diff --git a/README.md b/README.md index e976d58..89dd1b8 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ To drop DB and create new use: ```php bin/console doctrine:mig:mig``` -```php bin/console doctrine:fixtures:load``` +```php bin/console doctrine:fixtures:load --group=prod``` or dev group ### Run tests Before every test you need to delete, create, migrate and purge DB like in previuos step, now test can't be run more times in a row. @@ -33,5 +33,5 @@ To run test use ```composer test``` or ```php ./vendor/symfony/phpunit-bridge/bi ```symfony server:start``` -Documentation of API is [localhost:8000/api/doc](https://localhost:8000/api/doc) +Documentation of API is [localhost:8000/rest/doc](https://localhost:8000/rest/doc) Rest API is on [localhost:8000/rest](https://localhost:8000/rest) diff --git a/composer.json b/composer.json index 0151f47..0de292a 100644 --- a/composer.json +++ b/composer.json @@ -16,17 +16,17 @@ "netresearch/jsonmapper": "^4.0", "sensio/framework-extra-bundle": "^6.0", "symfony/apache-pack": "^1.0", - 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HTTP Integration", "homepage": "https://symfony.com", "support": { - "source": "https://github.com/symfony/security-http/tree/v5.2.9" + "source": "https://github.com/symfony/security-http/tree/v5.3.1" }, "funding": [ { @@ -5914,7 +6132,7 @@ "type": "tidelift" } ], - "time": "2021-05-18T23:02:18+00:00" + "time": "2021-06-01T15:43:02+00:00" }, { "name": "symfony/service-contracts", @@ -6059,16 +6277,16 @@ }, { "name": "symfony/string", - "version": "v5.2.8", + "version": "v5.3.0", "source": { "type": "git", "url": "https://github.com/symfony/string.git", - "reference": "01b35eb64cac8467c3f94cd0ce2d0d376bb7d1db" + "reference": "a9a0f8b6aafc5d2d1c116dcccd1573a95153515b" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/symfony/string/zipball/01b35eb64cac8467c3f94cd0ce2d0d376bb7d1db", - "reference": "01b35eb64cac8467c3f94cd0ce2d0d376bb7d1db", + "url": "https://api.github.com/repos/symfony/string/zipball/a9a0f8b6aafc5d2d1c116dcccd1573a95153515b", + "reference": "a9a0f8b6aafc5d2d1c116dcccd1573a95153515b", "shasum": "" }, "require": { @@ -6122,7 +6340,7 @@ "utf8" ], "support": { - 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"doctrine/annotations": "*", + "doctrine/annotations": "^1.7", "ext-json": "*", "php": ">=7.2", "symfony/finder": ">=2.2", @@ -6979,9 +7202,9 @@ ], "support": { "issues": "https://github.com/zircote/swagger-php/issues", - "source": "https://github.com/zircote/swagger-php/tree/3.1.0" + "source": "https://github.com/zircote/swagger-php/tree/3.2.1" }, - "time": "2020-09-03T20:18:43+00:00" + "time": "2021-05-20T21:46:24+00:00" } ], "packages-dev": [ @@ -7341,26 +7564,26 @@ }, { "name": "symfony/phpunit-bridge", - "version": "v5.2.9", + "version": "v5.3.0", "source": { "type": "git", "url": "https://github.com/symfony/phpunit-bridge.git", - "reference": "ea24e42c1ee04792f5d814da6f0814b20ece2907" + "reference": "15cab721487b7bf43ad545a1e7d0095782e26f8c" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/symfony/phpunit-bridge/zipball/ea24e42c1ee04792f5d814da6f0814b20ece2907", - "reference": "ea24e42c1ee04792f5d814da6f0814b20ece2907", + "url": "https://api.github.com/repos/symfony/phpunit-bridge/zipball/15cab721487b7bf43ad545a1e7d0095782e26f8c", + "reference": "15cab721487b7bf43ad545a1e7d0095782e26f8c", "shasum": "" }, "require": { - "php": ">=5.5.9" + "php": ">=7.1.3", + "symfony/deprecation-contracts": "^2.1" }, "conflict": { - "phpunit/phpunit": "<4.8.35|<5.4.3,>=5.0|<6.4,>=6.0|9.1.2" + "phpunit/phpunit": "<7.5|9.1.2" }, "require-dev": { - "symfony/deprecation-contracts": "^2.1", "symfony/error-handler": "^4.4|^5.0" }, "suggest": { @@ -7404,7 +7627,7 @@ "description": "Provides utilities for PHPUnit, especially user deprecation notices management", "homepage": "https://symfony.com", "support": { - "source": "https://github.com/symfony/phpunit-bridge/tree/v5.2.9" + "source": "https://github.com/symfony/phpunit-bridge/tree/v5.3.0" }, "funding": [ { @@ -7420,7 +7643,7 @@ "type": "tidelift" } ], - "time": "2021-05-16T13:07:46+00:00" + "time": "2021-05-26T17:57:12+00:00" }, { "name": "symfony/profiler-pack", @@ -7603,5 +7826,5 @@ "ext-json": "*" }, "platform-dev": [], - "plugin-api-version": "2.0.0" + "plugin-api-version": "2.1.0" } diff --git a/config/packages/nelmio_api_doc.yaml b/config/packages/nelmio_api_doc.yaml index d72b734..5e30fb2 100644 --- a/config/packages/nelmio_api_doc.yaml +++ b/config/packages/nelmio_api_doc.yaml @@ -13,4 +13,4 @@ nelmio_api_doc: in: header areas: # to filter documented areas path_patterns: - - ^/rest + - ^/rest(?!