feat: enabled cache and various bug fixes

Steinbeck-Lab · May 29, 2024 · 97f9acb · 97f9acb
1 parent b2697dc
commit 97f9acb
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Showing 11 changed files with 52 additions and 22 deletions.
diff --git a/app/Console/Commands/ImportClassyFire.php b/app/Console/Commands/ImportClassyFire.php
@@ -2,10 +2,10 @@
 
 namespace App\Console\Commands;
 
-use Illuminate\Console\Command;
-use Log;
 use App\Models\Properties;
 use DB;
+use Illuminate\Console\Command;
+use Log;
 
 class ImportClassyFire extends Command
 {
@@ -36,7 +36,7 @@ public function handle()
             return 1;
         }
 
-        Log::info("Reading file: " . $file);
+        Log::info('Reading file: '.$file);
 
         $batchSize = 10000;
         $header = null;
@@ -85,7 +85,7 @@ private function insertBatch(array $data)
             foreach ($data as $row) {
                 Properties::updateorCreate(
                     [
-                        'molecule_id' => $row['id']
+                        'molecule_id' => $row['id'],
                     ],
                     [
                         'chemical_class' => str_replace('"', '', $row['chemical_class']),

diff --git a/app/Console/Commands/ImportProperties.php b/app/Console/Commands/ImportProperties.php
@@ -2,10 +2,10 @@
 
 namespace App\Console\Commands;
 
-use Illuminate\Console\Command;
-use Log;
 use App\Models\Properties;
 use DB;
+use Illuminate\Console\Command;
+use Log;
 
 class ImportProperties extends Command
 {
@@ -36,7 +36,7 @@ public function handle()
             return 1;
         }
 
-        Log::info("Reading file: " . $file);
+        Log::info('Reading file: '.$file);
 
         $batchSize = 10000;
         $header = null;
@@ -85,7 +85,7 @@ private function insertBatch(array $data)
             foreach ($data as $row) {
                 Properties::updateorCreate(
                     [
-                        'molecule_id' => $row['id']
+                        'molecule_id' => $row['id'],
                     ],
                     [
                         'total_atom_count' => str_replace('"', '', $row['atom_count']),
@@ -110,7 +110,7 @@ private function insertBatch(array $data)
                         'contains_ring_sugars' => str_replace('"', '', $row['circular_sugars']),
                         'contains_sugar' => filter_var(str_replace('"', '', $row['linear_sugars']), FILTER_VALIDATE_BOOLEAN) || filter_var(str_replace('"', '', $row['circular_sugars']), FILTER_VALIDATE_BOOLEAN),
                         'murko_framework' => str_replace('"', '', $row['murko_framework']),
-                        'nplikeness' => str_replace('"', '', $row['nplikeness']),
+                        'np_likeness' => str_replace('"', '', $row['nplikeness']),
                         'molecular_formula' => str_replace('"', '', $row['molecular_formula']),
                     ]
                 );

diff --git a/app/Filament/Dashboard/Resources/CollectionResource/Widgets/CollectionStats.php b/app/Filament/Dashboard/Resources/CollectionResource/Widgets/CollectionStats.php
@@ -48,8 +48,9 @@ protected function getStats(): array
                 $molecules = $this->record->molecules;
                 $count = 0;
                 foreach ($molecules as $molecule) {
-                    $count += $molecule->geoLocations()->count();
+                    $count += $molecule->geo_locations()->count();
                 }
+
                 return $count;
             })),
         ];

diff --git a/...ment/Dashboard/Resources/MoleculeResource/RelationManagers/GeoLocationRelationManager.php b/...ment/Dashboard/Resources/MoleculeResource/RelationManagers/GeoLocationRelationManager.php
@@ -11,7 +11,7 @@
 
 class GeoLocationRelationManager extends RelationManager
 {
-    protected static string $relationship = 'geoLocations';
+    protected static string $relationship = 'geo_locations';
 
     public function form(Form $form): Form
     {

diff --git a/app/Livewire/DataSources.php b/app/Livewire/DataSources.php
@@ -3,16 +3,16 @@
 namespace App\Livewire;
 
 use App\Models\Collection;
-use Livewire\Component;
 use Cache;
+use Livewire\Component;
 
 class DataSources extends Component
 {
     public $collections = [];
 
     public function mount()
     {
-        $this->collections = Cache::rememberForever('collections', function (){
+        $this->collections = Cache::rememberForever('collections', function () {
             return Collection::limit(10)->pluck('title');
         });
     }

diff --git a/app/Livewire/MoleculeDepict2d.php b/app/Livewire/MoleculeDepict2d.php
@@ -18,7 +18,7 @@ class MoleculeDepict2d extends Component
     #[Computed]
     public function source()
     {
-        return env('CM_API').'depict/2D?smiles='.urlencode($this->smiles).'&height='.$this->height.'&width='.$this->width.'&CIP='.$this->CIP.'&toolkit=rdkit';
+        return env('CM_API').'depict/2D?smiles='.urlencode($this->smiles).'&height='.$this->height.'&width='.$this->width.'&toolkit=cdk';
     }
 
     public function render()

diff --git a/app/Livewire/MoleculeDetails.php b/app/Livewire/MoleculeDetails.php
@@ -3,6 +3,7 @@
 namespace App\Livewire;
 
 use App\Models\Molecule;
+use Cache;
 use Livewire\Attributes\Layout;
 use Livewire\Component;
 
