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##Project FMU - Fördjupade Medicinska Utredningar

##JIRA Link: Inera FMU

##Architecture Link: FMU Architecture

##Technology Stack:

###Backend (Server Side)

  1. Language(s): Java 1.7,Groovy
  2. Production Database: MySql 5.6.4+
  3. Test Database: H2
  4. Dependency & Build Management: Maven 3.0
  5. Database Migration Tool: Liquibase 3
  6. Logging Abstraction: SFL4J
  7. Logging Implementation: logback
  8. Unit Testing: JUnit 4 — The de-facto standard for unit testing Java applications.
  9. Persistence (Data Access): JPA, Hibernate 4 (One of the most popular JPA implementations.), Spring Data JPA (Makes it easy to easily implement JPA based repositories), Spring ORMs (Core ORM support from the Spring Framework)
  10. BPM: Activiti 5.15
  11. Mocking: Mockito
  12. Application Server (embedded): Tomcat
  13. Object to JSON Mapping: Jackson
  14. Date Time Utility: Joda-Time
  15. Assertion Library: Hamcrest - A library of matcher objects (also known as constraints or predicates) allowing assertThat style JUnit assertions.
  16. Integration Test Support: Spring Test — integration test support for Spring applications.
  17. JDBC Connection Pool: HikariCP - HikariCP is a high performance JDBC connection pool.
  18. Properties file format: YAML
  19. @ToString: lombok
  20. AOP: Spring AOP Logging, Transactions,
  21. Profiles: Maven & Spring Profiles
  22. Local Caching: Ehcache
  23. i18n:
  24. Templating Engine: thymeleaf (if a single Web page application isn't enough for our needs)
  25. Spring Boot: For easy configuration
  26. Security: Spring Security
  27. Mail:
  28. Guava EventBus EventBus allows publish-subscribe-style communication between components without requiring the components to explicitly register with one another (and thus be aware of each other). It is designed exclusively to replace traditional Java in-process event distribution using explicit registration.

###Frontend (Client Side) ####Build tools and optimization

  1. NodeJs: For builtools dependencies management
  2. Bower: For webapp package dependency management
  3. Gulp: is one of the most widely used build tool for your JavaScript and CSS assets. We moved from Grunt since the latest merge to provide better readability and maintainability

####Frameworks

  1. AngularJS
  2. Angular-resource: For backend REST communication
  3. Angular-animate: To provide event-based entry-points for animations (Not very frequently used in this project)
  4. Angular-sanitize: For secure Html loading
  5. HTML5 Boilerplate
  6. Twitter Bootstrap (Stripped down with minimal use, mostly to provide support for Angular-ui elements)
  7. Karma & PhantomJS & Jasmine: For unit-testing
  8. [SASS-SCSS]: CSS-preprocessor for more dynamic and maintainable CSS
  9. Susy-grid: For on demand grid-layout using SCSS
  10. Breakpoint: To simplify responsive styling and native support with Susy
  11. Typeplate: For more structured typepographic styling using SCSS (So far we only setup basic functionalities)
  12. Jquery: For dynamic DOM manipulation
  13. angular-gettext: For customizable text extraction and translation in both Html and Javascript code

####Gulp processes #####Development

  1. [wiredep]: Automatic Javascripts and CSS dependencies injection to indext.html
  2. [Sass]: Compile SCSS files to CSS files using Libsass
  3. [Serve]: Serving development resources as-is
  4. [Karma-inject]: Inject all dependencies to use during unit-tests
  5. [Test]: Run all unit-test and quit
  6. [Tdd]: Run all tests and watch for changes and rerun, useful for test driven development
  7. [Annotate]: Inject angular dependency injections to make uglify possible. [Html] task does this automatically for -Pprod profile but not -Pdev
  8. [Extract-pot]: Extract all static texts from the application to a .pot file which can be used for translation using any gettext compatible editors for example Poedit which also support update of existing translations
  9. [Compile-po]: Convert all translated .po files to a lookup module which apply translations to the angular application

