WOR-1141 Set up landing zone web endpoints (#313)

* WOR-1141 Set up landing zone web endpoints

* Isolate gradle scripts

* Add version endpoint.

* Exclude swagger generated code from spotless analysis

* Add landing zone create endpoint with tests

* Add endpoint to check result of landing zone create operation

* Add all existing landing zone endpoints

* Add unit tests for landing zone controller

* Add security to swagger/config to serve static content

* Fix artifactory conflict

* PR comments: unauthenticated-> public controller. sh file permission.

* Refactor test code.

build.gradle

@@ -0,0 +1,3 @@
+plugins {
+    id 'com.jfrog.artifactory' version '5.1.10' apply false
+}

buildSrc/src/main/groovy/bio.terra.landingzone.java-common-conventions.gradle

@@ -5,6 +5,7 @@ plugins {
 
     id 'com.diffplug.spotless'
     id 'com.github.spotbugs'
+    id 'org.hidetake.swagger.generator'
 }
 
 boolean isGithubAction = System.getenv().containsKey("GITHUB_ACTIONS")
@@ -41,6 +42,8 @@ repositories {
 dependencies {
     compileOnly "com.google.code.findbugs:annotations:3.0.1"
     implementation 'org.slf4j:slf4j-api:1.7.35'
+    implementation 'io.swagger.core.v3:swagger-annotations:2.1.12'
+    swaggerCodegen 'io.swagger.codegen.v3:swagger-codegen-cli:3.0.31'
 
     testImplementation 'ch.qos.logback:logback-classic:1.2.10'
     testImplementation 'org.hamcrest:hamcrest:2.2'
@@ -68,6 +71,7 @@ if (hasProperty("buildScan")) {
 spotless {
     java {
         targetExclude "${buildDir}/**"
+        targetExclude "**/swagger-code/**"
         googleJavaFormat()
     }
 }

buildSrc/src/main/groovy/bio.terra.landingzone.java-library-conventions.gradle

@@ -0,0 +1,4 @@
+plugins {
+    id 'bio.terra.landingzone.java-common-conventions'
+    id 'java-library'
+}

client/.swagger-codegen-ignore

@@ -0,0 +1,2 @@
+**
+!**/src/**

client/artifactory.gradle

@@ -0,0 +1,48 @@
+// This and the test below makes sure the build will fail reasonably if you try
+// to publish without the environment variables defined.
+def artifactory_username = System.getenv("ARTIFACTORY_USERNAME")
+def artifactory_password = System.getenv("ARTIFACTORY_PASSWORD")
+
+gradle.taskGraph.whenReady { taskGraph ->
+    if (taskGraph.hasTask(artifactoryPublish) &&
+            (artifactory_username == null || artifactory_password == null)) {
+        throw new GradleException("Set env vars ARTIFACTORY_USERNAME and ARTIFACTORY_PASSWORD to publish")
+    }
+}
+
+java {
+    // Builds sources into the published package as part of the 'assemble' task.
+    withSourcesJar()
+}
+
+publishing {
+    publications {
+        billingProfileManagerClientLibrary(MavenPublication) {
+            artifactId = "landing-zone-service-client"
+            from components.java
+            versionMapping {
+                usage("java-runtime") {
+                    fromResolutionResult()
+                }
+            }
+        }
+    }
+}
+
+artifactory {
+    publish {
+        contextUrl = "https://broadinstitute.jfrog.io/broadinstitute/"
+        repository {
+            repoKey = "libs-snapshot-local" // The Artifactory repository key to publish to
+            username = "${artifactory_username}" // The publisher user name
+            password = "${artifactory_password}" // The publisher password
+        }
+        defaults {
+            // This is how we tell the Artifactory Plugin which artifacts should be published to Artifactory.
+            // Reference to Gradle publications defined in the build script.
+            publications("landingZoneServiceClientLibrary")
+            publishArtifacts = true
+            publishPom = true
+        }
+    }
+}

client/build.gradle

@@ -0,0 +1,18 @@
+import org.springframework.boot.gradle.plugin.SpringBootPlugin
+
+plugins {
+    id 'bio.terra.landingzone.java-library-conventions'
+    id 'maven-publish'
+    id 'io.spring.dependency-management'
+    id 'com.jfrog.artifactory'
+    id 'org.hidetake.swagger.generator'
+}
+
+dependencyManagement {
+    imports {
+        mavenBom(SpringBootPlugin.BOM_COORDINATES)
+    }
+}
+
+apply from: 'artifactory.gradle'
+apply from: 'swagger.gradle'

