Merge pull request #1123 from NFDI4Chem/development

Development
NFDI4Chem · Apr 5, 2024 · b4eb382 · b4eb382
2 parents bde2fd3 + 4f9aa27
commit b4eb382
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Showing 21 changed files with 583 additions and 224 deletions.
diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php
@@ -238,13 +238,17 @@ public function prepareMoleculesSchemas($sample)
      */
     public function getSample($study)
     {
+        $prefix = '';
+        if (property_exists($study, 'project')) {
+            $prefix = $study->project->name.'.';
+        }
         $sample = $study->sample;
         $molecules = $this->prepareMoleculesSchemas($sample);
 
         $sampleSchema = Schema::ChemicalSubstance();
         $sampleSchema['@id'] = $study->doi;
         $sampleSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/types/ChemicalSubstance/0.3-RELEASE-2019_09_02']);
-        $sampleSchema->name($study->project->name.'.'.$sample->name);
+        $sampleSchema->name($prefix.$sample->name);
         $sampleSchema->description($sample->description);
         $sampleSchema->url(env('APP_URL').'/'.explode(':', $study->identifier ? $study->identifier : ':')[1]);
         $sampleSchema->hasBioChemEntityPart($this->prepareMoleculesSchemas($sample));
@@ -451,7 +455,11 @@ public function datasetLite($dataset)
     {
         $nmriumInfo = $this->prepareNMRiumInfo($dataset);
         if ($nmriumInfo) {
-            $prefix = $dataset->study->project->name.':'.$dataset->study->name.'.';
+            $study = $dataset->study;
+            $prefix = $dataset->study->name.'.';
+            if (property_exists($study, 'project')) {
+                $prefix = $study->project->name.':'.$prefix;
+            }
             $datasetSchema = Schema::Dataset();
             $datasetSchema['@id'] = $dataset->doi;
             $datasetSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://schema.org/Dataset', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#assay']);
@@ -504,7 +512,10 @@ public function dataset($dataset)
      */
     public function studyLite($study)
     {
-        $prefix = $study->project->name.':';
+        $prefix = '';
+        if (property_exists($study, 'project')) {
+            $prefix = $study->project->name.':';
+        }
         $studySchema = Bioschemas::Study();
         $studySchema['@id'] = $study->doi;
         $studySchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/types/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#study']);
@@ -534,7 +545,9 @@ public function studyLite($study)
     public function study($study)
     {
         $studySchema = $this->studyLite($study);
-        $studySchema->isPartOf($this->projectLite($study->project));
+        if (property_exists($study, 'project')) {
+            $studySchema->isPartOf($this->projectLite($study->project));
+        }
         $studySchema->hasPart($this->prepareDatasets($study));
 
         return $studySchema;

diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasHelper.php b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasHelper.php
@@ -127,7 +127,6 @@ public static function prepareCitations($model)
         $citationsSchemas = [];
         foreach ($model->citations as &$citation) {
             $citationSchema = Schema::CreativeWork();
-            $citationSchema->abstract($citation->abstract);
             $citationSchema->author($citation->authors);
             $citationSchema->headline($citation->title);
             $citationSchema->identifier($citation->doi);
@@ -149,11 +148,17 @@ public static function prepareDataDownload($dataset)
     {
         $url = env('APP_URL');
         $user = $dataset->owner->username;
-        $slug = $dataset->project->slug;
+        if (property_exists($dataset, 'project')) {
+            $slug = $dataset->project->slug;
+            $name = $dataset->project->name;
+        } else {
+            $slug = $dataset->study->slug;
+            $name = $dataset->study->name;
+        }
         $contentURL = $url.'/'.$user.'/datasets/'.$slug;
 
         $DataDownloadSchema = Schema::DataDownload();
-        $DataDownloadSchema->name($dataset->project->name);
+        $DataDownloadSchema->name($name);
         $DataDownloadSchema->encodingFormat('zip');
         $DataDownloadSchema->contentURL($contentURL);
 

diff --git a/app/Http/Controllers/DashboardController.php b/app/Http/Controllers/DashboardController.php
@@ -36,7 +36,7 @@ public function dashboard(Request $request)
         return Inertia::render('Dashboard', [
             'filters' => $request->all('action', 'draft_id'),
             'team' => $team,
-            'projects' => $projects->load('tags'),
+            'projects' => $projects->load('tags', 'draft'),
             'samples' => $samples->load('sample.molecules'),
             'teamRole' => $user->teamRole($team),
         ]);

diff --git a/app/Http/Controllers/DraftController.php b/app/Http/Controllers/DraftController.php
@@ -125,6 +125,7 @@ public function update(Request $request, Draft $draft)
         }
         $draft->name = $request->get('name') ? $request->get('name') : $draft->name;
         $draft->project_enabled = $project_enabled;
+        $draft->current_step = $request->get('current_step') ? $request->get('current_step') : 1;
         $draft->save();
 
         return $draft;
@@ -424,7 +425,7 @@ public function process(Request $request, Draft $draft)
                 }
             }
 
-            $draft->current_step = 2;
+            //$draft->current_step = 2;
             $draft->save();
 
             $studies = json_decode($project->studies()->orderBy('name')->get()->load(['datasets', 'sample.molecules', 'tags']));

diff --git a/app/Http/Controllers/UploadController.php b/app/Http/Controllers/UploadController.php
@@ -16,6 +16,7 @@ public function upload(Request $request)
     {
         return Inertia::render('Upload', [
             'draft_id' => $request->get('draft_id'),
+            'step' => $request->get('step'),
         ]);
     }
 

diff --git a/app/Http/Resources/ProjectResource.php b/app/Http/Resources/ProjectResource.php
@@ -48,6 +48,7 @@ public function toArray($request)
             'updated_at' => $this->updated_at,
             'download_url' => $this->download_url,
             'species' => json_decode($this->species),
+            'release_date' => $this->release_date,
             'stats' => [
                 'likes' => $this->likesCount(),
             ],

diff --git a/app/Models/Draft.php b/app/Models/Draft.php
@@ -24,6 +24,7 @@ class Draft extends Model
         'settings',
         'info',
         'project_enabled',
+        'current_step',
     ];
 
     public function files()
-Original file line number
+Diff line change
@@ Expand Up / @@ -16,6 +16,7 @@ public function upload(Request $request) @@
         {
             return Inertia::render('Upload', [
                 'draft_id' => $request->get('draft_id'),
+                'step' => $request->get('step'),
             ]);
         }
@@ Expand Down @@