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fix: updated molecule card and added counts to the molecules table
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@CS76
CS76 committed Jun 5, 2024
1 parent 2ce5b9d commit 4752a2e
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Showing 4 changed files with 206 additions and 29 deletions.
6 changes: 6 additions & 0 deletions database/migrations/2024_02_09_202858_create_molecules_table.php
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,12 @@ public function up(): void
$table->boolean('is_parent')->default(0);
$table->boolean('is_placeholder')->default(0);

$table->integer('organism_count')->default(0)->nullable();
$table->integer('geo_count')->default(0)->nullable();
$table->integer('citation_count')->default(0)->nullable();
$table->integer('collection_count')->default(0)->nullable();
$table->integer('synonym_count')->default(0)->nullable();

$table->json('comment')->nullable();

$table->timestamps();
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80 changes: 80 additions & 0 deletions resources/scripts/update-counts.sql
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@@ -0,0 +1,80 @@
CREATE TEMPORARY TABLE temp_organism_counts AS
SELECT
mo.molecule_id,
COUNT(mo.organism_id) AS organism_count
FROM
molecule_organism mo
GROUP BY
mo.molecule_id;

-- Then, update the molecules table using the temporary table
UPDATE molecules m
SET organism_count = toc.organism_count
FROM temp_organism_counts toc
WHERE m.id = toc.molecule_id;

-- Optionally, drop the temporary table if no longer needed
DROP TABLE temp_organism_counts;


-- First, create a temporary table to store the counts
CREATE TEMPORARY TABLE temp_geo_counts AS
SELECT
mgl.molecule_id,
COUNT(mgl.geo_location_id) AS geo_count
FROM
geo_location_molecule mgl
GROUP BY
mgl.molecule_id;

-- Then, update the molecules table using the temporary table
UPDATE molecules m
SET geo_count = tg.geo_count
FROM temp_geo_counts tg
WHERE m.id = tg.molecule_id;

-- Optionally, drop the temporary table if no longer needed
DROP TABLE temp_geo_counts;


-- First, create a temporary table to store the counts
CREATE TEMPORARY TABLE temp_collection_counts AS
SELECT
mc.molecule_id,
COUNT(mc.collection_id) AS collection_count
FROM
collection_molecule mc
GROUP BY
mc.molecule_id;

-- Then, update the molecules table using the temporary table
UPDATE molecules m
SET collection_count = tc.collection_count
FROM temp_collection_counts tc
WHERE m.id = tc.molecule_id;

-- Optionally, drop the temporary table if no longer needed
DROP TABLE temp_collection_counts;


-- First, create a temporary table to store the counts
CREATE TEMPORARY TABLE temp_citation_counts AS
SELECT
mc.citable_id,
COUNT(mc.citation_id) AS citation_count
FROM
citables mc
GROUP BY
mc.citable_id;

-- Then, update the molecules table using the temporary table
UPDATE molecules m
SET citation_count = tc.citation_count
FROM temp_citation_counts tc
WHERE m.id = tc.citable_id;

-- Optionally, drop the temporary table if no longer needed
DROP TABLE temp_citation_counts;

