From 7cea5c31def2b3da66e539648270ae5907ebcd46 Mon Sep 17 00:00:00 2001
From: "j.belova" <fridadet@gmail.com>
Date: Sat, 5 Mar 2022 13:07:41 +0300
Subject: [PATCH 1/4] OG-609 orthologs to purple form

---
 app/assets/js/gene.js                         | 74 ++++++++++++++--
 app/controllers/GeneController.php            |  7 +-
 app/models/LifespanExperiment.php             | 87 +++++++++++++++----
 app/models/Ortholog.php                       | 73 ++++++++++++++++
 app/widgets/views/full/lifespanExperiment.php | 23 +++++
 5 files changed, 241 insertions(+), 23 deletions(-)

diff --git a/app/assets/js/gene.js b/app/assets/js/gene.js
index 011d3b37..9c5298c1 100644
--- a/app/assets/js/gene.js
+++ b/app/assets/js/gene.js
@@ -177,12 +177,76 @@ $(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=' + $(this).attr('gene-id'), function (data) {
         container.html(data);
+    })
+})
+
+$(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();
+    });
+});
+
+$(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];
+    $('select#generallifespanexperiment-'+general_le_id+'-model_organism_id option').attr('disabled', 'disabled');
+    $('#select2-generallifespanexperiment-'+general_le_id+'-model_organism_id-container').css('cursor', 'not-allowed');
+    $('#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');
+    $('#select2-generallifespanexperiment-'+general_le_id+'-model_organism_id-container .select2-selection__clear').css('display', 'none');
+    let interval;
+    interval = setInterval(function () {
+        if($('[aria-controls="select2-generallifespanexperiment-'+general_le_id+'-model_organism_id-results"]').length) {
+            $('[aria-controls="select2-generallifespanexperiment-'+general_le_id+'-model_organism_id-results"]').hide();
+            clearInterval(interval);
+        }
+    }, 500)
+})
+
+$(document).on('change', '.js-lifespan-experiment [id$="gene_id"]', function() {
+    let t = $(this);
+    let gene_id = t.val();
+    let model_organism_id = t.parents('.js-lifespan-experiment').parents('.js-lifespan-experiment').find('[id$="model_organism_id"]').val();
+    $.get('/gene/get-orthologs?modelOrganismId='+model_organism_id+'&geneId='+gene_id, function (data) {
+        let orthologs = JSON.parse(data);
+        let select = t.parents('.gene-modulation.js-gene-link-section').find('.orthologs');
+        select.empty();
+        let options = Object.entries(orthologs);
+        for (const [id, symbol] of options) {
+            select.append($('<option>', {
+                value: id,
+                text: symbol
+            }));
+        }
+        if (options.length == 1) {
+            select.val(options[0][0]);
+        }
+        select.change();
     });
 });
\ No newline at end of file
diff --git a/app/controllers/GeneController.php b/app/controllers/GeneController.php
index b5ea294b..efeaeff2 100755
--- a/app/controllers/GeneController.php
+++ b/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.
diff --git a/app/models/LifespanExperiment.php b/app/models/LifespanExperiment.php
index 04240851..0b5a1910 100755
--- a/app/models/LifespanExperiment.php
+++ b/app/models/LifespanExperiment.php
@@ -8,6 +8,7 @@
 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;
@@ -24,6 +25,8 @@ class LifespanExperiment extends common\LifespanExperiment
     public $delete = false;
     public $tissuesIds;
     private $tissuesIdsArray;
+    private $orthologIds = [];
+    private $modelOrganismId;
 
     public function behaviors()
     {
@@ -58,7 +61,7 @@ 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 +110,15 @@ 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);
+        }
+        $this->orthologIds = $this->getOrthologsIdsByNames($this->orthologIds);
 
+        parent::afterSave($insert, $changedAttributes);
+    }
 
     /**
      * Gets query for [[GeneralLifespanExperiment]].
@@ -174,6 +185,8 @@ 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;
             }
@@ -187,6 +200,62 @@ public static function saveMultipleForGene(array $modelArrays)
         }
     }
 
