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Merge pull request #271 from Steinbeck-Lab/feat-italic-display-of-iup…
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…ac-names

feat: now IUPAC names are displayed with proper italicisation.
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@Kohulan
Kohulan authored Oct 14, 2024
2 parents fa75c27 + 22187a3 commit b37dde6
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205 changes: 204 additions & 1 deletion app/Helper.php
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
<?php

use App\Models\Citation;
use App\Models\Molecule;
use Filament\Forms\Components\KeyValue;
use Illuminate\Support\Facades\Event;
use OwenIt\Auditing\Events\AuditCustom;

Expand Down Expand Up @@ -180,6 +182,7 @@ function changeAudit(array $data): array
$whitelist = [
// 'id' => 'id',
'name' => 'name',
'title' => 'title',
// 'identifier' => 'identifier',
];

Expand All @@ -194,12 +197,14 @@ function changeAudit(array $data): array
$data[$key_type][$changed_model] = [];
foreach ($changed_data_values as $key => $value) {
$value = is_array($value) ? $value : $value->toArray();
if ($value) {
if (array_key_exists('name', $value)) {
if (array_key_exists('identifier', $value)) {
$value['name'] = $value['name'].' (ID: '.$value['id'].')'.' (COCONUT ID: '.$value['identifier'].')';
} else {
$value['name'] = $value['name'].' (ID: '.$value['id'].')';
}
} else {
$value['title'] = $value['title'].' (ID: '.$value['id'].')';
}
$data[$key_type][$changed_model][$key] = array_intersect_key($value, $whitelist);
}
Expand Down Expand Up @@ -232,3 +237,201 @@ function flattenArray(array $array, $prefix = ''): array

return $result;
}

function getChangesToDisplayModal($data)
{
$key_values = [];
$overall_changes = getOverallChanges($data);

foreach ($overall_changes as $key => $value) {
if (count($value['changes']) == 0) {
continue;
}
array_push($key_values, KeyValue::make($key)
->addable(false)
->deletable(false)
->keyLabel($value['key'])
->valueLabel($value['value'])
->editableKeys(false)
->editableValues(false)
->default(
$value['changes']
));
}

return $key_values;
}

function getOverallChanges($data)
{
$overall_changes = [];
$geo_location_changes = [];
$molecule = Molecule::where('identifier', $data['mol_id_csv'])->first();

$db_geo_locations = $molecule->geo_locations->pluck('name')->toArray();
$deletable_locations = array_key_exists('existing_geo_locations', $data) ? array_diff($db_geo_locations, $data['existing_geo_locations']) : [];
$new_locations = array_key_exists('new_geo_locations', $data) ? (is_string($data['new_geo_locations']) ? $data['new_geo_locations'] : implode(',', $data['new_geo_locations'])) : null;
if (count($deletable_locations) > 0 || $new_locations) {
$key = implode(',', $deletable_locations) == '' ? ' ' : implode(',', $deletable_locations);
$geo_location_changes[$key] = $new_locations;
$overall_changes['geo_location_changes'] = [
'key' => 'Delete',
'value' => 'Add',
'changes' => $geo_location_changes,
'delete' => $deletable_locations,
'add' => $new_locations,
];
}

$synonym_changes = [];
$db_synonyms = $molecule->synonyms;
$deletable_synonyms = array_key_exists('existing_synonyms', $data) ? array_diff($db_synonyms, $data['existing_synonyms']) : [];
$new_synonyms = array_key_exists('new_synonyms', $data) ? (is_string($data['new_synonyms']) ? $data['new_synonyms'] : implode(',', $data['new_synonyms'])) : null;
if (count($deletable_synonyms) > 0 || $new_synonyms) {
$key = implode(',', $deletable_synonyms) == '' ? ' ' : implode(',', $deletable_synonyms);
$synonym_changes[$key] = $new_synonyms;
$overall_changes['synonym_changes'] = [
'key' => 'Delete',
'value' => 'Add',
'changes' => $synonym_changes,
'delete' => $deletable_synonyms,
'add' => $new_synonyms,
];
}

$name_change = [];
if (array_key_exists('name', $data) && $data['name'] && $data['name'] != $molecule->name) {
$name_change[$molecule->name] = $data['name'];
$overall_changes['name_change'] = [
'key' => 'Old',
'value' => 'New',
'changes' => $name_change,
'old' => $molecule->name,
'new' => $data['name'],
];
}

