feat(agora): create a spec-first REST API prototype in Java-Spring

apps/agora/api-spring/.env.example

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+SERVER_PORT=8086

apps/agora/api-spring/.gitignore

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+.gradle
+bin/
+lib/*.jar
+maven-legacy/
+tmp/
+log/
+
+HELP.md
+target/
+!**/src/main/**/target/
+!**/src/test/**/target/
+
+### STS ###
+.apt_generated
+.classpath
+.factorypath
+.project
+.settings
+.springBeans
+.sts4-cache
+
+### IntelliJ IDEA ###
+.idea
+*.iws
+*.iml
+*.ipr
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/

apps/agora/api-spring/.openapi-generator-ignore

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+# OpenAPI Generator Ignore
+# Generated by openapi-generator https://github.com/openapitools/openapi-generator
+
+# Use this file to prevent files from being overwritten by the generator.
+# The patterns follow closely to .gitignore or .dockerignore.
+
+# As an example, the C# client generator defines ApiClient.cs.
+# You can make changes and tell OpenAPI Generator to ignore just this file by uncommenting the following line:
+# ApiClient.cs
+
+# You can match any string of characters against a directory, file or extension with a single asterisk (*):
+# foo/*/qux
+# The above matches foo/bar/qux and foo/baz/qux, but not foo/bar/baz/qux
+
+# You can recursively match patterns against a directory, file or extension with a double asterisk (**):
+# foo/**/qux
+# This matches foo/bar/qux, foo/baz/qux, and foo/bar/baz/qux
+
+# You can also negate patterns with an exclamation (!).
+# For example, you can ignore all files in a docs folder with the file extension .md:
+# docs/*.md
+# Then explicitly reverse the ignore rule for a single file:
+# !docs/README.md
+pom.xml
+README.md
+**/application.properties
+**/model/dto/*AllOf*.java
+**/OpenApiGeneratorApplication.java
+**/OpenApiGeneratorApplicationTests.java

apps/agora/api-spring/.openapi-generator/FILES

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+src/main/java/org/sagebionetworks/agora/api/OpenApiGeneratorApplication.java
+src/main/java/org/sagebionetworks/agora/api/RFC3339DateFormat.java
+src/main/java/org/sagebionetworks/agora/api/api/ApiUtil.java
+src/main/java/org/sagebionetworks/agora/api/api/BioDomainsApi.java
+src/main/java/org/sagebionetworks/agora/api/api/BioDomainsApiController.java
+src/main/java/org/sagebionetworks/agora/api/api/BioDomainsApiDelegate.java
+src/main/java/org/sagebionetworks/agora/api/api/DataversionApi.java
+src/main/java/org/sagebionetworks/agora/api/api/DataversionApiController.java
+src/main/java/org/sagebionetworks/agora/api/api/DataversionApiDelegate.java
+src/main/java/org/sagebionetworks/agora/api/api/DistributionApi.java
+src/main/java/org/sagebionetworks/agora/api/api/DistributionApiController.java
+src/main/java/org/sagebionetworks/agora/api/api/DistributionApiDelegate.java
+src/main/java/org/sagebionetworks/agora/api/api/GenesApi.java
+src/main/java/org/sagebionetworks/agora/api/api/GenesApiController.java
+src/main/java/org/sagebionetworks/agora/api/api/GenesApiDelegate.java
+src/main/java/org/sagebionetworks/agora/api/api/TeamsApi.java
+src/main/java/org/sagebionetworks/agora/api/api/TeamsApiController.java
+src/main/java/org/sagebionetworks/agora/api/api/TeamsApiDelegate.java
+src/main/java/org/sagebionetworks/agora/api/configuration/HomeController.java
+src/main/java/org/sagebionetworks/agora/api/configuration/SpringDocConfiguration.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/BasicErrorDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/BioDomainDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/BioDomainInfoDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/BioDomainsDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/DataversionDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/DistributionDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/DruggabilityDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/EnsemblInfoDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/ExperimentalValidationDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/GCTGeneDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/GCTGeneNominationsDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/GCTGeneTissueDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/GCTGenesListDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/GeneDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/MedianExpressionDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/NeuropathologicCorrelationDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/NominatedGenesListDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/OverallScoresDistributionDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/OverallScoresDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/ProteinDifferentialExpressionDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/ProteomicsDistributionDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/RnaDifferentialExpressionDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/RnaDistributionDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/SimilarGenesNetworkDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/SimilarGenesNetworkLinkDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/SimilarGenesNetworkNodeDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/TargetNominationDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/TeamDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/TeamMemberDto.java
+src/main/java/org/sagebionetworks/agora/api/model/dto/TeamsListDto.java
+src/main/resources/openapi.yaml
+src/test/java/org/sagebionetworks/agora/api/OpenApiGeneratorApplicationTests.java

apps/agora/api-spring/.openapi-generator/VERSION

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+7.0.0

apps/agora/api-spring/Dockerfile

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+FROM ghcr.io/sage-bionetworks/agora-api-spring-base:local
+
+USER root
+
+RUN apt-get update -qq -y && export DEBIAN_FRONTEND=noninteractive \
+  && apt-get install --no-install-recommends -qq -y \
+    curl jq \
+  && apt-get -y autoclean \
+  && apt-get -y autoremove \
+  && rm -rf /var/lib/apt/lists/*
+
+# Requires the environment variable SERVER_PORT at runtime
+HEALTHCHECK --interval=2s --timeout=3s --retries=20 --start-period=5s \
+  CMD curl --fail --silent "localhost:${SERVER_PORT}/actuator/health/readiness" | jq '.status' | grep UP || exit 1
+
+USER cnb

