Merge pull request #391 from NFDI4Chem/development

v1.6.0-alpha - Development merge into production
NFDI4Chem · Aug 26, 2022 · c6b9cf8 · c6b9cf8
2 parents 11808b2 + 45ba82b
commit c6b9cf8
Show file tree

Hide file tree

Showing 29 changed files with 1,995 additions and 47 deletions.
diff --git a/app/Actions/Project/UpdateProject.php b/app/Actions/Project/UpdateProject.php
@@ -116,4 +116,11 @@ public function updateAuthors(Project $project, $authors)
             $authors
         );
     }
+
+    public function updateCitation(Project $project, $citations, $user)
+    {
+        $project->citations()->syncWithPivotValues(
+            $citations,['user' => $user->id]
+        );
+    }
 }
diff --git a/app/Http/Controllers/API/Bioschema/BiochemaController.php b/app/Http/Controllers/API/Bioschema/BiochemaController.php
@@ -0,0 +1,136 @@
+<?php
+
+namespace App\Http\Controllers\API\Bioschema;
+
+use App\Http\Controllers\Controller;
+use Illuminate\Http\Request;
+use Spatie\SchemaOrg\Schema;
+use App\Models\Bioschema\BioSchema;
+use App\Models\Project;
+use App\Models\Study;
+use App\Models\Dataset;
+use App\Models\Bioschema\Study as StudySchema;
+use App\Models\User;
+use App\Models\Author;
+
+
+
+class BiochemaController extends Controller
+{
+    public function schema(Request $request, $username, $projectName, $studyName = null, $datasetName = null)
+    {
+        $user = User::where('username', $username)->firstOrFail();
+        if($user){
+            $project = Project::where([['slug', $projectName], ['owner_id', $user->id]])->firstOrFail();  
+        }
+        if($project){
+            $creativeWork = Schema::creativeWork();
+            $creativeWork['@id'] = 'https://bioschemas.org/profiles/Study/0.2-DRAFT';
+            $confromsTo = [];
+            $confromsTo['http://purl.org/dc/terms/conformsTo'] = $creativeWork;
+
+
+            $projectSchema = Schema::Project(); 
+            $projectSchema['@id']= $project->uuid;
+            $projectSchema['dct:conformsTo'] = $confromsTo;
+            $authors = [];
+            foreach ($project->authors as &$author) {
+                $authorSchema = Schema::Person(); 
+                $authorSchema-> givenName($author->given_name);
+                $authorSchema->familyName($author->family_name);
+                $authorSchema->identifier($author->orcid_id);
+                $authorSchema-> email($author->email_id);
+                $authorSchema-> affiliation($author->affiliation);
+                array_push($authors, $authorSchema);
+            }
+            $projectSchema['author']  = $authors;
+            $projectSchema->datePublished($project->release_date);
+            $projectSchema->description($project->description);
+            $projectSchema->name($project->name);
+            $projectSchema->dateCreated($project->created_at);
+            $tags = [];
+            foreach ($project->tags as &$tag) {
+                $tag = $tag->name; 
+                array_push($tags, $tag);
+            }
+            $projectSchema->keywords($tags);
+            $projectSchema->url($project->public_url);
+            $projectSchema->license($project->license->url);
+
+            $studies = [];
+            foreach ($project->studies as &$study) {
+                $studySchema = BioSchema::Study(); 
+                $studySchema->name($study->name);
+                $studySchema->url($study->public_url);
+
+                $datasets = [];
+                foreach ($study->datasets as &$dataset) {
+                    $datasetSchema = Schema::Dataset(); 
+                    $datasetSchema->name($dataset->name);
+                    $datasetSchema->url($dataset->public_url);
+                    array_push($datasets, $datasetSchema);
+                }
+                $studySchema->hasPart($datasets);
+                array_push($studies, $studySchema);   
+            }
+            $projectSchema->hasPart($studies);
+
+            if($studyName){
+                // send study back with project info added to it\
+                $study = Study::where([['slug', $studyName], ['owner_id', $user->id], ['project_id', $project->id]])->firstOrFail();
+                if($study){
+                    $studySchema = BioSchema::Study(); 
+                    $studySchema['@id']= $study->uuid;
+                    $studySchema['dct:conformsTo'] = $confromsTo;
+                    $studySchema->name($study->name);
+                    $studySchema->description($study->description);
