Merge development into production [minor]

.ai/guidelines/frontend.md

@@ -1,4 +1,6 @@
 # Frontend Build (BIOSPEX)
 
-- This project builds assets with Laravel Mix (`webpack.mix.js`), not Vite. Ignore Vite-specific guidance.
-- If the user doesn't see a frontend change reflected in the UI, they may need to run `yarn run dev` or `yarn run production`. Ask them.
+- This project builds assets with Vite (`vite.config.js`, `laravel-vite-plugin`) and yarn. Blade views load them with `@vite(...)`.
+- `yarn build` writes `public/build`; `yarn dev` runs the dev server. If the user doesn't see a frontend change reflected in the UI, they may need to run `yarn build` or `yarn dev`. Ask them.
+- The scripts are ES modules. jQuery and the libraries the pages call are globals set by `resources/js/jquery-global.js` and the `*-globals.js` files, imported first. An inline `<script>` in a Blade view that uses them while the page loads must be `type="module"`, and a CDN jQuery plugin it needs must be `defer`, so both run after the bundles.
+

.github/workflows/deploy-environment.yml

@@ -27,7 +27,7 @@ jobs:
     runs-on: ubuntu-latest
     environment: ${{ inputs.environment }}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
       - name: Get Runner IP
         id: ip
@@ -59,7 +59,7 @@ jobs:
         run: echo "dir=$(composer config cache-files-dir)" >> "$GITHUB_OUTPUT"
 
       - name: Cache Composer downloads
-        uses: actions/cache@v5
+        uses: actions/cache@v6
         with:
           path: ${{ steps.composer-cache.outputs.dir }}
           key: ${{ runner.os }}-composer-${{ hashFiles('composer.lock') }}
@@ -70,7 +70,7 @@ jobs:
         run: composer install --prefer-dist --no-progress --no-interaction --optimize-autoloader --no-scripts
 
       - name: Setup Node.js
-        uses: actions/setup-node@v6
+        uses: actions/setup-node@v7
         with:
           node-version: '24'
           cache: 'yarn'
@@ -79,12 +79,12 @@ jobs:
         run: yarn install --frozen-lockfile --ignore-engines
 
       - name: Build assets
-        run: npm run production
+        run: yarn build
         env:
-          MIX_REVERB_APP_KEY: ${{ vars[format('{0}_REVERB_APP_KEY', inputs.vars_prefix)] }}
-          MIX_REVERB_HOST: ${{ vars[format('{0}_REVERB_HOST', inputs.vars_prefix)] }}
-          MIX_REVERB_PORT: ${{ vars[format('{0}_REVERB_PORT', inputs.vars_prefix)] }}
-          MIX_REVERB_SCHEME: ${{ vars[format('{0}_REVERB_SCHEME', inputs.vars_prefix)] }}
+          VITE_REVERB_APP_KEY: ${{ vars[format('{0}_REVERB_APP_KEY', inputs.vars_prefix)] }}
+          VITE_REVERB_HOST: ${{ vars[format('{0}_REVERB_HOST', inputs.vars_prefix)] }}
+          VITE_REVERB_PORT: ${{ vars[format('{0}_REVERB_PORT', inputs.vars_prefix)] }}
+          VITE_REVERB_SCHEME: ${{ vars[format('{0}_REVERB_SCHEME', inputs.vars_prefix)] }}
 
       - name: Create deployment package
         run: |
@@ -94,7 +94,8 @@ jobs:
           # Create isolated temp dir
           TEMP_DIR=$(mktemp -d)
 
-          # Sync repo files to temp (exclusions prevent bloat/self-ref)
+          # Sync repo files to temp (exclusions prevent bloat/self-ref).
+          # This includes the Vite build in public/build, which each release keeps for itself.
           rsync -av \
             --exclude=node_modules \
             --exclude=.git \
@@ -104,8 +105,8 @@ jobs:
             --exclude=vendor \
             . "$TEMP_DIR/"
 
-          # Copy assets into temp/public/ (these are already built via npm run production)
-          cp -r public/css public/js public/fonts public/images public/svg public/mix-manifest.json "$TEMP_DIR/public/" || true
+          # Fail early if the build is missing, rather than deploying pages without assets
+          test -f "$TEMP_DIR/public/build/manifest.json"
 
