fix: various bug fixes and ux/ui improvements

app/Console/Commands/ImportEntries.php

@@ -39,6 +39,10 @@ public function handle()
         }
 
         foreach ($collections as $collection) {
+            $collection->jobs_status = 'PROCESSING';
+            $collection->job_info = 'Importing entries: Citations, Organism Info and other details';
+            $collection->save();
+
             $batchJobs = [];
             $i = 0;
             Entry::select('id')->where('status', 'PASSED')->where('collection_id', $collection->id)->chunk(100, function ($ids) use (&$batchJobs, &$i) {
@@ -47,7 +51,10 @@ public function handle()
             });
             $batch = Bus::batch($batchJobs)->then(function (Batch $batch) {
             })->catch(function (Batch $batch, Throwable $e) {
-            })->finally(function (Batch $batch) {
+            })->finally(function (Batch $batch) use ($collection) {
+                $collection->jobs_status = 'INCURATION';
+                $collection->job_info = '';
+                $collection->save();
             })->name('Import Entries '.$collection->id)
                 ->allowFailures(false)
                 ->onConnection('redis')

app/Console/Commands/ProcessEntries.php

@@ -3,6 +3,7 @@
 namespace App\Console\Commands;
 
 use App\Jobs\LoadEntriesBatch;
+use App\Models\Collection;
 use App\Models\Entry;
 use Artisan;
 use Illuminate\Bus\Batch;
@@ -35,18 +36,25 @@ public function handle()
         foreach ($collectionIds as $collectionId) {
             $batchJobs = [];
             $i = 0;
-            Entry::select('id')->where('status', 'SUBMITTED')->where('collection_id', $collectionId)->chunk(100, function ($ids) use (&$batchJobs, &$i) {
+
+            $collection = Collection::whereId($collectionId['collection_id'])->first();
+            $collection->jobs_status = 'PROCESSING';
+            $collection->job_info = 'Processing entries using ChEMBL Pipeline.';
+            $collection->save();
+
+            Entry::select('id')->where('status', 'SUBMITTED')->where('collection_id', $collectionId['collection_id'])->chunk(100, function ($ids) use (&$batchJobs, &$i) {
                 array_push($batchJobs, new LoadEntriesBatch($ids->pluck('id')->toArray()));
                 $i = $i + 1;
             });
             $batch = Bus::batch($batchJobs)->then(function (Batch $batch) {
             })->catch(function (Batch $batch, Throwable $e) {
-            })->finally(function (Batch $batch) use ($collectionId) {
-
+            })->finally(function (Batch $batch) use ($collection) {
                 Artisan::call('entries:import', [
-                    'collection_id' => $collectionId['collection_id'],
+                    'collection_id' => $collection->id,
                 ]);
-
+                $collection->jobs_status = 'INCURATION';
+                $collection->job_info = '';
+                $collection->save();
             })->name('Process Entries '.$collectionId['collection_id'])
                 ->allowFailures(false)
                 ->onConnection('redis')

app/Filament/Dashboard/Imports/EntryImporter.php

@@ -17,6 +17,7 @@ public static function getColumns(): array
         return [
             ImportColumn::make('canonical_smiles'),
             ImportColumn::make('reference_id'),
+            ImportColumn::make('name'),
             ImportColumn::make('doi'),
             ImportColumn::make('link'),
             ImportColumn::make('organism'),

app/Filament/Dashboard/Resources/CitationResource.php

@@ -20,6 +20,8 @@ class CitationResource extends Resource
 
     protected static ?string $model = Citation::class;
 
+    protected static ?string $recordTitleAttribute = 'title';
+
     protected static ?int $navigationSort = 2;
 
     protected static ?string $navigationIcon = 'heroicon-o-ticket';

app/Filament/Dashboard/Resources/CollectionResource.php

@@ -5,13 +5,14 @@
 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\Livewire\ShowJobStatus;
 use App\Models\Collection;
+use Filament\Forms\Components\Livewire;
 use Filament\Forms\Components\Section;
 use Filament\Forms\Components\Select;
 use Filament\Forms\Components\SpatieTagsInput;
 use Filament\Forms\Components\TextArea;
 use Filament\Forms\Components\TextInput;
-use Filament\Forms\Components\ToggleButtons;
 use Filament\Forms\Form;
 use Filament\Forms\Set;
 use Filament\Resources\Resource;
@@ -30,11 +31,16 @@ class CollectionResource extends Resource
 
     protected static ?string $navigationIcon = 'heroicon-o-swatch';
 
