gene_id, function (data) {
+        let orthologs = JSON.parse(data);
+        let select = t.parents('.js-lifespan-experiment').find('.js-lifespan-experiments-gene .orthologs');
+        select.empty();
+        let options = Object.entries(orthologs);
+        for (const [id, symbol] of options) {
+            select.append($('<option>', {
+                value: id,
+                text: symbol
+            }));
+        }
+        if (options.length == 1) {
+            select.val(options[0][0]);
+        }
+        select.change();
+    });
+});
+
+//запрет изменения организма при существующем доп воздействии
+$(document).on('click', '.js-add-lifespan-experiment-control, .js-add-lifespan-experiment-gene', function() {
+    let t = $(this);
+    let general_le_name = t.parents('.js-gene-link-section').find('input[name^="GeneralLifespanExperiment"')[0].name;
+    let matches = general_le_name.match(/GeneralLifespanExperiment\[(\d+)\]\[(\w+)\]/);
+    let general_le_id = matches[1];
+    let select = $('select#generallifespanexperiment-'+general_le_id+'-model_organism_id');
+
+    select.data('data-value', select.val())
+    $('select#generallifespanexperiment-'+general_le_id+'-model_organism_id').next().children().each(function () {
+        $(this).css('pointer-events', 'none');
+    });
+    $('#select2-generallifespanexperiment-'+general_le_id+'-model_organism_id-container')
+        .parents('[aria-labelledby="select2-generallifespanexperiment-'+general_le_id+'-model_organism_id-container"]')
+        .css('background-color', '#d6d8d9').css('border-color', '#c6c8ca');
+    $('#select2-generallifespanexperiment-'+general_le_id+'-model_organism_id-container .select2-selection__clear').css('display', 'none');
+})
+
+//ортологи при изменении гена в доп воздействии
+$(document).on('change', '.js-lifespan-experiment [id$="gene_id"]', function() {
+    let t = $(this);
+    let gene_id = t.val();
+    let select = t.parents('.js-lifespan-experiment').parents('.js-lifespan-experiment').find('[id$="model_organism_id"]');
+    console.log(select);
+    let model_organism_id = select.data('data-value');
+
+    $.get('/gene/get-orthologs?modelOrganismId='+model_organism_id+'&geneId='+gene_id, function (data) {
+        let orthologs = JSON.parse(data);
+        let select = t.parents('.gene-modulation.js-gene-link-section').find('.orthologs');
+        select.empty();
+        let options = Object.entries(orthologs);
+        for (const [id, symbol] of options) {
+            select.append($('<option>', {
+                value: id,
+                text: symbol
+            }));
+        }
+        if (options.length == 1) {
+            select.val(options[0][0]);
+        }
+        select.change();
     });
 });

app/controllers/GeneController.php

@@ -9,6 +9,7 @@
 use app\models\GeneToAdditionalEvidence;
 use app\models\GeneToLongevityEffect;
 use app\models\GeneToProgeria;
+use app\models\Ortholog;
 use app\models\Phylum;
 use app\models\CommentCause;
 use app\models\Gene;
@@ -47,7 +48,7 @@ public function behaviors()
                 'rules' => [
                     [
                         'allow' => true,
-                        'actions' => ['index', 'update', 'update-experiments', 'update-functions', 'update-age-related-changes', 'load-widget-form'],
+                        'actions' => ['index', 'update', 'update-experiments', 'update-functions', 'update-age-related-changes', 'load-widget-form', 'get-orthologs'],
                         'roles' => ['admin', 'editor', 'contributor'],
                     ],
                     [
@@ -233,6 +234,10 @@ public function actionLoadWidgetForm($id, string $modelName, string $widgetName,
         return $this->renderAjax('_geneLinkWidgetForm', ['model' => $model, 'widgetName' => $widgetName, 'params' => $params]);
     }
 
+    public function actionGetOrthologs(int $modelOrganismId, int $geneId) {
+        return json_encode(Ortholog::getByOrganismAndGene($modelOrganismId, $geneId));
+    }
+
     /**
      * Finds the Gene model based on its primary key value.
      * If the model is not found, a 404 HTTP exception will be thrown.

