Merge branch 'dev'

Author: temi

.gitignore

@@ -1,11 +1,13 @@
-.idea/
-target/
+Thumbs.db
+.DS_Store
+.gradle
+build/
 out/
+.idea
 *.iml
-*.zip
-*.sha1
-plugin.xml
-*.log
-*.tld
-node_modules/
-.slcache
+*.ipr
+*.iws
+.project
+.settings
+.classpath
+.asscache

.travis.yml

@@ -1,41 +1,51 @@
+dist: xenial
 language: groovy
-sudo: false
 jdk:
 - openjdk8
+
+sudo: false
 branches:
   only:
   - master
   - dev
-  - /^hotfix\/.*$/
   - /^feature\/.*$/
-  - ecodata-client-plugin
+before_cache:
+  - rm -f  $HOME/.gradle/caches/modules-2/modules-2.lock
+  - rm -fr $HOME/.gradle/caches/*/plugin-resolution/
+cache:
+  directories:
+  - $HOME/.m2
+  - $HOME/.gradle/caches/
+  - $HOME/.gradle/wrapper/
+
 before_install:
-- rm -rf ~/.nvm && git clone https://github.com/creationix/nvm.git ~/.nvm && (cd ~/.nvm && git checkout `git describe --abbrev=0 --tags`) && source ~/.nvm/nvm.sh && nvm install $TRAVIS_NODE_VERSION
-- git clone --depth=50 --branch=dev https://github.com/AtlasOfLivingAustralia/ecodata-client-plugin.git ../ecodata-client-plugin
-- rm -rf ~/.sdkman
-- curl -s get.sdkman.io > ~/install_sdkman.sh
-- chmod 775 ~/install_sdkman.sh
-- "~/install_sdkman.sh"
-- echo "sdkman_auto_answer=true" > ~/.sdkman/etc/config
-- source ~/.sdkman/bin/sdkman-init.sh
-- GRAILS_VERSION=`grep '^\s*app.grails.version' application.properties | sed -e 's/^\s*app\.grails\.version=//g'
-  | tr -d "\r"`
-- echo "GRAILS_VERSION:$GRAILS_VERSION"
-- sdk install grails $GRAILS_VERSION || true
+  - export TZ=Australia/Canberra
+  - rm -rf ~/.nvm && git clone https://github.com/creationix/nvm.git ~/.nvm && (cd ~/.nvm && git checkout `git describe --abbrev=0 --tags`)
+  - git clone --depth=50 --branch=$ECODATA_CLIENT_PLUGIN_BRANCH https://github.com/AtlasOfLivingAustralia/ecodata-client-plugin.git ../ecodata-client-plugin
+
+install:
+  - cd ~/.nvm
+  - source ~/.nvm/nvm.sh
+  - nvm install $TRAVIS_NODE_VERSION
+
 before_script:
-- mkdir -p ~/.grails; wget -q -O ~/.grails/settings.groovy https://raw.githubusercontent.com/AtlasOfLivingAustralia/travis-build-configuration/master/travis_grails_settings_new.groovy
-- MAVEN_REPO="ala-repo-snapshot"; grep '^app\.version=' ./application.properties |
-  grep -q "\-SNAPSHOT"; if [ "$?" = "1" ]; then MAVEN_REPO="ala-repo-release"; fi;
-- echo "MAVEN_REPO:$MAVEN_REPO"
-- node --version
-- npm install
+  - cd $TRAVIS_BUILD_DIR
+  - npm install
+
 script:
-- node_modules/karma/bin/karma start karma.conf.js --single-run --browsers PhantomJS
-- grails clean && grails refresh-dependencies --non-interactive && grails test-app
-  --non-interactive && grails prod maven-deploy --repository=$MAVEN_REPO --non-interactive
-  --stacktrace
+  - cd $TRAVIS_BUILD_DIR
+  - ./gradlew clean && ./gradlew build
+  - node_modules/karma/bin/karma start karma.conf.js --single-run --browsers ChromeHeadless
+
+
+after_success:
+  - '[ "${TRAVIS_PULL_REQUEST}" = "false" ] && travis_retry ./gradlew publish'
+
+
 env:
   global:
-  - TRAVIS_NODE_VERSION="0.10"
+  - TRAVIS_NODE_VERSION="10.8.0"
+  - ECODATA_CLIENT_PLUGIN_BRANCH="feature/map-extension"
   - secure: 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
   - secure: aDQyUOaNj+7D9ug0bhhtnxIbVikKnNrFc2GJe+cRgl0PgPHffuHVGndINcgJW6T3nlLkRwP8Z5Ic9Y2a+C0tzWxiGs2+sHHyw0VaASHzcxV5aH15jgb2MMOY2JkaYVSEp7rvlLeHfLposA1NcvTk9u9nKG0k8R96vTLH3c+cFc6wmKfOFtfUZKu+qi75idaxeHoFQGiNMjU81mzFUA5UeNsNEiazTp8x9HUlqWofOJfrzRzUcp1PKHTV1MJdWyeVDJHg+OWdiWKjA5F/gkpcIFfkxYuvb2WM63wTrYdHBEIfBeGWzFMmbHMwM0SEOkgJQVhEiOfIK67+S/p5hWl/R/gyaf9xj2eZ7DARNNIyuohyXYcOT0gzSoLRXSANU64nrwlgQAJOhHpgFOTdejpZm8XIEOyakCImnJxLjTEivBIujfqT80esomN7rcEj0dulM8uOy1fi4FeyonMyR65ZwduPFaOop93CFSgw9aHlFyRh6Z0n0YNCRbuWLPPRt9ZjaLte7eEIlf87CmS0DDS1vCtKjoHN165K/gpBTltmVZDqBfT70BqVG+DIf3oBZW7scroSlcdJj18axyCIxsPibbCu4ezHgNpM84J2+f7BSaBvKuh00csvu5P0e3h3laHI6jzc0MkWWbV6ZB5e7ctG2fptXIZxse3X0I1tdgL3x08=
+

