Merge pull request #49 from Steinbeck-Lab/development

Development
Steinbeck-Lab · Jun 3, 2024 · ae968dd · ae968dd
2 parents 4d359e4 + 61606ad
commit ae968dd
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Showing 23 changed files with 811 additions and 475 deletions.
diff --git a/app/Livewire/CollectionList.php b/app/Livewire/CollectionList.php
@@ -0,0 +1,47 @@
+<?php
+
+namespace App\Livewire;
+
+use App\Models\Collection;
+use Livewire\Attributes\Layout;
+use Livewire\Attributes\Url;
+use Livewire\Component;
+use Livewire\WithPagination;
+
+#[Layout('layouts.guest')]
+class CollectionList extends Component
+{
+    use WithPagination;
+
+    #[Url(except: '', keep: true, history: true, as: 'q')]
+    public $query = '';
+
+    #[Url(as: 'limit')]
+    public $size = 20;
+
+    #[Url()]
+    public $sort = null;
+
+    #[Url()]
+    public $page = null;
+
+    public function updatingQuery()
+    {
+        $this->resetPage();
+    }
+
+    public function render()
+    {
+        $search = $this->query;
+        $collections = Collection::query()
+            ->where(function ($query) use ($search) {
+                $query->whereRaw('LOWER(title) LIKE ?', ['%'.strtolower($search).'%'])
+                    ->orWhereRaw('LOWER(description) LIKE ?', ['%'.strtolower($search).'%']);
+            })
+            ->orderByRaw('title LIKE ? DESC', [$search.'%'])
+            ->orderByRaw('description LIKE ? DESC', [$search.'%'])
+            ->paginate($this->size);
+
+        return view('livewire.collection-list', ['collections' => $collections]);
+    }
+}
diff --git a/app/Livewire/CompoundClasses.php b/app/Livewire/CompoundClasses.php
@@ -6,6 +6,32 @@
 
 class CompoundClasses extends Component
 {
+    public $superClasses = [
+        'Acetylides',
+        'Alkaloids and derivatives',
+        'Allenes',
+        'Benzenoids',
+        'Hydrocarbon derivatives',
+        'Hydrocarbons',
+        'Lignans, neolignans and related compounds',
+        'Lipids and lipid-like molecules',
+        'Nucleosides, nucleotides, and analogues',
+        'Organoheterocyclic compounds',
+        'Organohalogen compounds',
+        'Organometallic compounds',
+        'Organophosphorus compounds',
+        'Organosulfur compounds',
+        'Organic 1,3-dipolar compounds',
+        'Organic Polymers',
+        'Organic acids and derivatives',
+        'Organic anions',
+        'Organic cations',
+        'Organic nitrogen compounds',
+        'Organic oxygen compounds',
+        'Organic salts',
+        'Phenylpropanoids and polyketides',
+    ];
+
     public $parentClasses = [
         'Acenaphthylenes',
         'Acetals',
@@ -985,7 +1011,8 @@ class CompoundClasses extends Component
 
     public function mount()
     {
-        $this->parentClasses = array_slice($this->parentClasses, 0, 50);
+        // $this->parentClasses = array_slice($this->parentClasses, 0, 50);
+        $this->superClasses = $this->superClasses;
     }
 
     public function render()

diff --git a/app/Livewire/MoleculeDetails.php b/app/Livewire/MoleculeDetails.php
@@ -4,7 +4,6 @@
 
 use App\Models\Molecule;
 use Cache;
-use Livewire\Attributes\Layout;
 use Livewire\Component;
 
 class MoleculeDetails extends Component
@@ -18,11 +17,20 @@ public function mount($id)
         });
     }
 
