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fix: added search history, collection url resolution bug fix, chemica…
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…l classes issue fix
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@CS76
CS76 committed Dec 11, 2024
1 parent 467de00 commit 9d520a3
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Showing 4 changed files with 162 additions and 73 deletions.
38 changes: 38 additions & 0 deletions app/Http/Controllers/CollectionController.php
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Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
<?php

namespace App\Http\Controllers;

use App\Models\Collection;
use Cache;
use Illuminate\Http\Request;

class CollectionController extends Controller
{
/**
* Handle the incoming request.
*/
public function __invoke(Request $request, $id)
{
if (! str_starts_with($id, 'CNPC')) {
abort(404);
}

$collection = Cache::remember('collections.'.$id, 172800, function () use ($id) {
return Collection::where('identifier', $id)->first();
});

if (! $collection) {
abort(404);
}

$query = [
'type' => 'tags',
'q' => urlencode($collection->title),
'tagType' => 'dataSource',
];

$baseUrl = config('app.url');

return redirect()->to($baseUrl.'/search?'.http_build_query($query));
}
}
4 changes: 0 additions & 4 deletions app/Models/Properties.php
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Original file line number Diff line number Diff line change
Expand Up @@ -60,10 +60,6 @@ class Properties extends Model implements Auditable
* @var array
*/
protected $casts = [
'chemical_class' => 'array',
'chemical_sub_class' => 'array',
'chemical_super_class' => 'array',
'direct_parent_classification' => 'array',
'pathway_results' => 'array',
'superclass_results' => 'array',
'class_results' => 'array',
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189 changes: 120 additions & 69 deletions resources/views/livewire/structure-editor.blade.php
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
smiles: @entangle('smiles'),
type: @entangle('type'),
draggedFile: null,
recentSearches: JSON.parse(localStorage.getItem('recentSearches') || '[]'),
fetchClipboardText() {
navigator.clipboard.readText().then(text => {
window.editor.setSmiles(text);
Expand All @@ -18,7 +19,7 @@
const allowedExtensions = ['.mol', '.sdf'];
const fileExtension = '.' + file.name.split('.').pop().toLowerCase();
if (!allowedExtensions.includes(fileExtension)) {
alert('Only .mol and .sdf files are allowed');
return;
Expand All @@ -35,8 +36,28 @@
}
};
reader.readAsText(file);
},
performSearch() {
const smiles = window.getEditorSmiles();
const query = { type: this.type, q: smiles };
this.recentSearches.push(query);
this.recentSearches = Array.from(
new Map(this.recentSearches.map(item => [item.q, item])).values()
);
localStorage.setItem('recentSearches', JSON.stringify(this.recentSearches));
window.location.href = `/search?type=${this.type}&q=${encodeURIComponent(smiles)}`;
},
deleteSearch(index) {
this.recentSearches.splice(index, 1);
localStorage.setItem('recentSearches', JSON.stringify(this.recentSearches));
},
loadSearch(search) {
this.type = search.type;
window.editor.setSmiles(search.q);
}
}" >
}">
<div x-init="$watch('isOpen', value => {
if (value) {
setTimeout(() => {
Expand All @@ -50,90 +71,120 @@
});">
<div x-show="isOpen" x-cloak class="fixed z-20 inset-0 overflow-y-auto" aria-labelledby="modal-title" role="dialog"
aria-modal="true">
<div class="flex items-end justify-center min-h-screen pt-4 px-4 pb-20 text-center sm:block sm:p-0">
<div class="flex items-center justify-center min-h-screen text-center px-8">
<div class="fixed inset-0 bg-gray-500 bg-opacity-75 transition-opacity" aria-hidden="true"></div>

