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Organism resource improvements #701

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ebe1cd7
feat(organisms): add preset views for inactive and unmapped organisms
vcnainala Nov 27, 2025
e831826
fix(organisms): correct isObsolete boolean check and family rank mapping
vcnainala Nov 27, 2025
3c553b7
feat(organisms): enhance organisms table with molecule count and IRI
vcnainala Nov 27, 2025
bb6820e
feat(organisms): add multi-source taxonomy search with modal selection
vcnainala Nov 27, 2025
e5f36c7
feat(organisms): redesign similar organisms UI
vcnainala Nov 27, 2025
c615a28
style(organisms): set full width for create/edit organism pages
vcnainala Nov 27, 2025
9bfa4d0
feat(organisms): click table rows to open view instead of edit
vcnainala Nov 28, 2025
30d095d
feat(organisms): improve similar organisms query
vcnainala Nov 28, 2025
441d1c0
feat(organisms): add merge functionality for similar organisms
vcnainala Nov 28, 2025
fad3fa7
Merge branch 'development' into feature/organism-improvements
vcnainala Feb 2, 2026
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8 changes: 6 additions & 2 deletions app/Console/Commands/MapOrganismNamesToOGG.php
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ public function handle()
} else {
$data = $this->getOLSIRI(explode(' ', $name)[0], 'family');
if ($data) {
$this->updateOrganismModel($name, $data, $organism, 'genus');
$this->updateOrganismModel($name, $data, $organism, 'family');
$this->info("Mapped and updated: $name");
} else {
$this->getGNFMatches($name, $organism);
Expand Down Expand Up @@ -155,7 +155,7 @@ protected function getOLSIRI($name, $rank)
if (isset($data['elements']) && count($data['elements']) > 0) {

$element = $data['elements'][0];
if (isset($element['iri'], $element['ontologyId']) && $element['isObsolete'] === 'false') {
if (isset($element['iri'], $element['ontologyId']) && $element['isObsolete'] === false) {
if ($rank && $rank == 'species') {
if (isset($element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank']) && $element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank'] == 'http://purl.obolibrary.org/obo/NCBITaxon_species') {
return urlencode($element['iri']);
Expand Down Expand Up @@ -188,6 +188,10 @@ protected function updateOrganismModel($name, $iri, $organism = null, $rank = nu
if ($organism) {
$organism->iri = $iri;
$organism->rank = $rank;
// Auto-generate slug if not exists
if (! $organism->slug) {
$organism->slug = \Illuminate\Support\Str::slug($name);
}
$organism->save();
} else {
$this->error("Organism not found in the database: $name");
Expand Down
111 changes: 52 additions & 59 deletions app/Filament/Dashboard/Resources/OrganismResource.php
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Original file line number Diff line number Diff line change
Expand Up @@ -17,16 +17,13 @@
use Filament\Actions\BulkActionGroup;
use Filament\Actions\DeleteBulkAction;
use Filament\Actions\EditAction;
use Filament\Actions\ViewAction;
use Filament\Resources\Resource;
use Filament\Schemas\Components\Grid;
use Filament\Schemas\Components\Group;
use Filament\Schemas\Components\Section;
use Filament\Schemas\Schema;
use Filament\Tables;
use Filament\Tables\Columns\TextColumn;
use Filament\Tables\Table;
use GuzzleHttp\Client;
use Illuminate\Contracts\View\View;
use Illuminate\Support\Facades\Cache;
use Illuminate\Support\Facades\DB;
use Illuminate\Support\Facades\Log;
Expand All @@ -46,30 +43,19 @@ public static function form(Schema $schema): Schema
{
return $schema
->components([
Grid::make()
Section::make('Organism Information')
->description('Enter the organism details below')
->schema(Organism::getForm()),

Section::make('Similar Organisms')
->description('View similar organisms in the database')
->schema([
Group::make()
->schema([
Section::make('')
->schema(Organism::getForm()),
])
->columnSpan(1),
Group::make()
->schema([
Section::make('')
->schema([
OrganismsTable::make('Custom Table'),
// \Livewire\Livewire::mount('similar-organisms', ['organismId' => function ($get) {
// return $get('name');
// }]),
]),
])
->hidden(function ($operation) {
return $operation === 'create';
})
->columnSpan(1),
OrganismsTable::make('Custom Table'),
])
->columns(2), // Defines the number of columns in the grid
->hidden(function ($operation) {
return $operation === 'create';
})
->collapsible(),
]);
}