UPDATE molecules
SET synonym_count = json_array_length(synonyms);
137 changes: 114 additions & 23 deletions resources/views/livewire/molecule-card.blade.php
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Original file line number Diff line number Diff line change
@@ -1,31 +1,122 @@
<div class="bg-white rounded-lg hover:shadow-xl shadow border">
@if($molecule->identifier)
@if ($molecule->identifier)
<a href="{{ route('compound', $molecule->identifier) }}" wire:navigate>
<div class="group relative flex flex-col overflow-hidden">
<div class="aspect-h-3 aspect-w-3 sm:aspect-none group-hover:opacity-75 h-56">
<livewire:molecule-depict2d :smiles="$molecule->canonical_smiles">
<div class="group relative flex flex-col overflow-hidden">
<div class="aspect-h-3 aspect-w-3 sm:aspect-none group-hover:opacity-75 h-56">
<livewire:molecule-depict2d :smiles="$molecule->canonical_smiles">
</div>
<div class="flex flex-1 border-t flex-col p-4 pb-2">
<div class="flex items-center">
@for ($i = 0; $i < $molecule->annotation_level; $i++)
<span class="text-amber-300">★</span>
@endfor
@for ($i = $molecule->annotation_level; $i < 5; $i++)
☆
@endfor
</div>
<div class="flex flex-1 flex-col justify-end">
<p class="text-sm font-medium text-gray-500">{{ $molecule->identifier }}</p>
</div>
<h3 class="mt-1 text-base font-bold text-gray-900 capitalize truncate" title="{{ $molecule->name }}">
@if ($molecule->name)
{{ $molecule->name }}
@else
{{ $molecule->iupac_name }}
@endif
</h3>
</div>
</div>
<div class="flex flex-1 border-t flex-col p-4">
<div class="flex items-center">
@for ($i = 0; $i < $molecule->annotation_level; $i++)
<span class="text-amber-300">★<span>
@endfor
@for ($i = $molecule->annotation_level; $i < 5; $i++)
☆
@endfor
<div class="flex justify-around p-4 py-2 border-t mt-1">
<div class="flex-1 flex justify-center items-center text-xs" title="Organism Count">
<svg fill="currentColor" class="w-4 h-4 inline mr-1" version="1.1" id="Layer_1"
xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"
viewBox="0 0 512 512" xml:space="preserve">
<g>
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</g>
</g>
<g>
<g>
<path d="M174.55,256c-25.67,0-46.545,20.876-46.545,46.545s20.876,46.545,46.545,46.545c25.67,0,46.545-20.876,46.545-46.545
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</g>
</g>
</svg>
<span>{{ $molecule->organism_count }}</span>
</div>
<div class="flex-1 flex justify-center items-center text-xs" title="Collection Count">
<svg class="w-4 h-5 inline mr-1" viewBox="0 0 16 16" xmlns="http://www.w3.org/2000/svg"
fill="currentColor">
<path
d="M2.5 3.5a.5.5 0 0 1 0-1h11a.5.5 0 0 1 0 1h-11zm2-2a.5.5 0 0 1 0-1h7a.5.5 0 0 1 0 1h-7zM0 13a1.5 1.5 0 0 0 1.5 1.5h13A1.5 1.5 0 0 0 16 13V6a1.5 1.5 0 0 0-1.5-1.5h-13A1.5 1.5 0 0 0 0 6v7zm1.5.5A.5.5 0 0 1 1 13V6a.5.5 0 0 1 .5-.5h13a.5.5 0 0 1 .5.5v7a.5.5 0 0 1-.5.5h-13z" />
</svg>
<span>{{ $molecule->collection_count }}</span>
</div>
<div class="flex-1 flex justify-center items-center text-xs" title="Geo Count">
<svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5"
stroke="currentColor" class="w-4 h-4 inline mr-1">
<path stroke-linecap="round" stroke-linejoin="round"
d="M15 10.5a3 3 0 1 1-6 0 3 3 0 0 1 6 0Z" />
<path stroke-linecap="round" stroke-linejoin="round"
d="M19.5 10.5c0 7.142-7.5 11.25-7.5 11.25S4.5 17.642 4.5 10.5a7.5 7.5 0 1 1 15 0Z" />
</svg>
<span>{{ $molecule->geo_count }}</span>
</div>
<div class="flex flex-1 flex-col justify-end">
<p class="text-sm font-medium text-gray-500">{{ $molecule->identifier }}</p>
<div class="flex-1 flex justify-center items-center text-xs" title="Citation Count">
<svg class="w-auto h-3 inline mr-1" viewBox="0 0 16 16" xmlns="http://www.w3.org/2000/svg"
fill="currentColor">
<path fill-rule="evenodd"
