Merge pull request #522 from NFDI4Chem/development

Development

.github/workflows/build.yml

@@ -1,4 +1,4 @@
-name : Deploy to GKE
+name : Deploy to Dev
 
 on:
   push:
@@ -16,7 +16,7 @@ env:
 
 jobs:
   setup-build-publish-deploy:
-    name: Setup, Build, Publish, and Deploy
+    name: Deploy to Dev
     if: github.ref == 'refs/heads/development'
     runs-on: ubuntu-latest
     #needs: build

app/Actions/Jetstream/DeleteTeam.php

@@ -2,6 +2,7 @@
 
 namespace App\Actions\Jetstream;
 
+use Illuminate\Validation\ValidationException;
 use Laravel\Jetstream\Contracts\DeletesTeams;
 
 class DeleteTeam implements DeletesTeams
@@ -14,6 +15,11 @@ class DeleteTeam implements DeletesTeams
      */
     public function delete($team)
     {
+        if ($team->projects()->count() > 0) {
+            throw ValidationException::withMessages([
+                'hasProject' => __('This team cannot be deletd as it has project associated with it. Please do not forget to wait for the cool off period of 30 days for your project to be deleted permanently.'),
+            ]);
+        }
         $team->purge();
 
         return redirect()->route('dashboard')->with('success', 'Team deleted successfully');

app/Actions/Project/AssignIdentifier.php

@@ -0,0 +1,105 @@
+<?php
+
+namespace App\Actions\Project;
+
+use App\Models\Project;
+use App\Models\Ticker;
+use App\Services\DOI\DOIService;
+
+class AssignIdentifier
+{
+    private $doiService;
+
+    /**
+     * Create a new class instance.
+     *
+     * @return void
+     */
+    public function __construct(DOIService $doiService)
+    {
+        $this->doiService = $doiService;
+    }
+
+    /**
+     * Archive the given project.
+     *
+     * @param  mixed  $project
+     * @return void
+     */
+    public function assign($project)
+    {
+        $projectIdentifier = $project->identifier ? $project->identifier : null;
+
+        if ($projectIdentifier == null) {
+            $projectTicker = Ticker::whereType('project')->first();
+            $projectIdentifier = $projectTicker->index + 1;
+            $projectTicker->index = $projectIdentifier;
+            $projectTicker->save();
+
+            $project->identifier = $projectIdentifier;
+            $project->save();
+        }
+
+        $studies = $project->studies;
+        foreach ($studies as $study) {
+            $studyIdentifier = $study->identifier ? $study->identifier : null;
+
+            if ($studyIdentifier == null) {
+                $studyTicker = Ticker::whereType('study')->first();
+                $studyIdentifier = $studyTicker->index + 1;
+                $study->identifier = $studyIdentifier;
+                $studyTicker->index = $studyIdentifier;
+                $studyTicker->save();
+            }
+
+            $sample = $study->sample;
+            $sampleIdentifier = $sample->identifier ? $sample->identifier : null;
+
+            if ($sampleIdentifier == null) {
+                $sampleTicker = Ticker::whereType('sample')->first();
+                $sampleIdentifier = $sampleTicker->index + 1;
+                $sample->identifier = $sampleIdentifier;
+                $sample->save();
+
+                $sampleTicker->index = $sampleIdentifier;
+                $sampleTicker->save();
+            }
+
+            $molecules = $sample->molecules;
+
+            foreach ($molecules as $molecule) {
+                $moleculeIdentifier = $molecule->identifier ? $molecule->identifier : null;
+                if ($moleculeIdentifier == null) {
+                    $moleculeTicker = Ticker::whereType('molecule')->first();
+                    $moleculeIdentifier = $moleculeTicker->index + 1;
+                    $molecule->identifier = $moleculeIdentifier;
+                    $molecule->save();
+
+                    $moleculeTicker->index = $moleculeIdentifier;
+                    $moleculeTicker->save();
+                }
+            }
+
+            $datasets = $study->datasets;
+            foreach ($datasets as $dataset) {
+                $dsIdentifier = $dataset->identifier ? $dataset->identifier : null;
+
+                if ($dsIdentifier == null) {
+                    $dsTicker = Ticker::whereType('dataset')->first();
+                    $dsIdentifier = $dsTicker->index + 1;
+                    $dataset->identifier = $dsIdentifier;
+
+                    $dsTicker->index = $dsIdentifier;
+                    $dsTicker->save();
+                }
+
+                $dataset->save();
+                $dataset->generateDOI($this->doiService);
+            }
+
+            $study->save();
+            $study->generateDOI($this->doiService);
+        }
+        $project->fresh()->generateDOI($this->doiService);
+    }
+}

