Update dependencies and for the way we're making services work these days

Dockerfile

@@ -18,21 +18,34 @@ RUN jlink --compress=2 --module-path /opt/jdk/jmods \
     && apk add --no-cache git sed findutils coreutils make npm curl gawk \
     && git config --global advice.detachedHead false
 
-ENV DOCKER=build
+RUN npm install -gs raml2html raml2html-modern-theme
 
-# copy files required to build dev environment and fetch dependencies
-COPY makefile build.gradle.kts settings.gradle.kts gradlew ./
+# download gradle
+COPY gradlew ./
 COPY gradle gradle
+RUN bash -c 'echo "\n\n" | ./gradlew init --type basic --dsl kotlin --no-daemon'
+
+# copy files required to build dev environment and fetch dependencies
+COPY build.gradle.kts settings.gradle.kts ./
 
-# cache build environment
-RUN make install-dev-env
+# download raml tools (these never change)
+RUN ./gradlew install-raml-4-jax-rs install-raml-merge
+
+# download project dependencies in advance
+RUN ./gradlew download-dependencies
+
+# copy raml over for merging, then perform code and documentation generation
+COPY api.raml ./
+COPY schema schema
+RUN ./gradlew generate-jaxrs generate-raml-docs
 
 # copy remaining files
 COPY . .
 
 # build the project
 RUN ./gradlew clean test shadowJar
 
+
 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
 #
 #   Run the service

api.raml

@@ -68,13 +68,18 @@ uses:
           application/json:
             type: error.ServerError
 
-# TODO: need the file upload patch in the gradle plugin for this
 /word-count:
   post:
     description: Counts the words in an uploaded file.
     body:
       multipart/form-data:
-        type: file
+        type: object
+        properties:
+          uploadMethod:
+            type: string
+            enum: [ 'url', 'file' ]
+          url?: string
+          file?: file
     responses:
       200:
         description: |

build.gradle.kts

@@ -2,7 +2,7 @@ import org.veupathdb.lib.gradle.container.util.Logger.Level
 
 plugins {
   java
-  id("org.veupathdb.lib.gradle.container.container-utils") version "4.5.3"
+  id("org.veupathdb.lib.gradle.container.container-utils") version "4.8.3"
   id("com.github.johnrengelman.shadow") version "7.1.2"
 }
 
@@ -41,19 +41,9 @@ containerBuild {
     dockerFile = "Dockerfile"
 
     // Resulting image tag
-    imageName = "example-service"
+    imageName = "example-async-service"
 
   }
-
-  generateJaxRS {
-    // List of custom arguments to use in the jax-rs code generation command
-    // execution.
-    arguments = listOf(/*arg1, arg2, arg3*/)
-
-    // Map of custom environment variables to set for the jax-rs code generation
-    // command execution.
-    environment = mapOf(/*Pair("env-key", "env-val"), Pair("env-key", "env-val")*/)
-  }
 }
 
 java {
@@ -95,21 +85,21 @@ dependencies {
   // repository:
 
   // Core lib
-  implementation("org.veupathdb.lib:jaxrs-container-core:6.10.1")
+  implementation("org.veupathdb.lib:jaxrs-container-core:6.14.4")
 
   // Jersey
-  implementation("org.glassfish.jersey.core:jersey-server:3.0.8")
+  implementation("org.glassfish.jersey.core:jersey-server:3.1.1")
 
   // Async platform core
-  implementation("org.veupathdb.lib:compute-platform:1.3.5")
+  implementation("org.veupathdb.lib:compute-platform:1.5.0")
 
   // Job IDs
   implementation("org.veupathdb.lib:hash-id:1.1.0")
 
   // Logging
   implementation("org.slf4j:slf4j-api:1.7.36")
-  implementation("org.apache.logging.log4j:log4j-core:2.19.0")
-  runtimeOnly("org.apache.logging.log4j:log4j-slf4j-impl:2.19.0")
+  implementation("org.apache.logging.log4j:log4j-core:2.20.0")
+  runtimeOnly("org.apache.logging.log4j:log4j-slf4j-impl:2.20.0")
 
 
   // Example Dependencies
@@ -120,7 +110,7 @@ dependencies {
   // Pico CLI
   // Only required if your project adds custom CLI/environment options, see
   // the "MyOptions" class in the demo source code.
-  implementation("info.picocli:picocli:4.6.3")
+  implementation("info.picocli:picocli:4.7.1")
 
   // Jackson
   // Only required if you are going to be directly using Jackson's JSON api.
@@ -138,9 +128,9 @@ dependencies {
   // These dependencies are not required, but are recommended.
 
