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feat(api): expose organism associations on molecules REST resource #794

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3 changes: 3 additions & 0 deletions app/Rest/Resources/MoleculeResource.php
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
use App\Rest\Resource as RestResource;
use Illuminate\Database\Eloquent\Model;
use Lomkit\Rest\Http\Requests\RestRequest;
use Lomkit\Rest\Relations\BelongsToMany;
use Lomkit\Rest\Relations\HasOne;

class MoleculeResource extends RestResource
Expand Down Expand Up @@ -37,6 +38,7 @@ public function fields(RestRequest $request): array
'name_trust_level',
'annotation_level',
'variants_count',
'organism_count',

'status',
'active',
Expand All @@ -55,6 +57,7 @@ public function relations(RestRequest $request): array
{
return [
HasOne::make('properties', PropertiesResource::class),
BelongsToMany::make('organisms', OrganismResource::class),
];
}

Expand Down
31 changes: 30 additions & 1 deletion docs/api-documentation.md
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Expand Up @@ -93,7 +93,7 @@ Search Molecules using various attributes. There are two tables invovled in this

#### Searchable fields
::: info molecules
'standard_inchi', 'standard_inchi_key', 'canonical_smiles', 'sugar_free_smiles', 'identifier', 'name', 'cas', 'iupac_name', 'murko_framework', 'structural_comments', 'name_trust_level', 'annotation_level', 'variants_count', 'status', 'active', 'has_variants', 'has_stereo', 'is_tautomer', 'is_parent', 'is_placeholder'
'standard_inchi', 'standard_inchi_key', 'canonical_smiles', 'sugar_free_smiles', 'identifier', 'name', 'cas', 'iupac_name', 'murko_framework', 'structural_comments', 'name_trust_level', 'annotation_level', 'variants_count', 'organism_count', 'status', 'active', 'has_variants', 'has_stereo', 'is_tautomer', 'is_parent', 'is_placeholder'
:::
::: info properties
'total_atom_count', 'heavy_atom_count', 'molecular_weight', 'exact_molecular_weight', 'molecular_formula', 'alogp', 'topological_polar_surface_area', 'rotatable_bond_count', 'hydrogen_bond_acceptors', 'hydrogen_bond_donors', 'hydrogen_bond_acceptors_lipinski', 'hydrogen_bond_donors_lipinski', 'lipinski_rule_of_five_violations', 'aromatic_rings_count', 'qed_drug_likeliness', 'formal_charge', 'fractioncsp3', 'number_of_minimal_rings', 'van_der_walls_volume', 'contains_sugar', 'contains_ring_sugars', 'contains_linear_sugars', 'murcko_framework', 'np_likeness', 'chemical_class', 'chemical_sub_class', 'chemical_super_class', 'direct_parent_classification', 'np_classifier_pathway', 'np_classifier_superclass', 'np_classifier_class', 'np_classifier_is_glycoside'
Expand All @@ -103,6 +103,35 @@ Search Molecules using various attributes. There are two tables invovled in this
The fields in the *molecules* table can be accessed directly with their column names. The fields in the *properties* table are to be accessed prefixing them with the table name. Ex: **properties.field-name**.
:::

#### Includable relations
::: info relations
'properties', 'organisms'
:::

Use the `includes` array in the search request to load related records. For example, to include organisms reported for a molecule:

**Request Body Example with organisms (application/json):**
```json
{
"search": {
"filters": [
{
"field": "identifier",
"operator": "=",
"value": "CNP0228556.0"
}
],
"includes": [
{
"relation": "organisms"
}
]
}
}
```

Each included organism exposes: `name`, `iri`, `rank`, `molecule_count`.