app/Actions/Project/CreateNewProject.php

@@ -4,6 +4,7 @@
 
 use App\Models\Project;
 use App\Models\User;
+use App\Models\Validation;
 use Illuminate\Support\Facades\DB;
 use Illuminate\Support\Facades\Validator;
 use Illuminate\Support\Str;
@@ -57,6 +58,10 @@ public function create(array $input)
                         $user, ['role' => 'creator']
                     );
                 }
+                $validaton = new Validation();
+                $validaton->save();
+                $project->associate($validation);
+                $project->save();
             });
         });
     }

app/Actions/Project/DeleteProject.php

@@ -17,15 +17,21 @@ public function delete($project)
         if ($project->is_public) {
             $project->studies()->update(['is_archived' => true]);
             foreach ($project->studies as $study) {
+                $study->update(['is_archived' => true]);
                 $study->datasets()->update(['is_archived' => true]);
             }
             $project->is_archived = true;
             $project->save();
         } else {
             $project->studies()->update(['is_deleted' => true]);
             foreach ($project->studies as $study) {
+                $study->update(['is_deleted' => true]);
                 $study->datasets()->update(['is_deleted' => true]);
             }
+            $draft = $project->draft;
+            if ($draft) {
+                $draft->update(['is_deleted' => true]);
+            }
             $project->is_deleted = true;
             $project->save();
         }

app/Actions/Project/PublishProject.php

@@ -0,0 +1,30 @@
+<?php
+
+namespace App\Actions\Project;
+
+use App\Models\Project;
+
+class PublishProject
+{
+    /**
+     * Publish the given project.
+     *
+     * @param  mixed  $project
+     * @return void
+     */
+    public function publish($project)
+    {
+        $project->is_public = true;
+        $project->save();
+        $studies = $project->studies;
+        foreach ($studies as $study) {
+            $study->is_public = true;
+            $study->save();
+            $datasets = $study->datasets;
+            foreach ($datasets as $dataset) {
+                $dataset->is_public = true;
+                $dataset->save();
+            }
+        }
+    }
+}

app/Actions/Project/UnPublishProject.php

@@ -0,0 +1,31 @@
+<?php
+
+namespace App\Actions\Project;
+
+use App\Models\Project;
+
+class UnPublishProject
+{
+    /**
+     * Publish the given project.
+     *
+     * @param  mixed  $project
+     * @return void
+     */
+    public function unPublish($project)
+    {
+        $project->is_public = false;
+        $project->release_date = null;
+        $project->save();
+        $studies = $project->studies;
+        foreach ($studies as $study) {
+            $study->is_public = false;
+            $study->save();
+            $datasets = $study->datasets;
+            foreach ($datasets as $dataset) {
+                $dataset->is_public = false;
+                $dataset->save();
+            }
+        }
+    }
+}

app/Actions/Project/UpdateProject.php

@@ -3,7 +3,7 @@
 namespace App\Actions\Project;
 
 use App\Models\Project;
-use Carbon\Carbon;
+use App\Models\Validation;
 use Illuminate\Support\Facades\DB;
 use Illuminate\Support\Facades\Storage;
 use Illuminate\Support\Facades\Validator;
@@ -47,10 +47,6 @@ public function update(Project $project, array $input)
             $licenseExists = array_key_exists('license_id', $input);
             $license_id = $licenseExists ? $input['license_id'] : $project->license_id;
 
