init: Create spring boot backend with gradle build and initial configuration. GNP-5451.

.idea/gpds.iml

@@ -4,7 +4,10 @@
     <exclude-output />
     <content url="file://$MODULE_DIR$">
       <excludeFolder url="file://$MODULE_DIR$/.gradle" />
+      <excludeFolder url="file://$MODULE_DIR$/.idea" />
+      <excludeFolder url="file://$MODULE_DIR$/backend/build" />
       <excludeFolder url="file://$MODULE_DIR$/build" />
+      <excludeFolder url="file://$MODULE_DIR$/frontend/.gradle" />
       <excludeFolder url="file://$MODULE_DIR$/frontend/dist" />
       <excludeFolder url="file://$MODULE_DIR$/frontend/tmp" />
     </content>

.idea/modules.xml

@@ -2,8 +2,11 @@
 <project version="4">
   <component name="ProjectModuleManager">
     <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/modules/frontend/frontend.iml" filepath="$PROJECT_DIR$/.idea/modules/frontend/frontend.iml" group="frontend" />
+      <module fileurl="file://$PROJECT_DIR$/.idea/modules/backend/backend.iml" filepath="$PROJECT_DIR$/.idea/modules/backend/backend.iml" group="backend" />
+      <module fileurl="file://$PROJECT_DIR$/.idea/modules/backend/backend_main.iml" filepath="$PROJECT_DIR$/.idea/modules/backend/backend_main.iml" group="backend" />
+      <module fileurl="file://$PROJECT_DIR$/.idea/modules/backend/backend_test.iml" filepath="$PROJECT_DIR$/.idea/modules/backend/backend_test.iml" group="backend" />
       <module fileurl="file://$PROJECT_DIR$/.idea/gpds.iml" filepath="$PROJECT_DIR$/.idea/gpds.iml" />
+      <module fileurl="file://$PROJECT_DIR$/.idea/modules/frontend/gpds-frontend.iml" filepath="$PROJECT_DIR$/.idea/modules/frontend/gpds-frontend.iml" group="frontend" />
     </modules>
   </component>
 </project>
\ No newline at end of file