+    protected static ?string $recordTitleAttribute = 'title';
+
     public static function form(Form $form): Form
     {
         return $form
             ->schema(
                 [
+
+                    Livewire::make(ShowJobStatus::class),
+
                     Section::make('Database details')
                         ->description('Provide details of the database and link to the resource.')
                         ->schema([
@@ -48,23 +54,15 @@ public static function form(Form $form): Form
                     Section::make('Meta data')
                         ->schema([
                             SpatieTagsInput::make('tags')
-                                 ->type('collections'),
+                                ->type('collections'),
                             TextInput::make('identifier'),
                         ]),
                     Section::make('Distribution')
                         ->schema([
                             Select::make('license')
-                                 ->relationship('license', 'title')
-                                 ->preload()
-                                 ->searchable(),
-                            // ToggleButtons::make('status')
-                            //     ->options([
-                            //         'DRAFT' => 'Draft',
-                            //         'REVIEW' => 'Review',
-                            //         'EMBARGO' => 'Embargo',
-                            //         'PUBLISHED' => 'Published',
-                            //         'REJECTED' => 'Rejected',
-                            //     ])->inline(),
+                                ->relationship('license', 'title')
+                                ->preload()
+                                ->searchable(),
                         ]),
                 ]
             )->columns(1);

app/Filament/Dashboard/Resources/CollectionResource/RelationManagers/EntriesRelationManager.php

@@ -30,6 +30,9 @@ public function form(Form $form): Form
                 Forms\Components\TextInput::make('canonical_smiles')
                     ->required()
                     ->maxLength(255),
+                Forms\Components\TextInput::make('name')
+                    ->required()
+                    ->maxLength(255),
                 Forms\Components\TextInput::make('doi')
                     ->required()
                     ->maxLength(255),
@@ -42,11 +45,20 @@ public function form(Form $form): Form
                 Forms\Components\TextInput::make('organism_part')
                     ->required()
                     ->maxLength(255),
+                Forms\Components\TextInput::make('mol_filename')
+                    ->required()
+                    ->maxLength(255),
                 Forms\Components\TextInput::make('molecular_formula')
                     ->required()
                     ->maxLength(255),
                 Forms\Components\TextArea::make('structural_comments')
                     ->required(),
+                Forms\Components\TextInput::make('geo_location')
+                    ->required()
+                    ->maxLength(255),
+                Forms\Components\TextInput::make('location')
+                    ->required()
+                    ->maxLength(255),
                 Forms\Components\TextArea::make('errors')
                     ->required(),
                 Forms\Components\TextInput::make('standardized_canonical_smiles')
@@ -66,12 +78,15 @@ public function infolist(Infolist $infolist): Infolist
                 Section::make()
                     ->schema([
                         TextEntry::make('reference_id'),
+                        TextEntry::make('name'),
                         TextEntry::make('doi'),
                         TextEntry::make('link'),
                         TextEntry::make('organism'),
                         TextEntry::make('organism_part'),
                         TextEntry::make('molecular_formula'),
                         TextEntry::make('structural_comments'),
+                        TextEntry::make('geo_location'),
+                        TextEntry::make('location'),
                         TextEntry::make('errors'),
                     ]),
                 Section::make()
@@ -122,7 +137,7 @@ public function table(Table $table): Table
                     ->height(200)
                     ->ring(5)
                     ->defaultImageUrl(url('/images/placeholder.png')),
-                Tables\Columns\TextColumn::make('identifier')->searchable(),
+                Tables\Columns\TextColumn::make('reference_id')->searchable(),
                 Tables\Columns\TextColumn::make('status'),
             ])
             ->filters([

app/Jobs/ImportEntry.php

@@ -5,6 +5,7 @@
 use App\Models\Citation;
 use App\Models\Molecule;
 use App\Models\Properties;
+use App\Models\Ticker;
 use Illuminate\Bus\Batchable;
 use Illuminate\Bus\Queueable;
 use Illuminate\Contracts\Queue\ShouldBeUnique;
@@ -29,6 +30,14 @@ public function __construct($entry)
         $this->entry = $entry;
     }
 
+    /**
+     * Get the unique ID for the job.
+     */
+    public function uniqueId(): string
+    {
+        return $this->entry->uuid;
+    }
+
     /**
      * Execute the job.
      */
@@ -41,61 +50,79 @@ public function handle(): void
                 if ($parent->wasRecentlyCreated) {
                     $parent->is_parent = true;
                     $parent->has_variants = true;
-                    $parent->identifier = $this->entry->coconut_id;
                     $parent->is_placeholder = true;
                     $parent->variants_count += $parent->variants_count;
                     $parent = $this->assignData($parent, $data);
                     $parent->save();
-
-                    $this->fetchIUPACNameFromPubChem($parent);
-                    $this->attachProperties('parent', $parent);
-                    $this->classify($parent);
+                    // $this->fetchIUPACNameFromPubChem($parent);
+                    // $this->attachProperties('parent', $parent);
+                    // $this->classify($parent);
                 }
-                $this->attachCollection($parent);
 
