fix: various fixes to the reporting workflow

Steinbeck-Lab · Oct 10, 2024 · ca3dfdf · ca3dfdf
1 parent 658ff2f
commit ca3dfdf
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Showing 4 changed files with 63 additions and 49 deletions.
diff --git a/app/Filament/Dashboard/Resources/MoleculeResource.php b/app/Filament/Dashboard/Resources/MoleculeResource.php
@@ -125,7 +125,9 @@ public static function table(Table $table): Table
                         ])
                         ->action(function (array $data, Molecule $record): void {
                             $record->active = ! $record->active;
-                            self::saveComment($record, $data['reason']);
+                            $record->active ? $record->status = 'APPROVED' : $record->status = 'REVOKED';
+                            $record->comment = prepareComment($data['reason']);
+                            $record->save();
                         })
                         ->modalHidden(function (Molecule $record) {
                             return ! $record['active'];
@@ -144,7 +146,9 @@ public static function table(Table $table): Table
                         ->action(function (array $data, Collection $records): void {
                             foreach ($records as $record) {
                                 $record->active = ! $record->active;
-                                self::saveComment($record, $data['reason']);
+                                $record->active ? $record->status = 'APPROVED' : $record->status = 'REVOKED';
+                                $record->comment = prepareComment($data['reason']);
+                                $record->save();
                             }
                         })
                         // ->modalHidden(function (Molecule $record) {
@@ -207,15 +211,4 @@ public static function getNavigationBadge(): ?string
     {
         return Cache::get('stats.molecules');
     }
-
-    public static function saveComment($record, $reason)
-    {
-        $record->comment = [[
-            'timestamp' => now(),
-            'changed_by' => auth()->user()->id,
-            'comment' => $reason,
-        ]];
-
-        $record->save();
-    }
 }
diff --git a/app/Filament/Dashboard/Resources/ReportResource.php b/app/Filament/Dashboard/Resources/ReportResource.php
@@ -79,11 +79,15 @@ public static function form(Form $form): Form
                         Actions::make([
                             Action::make('approve')
                                 ->form(function ($record, $livewire) {
-                                    self::$approved_changes = self::prepareApprovedChanges($record, $livewire);
-                                    $key_value_fields = getChangesToDisplayModal(self::$approved_changes);
-                                    array_unshift($key_value_fields, Textarea::make('reason'));
-
-                                    return $key_value_fields;
+                                    if ($record['is_change']) {
+                                        self::$approved_changes = self::prepareApprovedChanges($record, $livewire);
+                                        $key_value_fields = getChangesToDisplayModal(self::$approved_changes);
+                                        array_unshift($key_value_fields, Textarea::make('reason'));
+
+                                        return $key_value_fields;
+                                    } else {
+                                        return [Textarea::make('reason')];
+                                    }
                                 })
                                 ->hidden(function (Get $get, string $operation) {
                                     return ! auth()->user()->roles()->exists() || $get('status') == 'rejected' || $get('status') == 'approved' || $operation != 'edit';
@@ -107,8 +111,14 @@ public static function form(Form $form): Form
                             Action::make('viewCompoundPage')
                                 ->color('info')
                                 ->url(fn (string $operation, $record): string => $operation === 'create' ? env('APP_URL').'/compounds/'.request()->compound_id : env('APP_URL').'/compounds/'.$record->mol_id_csv)
-                                ->openUrlInNewTab(),
+                                ->openUrlInNewTab()
+                                ->hidden(function (Get $get, string $operation) {
+                                    return ! request()->has('type');
+                                }),
                         ])
+                            ->hidden(function (Get $get) {
+                                return $get('report_type') != 'molecule';
+                            })
                             ->verticalAlignment(VerticalAlignment::End)
                             ->columnStart(4),
                     ])
@@ -589,17 +599,6 @@ public static function prepareApprovedChanges(Report $record, $livewire)
     {
         $approved_changes = [];
 
-        // In case of reporting a synthetic molecule, Deactivate Molecules
-        if ($record['mol_id_csv'] && ! $record['is_change']) {
-            $molecule_ids = explode(',', $record['mol_id_csv']);
-            $molecule = Molecule::whereIn('id', $molecule_ids)->get();
-            foreach ($molecule as $mol) {
-                $mol->active = false;
-                $mol->save();
-            }
-        }
-
-        // In case of Changes, run SQL queries for the approved changes
         $approved_changes['mol_id_csv'] = $record['mol_id_csv'];
         if ($record['is_change']) {
 