           # Rename to package name
           mv "$TEMP_DIR" deployment-package

.github/workflows/deploy.yml

@@ -48,7 +48,7 @@ jobs:
       new_version: ${{ steps.new_version.outputs.new_version }}
       current_version: ${{ steps.version_bump.outputs.current_version }}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
 

.github/workflows/tests.yml

@@ -30,7 +30,7 @@ jobs:
           - 27017:27017
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0  # Pint --diff compares against the base branch
 
@@ -46,7 +46,7 @@ jobs:
         run: echo "dir=$(composer config cache-files-dir)" >> "$GITHUB_OUTPUT"
 
       - name: Cache Composer downloads
-        uses: actions/cache@v5
+        uses: actions/cache@v6
         with:
           path: ${{ steps.composer-cache.outputs.dir }}
           key: ${{ runner.os }}-composer-${{ hashFiles('composer.lock') }}
@@ -75,7 +75,7 @@ jobs:
     if: github.event_name == 'pull_request'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
       - name: Setup PHP
         uses: shivammathur/setup-php@v2

.gitignore

@@ -6,8 +6,8 @@ node_modules
 /public/css
 /public/js
 /public/fonts
-/public/images
-/public/mix-manifest.json
+/public/build
+/public/hot
 storage/cmd.txt
 storage/testing
 storage/app/classifications/*

AGENTS.md

@@ -3,8 +3,10 @@
 
 # Frontend Build (BIOSPEX)
 
-- This project builds assets with Laravel Mix (`webpack.mix.js`), not Vite. Ignore Vite-specific guidance.
-- If the user doesn't see a frontend change reflected in the UI, they may need to run `yarn run dev` or `yarn run production`. Ask them.
+- This project builds assets with Vite (`vite.config.js`, `laravel-vite-plugin`) and yarn. Blade views load them with `@vite(...)`.
+- `yarn build` writes `public/build`; `yarn dev` runs the dev server. If the user doesn't see a frontend change reflected in the UI, they may need to run `yarn build` or `yarn dev`. Ask them.
+- The scripts are ES modules. jQuery and the libraries the pages call are globals set by `resources/js/jquery-global.js` and the `*-globals.js` files, imported first. An inline `<script>` in a Blade view that uses them while the page loads must be `type="module"`, and a CDN jQuery plugin it needs must be `defer`, so both run after the bundles.
+
 
 === .ai/project-context rules ===
 

CLAUDE.md

@@ -3,8 +3,10 @@
 
 # Frontend Build (BIOSPEX)
 
-- This project builds assets with Laravel Mix (`webpack.mix.js`), not Vite. Ignore Vite-specific guidance.
-- If the user doesn't see a frontend change reflected in the UI, they may need to run `yarn run dev` or `yarn run production`. Ask them.
+- This project builds assets with Vite (`vite.config.js`, `laravel-vite-plugin`) and yarn. Blade views load them with `@vite(...)`.
+- `yarn build` writes `public/build`; `yarn dev` runs the dev server. If the user doesn't see a frontend change reflected in the UI, they may need to run `yarn build` or `yarn dev`. Ask them.
+- The scripts are ES modules. jQuery and the libraries the pages call are globals set by `resources/js/jquery-global.js` and the `*-globals.js` files, imported first. An inline `<script>` in a Blade view that uses them while the page loads must be `type="module"`, and a CDN jQuery plugin it needs must be `defer`, so both run after the bundles.
+
 
 === .ai/project-context rules ===
 

app/Console/Commands/CleanEfsDirsCommand.php

@@ -44,7 +44,11 @@ class CleanEfsDirsCommand extends Command
      *
      * @var string
      */
-    protected $description = 'Deletes files older than 72 hours from the /efs directory, leaving empty directories intact. Skipped while an import, export, OCR run or GeoLocate job is in progress.';
+    protected $description = 'Deletes files and empty directories older than 72 hours from the /efs directories BIOSPEX writes to (import, scratch, GeoLocate export). Skipped while an import, export, OCR run or GeoLocate job is in progress.';
+
+    private int $deletedFiles = 0;
+
+    private int $deletedDirectories = 0;
 
