Merge pull request #1099 from NFDI4Chem/bioschemas

fix: extend Bioschemas to cover samples with no projects
NFDI4Chem · Apr 4, 2024 · 8fb25e7 · 8fb25e7
2 parents ad0f34a + e3c5d5d
commit 8fb25e7
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Showing 2 changed files with 25 additions and 7 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);