wip full molecule GET single molecule endpoint

Author: MichelML

resources/config.json

@@ -3,12 +3,12 @@
     "host": "0.0.0.0",
     "port": 8000,
     "swaggerHost": "localhost:8000",
-    "dbConnectionString": "postgresql://postgres:db-pass@localhost:5432/postgres"
+    "dbConnectionString": "postgresql://postgres:db-pass@localhost:5432/molecules"
   },
   "local-docker": {
     "host": "0.0.0.0",
     "port": 8000,
     "swaggerHost": "localhost:8000",
-    "dbConnectionString": "postgresql://postgres:db-pass@db:5432/postgres"
+    "dbConnectionString": "postgresql://postgres:db-pass@db:5432/molecules"
   }
 }

src/controller/MoleculeController.hpp

@@ -0,0 +1,49 @@
+
+#ifndef MoleculeController_hpp
+#define MoleculeController_hpp
+
+#include "service/MoleculeService.hpp"
+
+#include "oatpp/web/server/api/ApiController.hpp"
+#include "oatpp/parser/json/mapping/ObjectMapper.hpp"
+#include "oatpp/core/macro/codegen.hpp"
+
+#include OATPP_CODEGEN_BEGIN(ApiController) //<- Begin Codegen
+
+/**
+ * User REST controller.
+ */
+class MoleculeController : public oatpp::web::server::api::ApiController {
+public:
+  MoleculeController(const std::shared_ptr<ObjectMapper>& objectMapper)
+    : oatpp::web::server::api::ApiController(objectMapper)
+  {}
+private:
+  MoleculeService m_moleculeService; // Create user service.
+public:
+
+  static std::shared_ptr<MoleculeController> createShared(
+    OATPP_COMPONENT(std::shared_ptr<ObjectMapper>, objectMapper) // Inject objectMapper component here as default parameter
+  ){
+    return std::make_shared<MoleculeController>(objectMapper);
+  }
+  
+  ENDPOINT_INFO(getMoleculeById) {
+    info->summary = "Get one molecule by molecule id";
+
+    info->addResponse<Object<UserDto>>(Status::CODE_200, "application/json");
+    info->addResponse<Object<StatusDto>>(Status::CODE_404, "application/json");
+    info->addResponse<Object<StatusDto>>(Status::CODE_500, "application/json");
+
+    info->pathParams["moleculeId"].description = "Molecule Identifier";
+  }
+  ENDPOINT("GET", "users/{moleculeId}", getMoleculeById,
+           PATH(String, moleculeId))
+  {
+    return createDtoResponse(Status::CODE_200, m_moleculeService.getMoleculeById(userId));
+  }
+};
+
+#include OATPP_CODEGEN_BEGIN(ApiController) //<- End Codegen
+
+#endif /* MoleculeController_hpp */

src/db/MoleculeDb.hpp

@@ -0,0 +1,41 @@
+
+#ifndef EXAMPLE_POSTGRESQL_MOLECULEDB_HPP
+#define EXAMPLE_POSTGRESQL_MOLECULEDB_HPP
+
+#include "dto/MoleculeDto.hpp"
+#include "oatpp-postgresql/orm.hpp"
+
+#include OATPP_CODEGEN_BEGIN(DbClient) //<- Begin Codegen
+
+/**
+ * MoleculeDb client definitions.
+ */
+class MoleculeDb : public oatpp::orm::DbClient {
+public:
+
+  MoleculeDb(const std::shared_ptr<oatpp::orm::Executor>& executor)
+    : oatpp::orm::DbClient(executor)
+  {
+
+    oatpp::orm::SchemaMigration migration(executor);
+    // We use a pre-filled, read-only database, therefore no migration files needed
+    // migration.addFile(1 /* start from version 1 */, DATABASE_MIGRATIONS "/001_init.sql");
+    // TODO - Add more migrations here.
+    // migration.migrate(); // <-- run migrations. This guy will throw on error.
+
+    auto version = executor->getSchemaVersion();
+    OATPP_LOGD("MoleculeDb", "Migration - OK. Version=%d.", version);
+
+  }
+
+
+  QUERY(getMoleculeById,
+        "SELECT id, m::text as smiles from mols where id=:id;",
+        PREPARE(true), //<-- user prepared statement!
+        PARAM(oatpp::String, id))
+
+};
+
+#include OATPP_CODEGEN_END(DbClient) //<- End Codegen
+
+#endif //EXAMPLE_POSTGRESQL_MOLECULEDB_HPP

src/dto/MoleculeDto.hpp

@@ -0,0 +1,19 @@
+#ifndef MoleculeDto_hpp
+#define MoleculeDto_hpp
+
+#include "oatpp/core/macro/codegen.hpp"
+#include "oatpp/core/Types.hpp"
+
+#include OATPP_CODEGEN_BEGIN(DTO)
+
+class MoleculeDto : public oatpp::DTO {
+  
+  DTO_INIT(MoleculeDto, DTO)
+
+  DTO_FIELD(String, id);
+  DTO_FIELD(String, smiles, "smiles");
+};
+
+#include OATPP_CODEGEN_END(DTO)
+
+#endif /* MoleculeDto_hpp */

src/service/MoleculeService.cpp

@@ -0,0 +1,17 @@
+
+#include "MoleculeService.hpp"
+
+oatpp::Object<UserDto>
+MoleculeService::getMoleculeById(const oatpp::String &id) {
+
+  auto dbResult = m_database->getMoleculeById(id);
+  OATPP_ASSERT_HTTP(dbResult->isSuccess(), Status::CODE_500,
+                    dbResult->getErrorMessage());
+  OATPP_ASSERT_HTTP(dbResult->hasMoreToFetch(), Status::CODE_404,
+                    "User not found");
+
+  auto result = dbResult->fetch<oatpp::Vector<oatpp::Object<UserDto>>>();
+  OATPP_ASSERT_HTTP(result->size() == 1, Status::CODE_500, "Unknown error");
+
+  return result[0];
+}

src/service/MoleculeService.hpp

@@ -0,0 +1,22 @@
+
+#ifndef EXAMPLE_POSTGRESQL_MOLECULESERVICE_HPP
+#define EXAMPLE_POSTGRESQL_MOLECULESERVICE_HPP
+
+#include "db/UserDb.hpp"
+#include "dto/PageDto.hpp"
+#include "dto/StatusDto.hpp"
+
+#include "oatpp/web/protocol/http/Http.hpp"
+#include "oatpp/core/macro/component.hpp"
+
+class MoleculeService {
+private:
+  typedef oatpp::web::protocol::http::Status Status;
+private:
+  OATPP_COMPONENT(std::shared_ptr<UserDb>, m_database); // Inject database component
+public:
+
+  oatpp::Object<UserDto> getMoleculeById(const oatpp::String& id);
+};
+
+#endif //EXAMPLE_POSTGRESQL_MOLECULESERVICE_HPP