Merge branch 'development' into feat-api-search-expansion

README.md

@@ -43,8 +43,6 @@ COCONUT infrastructure code is licensed under the MIT license - see the [LICENSE
 
 ### COCONUT 2.0
 -  Venkata Chandrasekhar, Kohulan Rajan, Sri Ram Sagar Kanakam, Nisha Sharma, Viktor Weißenborn, Jonas Schaub, Christoph Steinbeck, COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database, Nucleic Acids Research, 2024;, gkae1063, https://doi.org/10.1093/nar/gkae1063
-
-https://doi.org/10.1093/nar/gkae1063
 
 ### COCONUT (Legacy)
 -  Sorokina, M., Merseburger, P., Rajan, K. et al. (2021). COCONUT online: COlleCtion of Open Natural prodUcTs database. *Journal of Cheminformatics*, 13, 2. 

app/Actions/Coconut/AssignDOI.php

@@ -0,0 +1,50 @@
+<?php
+
+namespace App\Actions\Coconut;
+
+use App\Models\Collection;
+use App\Models\Ticker;
+use App\Services\DOI\DOIService;
+
+class AssignDOI
+{
+    private $doiService;
+
+    /**
+     * Create a new class instance.
+     *
+     * @return void
+     */
+    public function __construct(DOIService $doiService)
+    {
+        $this->doiService = $doiService;
+    }
+
+    /**
+     * Archive the given model.
+     *
+     * @param  mixed  $model
+     * @return void
+     */
+    public function assign($model)
+    {
+        $collection = null;
+        if ($model instanceof Collection) {
+            $collection = $model;
+        }
+        if ($collection) {
+            $collectionIdentifier = $collection->identifier ? $collection->identifier : null;
+            if ($collectionIdentifier == null) {
+                $collectionTicker = Ticker::whereType('collection')->first();
+                $collectionIdentifier = $collectionTicker->index + 1;
+                $collectionTicker->index = $collectionIdentifier;
+                $collectionTicker->save();
+
+                $collection->identifier = $collectionIdentifier;
+                $collection->save();
+            }
+            $collection->fresh()->generateDOI($this->doiService);
+            echo $collection->identifier."\r\n";
+        }
+    }
+}

app/Console/Commands/AssignCollectionsIdentifiers.php

@@ -50,7 +50,9 @@ public function handle()
 
     public function generateIdentifier($index)
     {
-        return 'CNPC'.str_pad($index, 4, '0', STR_PAD_LEFT);
+        $prefix = (env('APP_ENV') === 'production') ? 'CNPC' : 'CNPC_DEV';
+
+        return $prefix.str_pad($index, 6, '0', STR_PAD_LEFT);
     }
 
     public function fetchLastIndex()

app/Console/Commands/AssignDOIs.php

@@ -0,0 +1,45 @@
+<?php
+
+namespace App\Console\Commands;
+
+use App\Actions\Coconut\AssignDOI;
+use App\Models\Collection;
+use Illuminate\Console\Command;
+use Illuminate\Support\Facades\DB;
+
+class AssignDOIs extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'coconut:collection-assign-doi';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Assigns dois to all unassigned public collections';
+
+    /**
+     * Execute the console command.
+     *
+     * @return int
+     */
+    public function handle(AssignDOI $assigner)
+    {
+        return DB::transaction(function () use ($assigner) {
+            $collections = Collection::where([
+                ['is_public', true],
+                ['doi', null],
+            ])->get();
+
+            foreach ($collections as $collection) {
+                $collectionDOI = $collection->doi ? $collection->doi : null;
+                $assigner->assign($collection);
+            }
+        });
+    }
+}

app/Models/Collection.php

@@ -15,6 +15,7 @@
 
 class Collection extends Model implements Auditable, HasMedia
 {
+    use HasDOI;
     use HasFactory;
     use HasTags;
     use InteractsWithMedia;
@@ -41,6 +42,7 @@ protected static function booted()
         'image',
         'status',
         'release_date',
+        'datacite_schema',
     ];
 