+    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()
+    {
+        $modelOrganismId = $this->getModelOrganismId();
+
+        return Ortholog::find()
+            ->select('ortholog.id')
+            ->innerJoin('gene_to_ortholog', 'ortholog.id=gene_to_ortholog.ortholog_id')
+            ->where(['ortholog.model_organism_id' => $modelOrganismId])
+            ->andWhere(['gene_to_ortholog.gene_id' => $this->gene_id])
+            ->asArray()
+            ->column();
+    }
+
+    public function setModelOrganismId($id)
+    {
+        $this->modelOrganismId = $id;
+    }
+
+    public function getModelOrganismId()
+    {
+        return $this->getGeneralLifespanExperiment()
+            ->select('model_organism_id')->distinct()->one()->model_organism_id;
+    }
+
+    public function getOrthologsIdsByNames($arOrthologs)
+    {
+        foreach ($arOrthologs as &$ortholog) {
+            if(is_numeric($ortholog)) {
+                continue;
+            }
+            $ortholog = (string)Ortholog::getIdByName($ortholog)->id;
+        }
+        return $arOrthologs;
+    }
+
     private function saveTissues($tissuesIdsArray)
     {
         $currentTissuesIdsArray = $this->getTissuesIdsArray();
@@ -219,20 +288,4 @@ private function saveTissues($tissuesIdsArray)
             }
         }
     }
-
-
-    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;
-    }
-
 }
diff --git a/app/models/Ortholog.php b/app/models/Ortholog.php
index f4c130c9..d416b9cc 100644
--- a/app/models/Ortholog.php
+++ b/app/models/Ortholog.php
@@ -74,4 +74,77 @@ public function getLinkedGenesIds()
         return []; // todo implement for column with related genes
     }
 
+    public static function createNewByIds($ids, $generalLifespanId, $geneId)
+    {
+        $modelOrganismId = self::getCurrentModelOrganismId($generalLifespanId);
+        if (!empty($ids) && is_array($ids)) {
+            foreach ($ids as $id) {
+                if (is_numeric($id)) {
+                    continue;
+                }
+                $newOrtholog = self::createFromNameString($id, $modelOrganismId);
+                self::createRelationToGene($geneId, $newOrtholog->id);
+            }
+        }
+    }
+
+    public static function getIdByName($name) {
+        return self::find()->select('id')->where(
+                ['symbol' => $name]
+        )->one();
+    }
+
+    public static function getByOrganismAndGene($modelOrganismId, $geneId){
+        $orthologs = self::find()
+            ->select(['ortholog.id', 'ortholog.symbol'])
+            ->innerJoin('gene_to_ortholog', 'ortholog.id=gene_to_ortholog.ortholog_id')
+            ->where(['ortholog.model_organism_id' => $modelOrganismId])
+            ->andWhere(['gene_to_ortholog.gene_id' => $geneId])
+            ->asArray()
+            ->all();
+        $result = [];
+        foreach ($orthologs as $ortholog) {
+            $result[$ortholog['id']] = "{$ortholog['symbol']}";
+        }
+        return $result;
+
+    }
+
+    public static function getByGeneralLe($generalId, $geneId)
+    {
+        $modelOrganismId = self::getCurrentModelOrganismId($generalId);
+        return self::getByOrganismAndGene($modelOrganismId, $geneId);
+
+    }
+
+    private static function createRelationToGene($geneId, $orthologId) {
+        $geneToRelation = new GeneToOrtholog();
+        $geneToRelation->gene_id = $geneId;
+        $geneToRelation->ortholog_id = $orthologId;
+        $geneToRelation->save();
+    }
+
+
+    private static function createFromNameString(string $symbol, int $modelOrganismId) {
+        $model = parent::find()
+            ->where(['symbol' => $symbol])
+            ->andWhere(['model_organism_id' => $modelOrganismId])
+            ->one();
+        if(!$model) {
+            $model = new self();
+            $model->symbol = $symbol;
+            $model->model_organism_id = $modelOrganismId;
+            $model->save();
+        }
+        return $model;
+    }
+
+    private static function getCurrentModelOrganismId($generalLifespanId)
+    {
+        return GeneralLifespanExperiment::find()
+            ->select(['model_organism_id'])
+            ->where(['id' => $generalLifespanId])
+            ->one()
+            ->model_organism_id;
+    }
 }
diff --git a/app/widgets/views/full/lifespanExperiment.php b/app/widgets/views/full/lifespanExperiment.php
index 94390541..b77c9645 100644
--- a/app/widgets/views/full/lifespanExperiment.php
+++ b/app/widgets/views/full/lifespanExperiment.php
@@ -47,6 +47,29 @@
         <?php else: ?>
             <?= \yii\helpers\Html::hiddenInput('LifespanExperiment[' . $lifespanExperiment->id . '][gene_id]', $lifespanExperiment->gene_id) ?>
         <?php endif; ?>
+        <div class="row form-row">
+            <div class="col-xs-6 col-md-3">
+                <?= \kartik\select2\Select2::widget([
+                    'model' => $lifespanExperiment,
+                    'attribute' => '[' . $lifespanExperiment->id . ']orthologIds',
+                    'data' => \app\models\Ortholog::getByGeneralLe(
+                            $lifespanExperiment->general_lifespan_experiment_id,
+                            $lifespanExperiment->gene_id
+                    ),
+                    'options' => [
+                        'placeholder' => 'Ортологи',
+                        'multiple' => true,
+                        'class' => 'orthologs'
+                    ],
+                    'pluginOptions' => [
+                        'allowClear' => true,
+                        'tags' => true,
+                        'tokenSeparators' => ['##'],
+                    ],
+                ]);
+                ?>
+            </div>
+        </div>
         <div class="row form-row">
             <?= \yii\helpers\Html::hiddenInput('LifespanExperiment[' . $lifespanExperiment->id . '][type]', $lifespanExperiment->type) ?>
             <?= \yii\helpers\Html::hiddenInput('LifespanExperiment[' . $lifespanExperiment->id . '][general_lifespan_experiment_id]', $lifespanExperiment->general_lifespan_experiment_id) ?>

