Merge pull request #1134 from NFDI4Chem/development

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NFDI4Chem · May 2, 2024 · 294807a · 294807a
2 parents 72a05c5 + 2a833f6
commit 294807a
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Showing 10 changed files with 70 additions and 84 deletions.
diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml
@@ -14,20 +14,20 @@ jobs:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
-          node-version: 16
+          node-version: 20
           cache: npm
       - run: npm ci
       - name: Build
         run: npm run docs:build
-      - uses: actions/configure-pages@v2
-      - uses: actions/upload-pages-artifact@v1
+      - uses: actions/configure-pages@v5
+      - uses: actions/upload-pages-artifact@v3
         with:
           path: docs/.vitepress/dist
       - name: Deploy
         id: deployment
-        uses: actions/deploy-pages@v2.0.2
+        uses: actions/deploy-pages@v4
diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php
@@ -30,8 +30,8 @@ class BioschemasController extends Controller
      * @param  Illuminate\Http\Request  $request
      * @param  App\Models\User  $username
      * @param  App\Models\Project  $projectName
-     * @param  App\Models\Study  $studyName Optional
-     * @param  App\Models\Dataset  $datasetName Optional
+     * @param  App\Models\Study  $studyName  Optional
+     * @param  App\Models\Dataset  $datasetName  Optional
      * @return object
      */
     /**

diff --git a/app/Http/Controllers/API/Schemas/DataCite/DataCiteController.php b/app/Http/Controllers/API/Schemas/DataCite/DataCiteController.php
@@ -24,8 +24,8 @@ class DataCiteController extends Controller
      * @param  Illuminate\Http\Request  $request
      * @param  App\Models\User  $username
      * @param  App\Models\Project  $projectName
-     * @param  App\Models\Study  $studyName Optional
-     * @param  App\Models\Dataset  $datasetName Optional
+     * @param  App\Models\Study  $studyName  Optional
+     * @param  App\Models\Dataset  $datasetName  Optional
      * @return object
      */
     /**

diff --git a/app/Http/Controllers/API/SearchController.php b/app/Http/Controllers/API/SearchController.php
@@ -252,7 +252,7 @@ public function search(Request $request)
                     $statement = $statement.')';
                 }
                 $statement = $statement.' LIMIT '.$limit;
-            // dd($statement );
+                // dd($statement );
             } else {
                 if ($query) {
                     $query = str_replace("'", "''", $query);

diff --git a/app/Http/Controllers/Admin/UsersController.php b/app/Http/Controllers/Admin/UsersController.php
@@ -180,7 +180,7 @@ public function checkPassword(Request $request)
     /**
      * Delete the profile photo.
      *
-     *  @return \Illuminate\Http\RedirectResponse
+     * @return \Illuminate\Http\RedirectResponse
      */
     public function destroyPhoto(User $user, Request $request)
     {

diff --git a/app/Http/Controllers/ProjectController.php b/app/Http/Controllers/ProjectController.php
@@ -17,7 +17,6 @@
 use App\Models\User;
 use App\Models\Validation;
 use Auth;
-use Carbon\Carbon;
 use Illuminate\Auth\Access\AuthorizationException;
 use Illuminate\Contracts\Auth\StatefulGuard;
 use Illuminate\Http\JsonResponse;
@@ -328,83 +327,71 @@ public function publish(Request $request, Project $project, PublishProject $publ
         if ($project) {
             $input = $request->all();
             $release_date = $input['release_date'];
-            if (! $project->is_public && ! is_null($project->doi) && ! is_null($release_date)) {
-                $release_date = Carbon::parse($release_date);
-                if ($release_date->isPast()) {
-                    $updater->update($project, $request->all());
-                    $publisher->publish($project);
-                    $project->sendNotification('publish', $this->prepareSendList($project));
-                }
-            } else {
-
-                $enableProjectMode = $request->get('enableProjectMode');
-                if ($enableProjectMode) {
-                    $validation = $project->validation;
-                    $validation->process();
-                    $validation = $validation->fresh();
-                    if ($validation['report']['project']['status']) {
-                        $project->release_date = $request->get('release_date');
-                        $project->status = 'queued';
-                        $project->save();
-
-                        ProcessSubmission::dispatch($project);
-
-                        return response()->json([
-                            'project' => $project,
-                            'validation' => $validation,
-                        ]);
-                    } else {
-                        return response()->json([
-                            'errors' => 'Validation failing. Please provide all the required data and try again. If the problem persists, please contact us.',
-                            'validation' => $validation,
-                        ], 422);
-                    }
-                } else {
-                    $draft = $project->draft;
-                    $draft->project_enabled = false;
-                    $draft->save();
-
+            $enableProjectMode = $request->get('enableProjectMode');
+            if ($enableProjectMode) {
+                $validation = $project->validation;
+                $validation->process();
+                $validation = $validation->fresh();
+                if ($validation['report']['project']['status']) {
                     $project->release_date = $request->get('release_date');
                     $project->status = 'queued';
                     $project->save();
 