d="M6 1h6v7a.5.5 0 0 1-.757.429L9 7.083 6.757 8.43A.5.5 0 0 1 6 8V1z" />
<path
d="M3 0h10a2 2 0 0 1 2 2v12a2 2 0 0 1-2 2H3a2 2 0 0 1-2-2v-1h1v1a1 1 0 0 0 1 1h10a1 1 0 0 0 1-1V2a1 1 0 0 0-1-1H3a1 1 0 0 0-1 1v1H1V2a2 2 0 0 1 2-2z" />
<path
d="M1 5v-.5a.5.5 0 0 1 1 0V5h.5a.5.5 0 0 1 0 1h-2a.5.5 0 0 1 0-1H1zm0 3v-.5a.5.5 0 0 1 1 0V8h.5a.5.5 0 0 1 0 1h-2a.5.5 0 0 1 0-1H1zm0 3v-.5a.5.5 0 0 1 1 0v.5h.5a.5.5 0 0 1 0 1h-2a.5.5 0 0 1 0-1H1z" />
</svg>
<span>{{ $molecule->citation_count }}</span>
</div>
<h3 class="mt-1 text-base font-bold text-gray-900 capitalize">
@if($molecule->name)
{{ $molecule->name }}
@else
{{ $molecule->iupac_name }}
@endif
</h3>
</div>
</div>
</a>
</a>
@endif
</div>
12 changes: 6 additions & 6 deletions resources/views/livewire/welcome.blade.php
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ class="rounded-md bg-secondary-dark px-3.5 py-1.5 text-base font-semibold leadin
<div class="mt-5 flex items-center gap-x-6">
<div>
<button type="button" onclick="Livewire.dispatch('openModal', { smiles: query })"
class="bg-gray-50 justify-center items-center text-center rounded-md text-gray-900 mr-1 py-3 px-4 text-gray-400 hover:bg-gray-500 hover:text-white focus:outline-none focus:ring-2 focus:ring-secondary-dark focus:ring-offset-2">
class="bg-gray-50 justify-center items-center text-center rounded-md text-gray-900 mr-1 py-3 px-4 hover:bg-gray-100 focus:outline-none focus:ring-2 focus:ring-secondary-dark focus:ring-offset-2">
<svg class="w-12 h-12 mx-auto" viewBox="0 0 78 78" fill="none"
xmlns="http://www.w3.org/2000/svg">
<g clip-path="url(#clip0_1_2)">
Expand Down Expand Up @@ -131,27 +131,27 @@ class="bg-gray-50 justify-center items-center text-center rounded-md text-gray-9
</clipPath>
</defs>
</svg>
<small class="text-base font-semibold leading-7 text-gray-900">Draw Structure</small>
<small class="text-base font-semibold leading-7">Draw Structure</small>
</button>
</div>
<a href="/search"
class="bg-gray-50 text-secondary justify-center items-center text-center rounded-md text-gray-900 mr-1 py-3 px-4 text-gray-400 hover:bg-gray-500 hover:text-gray-700 focus:outline-none focus:ring-2 focus:ring-secondary-dark focus:ring-offset-2">
class="bg-gray-50 justify-center items-center text-center rounded-md text-gray-900 mr-1 py-3 px-4 hover:bg-gray-100 focus:outline-none focus:ring-2 focus:ring-secondary-dark focus:ring-offset-2">
<svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24"
stroke-width="1.5" stroke="currentColor" class="w-12 h-12 mx-auto">
<path stroke-linecap="round" stroke-linejoin="round"
d="M3.75 6.75h16.5M3.75 12h16.5m-16.5 5.25H12" />
</svg>
<small class="text-base font-semibold leading-7 text-gray-900">Browse Data</small>
<small class="text-base font-semibold leading-7">Browse Data</small>
</button>
</a>
<a href="/admin/collections/create"
class="bg-gray-50 justify-center items-center text-center rounded-md text-gray-900 mr-1 py-3 px-4 text-gray-400 hover:bg-gray-500 hover:text-gray-700 focus:outline-none focus:ring-2 focus:ring-secondary-dark focus:ring-offset-2">
class="bg-gray-50 justify-center items-center text-center rounded-md text-gray-900 mr-1 py-3 px-4 hover:bg-gray-100 focus:outline-none focus:ring-2 focus:ring-secondary-dark focus:ring-offset-2">
<svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24"
stroke-width="1.5" stroke="currentColor" class="w-12 h-12 mx-auto">
<path stroke-linecap="round" stroke-linejoin="round"
d="M3 4.5h14.25M3 9h9.75M3 13.5h5.25m5.25-.75L17.25 9m0 0L21 12.75M17.25 9v12" />
</svg>
<small class="text-base font-semibold leading-7 text-gray-900">Submit Data</small>
<small class="text-base font-semibold leading-7">Submit Data</small>
</button>
</a>
</div>
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