Developer’s guide
This REST API was developed in Java 17 with the version 1.06 of the tool InChI.
Dependencies required
This API rests on several dependencies :
To build the application :
Spring Boot Starter Web 3.2.5 : Starter for building web, including RESTful, applications using Spring MVC. Uses Tomcat as the default embedded container.
InChI 1.06 : Binary program which generates InChIs and InChI Keys of molecules.
Lombok 1.18.32 : Java library that provides annotations to simplify Java development by automating the generation of boilerplate code. Used to the automatic generation of getters and setters methods.
Microservice Core Lib 1.0.1 : Custom Java library with factorized code common between microservices from the MetaboCloud project.
Openapi Generator 7.2.0 : OpenAPI Generator allows generation of API client libraries, server stubs, documentation and configuration automatically, given an OpenAPI Specification
To test the application :
Spring Boot Starter Test 3.2.5 : Starter for testing Spring Boot applications with libraries including JUnit Jupiter, Hamcrest and Mockito.
To build the documentation :
Springdoc 2.5.0 : Java library that helps to automate the generation of API documentation using spring boot projects.
- Sphinx 7.2.6Tool to build this documentation.
Sphinx-rtd-theme 1.3.0 : Sphinx extension to use the “Read the Docs” sphinx-rtd-theme/
Note
All the dependencies are install and manage by Maven during the application compilation, except for the InChI binary program which is downloaded externally.
Unit and functional testing
Unit and functional tests are in the src/test/java directory. To run all tests, use the following command :
$ mvn test
Note
You can launch specific tests by using the argument -Dtest.
$ mvn test -Dtest=<name of the file>
Where <name of the file> is the file containing the tests you want to run without its extension (e.g. InChIGenerationControllerTest)
Code organisation
The structure of the InChI REST API follows the Standard Directory layout created by Maven.
.
├── doc # Folder with the source of the documentation
├── Dockerfile
├── LICENSE
├── Makefile
├── pom.xml
├── README.md
├── src # Folder with the code source of the application
│ ├── main
│ │ ├── java
│ │ │ └── fr
│ │ │ └── metabocloud
│ │ │ └── inchi
│ │ │ ├── Application.java
│ │ │ ├── controllers
│ │ │ │ ├── core
│ │ │ │ │ ├── AboutController.java
│ │ │ │ │ └── RootController.java
│ │ │ │ └── inchi
│ │ │ │ └── InChIGenerationController.java
│ │ │ ├── exception
│ │ │ │ └── GlobalExceptionHandler.java
│ │ │ ├── implementation
│ │ │ │ └── InChIGenerationImpl.java
│ │ │ └── utils
│ │ │ └── ConfigUtils.java
│ │ └── resources
│ │ ├── local
│ │ │ └── application.properties
│ │ ├── mesocentre
│ │ │ └── application.properties
│ │ ├── pfem
│ │ │ └── application.properties
│ │ ├── conf.properties
│ │ ├── infos.properties
│ │ └── static
│ │ └── metabocloud-inchi.yaml
│ └── test
│ ├── java
│ │ └── fr
│ │ └── metabocloud
│ │ └── inchi
│ │ ├── ApplicationTests.java
│ │ ├── controllers
│ │ │ │ ├── core
│ │ │ │ │ ├── AboutControllerTest.java
│ │ │ │ │ └── RootControllerTest.java
│ │ │ │ └── inchi
│ │ │ │ └── InChIGenerationControllerTest.java
│ │ ├── data
│ │ │ ├── model
│ │ │ │ └── Parameters.java
│ │ │ ├── providers
│ │ │ │ └── GenerationProvider.java
│ │ │ └── stub
│ │ │ ├── JsonStub.java
│ │ │ ├── MolStub.java
│ │ │ └── SdfStub.java
│ │ └── implementation
│ │ └── InChIGenerationImplTest.java
│ └── resources
│ ├── confTest.properties
│ └── input
│ ├── Caffeine
│ │ ├── Caffeine.mol
│ │ └── Caffeine.sdf
│ ├── Cholesterol
│ │ ├── Cholesterol.mol
│ │ └── Cholesterol.sdf
│ ├── D-Glucose
│ │ ├── D-Glucose.mol
│ │ └── D-Glucose.sdf
│ ├── MethylTryptophan
│ │ ├── MethylTryptophan.mol
│ │ └── MethylTryptophan.sdf
│ ├── Sphinganine1Phosphate
│ │ ├── Sphinganine1Phosphate.mol
│ │ └── Sphinganine1Phosphate.sdf
│ └── VitaminE
│ ├── VitaminE.mol
│ └── VitaminE.sdf
docDirectory containing the source of the documentation
pom.xmlXML File at the root of the repository that contains information about the project, configuration details and dependencies needed, used by Maven to build the project.