-                    $validation = $project->validation;
-                    $validation->process();
-                    $validation = $validation->fresh();
-
-                    foreach ($project->studies as $study) {
-                        $study->license_id = $project->license_id;
-                        $study->save();
-                        foreach ($study->datasets as $dataset) {
-                            $dataset->license_id = $project->license_id;
-                            $dataset->save();
-                        }
+                    ProcessSubmission::dispatch($project);
+
+                    return response()->json([
+                        'project' => $project,
+                        'validation' => $validation,
+                    ]);
+                } else {
+                    return response()->json([
+                        'errors' => 'Validation failing. Please provide all the required data and try again. If the problem persists, please contact us.',
+                        'validation' => $validation,
+                    ], 422);
+                }
+            } else {
+                $draft = $project->draft;
+                $draft->project_enabled = false;
+                $draft->save();
+
+                $project->release_date = $request->get('release_date');
+                $project->status = 'queued';
+                $project->save();
+
+                $validation = $project->validation;
+                $validation->process();
+                $validation = $validation->fresh();
+
+                foreach ($project->studies as $study) {
+                    $study->license_id = $project->license_id;
+                    $study->save();
+                    foreach ($study->datasets as $dataset) {
+                        $dataset->license_id = $project->license_id;
+                        $dataset->save();
                     }
+                }
 
-                    $status = true;
+                $status = true;
 
-                    foreach ($validation['report']['project']['studies'] as $study) {
-                        if (! $study['status']) {
-                            $status = false;
-                        }
-                    }
-                    // add license check
-                    if ($status) {
-                        ProcessSubmission::dispatch($project);
-
-                        return response()->json([
-                            'project' => $project,
-                            'validation' => $validation,
-                        ]);
-                    } else {
-                        return response()->json([
-                            'errors' => 'Validation failing. Please provide all the required data and try again. If the problem persists, please contact us.',
-                        ], 422);
+                foreach ($validation['report']['project']['studies'] as $study) {
+                    if (! $study['status']) {
+                        $status = false;
                     }
                 }
-
+                // add license check
+                if ($status) {
+                    ProcessSubmission::dispatch($project);
+
+                    return response()->json([
+                        'project' => $project,
+                        'validation' => $validation,
+                    ]);
+                } else {
+                    return response()->json([
+                        'errors' => 'Validation failing. Please provide all the required data and try again. If the problem persists, please contact us.',
+                    ], 422);
+                }
             }
-
         }
 
     }

diff --git a/app/Models/Project.php b/app/Models/Project.php
@@ -339,7 +339,7 @@ public function citations()
     /**
      * Send Notification via email.
      *
-     * @param  string  $notifyType (deletion / deletionReminder / archival / archivalAdmin)
+     * @param  string  $notifyType  (deletion / deletionReminder / archival / archivalAdmin)
      * @param  array  sendTo
      * @return void
      */

diff --git a/app/Models/Schemas/Study.php b/app/Models/Schemas/Study.php
@@ -101,7 +101,6 @@ public function studyDomain($studyDomain)
      * drugs, etc. investigated by the study.
      *
      * @param  \Spatie\SchemaOrg\Contracts\BioChemEntityContract|\Spatie\SchemaOrg\Contracts\MedicalEntityContract[]  $studySubject
-
      * @return static
      */
     public function studySubject($studySubject)

diff --git a/app/Policies/ProjectPolicy.php b/app/Policies/ProjectPolicy.php
@@ -65,7 +65,7 @@ public function createProject(User $user)
      */
     public function updateProject(User $user, Project $project)
     {
-        if ($project->is_public || $project->is_archived || $project->is_deleted || $project->is_published || (! $project->is_published && $project->doi)) {
+        if ($project->is_public || $project->is_archived || $project->is_deleted || $project->is_published) {
             return false;
         }
 

diff --git a/resources/js/App/MoleculeCard.vue b/resources/js/App/MoleculeCard.vue
@@ -51,7 +51,7 @@
                     </div>
                     <div class="font-bold text-md mb-2">
                         <a class="font-semibold text-gray-600 hover:underline"
-                            >#NMRXIV:{{ molecule.identifier }}</a
+                            >#NMRXIV:M{{ molecule.identifier }}</a
                         >
                     </div>
                     <div