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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,336 @@ | ||
| <?php | ||
|
|
||
| namespace App\Http\Controllers\API; | ||
|
|
||
| use App\Http\Controllers\Controller; | ||
| use App\Models\Molecule; | ||
| use Illuminate\Database\QueryException; | ||
| use Illuminate\Http\Request; | ||
| use Illuminate\Pagination\LengthAwarePaginator; | ||
| use Illuminate\Support\Facades\DB; | ||
|
|
||
| class SearchController extends Controller | ||
| { | ||
| /** | ||
| * Search DB based on the query and filter parameters | ||
| * | ||
| * @return \Illuminate\Http\Response | ||
| */ | ||
|
|
||
| /** | ||
| * @OA\Post( | ||
| * path="/api/v1/search", | ||
| * summary="Get compound details by Compound name, SMILES, InChi & InChiKey.", | ||
| * description="Get compound details by Compound name, SMILES, InChi & InChiKey.", | ||
| * operationId="search", | ||
| * tags={"search"}, | ||
| * | ||
| * @OA\RequestBody( | ||
| * required=true, | ||
| * description="Pass search query and type such as InChiKey, InChi, SMILES & text", | ||
| * | ||
| * @OA\JsonContent( | ||
| * required={"query","type"}, | ||
| * | ||
| * @OA\Property(property="query", type="string", format="query", example="AAAAWQOPBUPWEV-UHFFFAOYSA-N"), | ||
| * @OA\Property(property="type", type="string", format="type", example="InChiKey"), | ||
| * | ||
| * ), | ||
| * | ||
| * ), | ||
| * | ||
| * @OA\Response( | ||
| * response=200, | ||
| * description="Successful Operation" | ||
| * ), | ||
| * @OA\Response( | ||
| * response=404, | ||
| * description="Not Found" | ||
| * ) | ||
| * ) | ||
| */ | ||
| public function search(Request $request) | ||
| { | ||
| try { | ||
| set_time_limit(300); | ||
|
|
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| $queryType = 'text'; | ||
| $results = []; | ||
|
|
||
| //dd($request); | ||
|
|
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| $limit = $request->query('limit'); | ||
| $sort = $request->query('sort'); | ||
| $limit = $limit ? $limit : 24; | ||
| $page = $request->query('page'); | ||
| $tagType = $request->get('tagType') ? $request->get('tagType') : null; | ||
|
|
||
| $offset = | ||
| (($page != null && $page != 'null' && $page != 0 ? $page : 1) - | ||
| 1) * | ||
| $limit; | ||
|
|
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| $query = $request->get('query'); | ||
|
|
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| $type = $request->query('type') | ||
| ? $request->query('type') | ||
| : $request->get('type'); | ||
|
|
||
| if ($type) { | ||
| $queryType = $type; | ||
| } else { | ||
| //inchi | ||
| $re = | ||
| '/^((InChI=)?[^J][0-9BCOHNSOPrIFla+\-\(\)\\\\\/,pqbtmsih]{6,})$/i'; | ||
| preg_match_all($re, $query, $imatches, PREG_SET_ORDER, 0); | ||
|
|
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| if (count($imatches) > 0 && substr($query, 0, 6) == 'InChI=') { | ||
| $queryType = 'inchi'; | ||
| } | ||
|
|
||
| //inchikey | ||
| $re = '/^([0-9A-Z\-]+)$/i'; | ||
| preg_match_all($re, $query, $ikmatches, PREG_SET_ORDER, 0); | ||
| if ( | ||
| count($ikmatches) > 0 && | ||
| substr($query, 14, 1) == '-' && | ||
| strlen($query) == 27 | ||
| ) { | ||
| $queryType = 'inchikey'; | ||
| } | ||
|
|
||
| // smiles | ||
| $re = '/^([^J][0-9BCOHNSOPrIFla@+\-\[\]\(\)\\\\\/%=#$]{6,})$/i'; | ||