<!-- This element is to trick the browser into centering the modal contents. -->
<span class="hidden sm:inline-block sm:align-middle sm:h-screen" aria-hidden="true">&#8203;</span>
<div
class="z-20 inline-block align-bottom bg-white rounded-lg px-4 pt-5 pb-4 text-left overflow-hidden shadow-xl transform transition-all sm:my-8 sm:align-middle sm:max-w-lg sm:w-full sm:p-6">
class="z-20 inline-block align-bottom bg-white rounded-lg px-4 pt-5 pb-4 text-left overflow-hidden shadow-xl transform transition-all sm:my-8 sm:align-middle sm:w-full sm:p-6">
<div class="sm:flex sm:items-start">
<div class="mt-3 text-center sm:mt-0 sm:text-left w-full">
<h3 class="text-lg leading-6 font-medium text-gray-900" id="modal-title">
Structure Editor
</h3>
<div class="py-3">
<div
x-on:dragover.prevent="draggedFile = null"
x-on:drop.prevent="draggedFile = $event.dataTransfer.files[0]; handleFileUpload($event)"
class="border-2 border-dashed border-gray-300 p-6 text-center mb-3"
>
<input
type="file"
accept=".mol,.sdf"
class="hidden"
id="fileUpload"
x-on:change="handleFileUpload($event)"
/>
<label for="fileUpload" class="cursor-pointer">
<p class="text-gray-600">Drag and drop .mol or .sdf files here</p>
<p class="text-sm text-gray-500 mt-2">Or click to select a file</p>
</label>
</div>
<div id="structureSearchEditor" class="border mb-3" style="height: 400px; width: 100%">
</div>
<div
@click="fetchClipboardText"
class="hover:cursor-pointer w-full text-center rounded-md shadow-sm px-4 py-2 bg-white-600 text-base font-medium hover:bg-white-700 focus:outline-none sm:w-auto sm:text-sm border"
>
Paste from Clipboard
</div>
</div>
<fieldset class="mt-1">
<legend class="contents text-base font-medium text-gray-900">
Select search type
</legend>
<div class="mt-4 space-y-4">
<div class="flex items-center">
<label for="search-type-exact"
class="block cursor-pointer text-sm font-medium text-gray-700">
<input id="search-type-exact" name="search-type" x-model="type"
value="exact" type="radio"
class="mr-3 h-4 w-4 border-gray-300 text-secondary-dark focus:ring-secondary-dark" />
Exact match
</label>
<div class="grid grid-cols-1 sm:grid-cols-2 gap-6">
<div class="my-4">
<div id="structureSearchEditor" class="border mb-3"
style="height: 400px; width: 100%">
</div>
<div class="flex items-center">
<label for="search-type-sub"
class="block cursor-pointer text-sm font-medium text-gray-700">
<input id="search-type-sub" name="search-type" x-model="type"
value="substructure" type="radio"
class="mr-3 h-4 w-4 border-gray-300 text-secondary-dark focus:ring-secondary-dark" />
Substructure Search
</label>
<div class="py-3">
<div x-on:dragover.prevent="draggedFile = null"
x-on:drop.prevent="draggedFile = $event.dataTransfer.files[0]; handleFileUpload($event)"
class="border-2 border-dashed border-gray-300 p-6 text-center mb-3">
<input type="file" accept=".mol,.sdf" class="hidden" id="fileUpload"
x-on:change="handleFileUpload($event)" />
<label for="fileUpload" class="cursor-pointer">
<p class="text-gray-600">Drag and drop .mol or .sdf files here</p>
<p class="text-sm text-gray-500 mt-2">Or click to select a file</p>
</label>
</div>
<div @click="fetchClipboardText"
class="hover:cursor-pointer w-full text-center rounded-md shadow-sm px-4 py-2 bg-white-600 text-base font-medium hover:bg-white-700 focus:outline-none sm:w-auto sm:text-sm border">
Paste from Clipboard
</div>
</div>
<div class="flex items-center">
<label for="search-type-similar"
class="block cursor-pointer text-sm font-medium text-gray-700">
<input id="search-type-similar" name="search-type" x-model="type"
value="similarity" type="radio"
class="mr-3 h-4 w-4 border-gray-300 text-secondary-dark focus:ring-secondary-dark" />
Similarity Search (tanimoto_threshold=0.5)
</label>
</div>
<div>
<fieldset class="mt-1">
<legend class="contents text-base font-medium text-gray-900">
Select search type
</legend>
<div class="mt-4 space-y-4">
<div class="flex items-center">
<label for="search-type-exact"
class="block cursor-pointer text-sm font-medium text-gray-700">
<input id="search-type-exact" name="search-type" x-model="type"
value="exact" type="radio"
class="mr-3 h-4 w-4 border-gray-300 text-secondary-dark focus:ring-secondary-dark" />
Exact match
</label>
</div>
<div class="flex items-center">
<label for="search-type-sub"
class="block cursor-pointer text-sm font-medium text-gray-700">
<input id="search-type-sub" name="search-type" x-model="type"
value="substructure" type="radio"
class="mr-3 h-4 w-4 border-gray-300 text-secondary-dark focus:ring-secondary-dark" />
Substructure Search
</label>
</div>
<div class="flex items-center">
<label for="search-type-similar"
class="block cursor-pointer text-sm font-medium text-gray-700">
<input id="search-type-similar" name="search-type" x-model="type"
value="similarity" type="radio"
class="mr-3 h-4 w-4 border-gray-300 text-secondary-dark focus:ring-secondary-dark" />
Similarity Search (tanimoto_threshold=0.5)
</label>
</div>
</div>
</fieldset>
<div class="mt-6">
<h3 class="contents text-base font-medium text-gray-900">Previous searches</h3>
<ul class="mt-2">
<div class="grid grid-cols-2 gap-2">
<template x-for="(search, index) in recentSearches"
:key="index">
<div>
<div
class="group relative flex flex-col overflow-hidden rounded-lg border border-gray-200 bg-white">
<span class="cursor-pointer" @click="loadSearch(search)">
<img :src="`https://api.cheminf.studio/latest/depict/2D?smiles=${search.q}&height=300&width=300&CIP=true&toolkit=cdk`"
alt="Molecule Structure"
class="object-cover sm:h-36 sm:w-36 mx-auto my-2">
<div
class="flex flex-1 flex-col space-y-2 p-4 border-t">
<span x-text="`${search.type}`"
class="float rounded-lg pt-0.5 text-xs/6 font-semibold whitespace-nowrap text-slate-700">
</span>
<p x-text="`${search.q}`"
class="text-sm text-gray-500 truncate pt-0">
</p>

