#66 - Converting to a Gradle multi-module project, though currently o…

…nly with a single module, that being the existing project as-is
bobbylight · Mar 18, 2021 · 06d22d3 · 06d22d3
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diff --git a/README.md b/README.md
@@ -1,85 +1,11 @@
 # Random Acts of Kinase
 
-[![Build Status](https://travis-ci.org/bobbylight/random-acts-of-kinase.svg?branch=master)](https://travis-ci.org/bobbylight/random-acts-of-kinase)
-[![Coverage Status](https://coveralls.io/repos/github/bobbylight/random-acts-of-kinase/badge.svg?branch=master)](https://coveralls.io/github/bobbylight/random-acts-of-kinase?branch=master)
-
 A web frontend for SGC kinase information.
 
-A Spring Boot application exposes the data via a REST API.  The frontend is written in Vue.
-
-Note:  The actual kinase data is not included in this repository, for obvious reasons.
-You can still test the application without this data by running it with the `dev` Spring profile.
-
-## Hacking
-You can omit the `-xcreateSmileSvgs` options if you actually have openbabel installed
-and configured properly in your environment.  If you don't, you need to use this option to
-omit that build task to prevent a build failure:
-
-```sh
-git clone https://github.com/bobbylight/random-acts-of-kinase.git
-./gradlew build -xwebpack --warning-mode all -xcreateSmileSvgs
-./gradlew bootRun -xwebpack -xcreateSmileSvgs # Starts application at localhost:8080
-./gradlew webpackWatch      # In another window, run webpack watch for UI updates
-./gradlew copyStaticResourcesToBuildWatch # Copy webpack build into build/ for hot deploys
-```
-
-Unfortunately you need to start three processes to develop - annoying.  I couldn't get
-webpack to build directly into `build/` without Spring Boot getting cranky and clearing
-out the contents of `build/resources/main/static` on restarts.
-
-*Note:* Ctrl+C may not propagate the SIGKILL to the child npm tasks for `webpackWatch`
-and `copyStaticResourcesToBuildWatch`, which can cause race conditions on file copies
-and in turn weird behavior (stale static resources).  If you see this happening, you
-might consider running the wrapped npm tasks directly.  See
-[here](https://github.com/srs/gradle-node-plugin/issues/143) for more information.
-
-If you have data to develop against in a local postgres instance, you can run against
-via `./gradlew bootRun -Dspring.profiles.active=dev-postgres`.
-
-The server is a simple Spring Boot application exposing a REST API and a little
-static content.  The client is Vue/JS/TypeScript.
-
-The application will be hosted at [http://localhost:8080]().
-
-To run tests:
-```sh
-./gradlew test -xwebpack # Service tests
-npm test                 # Client tests
-npm run coverage         # Client tests + coverage report
-```
-
-The coverage report for the client-side tests lives here:
-```sh
-open reports/coverage/index.html
-```
-
-To deploy to AWS (we build a zip containing just the jar and a Procfile to launch
-it, as configured in `.elasticbeanstalk/config.yml`):
-```sh
-./gradlew clean build --warning-mode all # Be sure to perform a production build
-./gradlew makeAwsArchive
-eb deploy --label "something"
-```
-
-## Utilities
-
-The `util` folder contains shell scripts to do mundane tasks.  For these scripts
-to run you'll need to create a file named `env.sh` from the `env.sh.orig` template
-file with connection info for a database containing the SGC data.
-
-### Creating SVG images for compounds from SMILES strings
-The SVG images of compounds used by the application are generated from their
-SMILES strings.  Generate them by running `./create-smiles-svgs.sh`.  You'll
-need to have `psql` on your `PATH` or this script will fail silently.  This
-script is run as part of `./gradlew build` so you typically don't need to
-run it directly.
-
-### Exporting data from our database into CSV files
-To back up the database into CSV files, you can run `./export-to-csv.sh`.
+This projectr contains two modules:
 