-            if ($is_public == true) {
-                $release_date = Carbon::now()->toDateTimeString();
-            }
-
             $project
                 ->forceFill([
                     'name' => $input['name'],
@@ -76,8 +72,6 @@ public function update(Project $project, array $input)
                         : 'viewer',
                     'team_id' => $input['team_id'],
                     'owner_id' => $input['owner_id'],
-                    'is_public' => $is_public,
-                    'release_date' => $release_date,
                     'license_id' => $license_id,
                     'project_photo_path' => $s3filePath ? $s3filePath : $project->project_photo_path,
                 ])
@@ -94,10 +88,7 @@ public function update(Project $project, array $input)
                         $study->license_id = $license_id;
                     }
                 }
-                if ($is_public) {
-                    $study->is_public = $is_public;
-                    $study->release_date = $release_date;
-                }
+
                 $study->save();
 
                 $datasets = $study->datasets;
@@ -107,13 +98,29 @@ public function update(Project $project, array $input)
                             $dataset->license_id = $license_id;
                         }
                     }
-                    if ($is_public) {
-                        $dataset->is_public = $is_public;
-                        $dataset->release_date = $release_date;
-                    }
+
                     $dataset->save();
                 }
             }
+
+            $validation = $project->validation;
+
+            if (! $validation) {
+                $validation = new Validation();
+                $validation->save();
+                $project->validation()->associate($validation);
+                $project->save();
+
+                foreach ($project->studies as $study) {
+                    $study->validation()->associate($validation);
+                    $study->save();
+                    foreach ($study->datasets as $dataset) {
+                        $dataset->validation()->associate($validation);
+                        $dataset->save();
+                    }
+                }
+            }
+            $validation->process();
         });
     }
 
@@ -126,7 +133,7 @@ public function updateAuthors(Project $project, $authors)
 
     public function updateCitation(Project $project, $citations, $user)
     {
-        $project->citations()->syncWithPivotValues(
+        $project->citations()->sync(
             $citations, ['user' => $user->id]
         );
     }

app/Actions/Study/UpdateStudy.php

@@ -3,6 +3,7 @@
 namespace App\Actions\Study;
 
 use App\Models\Study;
+use App\Models\Ticker;
 use Illuminate\Support\Facades\DB;
 use Illuminate\Support\Facades\Validator;
 use Illuminate\Support\Str;
@@ -54,6 +55,34 @@ public function update(Study $study, array $input)
 
             if ($is_public == true) {
                 $release_date = Carbon::now()->timestamp;
+
+                $sample = $study->sample;
+                $sampleIdentifier = $sample->identifier ? $sample->identifier : null;
+
+                if ($sampleIdentifier == null) {
+                    $sampleTicker = Ticker::whereType('sample')->first();
+                    $sampleIdentifier = $sampleTicker->index + 1;
+                    $sample->identifier = $sampleIdentifier;
+                    $sample->save();
+
+                    $sampleTicker->index = $sampleIdentifier;
+                    $sampleTicker->save();
+                }
+
+                $molecules = $sample->molecules;
+
+                foreach ($molecules as $molecule) {
+                    $moleculeIdentifier = $molecule->identifier ? $molecule->identifier : null;
+                    if ($moleculeIdentifier == null) {
+                        $moleculeTicker = Ticker::whereType('molecule')->first();
+                        $moleculeIdentifier = $moleculeTicker->index + 1;
+                        $molecule->identifier = $moleculeIdentifier;
+                        $molecule->save();
+
+                        $moleculeTicker->index = $moleculeIdentifier;
+                        $moleculeTicker->save();
+                    }
+                }
             }
 
             $datasets = $study->datasets;
@@ -64,6 +93,17 @@ public function update(Study $study, array $input)
                     }
                 }
                 if ($is_public) {
+                    $dsIdentifier = $dataset->identifier ? $dataset->identifier : null;
+
+                    if ($dsIdentifier == null) {
+                        $dsTicker = Ticker::whereType('dataset')->first();
+                        $dsIdentifier = $dsTicker->index + 1;
+                        $dataset->identifier = $dsIdentifier;
+
+                        $dsTicker->index = $dsIdentifier;
+                        $dsTicker->save();
+                    }
+
                     $dataset->is_public = $is_public;
                     $dataset->release_date = $release_date;
                 }