   // JUnit 5
-  testImplementation("org.junit.jupiter:junit-jupiter-api:5.9.0")
-  testRuntimeOnly("org.junit.jupiter:junit-jupiter-engine:5.9.0")
+  testImplementation("org.junit.jupiter:junit-jupiter-api:5.9.2")
+  testRuntimeOnly("org.junit.jupiter:junit-jupiter-engine:5.9.2")
 
   // Mockito Test Mocking
-  testImplementation("org.mockito:mockito-core:4.7.0")
+  testImplementation("org.mockito:mockito-core:5.2.0")
 }

docker-compose/docker-compose.dev.yml

@@ -40,10 +40,7 @@ services:
       RABBITMQ_DEFAULT_USER: demouser
       RABBITMQ_DEFAULT_PASS: demopass
 
-  service:
-    build:
-      dockerfile: Dockerfile
-      context: ..
+  example:
     ports:
       - "8080:8080"
     depends_on:

docker-compose/docker-compose.prod.yml

@@ -7,19 +7,15 @@ services:
   #
   # Each new container in the Docker compose stack will need a service entry.
   example:
-    # The "build" field tells docker compose how to build the Docker image that
-    # backs this individual service.
-    build:
-      # Context is the root for the docker image to be built, including the
-      # Dockerfile.
-      context: ..
+    image: example-async-service:latest
+
     # The "environment" field defines a map of environment variables that will
     # be passed to the service container on startup.
     #
     # Fields here that do not have a value provided here will be required on
     # docker-compose startup.
     environment:
-      # The port this service will bind to in it's own container.
+      # The port this service will bind to in its own container.
       SERVER_PORT: 80
 
       # A comma separated list of LDAP servers this service should hit to fetch
@@ -68,4 +64,4 @@ services:
 # docker-compose stack.
 networks:
   traefik:
-    external: true
+    external: true

makefile

@@ -1,65 +1,65 @@
-<<<<<<< HEAD
-APP_PACKAGE  := $(shell ./gradlew -q print-package | tail -1)
-MAIN_DIR     := src/main/java/$(shell echo $(APP_PACKAGE) | sed 's/\./\//g')
-TEST_DIR     := $(shell echo $(MAIN_DIR) | sed 's/main/test/')
-BIN_DIR      := .tools/bin
+#
+# Help/Usage
+#
 
 C_BLUE := "\\033[94m"
 C_NONE := "\\033[0m"
-C_CYAN := "\\033[36m"
-C_RED  := "\\033[31m"
-
-=======
->>>>>>> template/master
-#
-# Development environment setup / teardown
-#
 
-<<<<<<< HEAD
-.PHONY: help
-help:
-	@echo "Targets:\n`cat makefile | grep '^[a-z\-]\+:' | sed 's/:.*//;s/^/  /'`"
+.PHONY: default
+default:
+	@echo "Please choose one of:"
+	@echo ""
+	@echo "$(C_BLUE)  make install-dev-env$(C_NONE)"
+	@echo "    Checks the development environment for initial build dependencies "
+	@echo "    and downloads them if necessary."
+	@echo ""
+	@echo "$(C_BLUE)  make raml-gen-code$(C_NONE)"
+	@echo "    Generates Java classes representing API interfaces as "
+	@echo "    defined in api.raml and child types."
+	@echo ""
+	@echo "$(C_BLUE)  make compile$(C_NONE)"
+	@echo "    Compiles the existing code in 'src/'.  Regenerates files if the"
+	@echo "    api spec has changed."
+	@echo ""
+	@echo "$(C_BLUE)  make test$(C_NONE)"
+	@echo "    Compiles the existing code in 'src/' and runs unit tests."
+	@echo "    Regenerates files if the api spec has changed."
+	@echo ""
+	@echo "$(C_BLUE)  make jar$(C_NONE)"
+	@echo "    Compiles a 'fat jar' from this project and its dependencies."
+	@echo ""
+	@echo "$(C_BLUE)  make docker$(C_NONE)"
+	@echo "    Builds a runnable docker image for this service"
+	@echo ""
+	@echo "$(C_BLUE)  make clean$(C_NONE)"
+	@echo "    Remove files generated by other targets; put project back in"
+	@echo "    its original state."
+	@echo ""
 