From fb5150b34d770a3a9717293a986674357b6968bf Mon Sep 17 00:00:00 2001
From: "j.belova" <fridadet@gmail.com>
Date: Fri, 25 Mar 2022 13:23:07 +0300
Subject: [PATCH 2/4] OG-609 bug fix

---
 app/assets/js/gene.js | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/app/assets/js/gene.js b/app/assets/js/gene.js
index 9c5298c1..ab249150 100644
--- a/app/assets/js/gene.js
+++ b/app/assets/js/gene.js
@@ -187,6 +187,7 @@ $(document).on('click', '#experiments-form .js-lifespan-experiment-short', funct
     })
 })
 
+//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();
@@ -209,30 +210,32 @@ $(document).on('change', '#experiments-form .js-lifespan-experiment-block [id$="
     });
 });
 
+//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];
-    $('select#generallifespanexperiment-'+general_le_id+'-model_organism_id option').attr('disabled', 'disabled');
-    $('#select2-generallifespanexperiment-'+general_le_id+'-model_organism_id-container').css('cursor', 'not-allowed');
+    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');
     $('#select2-generallifespanexperiment-'+general_le_id+'-model_organism_id-container .select2-selection__clear').css('display', 'none');
-    let interval;
-    interval = setInterval(function () {
-        if($('[aria-controls="select2-generallifespanexperiment-'+general_le_id+'-model_organism_id-results"]').length) {
-            $('[aria-controls="select2-generallifespanexperiment-'+general_le_id+'-model_organism_id-results"]').hide();
-            clearInterval(interval);
-        }
-    }, 500)
 })
 
+//ортологи при изменении гена в доп воздействии
 $(document).on('change', '.js-lifespan-experiment [id$="gene_id"]', function() {
     let t = $(this);
     let gene_id = t.val();
-    let model_organism_id = t.parents('.js-lifespan-experiment').parents('.js-lifespan-experiment').find('[id$="model_organism_id"]').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');

From 2af22fab114412cfb66c7ab2937b07a5f102af4a Mon Sep 17 00:00:00 2001
From: "j.belova" <fridadet@gmail.com>
Date: Fri, 25 Mar 2022 14:11:10 +0300
Subject: [PATCH 3/4] OG-609 migration le to ortholog