README.md

@@ -32,10 +32,30 @@ cd frontend
 npm install
 ```
 
+### Install Java JDK8
+
+See instructions for your operating system
+
+
+## Run backend development server
+
+If you just need access to API (to run the Angular serve on top) without the frontend interface, you can run:
+
+```sh
+./gradlew bootRun
+```
+
+Otherwise, for the complete server (backend API + frontend interface), you can run:
+
+```sh
+./gradlew assemble && java -jar backend/build/libs/gpds.jar
+```
+
+The server should then be accessible at http://localhost:8080/gnpis-core
+
 ## Run frontend development server
 
-The frontend requests are redirected to the production server API of GnpIS core 
-(https://urgi.versailles.inra.fr/gnpis-core-srv/swagger-ui.html) via the 
+The frontend requests are redirected to the local backend API server (see instructions above to launch) via the
 Angular proxy.
 
 You can run the development server with the following command:

backend/build.gradle.kts

+import org.gradle.api.tasks.testing.logging.TestExceptionFormat
+import org.springframework.boot.gradle.tasks.buildinfo.BuildInfo
+import org.springframework.boot.gradle.tasks.bundling.BootJar
+import org.springframework.boot.gradle.tasks.run.BootRun
+
+buildscript {
+    repositories {
+        mavenLocal()
+        mavenCentral()
+    }
+}
+
+plugins {
+    java
+    jacoco
+    id("org.springframework.boot") version "2.1.1.RELEASE"
+    id("com.gorylenko.gradle-git-properties") version "1.5.2"
+    id("io.spring.dependency-management") version "1.0.6.RELEASE"
+}
+
+
+java {
+    sourceCompatibility = JavaVersion.VERSION_1_8
+}
+
+repositories {
+    mavenCentral()
+}
+
+val snippetsDir = file("build/generated-snippets")
+
+tasks {
+
+    withType(JavaCompile::class.java) {
+        // make sur the parameter names are writtn in the byte code and available using reflection.
+        // this is useful for Jackson and Spring to automatically deduce propert names or path variable names
+        // based on the name of the parameter
+        options.compilerArgs.add("-parameters")
+    }
+
+    getByName<Copy>("processResources") {
+        inputs.property("app", "gnpis")
+
+        filesMatching("bootstrap.yml") {}
+    }
+
+    // this task is always out-of-date because it generates a properties file with the build time inside
+    // so the bootJar task is also always out of date, too, since it depends on it
+    // but it's better to do that than using the bootInfo() method of the springBoot closure, because that
+    // makes the test task out of date, which makes the build much longer.
+    // See https://github.com/spring-projects/spring-boot/issues/13152
+    val buildInfo by creating(BuildInfo::class) {
+        destinationDir = file("$buildDir/buildInfo")
+    }
+
+    val bootJar by getting(BootJar::class) {
+        archiveName = "${rootProject.name}.jar"
+        dependsOn(":frontend:assemble")
+        dependsOn(buildInfo)
+
+        into("BOOT-INF/classes/static") {
+            from("${project(":frontend").projectDir}/dist/frontend")
+        }
+        into("BOOT-INF/classes/META-INF") {
+            from(buildInfo.destinationDir)
+        }
+        launchScript()
+    }
+
+    val test by getting(Test::class) {
+        useJUnitPlatform()
+        testLogging {
+            exceptionFormat = TestExceptionFormat.FULL
+        }
+        outputs.dir(snippetsDir)
+    }
+
+    val jacocoTestReport by getting(JacocoReport::class) {
+        reports {
+            xml.setEnabled(true)
+            html.setEnabled(true)
+        }
+    }
+}
+
+dependencyManagement {
+    imports {
+        mavenBom("org.springframework.cloud:spring-cloud-dependencies:Finchley.SR1")
+    }
+}
+
+dependencies {
+    annotationProcessor("org.springframework.boot:spring-boot-configuration-processor")
+    implementation("org.springframework.boot:spring-boot-starter-web")
+    implementation("org.springframework.boot:spring-boot-starter-actuator")
+    implementation("org.springframework.cloud:spring-cloud-starter-config")
+
+    implementation("io.swagger:swagger-annotations:1.5.21")
+
+    // Elasticsearch
+    implementation("org.elasticsearch:elasticsearch:6.5.1")
+    implementation("org.elasticsearch.client:transport:6.5.1")
+
+    testImplementation("org.springframework.boot:spring-boot-starter-test") {
+        exclude(module = "junit")
+    }
+
+    testImplementation("org.junit.jupiter:junit-jupiter-api")
+    testImplementation("org.junit.jupiter:junit-jupiter-params")
+    testImplementation("org.mockito:mockito-junit-jupiter:2.23.0")
+    testImplementation("org.junit-pioneer:junit-pioneer:0.3.0")
+
+    testRuntimeOnly("org.junit.jupiter:junit-jupiter-engine")
+}

backend/src/main/java/fr/inra/urgi/gpds/Application.java

+package fr.inra.urgi.gpds;
+
+import fr.inra.urgi.gpds.config.GPDSProperties;
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
+import org.springframework.scheduling.annotation.EnableAsync;
+
+/**
+ * The main gpds Application
+ * @author gcornut
+ */
+@SpringBootApplication
+@EnableAsync
+@EnableConfigurationProperties(GPDSProperties.class)
+public class Application {
+    public static void main(String[] args) {
+        SpringApplication.run(Application.class, args);
+    }
+}

backend/src/main/java/fr/inra/urgi/gpds/IndexFilter.java

+package fr.inra.urgi.gpds;
+
+import org.springframework.stereotype.Component;
+
+import javax.servlet.*;
+import javax.servlet.annotation.WebFilter;