                 $data = $this->getRepresentations('standardized');
                 $molecule = Molecule::firstOrCreate(['standard_inchi' => $data['standard_inchi'], 'standard_inchi_key' => $data['standard_inchikey']]);
                 if ($molecule->wasRecentlyCreated) {
                     $molecule->has_stereo = true;
                     $molecule->parent_id = $parent->id;
-                    $parent->ticker = $parent->ticker + 1;
-                    $molecule->identifier = $this->entry->coconut_id.'.'.$parent->ticker;
-                    $molecule = $this->assignData($molecule, $data);
-                    $this->fetchIUPACNameFromPubChem($molecule);
-                    $this->attachProperties('standardized', $molecule);
                     $parent->save();
-                    $this->classify($molecule);
+                    $molecule = $this->assignData($molecule, $data);
+                    // $this->fetchIUPACNameFromPubChem($molecule);
+                    // $this->attachProperties('standardized', $molecule);
+                    // $this->classify($molecule);
                     $molecule->save();
                 }
                 $this->entry->molecule_id = $molecule->id;
                 $this->entry->save();
 
+                $this->attachCollection($parent);
                 $this->attachCollection($molecule);
             } else {
                 $data = $this->getRepresentations('standardized');
                 $molecule = Molecule::firstOrCreate(['standard_inchi' => $data['standard_inchi'], 'standard_inchi_key' => $data['standard_inchikey']]);
                 if ($molecule->wasRecentlyCreated) {
                     $molecule = $this->assignData($molecule, $data);
-                    $molecule->identifier = $this->entry->coconut_id;
                     $molecule->save();
-                    $this->fetchIUPACNameFromPubChem($molecule);
-                    $this->attachProperties('standardized', $molecule);
-                    $this->classify($molecule);
+                    // $this->fetchIUPACNameFromPubChem($molecule);
+                    // $this->attachProperties('standardized', $molecule);
+                    // $this->classify($molecule);
                 }
                 $this->entry->molecule_id = $molecule->id;
                 $this->entry->save();
                 $this->attachCollection($molecule);
             }
 
             if ($this->entry->doi && $this->entry->doi != '') {
-                $this->fetchCitation($this->entry->doi, $molecule);
+                $dois = explode('|', $this->entry->doi);
+
+                $doiRegex = '/\b(10[.][0-9]{4,}(?:[.][0-9]+)*)\b/';
+                foreach ($dois as $doi) {
+                    if (preg_match($doiRegex, $doi)) {
+                        $this->fetchDOICitation($doi, $molecule);
+                    } else {
+                        $this->fetchCitation($doi, $molecule);
+                    }
+                }
             }
         }
     }
 
-    public function classify($molecule)
+    public function fetchIdentifier()
     {
+        $ticker = Ticker::first();
+        $identifier = $ticker->index + 1;
+        $ticker->index = $identifier;
+        $ticker->save();
+        $CNP = 'CNP'.$identifier;
+
+        while (Molecule::where('identifier', $CNP)->exists()) {
+            return $this->fetchIdentifier();
+        }
 
+        return $CNP;
+    }
+
+    public function classify($molecule)
+    {
         $properties = $molecule->properties;
 
         if ($properties->chemical_class == null || $properties->chemical_sub_class == null || $properties->chemical_super_class == null || $properties->direct_parent_classification == null) {
@@ -146,19 +173,29 @@ public function classify($molecule)
 
     }
 
-    public function fetchCitation($doi, $molecule)
+    public function fetchCitation($citation_text, $molecule)
+    {
+        $citation = Citation::firstOrCreate(['citation_text' => $citation_text]);
+        $molecule->citations()->syncWithoutDetaching($citation);
+    }
+
+    public function fetchDOICitation($doi, $molecule)
     {
+
         $citation = null;
 
         // check if the doi is valid
         $isDOI = preg_match('/\b(10[.][0-9]{4,}(?:[.][0-9]+)*)\b/', $doi);
 
         if ($isDOI) {
 
+            echo $doi;
+            echo '/r/n';
+
             //check if citation already exists
-            $citation = Citation::where('doi', $doi)->first();
+            $citation = Citation::firstOrCreate(['doi' => $doi]);
             $citationResponse = null;
-            if (! $citation) {
+            if ($citation->wasRecentlyCreated) {
                 // fetch citation from EuropePMC
                 $europemcUrl = env('EUROPEPMC_WS_API');
                 $europemcParams = [
@@ -199,7 +236,6 @@ public function fetchCitation($doi, $molecule)
                 }
             }
 
-            // attach citation
             $molecule->citations()->syncWithoutDetaching($citation);
         }
     }

app/Livewire/ShowJobStatus.php

@@ -0,0 +1,24 @@
+<?php
+
+namespace App\Livewire;
+
+use Illuminate\Database\Eloquent\Model;
+use Livewire\Component;
+
+class ShowJobStatus extends Component
+{
+    public $collection;
+
+    public function mount(?Model $record = null)
+    {
+        $this->collection = $record;
+    }
+
+    public function render()
+    {
+        return view('livewire.show-job-status', [
+            'status' => $this->collection->jobs_status,
+            'info' => $this->collection->job_info,
+        ]);
+    }
+}

app/Models/Collection.php

@@ -31,6 +31,7 @@ protected static function booted()
         'title',
         'slug',
         'description',
+        'jobs_status',
         'comments',
         'identifier',
         'url',