client/swagger.gradle

@@ -0,0 +1,44 @@
+dependencies {
+    // Version controlled by dependency management plugin
+    implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310'
+    implementation 'org.glassfish.jersey.core:jersey-client'
+    implementation 'org.glassfish.jersey.media:jersey-media-json-jackson'
+    implementation 'org.glassfish.jersey.media:jersey-media-multipart'
+
+    implementation 'io.swagger.core.v3:swagger-annotations'
+    swaggerCodegen 'io.swagger.codegen.v3:swagger-codegen-cli'
+}
+
+def artifactGroup = "${group}.lz.futureservice"
+
+generateSwaggerCode {
+    inputFile = file('../service/src/main/resources/api/service_openapi.yaml')
+    language = 'java'
+    library = 'jersey2'
+
+    // For Swagger Codegen v3 on Java 16+
+    // See https://github.com/swagger-api/swagger-codegen/issues/10966
+    jvmArgs = ['--add-opens=java.base/java.util=ALL-UNNAMED']
+
+    components = [
+            apiDocs  : false, apiTests: false,
+            modelDocs: false, modelTests: false
+    ]
+
+    additionalProperties = [
+            modelPackage  : "${artifactGroup}.model",
+            apiPackage    : "${artifactGroup}.api",
+            invokerPackage: "${artifactGroup}.client",
+            dateLibrary   : 'java11',
+            java8         : true
+    ]
+
+    rawOptions = ['--ignore-file-override', "${projectDir}/.swagger-codegen-ignore"]
+}
+
+idea.module.generatedSourceDirs = [file("${generateSwaggerCode.outputDir}/src/main/java")]
+sourceSets.main.java.srcDir "${generateSwaggerCode.outputDir}/src/main/java"
+compileJava.dependsOn generateSwaggerCode
+sourcesJar.dependsOn generateSwaggerCode
+//why this is required?
+spotlessJava.dependsOn generateSwaggerCode

library/build.gradle

@@ -4,7 +4,7 @@ plugins {
     id 'com.google.cloud.tools.jib'
     id 'com.srcclr.gradle'
     id 'org.sonarqube'
-    id 'com.jfrog.artifactory' version '5.1.10'
+    id 'com.jfrog.artifactory'
     id 'org.liquibase.gradle' version '2.2.0'
 }
 

service/build.gradle

@@ -3,15 +3,27 @@ plugins {
     id 'de.undercouch.download'
     id 'com.google.cloud.tools.jib'
     id 'com.srcclr.gradle'
+    id 'com.gorylenko.gradle-git-properties' version '2.4.1'
 }
 
-apply from: 'publishing.gradle'
+project.ext {
+    includeDir = "$projectDir/gradle"
+    resourceDir = "${projectDir}/src/main/resources"
+}
+
+apply(from: "$includeDir/generators.gradle")
+apply(from: "$includeDir/publishing.gradle")
 
 dependencies {
-    implementation 'org.springframework.boot:spring-boot-starter-web'
     implementation project(':library')
+    implementation group: "org.springframework.boot", name: "spring-boot-starter-web"
+    implementation group: "org.springframework.boot", name: "spring-boot-starter-validation"
+    implementation group: "org.springframework.boot", name: "spring-boot-starter-data-jdbc"
+
+    //implementation group: "org.liquibase", name: "liquibase-core", version: "4.8.0"
 
     testImplementation 'org.springframework.boot:spring-boot-starter-test'
+    testImplementation group: "org.hamcrest", name: "hamcrest", version: "2.2"
 }
 
 test {

service/gradle/generators.gradle

@@ -0,0 +1,50 @@
+dependencies {
+    implementation 'io.swagger.core.v3:swagger-annotations'
+    runtimeOnly 'org.webjars.npm:swagger-ui-dist:4.5.0'
+    swaggerCodegen 'io.swagger.codegen.v3:swagger-codegen-cli'
+
+    // Versioned by Spring:
+    implementation 'javax.validation:validation-api'
+    implementation 'org.webjars:webjars-locator-core'
+
+    annotationProcessor 'org.springframework.boot:spring-boot-configuration-processor'
+}
+
+def artifactGroup = "${group}.lz.futureservice"
+
+generateSwaggerCode {
+    inputFile = file('src/main/resources/api/service_openapi.yaml')
+    language = 'spring'
+    components = ['models', 'apis']
+    // For Swagger Codegen v3 on Java 16+
+    // See https://github.com/swagger-api/swagger-codegen/issues/10966
+    jvmArgs = ['--add-opens=java.base/java.util=ALL-UNNAMED']
+    additionalProperties = [
+            modelPackage     : "${artifactGroup}.generated.model",
+            apiPackage       : "${artifactGroup}.generated.api",
+            modelNamePrefix  : "Api",
+            dateLibrary      : 'java8',
+            java8            : true,
+            interfaceOnly    : 'true',
+            useTags          : 'true',
+            springBootVersion: dependencyManagement.managedVersions['org.springframework.boot:spring-boot']
+    ]
+}
+
+String swaggerOutputSrc = "${generateSwaggerCode.outputDir}/src/main/java"
+
+idea.module.generatedSourceDirs = [file(swaggerOutputSrc)]
+sourceSets.main.java.srcDir swaggerOutputSrc
+compileJava.dependsOn generateSwaggerCode
+//why this is required?
+spotlessJava.dependsOn generateSwaggerCode
+
+// see https://github.com/n0mer/gradle-git-properties
+gitProperties {
+    keys = []
+    gitPropertiesName = "version.properties"
+    customProperty('landingzone.version.gitTag', { it.describe(tags: true) })
+    customProperty('landingzone.version.gitHash', { it.head().abbreviatedId })
+    customProperty('landingzone.version.github', { "https://github.com/DataBiosphere/terra-landing-zone-service/tree/${it.describe(tags: true)}" })
+    customProperty('landingzone.version.build', version)
+}