$cas_changes = [];
$db_cas = $molecule->cas;
$deletable_cas = array_key_exists('existing_cas', $data) ? array_diff($db_cas, $data['existing_cas']) : [];
$new_cas = array_key_exists('new_cas', $data) ? (is_string($data['new_cas']) ? $data['new_cas'] : implode(',', $data['new_cas'])) : null;
if (count($deletable_cas) > 0 || $new_cas) {
$key = implode(',', $deletable_cas) == '' ? ' ' : implode(',', $deletable_cas);
$cas_changes[$key] = $new_cas;
$overall_changes['cas_changes'] = [
'key' => 'Delete',
'value' => 'Add',
'changes' => $cas_changes,
'delete' => $deletable_cas,
'add' => $new_cas,
];
}

$organism_changes = [];
$db_organisms = $molecule->organisms->pluck('name')->toArray();
$deletable_organisms = array_key_exists('existing_organisms', $data) ? array_diff($db_organisms, $data['existing_organisms']) : [];
$new_organisms = [];
$new_organisms_form_data = [];
if (array_key_exists('new_organisms', $data)) {
foreach ($data['new_organisms'] as $organism) {
if ($organism['name']) {
$new_organisms[] = $organism['name'];
$new_organisms_form_data[] = $organism;
}
}
}
if (count($deletable_organisms) > 0 || count($new_organisms) > 0) {
$key = implode(',', $deletable_organisms) == '' ? ' ' : implode(',', $deletable_organisms);
$organism_changes[$key] = implode(',', $new_organisms);
$overall_changes['organism_changes'] = [
'key' => 'Delete',
'value' => 'Add',
'changes' => $organism_changes,
'delete' => $deletable_organisms,
'add' => $new_organisms_form_data,
];
}

$citation_changes = [];
$db_citations = $molecule->citations->where('title', '<>', null)->pluck('title')->toArray();
$deletable_citations = array_key_exists('existing_citations', $data) ? array_diff($db_citations, $data['existing_citations']) : [];
$new_citations = [];
$new_citations_form_data = [];
if (array_key_exists('new_citations', $data)) {
foreach ($data['new_citations'] as $ciation) {
if ($ciation['title']) {
$new_citations[] = $ciation['title'];
$new_citations_form_data[] = $ciation;
}
}
}
if (count($deletable_citations) > 0 || count($new_citations) > 0) {
$key = implode(',', $deletable_citations) == '' ? ' ' : implode(',', $deletable_citations);
$citation_changes[$key] = implode(',', $new_citations);
$overall_changes['citation_changes'] = [
'key' => 'Delete',
'value' => 'Add',
'changes' => $citation_changes,
'delete' => $deletable_citations,
'add' => $new_citations_form_data,
];
}

return $overall_changes;
}

function copyChangesToCuratorJSON($record, $data)
{
$temp = $data;
$data = $record->toArray();

$data['suggested_changes']['curator']['existing_geo_locations'] = $temp['existing_geo_locations'] ?? $record['suggested_changes']['curator']['existing_geo_locations'];
$data['suggested_changes']['curator']['new_geo_locations'] = $temp['new_geo_locations'] ?? $record['suggested_changes']['curator']['new_geo_locations'];
$data['suggested_changes']['curator']['approve_geo_locations'] = $temp['approve_geo_locations'] ?? false;

$data['suggested_changes']['curator']['existing_synonyms'] = $temp['existing_synonyms'] ?? $record['suggested_changes']['curator']['existing_synonyms'];
$data['suggested_changes']['curator']['new_synonyms'] = $temp['new_synonyms'] ?? $record['suggested_changes']['curator']['new_synonyms'];
$data['suggested_changes']['curator']['approve_synonyms'] = $temp['approve_synonyms'] ?? false;

$data['suggested_changes']['curator']['name'] = $temp['name'] ?? $record['suggested_changes']['curator']['name'];
$data['suggested_changes']['curator']['approve_name'] = $temp['approve_name'] ?? false;