app/migrations/m220325_103131_lifespan_experiment_to_ortholog.php

@@ -0,0 +1,58 @@
+<?php
+
+use yii\db\Migration;
+use yii\db\Schema;
+
+/**
+ * Class m220325_103131_lifespan_experiment_to_ortholog
+ */
+class m220325_103131_lifespan_experiment_to_ortholog extends Migration
+{
+    /**
+     * {@inheritdoc}
+     */
+    public function safeUp()
+    {
+        $this->createTable('lifespan_experiment_to_ortholog', [
+            'id' => Schema::TYPE_PK,
+            'lifespan_experiment_id' => Schema::TYPE_INTEGER,
+            'ortholog_id' => Schema::TYPE_INTEGER,
+        ], 'CHARACTER SET utf8 COLLATE utf8_general_ci ENGINE=InnoDB');
+
+        $this->addForeignKey('le_to_ortholog_to_le', 'lifespan_experiment_to_ortholog', 'lifespan_experiment_id', 'lifespan_experiment', 'id', 'CASCADE');
+        $this->addForeignKey('le_to_ortholog_to_ortholog', 'lifespan_experiment_to_ortholog', 'ortholog_id', 'ortholog', 'id', 'CASCADE');
+
+        Yii::$app->db->createCommand(
+            'INSERT INTO lifespan_experiment_to_ortholog (lifespan_experiment_id, ortholog_id)
+                    SELECT le.id, o.id FROM lifespan_experiment le
+                    JOIN general_lifespan_experiment gle ON le.general_lifespan_experiment_id = gle.id
+                    JOIN ortholog o ON gle.model_organism_id=o.model_organism_id
+                    JOIN gene_to_ortholog gto ON o.id = gto.ortholog_id
+                    WHERE le.gene_id = gto.gene_id');
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    public function safeDown()
+    {
+        $this->dropForeignKey('le_to_ortholog_to_le', 'lifespan_experiment_to_ortholog');
+        $this->dropForeignKey('le_to_ortholog_to_ortholog', 'lifespan_experiment_to_ortholog');
+        $this->dropTable('lifespan_experiment_to_ortholog');
+    }
+
+    /*
+    // Use up()/down() to run migration code without a transaction.
+    public function up()
+    {
+
+    }
+
+    public function down()
+    {
+        echo "m220325_103131_lifespan_experiment_to_ortholog cannot be reverted.\n";
+
+        return false;
+    }
+    */
+}

app/models/LifespanExperiment.php

@@ -5,9 +5,11 @@
 use app\models\behaviors\ChangelogBehavior;
 use app\models\common\GeneralLifespanExperimentQuery;
 use app\models\common\LifespanExperimentQuery;
+use app\models\common\LifespanExperimentToOrtholog;
 use app\models\exceptions\UpdateExperimentsException;
 use app\models\traits\ExperimentsActiveRecordTrait;
 use app\models\traits\ValidatorsTrait;
+use Yii;
 use yii\behaviors\TimestampBehavior;
 use yii\db\ActiveRecord;
 use yii\helpers\ArrayHelper;
@@ -21,9 +23,13 @@ class LifespanExperiment extends common\LifespanExperiment
     use ValidatorsTrait;
     use ExperimentsActiveRecordTrait;
 
+    public const TYPE_ORTHOLOG = 1;
+    public const TYPE_TISSUE = 2;
     public $delete = false;
     public $tissuesIds;
     private $tissuesIdsArray;
+    private $orthologIds = [];
+    private $modelOrganismId;
 
     public function behaviors()
     {
@@ -58,7 +64,7 @@ public function rules()
         return ArrayHelper::merge(
             parent::rules(), [
             [['gene_id', 'gene_intervention_method_id'], 'safe'], // todo OG-410
-            [['tissuesIds', 'intervention_result_id'], 'safe'],
+            [['tissuesIds', 'intervention_result_id', 'orthologIds'], 'safe'],
             [['age'], 'number', 'min' => 0],
             [['reference'], 'validateDOI']
         ]);
@@ -107,7 +113,14 @@ public function beforeValidate()
 
         return parent::beforeValidate();
     }
+    public function afterSave($insert, $changedAttributes)
+    {
+        if (Yii::$app instanceof \yii\console\Application) { // todo продумать нормальный фикс
+            return parent::afterSave($insert, $changedAttributes);
+        }
 
+        parent::afterSave($insert, $changedAttributes);
+    }
 
     /**
      * Gets query for [[GeneralLifespanExperiment]].
@@ -174,6 +187,8 @@ public static function saveMultipleForGene(array $modelArrays)
             self::setAttributeFromNewAR($modelArray, 'treatment_end_stage_of_development_id', 'TreatmentStageOfDevelopment', $modelAR);
             self::setAttributeFromNewAR($modelArray, 'genotype', 'Genotype', $modelAR);
 
+//            Ortholog::createNewByIds($modelArray['orthologIds'], $modelAR->general_lifespan_experiment_id, $modelAR->gene_id);
+
             if ($modelAR->organism_line_id === '') {
                 $modelAR->organism_line_id = null;
             }
@@ -183,10 +198,58 @@ public static function saveMultipleForGene(array $modelArrays)
             if (!$modelAR->validate() || !$modelAR->save()) {
                 throw new UpdateExperimentsException($id, $modelAR);
             }
-            $modelAR->saveTissues($modelArray['tissuesIdsArray']);
+            $modelAR->saveForeignEntity(self::TYPE_TISSUE, $modelArray['tissuesIdsArray']);
+//            $modelAR->saveTissues($modelArray['tissuesIdsArray']);
+//            $modelAR->saveOrthologs($modelArray['orthologIds']);
+            $modelAR->saveForeignEntity(self::TYPE_ORTHOLOG,
+                                                    $modelArray['orthologIds'],
+                                                    $modelAR->general_lifespan_experiment_id,
+                                                    $modelAR->gene_id
+            );
         }
     }
 