Expand All @@ -78,9 +64,13 @@ public static function table(Table $table): Table
return $table
->columns([
TextColumn::make('name')
->searchable(),
->searchable()
->description(fn (Organism $record): ?string => $record->iri ? urldecode($record->iri) : null),
TextColumn::make('rank')->wrap()
->searchable(),
TextColumn::make('molecule_count')
->label('Molecules')
->sortable(),
TextColumn::make('created_at')
->dateTime()
->sortable()
Expand All @@ -101,15 +91,19 @@ public static function table(Table $table): Table
->color('info')
->icon('heroicon-o-link')
->iconButton(),
// Tables\Actions\ViewAction::make(),
ViewAction::make()
->iconButton(),
EditAction::make()
->iconButton(),
])
->toolbarActions([
BulkActionGroup::make([
DeleteBulkAction::make(),
]),
]);
])
->recordUrl(
fn (Organism $record): string => self::getUrl('view', ['record' => $record]),
);
}

public static function getRelations(): array
Expand All @@ -129,7 +123,7 @@ public static function getPages(): array
'index' => ListOrganisms::route('/'),
'create' => CreateOrganism::route('/create'),
'edit' => EditOrganism::route('/{record}/edit'),
// 'view' => Pages\ViewOrganism::route('/{record}'),
'view' => Pages\ViewOrganism::route('/{record}'),
];
}

Expand Down Expand Up @@ -219,6 +213,10 @@ protected static function updateOrganismModel($name, $iri, $organism = null, $ra
$organism->name = $name;
$organism->iri = $iri;
$organism->rank = $rank;
// Auto-generate slug if not exists
if (! $organism->slug) {
$organism->slug = \Illuminate\Support\Str::slug($name);
}
$organism->save();
} else {
Log::error("Organism not found in the database: $name");
Expand All @@ -228,46 +226,41 @@ protected static function updateOrganismModel($name, $iri, $organism = null, $ra
protected static function getOLSIRI($name, $rank)
{
$client = new Client([
'base_uri' => 'https://www.ebi.ac.uk/ols4/api/',
'base_uri' => 'https://www.ebi.ac.uk/ols4/api/v2/',
]);

try {
$response = $client->get('search', [
$response = $client->get('entities', [
'query' => [
'q' => $name,
'ontology' => ['ncbitaxon', 'efo', 'obi', 'uberon', 'taxrank'],
'exact' => false,
'obsoletes' => false,
'format' => 'json',
'search' => $name,
'ontologyId' => 'ncbitaxon',
'exactMatch' => true,
'type' => 'class',
],
]);

$data = json_decode($response->getBody(), true);

return $data;
// var_dump($data);

// if (isset($data['elements']) && count($data['elements']) > 0) {
if (isset($data['elements']) && count($data['elements']) > 0) {

// $element = $data['elements'][0];
// if (isset($element['iri'], $element['ontologyId']) && $element['isObsolete'] === 'false') {
// if ($rank && $rank == 'species') {
// if (isset($element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank']) && $element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank'] == 'http://purl.obolibrary.org/obo/NCBITaxon_species') {
// return urlencode($element['iri']);
// }
// } elseif ($rank && $rank == 'genus') {
// if (isset($element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank']) && $element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank'] == 'http://purl.obolibrary.org/obo/NCBITaxon_genus') {
// return urlencode($element['iri']);
// }
// } elseif ($rank && $rank == 'family') {
// if (isset($element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank']) && $element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank'] == 'http://purl.obolibrary.org/obo/NCBITaxon_family') {
// return urlencode($element['iri']);
// }
// }
// }
// }
$element = $data['elements'][0];
if (isset($element['iri'], $element['ontologyId']) && $element['isObsolete'] === false) {
if ($rank && $rank == 'species') {
if (isset($element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank']) && $element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank'] == 'http://purl.obolibrary.org/obo/NCBITaxon_species') {
return urlencode($element['iri']);
}
} elseif ($rank && $rank == 'genus') {
if (isset($element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank']) && $element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank'] == 'http://purl.obolibrary.org/obo/NCBITaxon_genus') {
return urlencode($element['iri']);
}
} elseif ($rank && $rank == 'family') {
if (isset($element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank']) && $element['http://purl.obolibrary.org/obo/ncbitaxon#has_rank'] == 'http://purl.obolibrary.org/obo/NCBITaxon_family') {
return urlencode($element['iri']);
}
}
}
}
} catch (Exception $e) {
// Self::error("Error fetching IRI for $name: " . $e->getMessage());
Log::error("Error fetching IRI for $name: ".$e->getMessage());
}

Expand Down
5 changes: 5 additions & 0 deletions app/Filament/Dashboard/Resources/OrganismResource/Pages/CreateOrganism.php
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Original file line number Diff line number Diff line change
Expand Up @@ -8,4 +8,9 @@
class CreateOrganism extends CreateRecord
{
protected static string $resource = OrganismResource::class;

public function getMaxContentWidth(): ?string
{
return 'full';
}
}
122 changes: 122 additions & 0 deletions app/Filament/Dashboard/Resources/OrganismResource/Pages/EditOrganism.php
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,11 @@
namespace App\Filament\Dashboard\Resources\OrganismResource\Pages;

use App\Filament\Dashboard\Resources\OrganismResource;
use App\Models\Organism;
use Filament\Actions\DeleteAction;
use Filament\Notifications\Notification;
use Filament\Resources\Pages\EditRecord;
use Illuminate\Support\Facades\DB;

class EditOrganism extends EditRecord
{
Expand All @@ -16,4 +19,123 @@ protected function getHeaderActions(): array
DeleteAction::make(),
];
}

public function getMaxContentWidth(): ?string
{
return 'full';
}

/**
* Merge current organism into target organism
*/
public function mergeOrganism(int $targetId): void
{
$this->executeMerge($targetId);
}