/doc.*$) diff --git a/config/routes/nelmio_api_doc.yaml b/config/routes/nelmio_api_doc.yaml index f350dd6..f2eedcb 100644 --- a/config/routes/nelmio_api_doc.yaml +++ b/config/routes/nelmio_api_doc.yaml @@ -1,12 +1,12 @@ # Expose your documentation as JSON swagger compliant app.swagger: - path: /api/doc.json + path: /rest/doc.json methods: GET defaults: { _controller: nelmio_api_doc.controller.swagger } ## Requires the Asset component and the Twig bundle ## $ composer require twig asset app.swagger_ui: - path: /api/doc + path: /rest/doc methods: GET defaults: { _controller: nelmio_api_doc.controller.swagger_ui } diff --git a/src/Base/ReferenceHelper.php b/src/Base/ReferenceHelper.php index da02ba4..03ba047 100644 --- a/src/Base/ReferenceHelper.php +++ b/src/Base/ReferenceHelper.php @@ -11,9 +11,10 @@ class ReferenceHelper { const SMILES = "SMILES: "; + const CHEBI = 'CHEBI: '; public static function reference($database, $reference, $smiles) { - if ($reference == 0) { + if (!isset($reference) || $reference === '') { return self::defaultValue($smiles); } switch ($database) { @@ -24,7 +25,19 @@ public static function reference($database, $reference, $smiles) { case ServerEnum::PDB: return ServerEnum::$cycloBranchValues[ServerEnum::PDB] . $reference; case ServerEnum::NORINE: + case ServerEnum::COCONUT: + case ServerEnum::NP_ATLAS: return $reference; + case ServerEnum::CHEBI: + if (str_contains($reference, 'CHEBI:')) { + if (str_contains($reference, self::CHEBI)) { + return strtoupper($reference); + } else { + return self::CHEBI . substr($reference, 6); + } + } else { + return self::CHEBI . $reference; + } case ServerEnum::SIDEROPHORE_BASE: return ServerEnum::$cycloBranchValues[ServerEnum::SIDEROPHORE_BASE] . $reference; case ServerEnum::DOI: diff --git a/src/Base/SequenceHelper.php b/src/Base/SequenceHelper.php index 397f205..c8e0092 100644 --- a/src/Base/SequenceHelper.php +++ b/src/Base/SequenceHelper.php @@ -77,6 +77,8 @@ function findBlocks(Container $container, BlockRepository $blockRepository): arr if (!isset($block)) { return []; } + $b2s->setBlockOriginalId($len); + $b2s->setSort($len); $b2s->setBlock($block); $b2s->setIsBranch($this->branch); $branchNextAcronym = $this->branchNext(true); diff --git a/src/Controller/SmilesController.php b/src/Controller/SmilesController.php index 532a4cc..528da61 100644 --- a/src/Controller/SmilesController.php +++ b/src/Controller/SmilesController.php @@ -159,7 +159,7 @@ public function similarityContainer(Container $container, Request $request, Logg } $setup = $setupRepository->findOneBy(['id' => 1]); if ($setup->getSimilarity() === 'name') { - return new JsonResponse($sequenceFamilyRepository->similarity(1, $trans->sequenceName)); + return new JsonResponse($sequenceFamilyRepository->similarity($container->getId(), $trans->sequenceName)); } else { if ($trans->blockLengthUnique === 0) { return ResponseHelper::jsonResponse(new Message(ErrorConstants::ERROR_EMPTY_PARAMS, Response::HTTP_BAD_REQUEST)); diff --git a/src/Enum/ServerEnum.php b/src/Enum/ServerEnum.php index f5bdc67..9cc5474 100644 --- a/src/Enum/ServerEnum.php +++ b/src/Enum/ServerEnum.php @@ -14,22 +14,8 @@ class ServerEnum { const DOI = 6; const SIDEROPHORE_BASE = 7; const LIPID_MAPS = 8; - - /** @var array mapping int code to string */ - public static $values = [ - self::PUBCHEM => "PubChem", - self::CHEMSPIDER => "ChemSpider", - self::NORINE => "Norine", - self::PDB => "PDB", - self::CHEBI => "ChEBI", - ]; - - public static $backValues = [ - 'CID: ' => self::PUBCHEM, - 'CSID: ' => self::CHEMSPIDER, - ':' => self::NORINE, - 'PDB: ' => self::PDB, - ]; + const COCONUT = 9; + const NP_ATLAS = 10; /** @var array mapping int code to CycloBranch format string */ public static $cycloBranchValues = [ @@ -42,7 +28,7 @@ class ServerEnum { ]; public