diff --git a/.env.example b/.env.example index 8d59baba..befea717 100644 --- a/.env.example +++ b/.env.example @@ -86,3 +86,7 @@ CSP_ENABLED_WHILE_HOT_RELOADING=false # External Services for CSP # TAWK_URL: URL for Tawk.to live chat widget. Add the widget's domain here if you use Tawk.to and need to allow it in your Content Security Policy. TAWK_URL= + +CAS_KEY= +CAS_BASE_URL=https://commonchemistry.cas.org/direct-api +CAS_ORIGIN=https://commonchemistry.cas.org/api-overview diff --git a/app/Console/Commands/SubmissionsAutoProcess/FetchCASNumbersAuto.php b/app/Console/Commands/SubmissionsAutoProcess/FetchCASNumbersAuto.php index 1b842ec6..c58826b2 100644 --- a/app/Console/Commands/SubmissionsAutoProcess/FetchCASNumbersAuto.php +++ b/app/Console/Commands/SubmissionsAutoProcess/FetchCASNumbersAuto.php @@ -10,6 +10,7 @@ use Illuminate\Support\Facades\Http; use Illuminate\Support\Facades\Log; use Illuminate\Support\Facades\RateLimiter; +use Illuminate\Support\Str; class FetchCASNumbersAuto extends Command { @@ -32,13 +33,15 @@ class FetchCASNumbersAuto extends Command */ private $batchSize = 100; // Number of molecules per batch - private $apiBaseUrl = 'https://commonchemistry.cas.org/api'; + private string $apiBaseUrl = ''; /** * Execute the console command. */ public function handle() { + $this->apiBaseUrl = rtrim((string) config('services.cas.base_url'), '/'); + $collection_id = $this->argument('collection_id'); if (! $collection_id && ! $this->option('all')) { @@ -176,30 +179,49 @@ private function fetchCASFromAPI(Molecule $molecule): ?string continue; } - $casNumber = $this->fetchCASFromCommonChemistryAPI($candidate, 'search'); - Log::info("Received CAS number: {$casNumber}"); - if ($casNumber) { - // Get the details using this CAS number. + // A search can return several matches and the first is not always the right compound + // (e.g. a deuterated variant), so verify every candidate against the molecule. + $matches = []; + foreach ($this->searchCASNumbers($candidate) as $casNumber) { $details = $this->fetchCASFromCommonChemistryAPI($casNumber, 'detail'); if (! $details) { Log::warning("Failed to fetch details for CAS number: {$casNumber}"); continue; } - // Use the SMILE (if not then use Canonical SMILE), InChI, InChIKey from details to verify if this is the correct molecule. - // First need to standardise the SMILES using CMS pre-processing pipeline. + $isTheCorrectMolecule = $this->verifyMoleculeIdentity($molecule, $details); - Log::info(sprintf('Is the correct molecule: %s', $isTheCorrectMolecule ? 'yes' : 'no')); + Log::info(sprintf('CAS %s is the correct molecule: %s', $casNumber, $isTheCorrectMolecule ? 'yes' : 'no')); if ($isTheCorrectMolecule) { - return $casNumber; + $matches[] = $casNumber; } } + + if (count($matches) === 1) { + return $matches[0]; + } + if (count($matches) > 1) { + Log::warning('Ambiguous CAS match, not saving: '.implode(', ', $matches), ['molecule_id' => $molecule->id]); + } } return null; } + /** + * Search Common Chemistry and return all matching CAS numbers. + * + * @return string[] + */ + private function searchCASNumbers(string $query): array + { + $response = $this->makeAPIRequest("{$this->apiBaseUrl}/search", ['q' => $query]); + $data = $response?