/**
* Execute the merge operation
*/
protected function executeMerge(int $targetOrganismId): void
{
$currentOrganism = $this->record;
$targetOrganism = Organism::findOrFail($targetOrganismId);

if ($currentOrganism->id === $targetOrganismId) {
Notification::make()
->title('Cannot merge organism into itself')
->danger()
->send();

return;
}

DB::beginTransaction();

try {
// Get all molecule_organism records for the current organism
$currentRelations = DB::table('molecule_organism')
->where('organism_id', $currentOrganism->id)
->get();

$transferred = 0;
$skipped = 0;

foreach ($currentRelations as $relation) {
// Check if this exact combination already exists for the target organism
$exists = DB::table('molecule_organism')
->where('organism_id', $targetOrganismId)
->where('molecule_id', $relation->molecule_id)
->where(function ($query) use ($relation) {
$query->where('sample_location_id', $relation->sample_location_id)
->orWhere(function ($q) use ($relation) {
$q->whereNull('sample_location_id')
->where(DB::raw('1'), $relation->sample_location_id === null ? 1 : 0);
});
})
->where(function ($query) use ($relation) {
$query->where('geo_location_id', $relation->geo_location_id)
->orWhere(function ($q) use ($relation) {
$q->whereNull('geo_location_id')
->where(DB::raw('1'), $relation->geo_location_id === null ? 1 : 0);
});
})
->where(function ($query) use ($relation) {
$query->where('ecosystem_id', $relation->ecosystem_id)
->orWhere(function ($q) use ($relation) {
$q->whereNull('ecosystem_id')
->where(DB::raw('1'), $relation->ecosystem_id === null ? 1 : 0);
});
})
->exists();

if (! $exists) {
// Update the record to point to the target organism
DB::table('molecule_organism')
->where('id', $relation->id)
->update(['organism_id' => $targetOrganismId]);
$transferred++;
} else {
// Delete the duplicate record from current organism
DB::table('molecule_organism')
->where('id', $relation->id)
->delete();
$skipped++;
}
}

// Update molecule counts for both organisms
$currentOrganism->molecule_count = DB::table('molecule_organism')
->where('organism_id', $currentOrganism->id)
->distinct('molecule_id')
->count('molecule_id');
$currentOrganism->save();

$targetOrganism->molecule_count = DB::table('molecule_organism')
->where('organism_id', $targetOrganismId)
->distinct('molecule_id')
->count('molecule_id');
$targetOrganism->save();

DB::commit();

Notification::make()
->title('Organisms merged successfully')
->body("Transferred {$transferred} molecule relations to \"{$targetOrganism->name}\". {$skipped} duplicates were skipped.")
->success()
->send();

// Redirect to the target organism's edit page
$this->redirect(OrganismResource::getUrl('edit', ['record' => $targetOrganism]));

} catch (\Exception $e) {
DB::rollBack();

Notification::make()
->title('Merge failed')
->body($e->getMessage())
->danger()
->send();
}
}
}
11 changes: 10 additions & 1 deletion app/Filament/Dashboard/Resources/OrganismResource/Pages/ListOrganisms.php
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Original file line number Diff line number Diff line change
Expand Up @@ -31,11 +31,20 @@
->badge((string) Organism::query()->where('molecule_count', '>', 0)->count())
->preserveAll()
->default(),
'inactive entries' => PresetView::make()
'inactive' => PresetView::make()
->modifyQueryUsing(fn ($query) => $query->where('molecule_count', '<=', 0))
->favorite()
->badge((string) Organism::query()->where('molecule_count', '<=', 0)->count())
->preserveAll(),
'unmapped' => PresetView::make()
->modifyQueryUsing(fn ($query) => $query->where(function ($q) {
$q->whereNull('rank')->orWhere('rank', '');
}))
->favorite()
->badge(Organism::query()->where(function ($q) {

Check failure on line 44 in app/Filament/Dashboard/Resources/OrganismResource/Pages/ListOrganisms.php

View workflow job for this annotation

GitHub Actions / PHPStan Analysis / PHPStan Analysis (Level 5) 

Parameter #1 $badge of method Archilex\AdvancedTables\Components\PresetView::badge() expects Closure|string|null, int<0, max> given.
$q->whereNull('rank')->orWhere('rank', '');
})->count())
->preserveAll(),
];
}
}
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