Merge pull request #242 from Steinbeck-Lab/development

Development
Steinbeck-Lab · Sep 11, 2024 · 8a35a45 · 8a35a45
2 parents 0ba3726 + 50dda62
commit 8a35a45
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diff --git a/README.md b/README.md
@@ -39,9 +39,15 @@ COCONUT data curation and descriptors calculation are performed using our [micro
 
 COCONUT infrastructure code is licensed under the MIT license - see the [LICENSE](https://GitHub.com/Steinbeck-Lab/coconut/blob/documentation/LICENSE). Every source on COCONUT comes with its own specific license. It is essential to review the license details for each dataset before using it.
 
-## ![Citation](https://www.google.com/s2/favicons?domain=doi.org) COCONUT (Legacy) - Citation
+## ![Citations](https://www.google.com/s2/favicons?domain=doi.org)Citations
 
-Sorokina, M., Merseburger, P., Rajan, K. et al. COCONUT online: COlleCtion of Open Natural prodUcTs database. J Cheminform 13, 2 (2021). https://doi.org/10.1186/s13321-020-00478-9
+### COCONUT (Legacy)
+-  Sorokina, M., Merseburger, P., Rajan, K. et al. (2021). COCONUT online: COlleCtion of Open Natural prodUcTs database. *Journal of Cheminformatics*, 13, 2. 
+https://doi.org/10.1186/s13321-020-00478-9
+
+### COCONUT 2.0
+-  Nainala, V.C., Rajan, K., Kanakam, S.R.S., Sharma, N., Weißenborn, V., Schaub, J., et al. (2024). COCONUT 2.0: A comprehensive overhaul and curation of the collection of open natural products database. *ChemRxiv*. 
+https://doi.org/10.26434/chemrxiv-2024-fxq2s
 
 ## ![Maintained](https://www.google.com/s2/favicons?domain=uni-jena.de) Maintained by
 

diff --git a/app/Console/Commands/DashWidgetsRefresh.php b/app/Console/Commands/DashWidgetsRefresh.php
@@ -32,49 +32,49 @@ public function handle()
         // Cache::flush();
 
         // Create the cache for all DashboardStats widgets
-        Cache::rememberForever('stats.collections', function () {
+        Cache::remember('stats.collections', 172800, function () {
             return DB::table('collections')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for collections refreshed.');
 
-        Cache::rememberForever('stats.citations', function () {
+        Cache::remember('stats.citations', 172800, function () {
             return DB::table('citations')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for citations refreshed.');
 
-        Cache::rememberForever('stats.organisms', function () {
+        Cache::remember('stats.organisms', 172800, function () {
             return DB::table('organisms')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for organisms refreshed.');
 
-        Cache::rememberForever('stats.geo_locations', function () {
+        Cache::remember('stats.geo_locations', 172800, function () {
             return DB::table('geo_locations')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for geo locations refreshed.');
 
-        Cache::rememberForever('stats.reports', function () {
+        Cache::remember('stats.reports', 172800, function () {
             return DB::table('reports')->selectRaw('count(*)')->get()[0]->count;
         });
         $this->info('Cache for reports refreshed.');
 
         // Create the cache for all DashboardStatsMid widgets
 
-        Cache::rememberForever('stats.molecules.non_stereo', function () {
+        Cache::remember('stats.molecules.non_stereo', 172800, function () {
             return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=false and is_parent=false')->get()[0]->count;
         });
         $this->info('Cache for molecules non-stereo refreshed.');
 
-        Cache::rememberForever('stats.molecules.stereo', function () {
+        Cache::remember('stats.molecules.stereo', 172800, function () {
             return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=true')->get()[0]->count;
         });
         $this->info('Cache for molecules stereo refreshed.');
 
-        Cache::rememberForever('stats.molecules.parent', function () {
+        Cache::remember('stats.molecules.parent', 172800, function () {
             return DB::table('molecules')->selectRaw('count(*)')->whereRaw('has_stereo=false and is_parent=true')->get()[0]->count;
         });
         $this->info('Cache for molecules parent refreshed.');
 
-        Cache::rememberForever('stats.molecules', function () {
+        Cache::remember('stats.molecules', 172800, function () {
             return DB::table('molecules')->selectRaw('count(*)')->whereRaw('active=true and NOT (is_parent=true AND has_variants=true)')->get()[0]->count;
         });
         $this->info('Cache for molecules refreshed.');

diff --git a/app/Filament/Dashboard/Resources/CollectionResource/Widgets/CollectionStats.php b/app/Filament/Dashboard/Resources/CollectionResource/Widgets/CollectionStats.php
@@ -17,7 +17,7 @@ protected function getStats(): array
         return [
             // Commented is the model query that we can use in case we decide not to use app level caching as the app scales up.
 
