From 6130df4eea4e3cedb39021eaafc3b79626706e72 Mon Sep 17 00:00:00 2001
From: Sagar <sriramkanakam87@gmail.com>
Date: Fri, 10 May 2024 17:19:22 +0200
Subject: [PATCH 1/7] feat: created molecule relation manger for collection
 resource, added functionality for processing molecules in entries table, and
 added forget the collection molecules count at the end of import

---
 app/Console/Commands/ImportEntries.php        |  2 +
 .../Resources/CollectionResource.php          |  9 +++-
 .../EntriesRelationManager.php                |  9 ++++
 .../MoleculesRelationManager.php              | 50 +++++++++++++++++++
 4 files changed, 69 insertions(+), 1 deletion(-)
 create mode 100644 app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php

diff --git a/app/Console/Commands/ImportEntries.php b/app/Console/Commands/ImportEntries.php
index f3e85b81..9906d9b7 100644
--- a/app/Console/Commands/ImportEntries.php
+++ b/app/Console/Commands/ImportEntries.php
@@ -8,6 +8,7 @@
 use Illuminate\Bus\Batch;
 use Illuminate\Console\Command;
 use Illuminate\Support\Facades\Bus;
+use Illuminate\Support\Facades\Cache;
 
 class ImportEntries extends Command
 {
@@ -55,6 +56,7 @@ public function handle()
                 $collection->jobs_status = 'INCURATION';
                 $collection->job_info = '';
                 $collection->save();
+                Cache::forget('stats.collections'.$collection->id.'molecules.count');
             })->name('Import Entries '.$collection->id)
                 ->allowFailures(false)
                 ->onConnection('redis')
diff --git a/app/Filament/Dashboard/Resources/CollectionResource.php b/app/Filament/Dashboard/Resources/CollectionResource.php
index bbe9848b..a8548c39 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource.php
@@ -5,6 +5,7 @@
 use App\Filament\Dashboard\Resources\CollectionResource\Pages;
 use App\Filament\Dashboard\Resources\CollectionResource\RelationManagers\CitationsRelationManager;
 use App\Filament\Dashboard\Resources\CollectionResource\RelationManagers\EntriesRelationManager;
+use App\Filament\Dashboard\Resources\CollectionResource\RelationManagers\MoleculesRelationManager;
 use App\Filament\Dashboard\Resources\CollectionResource\Widgets\CollectionStats;
 use App\Livewire\ShowJobStatus;
 use App\Models\Collection;
@@ -21,6 +22,7 @@
 use Filament\Tables\Table;
 use Illuminate\Support\Str;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
+use Illuminate\Database\Eloquent\Model;
 
 class CollectionResource extends Resource
 {
@@ -91,11 +93,16 @@ public static function table(Table $table): Table
 
     public static function getRelations(): array
     {
-        return [
+        // $record = static::getOwner();
+        // dd(static::getOwner());
+        // dd(static::$model::molecules()->get());
+        $arr = [
             EntriesRelationManager::class,
             CitationsRelationManager::class,
             AuditsRelationManager::class,
+            MoleculesRelationManager::class,
         ];
+        return $arr;
     }
 
     public static function getPages(): array
diff --git a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
index 53831fbe..5b49073f 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
@@ -15,6 +15,8 @@
 use Filament\Tables\Columns\ImageColumn;
 use Filament\Tables\Filters\SelectFilter;
 use Filament\Tables\Table;
+use Filament\Tables\Actions\Action;
+use Illuminate\Support\Facades\Artisan;
 