| preg_match_all($re, $query, $matches, PREG_SET_ORDER, 0); | ||
|
|
||
| if (count($matches) > 0 && substr($query, 14, 1) != '-') { | ||
| $queryType = 'smiles'; | ||
| } | ||
| } | ||
|
|
||
| $filterMap = [ | ||
| 'mf' => 'molecular_formula', | ||
|
|
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| 'mw' => 'molecular_weight', | ||
| 'hac' => 'heavy_atom_count', | ||
| 'tac' => 'total_atom_count', | ||
|
|
||
| 'arc' => 'aromatic_ring_count', | ||
| 'rbc' => 'rotatable_bond_count', | ||
| 'mrc' => 'minimal_number_of_rings', | ||
| 'fc' => 'formal_charge', | ||
| 'cs' => 'contains_sugar', | ||
| 'crs' => 'contains_ring_sugars', | ||
| 'cls' => 'contains_linear_sugars', | ||
|
|
||
| 'npl' => 'np_likeness_score', | ||
| 'alogp' => 'alogp', | ||
| 'topopsa' => 'topo_psa', | ||
| 'fsp3' => 'fsp3', | ||
| 'hba' => 'h_bond_acceptor_count', | ||
| 'hbd' => 'h_bond_donor_count', | ||
| 'ro5v' => 'rule_of_5_violations', | ||
| 'lhba' => 'lipinski_h_bond_acceptor_count', | ||
| 'lhbd' => 'lipinski_h_bond_donor_count', | ||
| 'lro5v' => 'lipinski_rule_of_5_violations', | ||
| 'ds' => 'found_in_databases', | ||
|
|
||
| 'class' => 'chemical_class', | ||
| 'subclass' => 'chemical_sub_class', | ||
| 'superclass' => 'chemical_super_class', | ||
| 'parent' => 'direct_parent_classification', | ||
|
|
||
| ]; | ||
|
|
||
| $queryType = strtolower($queryType); | ||
|
|
||
| $statement = null; | ||
|
|
||
| if ($queryType == 'smiles' || $queryType == 'substructure') { | ||
| $statement = | ||
| "select id, COUNT(*) OVER () from mols where m@>'". | ||
| $query. | ||
| "' limit ". | ||
| $limit. | ||
| ' offset '. | ||
| $offset; | ||
| } elseif ($queryType == 'inchi') { | ||
| $statement = | ||
| "select id, COUNT(*) OVER () from molecules WHERE identifier NOTNULL AND standard_inchi LIKE '%". | ||
| $query. | ||
| "%' limit ". | ||
| $limit. | ||
| ' offset '. | ||
| $offset; | ||
| } elseif ($queryType == 'inchikey') { | ||
| $statement = | ||
| "select id, COUNT(*) OVER () from molecules WHERE identifier NOTNULL AND standard_inchi_key LIKE '%". | ||
| $query. | ||
| "%' limit ". | ||
| $limit. | ||
| ' offset '. | ||
| $offset; | ||
| } elseif ($queryType == 'exact') { | ||
| $statement = | ||
| "select id, COUNT(*) OVER () from mols where m@='". | ||
| $query. | ||
| "' limit ". | ||
| $limit. | ||
| ' offset '. | ||
| $offset; | ||
| } elseif ($queryType == 'similarity') { | ||
| $statement = | ||
| "select id, COUNT(*) OVER () from fps where mfp2%morganbv_fp('". | ||
| $query. | ||
| "') limit ". | ||
| $limit. | ||
| ' offset '. | ||
| $offset; | ||
| } elseif ($queryType == 'tags') { | ||
| $results = Molecule::withAnyTags([$query], $tagType)->paginate($limit)->items(); | ||
| $count = Molecule::withAnyTags([$query], $tagType)->count(); | ||
| } elseif ($queryType == 'filters') { | ||
| $orConditions = explode('OR', $query); | ||
| $isORInitial = true; | ||
| $statement = | ||
| 'select molecule_id as id, COUNT(*) OVER () from properties where '; | ||
| foreach ($orConditions as $orCondition) { | ||
| if ($isORInitial === false) { | ||
| $statement = $statement.' OR '; | ||
| } | ||
| $isORInitial = false; | ||
| $statement = $statement.'('; | ||
| $andConditions = explode(' ', trim($orCondition, ' ')); | ||
| $isANDInitial = true; | ||
