Merge pull request #146 from Steinbeck-Lab/development

Development
Steinbeck-Lab · Aug 9, 2024 · 07ba7ef · 07ba7ef
2 parents 7bf807c + e461c89
commit 07ba7ef
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diff --git a/.github/workflows/docs-deploy.yml b/.github/workflows/docs-deploy.yml
@@ -0,0 +1,64 @@
+# Sample workflow for building and deploying a VitePress site to GitHub Pages
+#
+name: Deploy Coconut docs to Pages
+
+on:
+  # Runs on pushes targeting the `main` branch. Change this to `master` if you're
+  # using the `master` branch as the default branch.
+  push:
+    branches: [main]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Not needed if lastUpdated is not enabled
+      # - uses: pnpm/action-setup@v3 # Uncomment this if you're using pnpm
+      # - uses: oven-sh/setup-bun@v1 # Uncomment this if you're using Bun
+      - name: Setup Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm # or pnpm / yarn
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      - name: Install dependencies
+        run: npm ci # or pnpm install / yarn install / bun install
+      - name: Build with VitePress
+        run: npm run docs:build # or pnpm docs:build / yarn docs:build / bun run docs:build
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/.vitepress/dist
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    needs: build
+    runs-on: ubuntu-latest
+    name: Deploy
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
diff --git a/app/Actions/Coconut/SearchMolecule.php b/app/Actions/Coconut/SearchMolecule.php
@@ -2,6 +2,7 @@
 
 namespace App\Actions\Coconut;
 
+use App\Models\Citation;
 use App\Models\Collection;
 use App\Models\Molecule;
 use App\Models\Organism;
@@ -26,6 +27,8 @@ class SearchMolecule
 
     public $organisms = null;
 
+    public $citations = null;
+
     /**
      * Search based on given query.
      */
@@ -140,6 +143,8 @@ private function getFilterMap()
             'subclass' => 'chemical_sub_class',
             'superclass' => 'chemical_super_class',
             'parent' => 'direct_parent_classification',
+            'org' => 'organism',
+            'cite' => 'ciatation',
         ];
     }
 
@@ -233,6 +238,18 @@ private function buildTagsStatement($offset)
             return Molecule::whereHas('organisms', function ($query) use ($organismIds) {
                 $query->whereIn('organism_id', $organismIds);
             })->where('active', true)->where('is_parent', false)->orderBy('annotation_level', 'DESC')->paginate($this->size);
+        } elseif ($this->tagType == 'citations') {
+            $this->citations = array_map('strtolower', array_map('trim', explode(',', $this->query)));
+            $citationIds = Citation::where(function ($query) {
+                foreach ($this->citations as $name) {
+                    $query->orWhereRaw('LOWER(doi) LIKE ?', ['%'.strtolower($name).'%'])
+                        ->orWhereRaw('LOWER(title) LIKE ?', ['%'.strtolower($name).'%']);
+                }
+            })->pluck('id');
+
+            return Molecule::whereHas('citations', function ($query) use ($citationIds) {
+                $query->whereIn('citation_id', $citationIds);
+            })->where('active', true)->where('is_parent', false)->orderBy('annotation_level', 'DESC')->paginate($this->size);
         } else {
             return Molecule::withAnyTags([$this->query], $this->tagType)->where('active', true)->where('is_parent', false)->paginate($this->size);
         }

diff --git a/app/Actions/Fortify/CreateNewUser.php b/app/Actions/Fortify/CreateNewUser.php
@@ -30,7 +30,7 @@ public function create(array $input): User
         ])->validate();
 
         return User::create([
-            'name' => $input['username'],
+            'name' => $input['first_name'].' '.$input['last_name'],
             'email' => $input['email'],
             'password' => Hash::make($input['password']),
 

diff --git a/app/Console/Commands/DashWidgetsRefresh.php b/app/Console/Commands/DashWidgetsRefresh.php
@@ -32,7 +32,7 @@ class DashWidgetsRefresh extends Command
     public function handle()
     {
         // Clear the cache for all widgets
-        Cache::flush();
+        // Cache::flush();
 
         // Create the cache for all DashboardStats widgets
         Cache::rememberForever('stats.collections', function () {

diff --git a/app/Http/Controllers/API/Auth/RegisterController.php b/app/Http/Controllers/API/Auth/RegisterController.php
@@ -25,7 +25,7 @@ public function register(Request $request): JsonResponse
             'last_name' => $validatedData['last_name'],
             'email' => $validatedData['email'],
             'username' => $validatedData['username'],
-            'name' => $validatedData['username'],
+            'name' => $validatedData['first_name'].' '.$validatedData['last_name'],
             'orcid_id' => $request['orcid_id'],
             'affiliation' => $request['affiliation'],
             'password' => Hash::make($validatedData['password']),

diff --git a/app/Livewire/Search.php b/app/Livewire/Search.php
@@ -37,6 +37,9 @@ class Search extends Component
 
     public $organisms = null;
 
+    #[Url(as: 'activeTab')]
+    public $activeTab = 'molecules';
+
     public function placeholder()
     {
         return <<<'HTML'
@@ -65,23 +68,18 @@ public function placeholder()
         HTML;
     }
 