---
 ...103131_lifespan_experiment_to_ortholog.php | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 app/migrations/m220325_103131_lifespan_experiment_to_ortholog.php

diff --git a/app/migrations/m220325_103131_lifespan_experiment_to_ortholog.php b/app/migrations/m220325_103131_lifespan_experiment_to_ortholog.php
new file mode 100644
index 00000000..919def80
--- /dev/null
+++ b/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;
+    }
+    */
+}

From 5b32dc03a4fae6b11314ea2edc0d81df823910f0 Mon Sep 17 00:00:00 2001
From: "j.belova" <fridadet@gmail.com>
Date: Mon, 28 Mar 2022 14:21:50 +0300
Subject: [PATCH 4/4] OG-609 orthologs refactor

---
 app/models/LifespanExperiment.php             | 116 ++++++++++++++----
 app/models/LifespanExperimentToOrtholog.php   |  77 ++++++++++++
 app/models/Ortholog.php                       |  29 +++--
 .../common/LifespanExperimentToOrtholog.php   |  79 ++++++++++++
 .../LifespanExperimentToOrthologQuery.php     |  34 +++++
 5 files changed, 305 insertions(+), 30 deletions(-)
 create mode 100644 app/models/LifespanExperimentToOrtholog.php
 create mode 100644 app/models/common/LifespanExperimentToOrtholog.php
 create mode 100644 app/models/common/LifespanExperimentToOrthologQuery.php

diff --git a/app/models/LifespanExperiment.php b/app/models/LifespanExperiment.php
index 0b5a1910..7c7d6be9 100755
--- a/app/models/LifespanExperiment.php
+++ b/app/models/LifespanExperiment.php
@@ -5,6 +5,7 @@
 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;
@@ -22,6 +23,8 @@ 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 $tissuesIdsArray;
@@ -115,7 +118,6 @@ public function afterSave($insert, $changedAttributes)
         if (Yii::$app instanceof \yii\console\Application) { // todo продумать нормальный фикс
             return parent::afterSave($insert, $changedAttributes);
         }
-        $this->orthologIds = $this->getOrthologsIdsByNames($this->orthologIds);
 
         parent::afterSave($insert, $changedAttributes);
     }
@@ -185,7 +187,7 @@ 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, $modelAR->gene_id);
+//            Ortholog::createNewByIds($modelArray['orthologIds'], $modelAR->general_lifespan_experiment_id, $modelAR->gene_id);
 
             if ($modelAR->organism_line_id === '') {
                 $modelAR->organism_line_id = null;
@@ -196,7 +198,14 @@ 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
+            );
         }
     }
 
@@ -223,13 +232,9 @@ public function setOrthologIds($ids)
 
     public function getOrthologIds()
     {
-        $modelOrganismId = $this->getModelOrganismId();
-
-        return Ortholog::find()
-            ->select('ortholog.id')
-            ->innerJoin('gene_to_ortholog', 'ortholog.id=gene_to_ortholog.ortholog_id')
-            ->where(['ortholog.model_organism_id' => $modelOrganismId])
-            ->andWhere(['gene_to_ortholog.gene_id' => $this->gene_id])
+        return LifespanExperimentToOrtholog::find()
+            ->select('ortholog_id')
+            ->where(['lifespan_experiment_id' => $this->id])
             ->asArray()
             ->column();
     }
@@ -245,17 +250,6 @@ public function getModelOrganismId()
             ->select('model_organism_id')->distinct()->one()->model_organism_id;
     }
 