**Request Body Example (application/json):**
```json
Expand Down
153 changes: 134 additions & 19 deletions public/vendor/rest/openapi.json
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@
"name_trust_level",
"annotation_level",
"variants_count",
"organism_count",
"status",
"active",
"has_variants",
Expand All @@ -73,6 +74,17 @@
"prohibited_on_update": false
},
"name": "HasOne"
},
{
"resource": "App\\Rest\\Resources\\OrganismResource",
"relation": "organisms",
"constraints": {
"required_on_creation": false,
"prohibited_on_creation": false,
"required_on_update": false,
"prohibited_on_update": false
},
"name": "BelongsToMany"
}
],
"rules": {
Expand Down Expand Up @@ -224,6 +236,11 @@
"operator": "=",
"value": ""
},
{
"field": "organism_count",
"operator": "=",
"value": ""
},
{
"field": "status",
"operator": "=",
Expand Down Expand Up @@ -313,6 +330,10 @@
"field": "variants_count",
"direction": "desc"
},
{
"field": "organism_count",
"direction": "desc"
},
{
"field": "status",
"direction": "desc"
Expand Down Expand Up @@ -382,6 +403,9 @@
{
"field": "variants_count"
},
{
"field": "organism_count"
},
{
"field": "status"
},
Expand All @@ -407,6 +431,9 @@
"includes": [
{
"relation": "properties"
},
{
"relation": "organisms"
}
],
"aggregates": [],
Expand Down Expand Up @@ -476,6 +503,7 @@
"name_trust_level": "",
"annotation_level": "",
"variants_count": "",
"organism_count": "",
"status": "",
"active": "",
"has_variants": "",
Expand All @@ -488,6 +516,10 @@
"properties": {
"operation": "update",
"key": 1
},
"organisms": {
"operation": "update",
"key": 1
}
}
}
Expand Down Expand Up @@ -629,9 +661,9 @@
"application\/json": {
"example": {
"data": {
"title": "Est consectetur labore ut.",
"description": "Distinctio assumenda eum itaque veritatis in aut. Rem aut exercitationem occaecati rerum quo. Illo veritatis aut non non. Quia ipsum doloribus fugiat vel corrupti fugit quasi.",
"url": "http:\/\/crooks.com\/",
"title": "Vero velit sint aut voluptatum.",
"description": "Saepe omnis ut corrupti placeat iure provident. Accusamus dolorem tenetur consequuntur sed. Aut sunt voluptates incidunt qui omnis.",
"url": "http:\/\/tillman.info\/dolorem-assumenda-dolores-ad-odio.html",
"identifier": null
},
"meta": []
Expand Down Expand Up @@ -674,10 +706,10 @@
"application\/json": {
"example": {
"data": {
"title": "Et alias rerum incidunt et.",
"description": "Libero nesciunt placeat magnam sint. Ut in voluptas consequatur. Laborum aspernatur sint ut optio. Voluptatem illo distinctio culpa laborum.",
"url": "http:\/\/kutch.com\/ab-voluptatem-consequatur-minus-voluptas-repudiandae-perferendis",
"identifier": null
"title": "Enim ratione enim accusantium quia.",
"description": "Temporibus sit eum qui sint sequi ratione dolorem. Esse eum cupiditate quis quasi cum et. Qui eius voluptas amet autem accusamus.",
"url": "https:\/\/www.grady.net\/id-commodi-ratione-aut-iste-ducimus-mollitia-aut-eos",
"identifier": "Sint et repudiandae et earum et itaque ratione."
},
"meta": []
}
Expand Down Expand Up @@ -946,9 +978,9 @@
"application\/json": {
"example": {
"data": {
"doi": "10.1016\/j.bbrep.2025.102032~58",
"title": "RNA signaling in medicinal plants: An overlooked mechanism for phytochemical regulation.",
"authors": "Alum EU, Udechukwu CD, Obasi DC.",
"doi": "10.1038\/s41598-026-45889-0~78",
"title": "The impact of herbal medicine development on the population health in China.",
"authors": "Wang Y, Zheng X, Masron TA.",
"citation_text": ""
},
"meta": []
Expand Down Expand Up @@ -991,9 +1023,9 @@
"application\/json": {
"example": {
"data": {
"doi": "10.1039\/b700306b~29",
"title": "Natural product isolation.",
"authors": "Sticher O.",
"doi": "10.1016\/j.jaim.2026.101328~60",
"title": "The Delhi Declaration on Traditional Medicine: Outcome of the Second WHO Global Summit on Traditional Medicine (2025).",
"authors": null,
"citation_text": ""
},
"meta": []
Expand Down Expand Up @@ -1568,8 +1600,8 @@
"application\/json": {
"example": {
"data": {
"name": "Annabel Medhurst",
"email": "veum.adolphus@example.com"
"name": "Grayce Bauch",
"email": "pabernathy@example.org"
},
"meta": []
}
Expand Down Expand Up @@ -1611,8 +1643,8 @@
"application\/json": {
"example": {
"data": {
"name": "Dr. Gonzalo Simonis II",
"email": "ssimonis@example.net"
"name": "Cathy Boyer",
"email": "hand.octavia@example.com"
},
"meta": []
}
Expand Down Expand Up @@ -2535,7 +2567,8 @@
"title",
"evidence",
"comment",
"suggested_changes"
"suggested_changes",
"mol_ids"
],
"scout_fields": [],
"limits": [
Expand Down Expand Up @@ -2654,6 +2687,11 @@
"field": "suggested_changes",
"operator": "=",
"value": ""
},
{
"field": "mol_ids",
"operator": "=",
"value": ""
}
],
"sorts": [
Expand All @@ -2668,6 +2706,10 @@
{
"field": "comment",
"direction": "desc"
},
{
"field": "mol_ids",
"direction": "desc"
}
],
"selects": [
Expand All @@ -2682,6 +2724,9 @@
},
{
"field": "suggested_changes"
},
{
"field": "mol_ids"
}
],
"includes": [],
Expand Down Expand Up @@ -2742,7 +2787,8 @@
"title": "",
"evidence": "",
"comment": "",
"suggested_changes": ""
"suggested_changes": "",
"mol_ids": ""
},
"relations": []
}
Expand Down Expand Up @@ -3063,6 +3109,75 @@
}
}
}
},
"\/api\/auth\/verify\/{user_id}": {
"get": {
"tags": [
"Authentication"
],
"summary": "Email verification endpoint",
"responses": {
"default": {
"description": "Email verification successful and redirected",
"headers": {
"Location": {
"description": "URL to redirect to",
"schema": {
"type": "string"
}
},
"Http-Response-Code": {
"description": "HTTP Response Code",
"schema": {
"type": "integer"
}
}
}
},
"\"401\"": {
"description": "Invalid\/Expired URL provided"
}
},
"requestBody": {
"content": {
"application\/json": {
"example": {
"user": {
"id": "example_user_id",
"name": "example_name",
"email": "example_email",
"password": "example_password"
},
"signature": "example_signature"
}
}
},
"description": "User object and Request Signature"
},
"security": [
{
"sanctum": []
}
]
}
},
"\/api\/auth\/email\/resend": {
"get": {
"tags": [
"Authentication"
],
"summary": "Resend email verification endpoint",
"responses": {
"default": {
"description": "Email verification link sent to your email address"
}
},
"security": [
{
"sanctum": []
}
]
}
}
},
"servers": [
Expand Down
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