-            // Stat::make('Entries', Cache::rememberForever('stats.collections'.$this->record->id.'entries.count', function () {
+            // Stat::make('Entries', Cache::remember('stats.collections'.$this->record->id.'entries.count', 172800, function () {
             //     return DB::table('entries')->selectRaw('count(*)')->whereRaw('collection_id='.$this->record->id)->get()[0]->count;
             // }))
             //     ->description('Total count')

diff --git a/app/Filament/Dashboard/Resources/MoleculeResource/Widgets/MoleculeStats.php b/app/Filament/Dashboard/Resources/MoleculeResource/Widgets/MoleculeStats.php
@@ -15,10 +15,10 @@ class MoleculeStats extends BaseWidget
     protected function getStats(): array
     {
         return [
-            Stat::make('Total Organisms', Cache::rememberForever('stats.molecules'.$this->record->id.'organisms.count', function () {
+            Stat::make('Total Organisms', Cache::remember('stats.molecules'.$this->record->id.'organisms.count', 172800, function () {
                 return DB::table('molecule_organism')->selectRaw('count(*)')->whereRaw('molecule_id='.$this->record->id)->get()[0]->count;
             })),
-            Stat::make('Total Geo Locations', Cache::rememberForever('stats.molecules'.$this->record->id.'geo_locations.count', function () {
+            Stat::make('Total Geo Locations', Cache::remember('stats.molecules'.$this->record->id.'geo_locations.count', 172800, function () {
                 return DB::table('geo_location_molecule')->selectRaw('count(*)')->whereRaw('molecule_id='.$this->record->id)->get()[0]->count;
             })),
         ];

diff --git a/app/Filament/Dashboard/Resources/OrganismResource/Widgets/OrganismStats.php b/app/Filament/Dashboard/Resources/OrganismResource/Widgets/OrganismStats.php
@@ -15,10 +15,10 @@ class OrganismStats extends BaseWidget
     protected function getStats(): array
     {
         return [
-            Stat::make('Total Molecules', Cache::rememberForever('stats.organisms'.$this->record->id.'molecules.count', function () {
+            Stat::make('Total Molecules', Cache::remember('stats.organisms'.$this->record->id.'molecules.count', 172800, function () {
                 return DB::table('molecule_organism')->selectRaw('count(*)')->whereRaw('organism_id='.$this->record->id)->get()[0]->count;
             })),
-            Stat::make('Total Geo Locations', Cache::rememberForever('stats.organisms'.$this->record->id.'geo_locations.count', function () {
+            Stat::make('Total Geo Locations', Cache::remember('stats.organisms'.$this->record->id.'geo_locations.count', 172800, function () {
                 return DB::table('molecule_organism')->selectRaw('count(*)')->whereRaw('organism_id='.$this->record->id)->Join('geo_location_molecule', 'molecule_organism.molecule_id', '=', 'geo_location_molecule.molecule_id')->get()[0]->count;
             })),
         ];

diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/MolecularEntityController.php b/app/Http/Controllers/API/Schemas/Bioschemas/MolecularEntityController.php
@@ -15,7 +15,7 @@ class MolecularEntityController extends Controller
 {
     public function moleculeSchema(Request $request, $identifier)
     {
-        $molecule = Cache::rememberForever('molecules.'.$identifier, function () use ($identifier) {
+        $molecule = Cache::remember('molecules.'.$identifier, 172800, function () use ($identifier) {
             return Molecule::where('identifier', $identifier)->first();
         });
 

diff --git a/app/Http/Controllers/MoleculeController.php b/app/Http/Controllers/MoleculeController.php
@@ -17,7 +17,7 @@ public function __invoke(Request $request, $id)
             $id .= '.0';
         }
 
-        $molecule = Cache::rememberForever('molecules.'.$id, function () use ($id) {
+        $molecule = Cache::remember('molecules.'.$id, 172800, function () use ($id) {
             return Molecule::where('identifier', $id)->first();
         });
 

diff --git a/app/Livewire/DataSources.php b/app/Livewire/DataSources.php
@@ -12,7 +12,7 @@ class DataSources extends Component
 
     public function mount()
     {
-        $this->collections = Cache::rememberForever('collections', function () {
+        $this->collections = Cache::remember('collections', 172800, function () {
             return Collection::where('promote', true)->orderBy('sort_order')->take(10)->get(['title', 'image'])->toArray();
         });
     }

diff --git a/app/Livewire/MoleculeDepict2d.php b/app/Livewire/MoleculeDepict2d.php
@@ -27,6 +27,12 @@ public function source()
         return env('CM_API').'depict/2D?smiles='.urlencode($this->smiles).'&height='.$this->height.'&width='.$this->width;
     }
 
+    #[Computed]
+    public function preview()
+    {
+        return env('CM_API').'depict/2D?smiles='.urlencode($this->smiles);
+    }
+
     public function render()
     {
         return view('livewire.molecule-depict2d');

diff --git a/app/Livewire/MoleculeDetails.php b/app/Livewire/MoleculeDetails.php
@@ -24,7 +24,7 @@ public function rendered()
         $_molecule = Cache::get('molecules.'.$id);
         if (! $_molecule->relationLoaded('properties')) {
             Cache::forget('molecules.'.$id);
-            Cache::rememberForever('molecules.'.$id, function () use ($molecule) {
+            Cache::remember('molecules.'.$id, 172800, function () use ($molecule) {
                 $molecule['schema'] = $molecule->getSchema();
 
                 return $molecule;

diff --git a/app/Livewire/RecentMolecules.php b/app/Livewire/RecentMolecules.php
@@ -16,7 +16,7 @@ class RecentMolecules extends Component
     public function render()
     {
         return view('livewire.recent-molecules', [
-            'molecules' => Cache::rememberForever('molecules.recent', function () {
+            'molecules' => Cache::remember('molecules.recent', 172800, function () {
                 return Molecule::where('is_parent', false)->where('active', true)->where('name', '!=', null)->where('annotation_level', '=', 5)->orderByDesc('updated_at')->paginate($this->size);
             }),
         ]);

diff --git a/config/rest.php b/config/rest.php
@@ -38,7 +38,7 @@
     'authorizations' => [
         'enabled' => true,
         'cache' => [
-            'enabled' => true,
+            'enabled' => false,
             'default' => 5, // Cache minutes by default
         ],
     ],