</div>
</span>
<button @click="deleteSearch(index)"
class="p-2 border-t text-red-600 hover:text-red-700 text-sm font-medium hover:underline">
Delete
</button>
</div>

</div>

</template>
</div>
</ul>
</div>
</div>
</fieldset>
</div>
</div>
</div>
<div class="mt-5 sm:mt-4 sm:flex sm:flex-row-reverse">
<div class="mt-2 sm:mt-4 sm:flex sm:flex-row-reverse border-t pt-3 px-6 -mx-6">
<button @click="isOpen = false" type="button"
class="mt-3 w-full inline-flex justify-center rounded-md border border-transparent shadow-sm px-4 py-2 bg-red-600 text-base font-medium text-white hover:bg-red-700 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-red-500 sm:mt-0 sm:ml-3 sm:w-auto sm:text-sm">
class="w-full inline-flex justify-center rounded-md border border-transparent shadow-sm px-4 py-2 bg-red-600 text-base font-medium text-white hover:bg-red-700 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-red-500 sm:mt-0 sm:ml-3 sm:w-auto sm:text-sm">
Close
</button>
<button
@click="const smiles = window.getEditorSmiles(); window.location.href = `/search?type=${type}&q=${encodeURIComponent(smiles)}`"
type="button"
class="mt-3 w-full inline-flex justify-center rounded-md border border-transparent shadow-sm px-4 py-2 bg-blue-600 text-base font-medium text-white hover:bg-blue-700 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-blue-500 sm:mt-0 sm:ml-3 sm:w-auto sm:text-sm">
<button @click="performSearch()" type="button"
class="w-full inline-flex justify-center rounded-md border border-transparent shadow-sm px-4 py-2 bg-blue-600 text-base font-medium text-white hover:bg-blue-700 focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-blue-500 sm:mt-0 sm:ml-3 sm:w-auto sm:text-sm">
Search
</button>
</div>
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4 changes: 4 additions & 0 deletions routes/web.php
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

use App\Http\Controllers\ApplicationController;
use App\Http\Controllers\Auth\SocialController;
use App\Http\Controllers\CollectionController;
use App\Http\Controllers\MoleculeController;
use App\Livewire\About;
use App\Livewire\CollectionList;
Expand Down Expand Up @@ -45,4 +46,7 @@
// Compound pages
Route::get('compound/coconut_id/{id}', MoleculeController::class)->name('old_compound');
Route::get('compounds/{id}', MoleculeController::class)->name('compound');

Route::get('collections/{id}', CollectionController::class)->name('collection');

Route::get('/search', Search::class)->name('browse');

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