src/main/javaSource code of the Application- fr.metabocloud.inchi :
Application.java : Enables to run the application using the Web framework SpringBoot.
- fr.metabocloud.inchi.controllers.corePackage containing controllers associated to the REST API
AboutController.java : Controller for the endpoint “/about” to retrieve the metadata associated to the REST API
RootController : Controller for the root “/” of the REST API
- fr.metabocloud.inchi.controllers.inchiPackage containing controllers associated to the tool InChI
InChIGenerationController.java : Controller for the endpoint “/generation” gor the generation of the InChI and InChI Key of a compound
- fr.metabocloud.inchi.exceptionPackage managing the exceptions that can be thrown by the REST API
GlobalExceptionHandler.java : Global handler which manage exceptions for all controllers
- fr.metabocloud.inchi.implementationPackage containing classes which implement methods to process the received requests
InChIGenerationImpl.java : Implementation for the endpoint “/generation”
- fr.metabocloud.inchi.utilsPackage containing model objects
ConfigUtils.java : Utils for configuring the path of the binary program
src/main/resources :Resources associated to the applicationlocal/Resource for building the application to use it in localapplication.properties : Configuration file of the application properties
mesocentre/Resource for building the application to use it on the MetaboCloud productionapplication.properties : Configuration file of the application properties
pfem/Resource for building the application to use it on the PFEM dev serverapplication.properties : Configuration file of the application properties
static/Folder containing the static filesmetabocloud-inchi.yaml : OpenAPI file describing the InChI REST API
src/test/javaContain the Java sources of the unit tests- fr.metabocloud.inchi :
ApplicationTests.java : Test on the main application
- fr.metabocloud.inchi.controllers.corePackage containing tests on controllers associated to the REST API
AboutControllerTest.java : Tests on the controller for the endpoint “/about” to retrieve the metadata associated to the REST API
RootControllerTest : Tests on the controller for the root “/” of the REST API
- fr.metabocloud.inchi.controllers.inchiPackage containing tests on controllers associated to the tool InChI
InChIGenerationControllerTest.java : Tests on the controller for the endpoint “/generation”
- fr.metabocloud.inchi.data.modelPackage containing the model used for tests
Parameters.java : Model with all available parameters to query the application
- fr.metabocloud.inchi.data.providersPackage containing the providers used to import data into tests
GenerationProvider.java : Provider for the “/generation” endpoint
- fr.metabocloud.inchi.data.stubPackage containing classes which store the input to used in tests
JsonStub.java : Store JSON response several compounds
MolStub.java : Store MOLs of several compounds
SdfStub.java : Store SDFs of several compounds
- fr.metabocloud.inchi.implementation: Package containing tests on the implemented methods to process the received requests
InChIGenerationImplTest.java : Tests on the implementation for the endpoint “/generation”
src/test/resourcesHost the files that are not Java sources but are necessary to run the tests.input/: Folder containing the input used to run the tests
Note
A Controller is a class that implements operations defined by the API. It will receive the request, process it and send back the response.
Note
The highlight is a source folder, the italic a package, and the bold a file.