#####Distribution

  1. [Jshint]: Perform static Javascript code-inspection
  2. [Html]: Collect, concaternate and uglify all CSS and Javascript dependencies
  3. [Templatecache]: Convert all Html fragments to Angular templatecache for easier access especially during unit-tests
  4. [images]: Collect and optimize all image-resources
  5. [Fonts]: Collect all fonts
  6. [Extras]: Copy all related resources missing from other tasks for example favicons, .httpaccess file etc.
  7. [Serve-prod]: Serve the distribution webapp, this provide quick preview of the client application
  8. [Build]: Assemble the application for distribution

####Coding standards

  1. Folders and files are organized based on functionality and not by type
  2. Immediately Invoked Function Expression (IIFE) for more consistent code structure
  3. Jshint
  4. Functionalities are devided in different modules
  5. Services and controllers exposes its API before everything else specific implementations, avoid anonymous function declarations for better readability and consistentcy

####Setup

  1. Install node using installer from http://nodejs.org/
  2. Install bower with npm install -g bower from commandline
  3. Navigate to the application rootfolder and run npm install to fetch all nodejs build dependencies. sudo might be required on OSX and Linux
  4. Run bower install to fetch all app-dependencies
  5. Run npm install --global gulp to install gulp globally
  6. run gulp to build and wire all dependencies and make sure everything is ok
  7. Now the application should have all required dependencies and can be run, either with both client- and backend-application using maven commands further down or with only client-application with gulp serve or gulp serve-prod
  8. Log in with fake id by clicking the user icon at the top right corner

#####NOTE

  1. When serving the application using gulp all rest requests are proxied to the defined backend server URL with the key backendServerUrl defined in GulpConfig.js file. Depending on where the backend-application is running from this should be changed accordingly.
  2. The application was tested using node v0.10.34 and npm v1.4.28, other versions might cause errors.
  3. If maven fails because some node task does not run correctly, try remove node_modules folder and rerun npm install.
  4. When run with Pprod profile maven will download node, npm and bower and run them locally, the idea is to make it possible to run the app independently. This can be changed in the pom.xml to enable maven to run with node and npm on the machine instead.
  5. Make sure mysql service is running if maven throw errors related to SQL INSERT. It might be a good idea to drop and recreate the existing database. The scripts for doing so can be located at src/main/resources/scripts/database/mysql/

###Other

  1. Source Code Management: Git
  2. IDE: IntelliJ (Recommended), STS, Eclipse Juno (Must for Activiti) or NetBeans
  3. REST API Documentation: Swagger
  4. Monitoring: Metrics

###Code Base

  1. Download and install Git.
  2. Right the folder which you want to be the home for the codebase, and choose Git Bash.(For integration of IntelliJ with Git, refer to the section below Setting Up the Environment->IntelliJ point 4 onward)
  3. Paste git clone https://github.com/rasheedamir/fmu.git
  4. Give the password (if) prompted.

###Project Structure

  1. src\integration-test - Specifically for integration tests!

    • src\integration-test\java

    • src\integration-test\resources

  2. src\main

    • src\main\java

    • src\main\resources

    • src\main\webapp

  3. src\test - Pure unit tests only!

    • src\test\java

    • src\test\javascript

    • src\test\resources

##Setting up the Environment:

###- JAVA

  • Ubuntu (Manually):
  1. Create "Tools" folder in your home directory. (If not present already)
  2. Create "Java" folder inside "Tools" folder.
  3. Go to oracle website to download [Java 7] (http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html). Download the binary (usually its a zip file) of required version. [I downloaded jdk-7u67-linux-x64.tar.gz so, I will use it in upcoming steps]
  4. Copy the downloaded file and paste it in "Java" folder. Then right click and extract. Delete the zip file; its not required anymore now
  5. Create a symlink at "~/Tools/java" and that link points to one of the specific Java version directories. Run this command (open terminal CTR+ALT+T): ln -s ~/Tools/Java/jdk1.7.0 _ 67 ~/Tools/java
  6. From command terminal run: nano .bashrc The .bashrc file will open in editor. (Please note this file is usually hidden in the home folder.)
  7. Update the JAVA_HOME to point the symlink I update the ".bashrc" file in my home folder. And I do this: (The file has been opened above). export JAVA_HOME=~/Tools/java export PATH=$JAVA_HOME/bin:$PATH CTRL+O & then CTRL+X
  8. Add different aliases for the versions you have to first remove existing symlink and then create new symlink. E.g. for Java I have defined following aliases in my .bashrc file: alias java7='rm ~/Tools/java && ln -s ~/Tools/Java/jdk1.7.0 _ 67 ~/Tools/java' Close terminal and open again!
  9. To switch the version just open the terminal and type: java7 and you are done! This way you can switch to different versions.
  10. To verify the installation of Java. Run this command on terminal: java -version