apps/agora/api-spring/build.gradle

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+buildscript {
+  repositories {
+    mavenCentral()
+  }
+}
+
+plugins {
+  id 'io.spring.dependency-management' version "${springDependencyManagementVersion}"
+  id 'java'
+  id 'jvm-test-suite'
+  id 'org.springframework.boot' version "${springBootVersion}"
+  id 'jacoco'
+  id "org.sonarqube" version "${sonarqubeVersion}"
+}
+
+repositories {
+  mavenCentral()
+  mavenLocal()
+}
+
+testing {
+  suites {
+    test {
+      useJUnitJupiter()
+    }
+
+    integrationTest(JvmTestSuite) {
+      sources {
+        java {
+          srcDirs = ['src/integrationTest/java']
+        }
+      }
+      targets {
+        all {
+          testTask.configure {
+            shouldRunAfter(test)
+          }
+        }
+      }
+    }
+  }
+}
+
+dependencies {
+  annotationProcessor "org.projectlombok:lombok:${lombokVersion}"
+  compileOnly "org.projectlombok:lombok:${lombokVersion}"
+  implementation 'com.google.code.findbugs:jsr305:3.0.2'
+  implementation 'org.openapitools:jackson-databind-nullable:0.2.6'
+  implementation 'org.springdoc:springdoc-openapi-ui:1.7.0'
+  implementation "com.fasterxml.jackson.core:jackson-databind:${fasterxmlVersion}"
+  implementation "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:${fasterxmlVersion}"
+  implementation "com.fasterxml.jackson.datatype:jackson-datatype-jsr310:${fasterxmlVersion}"
+  // implementation "org.sagebionetworks:util:${openchallengesVersion}"
+  implementation "org.springframework.boot:spring-boot-devtools:${springBootVersion}"
+  implementation "org.springframework.boot:spring-boot-starter-actuator:${springBootVersion}"
+  implementation "org.springframework.boot:spring-boot-starter-validation:${springBootVersion}"
+  implementation "org.springframework.boot:spring-boot-starter-web:${springBootVersion}"
+  implementation "org.springframework.boot:spring-boot-starter-data-mongodb:${springBootVersion}"
+  // implementation "org.springframework.cloud:spring-cloud-starter-netflix-eureka-client:${springCloudVersion}"
+  implementation "org.springframework.data:spring-data-commons:${springDataVersion}"
+  testImplementation 'org.assertj:assertj-core:3.23.1'
+  testImplementation "org.springframework.boot:spring-boot-starter-test:${springBootVersion}"
+
+  // Enable distributed tracing
+  // implementation "org.springframework.cloud:spring-cloud-starter-sleuth:${springCloudVersion}"
+  // implementation "org.springframework.cloud:spring-cloud-sleuth-zipkin:${springCloudVersion}"
+
+  // implementation "org.springframework.cloud:spring-cloud-starter-config:${springCloudVersion}"
+
+  // implementation 'io.micrometer:micrometer-registry-prometheus:1.10.4'
+  implementation 'com.squareup:pollexor:3.0.0'
+}
+
+group = 'org.sagebionetworks.agora'
+version = '0.0.1-SNAPSHOT'
+
+java {
+  toolchain {
+    languageVersion = JavaLanguageVersion.of(17)
+  }
+}
+
+tasks.withType(JavaCompile) {
+  options.encoding = 'UTF-8'
+}
+
+bootBuildImage {
+  imageName = "ghcr.io/sage-bionetworks/${project.name}-base:local"
+}
+
+test {
+	useJUnitPlatform()
+
+  testLogging.showStandardStreams = true
+
+  beforeTest { descriptor ->
+     logger.lifecycle("Running test: " + descriptor)
+  }
+
+  failFast = true
+
+  testLogging {
+    events("passed", "skipped", "failed")
+  }
+
+  finalizedBy jacocoTestReport
+}
+
+jacocoTestReport {
+  reports {
+    xml.required = true
+  }
+
+  afterEvaluate {
+    // A single star (*) selects files AND subdirectories.
+    // Exclude Java classes from the JaCoCo report. These files must be excluded from SonarCloud
+    // report separatedly (see SonarCloud config)
+    def autoGeneratedFiles = [
+      '**/api/*.*',
+      '**/configuration/EnumConverterConfiguration*.*',
+      '**/configuration/HomeController*.*',
+      '**/configuration/SpringDocConfiguration*.*',
+      '**/model/dto/**',
+      '**/RFC3339DateFormat.*'
+    ]
+    classDirectories.setFrom(files(classDirectories.files.collect {
+        fileTree(dir: it, exclude: autoGeneratedFiles
+        )
+    }))
+  }
+}

apps/agora/api-spring/config/application-local.yml

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+agora-api:
+  welcome-message: 'Welcome to the Agora API (local config).'

apps/agora/api-spring/gradle.properties

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+# Updating fasterxml to v2.15.3 results in an error (see #2373)
+fasterxmlVersion=2.13.4
+flywaydbVersion=9.4.0
+hibernateSearchVersion=6.1.7.Final
+lombokVersion=1.18.30
+openchallengesVersion=0.0.1-SNAPSHOT
+sonarqubeVersion=4.3.0.3225
+springBootVersion=2.7.8
+springCloudVersion=3.1.4
+springDataVersion=2.7.7
+springDependencyManagementVersion=1.0.14.RELEASE

apps/agora/api-spring/gradle/wrapper/gradle-wrapper.properties

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+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists