Development

app/Events/DraftProcessed.php

@@ -12,14 +12,17 @@ class DraftProcessed implements ShouldBroadcastNow
 
     public $project;
 
+    public $sendTo;
+
     /**
      * Create a new event instance.
      *
      * @return void
      */
-    public function __construct($project)
+    public function __construct($project, $sendTo)
     {
         $this->project = $project;
+        $this->sendTo = $sendTo;
     }
 
     /**

app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php

@@ -199,9 +199,13 @@ public function prepareMoleculesSchemas($sample)
         foreach ($sample->molecules as &$molecule) {
             $inchiKey = $molecule->inchi_key;
             $pubchemLink = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/'.$inchiKey.'/property/IUPACName/JSON';
-            $json = json_decode(Http::get($pubchemLink)->body(), true);
-            $cid = $json['PropertyTable']['Properties'][0]['CID'];
-            $iupacName = $json['PropertyTable']['Properties'][0]['IUPACName'];
+            $pubchemDataJSON = json_decode(Http::get($pubchemLink)->body(), true);
+            $cid = '';
+            $iupacName = '';
+            if (array_key_exists('PropertyTable', $pubchemDataJSON)) {
+                $cid = $pubchemDataJSON['PropertyTable']['Properties'][0]['CID'];
+                $iupacName = $pubchemDataJSON['PropertyTable']['Properties'][0]['IUPACName'];
+            }
 
             $moleculeSchema = Schema::MolecularEntity();
             $moleculeSchema['@id'] = $inchiKey;

app/Http/Controllers/DatasetController.php

@@ -137,10 +137,17 @@ public function preview(Request $request, Dataset $dataset)
         $content = $request->get('img');
         $study = $dataset->study;
         if ($content) {
-            $path = '/projects/'.$study->project->uuid.'/'.$study->uuid.'/'.$dataset->slug.'.svg';
-            Storage::disk(env('FILESYSTEM_DRIVER_PUBLIC'))->put($path, $content, 'public');
-            $dataset->dataset_photo_path = $path;
-            $dataset->save();
+            if ($study->project) {
+                $path = '/projects/'.$study->project->uuid.'/'.$study->uuid.'/'.$dataset->slug.'.svg';
+                Storage::disk(env('FILESYSTEM_DRIVER_PUBLIC'))->put($path, $content, 'public');
+                $dataset->dataset_photo_path = $path;
+                $dataset->save();
+            } else {
+                $path = '/samples/'.$study->uuid.'/'.$dataset->slug.'.svg';
+                Storage::disk(env('FILESYSTEM_DRIVER_PUBLIC'))->put($path, $content, 'public');
+                $dataset->dataset_photo_path = $path;
+                $dataset->save();
+            }
         }
     }
 }

app/Http/Controllers/OEmbedController.php

@@ -0,0 +1,66 @@
+<?php
+
+namespace App\Http\Controllers;
+
+use App\Http\Resources\StudyResource;
+use Illuminate\Http\Request;
+use Inertia\Inertia;
+use Response;
+
+class OEmbedController extends Controller
+{
+    public function spectra(Request $request)
+    {
+        $url = $request->get('url');
+        $format = $request->get('format');
+        $height = $request->get('height');
+        $width = $request->get('width');
+        $parsedURL = parse_url($url);
+        $URLPath = $parsedURL['path'];
+        $identifier = preg_split('#/#', $URLPath)[1];
+        if ($identifier) {
+            $resolvedModel = resolveIdentifier($identifier);
+            $namespace = $resolvedModel['namespace'];
+            $model = $resolvedModel['model'];
+            // dd($model);
+            if ($model) {
+                $data = [
+                    'success' => true,
+                    'type' => 'rich',
+                    'version' => '1.0',
+                    'provider_name' => config('app.name'),
+                    'provider_url' => config('app.url'),
+                    'title' => $model->name,
+                    'author_name' => $model->owner->name,
+                    'author_url' => config('app.url').'/author/'.$model->owner->username,
+                    'height' => $height ? $height : '300',
+                    'width' => $width ? $width : '320',
+                    'thumbnail_width' => '300',
+                    'thumbnail_height' => '125',
+                    'thumbnail_url' => $model->study_preview_urls[0],
+                    'html' => '<iframe id="nmrxiv_embed" class="nmrxiv_embed_iframe" style="width: 100%; overflow: hidden;" src="'.config('app.url').'/embed/'.$model->identifier.'" width="300" height="300" frameborder="0" scrolling="no"></iframe>',
+                ];
+
+                return Response::json($data);
+            }
+        }
+    }
+
+    public function embed(Request $request, $identifier)
+    {
+        $resolvedModel = resolveIdentifier($identifier);
+        $namespace = $resolvedModel['namespace'];
+        $model = $resolvedModel['model'];
+        if ($model) {
+            if ($namespace == 'Study') {
+                $study = $model;
+
+                return Inertia::render('Public/Embed/Sample', [
+                    'study' => (new StudyResource($study))->lite(false, ['tags', 'sample', 'datasets', 'molecules', 'owner', 'license']),
+                ]);
+            } elseif ($namespace == 'Dataset') {
+                $dataset = $model;
+            }
+        }
+    }
+}

app/Jobs/ProcessSubmission.php

@@ -109,7 +109,7 @@ public function handle(AssignIdentifier $assigner, PublishProject $projectPublis
 