###- Maven

  • Ubuntu (Manually)
  1. Create "Tools" folder in your home directory. (If not present already)
  2. Create "Maven" folder inside "Tools" folder.
  3. Download Maven. Download the binary (usually its a zip file) of required version. [I downloaded apache-maven-3.2.3 so, I will use it in upcoming steps]
  4. Copy the downloaded file and paste it in "Maven" folder. Then right click and extract. Delete the zip file; its not required anymore now.
  5. Create a symlink at "~/Tools/Maven" and that link points to one of the specific Maven version directories. Run this command (open terminal CTR+ALT+T): ln -s ~/Tools/Maven/apache-maven-3.2.1 ~/Tools/maven
  6. From command terminal run: nano .bashrc The .bashrc file will open in editor. (Please note this file is usually hidden in the home folder.)
  7. Update the MAVEN_HOME to point the symlink I update the ".bashrc" file in my home folder. And I do this: (The file has been opened above). export MAVEN_HOME=~/Tools/maven export PATH=$MAVEN_HOME/bin:$PATH CTRL+O & then CTRL+X
  8. Add different aliases for the versions you have to first remove existing symlink and then create new symlink. E.g. for Maven I have defined following aliases in my .bashrc file: alias mvn323='rm ~/Tools/maven && ln -s ~/Tools/Maven/apache-maven-3.2.3 ~/Tools/maven'
  9. To switch the version just open the terminal and type: mvn323 or mvn305 and you are done! This way you can switch to different versions.
  10. To verify the installation of Maven. Run this command on terminal: mvn -version

###- IntelliJ

  1. Install an IDE. Here we will assume the usage of IntelliJ. Download IntelliJ IDEA. Ultimate version needs to be bought. Install IntelliJ.
  2. Configure Groovy in IntelliJ.
    • At startup after IntelliJ installation, add support for the plugin of Grails.
    • Otherwise, you can later change it from File -> Settings. Then choose plugins, and check Grails.
  3. Enable Git in IntelliJ, as mentioned in the step above.
  4. After that, go to Project->Settings, under Version Control, click Git. On the right hand panel, you need to give the address to the git executable, named git.exe, present in .../Git/bin/.
  5. For the ssh drop down right below the executable field, its preferable to choose "Built In".
  6. For more information on this issue, refer to jetbrains website.
  7. For projects being developed on cross-platform operatins systems, windows uses CRLF line endings(a format) and Linux, OS X use LF line ending format. If not taken care of these line endings will be changed from one format to the other, causing in merge conflicts. There are 2 possible solutions:
    • If using from Git, you need to change the 'core.autocrlf' property in the Git config to 'true'(for Windows) or to 'input' in case of Linux.
    • From IntelliJ itself wth Git integrated, you need to place an xml file here: .IntelliJIdea12\config\codestyles\Default _1_.xml, which contains policies for the commiting.

More info on this topic can be found here

###- Eclipse (for Activiti Diagram Only)

Install Eclipse Juno

In addition to installing the maven package and the eclipse package, and all their dependencies, you need to install the m2e extension. The best way to do this is using the Eclipse Marketplace, but the marketplace is not installed by default in the Ubuntu package.