     /**

app/Models/HasDOI.php

@@ -0,0 +1,114 @@
+<?php
+
+namespace App\Models;
+
+trait HasDOI
+{
+    public function generateDOI($doiService)
+    {
+        $doi_host = env('DOI_HOST', null);
+        if (! is_null($doi_host)) {
+            $identifier = $this->getIdentifier($this, 'identifier');
+            if ($this->doi == null) {
+                $url = 'https://coconut.naturalproducts.net/collections/'.$identifier;
+                $attributes = $this->getMetadata();
+                $attributes['url'] = $url;
+                $doiResponse = $doiService->createDOI($identifier, $attributes);
+                $this->doi = $doiResponse['data']['id'];
+                $this->datacite_schema = $doiResponse;
+                $this->save();
+            }
+
+        }
+
+    }
+
+    public function getIdentifier($model, $key)
+    {
+        return $model->getAttributes()[$key];
+    }
+
+    public function getMetadata()
+    {
+        $title = $this->title;
+        $creators = [
+            ['name' => 'COCONUT',
+                'nameType' => 'Organizational', ],
+        ];
+        $description = [
+            'description' => $this->description,
+            'descriptionType' => 'Other',
+        ];
+        $relatedIdentifiers = [
+            [
+                'relatedIdentifier' => $this->url,
+                'relatedIdentifierType' => 'URL',
+                'relationType' => 'References',
+            ],
+        ];
+        $dates = [
+            [
+                'date' => $this->created_at,
+                'dateType' => 'Available',
+            ],
+            [
+                'date' => $this->created_at,
+                'dateType' => 'Submitted',
+            ],
+            [
+                'date' => $this->updated_at,
+                'dateType' => 'Updated',
+            ],
+        ];
+
+        $rights = [
+            [
+                'rights' => 'Creative Commons Attribution 4.0 International',
+                'rightsUri' => 'https://creativecommons.org/licenses/by/4.0/legalcode',
+                'rightsIdentifier' => 'CC-BY-4.0',
+                'rightsIdentifierScheme' => 'SPDX',
+                'schemeUri' => 'https://spdx.org/licenses/',
+            ],
+        ];
+        $publicationYear = explode('-', $this->created_at)[0];
+        $subjects = [
+            ['subject' => 'Natural Product',
+                'subjectScheme' => 'NCI Thesaurus OBO Edition',
+                'schemeURI' => 'http://purl.obolibrary.org/obo/ncit/releases/2022-08-19/ncit.owl',
+                'valueURI' => 'http://purl.obolibrary.org/obo/NCIT_C66892',
+                'classificationCode' => 'NCIT:C66892',
+            ],
+        ];
+        $attributes = [
+            'creators' => $creators,
+            'titles' => [
+                [
+                    'title' => $title,
+                ],
+            ],
+            'dates' => $dates,
+            'language' => 'en',
+            'rightsList' => $rights,
+            'descriptions' => [$description],
+            'relatedIdentifiers' => $relatedIdentifiers,
+            'resourceType' => 'Collection',
+            'resourceTypeGeneral' => 'Collection',
+            'publicationYear' => $publicationYear,
+            'subjects' => $subjects,
+            'types' => [
+                'ris' => 'DATA',
+                'bibtex' => 'misc',
+                'schemaOrg' => 'Collection',
+                'resourceType' => 'Collection',
+                'resourceTypeGeneral' => 'Collection',
+            ],
+            'isActive' => true,
+            'event' => 'publish',
+            'state' => 'findable',
+            'schemaVersion' => 'http://datacite.org/schema/kernel-4',
+
+        ];
+
+        return $attributes;
+    }
+}

app/Providers/DOIServiceProvider.php

@@ -0,0 +1,24 @@
+<?php
+
+namespace App\Providers;
+
+use App\Services\DOI\DataCite;
+use App\Services\DOI\DOIService;
+use Illuminate\Support\ServiceProvider;
+
+class DOIServiceProvider extends ServiceProvider
+{
+    /**
+     * Register any application services.
+     *
+     * @return void
+     */
+    public function register()
+    {
+        $this->app->bind(DOIService::class, function ($app) {
+            return match (config('doi.default')) {
+                'datacite' => new DataCite
+            };
+        });
+    }
+}

app/Services/DOI/DOIService.php

@@ -0,0 +1,18 @@
+<?php
+
+namespace App\Services\DOI;
+
+interface DOIService
+{
+    public function getDOIs();
+
+    public function createDOI($identifier, $attributes = []);
+
+    public function getDOI($doi);
+
+    public function updateDOI($doi);
+
+    public function deleteDOI($doi);
+
+    public function getDOIActivity($doi);
+}