->json(); + + return collect($data['results'] ?? [])->pluck('rn')->filter()->values()->all(); + } + /** * Single search helper that queries the Common Chemistry /search endpoint. */ @@ -217,11 +239,9 @@ private function fetchCASFromCommonChemistryAPI(string $query, string $searchTyp if ($searchType === 'detail') { return $this->extractDetailsFromResponse($response); - } else { - $extractedCAS = $this->extractCASFromResponse($response); - - return $extractedCAS; } + + return $this->extractCASFromResponse($response); } /** @@ -267,6 +287,8 @@ private function doActualRequest(string $url, array $params): ?Response $response = Http::timeout(120) ->connectTimeout(60) ->withHeaders([ + 'accept' => 'application/json', + 'x-origin' => config('services.cas.origin'), 'X-API-KEY' => config('services.cas.cas_key'), ]) ->get($url, $params); @@ -275,7 +297,8 @@ private function doActualRequest(string $url, array $params): ?Response return $response; } - Log::warning("HTTP request failed for URL: {$url}, Status: ".$response->status()." (attempt $attempt/$maxRetries)"); + // Never log request headers: they contain the API key. + Log::warning("HTTP request failed for URL: {$url}, Status: ".$response->status().', Body: '.Str::limit($response->body(), 500)." (attempt $attempt/$maxRetries)"); } catch (\Exception $e) { Log::warning("HTTP request exception (attempt $attempt/$maxRetries) for URL: {$url}, Error: ".$e->getMessage()); @@ -352,7 +375,7 @@ private function extractDetailsFromResponse($response): ?array 'smile' => $data['smile'] ?? null, 'canonical_smiles' => $data['canonicalSmile'] ?? null, 'inchi' => $data['inchi'] ?? null, - 'inchikey' => $data['inchikey'] ?? null, + 'inchikey' => $data['inchiKey'] ?? null, ]; } diff --git a/composer.lock b/composer.lock index 2bf5cf50..1c7ee96a 100644 --- a/composer.lock +++ b/composer.lock @@ -8,16 +8,16 @@ "packages": [ { "name": "anourvalar/eloquent-serialize", - "version": "1.3.10", + "version": "1.3.12", "source": { "type": "git", "url": "https://github.com/AnourValar/eloquent-serialize.git", - "reference": "2be26f176b764a2d6f20118bfa4b125f71fa88f8" + "reference": "eb46e698efe7e20c311f1f93830111fcdcdabd96" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/AnourValar/eloquent-serialize/zipball/2be26f176b764a2d6f20118bfa4b125f71fa88f8", - "reference": "2be26f176b764a2d6f20118bfa4b125f71fa88f8", + "url": "https://api.github.com/repos/AnourValar/eloquent-serialize/zipball/eb46e698efe7e20c311f1f93830111fcdcdabd96", + "reference": "eb46e698efe7e20c311f1f93830111fcdcdabd96", "shasum": "" }, "require": { @@ -67,18 +67,18 @@ ], "support": { "issues": "https://github.com/AnourValar/eloquent-serialize/issues", - "source": "https://github.com/AnourValar/eloquent-serialize/tree/1.3.10" + "source": "https://github.com/AnourValar/eloquent-serialize/tree/1.3.12" }, - "time": "2026-06-20T14:30:25+00:00" + "time": "2026-09-13T06:25:37+00:00" }, { "name": "archilex/filament-filter-sets", - "version": "4.3.9", + "version": "4.5.1", "dist": { "type": "zip", - "url": "https://filament-filter-sets.composer.sh/download/a2019a97-005a-446a-9d41-5ba6d2e62d1a/advanced-tables-for-filament-4.3.9.zip", - "reference": "ad045fa1a4631d8bcb26f4a6e15374a05f058737", - "shasum": "f29141f2d61b79299f9fc049e21fd0bb6fd7f1c1" + "url": "https://filament-filter-sets.composer.sh/download/a2e7e7ff-2b98-4b13-984f-a58333af8c54/advanced-tables-for-filament-4.5.1.zip", + "reference": "9593027b488da14ab337bd0853a20ef75bee9942", + "shasum": "fc56633e4f09b7596af1914737067794c2231655" }, "require": { "filament/tables": "^4.6.0", @@ -138,6 +138,9 @@ ], "test:sqlite": [ "vendor/bin/pest --configuration=phpunit.sqlite.xml" + ], + "test:sqlsrv": [ + "vendor/bin/pest --configuration=phpunit.sqlsrv.xml" ] }, "license": [ @@ -161,7 +164,7 @@ "tables", "views" ], - "time": "2026-06-12T15:22:03+00:00" + "time": "2026-10-05T02:58:54+00:00" }, { "name": "aws/aws-crt-php", @@ -219,16 +222,16 @@ }, { "name": "aws/aws-sdk-php", - "version": "3.385.3", + "version": "3.399.1", "source": { "type": "git", "url": "https://github.com/aws/aws-sdk-php.git", - "reference": "1952d9ce58aca5a5d444f74ed1034f7ba9125002" + "reference": "cd7cf43b7d42e49579bf3f09ab58d4724d64152c" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/aws/aws-sdk-php/zipball/1952d9ce58aca5a5d444f74ed1034f7ba9125002", - "reference": "1952d9ce58aca5a5d444f74ed1034f7ba9125002", + "url": "https://api.github.com/repos/aws/aws-sdk-php/zipball/cd7cf43b7d42e49579bf3f09ab58d4724d64152c", + "reference": "cd7cf43b7d42e49579bf3f09ab58d4724d64152c", "shasum": "" }, "require": { @@ -236,9 +239,9 @@ "ext-json": "*", "ext-pcre": "*", "ext-simplexml": "*", - "guzzlehttp/guzzle": "^7.4.5", - "guzzlehttp/promises": "^2.0", - "guzzlehttp/psr7": "^2.4.5", + "guzzlehttp/guzzle": "^7.8.2 || ^8.0", + "guzzlehttp/promises": "^2.0.3 || ^3.0", + "guzzlehttp/psr7": "^2.6.3 || ^3.0", "mtdowling/jmespath.php": "^2.9.1", "php": ">=8.1", "psr/http-message": "^1.0 || ^2.0", @@ -310,9 +313,9 @@ "support": { "forum": "https://github.com/aws/aws-sdk-php/discussions", "issues": "https://github.com/aws/aws-sdk-php/issues", - "source": "https://github.com/aws/aws-sdk-php/tree/3.385.3" + "source": "https://github.com/aws/aws-sdk-php/tree/3.399.1" }, - "time": "2026-06-19T18:07:45+00:00" + "time": "2026-10-02T18:16:16+00:00" }, { "name": "bacon/bacon-qr-code", @@ -375,12 +378,12 @@ "source": { "type": "git", "url": "https://github.com/bezhanSalleh/filament-exceptions.git", - "reference": "908918a5875db2e127bb631ef1dcf0981897241c" + "reference": "cb9af2efd9291dbc924212d9421c4f2fa15dc239" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/bezhanSalleh/filament-exceptions/zipball/908918a5875db2e127bb631ef1dcf0981897241c", - "reference": "908918a5875db2e127bb631ef1dcf0981897241c", + "url": "https://api.github.com/repos/bezhanSalleh/filament-exceptions/zipball/cb9af2efd9291dbc924212d9421c4f2fa15dc239", + "reference": "cb9af2efd9291dbc924212d9421c4f2fa15dc239", "shasum": "" }, "require": { @@ -455,7 +458,7 @@ "type": "github" } ], - "time": "2026-03-29T04:13:27+00:00" + "time": "2026-06-27T23:41:10+00:00" }, { "name": "bezhansalleh/filament-panel-switch", @@ -534,16 +537,16 @@ }, { "name": "bezhansalleh/filament-plugin-essentials", - "version": "1.2.1", + "version": "1.3.0", "source": { "type": "git", "url": "https://github.com/bezhanSalleh/filament-plugin-essentials.git", - "reference": "de3a8a07edcf1bc9fe829480ae09aa00265e7f03" + "reference": "3ccec939e6e3fb51ce08cacf73c3cc3d3f59640c" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/bezhanSalleh/filament-plugin-essentials/zipball/de3a8a07edcf1bc9fe829480ae09aa00265e7f03", - "reference": "de3a8a07edcf1bc9fe829480ae09aa00265e7f03", + "url": "https://api.github.com/repos/bezhanSalleh/filament-plugin-essentials/zipball/3ccec939e6e3fb51ce08cacf73c3cc3d3f59640c", + "reference": "3ccec939e6e3fb51ce08cacf73c3cc3d3f59640c", "shasum": "" }, "require": { @@ -600,7 +603,7 @@ ], "support": { "issues": "https://github.com/bezhanSalleh/filament-plugin-essentials/issues", - "source": "https://github.com/bezhanSalleh/filament-plugin-essentials/tree/1.2.1" + "source": "https://github.com/bezhanSalleh/filament-plugin-essentials/tree/1.3.0" }, "funding": [ { @@ -608,20 +611,20 @@ "type": "github" } ], - "time": "2026-03-22T08:15:32+00:00" + "time": "2026-07-25T02:30:23+00:00" }, { "name": "bezhansalleh/filament-shield", - "version": "4.2.0", + "version": "4.3.1", "source": { "type": "git", "url": "https://github.com/bezhanSalleh/filament-shield.git", - "reference": "a48ea9ca115c644ce40380b853142afcd65e38d1" + "reference": "1ff51f53985275f5bd37e9277cf810d391e7c3ca" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/bezhanSalleh/filament-shield/zipball/a48ea9ca115c644ce40380b853142afcd65e38d1", - "reference": "a48ea9ca115c644ce40380b853142afcd65e38d1", + "url": "https://api.github.com/repos/bezhanSalleh/filament-shield/zipball/1ff51f53985275f5bd37e9277cf810d391e7c3ca", + "reference": "1ff51f53985275f5bd37e9277cf810d391e7c3ca", "shasum": "" }, "require": { @@ -631,7 +634,7 @@ "illuminate/support": "^11.28|^12.0|^13.0", "php": "^8.2|^8.3", "spatie/laravel-package-tools": "^1.0", - "spatie/laravel-permission": "^6.0|^7.0" + "spatie/laravel-permission": "^6.0|^7.0|^8.0" }, "require-dev": { "larastan/larastan": "^3.0", @@ -695,7 +698,7 @@ ], "support": { "issues": "https://github.com/bezhanSalleh/filament-shield/issues", - "source": "https://github.com/bezhanSalleh/filament-shield/tree/4.2.0" + "source": "https://github.com/bezhanSalleh/filament-shield/tree/4.3.1" }, "funding": [ { @@ -703,7 +706,7 @@ "type": "github" } ], - "time": "2026-03-22T08:31:44+00:00" + "time": "2026-07-25T03:31:26+00:00" }, { "name": "blade-ui-kit/blade-heroicons", @@ -776,16 +779,16 @@ }, { "name": "blade-ui-kit/blade-icons", - "version": "1.10.0", + "version": "1.10.1", "source": { "type": "git", "url": "https://github.com/driesvints/blade-icons.git", - "reference": "74189a80bbaa4966aebaee54fec3a3c2ef0a5f3a" + "reference": "6e072d021ea6249986c330b93293c33d0c4f0e34" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/driesvints/blade-icons/zipball/74189a80bbaa4966aebaee54fec3a3c2ef0a5f3a", - "reference": "74189a80bbaa4966aebaee54fec3a3c2ef0a5f3a", + "url": "https://api.github.com/repos/driesvints/blade-icons/zipball/6e072d021ea6249986c330b93293c33d0c4f0e34", + "reference": "6e072d021ea6249986c330b93293c33d0c4f0e34", "shasum": "" }, "require": { @@ -853,7 +856,7 @@ "type": "paypal" } ], - "time": "2026-04-23T19:03:45+00:00" + "time": "2026-06-30T09:44:12+00:00" }, { "name": "brick/math", @@ -917,16 +920,16 @@ }, { "name": "carbonphp/carbon-doctrine-types", - "version": "3.2.0", + "version": "3.2.1", "source": { "type": "git", "url": "https://github.com/CarbonPHP/carbon-doctrine-types.git", - "reference": "18ba5ddfec8976260ead6e866180bd5d2f71aa1d" + "reference": "5fa5eacafd9ef47c8c6ab9143fc901ba0194d3dc" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/CarbonPHP/carbon-doctrine-types/zipball/18ba5ddfec8976260ead6e866180bd5d2f71aa1d", - "reference": "18ba5ddfec8976260ead6e866180bd5d2f71aa1d", + "url": "https://api.github.com/repos/CarbonPHP/carbon-doctrine-types/zipball/5fa5eacafd9ef47c8c6ab9143fc901ba0194d3dc", + "reference": "5fa5eacafd9ef47c8c6ab9143fc901ba0194d3dc", "shasum": "" }, "require": { @@ -941,6 +944,11 @@ "phpunit/phpunit": "^10.3" }, "type": "library", + "extra": { + "branch-alias": { + "dev-main": "3.x-dev" + } + }, "autoload": { "psr-4": { "Carbon\\Doctrine\\": "src/Carbon/Doctrine/" @@ -966,7 +974,7 @@ ], "support": { "issues": "https://github.com/CarbonPHP/carbon-doctrine-types/issues", - "source": "https://github.com/CarbonPHP/carbon-doctrine-types/tree/3.2.0" + "source": "https://github.com/CarbonPHP/carbon-doctrine-types/tree/3.2.1" }, "funding": [ { @@ -982,7 +990,7 @@ "type": "tidelift" } ], - "time": "2024-02-09T16:56:22+00:00" + "time": "2026-09-06T14:11:38+00:00" }, { "name": "chillerlan/php-qrcode", @@ -1146,6 +1154,75 @@ ], "time": "2026-03-20T21:10:52+00:00" }, + { + "name": "composer/class-map-generator", + "version": "1.8.0", + "source": { + "type": "git", + "url": "https://github.com/composer/class-map-generator.git", + "reference": "c0efbeb2f3fd7e23c7f180a59765c0b48a31fbc4" + }, + "dist": { + "type": "zip", + "url": "https://api.github.com/repos/composer/class-map-generator/zipball/c0efbeb2f3fd7e23c7f180a59765c0b48a31fbc4", + "reference": "c0efbeb2f3fd7e23c7f180a59765c0b48a31fbc4", + "shasum": "" + }, + "require": { + "composer/pcre": "^2.1 || ^3.1", + "php": "^7.2 || ^8.0", + "symfony/finder": "^4.4 || ^5.3 || ^6 || ^7 || ^8" + }, + "require-dev": { + "phpstan/phpstan": "^1.12 || ^2", + "phpstan/phpstan-deprecation-rules": "^1 || ^2", + "phpstan/phpstan-phpunit": "^1 || ^2", + "phpstan/phpstan-strict-rules": "^1.1 || ^2", + "phpunit/phpunit": "^8", + "symfony/filesystem": "^5.4 || ^6 || ^7 || ^8" + }, + "type": "library", + "extra": { + "branch-alias": { + "dev-main": "1.x-dev" + } + }, + "autoload": { + "psr-4": { + "Composer\\ClassMapGenerator\\": "src" + } + }, + "notification-url": "https://packagist.org/downloads/", + "license": [ + "MIT" + ], + "authors": [ + { + "name": "Jordi Boggiano", + "email": "j.boggiano@seld.be", + "homepage": "https://seld.be" + } + ], + "description": "Utilities to scan PHP code and generate class maps.", + "keywords": [ + "classmap" + ], + "support": { + "issues": "https://github.com/composer/class-map-generator/issues", + "source": "https://github.com/composer/class-map-generator/tree/1.8.0" + }, + "funding": [ + { + "url": "https://packagist.com", + "type": "custom" + }, + { + "url": "https://github.com/composer", + "type": "github" + } + ], + "time": "2026-09-25T15:24:19+00:00" + }, { "name": "composer/pcre", "version": "3.4.0", @@ -1224,16 +1301,16 @@ }, { "name": "composer/semver", - "version": "3.4.4", + "version": "3.5.1", "source": { "type": "git", "url": "https://github.com/composer/semver.git", - "reference": "198166618906cb2de69b95d7d47e5fa8aa1b2b95" + "reference": "528948210cc46f967a4b98e83b19e76f2b504993" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/composer/semver/zipball/198166618906cb2de69b95d7d47e5fa8aa1b2b95", - "reference": "198166618906cb2de69b95d7d47e5fa8aa1b2b95", + "url": "https://api.github.com/repos/composer/semver/zipball/528948210cc46f967a4b98e83b19e76f2b504993", + "reference": "528948210cc46f967a4b98e83b19e76f2b504993", "shasum": "" }, "require": { @@ -1275,7 +1352,7 @@ "homepage": "http://robbast.nl" } ], - "description": "Semver library that offers utilities, version constraint parsing and validation.", + "description": "Version comparison library that offers utilities, version constraint parsing and validation.", "keywords": [ "semantic", "semver", @@ -1285,7 +1362,7 @@ "support": { "irc": "ircs://irc.libera.chat:6697/composer", "issues": "https://github.com/composer/semver/issues", - 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"reference": "e5cc34d491a90e79c216d824f60fe21fd4d93bd6", + "url": "https://api.github.com/repos/phpstan/phpstan/zipball/b1f9890d9af53a25c58129e78f0aadd31f90d7f4", + "reference": "b1f9890d9af53a25c58129e78f0aadd31f90d7f4", "shasum": "" }, "require": { @@ -16819,7 +17102,7 @@ "type": "github" } ], - "time": "2026-06-05T09:00:01+00:00" + "time": "2026-10-06T06:15:36+00:00" }, { "name": "phpunit/php-code-coverage", @@ -17170,26 +17453,26 @@ }, { "name": "phpunit/phpunit", - "version": "11.5.55", + "version": "11.5.57", "source": { "type": "git", "url": "https://github.com/sebastianbergmann/phpunit.git", - "reference": "adc7262fccc12de2b30f12a8aa0b33775d814f00" + "reference": "36b75bf56a8535623f5b3e24b27ea1823759da1a" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/sebastianbergmann/phpunit/zipball/adc7262fccc12de2b30f12a8aa0b33775d814f00", - "reference": "adc7262fccc12de2b30f12a8aa0b33775d814f00", + "url": "https://api.github.com/repos/sebastianbergmann/phpunit/zipball/36b75bf56a8535623f5b3e24b27ea1823759da1a", + "reference": "36b75bf56a8535623f5b3e24b27ea1823759da1a", "shasum": "" }, "require": { "ext-dom": "*", + "ext-filter": "*", "ext-json": "*", "ext-libxml": "*", "ext-mbstring": "*", - "ext-xml": "*", "ext-xmlwriter": "*", - "myclabs/deep-copy": "^1.13.4", + "myclabs/deep-copy": "^1.14.0", "phar-io/manifest": "^2.0.4", "phar-io/version": "^3.2.1", "php": ">=8.2", @@ -17252,31 +17535,15 @@ "support": { "issues": "https://github.com/sebastianbergmann/phpunit/issues", "security": "https://github.com/sebastianbergmann/phpunit/security/policy", - "source": "https://github.com/sebastianbergmann/phpunit/tree/11.5.55" + "source": "https://github.com/sebastianbergmann/phpunit/tree/11.5.57" }, "funding": [ { - "url": "https://phpunit.de/sponsors.html", - "type": "custom" - }, - { - "url": "https://github.com/sebastianbergmann", - "type": "github" - }, - { - "url": "https://liberapay.com/sebastianbergmann", - "type": "liberapay" - }, - { - "url": "https://thanks.dev/u/gh/sebastianbergmann", - "type": "thanks_dev" - }, - { - "url": "https://tidelift.com/funding/github/packagist/phpunit/phpunit", - "type": "tidelift" + "url": "https://phpunit.de/sponsoring.html", + "type": "other" } ], - "time": "2026-02-18T12:37:06+00:00" + "time": "2026-10-05T05:47:54+00:00" }, { "name": "sebastian/cli-parser", @@ -18703,16 +18970,16 @@ }, { "name": "symfony/yaml", - "version": "v8.1.0", + "version": "v8.1.8", "source": { "type": "git", "url": "https://github.com/symfony/yaml.git", - "reference": "efb42bd2c6f4f3ccfd4683583449938b5fc146b0" + "reference": "030e96eed0303223bfca3af9109e9e64830b6ec3" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/symfony/yaml/zipball/efb42bd2c6f4f3ccfd4683583449938b5fc146b0", - "reference": "efb42bd2c6f4f3ccfd4683583449938b5fc146b0", + "url": "https://api.github.com/repos/symfony/yaml/zipball/030e96eed0303223bfca3af9109e9e64830b6ec3", + "reference": "030e96eed0303223bfca3af9109e9e64830b6ec3", "shasum": "" }, "require": { @@ -18755,7 +19022,7 @@ "description": "Loads and dumps YAML files", "homepage": "https://symfony.com", "support": { - "source": "https://github.com/symfony/yaml/tree/v8.1.0" + "source": "https://github.com/symfony/yaml/tree/v8.1.8" }, "funding": [ { @@ -18775,7 +19042,7 @@ "type": "tidelift" } ], - "time": "2026-05-29T05:06:50+00:00" + "time": "2026-09-26T06:33:49+00:00" }, { "name": "theseer/tokenizer", @@ -18839,5 +19106,5 @@ "php": "^8.3" }, "platform-dev": {}, - "plugin-api-version": "2.6.0" + "plugin-api-version": "2.9.0" } diff --git a/config/services.php b/config/services.php index db4792b8..7a37c94c 100644 --- a/config/services.php +++ b/config/services.php @@ -91,6 +91,8 @@ 'cas' => [ 'cas_key' => env('CAS_KEY'), + 'base_url' => env('CAS_BASE_URL', 'https://commonchemistry.cas.org/direct-api'), + 'origin' => env('CAS_ORIGIN', 'https://commonchemistry.cas.org/api-overview'), ], 'nominatim' => [ diff --git a/resources/css/filament/control-panel/theme.css b/resources/css/filament/control-panel/theme.css index b32b296a..f152c06e 100644 --- a/resources/css/filament/control-panel/theme.css +++ b/resources/css/filament/control-panel/theme.css @@ -1,6 +1,6 @@ @import "tailwindcss"; @import '../../../../vendor/filament/filament/resources/css/theme.css'; -@import '../../../../vendor/archilex/filament-filter-sets/resources/dist/advanced-tables.css'; +@import '../../../../vendor/archilex/filament-filter-sets/resources/css/plugin.css'; @import '../../../../vendor/pxlrbt/filament-spotlight-pro/resources/spotlight.css'; @plugin "@tailwindcss/forms"; diff --git a/resources/css/filament/dashboard/theme.css b/resources/css/filament/dashboard/theme.css index 66384d9a..0945bea2 100644 --- a/resources/css/filament/dashboard/theme.css +++ b/resources/css/filament/dashboard/theme.css @@ -1,6 +1,6 @@ @import "tailwindcss"; @import '../../../../vendor/filament/filament/resources/css/theme.css'; -@import '../../../../vendor/archilex/filament-filter-sets/resources/dist/advanced-tables.css'; +@import '../../../../vendor/archilex/filament-filter-sets/resources/css/plugin.css'; @import '../../../../vendor/pxlrbt/filament-spotlight-pro/resources/spotlight.css'; @plugin "@tailwindcss/forms"; diff --git a/tests/Unit/FetchCASNumbersAutoTest.php b/tests/Unit/FetchCASNumbersAutoTest.php new file mode 100644 index 00000000..faff6454 --- /dev/null +++ b/tests/Unit/FetchCASNumbersAutoTest.php @@ -0,0 +1,82 @@ + 'https://commonchemistry.cas.org/direct-api', + 'services.cas.origin' => 'https://commonchemistry.cas.org/api-overview', + 'services.cas.cas_key' => 'secret-key', + ]); + + $command = new FetchCASNumbersAuto; + $property = new \ReflectionProperty($command, 'apiBaseUrl'); + $property->setValue($command, config('services.cas.base_url')); + + return $command; + } + + private function invoke(FetchCASNumbersAuto $command, string $method, array $args) + { + return (new \ReflectionMethod($command, $method))->invoke($command, ...$args); + } + + public function test_detail_request_uses_direct_api_and_sends_x_origin_header(): void + { + Http::fake([ + 'commonchemistry.cas.org/direct-api/detail*' => Http::response(['rn' => '58-08-2', 'name' => 'Caffeine']), + ]); + + $details = $this->invoke($this->command(), 'fetchCASFromCommonChemistryAPI', ['58-08-2', 'detail']); + + $this->assertIsArray($details); + Http::assertSent(function (Request $request) { + return str_starts_with($request->url(), 'https://commonchemistry.cas.org/direct-api/detail?cas_rn=58-08-2') + && $request->header('x-origin') === ['https://commonchemistry.cas.org/api-overview'] + && $request->header('X-API-KEY') === ['secret-key']; + }); + } + + public function test_search_returns_all_matches_not_just_the_first(): void + { + Http::fake([ + 'commonchemistry.cas.org/direct-api/search*' => Http::response([ + 'count' => 2, + 'results' => [['rn' => '26351-04-2'], ['rn' => '58-08-2']], + ]), + ]); + + $result = $this->invoke($this->command(), 'searchCASNumbers', ['CN1C=NC2=C1C(=O)N(C(=O)N2C)C']); + + $this->assertSame(['26351-04-2', '58-08-2'], $result); + Http::assertSent(fn (Request $request) => $request->header('x-origin') === ['https://commonchemistry.cas.org/api-overview']); + } + + public function test_failed_request_logs_status_and_body_but_not_the_api_key(): void + { + Http::fake(['*' => Http::response(['message' => 'Unauthorized'], 401)]); + $logged = []; + Log::shouldReceive('warning')->andReturnUsing(function ($message) use (&$logged) { + $logged[] = $message; + }); + Log::shouldReceive('info')->andReturnNull(); + + $command = $this->command(); + $result = $this->invoke($command, 'doActualRequest', ['https://commonchemistry.cas.org/direct-api/detail', ['cas_rn' => '58-08-2']]); + + $this->assertNull($result); + $all = implode("\n", $logged); + $this->assertStringContainsString('Status: 401', $all); + $this->assertStringContainsString('Unauthorized', $all); + $this->assertStringNotContainsString('secret-key', $all); + } +}