Install the Eclipse Marketplace

  1. Open Eclipse, go to Help -> Install New Software...
  2. Select All Available Sites in the Work with dropdown menu.
  3. Wait for the list of software to populate; sometimes it takes a very long time.
  4. Expand the General Purpose Tools group, and tick Marketplace Client.
  5. Click Next, and again, accept the terms and conditions and click Finish.

This will install the marketplace. You will need to restart Eclipse for the change to take effect.

Install m2e

  1. Open Eclipse, go to Help -> Eclipse Marketplace...
  2. Wait for it to finish loading.
  3. Enter "maven" in the search box and press return.
  4. Click the Install button next to Maven Integration for Eclipse by Eclipse.org (NB: there is a similar item above called "Maven Integration for Eclipse WTP" by Red Hat, Inc; this is not the correct one).

Again, you will need to restart Eclipse for this to take effect.

Install Activiti BPMN 2.0 Designer

The following installation instructions are verified on Eclipse Juno.

Go to Help -> Install New Software. In the following panel, click on Add button and fill in the following fields:

Name: Activiti BPMN 2.0 designer Location: http://activiti.org/designer/update/

Make sure the "Contact all updates sites.." checkbox is checked, because all the necessary plugins will then be downloaded by Eclipse.

###- Git

  • Window users:
  1. Download latest version of git
  2. Select point 3 Run git and included unix tools from the windows command prompt, when needed. Path will be updated during installation.
  3. Open console and check git --version. The result should be like git version 1.9.0.msysgit.0.
  4. If git installation successful, generate ssh keys and add it to GitHub/Bitbucket account, follow to the Bitbuckt official guide.
  • Ubuntu/Debian users:
  1. Git Core: sudo apt-get install git
  2. Git GUI: sudo apt-get install git-gui

IMPORTANT! For projects being developed on cross-platform operating systems, windows uses CRLF line endings(a format) and Linux, OS X use LF line ending format. If not taken care of these line endings will be changed from one format to the other, causing in merge conflicts. You need to change the core.autocrlf property in the Git config to true(for Windows) or to input in case of Linux.

On Ubuntu you can find the ".gitconfig" under the home directory. It's usually hidden.

###- Node

Node.js is a Javascript platform for server-side programming that allows users to build network applications quickly. In most cases, you'll also want to also install npm, which is the Node.js package manager. This will allow you to easily install modules and packages to use with Node.js.

  • Ubuntu 14.04:

An alternative that can get you a more recent version of Node.js is to add a PPA (personal package archive) maintained by Chris Lea. This will probably have more up-to-date versions of Node.js than the official Ubuntu repositories.

  1. First, you need to install the PPA in order to get access to its contents: sudo add-apt-repository ppa:chris-lea/node.js
  2. The PPA will be added to your configuration. However, you still need to update your local package cache for your server to become aware of the new packages: sudo apt-get update
  3. After that, you can install the Node.js package: sudo apt-get install nodejs and you can verify it by running node --version
  4. You'll probably want to install npm as well: sudo apt-get install npm and you can verify it by running npm --version
  • Windows:
  1. If you don't already have Node.js installed, download the latest Node.js (if you use the .msi installer a reboot might be required for the npm to be registerd correctly)
  2. Open a command line prompt and run the following commands
    • npm update -g npm , to ensure that you have the latest version of npm

###- Bower

  • Ubuntu 14.04:
  1. sudo npm install -g bower
  2. Now verify the version by running bower --version
  • Windows:
  1. npm install -g bower ,`to install Bower. Make sure that Git is installed prior becasue Bower is dependent on it
  2. Now verify the version by running bower --version

###- Gulp

  1. Install gulp globally:

$ npm install --global gulp 2. Install gulp in your project devDependencies:

$ npm install --save-dev gulp

###- MySql

  • Window users:
  1. Download latest version of MySql community server
  2. Run .exe or .msi file and follow the instructions.
  3. Select Developer default.
  4. Specify password for root user.

Follow this guide, if there is any questions.