+import javax.servlet.http.HttpServletRequest;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * Filter that forwards all GET requests to non-static and non-api resources to index.html. This filter is necessary
+ * to support deep-linking for URLs generated by the Angular router.
+ *
+ * @author JB Nizet
+ */
+@Component
+@WebFilter("/*")
+public class IndexFilter implements Filter {
+
+    @Override
+    public void doFilter(ServletRequest req,
+                         ServletResponse response,
+                         FilterChain chain) throws IOException, ServletException {
+        HttpServletRequest request = (HttpServletRequest) req;
+        if (mustForward(request)) {
+            request.getRequestDispatcher("/index.html").forward(request, response);
+            return;
+        }
+
+        chain.doFilter(request, response);
+    }
+
+    private boolean mustForward(HttpServletRequest request) {
+        if (!request.getMethod().equals("GET")) {
+            return false;
+        }
+
+        String fullUri = request.getRequestURI();
+        String contextPath = request.getContextPath();
+        String uri = fullUri.substring(contextPath.length());
+
+        return !(isApi(uri) || isStaticResource(uri));
+    }
+
+    private boolean isApi(String uri) {
+        return uri.startsWith("/brapi") || uri.startsWith("/actuator") || uri.startsWith("/gnpis/v1");
+    }
+
+    private boolean isStaticResource(String uri) {
+        if (uri.startsWith("/index.html")) {
+            return true;
+        }
+
+        List<String> suffixes = Arrays.asList(
+            ".js", ".css", ".ico", ".png", ".jpg", ".gif", ".eot", ".svg", ".woff2", ".ttf", ".woff"
+        );
+        for (String suffix : suffixes) {
+            if (uri.endsWith(suffix)) return true;
+        }
+        return false;
+    }
+
+
+    @Override
+    public void init(FilterConfig filterConfig) {
+        // nothing to do
+    }
+
+    @Override
+    public void destroy() {
+        // nothing to do
+    }
+}

backend/src/main/java/fr/inra/urgi/gpds/api/brapi/v1/CallsController.java

+package fr.inra.urgi.gpds.api.brapi.v1;
+
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.bind.annotation.RestController;
+
+/**
+ * @author gcornut
+ *
+ *         Copyright (c) 2019 INRA URGI
+ */
+@Api(tags = { "Breeding API" }, description = "BrAPI endpoints")
+@RestController
+@RequestMapping("/brapi/v1/calls")
+public class CallsController {
+
+    /**
+	 * @link https://github.com/plantbreeding/API/blob/master/Specification/Calls/Calls.md
+	 */
+	@ApiOperation("List implemented Breeding API calls")
+	@ResponseBody
+    @GetMapping
+	public String calls() {
+        return "ok";
+	}
+
+}

backend/src/main/java/fr/inra/urgi/gpds/api/gnpis/v1/DataDiscoveryController.java

+package fr.inra.urgi.gpds.api.gnpis.v1;
+
+import io.swagger.annotations.Api;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.bind.annotation.RestController;
+
+/**
+ * @author gcornut
+ *
+ *         Copyright (c) 2019 INRA URGI
+ */
+@Api(tags = { "GnpIS API", "Data discovery" }, description = "GnpIS API data discovery endpoint")
+@RestController
+@RequestMapping("/gnpis/v1/datadiscovery")
+public class DataDiscoveryController {
+
+    @ResponseBody
+    @PostMapping("/suggest")
+    public String calls() {
+        return "ok";
+    }
+
+}

backend/src/main/java/fr/inra/urgi/gpds/config/GPDSProperties.java

+package fr.inra.urgi.gpds.config;
+
+import org.springframework.boot.context.properties.ConfigurationProperties;
+
+/**
+ * Properties class holding the properties of the application (typically stored in application.yml)
+ *
+ * @author gcornut
+ */
+@ConfigurationProperties(prefix = "gpds")
+public class GPDSProperties {
+}

backend/src/main/resources/application.yml

+data:
+  elasticsearch:
+      cluster:
+        name: es-gpds
+      host: 127.0.0.1
+      port: 9300
+
+management:
+  endpoint:
+    health:
+      show-details: 'always'
+  endpoints:
+    web:
+      exposure:
+        include: '*'
+
+server:
+  compression:
+    enabled: true
+    mime-types:
+      - application/json
+      - application/javascript
+      - text/html
+      - text/css
+
+logging.level:
+  root: ERROR
+  org.springframework:
+    boot.web.embedded.tomcat.TomcatWebServer: INFO
+    web.client.RestTemplate: DEBUG
+
+---
+spring:
+  profiles: gnpis
+  cloud.config.name: gpds
+
+server:
+  port: 8080
+  servlet:
+    context-path: /gnpis-core

backend/src/main/resources/bootstrap.yml

+spring:
+  application:
+    name: gpds
+  cloud:
+    config:
+      uri: ${SPRING_CONFIG_URI:http://localhost:8888}
+  profiles:
+    active: gnpis

frontend/build.gradle.kts

@@ -47,7 +47,6 @@ tasks {
     // Build assemble
     val assemble by getting {
         dependsOn("npm_run_build")
-        dependsOn(lint)
     }
 
 }

frontend/proxy.conf.js

@@ -4,7 +4,7 @@ const PROXY_CONFIG = [
             "/brapi",
             "/gnpis",
         ],
-        target: "https://urgi.versailles.inra.fr/beta/gnpis-core-srv",
+        target: "http://localhost:8080/gnpis-core",
         secure: false
     }
 ];

frontend/src/index.html

@@ -3,7 +3,7 @@
   <head>
     <meta charset="utf-8">
     <title>GnpIS Plant Data Search</title>
-    <base href="/">
+    <base href="./">
 
     <meta name="viewport" content="width=device-width, initial-scale=1">
     <link rel="icon" type="image/x-icon" href="favicon.ico">

settings.gradle.kts

 rootProject.name = "gpds"
-include("frontend")
+include("backend", "frontend")