                 ArchiveProject::dispatch($project);
 
-                Notification::send($project->owner, new DraftProcessedNotification($project));
+                $project->sendNotification('publish', $this->prepareSendList($project));
             }
         } else {
             $logs = 'Moving files in progress';
@@ -203,4 +203,24 @@ public function moveFolder($fsObject, $draft, $path)
             }
         }
     }
+
+    /**
+     * Prepare Sent to list.
+     *
+     * @param  App\Models\Project  $project
+     * @return void
+     */
+    public function prepareSendList($project)
+    {
+        $sendTo = [];
+        foreach ($project->allUsers() as $member) {
+            if ($member->projectMembership->role == 'creator' || $member->projectMembership->role == 'owner') {
+                array_push($sendTo, $member);
+            } else {
+                array_push($sendTo, $project->owner);
+            }
+        }
+
+        return $sendTo;
+    }
 }

app/Listeners/ProjectArchival.php

@@ -22,7 +22,7 @@ public function __construct()
      */
     public function handle(object $event): void
     {
-        Notification::send($event->$sendTo, new ProjectArchivalNotification($event->project));
-        Notification::send(User::role(['super-admin'])->get(), new ProjectArchivalNotificationToAdmins($this));
+        Notification::send($event->sendTo, new ProjectArchivalNotification($event->project));
+        Notification::send(User::role(['super-admin'])->get(), new ProjectArchivalNotificationToAdmins($event->project));
     }
 }

app/Listeners/SendDraftProcessedNotification.php

@@ -2,7 +2,9 @@
 
 namespace App\Listeners;
 
+use App\Models\User;
 use App\Notifications\DraftProcessedNotification;
+use App\Notifications\ProjectPublishNotificationToAdmins;
 use Illuminate\Support\Facades\Notification;
 
 class SendDraftProcessedNotification
@@ -19,14 +21,10 @@ public function __construct()
 
     /**
      * Handle the event.
-     *
-     * @param  object  $event
-     * @return void
      */
-    public function handle($event)
+    public function handle(object $event): void
     {
-        $project = $event->project;
-        $owner = $project->owner;
-        Notification::send($owner, new DraftProcessedNotification($project));
+        Notification::send($event->sendTo, new DraftProcessedNotification($event->project));
+        Notification::send(User::role(['super-admin'])->get(), new ProjectPublishNotificationToAdmins($event->project));
     }
 }

app/Mail/ProjectPublishNotifyAdmins.php

@@ -0,0 +1,38 @@
+<?php
+
+namespace App\Mail;
+
+use Illuminate\Bus\Queueable;
+use Illuminate\Mail\Mailable;
+use Illuminate\Queue\SerializesModels;
+
+class ProjectPublishNotifyAdmins extends Mailable
+{
+    use Queueable, SerializesModels;
+
+    public $project;
+
+    /**
+     * Create a new message instance.
+     *
+     * @return void
+     */
+    public function __construct($project)
+    {
+        $this->project = $project;
+    }
+
+    /**
+     * Build the message.
+     *
+     * @return $this
+     */
+    public function build()
+    {
+        return $this->markdown('vendor.mail.project-publish-notify-admins', [
+            'url' => url(config('app.url').'/dashboard/projects/'.$this->project->id),
+            'projectName' => $this->project->name,
+            'projectId' => $this->project->id,
+        ])->subject(__('A project has been published'.' - '.$this->project->name));
+    }
+}

app/Models/Project.php

@@ -2,6 +2,7 @@
 
 namespace App\Models;
 