@@ -12,7 +13,9 @@ class MoleculeDetails extends Component
 
     public function mount($id)
     {
-        $this->molecule = Molecule::with('properties', 'citations', 'collections', 'audits', 'variants')->where('identifier', $id)->first();
+        $this->molecule = Cache::remember('molecules.'.$id, 1440, function () use ($id) {
+            return Molecule::with('properties', 'citations', 'collections', 'audits', 'variants', 'organisms', 'geo_locations', 'related')->where('identifier', $id)->first();
+        });
     }
 
     #[Layout('layouts.guest')]

diff --git a/app/Livewire/RecentMolecules.php b/app/Livewire/RecentMolecules.php
@@ -4,9 +4,9 @@
 
 use App\Http\Resources\MoleculeResource;
 use App\Models\Molecule;
+use Cache;
 use Livewire\Component;
 use Livewire\WithPagination;
-use Cache;
 
 class RecentMolecules extends Component
 {
@@ -17,10 +17,9 @@ class RecentMolecules extends Component
     public function render()
     {
         return view('livewire.recent-molecules', [
-            'molecules' => 
-            Cache::rememberForever('molecules.recent', function (){
+            'molecules' => Cache::rememberForever('molecules.recent', function () {
                 return MoleculeResource::collection(Molecule::where('has_variants', true)->where('name', '!=', null)->orderByDesc('updated_at')->paginate($this->size));
-            })
+            }),
         ]);
     }
 }
diff --git a/app/Models/Molecule.php b/app/Models/Molecule.php
@@ -120,7 +120,7 @@ public function organisms(): BelongsToMany
     /**
      * Get all of the geo-locations for the molecule.
      */
-    public function geoLocations(): BelongsToMany
+    public function geo_locations(): BelongsToMany
     {
         return $this->belongsToMany(GeoLocation::class)->withPivot('locations')->withTimestamps();
     }

diff --git a/resources/views/livewire/molecule-details.blade.php b/resources/views/livewire/molecule-details.blade.php
@@ -99,6 +99,33 @@ class="flex items-baseline flex-wrap justify-between gap-y-2 gap-x-4 border-t bo
         <div
             class="mx-auto mt-8 grid max-w-3xl grid-cols-1 gap-6 sm:px-6 lg:max-w-7xl lg:grid-flow-col-dense lg:grid-cols-3">
             <div class="space-y-6 lg:col-span-2 lg:col-start-1">
+             @if ($molecule->organisms && count($molecule->organisms) > 0)
+             <section>
+                    <div class="bg-white border shadow sm:rounded-lg">
+                        <div class="px-4 py-5 sm:px-6">
+                            <h2 id="applicant-information-title" class="text-lg font-medium leading-6 text-gray-900">
+                                Organisms</h2>
+                        </div>
+                        <div class="border-t border-gray-200">
+                            <div class="no-scrollbar px-4 py-4 lg:px-8 min-w-0">
+                                    <ul role="list" class="mt-2 leading-8">
+                                        @foreach ($molecule->organisms as $organism)
+                                            @if ($organism != '')
+                                                <li class="inline">
+                                                    <a class="text-sm relative mr-2 inline-flex items-center rounded-md border border-gray-300 px-3 py-0.5"
+                                                        href="{{ urldecode($organism->iri) }}"
+                                                        target="_blank">
+                                                        {{ $organism->name }} | {{ $organism->rank }}
+                                                    </a>
+                                                </li>
+                                            @endif
+                                        @endforeach
+                                    </ul>
+                            </div>
+                        </div>
+                    </div>
+                </section>
+                @endif
                 <section>
                     <div class="bg-white border shadow sm:rounded-lg">
                         <div class="px-4 py-5 sm:px-6">
@@ -157,7 +184,7 @@ class="text-sm font-medium text-gray-500 sm:flex sm:justify-between">
                                             <div class="group/item -ml-4 rounded-xl p-4 hover:bg-slate-100">
                                                 <dt
                                                     class="text-sm font-medium text-gray-500 sm:flex sm:justify-between">
-                                                    Canonical SMILES (CDK)
+                                                    Canonical SMILES (RDKit)
                                                 </dt>
                                                 <div class="mt-1 break-all text-sm text-gray-900">
                                                     {{ $molecule->canonical_smiles }}

diff --git a/resources/views/livewire/search.blade.php b/resources/views/livewire/search.blade.php
@@ -79,7 +79,7 @@ class="rounded-md bg-white text-gray-900 mr-3 py-3 px-2 text-gray-400 hover:bg-g
         <livewire:molecule-editor />
     </div>
     <div class="mx-auto max-w-2xl px-4 py-8 sm:px-6 sm:py-8 lg:max-w-7xl lg:px-8">
-        <div class="p-4">
+        <div class="p-4 w-full">
             {{ $molecules->links() }}
         </div>
         <div class="grid grid-cols-1 gap-y-4 sm:grid-cols-2 sm:gap-x-6 sm:gap-y-10 lg:grid-cols-4 lg:gap-x-8">