Merge pull request #152 from privrja/devel

Version 1.0.2

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)

composer.json

@@ -16,17 +16,17 @@
     "netresearch/jsonmapper": "^4.0",
     "sensio/framework-extra-bundle": "^6.0",
     "symfony/apache-pack": "^1.0",
-    "symfony/asset": "5.2.*",
-    "symfony/console": "5.2.*",
-    "symfony/dotenv": "5.2.*",
-    "symfony/expression-language": "5.2.*",
+    "symfony/asset": "5.3.*",
+    "symfony/console": "5.3.*",
+    "symfony/dotenv": "5.3.*",
+    "symfony/expression-language": "5.3.*",
     "symfony/flex": "^1.3.1",
-    "symfony/framework-bundle": "5.2.*",
+    "symfony/framework-bundle": "5.3.*",
     "symfony/monolog-bundle": "^3.5",
     "symfony/orm-pack": "^2.0",
-    "symfony/security-bundle": "5.2.*",
+    "symfony/security-bundle": "5.3.*",
     "symfony/twig-pack": "^1.0",
-    "symfony/yaml": "5.2.*"
+    "symfony/yaml": "5.3.*"
   },
   "require-dev": {
     "symfony/maker-bundle": "^1.14",

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.*$)

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 }

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:

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);

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));

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;
     }
 
 }

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) {

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();

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]);