@@ -650,22 +649,33 @@ public static function prepareApprovedChanges(Report $record, $livewire)
 
     public static function approveReport(array $data, Report $record, Molecule $molecule, $livewire): void
     {
-        // Run SQL queries for the approved changes
-        self::runSQLQueries($record);
-
-        $suggested_changes = $record['suggested_changes'];
-
-        $suggested_changes['curator']['approved_changes'] = self::$overall_changes;
-        $record['suggested_changes'] = $suggested_changes;
-        $record['comment'] = $data['reason'];
-        $record['status'] = 'approved';
-        $formData = copyChangesToCuratorJSON($record, $livewire->data);
-        $suggested_changes['curator'] = $formData['suggested_changes']['curator'];
-        $record['suggested_changes'] = $suggested_changes;
-
-        // Save the report record in any case
-        $record->save();
-
+        // In case of reporting a synthetic molecule, Deactivate Molecules
+        if ($record['mol_id_csv'] && ! $record['is_change']) {
+            $molecule_ids = explode(',', $record['mol_id_csv']);
+            $molecule = Molecule::whereIn('identifier', $molecule_ids)->get();
+            foreach ($molecule as $mol) {
+                $mol->active = false;
+                $mol->status = 'REVOKED';
+                $mol->comment = prepareComment($data['reason']);
+                $mol->save();
+            }
+        } else {
+            // In case of Changes
+            // Run SQL queries for the approved changes
+            self::runSQLQueries($record);
+
+            $suggested_changes = $record['suggested_changes'];
+
+            $suggested_changes['curator']['approved_changes'] = self::$overall_changes;
+            $record['suggested_changes'] = $suggested_changes;
+            $record->comment = prepareComment($data['reason']);
+            $record['status'] = 'approved';
+            $formData = copyChangesToCuratorJSON($record, $livewire->data);
+            $suggested_changes['curator'] = $formData['suggested_changes']['curator'];
+            $record['suggested_changes'] = $suggested_changes;
+
+            $record->save();
+        }
         $livewire->redirect(ReportResource::getUrl('view', ['record' => $record->id]));
     }
 

diff --git a/app/Filament/Dashboard/Resources/ReportResource/Pages/CreateReport.php b/app/Filament/Dashboard/Resources/ReportResource/Pages/CreateReport.php
@@ -43,9 +43,11 @@ protected function afterFill(): void
             $this->data['is_change'] = true;
             $this->data['existing_geo_locations'] = $this->molecule->geo_locations->pluck('name')->toArray();
             $this->data['existing_synonyms'] = $this->molecule->synonyms;
-            $this->data['existing_cas'] = array_values($this->molecule->cas);
+            $this->data['existing_cas'] = array_values($this->molecule->cas ?? []);
             $this->data['existing_organisms'] = $this->molecule->organisms->pluck('name')->toArray();
             $this->data['existing_citations'] = $this->molecule->citations->where('title', '!=', null)->pluck('title')->toArray();
+        } else {
+            $this->data['is_change'] = false;
         }
 
         if ($request->has('collection_uuid')) {
@@ -94,8 +96,7 @@ protected function mutateFormDataBeforeCreate(array $data): array
     {
         $data['user_id'] = auth()->id();
         $data['status'] = 'submitted';
-
-        if ($data['is_change'] == true) {
+        if ($data['is_change']) {
             $suggested_changes = [];
             $suggested_changes['existing_geo_locations'] = $data['existing_geo_locations'];
             $suggested_changes['new_geo_locations'] = $data['new_geo_locations'];
@@ -153,6 +154,7 @@ protected function getCreateFormAction(): Action
         if (! $this->data['is_change']) {
             return parent::getCreateFormAction();
         }
+
         return parent::getCreateFormAction()
             ->submit(null)
             ->form(function () {

diff --git a/app/Helper.php b/app/Helper.php
@@ -410,3 +410,12 @@ function copyChangesToCuratorJSON($record, $data)
 
     return $data;
 }
+
+function prepareComment($reason)
+{
+    return [[
+        'timestamp' => now(),
+        'changed_by' => auth()->user()->id,
+        'comment' => $reason,
+    ]];
+}