Combined 500 752 753

app/Actions/ReportVcepGenesMake.php

@@ -47,9 +47,6 @@ private function pullData(): array
                     })
                     ->orderBy('gene_symbol')
                     ->with([
-                        'disease' => function ($q) {
-                            $q->select(['mondo_id','name']);
-                        },
                         'expertPanel' => function ($q) {
                             $q->select(['id', 'long_base_name', 'expert_panel_type_id']);
                         },
@@ -60,6 +57,20 @@ private function pullData(): array
                         'expertPanel.group.type'
                     ])
                     ->get();
+        $gtApi = app(\App\Services\Api\GtApiService::class);
+
+        $mondoIds = $genes->pluck('mondo_id')->unique()->values()->all();
+        $diseaseData = $gtApi->getDiseasesByMondoIds($mondoIds);
+
+        $diseaseMap = collect($diseaseData)
+                        ->keyBy('mondo_id')
+                        ->map(fn($d) => (object)[
+                            'mondo_id' => $d['mondo_id'],
+                            'name' => $d['name']
+                        ]);
+        $genes->each(function ($gene) use ($diseaseMap) {
+            $gene->setRelation('disease', $diseaseMap[$gene->mondo_id] ?? (object)[]);
+        });
 
         return $genes
             ->groupBy(function ($g) {
@@ -79,5 +90,4 @@ private function pullData(): array
             ->values()
             ->toArray();
     }
-
-}
+}

app/DataTransferObjects/GtDiseaseDto.php

@@ -0,0 +1,25 @@
+<?php
+
+namespace App\DataTransferObjects;
+
+class GtDiseaseDto
+{
+    public function __construct(
+        public string $mondo_id,
+        public ?string $doid_id = null,
+        public string $name,
+        public ?string $is_obsolete = null,
+        public ?string $replaced_by = null,
+    ) {}
+
+    public static function fromArray(array $data): self
+    {
+        return new self(            
+            mondo_id    : $data['mondo_id'],
+            doid_id     : $data['doid_id'] ?? null,
+            name        : $data['name'],
+            is_obsolete : $data['is_obsolete'] ?? null,
+            replaced_by : $data['replaced_by'] ?? null,
+        );
+    }
+}

app/DataTransferObjects/GtGeneDto.php

@@ -0,0 +1,26 @@
+<?php 
+
+namespace App\DataTransferObjects;
+
+class GtGeneDto
+{
+    public function __construct(        
+        public int $hgnc_id,        
+        public string $gene_symbol,
+        public ?int $omim_id = null,
+        public ?string $hgnc_name = null,
+        public ?string $hgnc_status = null,
+    ) {}
+
+    public static function fromArray(array $data): self
+    {
+        return new self(
+            hgnc_id     : $data['hgnc_id'],
+            gene_symbol : $data['gene_symbol'],
+            omim_id     : $data['omim_id'] ?? null,
+            hgnc_name   : $data['hgnc_name'] ?? null,
+            hgnc_status : $data['hgnc_status'] ?? null
+
+        );
+    }
+}

app/Http/Controllers/Api/DiseaseLookupController.php

@@ -3,13 +3,20 @@
 namespace App\Http\Controllers\Api;
 
 use Illuminate\Http\Request;
-use Illuminate\Support\Facades\DB;
 use App\Http\Controllers\Controller;
 use Illuminate\Support\Facades\Validator;
 use Illuminate\Validation\ValidationException;
+use App\Services\Api\GtApiService;
 
 class DiseaseLookupController extends Controller
 {
+    protected GtApiService $gtApi;
+
+    public function __construct(GtApiService $gtApi)
+    {
+        $this->gtApi = $gtApi;
+    }
+
     public function show($mondoId)
     {
         $validator = Validator::make(['mondo_id' => $mondoId], [
@@ -19,24 +26,17 @@ public function show($mondoId)
             throw new ValidationException($validator);
         }
 
-        return DB::connection(config('database.gt_db_connection'))->table('diseases')->where('mondo_id', $mondoId)->sole();
+        $mondo_id = strtolower($validator->validated()['mondo_id']);
+        return $this->gtApi->getDiseasesByMondoIds($mondo_id);
     }
 
     public function search(Request $request)
-    {
+    {       
         $queryString = strtolower(($request->query_string ?? ''));
         if (strlen($queryString) < 3) {
             return [];
         }
 
-        $results = DB::connection(config('database.gt_db_connection'))->table('diseases')
-                    ->select('id', 'mondo_id', 'doid_id', 'name',)
-                    ->where('name', 'like', '%'.$queryString.'%')
-                    ->orWhere('mondo_id', 'like', '%'.$queryString.'%')
-                    ->orWhere('doid_id', 'like', '%'.$queryString.'%')
-                    ->limit(50)
-                    ->get();
-
-        return $results->toArray();
+        return $this->gtApi->searchDiseases($queryString);
     }
-}
+}

app/Http/Controllers/Api/GeneLookupController.php

@@ -5,31 +5,54 @@
 use Illuminate\Http\Request;
 use Illuminate\Support\Facades\DB;
 use App\Http\Controllers\Controller;
+use Illuminate\Support\Facades\Log;
+use App\Services\Api\GtApiService;
 
 class GeneLookupController extends Controller
 {
+    protected GtApiService $gtApi;
 