 #
-# Project & Environment Setup Targets
+# Development environment setup / teardown
 #
 
-.PHONY: new-project-initialization
-new-project-initialization:
-	@if [ ! 1 -eq `git rev-list --all --count` ]; then \
-	  echo ; \
-	  echo "$(C_RED)-- ERROR -----------------------------------------------------------------------$(C_NONE)"; \
-	  echo "This make target cannot not be used after a new project already has commits.";\
-	  echo "Merging the histories of the template repository and a project based on it may";\
-	  echo "cause issues and must be done with care.";\
-	  echo "$(C_RED)--------------------------------------------------------------------------------$(C_NONE)";\
-	  echo ; \
-	  exit 1; \
-	fi
-	$(MAKE) register-template-repo
-	@git fetch template
-	@git merge template/master --allow-unrelated-histories
-
-.PHONY: link-template-repo
-link-template-repo:
-	@git remote add template [email protected]:VEuPathDB/example-jaxrs-container-service.git
-
-# Merges in changes from the template/example repo.
-.PHONY: merge-template-repo
-merge-template-repo:
-	@git remote show template > /dev/null 2>&1 || (echo "\n$(C_RED)Template repo has not been registered.$(C_NONE)\n\nRun 'make link-template-repo'\n"; exit 1)
-	@git fetch template
-	@git merge template/master
-
-=======
->>>>>>> template/master
 .PHONY: install-dev-env
 install-dev-env:
 	./gradlew check-env
 
 .PHONY: clean
 clean:
-	@rm -rf .bin .gradle .tools build vendor
+	@./gradlew clean
+	@rm -rf .bin .gradle
+
+#
+# Code & Doc Generation
+#
+
+.PHONY: raml-gen-code
+raml-gen-code:
+	./gradlew generate-jaxrs
+
+.PHONY: raml-gen-docs
+raml-gen-docs:
+	./gradlew generate-raml-docs
 
 #
 # Build & Test Targets
@@ -80,42 +80,9 @@ jar: build/libs/service.jar
 docker:
 	./gradlew build-docker --stacktrace
 
-#
-# Code & Doc Generation
-#
-
-.PHONY: raml-gen-code
-raml-gen-code:
-	./gradlew generate-jaxrs
-
-.PHONY: raml-gen-docs
-raml-gen-docs:
-	./gradlew generate-raml-docs
-
-
-.PHONY: example-build
-example-build:
-	@docker compose -f docker-compose/docker-compose.dev.yml build \
-		--build-arg=GITHUB_USERNAME=${GITHUB_USERNAME} \
-		--build-arg=GITHUB_TOKEN=${GITHUB_TOKEN}
-
-.PHONY: example-run
-example-run:
-	@docker compose -f docker-compose/docker-compose.dev.yml up
-
-.PHONY: example-clean
-example-clean:
-	@docker compose -f docker-compose/docker-compose.dev.yml down
-
 #
 # File based targets
 #
 
 build/libs/service.jar: build.gradle.kts
-<<<<<<< HEAD
-	@echo "$(C_BLUE)Building application jar$(C_NONE)"
-	@./gradlew clean test shadowJar
-
-=======
 	./gradlew clean test generate-raml-docs shadowJar
->>>>>>> template/master

settings.gradle.kts

@@ -1,45 +1,4 @@
-pluginManagement {
-  fun requireNonBlankGitHubCred(key: String, env: String) : String {
-
-    // First try and load the gradle.properties entry.
-    if (extra.has(key)) {
-      val cred = extra[key] as String?
-
-      // Well, they defined it, but they did it wrong, so throw an error here.
-      if (cred.isNullOrBlank()) {
-        println("Gradle property \"$key\" has been set to a null or blank value.")
-        throw RuntimeException("Gradle property \"$key\" has been set to a null or blank value.")
-      }
-
-      return cred
-    }
-
-    // They don't have a gradle.properties entry.  Check the environment.
-
-    val cred = System.getenv(env)
-
-    if (cred.isNullOrBlank()) {
-      println("Environment variable \"$env\" is missing or blank.")
-      throw RuntimeException("Environment variable \"$env\" is missing or blank.")
-    }
-
-    return cred
-  }
-
-  fun requireGitHubUsername() = requireNonBlankGitHubCred("gpr.user", "GITHUB_USERNAME")
-  fun requireGitHubToken() = requireNonBlankGitHubCred("gpr.key", "GITHUB_TOKEN")
-
-  repositories {
-    mavenLocal()
-    mavenCentral()
-    gradlePluginPortal()
-    maven {
-      name = "GitHubPackages"
-      url  = uri("https://maven.pkg.github.com/veupathdb/maven-packages")
-      credentials {
-        username = requireGitHubUsername()
-        password = requireGitHubToken()
-      }
-    }
-  }
+// adds repos for gradle plugin resolution and ensures github creds are provided to the build
+apply {
+  from("https://raw.githubusercontent.com/VEuPathDB/lib-gradle-container-utils/v4.8.3/includes/common.settings.gradle.kts")
 }