+    public function getTissuesIdsArray()
+    {
+        return LifespanExperimentToTissue::find()
+            ->select('tissue_id')
+            ->where(['lifespan_experiment_id' => $this->id])
+            ->asArray()
+            ->column();
+    }
+
+    public function setTissuesIdsArray(array $ids)
+    {
+        $this->tissuesIdsArray = $ids;
+    }
+    public function setOrthologIds($ids)
+    {
+        if (!$ids) {
+            $ids = [];
+        }
+        $this->orthologIds = $ids;
+    }
+
+    public function getOrthologIds()
+    {
+        return LifespanExperimentToOrtholog::find()
+            ->select('ortholog_id')
+            ->where(['lifespan_experiment_id' => $this->id])
+            ->asArray()
+            ->column();
+    }
+
+    public function setModelOrganismId($id)
+    {
+        $this->modelOrganismId = $id;
+    }
+
+    public function getModelOrganismId()
+    {
+        return $this->getGeneralLifespanExperiment()
+            ->select('model_organism_id')->distinct()->one()->model_organism_id;
+    }
+
     private function saveTissues($tissuesIdsArray)
     {
         $currentTissuesIdsArray = $this->getTissuesIdsArray();
@@ -220,19 +283,83 @@ private function saveTissues($tissuesIdsArray)
         }
     }
 
-
-    public function getTissuesIdsArray()
+    private function saveOrthologs($orthologIds, $typeRelations, $generalLe = false, $geneId = false)
     {
-        return LifespanExperimentToTissue::find()
-            ->select('tissue_id')
-            ->where(['lifespan_experiment_id' => $this->id])
-            ->asArray()
-            ->column();
+        $currentOrthologIds = $this->getOrthologIds();
+
+        if ($currentOrthologIds !== $orthologIds) {
+            if ($orthologIds) {
+                $orthologIdsToDelete = array_diff($currentOrthologIds, $orthologIds);
+                $orthologIdsToAdd = array_diff($orthologIds, $currentOrthologIds);
+
+                foreach ($orthologIdsToAdd as $orthologIdToAdd) {
+                    if (!is_numeric($orthologIdToAdd)) {
+                        $orthologToAdd = Ortholog::createNewByName($orthologIdToAdd, $generalLe, $geneId);
+                        $orthologIdToAdd = $orthologToAdd->id;
+                    }
+                    $lifespanExperimentToTissue = new LifespanExperimentToOrtholog();
+                    $lifespanExperimentToTissue->lifespan_experiment_id = $this->id;
+                    $lifespanExperimentToTissue->tissue_id = $orthologIdToAdd;
+                    $lifespanExperimentToTissue->save();
+                }
+            } else {
+                $orthologIdsToDelete = $currentOrthologIds;
+            }
+
+            $arsToDelete = LifespanExperimentToOrtholog::find()->where(
+                ['and', ['lifespan_experiment_id' => $this->id],
+                    ['in', 'ortholog_id', $orthologIdsToDelete]]
+            )->all();
+            foreach ($arsToDelete as $arToDelete) { // one by one for properly triggering "afterDelete" event
+                $arToDelete->delete();
+            }
+        }
     }
 
-    public function setTissuesIdsArray(array $ids)
+    private function saveForeignEntity($typeRelations, $newIds, $generalLe = false, $geneId = false)
     {
-        $this->tissuesIdsArray = $ids;
-    }
+        if($typeRelations == 1) {
+            $relationKey = 'ortholog_id';
+            $relationClass = LifespanExperimentToOrtholog::class;
+            $currentIds = $this->getOrthologIds();
+        }
+        elseif($typeRelations == 2){
+            $relationKey = 'tissue_id';
+            $relationClass = LifespanExperimentToTissue::class;
+            $currentIds = $this->getTissuesIdsArray();
+        }
+
+        if ($currentIds !== $newIds) {
+            if ($newIds) {
+                $IdsToDelete = array_diff($currentIds, $newIds);
+                $idsToAdd = array_diff($newIds, $currentIds);
+
+                foreach ($idsToAdd as $idToAdd) {
+                    if (!is_numeric($idToAdd)) {
+                        if ($typeRelations == 1) {
+                            $entityToAdd = Ortholog::createNewByName($idToAdd, $generalLe, $geneId);
+                        }
+                        elseif($typeRelations == 2) {
+                            $entityToAdd = Sample::createFromNameString($idToAdd);
+                        }
+                        $idToAdd = $entityToAdd->id;
+                    }
+                    $lifespanExperimentToEntity = new $relationClass;
+                    $lifespanExperimentToEntity->lifespan_experiment_id = $this->id;
+                    $lifespanExperimentToEntity->$relationKey = $idToAdd;
+                    $lifespanExperimentToEntity->save();
+                }
+            } else {
+                $IdsToDelete = $currentIds;
+            }
 
+            $arsToDelete = $relationClass::find()->where(
+                ['and', ['lifespan_experiment_id' => $this->id],
+                    ['in', $relationKey, $IdsToDelete]]
+            )->all();
+            foreach ($arsToDelete as $arToDelete) { // one by one for properly triggering "afterDelete" event
+                $arToDelete->delete();
+            }
+        }
+    }
 }