Merge pull request #1139 from NFDI4Chem/development

Development

app/Actions/Project/UpdateDOI.php

@@ -0,0 +1,59 @@
+<?php
+
+namespace App\Actions\Project;
+
+use App\Models\Dataset;
+use App\Models\Project;
+use App\Models\Study;
+use App\Services\DOI\DOIService;
+use Illuminate\Support\Collection;
+
+class UpdateDOI
+{
+    private $doiService;
+
+    /**
+     * Create a new class instance.
+     *
+     * @return void
+     */
+    public function __construct(DOIService $doiService)
+    {
+        $this->doiService = $doiService;
+    }
+
+    /**
+     * Update the given model DOI metadata.
+     *
+     * @param  mixed  $model
+     * @return void
+     */
+    public function update($model)
+    {
+        $project = null;
+        $studies = null;
+        if ($model instanceof Project) {
+            $project = $model;
+        } elseif ($model instanceof Collection) {
+            $studies = $model;
+        }
+
+        if ($project) {
+            $project->addRelatedIdentifiers($this->doiService);
+            $studies = $project->studies;
+        }
+        if ($studies) {
+            foreach ($studies as $study) {
+                if ($study instanceof Study) {
+                    $study->addRelatedIdentifiers($this->doiService);
+                    $datasets = $study->datasets;
+                    foreach ($datasets as $dataset) {
+                        if ($dataset instanceof Dataset) {
+                            $dataset->addRelatedIdentifiers($this->doiService);
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php

@@ -281,7 +281,6 @@ public function prepareExperiment($dataset)
                         $experiment = 'c13';
                     }
                 }
-
                 if ($experiment == 'proton') {
                     $experimentSchema = BioschemasHelper::prepareDefinedTerm('1H nuclear magnetic resonance spectroscopy', ['1H-NMR spectrometry', 'proton nuclear magnetic resonance spectroscopy', '1H-NMR spectroscopy', '1H-NMR', '1H NMR', '1H NMR spectroscopy', '1H nuclear magnetic resonance spectrometry', 'proton NMR'], 'CHMO:0000593', 'http://purl.obolibrary.org/obo/CHMO_0000593', $chmo);
                 } elseif ($experiment == 'c13') {
@@ -379,12 +378,12 @@ public function prepareNMRiumInfo($dataset)
             $dimensionProperty = BioschemasHelper::preparePropertyValue('NMR spectrum by dimensionality', 'NMR:1000117', $dimension, null);
             $probeNameProperty = BioschemasHelper::preparePropertyValue('NMR probe', 'OBI:0000516', $probeName, null);
             //$experimentProperty = BioschemasHelper::preparePropertyValue('pulsed nuclear magnetic resonance spectroscopy', 'CHMO:0000613', $experiment, null);
-            $temperatureProperty = BioschemasHelper::preparePropertyValue('Temperature', 'NCIT:C25206', $temperature, 'https://ontobee.org/ontology/UO?iri=http://purl.obolibrary.org/obo/UO_0000012');
+            $temperatureProperty = BioschemasHelper::preparePropertyValue('Temperature', 'NCIT:C25206', $temperature, 'http://purl.obolibrary.org/obo/UO_0000012');
             $baseFrequencyProperty = BioschemasHelper::preparePropertyValue('irradiation frequency', 'NMR:1400026', $baseFrequency, 'http://purl.obolibrary.org/obo/UO_0000325');
             $fieldStrengthProperty = BioschemasHelper::preparePropertyValue('magnetic field strength', 'MR:1400253', $fieldStrength, 'http://purl.obolibrary.org/obo/UO_0000228');
             $numberOfScansProperty = BioschemasHelper::preparePropertyValue('number of scans', 'NMR:1400087', $numberOfScans, 'scans');
             $pulseSequenceProperty = BioschemasHelper::preparePropertyValue('nuclear magnetic resonance pulse sequence', 'CHMO:0001841', $pulseSequence, null);
-            $spectralWidthProperty = BioschemasHelper::preparePropertyValue('Spectral Width', 'NCIT:C156496', $spectralWidth, null); //todo: add unit
+            $spectralWidthProperty = BioschemasHelper::preparePropertyValue('Spectral Width', 'NCIT:C156496', $spectralWidth, 'http://purl.obolibrary.org/obo/UO_0000169');
             $numberOfPointsProperty = BioschemasHelper::preparePropertyValue('number of data points', 'NMR:1000176', $numberOfPoints, 'points');
             $relaxationTimeProperty = BioschemasHelper::preparePropertyValue('relaxation time measurement', 'FIX:0000202', $relaxationTime, 'http://purl.obolibrary.org/obo/UO_0000010');
 

