Merge pull request #1162 from NFDI4Chem/datacite-bioschemas

fix: unify studies and datasets naming in bioschemas and datacite
NFDI4Chem · Aug 14, 2024 · 79bd14c · 79bd14c
2 parents 3ed669a + 31ed8e9
commit 79bd14c
Showing 1 changed file with 11 additions and 18 deletions.
diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php
@@ -238,17 +238,13 @@ 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']);
-        $sampleSchema->name($prefix.$sample->name);
+        $sampleSchema->name($sample->name);
         $sampleSchema->description($sample->description);
         $sampleSchema->url(env('APP_URL').'/'.explode(':', $study->identifier ? $study->identifier : ':')[1]);
         $sampleSchema->hasBioChemEntityPart($this->prepareMoleculesSchemas($sample));
@@ -455,14 +451,12 @@ public function datasetLite($dataset)
         $nmriumInfo = $this->prepareNMRiumInfo($dataset);
         if ($nmriumInfo) {
             $study = $dataset->study;
-            $prefix = $dataset->study->name.'.';
-            if (property_exists($study, 'project')) {
-                $prefix = $study->project->name.':'.$prefix;
-            }
+            $prefix = $dataset->study->name;
+
             $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']);
-            $datasetSchema->name($prefix.$nmriumInfo[2]);
+            $datasetSchema->name($prefix.'['.$dataset->name.']');
             $datasetSchema->description($dataset->description);
             $datasetSchema->keywords($nmriumInfo[0]);
             $datasetSchema->license($dataset->study->license->url);
@@ -491,11 +485,13 @@ public function datasetLite($dataset)
      */
     public function dataset($dataset)
     {
-        $projectSchema = $this->projectLite($dataset->project);
-        $studySchema = $this->studyLite($dataset->study);
         $datasetSchema = $this->datasetLite($dataset);
+        $studySchema = $this->studyLite($dataset->study);
 
-        $studySchema->isPartOf($projectSchema);
+        if ($dataset->project) {
+            $projectSchema = $this->projectLite($dataset->project);
+            $studySchema->isPartOf($projectSchema);
+        }
         $datasetSchema->isPartOf($studySchema);
 
         return $datasetSchema;
@@ -511,14 +507,11 @@ public function dataset($dataset)
      */
     public function studyLite($study)
     {
-        $prefix = '';
-        if (property_exists($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']);
-        $studySchema->name($prefix.$study->name);
+        $studySchema->name($study->name);
         $studySchema->description($study->description);
         $studySchema->keywords(BioschemasHelper::getTags($study));
         $studySchema->license($study->license->url);