-    public function getOrthologsIdsByNames($arOrthologs)
-    {
-        foreach ($arOrthologs as &$ortholog) {
-            if(is_numeric($ortholog)) {
-                continue;
-            }
-            $ortholog = (string)Ortholog::getIdByName($ortholog)->id;
-        }
-        return $arOrthologs;
-    }
-
     private function saveTissues($tissuesIdsArray)
     {
         $currentTissuesIdsArray = $this->getTissuesIdsArray();
@@ -288,4 +282,84 @@ private function saveTissues($tissuesIdsArray)
             }
         }
     }
+
+    private function saveOrthologs($orthologIds, $typeRelations, $generalLe = false, $geneId = false)
+    {
+        $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
+                $arToDelete->delete();
+            }
+        }
+    }
+
+    private function saveForeignEntity($typeRelations, $newIds, $generalLe = false, $geneId = false)
+    {
+        if($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();
+            }
+        }
+    }
 }
diff --git a/app/models/LifespanExperimentToOrtholog.php b/app/models/LifespanExperimentToOrtholog.php
new file mode 100644
index 00000000..6a641a79
--- /dev/null
+++ b/app/models/LifespanExperimentToOrtholog.php
@@ -0,0 +1,77 @@
+<?php
+
+namespace app\models;
+
+use app\models\behaviors\ChangelogBehavior;
+use app\models\traits\RuEnActiveRecordTrait;
+use Yii;
+
+/**
+ * This is the model class for table "lifespan_experiment_to_ortholog".
+ *
+ * @property int $id
+ * @property int|null $lifespan_experiment_id
+ * @property int|null $ortholog_id
+ *
+ * @property LifespanExperiment $lifespanExperiment
+ * @property Ortholog $ortholog
+ */
+class LifespanExperimentToOrtholog extends common\LifespanExperimentToOrtholog
+{
+    use RuEnActiveRecordTrait;
+
+    public $name;
+
+    /**
+    * {@inheritdoc}
+    */
+    public function behaviors()
+    {
+        return [
+            ChangelogBehavior::class
+        ];
+    }
+
+    /**
+    * {@inheritdoc}
+    */
+    public function attributeLabels()
+    {
+        return [
+                    'id' => 'ID',
+                    'lifespan_experiment_id' => 'Lifespan Experiment ID',
+                    'ortholog_id' => 'Ortholog ID',
+                ];
+    }
+
+
+    /**
+    * Gets query for [[LifespanExperiment]].
+    *
+    * @return \yii\db\ActiveQuery|\app\models\common\LifespanExperimentQuery
+    */
+    public function getLifespanExperiment()
+    {
+    return $this->hasOne(LifespanExperiment::class, ['id' => 'lifespan_experiment_id']);
+    }
+
+    /**
+    * Gets query for [[Ortholog]].
+    *
+    * @return \yii\db\ActiveQuery|\app\models\common\OrthologQuery
+    */
+    public function getOrtholog()
+    {
+    return $this->hasOne(Ortholog::class, ['id' => 'ortholog_id']);
+    }
+
+    public function getLinkedGenesIds()
+    {
+        return []; // todo implement for column with related genes
+    }
+
+    public static function getOrthologByName($name) {
+        return self::find()->select('ortholog_id')
+            ->where(['symbol' => $name])->one();
+    }
+}
diff --git a/app/models/Ortholog.php b/app/models/Ortholog.php
index d416b9cc..6fd42901 100644
--- a/app/models/Ortholog.php
+++ b/app/models/Ortholog.php
@@ -74,18 +74,29 @@ public function getLinkedGenesIds()
         return []; // todo implement for column with related genes
     }
 
-    public static function createNewByIds($ids, $generalLifespanId, $geneId)
+//    public static function createNewByIds($ids, $generalLifespanId, $geneId)
+//    {
+//        $modelOrganismId = self::getCurrentModelOrganismId($generalLifespanId);
+//        if (!empty($ids) && is_array($ids)) {
+//            foreach ($ids as $id) {
+//                if (is_numeric($id)) {
+//                    continue;
+//                }
+//                $newOrtholog = self::createFromNameString($id, $modelOrganismId);
+//                self::createRelationToGene($geneId, $newOrtholog->id);
+//            }
+//        }
+//    }
+
+    public static function createNewByName($name, $generalLifespanId, $geneId)
     {
+        $newOrtholog = [];
         $modelOrganismId = self::getCurrentModelOrganismId($generalLifespanId);
-        if (!empty($ids) && is_array($ids)) {
-            foreach ($ids as $id) {
-                if (is_numeric($id)) {
-                    continue;
-                }
-                $newOrtholog = self::createFromNameString($id, $modelOrganismId);
-                self::createRelationToGene($geneId, $newOrtholog->id);
-            }
+        if (!empty($name)) {
+            $newOrtholog = self::createFromNameString($name, $modelOrganismId);
+            self::createRelationToGene($geneId, $newOrtholog->id);
         }
+        return $newOrtholog;
     }
 