     /**
      * Execute the console command.
@@ -61,9 +65,34 @@ public function handle(): void
             return;
         }
 
-        $deletedFiles = $this->cleanDirectory(config('filesystems.disks.efs.root'));
+        $threshold = Carbon::now()->subHours(72)->getTimestamp();
+
+        foreach ($this->directories() as $directory) {
+            if (File::isDirectory($directory)) {
+                $this->cleanDirectory($directory, $threshold);
+            }
+        }
+
+        Log::info("Cleanup completed. Files deleted: {$this->deletedFiles}. Directories deleted: {$this->deletedDirectories}.");
+    }
+
+    /**
+     * Get the /efs directories that BIOSPEX writes to.
+     *
+     * /efs is shared by both servers and holds other files too, such as database dumps, so nothing outside these
+     * directories is touched.
+     *
+     * @return list<string>
+     */
+    private function directories(): array
+    {
+        $root = config('filesystems.disks.efs.root');
 
-        Log::info("Cleanup completed. Files deleted: $deletedFiles");
+        return [
+            "$root/".config('config.import_dir'),
+            "$root/".config('config.scratch_dir'),
+            "$root/".config('geolocate.dir.export'),
+        ];
     }
 
     /**
@@ -100,32 +129,27 @@ private function queueHasJobs(string $queue): bool
     }
 
     /**
-     * Recursively clean files older than 72 hours in a directory.
+     * Recursively delete the files, and then the empty subdirectories, last modified before the threshold.
+     *
+     * The directory itself is kept. A subdirectory emptied by this run was just modified, so it's removed by a
+     * later run. Hidden files aren't deleted, and a subdirectory holding one isn't empty: on EFS a deleted file
+     * that is still open becomes a hidden .nfs file until it's closed.
      */
-    private function cleanDirectory(string $path): int
+    private function cleanDirectory(string $path, int $threshold): void
     {
-        $deletedFiles = 0;
-
-        // Iterate through directory contents
-        $items = File::files($path);
-        $directories = File::directories($path);
-
-        // Delete files older than 72 hours
-        foreach ($items as $file) {
-            $lastModified = Carbon::createFromTimestamp(File::lastModified($file));
-            $threshold = Carbon::now()->subHours(72);
-
-            if ($lastModified->lessThan($threshold)) {
-                File::delete($file); // Use the File facade to delete
-                $deletedFiles++;
+        foreach (File::files($path) as $file) {
+            if (File::lastModified($file) < $threshold) {
+                File::delete($file);
+                $this->deletedFiles++;
             }
         }
 
-        // Recursively scan subdirectories
-        foreach ($directories as $directory) {
-            $deletedFiles += $this->cleanDirectory($directory);
-        }
+        foreach (File::directories($path) as $directory) {
+            $this->cleanDirectory($directory, $threshold);
 
-        return $deletedFiles;
+            if (File::isEmptyDirectory($directory) && File::lastModified($directory) < $threshold && File::deleteDirectory($directory)) {
+                $this->deletedDirectories++;
+            }
+        }
     }
 }

app/Http/Controllers/Admin/ExpertReconcileController.php

@@ -56,14 +56,14 @@ public function index(Expedition $expedition)
         $expedition->load(['project.group.owner', 'panoptesProject']);
 
         if (! CheckPermission::handle('updateProject', $expedition->project->group)) {
-            return Redirect::route('admin.expeditions.show', [$expedition->project_id, $expedition->id]);
+            return Redirect::route('admin.expeditions.show', [$expedition]);
         }
 
         $reconciles = $this->expertReconcileService->getPagination((int) $expedition->id);
 
         if ($reconciles->isEmpty()) {
 
-            return Redirect::route('admin.expeditions.show', [$expedition->project_id, $expedition->id])
+            return Redirect::route('admin.expeditions.show', [$expedition])
                 ->with('danger', t('Reconcile data for processing is missing.'));
         }
 