+                    $tags = [];
+                    foreach ($study->tags as &$tag) {
+                        $tag = $tag->name; 
+                        array_push($tags, $tag);
+                    }
+                    $studySchema->keywords($tags);
+                    $studySchema->url($study->public_url);
+                    $studySchema->license($study->license->url);
+                    $datasets = [];
+                    foreach ($study->datasets as &$dataset) {
+                        $datasetSchema = Schema::Dataset(); 
+                        $datasetSchema->name($dataset->name);
+                        $datasetSchema->url($dataset->public_url);
+                        array_push($datasets, $datasetSchema);
+                    }
+                    $studySchema->hasPart($datasets);
+                    $projectSchema->relatedStudy($studySchema);
+
+
+                    if($datasetName){
+                        $dataset = Dataset::where([['slug', $datasetName], ['owner_id', $user->id], ['project_id', $project->id], ['study_id', $study->id]])->firstOrFail();
+                        // send dataset with project and study details
+                        if($dataset){
+                            $dataCatalog = Schema::dataCatalog();
+                            $dataCatalog->name(env('APP_NAME'));
+                            $dataCatalog->url('https://nmrxiv.org');
+
+                            $creativeWorkDataset = Schema::creativeWork();
+                            $creativeWorkDataset['@id'] = 'https://bioschemas.org/profiles/Dataset/1.0-RELEASE';
+                            $DatasetconfromsTo = [];
+                            $DatasetconfromsTo['http://purl.org/dc/terms/conformsTo'] = $creativeWorkDataset;
+                            $datasetSchema = Schema::Dataset(); 
+                            $datasetSchema['@id']= $dataset->uuid;
+                            $datasetSchema['dct:conformsTo'] = $DatasetconfromsTo;
+                            $datasetSchema->description($dataset->description);
+                            $datasetSchema->name($dataset->name);
+                            $datasetSchema->url($dataset->public_url);
+                            $datasetSchema->license($study->license->url);
+                            $datasetSchema->includedInDataCatalog($dataCatalog);
+                            $datasetSchema->measurementTechnique("https://terminology.nfdi4chem.de/ts/ontologies/chmo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0000591");
+                            $datasetSchema->isPartOf([$projectSchema]);
+                            return $datasetSchema;
+                        }
+                    }
+                }
+            }
+            return $projectSchema;
+        }
+    }
+}
diff --git a/app/Http/Controllers/CitationController.php b/app/Http/Controllers/CitationController.php
@@ -0,0 +1,36 @@
+<?php
+
+namespace App\Http\Controllers;
+
+
+use App\Actions\Project\UpdateProject;
+use App\Models\Citation;
+use App\Models\Project;
+use Illuminate\Http\Request;
+use Illuminate\Support\Facades\DB;
+
+class CitationController extends Controller
+{
+    public function updateCitation(Request $request, UpdateProject $updater, Project $project)
+    {
+        $input = $request->citationList;
+        $user = $request->user();
+        //dd($request->citationList);
+        //DB transaction
+        $citations = [];
+
+        foreach ($input as $item) {
+            $citation = Citation::create([
+                'doi' => array_key_exists('doi', $item) ? $item['doi'] : null,
+                'title' => array_key_exists('title', $item) ? $item['title'] : null,
+                'authors' => array_key_exists('authors', $item) ? $item['authors'] : null,
+                'abstract' => array_key_exists('abstract', $item) ? $item['abstract'] : null,
+                'citation_text' => array_key_exists('citation_text', $item) ? $item['citation_text'] : null,
+                ]);
+            array_push($citations, $citation->id);
+        }
+        $updater->updateCitation($project, $citations, $user);
+
+        return $request->wantsJson() ? new JsonResponse('', 200) : back()->with('success', 'Citation updated successfully');
+    }
+}
diff --git a/app/Http/Controllers/ProjectController.php b/app/Http/Controllers/ProjectController.php
@@ -40,7 +40,7 @@ public function publicProjectView(Request $request, $owner, $slug)
 