$data['suggested_changes']['curator']['existing_cas'] = $temp['existing_cas'] ?? $record['suggested_changes']['curator']['existing_cas'];
$data['suggested_changes']['curator']['new_cas'] = $temp['new_cas'] ?? $record['suggested_changes']['curator']['new_cas'];
$data['suggested_changes']['curator']['approve_cas'] = $temp['approve_cas'] ?? false;

$data['suggested_changes']['curator']['existing_organisms'] = $temp['existing_organisms'] ?? $record['suggested_changes']['curator']['existing_organisms'];
$data['suggested_changes']['curator']['new_organisms'] = $temp['new_organisms'] ?? $record['suggested_changes']['curator']['new_organisms'];
$data['suggested_changes']['curator']['approve_existing_organisms'] = $temp['approve_existing_organisms'] ?? false;

$data['suggested_changes']['curator']['existing_citations'] = $temp['existing_citations'] ?? $record['suggested_changes']['curator']['existing_citations'];
$data['suggested_changes']['curator']['new_citations'] = $temp['new_citations'] ?? $record['suggested_changes']['curator']['new_citations'];
$data['suggested_changes']['curator']['approve_existing_citations'] = $temp['approve_existing_citations'] ?? false;

return $data;
}

function prepareComment($reason)
{
return [[
'timestamp' => now(),
'changed_by' => auth()->user()->id,
'comment' => $reason,
]];
}

function convert_italics_notation($text)
{
// Use preg_replace to replace ~{text} with <i>text</i>
$converted_text = preg_replace('/~\{([^}]*)\}/', '<i>$1</i>', $text);

return $converted_text;
}

function remove_italics_notation($text)
{
// Use preg_replace to find all instances of ~{something} and replace with just something
$converted_text = preg_replace('/~\{([^}]*)\}/', '$1', $text);

return $converted_text;
}
6 changes: 1 addition & 5 deletions resources/views/livewire/molecule-card.blade.php
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Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,7 @@
</div>
<div>
<h3 class="mt-1 text-base font-bold text-gray-900 capitalize text-clip overflow-hidden truncate ..." title="{{ $molecule->name }}">
@if ($molecule->name)
{{ $molecule->name }}
@else
{{ $molecule->iupac_name }}
@endif
{!! convert_italics_notation( $molecule->name ? $molecule->name : $molecule->iupac_name) !!}
</h3>
</div>
</div>
Expand Down
8 changes: 4 additions & 4 deletions resources/views/livewire/molecule-details.blade.php
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ class="lg:py-10 py-5 mx-auto max-w-3xl px-4 sm:px-6 md:flex md:items-center md:j
<p class="text-secondary-dark text-lg my-0">{{ $molecule->identifier }}</p>
<h1
class="mb-2 text-2xl break-all font-bold leading-7 break-words text-gray-900 sm:text-3xl sm:tracking-tight">
{{ $molecule->name ? $molecule->name : $molecule->iupac_name }}
{!! convert_italics_notation($molecule->name ? $molecule->name : $molecule->iupac_name) !!}
</h1>
<p class="text-sm font-medium text-gray-500">Created on <time
datetime="{{ $molecule->created_at }}">{{ $molecule->created_at }}</time> &middot; Last
Expand Down Expand Up @@ -252,7 +252,7 @@ class="text-sm font-medium text-gray-500 sm:flex sm:justify-between">
Name
</dt>
<div class="mt-1 break-all text-sm text-gray-900">
{{ $molecule->name ? $molecule->name : '-' }}
{!! convert_italics_notation($molecule->name ? $molecule->name : '-') !!}
<span class="float-end mr-2 group-hover:block hidden">
<livewire:copy-button text-to-copy="{{ $molecule->name }}" />
</span>
Expand All @@ -264,10 +264,10 @@ class="text-sm font-medium text-gray-500 sm:flex sm:justify-between">
IUPAC name
</dt>
<div class="mt-1 break-all text-sm text-gray-900">
{{ $molecule->iupac_name }}
{!! convert_italics_notation($molecule->iupac_name) !!}
<span class="float-end mr-2 group-hover:block hidden">
<livewire:copy-button
text-to-copy="{{ $molecule->iupac_name }}" />
text-to-copy="{{ remove_italics_notation($molecule->iupac_name) }}" />
</span>
</div>
</div>
Expand Down

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