@@ -87,7 +87,7 @@ public function create(Expedition $expedition, ReconcileService $reconcileLambda
         $expedition->load('project.group.owner');
 
         if (! CheckPermission::handle('updateProject', $expedition->project->group)) {
-            return Redirect::route('admin.expeditions.show', [$expedition->project_id, $expedition->id]);
+            return Redirect::route('admin.expeditions.show', [$expedition]);
         }
 
         if ($this->skipReconcile($expedition->id)) {

app/Jobs/DwcBatchImportJob.php

@@ -466,9 +466,11 @@ private function cleanupFiles(string $scratchFileDir, string $importFilePath): v
      */
     private function cleanupScratchDirectory(string $scratchFileDir): void
     {
-        if (File::isDirectory($scratchFileDir)) {
-            File::cleanDirectory($scratchFileDir);
-            File::deleteDirectory($scratchFileDir);
+        if (File::isDirectory($scratchFileDir) && ! File::deleteDirectory($scratchFileDir)) {
+            Log::warning('Could not remove the import scratch directory', [
+                'import_id' => $this->import->id,
+                'directory' => $scratchFileDir,
+            ]);
         }
     }
 }

app/Jobs/ZooniverseExportDeleteFilesJob.php

@@ -62,10 +62,6 @@ public function handle(): void
             Storage::disk('s3')->deleteDirectory($processDir);
         }
 
-        if (Storage::disk('efs')->exists($processDir)) {
-            Storage::disk('efs')->deleteDirectory($processDir);
-        }
-
         $this->exportQueue->delete();
     }
 

app/Services/Csv/Csv.php

@@ -20,8 +20,11 @@
 
 namespace App\Services\Csv;
 
+use League\Csv\CannotInsertRecord;
 use League\Csv\CharsetConverter;
+use League\Csv\Exception;
 use League\Csv\Reader;
+use League\Csv\SyntaxError;
 use League\Csv\Writer;
 
 /**
@@ -57,6 +60,16 @@ public function readerCreateFromPath($file)
         $this->reader = Reader::createFromPath($file);
     }
 
+    /**
+     * Release the reader, closing its file.
+     *
+     * On EFS (NFS) a file that is still open can't really be deleted, so its directory can't be removed either.
+     */
+    public function closeReader(): void
+    {
+        unset($this->reader);
+    }
+
     /**
      * Create reader from stream.
      *
@@ -88,7 +101,7 @@ public function writerCreateFromStream($stream)
     /**
      * Set delimiter.
      *
-     * @throws \League\Csv\Exception
+     * @throws Exception
      */
     public function setDelimiter(string $delimiter = ',')
     {
@@ -98,7 +111,7 @@ public function setDelimiter(string $delimiter = ',')
     /**
      * Set enclosure.
      *
-     * @throws \League\Csv\Exception
+     * @throws Exception
      */
     public function setEnclosure(string $enclosure = '"')
     {
@@ -108,7 +121,7 @@ public function setEnclosure(string $enclosure = '"')
     /**
      * Set escape.
      *
-     * @throws \League\Csv\Exception
+     * @throws Exception
      */
     public function setEscape(string $escape = '\\')
     {
@@ -119,7 +132,7 @@ public function setEscape(string $escape = '\\')
      * Set header offset.
      *
      *
-     * @throws \League\Csv\Exception
+     * @throws Exception
      */
     public function setHeaderOffset(int $offset = 0): void
     {
@@ -131,7 +144,7 @@ public function setHeaderOffset(int $offset = 0): void
      *
      * @return string[]
      *
-     * @throws \League\Csv\SyntaxError
+     * @throws SyntaxError
      */
     public function getHeader(): array
     {
@@ -141,7 +154,7 @@ public function getHeader(): array
     /**
      * Fetch all rows.
      *
-     * @throws \League\Csv\Exception
+     * @throws Exception
      */
     public function getRecords(array $header = []): \Iterator
     {
@@ -151,7 +164,7 @@ public function getRecords(array $header = []): \Iterator
     /**
      * Insert one row.
      *
-     * @throws \League\Csv\CannotInsertRecord|\League\Csv\Exception
+     * @throws CannotInsertRecord|Exception
      */
     public function insertOne($row): void
     {