+* `service/` contains a Spring Boot application that exposes the data via a
+  REST API
+* `ui/` contains the static content.  It's a built and minified Vue application
 
-## Updating the AWS database
-We won't have to keep doing this once we have the data exported in a format we like...
-```sh
-psql --host=<host-name> --username=<user> --dbname=<db> -f create-db.ddl
-```
+See the `README.md` in each module for instructions on how to run locally.
diff --git a/build.gradle b/build.gradle
@@ -1,211 +1,31 @@
 buildscript {
     repositories {
         mavenCentral()
-        jcenter()
     }
     dependencies {
-        classpath 'org.springframework.boot:spring-boot-gradle-plugin:2.4.3'
     }
 }
-plugins {
-    id 'com.github.node-gradle.node' version '3.0.1'
-    id 'jacoco'
-    id 'com.github.kt3k.coveralls' version '2.10.2'
-    id 'com.github.spotbugs' version '4.6.2'
-}
-apply plugin: 'java'
 apply plugin: 'idea'
-apply plugin: 'org.springframework.boot'
-apply plugin: 'io.spring.dependency-management'
-apply plugin: 'com.github.node-gradle.node'
-apply plugin: 'com.github.spotbugs'
-apply plugin: 'checkstyle'
-
-import static org.gradle.api.JavaVersion.*
-
-// We require building with JDK 14 or later, but there is no 14 check yet
-assert current().isJava12Compatible()
-
-group = 'org.sgc'
-version = '1.4.0-SNAPSHOT'
-
-repositories {
-    mavenCentral()
-}
-
-node {
-    version = '14.16.0'
-    npmVersion = '6.14.11'
-    download = true
-
-    // Node and npm should work in our 'frontend' folder
-    workDir = file("${project.buildDir}/nodejs")
-    npmWorkDir = file("${project.buildDir}/npm")
-    yarnWorkDir = file("${project.buildDir}/yarn")
-
-    // Where node_modules should be located
-    nodeModulesDir = file("${project.projectDir}/src/main/frontend")
-}
-
-dependencies {
-
-    implementation 'org.springframework.boot:spring-boot-starter-web'
-    implementation 'org.springframework.boot:spring-boot-starter-validation'
-    implementation 'org.springframework.boot:spring-boot-devtools'
-    implementation 'org.springframework.boot:spring-boot-starter-actuator'
-    implementation 'org.springframework.boot:spring-boot-starter-data-jpa'
-    implementation 'org.springframework.boot:spring-boot-starter-security'
-
-    implementation 'org.slf4j:slf4j-api'
-    implementation 'ch.qos.logback:logback-classic'
-    implementation 'ch.qos.logback:logback-core'
-
-    implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-csv'
-    implementation 'org.apache.commons:commons-lang3:3.12.0'
-    implementation 'org.postgresql:postgresql'
-    implementation 'org.apache.xmlgraphics:batik-transcoder:1.14'
-    implementation 'org.apache.xmlgraphics:batik-codec:1.14'
-    implementation 'com.h2database:h2'
 
-    testImplementation 'org.springframework.boot:spring-boot-starter-test'
-    testImplementation 'org.springframework.security:spring-security-test'
-    // TODO: Remove and update tests to JUnit 5 syntax
-    testImplementation('org.junit.vintage:junit-vintage-engine') {
-        exclude group: 'org.hamcrest', module: 'hamcrest-core'
-    }
-}
+group 'org.sgc'
+// NOTE: Local Java 8:  /Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home
 
 wrapper {
     gradleVersion = '6.8.3'
 }
 
-checkstyle {
-    toolVersion '8.41'
-    configDirectory = file("${project.projectDir}/config/checkstyle")
-}
-
 idea {
     module {
         downloadSources = true
     }
 }
 