-    protected $listeners = ['updateSmiles' => 'setSmiles'];
-
-    public function setSmiles($smiles, $searchType)
-    {
-        $this->query = $smiles;
-        $this->type = $searchType;
-        $this->page = null;
-        $this->tagType = null;
-    }
-
     public function updatedQuery()
     {
         $this->page = 1;
         $this->type = null;
         $this->tagType = null;
     }
 
+    public function search(SearchMolecule $search)
+    {
+        $this->render($search);
+    }
+
     public function render(SearchMolecule $search)
     {
         try {

diff --git a/app/Livewire/StructureEditor.php b/app/Livewire/StructureEditor.php
@@ -10,6 +10,8 @@ class StructureEditor extends Component
 
     public $smiles;
 
+    public $type = 'substructure';
+
     public function mount($smiles)
     {
         $this->smiles = $smiles;

diff --git a/app/Livewire/Welcome.php b/app/Livewire/Welcome.php
@@ -18,13 +18,6 @@ class Welcome extends Component
 
     public $citationsMapped;
 
-    protected $listeners = ['updateSmiles' => 'setSmiles'];
-
-    public function setSmiles($smiles, $searchType)
-    {
-        return redirect()->to('/search?q='.urlencode($smiles).'&type='.urlencode($searchType));
-    }
-
     public function placeholder()
     {
         return <<<'HTML'

diff --git a/app/Models/User.php b/app/Models/User.php
@@ -87,4 +87,16 @@ public function linkedSocialAccounts()
     {
         return $this->hasMany(LinkedSocialAccount::class);
     }
+
+    /**
+     * Check if user can access a particular panel.
+     */
+    public function canAccessPanel(Panel $panel): bool
+    {
+        if ($panel->getId() === 'control-panel') {
+            return $this->roles()->exists();
+        }
+
+        return true;
+    }
 }
diff --git a/database/migrations/2014_10_12_000000_create_users_table.php b/database/migrations/2014_10_12_000000_create_users_table.php
@@ -13,13 +13,8 @@ public function up(): void
     {
         Schema::create('users', function (Blueprint $table) {
             $table->id();
-            $table->string('name')->nullable();
+            $table->string('name');
             $table->string('email')->unique();
-            $table->string('username')->unique();
-            $table->string('first_name');
-            $table->string('last_name');
-            $table->string('orcid_id')->nullable();
-            $table->string('affiliation')->nullable();
             $table->timestamp('email_verified_at')->nullable();
             $table->string('password')->nullable();
             $table->rememberToken();

diff --git a/database/migrations/2024_08_08_150749_add_columns_to_users_table.php b/database/migrations/2024_08_08_150749_add_columns_to_users_table.php
@@ -0,0 +1,33 @@
+<?php
+
+use Illuminate\Database\Migrations\Migration;
+use Illuminate\Database\Schema\Blueprint;
+use Illuminate\Support\Facades\Schema;
+
+return new class extends Migration
+{
+    /**
+     * Run the migrations.
+     */
+    public function up(): void
+    {
+        Schema::table('users', function (Blueprint $table) {
+            $table->string('name')->nullable()->change();
+            $table->string('username')->unique()->nullable();
+            $table->string('first_name')->nullable();
+            $table->string('last_name')->nullable();
+            $table->string('orcid_id')->nullable();
+            $table->string('affiliation')->nullable();
+        });
+    }
+
+    /**
+     * Reverse the migrations.
+     */
+    public function down(): void
+    {
+        Schema::table('users', function (Blueprint $table) {
+            $table->dropColumn(['username', 'first_name', 'last_name', 'orcid_id', 'affiliation']);
+        });
+    }
+};
diff --git a/docs/.vitepress/cache/deps/_metadata.json b/docs/.vitepress/cache/deps/_metadata.json
@@ -1,31 +1,31 @@
 {
-  "hash": "f6991786",
+  "hash": "911d3a82",
   "configHash": "a6dc731f",
-  "lockfileHash": "ba8dc5dd",
-  "browserHash": "6d39fbea",
+  "lockfileHash": "65d0b609",
+  "browserHash": "3f416605",
   "optimized": {
     "vue": {
       "src": "../../../../node_modules/vue/dist/vue.runtime.esm-bundler.js",
       "file": "vue.js",
-      "fileHash": "81b3a260",
+      "fileHash": "698daf6a",
       "needsInterop": false
     },
     "vitepress > @vue/devtools-api": {
       "src": "../../../../node_modules/@vue/devtools-api/dist/index.js",
       "file": "vitepress___@vue_devtools-api.js",
-      "fileHash": "085c132f",
+      "fileHash": "abeac802",
       "needsInterop": false
     },
     "vitepress > @vueuse/core": {
       "src": "../../../../node_modules/@vueuse/core/index.mjs",
       "file": "vitepress___@vueuse_core.js",
-      "fileHash": "d9cc147b",
+      "fileHash": "354fcef1",
       "needsInterop": false
     },
     "@theme/index": {
       "src": "../../../../node_modules/vitepress/dist/client/theme-default/index.js",
       "file": "@theme_index.js",
-      "fileHash": "5ba4d4f8",
+      "fileHash": "d4ea2476",
       "needsInterop": false
     }
   },