README.md

@@ -19,20 +19,19 @@ New server side classes that are custom to Biocollect should be under the packag
 ## General Information
 
 ### Technologies
-  * Grails framework: 2.4.5
+  * Grails framework: 3.3.11
+  * Java 8
   * Knockout JS
   * JQuery
+  * Gradle
+  
+
+### Development Setup
+
+* This project requires you to run the [ecodata project](https://github.com/AtlasOfLivingAustralia/ecodata) on port `8081`.
+
+* [Use this guide to setup Biocollect in Intellij](setup.md)
 
-### Setup
-* This project requires you to run the [ecodata project](https://github.com/AtlasOfLivingAustralia/ecodata) on port `8080`.
-* You will need the following local directories:
-```
-  /data/biocollect/config
-  /data/biocollect/images
-```
-* Add the external config file.
-* The app is expected to run in port 8087 locally. Just add the option `-Dserver.port=8087` to the run-app command:
-![Imgur](http://i.imgur.com/syIKPgy.png)
 
 ### Running Javascript automatic tests
 * Executing the tests requires node.js

_events.groovy

@@ -0,0 +1,58 @@
+import java.nio.file.Files
+import java.nio.file.Paths
+import java.nio.file.attribute.BasicFileAttributes
+import java.nio.file.attribute.FileTime
+import org.apache.commons.io.FileUtils
+
+Boolean doesTemplateNeedCompiling (File templateDirectory, File compiledTemplateFile) {
+    Boolean compile = false
+    if (templateDirectory != null) {
+        BasicFileAttributes attr = Files.readAttributes(Paths.get(compiledTemplateFile.canonicalPath), BasicFileAttributes.class)
+        FileTime lastModifiedTime = attr.lastModifiedTime()
+        def templateFiles = templateDirectory.listFiles()
+
+        for (templateFile in templateFiles) {
+            BasicFileAttributes templateFileAttributes = Files.readAttributes(Paths.get(templateFile.canonicalPath), BasicFileAttributes.class)
+            if (templateFileAttributes.lastModifiedTime().compareTo(lastModifiedTime) > 0 ) {
+                return true
+            }
+        }
+    }
+
+    return compile
+}
+
+
+void generateTemplateFile(File compiledTemplateFile, File templateDirectory) {
+    if (!compiledTemplateFile.getParentFile().exists()) {
+        compiledTemplateFile.getParentFile().mkdirs()
+    }
+
+    FileUtils.writeStringToFile(compiledTemplateFile, '/* Do not edit or commit this file. This file built at compile by _Events.groovy */\n')
+    def templates = templateDirectory.listFiles()
+    templates.each { File template ->
+        def fileParts = template.getName().split("\\.")
+        if (fileParts.length >= 1) {
+            def componentName = fileParts[0]
+
+            if (template.exists()) {
+                def content = template.getText().replaceAll("[\n\r]", "")
+                        .replaceAll("\"", "\\\\\"")
+                        .replaceAll('\\s+', ' ')
+                FileUtils.writeStringToFile(compiledTemplateFile,
+                        "componentService.setTemplate(\"${componentName}\", \"" + content + "\");" as String, true)
+            }
+        }
+    }
+}
+
+def buildTemplateFile(String templateDirectoryName, String compiledTemplateFileName) {
+    File templateDir = new File(templateDirectoryName)
+    File compiledTemplateFile = new File(compiledTemplateFileName)
+    if (!compiledTemplateFile?.exists() || doesTemplateNeedCompiling(templateDir, compiledTemplateFile)) {
+        generateTemplateFile(compiledTemplateFile, templateDir)
+    }
+
+}
+
+buildTemplateFile("${projectDir}/grails-app/assets/components/template", "${projectDir}/grails-app/assets/components/compile/biocollect-templates.js")