-compileJava {
-    sourceCompatibility javaVersion
-    targetCompatibility javaVersion
-    options.debug = true
-    options.debugOptions.debugLevel = 'source,vars,lines'
-    options.compilerArgs << '-Xlint:deprecation' << '-Xlint:unchecked'
-}
-
-compileTestJava {
-    sourceCompatibility javaVersion
-    targetCompatibility javaVersion
-    options.debug = true
-    options.debugOptions.debugLevel = 'source,vars,lines'
-    options.compilerArgs << '-Xlint:deprecation' << '-Xlint:unchecked'
-}
-
-sourceSets {
-    integrationTest {
-        java.srcDirs = [ 'src/integration-test/java' ]
-        resources.srcDirs = [ 'src/integration-test/resources' ]
-        compileClasspath += main.output + test.output
-        runtimeClasspath += main.output + test.output
-    }
-}
-
-configurations {
-    integrationTestCompile.extendsFrom testImplementation
-    integrationTestRuntime.extendsFrom testRuntime
-}
-
-task integration(type: Test, description: 'Runs the integration tests.', group: 'Verification') {
-    testClassesDirs = sourceSets.integrationTest.output.classesDirs
-    classpath = sourceSets.integrationTest.runtimeClasspath
-}
-
-clean.doLast {
-    // Must disambiguate with project.delete since we're doing this in clean's doLast
-    project.delete "${rootDir}/aws-archive.zip"
-}
-
-task webpack(type: NpmTask, dependsOn: 'npmInstall') {
-    execOverrides {
-        it.workingDir = "${project.projectDir}/src/main/frontend/"
-    }
-    args = [ 'run', 'build' ]
-}
-
-processResources.dependsOn 'webpack'
-
-// Generate SVG files for each compound in the local database.  This
-// assumes openbabel (obabel) is on your PATH.  If you don't have openbabel
-// set up, the app will be built but without images for compounds.
-task createSmileSvgs(type: Exec) {
-    workingDir "${rootDir}"
-    if (System.getProperty('os.name').toLowerCase(Locale.ROOT).contains('windows')) {
-        def dir = rootDir.absolutePath.replace('\\', '/')
-        commandLine 'cmd', '/c', "C:\\Progra~1\\Git\\bin\\sh.exe --login -c '${dir}/util/create-smiles-svgs.sh'"
-    }
-    else {
-        commandLine '/bin/sh', '-c', './util/create-smiles-svgs.sh'
-    }
-}
-processResources.dependsOn 'createSmileSvgs'
-createSmileSvgs.onlyIf { !file('src/main/resources/static/img/smiles').exists() }
-createSmileSvgs.dependsOn 'webpack' // Ensure smiles generation occurs after webpack build
-
-task webpackWatch(type: NpmTask) {
-    args = [ 'run', 'watch' ]
-}
-
-task copyStaticResourcesToBuildWatch(type: NpmTask) {
-    args = [ 'run', 'watch-static-into-build' ]
-}
-
-task makeAwsArchive(type: Zip) {
-    from "${rootDir}/build/libs/"
-    include 'random-acts-of-kinase*.jar'
-    from '.'
-    include 'Procfile'
-    include '.ebextensions/**'
-    archiveFileName = 'aws-archive.zip'
-    destinationDirectory = file(rootDir)
-}
-
-spotbugs {
-    includeFilter = file('spotbugs-exclude.xml')
-}
-
-spotbugsMain {
-    reports {
-        xml.enabled = false
-        html.enabled = true
-    }
-}
-spotbugsTest {
-    reports {
-        xml.enabled = false
-        html.enabled = true
-    }
-}
-
-bootRun {
-
-    jvmArgs = [ '-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=10356' ]
+allprojects {
 
-    if (System.getProperty('spring.profiles.active') == null) {
-        println 'Defaulting to dev Spring profile'
-        System.setProperty('spring.profiles.active', 'dev')
+    repositories {
+        mavenCentral()
     }
-    // Forward -D properties to the Spring Boot app
-    systemProperties = System.properties
 }
 