-    #[Layout('layouts.guest')]
     public function render()
     {
         return view('livewire.molecule-details', [
             'molecule' => $this->molecule,
-        ]);
+        ])->layout('layouts.guest')
+            ->layoutData([
+                'title' => $this->molecule->name ? $this->molecule->name : $this->molecule->iupac_name,
+                'description' => $this->molecule->description ?? 'Molecule details for '.($this->molecule->name ? $this->molecule->name : $this->molecule->iupac_name),
+                'keywords' => 'natural products, '.$this->molecule->name.', '.$this->molecule->iupac_name.', '.implode(',', $this->molecule->synonyms ?? []),
+                'author' => $this->molecule->author ?? 'COCONUT Team',
+                'ogTitle' => $this->molecule->name ? $this->molecule->name : $this->molecule->iupac_name,
+                'ogDescription' => $this->molecule->description ?? 'Molecule details for '.($this->molecule->name ? $this->molecule->name : $this->molecule->iupac_name),
+                'ogImage' => env('CM_API').'depict/2D?smiles='.urlencode($this->molecule->canonical_smiles).'&height=200&width=200&toolkit=cdk' ?? asset('img/coconut-og-image.png'),
+                'ogSiteName' => 'Coconut 2.0',
+            ]);
     }
 }
diff --git a/app/Livewire/MoleculeEditor.php b/app/Livewire/MoleculeEditor.php
diff --git a/app/Livewire/Search.php b/app/Livewire/Search.php
@@ -2,16 +2,17 @@
 
 namespace App\Livewire;
 
-use App\Http\Resources\MoleculeResource;
 use App\Models\Collection;
 use App\Models\Molecule;
+use App\Models\Organism;
 use Illuminate\Pagination\LengthAwarePaginator;
 use Illuminate\Support\Facades\DB;
 use Livewire\Attributes\Layout;
 use Livewire\Attributes\Url;
 use Livewire\Component;
 use Livewire\WithPagination;
 
+#[Layout('layouts.guest')]
 class Search extends Component
 {
     use WithPagination;
@@ -36,12 +37,21 @@ class Search extends Component
 
     public $collection = null;
 
+    public $organisms = null;
+
     public function gotoPage($page)
     {
         $this->page = $page;
     }
 
-    #[Layout('layouts.guest')]
+    protected $listeners = ['updateSmiles' => 'setSmiles'];
+
+    public function setSmiles($smiles, $searchType)
+    {
+        $this->query = $smiles;
+        $this->type = $searchType;
+    }
+
     public function render()
     {
 
@@ -173,7 +183,31 @@ public function render()
             } elseif ($queryType == 'tags') {
                 if ($this->tagType == 'dataSource') {
                     $this->collection = Collection::where('title', $this->query)->first();
-                    $results = $this->collection->molecules()->orderBy('annotation_level', 'desc')->paginate($this->size);
+                    if ($this->collection) {
+                        $results = $this->collection->molecules()->orderBy('annotation_level', 'desc')->paginate($this->size);
+                    } else {
+                        $results = new LengthAwarePaginator(
+                            [],
+                            0,
+                            $this->size,
+                            $this->page
+                        );
+                    }
+                } elseif ($this->tagType == 'organisms') {
+                    $this->organisms = array_map(function ($name) {
+                        return strtolower(trim($name));
+                    }, explode(',', $this->query));
+
+                    $organismIds = Organism::where(function ($query) {
+                        foreach ($this->organisms as $name) {
+                            $query->orWhereRaw('LOWER(name) = ?', [$name]);
+                        }
+                    })->pluck('id');
+
+                    $results = Molecule::whereHas('organisms', function ($query) use ($organismIds) {
+                        $query->whereIn('organism_id', $organismIds);
+                    })->orderBy('annotation_level', 'DESC')->paginate($this->size);
+
                 } else {
                     $results = Molecule::withAnyTags([$this->query], $this->tagType)->paginate($this->size);
                 }
@@ -235,11 +269,12 @@ public function render()
                             }
                             $statement =
                                 $statement.
-                                '('.$filterMap[$_filter[0]].'::TEXT ILIKE \'%'.$_filter[1].'%\')';
+                                '(LOWER(REGEXP_REPLACE('.$filterMap[$_filter[0]].' , \'\s+\', \'-\', \'g\'))::TEXT ILIKE \'%'.$_filter[1].'%\')';
                         }
                     }
                     $statement = $statement.')';
                 }
+                // dd($statement);
                 $statement = $statement.' LIMIT '.$this->size;
             } else {
                 if ($this->query) {
@@ -335,10 +370,5 @@ public function render()
                 500
             );
         }
-        // return view('livewire.search', [
-        //     'molecules' => MoleculeResource::collection(
-        //         Molecule::where('active', true)->orderByDesc('updated_at')->paginate($this->size)
-        //     ),
-        // ]);
     }
 }
diff --git a/app/Livewire/StructureEditor.php b/app/Livewire/StructureEditor.php
@@ -0,0 +1,30 @@
+<?php
+
+namespace App\Livewire;
+
+use Livewire\Component;
+
+class StructureEditor extends Component
+{
+    public $isOpen = false;
+
+    public $smiles = '';
+
+    protected $listeners = ['openModal'];
+
+    public function openModal($smiles = '')
+    {
+        $this->smiles = $smiles;
+        $this->isOpen = true;
+    }
+
+    public function closeModal()
+    {
+        $this->isOpen = false;
+    }
+
+    public function render()
+    {
+        return view('livewire.structure-editor');
+    }
+}
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -23,6 +23,6 @@
         "vitepress": "^1.2.2"
     },
     "dependencies": {
-        "openchemlib": "^8.9.0"
+        "openchemlib": "^8.13.0"
     }
 }
diff --git a/public/img/coconut-og-image.png b/public/img/coconut-og-image.png
diff --git a/resources/css/app.css b/resources/css/app.css
@@ -293,4 +293,12 @@
 .tooltip:hover .tooltiptext {
   visibility: visible;
   opacity: 1;
+}
+
+.organism::first-letter {
+  text-transform: capitalize !important;
+}
+
+.organism {
+  font-style: italic;
 }
diff --git a/resources/js/app.js b/resources/js/app.js
@@ -1,4 +1,4 @@
 import "./bootstrap";
 
 import OCL from "openchemlib/full";
-window.OCL = OCL;
+window.OCL = OCL;
diff --git a/resources/views/layouts/guest.blade.php b/resources/views/layouts/guest.blade.php
@@ -7,6 +7,19 @@
 
         <title>{{ config('app.name', 'Coconut') }}</title>
 
+        <!-- Meta Tags -->
+        <meta name="description" content="{{ $description ?? 'An aggregated dataset of elucidated and predicted natural products collected from open sources and a web interface to browse, search, and easily download NPs.' }}">
+        <meta name="keywords" content="{{ $keywords ?? 'natural products, COCONUT, open data, molecule database' }}">
+        <meta name="author" content="{{ $author ?? 'COCONUT Team' }}">
+        <meta property="og:title" content="{{ $ogTitle ?? 'COCONUT: Collection of Open Natural Products' }}">
+        <meta property="og:description" content="{{ $ogDescription ?? 'An aggregated dataset of elucidated and predicted natural products collected from open sources and a web interface to browse, search, and easily download NPs.' }}">
+        <meta property="og:type" content="website">
+        <meta property="og:url" content="{{ $ogUrl ?? url()->current() }}">
+        <meta property="og:image" content="{{ $ogImage ?? asset('img/coconut-og-image.png') }}">
+        <meta property="og:image:width" content="1200">
+        <meta property="og:image:height" content="630">
+        <meta property="og:site_name" content="{{ $ogSiteName ?? config('app.name', 'Coconut') }}">
+
         <!-- Fonts -->
         <link rel="preconnect" href="https://fonts.bunny.net">
         <link href="https://fonts.bunny.net/css?family=figtree:400,500,600&display=swap" rel="stylesheet" />