application.properties

@@ -0,0 +1,189 @@
+import static org.springframework.boot.gradle.SpringBootPluginExtension.LayoutType.*
+
+buildscript {
+    repositories {
+        mavenLocal()
+        maven { url "https://repo.grails.org/grails/core" }
+        maven { url "https://nexus.ala.org.au/content/groups/public/" }
+    }
+    dependencies {
+        classpath "org.grails:grails-gradle-plugin:$grailsVersion"
+        //classpath "org.grails.plugins:hibernate5:${gormVersion-".RELEASE"}"
+        classpath "com.bertramlabs.plugins:asset-pipeline-gradle:2.15.1"
+    }
+}
+
+plugins {
+    id 'war'
+}
+
+version "5.0-SNAPSHOT"
+group "au.org.ala"
+
+apply plugin:"eclipse"
+apply plugin:"idea"
+apply plugin:"war"
+apply plugin:"org.grails.grails-web"
+apply plugin:"asset-pipeline"
+apply plugin:"org.grails.grails-gsp"
+apply from: 'https://raw.githubusercontent.com/AtlasOfLivingAustralia/travis-build-configuration/master/travis_grails_publish.gradle'
+//apply plugin:"org.grails.grails-plugin-publish"
+
+
+repositories {
+    mavenLocal()
+    //for missing jai_core.jar
+  //  maven { url "http://download.osgeo.org/webdav/geotools"}
+    maven { url "https://repo.grails.org/grails/core" }
+    maven { url "https://nexus.ala.org.au/content/groups/public/" }
+    mavenCentral()
+   // maven { url "http://maven.geotoolkit.org"}
+
+}
+
+//def tomcatVersion = '7.0.55.2'
+def metadataExtractorVersion = "2.6.2"
+def imgscalrVersion = "4.2"
+def httpmimeVersion = "4.2.1"
+def jtsVersion = "1.8"
+def geoToolsVersion = "11.1"
+// Set to true it needed only for development
+boolean inplace = false
+
+
+dependencies {
+    compile "org.springframework.boot:spring-boot-starter-logging"
+    compile "org.springframework.boot:spring-boot-autoconfigure"
+    compile "org.grails:grails-core"
+    compile "org.springframework.boot:spring-boot-starter-actuator"
+    compile "org.springframework.boot:spring-boot-starter-tomcat"
+
+    compile "org.grails:grails-dependencies"
+    compile "org.grails:grails-logging"
+    compile "org.grails:grails-web-boot"
+    compile "org.grails:grails-plugin-i18n"
+    compile "org.grails:grails-plugin-services"
+    compile "org.grails:grails-plugin-url-mappings"
+    compile "org.grails:grails-plugin-interceptors"
+    compile "org.grails.plugins:cache"
+    compile "org.grails.plugins:scaffolding"
+    console "org.grails:grails-console"
+    profile "org.grails.profiles:web"
+    compile "com.bertramlabs.plugins:asset-pipeline-grails:2.15.1"
+    //runtime "com.h2database:h2"
+    testCompile "org.grails:grails-plugin-testing"
+    testCompile "org.grails.plugins:geb"
+    testRuntime "org.seleniumhq.selenium:selenium-htmlunit-driver:2.47.1"
+    testRuntime "net.sourceforge.htmlunit:htmlunit:2.18"
+    compile "commons-io:commons-io:2.6"
+    compile "com.drewnoakes:metadata-extractor:${metadataExtractorVersion}"
+    compile "org.imgscalr:imgscalr-lib:${imgscalrVersion}"
+    compile "org.apache.httpcomponents:httpmime:${httpmimeVersion}"
+    compile "com.vividsolutions:jts:${jtsVersion}"
+    //compile "org.geotools.xsd:gt-xsd-kml:${geoToolsVersion}"
+    compile ("org.geotools.xsd:gt-xsd-kml:${geoToolsVersion}") {
+        exclude group: 'javax.media', module: 'jai_core'
+    }
+
+    compile "joda-time:joda-time:2.3"
+  //  compile "org.codehaus.groovy.modules.http-builder:http-builder:0.7.1"
+
+    // Used by the scripts
+    compile ('org.grails.plugins:http-builder-helper:1.1.0')  {
+        exclude group: 'org.apache.httpcomponents', module: 'httpclient'
+    }
+
+
+  //  compile "org.grails:http-client"
+
+   // compile "org.apache.httpcomponents:httpcore:4.4.1"
+   // compile "org.apache.httpcomponents:httpclient:4.4.1"
+    compile "org.apache.httpcomponents:httpclient:4.5.7"
+
+    testCompile "org.grails:grails-test-mixins:3.3.0"
+    testRuntime 'com.github.detro:phantomjsdriver:1.2.0'
+
+    //JSON converter
+    //compile 'org.grails.plugins:converters'
+    runtime 'org.webjars:jquery:1.12.4'
+    //mimic grails.config.locations like in Grails 2.x
+    compile 'org.grails.plugins:external-config:1.4.0'
+//    compile 'org.grails.plugins:external-config:2.0.0.RC1'
+    compile "org.grails.plugins:excel-import:3.0.2"
+    compile "org.grails.plugins:excel-export:0.2.1"
+    compile 'org.grails.plugins:grails-google-visualization:2.2.1'
+    compile group: 'org.apache.poi', name: 'poi', version: '3.17'
+    compile 'org.grails.plugins:mail:2.0.0.RC6'
+
+
+    compile 'org.grails.plugins:grails-markdown:3.0.0'
+    compile 'org.grails.plugins:grails-cookie:2.0.3'
+
+    compile 'org.grails.plugins:cache:5.0.0.RC1'
+
+    //ALA plugins
+    //TODO Same namespace?
+    compile ("au.org.ala.plugins.grails:images-client-plugin:1.2") {
+        exclude group: 'commons-httpclient', module: 'commons-httpclient'
+    }
+
+  //  compile "au.org.ala.plugins.grails:images-client-plugin:0.9-SNAPSHOT"
+    compile "org.grails.plugins:ala-auth:3.0.4"
+    runtime "org.grails.plugins:ala-bootstrap3:3.0.4"
+    compile "org.grails.plugins:ala-admin-plugin:2.1"
+    if (!inplace) {
+        compile "org.grails.plugins:ala-map-plugin:3.0"
+        compile "org.grails.plugins:ecodata-client-plugin:3.0"
+    }
+}
+
+springBoot {
+    buildInfo()
+    layout = WAR
+}
+
+
+bootRun {
+    jvmArgs('-Dspring.output.ansi.enabled=always', '-Xmx6000m')
+    addResources = true
+}
+
+bootRepackage {
+    enabled = true
+    executable = true
+    classifier = 'exec'
+}
+
+assets {
+    minifyJs = true
+    minifyCss = true
+
+}
+
+if (inplace) {
+    grails {
+        exploded = true
+        plugins {
+            compile (project(':ecodata-client-plugin'))
+            compile (project(':ala-map-plugin'))
+        }
+    }
+
+    // Make ecodata-client-plugin _Events task is called
+    assetCompile.dependsOn("ecodata-client-plugin:_Events")
+    compileGroovy.dependsOn("ecodata-client-plugin:_Events")
+    bootRun.dependsOn("ecodata-client-plugin:_Events")
+}
+
+task _Events {
+    doLast {
+        println "Running biocollect _events.groovy script"
+        println "${project.projectDir}/_events.groovy"
+        new GroovyScriptEngine(["${project.projectDir}"] as String[]).run("_events.groovy", new Binding(['projectDir': project.projectDir]))
+    }
+}
+
+// the tasks used here for dependsOn may be incomplete/incorrect
+assetCompile.dependsOn(_Events)
+compileGroovy.dependsOn(_Events)
+bootRun.dependsOn(_Events)

build.gradle

@@ -0,0 +1,3 @@
+grailsVersion=3.3.11
+gormVersion=6.1.12.RELEASE
+gradleWrapperVersion=3.5