static function isOneOf(int $source): bool { - return $source >= self::PUBCHEM && $source <= self::LIPID_MAPS; + return $source >= self::PUBCHEM && $source <= self::NP_ATLAS; } } diff --git a/src/Model/ContainerModel.php b/src/Model/ContainerModel.php index 5bda835..6c51a9a 100644 --- a/src/Model/ContainerModel.php +++ b/src/Model/ContainerModel.php @@ -199,8 +199,12 @@ private function updateBlockProperties(Container $container, BlockTransformed $t $acronym = $block->getAcronym(); $this->entityManager->beginTransaction(); $block = $this->setupBlock($container, $block, $trans); - $this->entityManager->persist($block); - $this->entityManager->flush(); + try { + $this->entityManager->persist($block); + $this->entityManager->flush(); + } catch (UniqueConstraintViolationException $exception) { + return new Message('Block with this acronym is already in container'); + } if ($acronym !== $trans->getAcronym()) { $blockUsages = $this->blockRepository->blockUsage($block->getContainer()->getId(), $block->getId(), []); foreach ($blockUsages as $usage) { diff --git a/src/Repository/BlockRepository.php b/src/Repository/BlockRepository.php index ecc5e6e..4c8bebe 100644 --- a/src/Repository/BlockRepository.php +++ b/src/Repository/BlockRepository.php @@ -109,25 +109,32 @@ function findMergeByFormula(int $containerId) { $conn = $this->getEntityManager()->getConnection(); $sql = ' select - group_concat(distinct src.block_name order by src.block_name separator \'/\') as block_name, - group_concat(distinct src.acronym order by src.block_name separator \'/\') as acronym, + group_concat(src.block_name order by src.block_name separator \'/\') as block_name, -- + group_concat(src.acronym order by src.block_name separator \'/\') as acronym, -- src.residue, coalesce(src.block_mass, \'\') as block_mass, - group_concat(distinct coalesce(src.losses, \'\') order by src.block_name separator \'/\') as losses, - group_concat(distinct + group_concat(distinct coalesce(src.losses, \'\') order by src.block_name separator \'/\') as losses, -- + group_concat( -- case when src.source is not null then concat(case when src.source = 0 then \'CID: \' when src.source = 1 then \'CSID: \' when src.source = 2 then \'\' when src.source = 3 then \'PDB: \' + when src.source = 4 then \'\' + when src.source = 6 then \'DOI: \' + when src.source = 7 then \'SB: \' + when src.source = 8 then \'\' + when src.source = 9 then \'\' + when src.source = 10 then \'\' else \'SMILES: \' - end, case when src.source > 3 then src.usmiles else src.identifier end) + end, case when src.source > 10 or src.source = 5 then src.usmiles else src.identifier end) else \'\' end order by src.block_name separator \'/\') as ref from msb_block src where src.container_id = :containerId - group by src.residue, src.block_mass'; + group by src.residue, src.block_mass; + '; $stmt = $conn->prepare($sql); $stmt->execute(['containerId' => $containerId]); return $stmt->fetchAll(); diff --git a/src/Repository/SequenceFamilyRepository.php b/src/Repository/SequenceFamilyRepository.php index 1900839..bafee16 100644 --- a/src/Repository/SequenceFamilyRepository.php +++ b/src/Repository/SequenceFamilyRepository.php @@ -21,10 +21,16 @@ public function __construct(ManagerRegistry $registry) { public function similarity(int $containerId, string $sequenceName) { $conn = $this->getEntityManager()->getConnection(); $sql = ' - select fam.id as value, fam.sequence_family_name as label - from msb_sequence_family fam - where :sequenceName like concat(\'%\', fam.sequence_family_name, \'%\') - and container_id = :containerId + select fam.id as value, fam.sequence_family_name as label + from ( + select seq.id, row_number() over (order by abs(length(:sequenceName) - length(seq.sequence_name)) asc) as RN + from msb_sequence seq + where lower(substring_index(:sequenceName, \' \', 1)) like concat(\'%\', lower(substring_index(seq.sequence_name, \' \', 1)), \'%\') + and seq.container_id = :containerId + ) seq + left join msb_s2f s2f on s2f.sequence_id = seq.id + left join msb_sequence_family fam on fam.id = s2f.family_id + where seq.RN = 1; '; $stmt = $conn->prepare($sql); $stmt->execute(['sequenceName' => $sequenceName, 'containerId' => $containerId]);