app/Http/Controllers/API/Schemas/DataCite/DOIController.php

@@ -0,0 +1,37 @@
+<?php
+
+namespace App\Http\Controllers\API\Schemas\DataCite;
+
+use App\Http\Controllers\Controller;
+use App\Services\DOI\DOIService;
+use Illuminate\Http\Request;
+
+class DOIController extends Controller
+{
+    /**
+     * Create a new class instance.
+     *
+     * @param  App\Services\DOI\DOIService  $doiService
+     * @return void
+     */
+    public function __construct(DOIService $doiService)
+    {
+        $this->doiService = $doiService;
+    }
+
+    /**
+     * Update Model's DataCite metadata
+     *
+     * @param  Illuminate\Http\Request  $request
+     * @param  string  $identifier
+     * @return void
+     */
+    public function update(Request $request, $identifier)
+    {
+        $resolvedModel = resolveIdentifier($identifier);
+        $model = $resolvedModel['model'];
+
+        // Call the updateDOI function
+        $model->updateDOIMetadata($this->doiService);
+    }
+}

app/Jobs/ProcessProject.php

@@ -4,6 +4,7 @@
 
 use App\Actions\Project\AssignIdentifier;
 use App\Actions\Project\PublishProject;
+use App\Actions\Project\UpdateDOI;
 use App\Models\FileSystemObject;
 use App\Models\Project;
 use App\Notifications\DraftProcessedNotification;
@@ -45,7 +46,7 @@ public function __construct(Project $project)
      *
      * @return void
      */
-    public function handle(AssignIdentifier $assigner, PublishProject $publisher)
+    public function handle(AssignIdentifier $assigner, UpdateDOI $updater, PublishProject $publisher)
     {
         $project = $this->project;
 
@@ -109,6 +110,7 @@ public function handle(AssignIdentifier $assigner, PublishProject $publisher)
             if ($release_date->isPast()) {
                 $publisher->publish($project);
             }
+            $updater->update($project->fresh());
 
             Notification::send($project->owner, new DraftProcessedNotification($project));
         }

app/Jobs/ProcessSubmission.php

@@ -4,6 +4,7 @@
 
 use App\Actions\Project\AssignIdentifier;
 use App\Actions\Project\PublishProject;
+use App\Actions\Project\UpdateDOI;
 use App\Actions\Study\PublishStudy;
 use App\Events\StudyPublish;
 use App\Models\FileSystemObject;
@@ -41,7 +42,7 @@ public function __construct(Project $project)
     /**
      * Execute the job.
      */
-    public function handle(AssignIdentifier $assigner, PublishProject $projectPublisher, PublishStudy $studyPublisher)
+    public function handle(AssignIdentifier $assigner, UpdateDOI $updater, PublishProject $projectPublisher, PublishStudy $studyPublisher)
     {
         $project = $this->project;
 
@@ -107,7 +108,7 @@ public function handle(AssignIdentifier $assigner, PublishProject $projectPublis
                 if ($release_date->isPast()) {
                     $projectPublisher->publish($project);
                 }
-
+                $updater->update($project->fresh());
                 ArchiveProject::dispatch($project);
 
                 $project->sendNotification('publish', $this->prepareSendList($project));

app/Models/HasDOI.php

@@ -65,8 +65,25 @@ public function generateDOI($doiService)
         }
     }
 
-    public function updateDOI($doiService)
+    /**
+     * Update Model's DataCite metadata
+     *
+     * @param  mixed  $doiService
+     * @return void
+     */
+    public function updateDOIMetadata($doiService)
     {
+        $doi_host = env('DOI_HOST', null);
+
+        if (! is_null($doi_host)) {
+            $doi = $this->doi;
+            if ($doi !== null) {
+                $attributes = $this->getMetadata();
+                $doiResponse = $doiService->updateDOI($doi, $attributes);
+                $this->datacite_schema = $doiResponse;
+                $this->save();
+            }
+        }
     }
 