 class EntriesRelationManager extends RelationManager
 {
@@ -157,6 +159,13 @@ public function table(Table $table): Table
                     ->options([
                         'collection_id' => $this->ownerRecord->id,
                     ]),
+                Action::make('process')
+                    ->hidden(function () {
+                        return $this->ownerRecord->entries()->where('status', 'SUBMITTED')->count() < 1;
+                    })
+                    ->action(function () {
+                        Artisan::call('entries:process');
+                    }),
                 // Tables\Actions\CreateAction::make(),
             ])
             ->actions([
diff --git a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php
new file mode 100644
index 00000000..ccd0e21a
--- /dev/null
+++ b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php
@@ -0,0 +1,50 @@
+<?php
+
+namespace App\Filament\Dashboard\Resources\CollectionResource\RelationManagers;
+
+use Filament\Forms;
+use Filament\Forms\Form;
+use Filament\Resources\RelationManagers\RelationManager;
+use Filament\Tables;
+use Filament\Tables\Table;
+use Illuminate\Database\Eloquent\Builder;
+use Illuminate\Database\Eloquent\SoftDeletingScope;
+
+class MoleculesRelationManager extends RelationManager
+{
+    protected static string $relationship = 'molecules';
+
+    public function form(Form $form): Form
+    {
+        return $form
+            ->schema([
+                Forms\Components\TextInput::make('canonical_smiles')
+                    ->required()
+                    ->maxLength(255),
+            ]);
+    }
+
+    public function table(Table $table): Table
+    {
+        return $table
+            ->recordTitleAttribute('canonical_smiles')
+            ->columns([
+                Tables\Columns\TextColumn::make('canonical_smiles'),
+            ])
+            ->filters([
+                //
+            ])
+            ->headerActions([
+                Tables\Actions\CreateAction::make(),
+            ])
+            ->actions([
+                Tables\Actions\EditAction::make(),
+                Tables\Actions\DeleteAction::make(),
+            ])
+            ->bulkActions([
+                Tables\Actions\BulkActionGroup::make([
+                    Tables\Actions\DeleteBulkAction::make(),
+                ]),
+            ]);
+    }
+}

From 98d3ba4f930faaac44a132f27585c74ba6ef296d Mon Sep 17 00:00:00 2001
From: Sagar <sriramkanakam87@gmail.com>
Date: Fri, 10 May 2024 17:21:18 +0200
Subject: [PATCH 2/7] feat: added button for publishing the collection.

---
 .../RelationManagers/EntriesRelationManager.php        | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
index 5b49073f..e779f96e 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
@@ -166,6 +166,16 @@ public function table(Table $table): Table
                     ->action(function () {
                         Artisan::call('entries:process');
                     }),
+                Action::make('publish')
+                    ->hidden(function () {
+                        return $this->ownerRecord->molecules()->where('status', 'DRAFT')->count() < 1;
+                    })
+                    ->action(function () {
+                        $this->ownerRecord->status = 'PUBLISHED';
+                        $this->ownerRecord->is_public = true;
+                        $this->ownerRecord->molecules()->where('status', 'DRAFT')->update(['status' => 'APPROVED']);
+                        $this->ownerRecord->save();
+                    }),
                 // Tables\Actions\CreateAction::make(),
             ])
             ->actions([

From d825bc30b95b4715119d528a8938a7933f281e1d Mon Sep 17 00:00:00 2001
From: Sagar <sriramkanakam87@gmail.com>
Date: Fri, 10 May 2024 18:03:46 +0200
Subject: [PATCH 3/7] feat: scheduled a refresh of cache for dashboard widgets

---
 app/Console/Commands/DashWidgetsRefresh.php | 85 +++++++++++++++++++++
 app/Console/Kernel.php                      |  1 +
 2 files changed, 86 insertions(+)
 create mode 100644 app/Console/Commands/DashWidgetsRefresh.php