         if ($tab == 'info') {
             return Inertia::render('Public/Project/Show', [
-                'project' => (new ProjectResource($project))->lite(false, ['users', 'authors']),
+                'project' => (new ProjectResource($project))->lite(false, ['users', 'authors', 'citations']),
                 'tab' => $tab,
             ]);
         } elseif ($tab == 'studies') {
@@ -69,7 +69,7 @@ public function publicProjectView(Request $request, $owner, $slug)
             ]);
         } else {
             return Inertia::render('Public/Project/Show', [
-                'project' => (new ProjectResource($project))->lite(false, ['users', 'authors']),
+                'project' => (new ProjectResource($project))->lite(false, ['users', 'authors', 'citations']),
                 'tab' => 'info',
             ]);
         }
@@ -110,7 +110,7 @@ public function show(Request $request, Project $project, GetLicense $getLicense)
         }
 
         return Inertia::render('Project/Show', [
-            'project' => $project->load('projectInvitations', 'tags', 'authors'),
+            'project' => $project->load('projectInvitations', 'tags', 'authors', 'citations'),
             'team' => $team ? $team->load(['users', 'owner']) : null,
             'members' => $project->allUsers(),
             'availableRoles' => array_values(Jetstream::$roles),

diff --git a/app/Http/Controllers/StudyController.php b/app/Http/Controllers/StudyController.php
@@ -140,6 +140,7 @@ public function moleculeDetach(Request $request, Study $study, Molecule $molecul
             $sample = $study->sample;
             $sample->molecules()->detach([$molecule->id]);
             $sample = $sample->fresh();
+
             return $sample->molecules;
         }
     }

diff --git a/app/Http/Middleware/HandleInertiaRequests.php b/app/Http/Middleware/HandleInertiaRequests.php
@@ -70,6 +70,7 @@ public function share(Request $request)
             'MEILISEARCH_PUBLICKEY' => (env('MEILISEARCH_PUBLICKEY')),
             'SCOUT_PREFIX' => (env('SCOUT_PREFIX')),
             'getDetailsbyDOIApi' => (env('GET_DETAILS_BY_DOI_API')),
+            'getCitationbyDOIApi' => (env('GET_CITATION_BY_DOI_API')),
         ]);
     }
 }
diff --git a/app/Http/Resources/CitationResource.php b/app/Http/Resources/CitationResource.php
@@ -0,0 +1,25 @@
+<?php
+
+namespace App\Http\Resources;
+
+use Illuminate\Http\Resources\Json\JsonResource;
+
+class CitationResource extends JsonResource
+{
+    /**
+     * Transform the resource into an array.
+     *
+     * @param  \Illuminate\Http\Request  $request
+     * @return array|\Illuminate\Contracts\Support\Arrayable|\JsonSerializable
+     */
+    public function toArray($request)
+    {
+        return [
+            'doi' => $this->doi,
+            'title' => $this->title,
+            'authors' => $this->authors,
+            'abstract' => $this->abstract,
+            'citation_text' => $this->citation_text,
+        ];
+    }
+}
diff --git a/app/Http/Resources/LicenseResource.php b/app/Http/Resources/LicenseResource.php
@@ -25,4 +25,4 @@ public function toArray($request)
             'body'        => $this->body,
         ];
     }
-}
+}
diff --git a/app/Http/Resources/ProjectResource.php b/app/Http/Resources/ProjectResource.php
@@ -9,7 +9,7 @@ class ProjectResource extends JsonResource
 {
     private bool $lite = true;
 
-    private array $properties = ['users', 'studies', 'files', 'authors'];
+    private array $properties = ['users', 'studies', 'files', 'authors', 'citations'];
 
     public function lite(bool $lite, array $properties): self
     {
@@ -94,6 +94,16 @@ function () {
                             ];
                         }
                     ),
+                    $this->mergeWhen(
+                        in_array('citations', $this->properties),
+                        function () {
+                            return [
+                                'citations' => CitationResource::collection(
+                                    $this->citations
+                                ),
+                            ];
+                        }
+                    ),
                 ];
             }),
         ];

diff --git a/app/Models/Bioschema/BioSchema.php b/app/Models/Bioschema/BioSchema.php
@@ -0,0 +1,17 @@
+<?php
+
+namespace App\Models\Bioschema;
+
+use App\Models\Bioschema\Study;
+use \Spatie\SchemaOrg\Schema;
+
+/**
+ * Factory class for all Schema.org types.
+ */
+class BioSchema extends Schema
+{
+    public static function study(): Study
+    {
+        return new Study();
+    }
+}
-Original file line number
+Diff line change
@@ Expand Up / @@ -25,4 +25,4 @@ public function toArray($request) @@
                 'body'        => $this->body,
             ];
         }
-    }
+    }