     public function getIdentifier($model, $key)
@@ -230,4 +247,65 @@ public function getMetadata()
 
         return $attributes;
     }
+
+    public function addRelatedIdentifiers($doiService)
+    {
+        $attributes = $this->getMetadata();
+        if ($this instanceof Project) {
+            foreach ($this->studies as &$study) {
+                $relatedIdentifier = [
+                    'relatedIdentifier' => $study->doi,
+                    'relatedIdentifierType' => 'DOI',
+                    'relationType' => 'HasPart',
+                ];
+                array_push($attributes['relatedIdentifiers'], $relatedIdentifier);
+                foreach ($study->datasets as &$dataset) {
+                    $relatedIdentifier = [
+                        'relatedIdentifier' => $dataset->doi,
+                        'relatedIdentifierType' => 'DOI',
+                        'relationType' => 'HasPart',
+                    ];
+                    array_push($attributes['relatedIdentifiers'], $relatedIdentifier);
+                }
+            }
+            $doiResponse = $doiService->updateDOI($this->doi, $attributes);
+            $this->datacite_schema = $doiResponse;
+            $this->save();
+
+        } elseif ($this instanceof Study) {
+            $relatedIdentifier = [
+                'relatedIdentifier' => $this->project->doi,
+                'relatedIdentifierType' => 'DOI',
+                'relationType' => 'IsPartOf',
+            ];
+            array_push($attributes['relatedIdentifiers'], $relatedIdentifier);
+            foreach ($this->datasets as &$dataset) {
+                $relatedIdentifier = [
+                    'relatedIdentifier' => $dataset->doi,
+                    'relatedIdentifierType' => 'DOI',
+                    'relationType' => 'HasPart',
+                ];
+                array_push($attributes['relatedIdentifiers'], $relatedIdentifier);
+            }
+            $doiResponse = $doiService->updateDOI($this->doi, $attributes);
+            $this->datacite_schema = $doiResponse;
+            $this->save();
+        } elseif ($this instanceof Dataset) {
+            $relatedIdentifier = [
+                'relatedIdentifier' => $this->project->doi,
+                'relatedIdentifierType' => 'DOI',
+                'relationType' => 'IsPartOf',
+            ];
+            array_push($attributes['relatedIdentifiers'], $relatedIdentifier);
+            $relatedIdentifier = [
+                'relatedIdentifier' => $this->study->doi,
+                'relatedIdentifierType' => 'DOI',
+                'relationType' => 'IsPartOf',
+            ];
+            array_push($attributes['relatedIdentifiers'], $relatedIdentifier);
+            $doiResponse = $doiService->updateDOI($this->doi, $attributes);
+            $this->datacite_schema = $doiResponse;
+            $this->save();
+        }
+    }
 }

app/Services/DOI/DOIService.php

@@ -10,7 +10,7 @@ public function createDOI($suffix, $attributes = []);
 
     public function getDOI($doi);
 
-    public function updateDOI($doi);
+    public function updateDOI($doi, $attributes = []);
 
     public function deleteDOI($doi);
 

app/Services/DOI/DataCite.php

@@ -70,9 +70,35 @@ public function createDOI($suffix, $metadata = [])
         return json_decode($contents, true);
     }
 
-    public function updateDOI($doi)
+    /**
+     * Update DataCite metadata based on DOI
+     *
+     * @param  string  $doi
+     * @param  array  $metadata
+     * @return array $contents
+     */
+    public function updateDOI($doi, $metadata = [])
     {
-        return 'Datacite';
+        foreach ($metadata as $key => $value) {
+            $attributes[$key] = $value;
+        }
+
+        $body = [
+            'data' => [
+                'type' => 'dois',
+                'attributes' => $attributes,
+            ],
+        ];
+
+        $response = $this->client->put('/dois/'.urlencode($doi),
+            [RequestOptions::JSON => $body]
+        );
+
+        $stream = $response->getBody();
+        $contents = $stream->getContents();
+        $contents = json_decode($contents, true);
+
+        return $contents;
     }
 
     public function deleteDOI($doi)