Merge pull request #1 from TheJacksonLaboratory/feature/framing

Feature/framing

.gitignore

@@ -13,3 +13,5 @@ out/
 .settings
 .classpath
 .factorypath
+
+oan-etl/data/

README.md

@@ -1,38 +1,46 @@
-## Micronaut 4.1.2 Documentation
+## Ontology Annotation Network
 
+*A graph to maintain our ontology annotation connections.*
+
+Java 17
+
+Micronaut 4.1.2
 - [User Guide](https://docs.micronaut.io/4.1.2/guide/index.html)
 - [API Reference](https://docs.micronaut.io/4.1.2/api/index.html)
 - [Configuration Reference](https://docs.micronaut.io/4.1.2/guide/configurationreference.html)
 - [Micronaut Guides](https://guides.micronaut.io/index.html)
 ---
 
-- [Shadow Gradle Plugin](https://plugins.gradle.org/plugin/com.github.johnrengelman.shadow)
-- [Micronaut Gradle Plugin documentation](https://micronaut-projects.github.io/micronaut-gradle-plugin/latest/)
-- [GraalVM Gradle Plugin documentation](https://graalvm.github.io/native-build-tools/latest/gradle-plugin.html)
-## Feature serialization-jackson documentation
-
-- [Micronaut Serialization Jackson Core documentation](https://micronaut-projects.github.io/micronaut-serialization/latest/guide/)
-
-
-## Feature neo4j-bolt documentation
-
-- [Micronaut Neo4j Bolt Driver documentation](https://micronaut-projects.github.io/micronaut-neo4j/latest/guide/index.html)
-
-
-## Feature openapi documentation
+### Modules
 
-- [Micronaut OpenAPI Support documentation](https://micronaut-projects.github.io/micronaut-openapi/latest/guide/index.html)
+#### OAN-ETL
+    A ontologyModule to load our graph data which includes phenotypes, diseases, genes, assays. There
+    are multiple loaders for the different ontologies that are supported
 
-- [https://www.openapis.org](https://www.openapis.org)
+Running
 
+```
+    ./gradlew oan-etl:run
+```
 
-## Feature micronaut-aot documentation
+Testing
 
-- [Micronaut AOT documentation](https://micronaut-projects.github.io/micronaut-aot/latest/guide/)
+```
+    ./gradlew oan-etl:test
+```
 
+#### OAN-REST
+    A ontologyModule that exposes our graph via a REST-API. This will be used for the hpo web application
+    and deployed to google cloud.
 
-## Feature github-workflow-ci documentation
+Running
 
-- [https://docs.github.com/en/actions](https://docs.github.com/en/actions)
+```
+    ./gradlew oan-rest:run
+```
 
+Testing
 
+```
+    ./gradlew oan-rest:test
+```

build.gradle

@@ -18,6 +18,15 @@ dependencies {
     implementation("io.micronaut.neo4j:micronaut-neo4j-bolt")
     implementation("io.micronaut.serde:micronaut-serde-jackson")
     implementation("io.swagger.core.v3:swagger-annotations")
+    implementation("org.monarchinitiative.phenol:phenol-core:2.0.3"){
+        exclude group: 'org.slf4j', module: 'slf4j-api'
+    }
+    implementation("org.monarchinitiative.phenol:phenol-io:2.0.3"){
+        exclude group: 'org.slf4j', module: 'slf4j-api'
+    }
+    implementation("org.monarchinitiative.phenol:phenol-annotations:2.0.3"){
+        exclude group: 'org.slf4j', module: 'slf4j-api'
+    }
     compileOnly("org.graalvm.nativeimage:svm")
     runtimeOnly("ch.qos.logback:logback-classic")
     testImplementation("io.micronaut:micronaut-http-client")

oan-etl/build.gradle

@@ -0,0 +1,68 @@
+plugins {
+    id("com.github.johnrengelman.shadow") version "8.1.1"
+    id("io.micronaut.application") version "4.0.3"
+    id('jacoco')
+}
+
+group = 'org.jax'
+version = '0.1'
+
+repositories {
+    mavenCentral()
+}
+
+dependencies {
+    implementation project(':oan-model')
+    annotationProcessor("info.picocli:picocli-codegen")
+    annotationProcessor("io.micronaut.serde:micronaut-serde-processor")
+    testAnnotationProcessor("io.micronaut:micronaut-inject-java")
+    implementation("info.picocli:picocli")
+    implementation("io.micronaut.picocli:micronaut-picocli")
+    implementation("io.micronaut.serde:micronaut-serde-jackson")
+    implementation("io.micronaut.neo4j:micronaut-neo4j-bolt")
+    implementation("org.monarchinitiative.phenol:phenol-core:2.0.3"){
+        exclude group: 'org.slf4j', module: 'slf4j-api'
+    }
+    implementation("org.monarchinitiative.phenol:phenol-io:2.0.3"){
+        exclude group: 'org.slf4j', module: 'slf4j-api'
+    }
+    implementation("org.monarchinitiative.phenol:phenol-annotations:2.0.3"){
+        exclude group: 'org.slf4j', module: 'slf4j-api'
+    }
+    runtimeOnly("ch.qos.logback:logback-classic")
+    testImplementation("io.micronaut.test:micronaut-test-junit5")
+    testImplementation("org.neo4j.test:neo4j-harness")
+    testRuntimeOnly("javax.validation:validation-api:2.0.1.Final")
+    testRuntimeOnly("javax.annotation:javax.annotation-api:1.3.2")
+    testRuntimeOnly('javax.ws.rs:javax.ws.rs-api:2.1.1')
+    testImplementation platform('org.junit:junit-bom:5.9.1')
+    testImplementation('org.junit.jupiter:junit-jupiter')
+}
+
+application {
+    mainClass.set("org.jacksonlaboratory.GraphCommand")
+}
+java {
+    sourceCompatibility = JavaVersion.toVersion("17")
+    targetCompatibility = JavaVersion.toVersion("17")
+}
+
+micronaut {
+    testRuntime("junit5")
+    processing {
+        incremental(true)
+        annotations("org.jacksonlaboratory.*")
+    }
+}
+
+test {
+    finalizedBy jacocoTestReport // report is always generated after tests run
+}
+jacocoTestReport {
+    dependsOn test // tests are required to run before generating the report
+    reports {
+        xml.required = false
+        csv.required = false
+        html.outputLocation = layout.buildDirectory.dir('jacocoHtml')
+    }
+}