diff --git a/app/Console/Commands/DashWidgetsRefresh.php b/app/Console/Commands/DashWidgetsRefresh.php
new file mode 100644
index 00000000..210c06b7
--- /dev/null
+++ b/app/Console/Commands/DashWidgetsRefresh.php
@@ -0,0 +1,85 @@
+<?php
+
+namespace App\Console\Commands;
+
+use Illuminate\Console\Command;
+use Illuminate\Support\Facades\Cache;
+use App\Models\Citation;
+use App\Models\Collection;
+use App\Models\GeoLocation;
+use App\Models\Organism;
+use App\Models\Report;
+use App\Models\Molecule;
+
+class DashWidgetsRefresh extends Command
+{
+    /**
+     * The name and signature of the console command.
+     *
+     * @var string
+     */
+    protected $signature = 'app:dash-widgets-refresh';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'This refreshes the dashboard widgets.';
+
+    /**
+     * Execute the console command.
+     */
+    public function handle()
+    {
+        // Clear the cache for all dashboard widgets
+        Cache::forget('stats.collections');
+        Cache::forget('stats.citations');
+        Cache::forget('stats.organisms');
+        Cache::forget('stats.geo_locations');
+        Cache::forget('stats.reports');
+        Cache::forget('stats.molecules');
+        Cache::forget('stats.molecules.non_stereo');
+        Cache::forget('stats.molecules.stereo');
+        Cache::forget('stats.molecules.parent');
+
+        // Create the cache for all DashboardStats widgets
+        Cache::rememberForever('stats.collections', function () {
+            return Collection::count();
+        });
+        Cache::rememberForever('stats.citations', function () {
+            return Citation::count();
+        });
+        Cache::rememberForever('stats.organisms', function () {
+            return Organism::count();
+        });
+        Cache::rememberForever('stats.geo_locations', function () {
+            return GeoLocation::count();
+        });
+        Cache::rememberForever('stats.reports', function () {
+            return Report::count();
+        });
+
+        // Create the cache for all DashboardStatsMid widgets
+        Cache::rememberForever('stats.molecules', function () {
+            return Molecule::count();
+        });
+        Cache::rememberForever('stats.molecules.non_stereo', function () {
+            return Molecule::where([
+                ['has_stereo', false],
+                ['is_parent', false],
+            ])->count();
+        });
+        Cache::rememberForever('stats.molecules.stereo', function () {
+            return Molecule::where([
+                ['has_stereo', true],
+            ])->count();
+        });
+        Cache::rememberForever('stats.molecules.parent', function () {
+            return Molecule::where([
+                ['has_stereo', false],
+                ['is_parent', true],
+            ])->count();
+        });
+    }
+}
diff --git a/app/Console/Kernel.php b/app/Console/Kernel.php
index 1c34480c..e341c0ba 100644
--- a/app/Console/Kernel.php
+++ b/app/Console/Kernel.php
@@ -15,6 +15,7 @@ protected function schedule(Schedule $schedule): void
         // $schedule->command('inspire')->hourly();
         $schedule->command('entries:process')->everyMinute()->withoutOverlapping();
         $schedule->command('entries:import')->everyMinute()->withoutOverlapping();
+        $schedule->command('app:dash-widgets-refresh')->everyFifteenMinutes()->withoutOverlapping();
     }
 
     /**

From c6a1489c729b6577931e6fc78f585ca1463aeb85 Mon Sep 17 00:00:00 2001
From: Sagar <sriramkanakam87@gmail.com>
Date: Tue, 14 May 2024 09:30:00 +0200
Subject: [PATCH 4/7] chore: ran pint

---
 app/Console/Commands/DashWidgetsRefresh.php                 | 6 +++---
 app/Filament/Dashboard/Resources/CollectionResource.php     | 2 +-
 .../RelationManagers/EntriesRelationManager.php             | 2 +-
 .../RelationManagers/MoleculesRelationManager.php           | 2 --
 4 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/app/Console/Commands/DashWidgetsRefresh.php b/app/Console/Commands/DashWidgetsRefresh.php
index 210c06b7..d21a4e62 100644
--- a/app/Console/Commands/DashWidgetsRefresh.php
+++ b/app/Console/Commands/DashWidgetsRefresh.php
@@ -2,14 +2,14 @@
 
 namespace App\Console\Commands;
 
-use Illuminate\Console\Command;
-use Illuminate\Support\Facades\Cache;
 use App\Models\Citation;
 use App\Models\Collection;
 use App\Models\GeoLocation;
+use App\Models\Molecule;
 use App\Models\Organism;
 use App\Models\Report;
-use App\Models\Molecule;
+use Illuminate\Console\Command;
+use Illuminate\Support\Facades\Cache;
 
 class DashWidgetsRefresh extends Command
 {
diff --git a/app/Filament/Dashboard/Resources/CollectionResource.php b/app/Filament/Dashboard/Resources/CollectionResource.php
index a8548c39..e013be93 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource.php
@@ -22,7 +22,6 @@
 use Filament\Tables\Table;
 use Illuminate\Support\Str;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
-use Illuminate\Database\Eloquent\Model;
 
 class CollectionResource extends Resource
 {
@@ -102,6 +101,7 @@ public static function getRelations(): array
             AuditsRelationManager::class,
             MoleculesRelationManager::class,
         ];
+
         return $arr;
     }
 
diff --git a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
index e779f96e..4e57a22d 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
@@ -11,11 +11,11 @@
 use Filament\Infolists\Infolist;
 use Filament\Resources\RelationManagers\RelationManager;
 use Filament\Tables;
+use Filament\Tables\Actions\Action;
 use Filament\Tables\Actions\ImportAction;
 use Filament\Tables\Columns\ImageColumn;
 use Filament\Tables\Filters\SelectFilter;
 use Filament\Tables\Table;
-use Filament\Tables\Actions\Action;
 use Illuminate\Support\Facades\Artisan;
 
 class EntriesRelationManager extends RelationManager
diff --git a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php
index ccd0e21a..9ec3fd20 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php
@@ -7,8 +7,6 @@
 use Filament\Resources\RelationManagers\RelationManager;
 use Filament\Tables;
 use Filament\Tables\Table;
-use Illuminate\Database\Eloquent\Builder;
-use Illuminate\Database\Eloquent\SoftDeletingScope;
 
 class MoleculesRelationManager extends RelationManager
 {

From ceb3a5afeee65b2c17510fda0e32d852a359a6c0 Mon Sep 17 00:00:00 2001
From: Sagar <sriramkanakam87@gmail.com>
Date: Tue, 14 May 2024 09:30:26 +0200
Subject: [PATCH 5/7] chore: ran pint

---
 app/Filament/Dashboard/Resources/CollectionResource.php         | 2 +-
 .../RelationManagers/EntriesRelationManager.php                 | 2 +-
 .../RelationManagers/MoleculesRelationManager.php               | 2 --
 3 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/app/Filament/Dashboard/Resources/CollectionResource.php b/app/Filament/Dashboard/Resources/CollectionResource.php
index a8548c39..e013be93 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource.php
@@ -22,7 +22,6 @@
 use Filament\Tables\Table;
 use Illuminate\Support\Str;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
-use Illuminate\Database\Eloquent\Model;
 
 class CollectionResource extends Resource
 {
@@ -102,6 +101,7 @@ public static function getRelations(): array
             AuditsRelationManager::class,
             MoleculesRelationManager::class,
         ];
+
         return $arr;
     }
 
diff --git a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
index e779f96e..4e57a22d 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
@@ -11,11 +11,11 @@
 use Filament\Infolists\Infolist;
 use Filament\Resources\RelationManagers\RelationManager;
 use Filament\Tables;
+use Filament\Tables\Actions\Action;
 use Filament\Tables\Actions\ImportAction;
 use Filament\Tables\Columns\ImageColumn;
 use Filament\Tables\Filters\SelectFilter;
 use Filament\Tables\Table;
-use Filament\Tables\Actions\Action;
 use Illuminate\Support\Facades\Artisan;
 
 class EntriesRelationManager extends RelationManager
diff --git a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php
index ccd0e21a..9ec3fd20 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php
@@ -7,8 +7,6 @@
 use Filament\Resources\RelationManagers\RelationManager;
 use Filament\Tables;
 use Filament\Tables\Table;
-use Illuminate\Database\Eloquent\Builder;
-use Illuminate\Database\Eloquent\SoftDeletingScope;
 
 class MoleculesRelationManager extends RelationManager
 {

From 3765492654bbefcdf11958ca3252470224c8ad7d Mon Sep 17 00:00:00 2001
From: Sagar <sriramkanakam87@gmail.com>
Date: Tue, 14 May 2024 09:30:55 +0200
Subject: [PATCH 6/7] chore: ran pint

---
 app/Filament/Dashboard/Resources/CollectionResource.php         | 2 +-
 .../RelationManagers/EntriesRelationManager.php                 | 2 +-
 .../RelationManagers/MoleculesRelationManager.php               | 2 --
 3 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/app/Filament/Dashboard/Resources/CollectionResource.php b/app/Filament/Dashboard/Resources/CollectionResource.php
index a8548c39..e013be93 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource.php
@@ -22,7 +22,6 @@
 use Filament\Tables\Table;
 use Illuminate\Support\Str;
 use Tapp\FilamentAuditing\RelationManagers\AuditsRelationManager;
-use Illuminate\Database\Eloquent\Model;
 
 class CollectionResource extends Resource
 {
@@ -102,6 +101,7 @@ public static function getRelations(): array
             AuditsRelationManager::class,
             MoleculesRelationManager::class,
         ];
+
         return $arr;
     }
 
diff --git a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
index 5b49073f..57a22039 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php
@@ -11,11 +11,11 @@
 use Filament\Infolists\Infolist;
 use Filament\Resources\RelationManagers\RelationManager;
 use Filament\Tables;
+use Filament\Tables\Actions\Action;
 use Filament\Tables\Actions\ImportAction;
 use Filament\Tables\Columns\ImageColumn;
 use Filament\Tables\Filters\SelectFilter;
 use Filament\Tables\Table;
-use Filament\Tables\Actions\Action;
 use Illuminate\Support\Facades\Artisan;
 
 class EntriesRelationManager extends RelationManager
diff --git a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php
index ccd0e21a..9ec3fd20 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/MoleculesRelationManager.php
@@ -7,8 +7,6 @@
 use Filament\Resources\RelationManagers\RelationManager;
 use Filament\Tables;
 use Filament\Tables\Table;
-use Illuminate\Database\Eloquent\Builder;
-use Illuminate\Database\Eloquent\SoftDeletingScope;
 
 class MoleculesRelationManager extends RelationManager
 {

From e14219b2451bc9b15a8cf879ddf76f4ec4a53599 Mon Sep 17 00:00:00 2001
From: Sagar <sriramkanakam87@gmail.com>
Date: Tue, 14 May 2024 13:17:14 +0200
Subject: [PATCH 7/7] feat: added functionality to display the status of the
 collection

---
 app/Filament/Dashboard/Resources/CollectionResource.php | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/app/Filament/Dashboard/Resources/CollectionResource.php b/app/Filament/Dashboard/Resources/CollectionResource.php
index e013be93..a745e0ee 100644
--- a/app/Filament/Dashboard/Resources/CollectionResource.php
+++ b/app/Filament/Dashboard/Resources/CollectionResource.php
@@ -75,6 +75,15 @@ public static function table(Table $table): Table
         return $table
             ->columns([
                 Tables\Columns\TextColumn::make('title')->wrap(),
+                Tables\Columns\TextColumn::make('status')
+                    ->badge()
+                    ->color(fn (string $state): string => match ($state) {
+                        'DRAFT' => 'info',
+                        'REVIEW' => 'warning',
+                        'EMBARGO' => 'warning',
+                        'PUBLISHED' => 'success',
+                        'REJECTED' => 'danger',
+                    }),
             ])
             ->filters([
                 //