     public static function getIdByName($name) {
diff --git a/app/models/common/LifespanExperimentToOrtholog.php b/app/models/common/LifespanExperimentToOrtholog.php
new file mode 100644
index 00000000..b366eb9b
--- /dev/null
+++ b/app/models/common/LifespanExperimentToOrtholog.php
@@ -0,0 +1,79 @@
+<?php
+
+namespace app\models\common;
+
+use Yii;
+
+/**
+ * This is the model class for table "lifespan_experiment_to_ortholog".
+ *
+ * @property int $id
+ * @property int|null $lifespan_experiment_id
+ * @property int|null $ortholog_id
+ *
+ * @property LifespanExperiment $lifespanExperiment
+ * @property Ortholog $ortholog
+ */
+class LifespanExperimentToOrtholog extends \yii\db\ActiveRecord
+{
+    /**
+     * {@inheritdoc}
+     */
+    public static function tableName()
+    {
+        return 'lifespan_experiment_to_ortholog';
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    public function rules()
+    {
+        return [
+            [['lifespan_experiment_id', 'ortholog_id'], 'integer'],
+            [['lifespan_experiment_id'], 'exist', 'skipOnError' => true, 'targetClass' => LifespanExperiment::class, 'targetAttribute' => ['lifespan_experiment_id' => 'id']],
+            [['ortholog_id'], 'exist', 'skipOnError' => true, 'targetClass' => Ortholog::class, 'targetAttribute' => ['ortholog_id' => 'id']],
+        ];
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    public function attributeLabels()
+    {
+        return [
+            'id' => 'ID',
+            'lifespan_experiment_id' => 'Lifespan Experiment ID',
+            'ortholog_id' => 'Ortholog ID',
+        ];
+    }
+
+    /**
+     * Gets query for [[LifespanExperiment]].
+     *
+     * @return \yii\db\ActiveQuery|LifespanExperimentQuery
+     */
+    public function getLifespanExperiment()
+    {
+        return $this->hasOne(LifespanExperiment::class, ['id' => 'lifespan_experiment_id']);
+    }
+
+    /**
+     * Gets query for [[Ortholog]].
+     *
+     * @return \yii\db\ActiveQuery|OrthologQuery
+     */
+    public function getOrtholog()
+    {
+        return $this->hasOne(Ortholog::class, ['id' => 'ortholog_id']);
+    }
+
+    /**
+     * {@inheritdoc}
+     * @return LifespanExperimentToOrthologQuery the active query used by this AR class.
+     */
+    public static function find()
+    {
+        return new LifespanExperimentToOrthologQuery(get_called_class());
+    }
+}
diff --git a/app/models/common/LifespanExperimentToOrthologQuery.php b/app/models/common/LifespanExperimentToOrthologQuery.php
new file mode 100644
index 00000000..8537e7f3
--- /dev/null
+++ b/app/models/common/LifespanExperimentToOrthologQuery.php
@@ -0,0 +1,34 @@
+<?php
+
+namespace app\models\common;
+
+/**
+ * This is the ActiveQuery class for [[\app\models\LifespanExperimentToOrtholog]].
+ *
+ * @see \app\models\LifespanExperimentToOrtholog
+ */
+class LifespanExperimentToOrthologQuery extends \yii\db\ActiveQuery
+{
+    /*public function active()
+    {
+        return $this->andWhere('[[status]]=1');
+    }*/
+
+    /**
+     * {@inheritdoc}
+     * @return \app\models\LifespanExperimentToOrtholog[]|array
+     */
+    public function all($db = null)
+    {
+        return parent::all($db);
+    }
+
+    /**
+     * {@inheritdoc}
+     * @return \app\models\LifespanExperimentToOrtholog|array|null
+     */
+    public function one($db = null)
+    {
+        return parent::one($db);
+    }
+}