service/local-dev/local-postgres-init.sql

@@ -0,0 +1,4 @@
+CREATE DATABASE landingzone_db;
+CREATE ROLE landingzoneuser WITH LOGIN ENCRYPTED PASSWORD 'landingzonepwd';
+CREATE DATABASE landingzone_stairway_db;
+CREATE ROLE landingzonestairwayuser WITH LOGIN ENCRYPTED PASSWORD 'landingzonestairwaypwd';

service/local-dev/run_postgres.sh

@@ -0,0 +1,50 @@
+#!/usr/bin/env bash
+# Start up a postgres container with initial user/database setup.
+POSTGRES_VERSION=13.1
+
+start() {
+    echo "attempting to remove old $CONTAINER container..."
+    docker rm -f $CONTAINER
+
+    # start up postgres
+    echo "starting up postgres container..."
+    BASEDIR=$(dirname "$0")
+    docker create --name $CONTAINER --rm -e POSTGRES_PASSWORD=password -p "$POSTGRES_PORT:5432" postgres:$POSTGRES_VERSION
+    docker cp $BASEDIR/local-postgres-init.sql $CONTAINER:/docker-entrypoint-initdb.d/docker_postgres_init.sql
+    docker start $CONTAINER
+
+    # validate postgres
+    echo "running postgres validation..."
+    docker exec $CONTAINER sh -c "$(cat $BASEDIR/sql_validate.sh)"
+    if [ 0 -eq $? ]; then
+        echo "postgres validation succeeded."
+    else
+        echo "postgres validation failed."
+        exit 1
+    fi
+
+}
+
+stop() {
+    echo "Stopping docker $CONTAINER container..."
+    docker stop $CONTAINER || echo "postgres stop failed. container already stopped."
+    docker rm -v $CONTAINER
+    exit 0
+}
+
+CONTAINER=postgres_lz
+COMMAND=$1
+POSTGRES_PORT=${2:-"5432"}
+
+if [ ${#@} == 0 ]; then
+    echo "Usage: $0 stop|start"
+    exit 1
+fi
+
+if [ $COMMAND = "start" ]; then
+    start
+elif [ $COMMAND = "stop" ]; then
+    stop
+else
+    exit 1
+fi

service/local-dev/sql_validate.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+# validate postgres
+echo "sleeping for 5 seconds during postgres boot..."
+sleep 5
+PGPASSWORD=dbpwd psql --username landingzoneuser -d landingzone_db -c "SELECT VERSION();SELECT NOW()"

service/src/main/java/bio/terra/lz/futureservice/app/LandingZoneApplication.java

@@ -0,0 +1,31 @@
+package bio.terra.lz.futureservice.app;
+
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration;
+import org.springframework.context.annotation.ComponentScan;
+
+// temporarily disable autoconfiguration since we don't have any related db yet.
+// this prevents from running application
+@SpringBootApplication(exclude = {DataSourceAutoConfiguration.class})
+@ComponentScan(
+    basePackages = {
+      // Dependencies for Stairway
+      "bio.terra.common.kubernetes",
+      // Scan for iam token handling
+      "bio.terra.common.iam",
+      // Stairway initialization and status
+      "bio.terra.common.stairway",
+      // Scan all landing zone service packages; from 'library' module
+      "bio.terra.landingzone",
+      // Scan for Liquibase migration components & configs
+      "bio.terra.common.migrate",
+      // future lz service
+      "bio.terra.lz.futureservice"
+    })
+public class LandingZoneApplication {
+
+  public static void main(String[] args) {
+    SpringApplication.run(LandingZoneApplication.class, args);
+  }
+}

service/src/main/java/bio/terra/lz/futureservice/app/StartupInitializer.java

@@ -0,0 +1,14 @@
+package bio.terra.lz.futureservice.app;
+
+import bio.terra.common.migrate.LiquibaseMigrator;
+import bio.terra.landingzone.library.LandingZoneMain;
+import org.springframework.context.ApplicationContext;
+
+public class StartupInitializer {
+  public static void initialize(ApplicationContext applicationContext) {
+    LiquibaseMigrator migrateService = applicationContext.getBean(LiquibaseMigrator.class);
+
+    // Initialize Terra Landing Zone library
+    LandingZoneMain.initialize(applicationContext, migrateService);
+  }
+}