-    public function show($hgncId)
+    public function __construct(GtApiService $gtApi)
     {
-        return DB::connection(config('database.gt_db_connection'))->table('hgnc_genes')->where('hgnc_id', $hgncId)->sole();
+        $this->gtApi = $gtApi;
     }
 
-
     public function search(Request $request)
     {
         $queryString = strtolower(($request->query_string ?? ''));
 
         if (strlen($queryString) < 3) {
             return [];
         }
-        $results = DB::connection(config('database.gt_db_connection'))->table('genes')
-                        ->where('gene_symbol', 'like', '%'.$queryString.'%')
-                        ->orWhere('hgnc_id', 'like', '%'.$queryString.'%')
-                        ->limit(250)
-                        ->get();
+        return $this->gtApi->searchGenes($queryString);
+    }
+
+    public function check(Request $request)
+    {
+        $symbols = $request->input('gene_symbol') ?? '';
+        if (! $symbols) {
+            return response()->json([], 200);
+        }
+        return $this->gtApi->lookupGenesBulk($symbols);
+    }
+
+    public function curations(Request $request)
+    {        
+        $query = $request->get('query');
+
+        if (! $query || strlen($query) < 3) {
+            return response()->json([], 200);
+        }
 
-        return $results->toArray();
+        return $this->gtApi->searchCurations($query);
+    }
+
+    public function curationids(Request $request)
+    {        
+        $curationIDs = $request->input('curation_ids') ?? '';
+        if (! $curationIDs) {
+            return response()->json([], 200);
+        }
+        return $this->gtApi->getCurationByID($curationIDs);
     }
-
-
-}
+}

app/Http/Controllers/Api/MoiLookupController.php

@@ -0,0 +1,23 @@
+<?php
+
+namespace App\Http\Controllers\Api;
+
+use Illuminate\Http\Request;
+use App\Http\Controllers\Controller;
+use App\Services\Api\GtApiService;
+
+class MoiLookupController extends Controller
+{
+    protected GtApiService $gtApi;
+
+    public function __construct(GtApiService $gtApi)
+    {
+        $this->gtApi = $gtApi;
+    }
+
+    public function index(Request $request)
+    {
+        return $this->gtApi->mois();
+    }
+
+}

app/Modules/ExpertPanel/Models/Gene.php

@@ -3,12 +3,14 @@
 namespace App\Modules\ExpertPanel\Models;
 
 use Illuminate\Database\Eloquent\Model;
-use App\Models\GeneTracker\Gene as GtGene;
 use Illuminate\Database\Eloquent\SoftDeletes;
-use App\Models\GeneTracker\Disease as GtDisease;
 use Database\Factories\GeneFactory;
 use Illuminate\Database\Eloquent\Relations\BelongsTo;
 use Illuminate\Database\Eloquent\Factories\HasFactory;
+use Illuminate\Support\Facades\Cache;
+use App\DataTransferObjects\GtGeneDto;
+use App\DataTransferObjects\GtDiseaseDto;
+use App\Services\Api\GtApiService;
 
 /**
  * @property int $id
@@ -25,12 +27,6 @@ class Gene extends Model
 {
     use HasFactory, SoftDeletes;
 
-    public function getConnectionName()
-    {
-        return config('database.default');
-    }
-
-
     /**
      * The attributes that are mass assignable.
      *
@@ -40,9 +36,12 @@ public function getConnectionName()
         'hgnc_id',
         'expert_panel_id',
         'gene_symbol',
+        'tier',
         'mondo_id',
         'disease_name',
         'date_approved',
+        'moi',
+        'plan',
     ];
 
     /**
@@ -54,7 +53,9 @@ public function getConnectionName()
         'id' => 'integer',
         'hgnc_id' => 'integer',
         'expert_panel_id' => 'integer',
+        'tier' => 'integer',
         'date_approved' => 'datetime',
+        'plan' => 'array',
     ];
 
     /**
@@ -65,24 +66,30 @@ public function expertPanel()
         return $this->belongsTo(ExpertPanel::class);
     }
 
-    /**
-     * Get the gene that owns the Gene
-     *
-     * @return \Illuminate\Database\Eloquent\Relations\BelongsTo
-     */
-    public function gene(): BelongsTo
+    public function gene(): ?GtGeneDto
     {
-        return $this->belongsTo(GtGene::class, 'hgnc_id', 'hgnc_id');
+        try {
+            return Cache::remember("hgnc_id_{$this->hgnc_id}", 300, function () {
+                $data = app(GtApiService::class)->getGeneSymbolById($this->hgnc_id);
+                return $data ? GtGeneDto::fromArray($data) : null;
+            });
+        } catch (\Throwable $e) {
+            report($e);
+            return null;
+        }
     }
 
-    /**
-     * Get the disease that owns the Gene
-     *
-     * @return \Illuminate\Database\Eloquent\Relations\BelongsTo
-     */
-    public function disease(): BelongsTo
+    public function disease(): ?GtDiseaseDto
     {
-        return $this->belongsTo(GtDisease::class, 'mondo_id', 'mondo_id');
+        try {
+            return Cache::remember("mondo_id_{$this->mondo_id}", 300, function () {
+                $data = app(GtApiService::class)->getDiseasesByMondoIds([$this->mondo_id]);
+                return $data ? GtDiseaseDto::fromArray($data) : null;
+            });
+        } catch (\Throwable $e) {
+            report($e);
+            return null;
+        }
     }
 
     /**