| foreach ($andConditions as $andCondition) { | ||
| if ($isANDInitial === false) { | ||
| $statement = $statement.' AND '; | ||
| } | ||
| $isANDInitial = false; | ||
| $_filter = explode(':', $andCondition); | ||
| if (str_contains($_filter[1], '..')) { | ||
| $range = array_values(explode('..', $_filter[1])); | ||
| $statement = | ||
| $statement. | ||
| '('. | ||
| $filterMap[$_filter[0]]. | ||
| ' between '. | ||
| $range[0]. | ||
| ' and '. | ||
| $range[1]. | ||
| ')'; | ||
| } elseif ( | ||
| $_filter[1] === 'true' || | ||
| $_filter[1] === 'false' | ||
| ) { | ||
| $statement = | ||
| $statement. | ||
| '('. | ||
| $filterMap[$_filter[0]]. | ||
| ' = '. | ||
| $_filter[1]. | ||
| ')'; | ||
| } elseif (str_contains($_filter[1], '|')) { | ||
| $dbFilters = explode('|', $_filter[1]); | ||
| $dbs = explode('+', $dbFilters[0]); | ||
| $statement = | ||
| $statement. | ||
| '('. | ||
| $filterMap[$_filter[0]]. | ||
| " @> '[\"". | ||
| implode('","', $dbs). | ||
| "\"]')"; | ||
| } else { | ||
| if (str_contains($_filter[1], '+')) { | ||
| $_filter[1] = str_replace('+', ' ', $_filter[1]); | ||
| } | ||
| $statement = | ||
| $statement. | ||
| '('.$filterMap[$_filter[0]].'::TEXT ILIKE \'%'.$_filter[1].'%\')'; | ||
| } | ||
| } | ||
| $statement = $statement.')'; | ||
| } | ||
| $statement = $statement.' LIMIT '.$limit; | ||
| // dd($statement ); | ||
| } else { | ||
| if ($query) { | ||
| $query = str_replace("'", "''", $query); | ||
| $statement = | ||
| "select id, COUNT(*) OVER () from molecules WHERE identifier NOTNULL AND (\"name\"::TEXT ILIKE '%". | ||
| $query. | ||
| "%') OR (\"synonyms\"::TEXT ILIKE '%". | ||
| $query. | ||
| "%') OR (\"identifier\"::TEXT ILIKE '%". | ||
| $query. | ||
| "%') limit ". | ||
| $limit. | ||
| ' offset '. | ||
| $offset; | ||
| } else { | ||
| $statement = | ||
| 'select id, COUNT(*) OVER () from mols limit '. | ||
| $limit. | ||
| ' offset '. | ||
| $offset; | ||
| } | ||
| } | ||
| if ($statement) { | ||
| $expression = DB::raw($statement); | ||
| $qString = $expression->getValue( | ||
| DB::connection()->getQueryGrammar() | ||
| ); | ||
|
|
||
| $hits = DB::select($qString); | ||
|
|
||
| $count = count($hits) > 0 ? $hits[0]->count : 0; | ||
|
|
||
| $ids = implode( | ||
| ',', | ||
| collect($hits) | ||
| ->pluck('id') | ||
| ->toArray() | ||
| ); | ||
|
|
||
| if ($ids != '') { | ||
| $statement = | ||
| 'SELECT * FROM molecules WHERE identifier NOTNULL AND ID IN ('. | ||
| implode( | ||
| ',', | ||
| collect($hits) | ||
| ->pluck('id') | ||
| ->toArray() | ||
| ). | ||
| ')'; | ||
| if ($sort == 'recent') { | ||
| $statement = $statement.' ORDER BY created_at DESC'; | ||
| } | ||
| $expression = DB::raw($statement); | ||
| $string = $expression->getValue( | ||
| DB::connection()->getQueryGrammar() | ||
| ); | ||
| $results = DB::select($string); | ||
| } else { | ||
| $results = []; | ||
| $count = 0; | ||
| } | ||
| } | ||
| $pagination = new LengthAwarePaginator( | ||
| $results, | ||
| $count, | ||
| $limit, | ||
| $page | ||
| ); | ||
|
|
||
| //dd($pagination); | ||
| return $pagination; | ||
| } catch (QueryException $exception) { | ||
| return response()->json( | ||
| [ | ||
| 'message' => $exception->getMessage(), | ||
| ], | ||
| 500 | ||
| ); | ||
| } | ||
| } | ||
| } |
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