-jacocoTestReport {
-    reports {
-        xml.enabled = true // coveralls plugin depends on xml format report
-        html.enabled = true
-    }
+subprojects {
 }
diff --git a/Procfile → service/Procfile b/Procfile → service/Procfile
diff --git a/service/README.md b/service/README.md
@@ -0,0 +1,85 @@
+# Random Acts of Kinase
+
+[![Build Status](https://travis-ci.org/bobbylight/random-acts-of-kinase.svg?branch=master)](https://travis-ci.org/bobbylight/random-acts-of-kinase)
+[![Coverage Status](https://coveralls.io/repos/github/bobbylight/random-acts-of-kinase/badge.svg?branch=master)](https://coveralls.io/github/bobbylight/random-acts-of-kinase?branch=master)
+
+A web frontend for SGC kinase information.
+
+A Spring Boot application exposes the data via a REST API.  The frontend is written in Vue.
+
+Note:  The actual kinase data is not included in this repository, for obvious reasons.
+You can still test the application without this data by running it with the `dev` Spring profile.
+
+## Hacking
+You can omit the `-xcreateSmileSvgs` options if you actually have openbabel installed
+and configured properly in your environment.  If you don't, you need to use this option to
+omit that build task to prevent a build failure:
+
+```sh
+git clone https://github.com/bobbylight/random-acts-of-kinase.git
+./gradlew build -xwebpack --warning-mode all -xcreateSmileSvgs
+./gradlew bootRun -xwebpack -xcreateSmileSvgs # Starts application at localhost:8080
+./gradlew webpackWatch      # In another window, run webpack watch for UI updates
+./gradlew copyStaticResourcesToBuildWatch # Copy webpack build into build/ for hot deploys
+```
+
+Unfortunately you need to start three processes to develop - annoying.  I couldn't get
+webpack to build directly into `build/` without Spring Boot getting cranky and clearing
+out the contents of `build/resources/main/static` on restarts.
+
+*Note:* Ctrl+C may not propagate the SIGKILL to the child npm tasks for `webpackWatch`
+and `copyStaticResourcesToBuildWatch`, which can cause race conditions on file copies
+and in turn weird behavior (stale static resources).  If you see this happening, you
+might consider running the wrapped npm tasks directly.  See
+[here](https://github.com/srs/gradle-node-plugin/issues/143) for more information.
+
+If you have data to develop against in a local postgres instance, you can run against
+via `./gradlew bootRun -Dspring.profiles.active=dev-postgres`.
+
+The server is a simple Spring Boot application exposing a REST API and a little
+static content.  The client is Vue/JS/TypeScript.
+
+The application will be hosted at [http://localhost:8080]().
+
+To run tests:
+```sh
+./gradlew test -xwebpack # Service tests
+npm test                 # Client tests
+npm run coverage         # Client tests + coverage report
+```
+
+The coverage report for the client-side tests lives here:
+```sh
+open reports/coverage/index.html
+```
+
+To deploy to AWS (we build a zip containing just the jar and a Procfile to launch
+it, as configured in `.elasticbeanstalk/config.yml`):
+```sh
+./gradlew clean build --warning-mode all # Be sure to perform a production build
+./gradlew makeAwsArchive
+eb deploy --label "something"
+```
+
+## Utilities
+
+The `util` folder contains shell scripts to do mundane tasks.  For these scripts
+to run you'll need to create a file named `env.sh` from the `env.sh.orig` template
+file with connection info for a database containing the SGC data.
+
+### Creating SVG images for compounds from SMILES strings
+The SVG images of compounds used by the application are generated from their
+SMILES strings.  Generate them by running `./create-smiles-svgs.sh`.  You'll
+need to have `psql` on your `PATH` or this script will fail silently.  This
+script is run as part of `./gradlew build` so you typically don't need to
+run it directly.
+
+### Exporting data from our database into CSV files
+To back up the database into CSV files, you can run `./export-to-csv.sh`.
+
+
+## Updating the AWS database
+We won't have to keep doing this once we have the data exported in a format we like...
+```sh
+psql --host=<host-name> --username=<user> --dbname=<db> -f create-db.ddl
+```