+use App\Events\DraftProcessed;
 use App\Events\ProjectArchival;
 use App\Events\ProjectDeletion;
 use App\Notifications\ProjectDeletionFailureNotification;
@@ -356,6 +357,9 @@ public function sendNotification($notifyType, $sendTo)
             case 'deletionFailure':
                 Notification::send($sendTo, new ProjectDeletionFailureNotification($this));
                 break;
+            case 'publish':
+                event(new DraftProcessed($this, $sendTo));
+                break;
         }
     }
 }

app/Notifications/ProjectPublishNotificationToAdmins.php

@@ -0,0 +1,60 @@
+<?php
+
+namespace App\Notifications;
+
+use App\Mail\ProjectPublishNotifyAdmins;
+use Illuminate\Bus\Queueable;
+use Illuminate\Contracts\Queue\ShouldQueue;
+use Illuminate\Notifications\Notification;
+
+class ProjectPublishNotificationToAdmins extends Notification implements ShouldQueue
+{
+    use Queueable;
+
+    private $project;
+
+    /**
+     * Create a new notification instance.
+     *
+     * @return void
+     */
+    public function __construct($project)
+    {
+        $this->project = $project;
+    }
+
+    /**
+     * Get the notification's delivery channels.
+     *
+     * @param  mixed  $notifiable
+     * @return array
+     */
+    public function via($notifiable)
+    {
+        return ['mail'];
+    }
+
+    /**
+     * Get the mail representation of the notification.
+     *
+     * @param  mixed  $notifiable
+     * @return \Illuminate\Notifications\Messages\MailMessage
+     */
+    public function toMail($notifiable)
+    {
+        return (new ProjectPublishNotifyAdmins($this->project))->to($notifiable->email);
+    }
+
+    /**
+     * Get the array representation of the notification.
+     *
+     * @param  mixed  $notifiable
+     * @return array
+     */
+    public function toArray($notifiable)
+    {
+        return [
+            //
+        ];
+    }
+}

docs/.vitepress/config.mjs

@@ -13,8 +13,8 @@ export default defineConfig({
     },
 
     logo:  { 
-      light: "/logo.svg",
-      dark: "/logo-dark.svg",
+      light: "/img/logo.svg",
+      dark: "/img/dark-logo.svg",
       alt : "nmrXiv" 
     },
 

docs/developer-guides/api.md

@@ -1,16 +1,4 @@
 # API
 
-nmrXiv infrastructure supports API through which software developers can interact with the data programmatically. Postman tool is used to document how nmrXiv API should be used, methods, status, and error codes supported.
+The infrastructure of nmrXiv facilitates API access, enabling software developers to interact with the data programmatically. The documentation for nmrXiv API, including information on methods, status, and supported error codes, is provided using [Swagger](https://swagger.io/). For detailed insights into API usage, please refer to our [Swagger documentation](https://nmrxiv.org/api/documentation).
 
-Postman allows you to publish documentation quickly and easily. Postman automatically pulls your sample requests, headers, code snippets, etc., to populate your documentation page with dynamic examples and machine-readable instructions so you can easily share your API with the rest of the world.
-
-## [nmrXiv APIs](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17173369-2ef7d5a8-0121-418b-8762-cc47d7a5b7cd)
-
-<img src="/img/postman.png"/>
-
-<br/><br/>
-If you are interested in specific endpoints, check out the following quick links:
-
-- [Authentication and Authorisation](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/collection/17173369-f372ec15-9b92-4902-8844-b129ab0c17d1?ctx=documentation)
-- [Projects/Studies/Dataset](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/collection/17173369-b00475c3-6171-4e58-97ab-cb88b3ac4c59?ctx=documentation)
-- [Bioschemas](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/folder/17195598-561a4bcc-7c84-4669-b245-c8416dfc8e90?ctx=documentation)

public/vendor/horizon/mix-manifest.json

@@ -1,5 +1,5 @@
 {
-    "/app.js": "/app.js?id=7e1968acfd75b8dc843675097962e3ce",
+    "/app.js": "/app.js?id=79bae40dcb18de9ca1b5d0008c577471",
     "/app-dark.css": "/app-dark.css?id=15c72df05e2b1147fa3e4b0670cfb435",
     "/app.css": "/app.css?id=4d6a1a7fe095eedc2cb2a4ce822ea8a5",
     "/img/favicon.png": "/img/favicon.png?id=1542bfe8a0010dcbee710da13cce367f",

resources/js/Pages/Public/Embed/Sample.vue

@@ -0,0 +1,29 @@
+<template>
+    <div>
+        <SpectraViewer
+            ref="spectraViewerREF"
+            :study="study.data"
+        ></SpectraViewer>
+    </div>
+</template>
+
+<script>
+import SpectraViewer from "@/Shared/SpectraViewer.vue";
+import Depictor2D from "@/Shared/Depictor2D.vue";
+import DOIBadge from "@/Shared/DOIBadge.vue";
+
+export default {
+    components: {
+        SpectraViewer,
+        Depictor2D,
+        DOIBadge,
+    },
+    props: ["study"],
+    data() {
+        return {};
+    },
+    computed: {},
+    mounted() {},
+    methods: {},
+};
+</script>