  • Ubuntu/Debian users: sudo apt-get install mysql-server mysql-client

Database Setup

  1. Create a new database named fmu
  2. MySql Settings:
    • username = root,
    • password = root,
    • host = localhost,
    • port = 3306.
  3. Open the terminal and type mysql -u root -p
  4. Enter the password when prompted root
  5. Create database CREATE DATABASE fmu CHARACTER SET utf8 COLLATE utf8_general_ci; (The output should be "Query OK, 1 row affected")

In case you need to drop existing database; DROP DATABASE fmu;

HikariCP MySQL recommended settings can be found here: https://github.com/brettwooldridge/HikariCP/wiki/MySQL-Configuration

###- kdiff3

  • Ubuntu/Debian users
  1. It's helps when you need to merge conflicting files! watch some youtube video to learn how to use it!
  2. Go to kdiff3
  3. Select your ubuntu version from the left
  4. Then simply click the install button!
  5. Change merge tool in "Git Gui" options; Edit -> Options...

###- dbVisualizer

##Logging

###Log file location

  • Application logs can be found here: fmu/logs

###Log configuration

  • For unit testing log configuration can be found here: fmu/src/test/resources/logback-test.xml
  • For production log configuration can be found here: fmu/src/main/resources/logback.xml

##Generating Liquibase ChangeLog

mvn resources:resources liquibase:update -P<profile_name> e.g. mvn resources:resources liquibase:diff -Pprod

Invoking the resources is necessary in order to have the liquibase.properties placeholders filtered. The -P option tells Maven the profile to use and thus the set of values (from the filter properties file) to use for filtering.

##Running/Debugging the Application

###Eclipse

#####Eclipse set and forget run configurations Right-click on the project folder -> Run as -> From here there should be many different Maven run configurations but if you want to add your own configurations or run any Maven commands.

#####Create ´dev´ run configuration

  1. Right-click on the project folder -> Run as
  2. click Run Configurations
  3. fill in a name, lets call it fmu-dev in the Name field
  4. browse to the correct Base directory, it should be something like ${workspace_loc:/fmu}
  5. fill in spring-boot:run -Pdev maven command under Goals
  6. fill in ``devunderProfiles` and Click Run.

Now the dev run configuration should be available directly from the dropdown menu at the green triangle Run icon.

Repeat the same step for other profiles if needed.

#####Increase permGem size while building with Maven Maven is currently having issues with memory. To increase the pemGem memory size include this VM arguments XX:MaxPermSize=512m in the run-configuration -> JRE. 512m can be adjusted to any number you see fit

###IntelliJ

#####Add 'resources' directory to classpath in IntelliJ 13

  1. Click on the Project view or unhide it by clicking on the "1: Project" button on the left border of the window or by pressing Alt + 1
  2. Find your project or sub-module and click on it to highlight it, then press F4, or right click and choose "Open Module Settings"
  3. Click on the dependencies tab
  4. Click the "+" button on the right and select "Jars or directories..."
  5. Find your path and click OK
  6. In the dialog with "Choose Categories of Selected File", choose classes (even if it's properties), press OK and OK again

You can now run your application and it will have the selected path in the classpath.

#####As a "main" Java class

  1. Go to Run then Edit Configurations...
  2. Then click on + sign on the top left corner then select Application
  3. Give name Application (or whatever you like)
  4. Main class se.inera.fmu.Application
  5. VM Options -XX:MaxPermSize=256M (this is must otherwise you might run in to PermGem or OutOfMemory issues)

From your IDE, right-click on the se.inera.fmu.Application class at the root of your Java package hierarchy, and run it directly. You should also be able to debug it as easily.

The application will be available on http://localhost:8080. Note: The default profile is dev so, it will run on port 8080

#####Deploy both frontend & backend (Maven) You can launch the Java server with Maven by running following command at the project root folder:

mvn spring-boot:run -P<profile_name> e.g. mvn spring-boot:run -Pprod -Drun.jvmArguments="-XX:MaxPermSize=256M"

The application will be available on http://localhost:9090

Please note that due to PerGem & OutOfMemory issues on few systems we have to pass this extra argument when running through maven: -Drun.jvmArguments="-XX:MaxPermSize=256M"

If you want more information on using Maven, please go to http://maven.apache.org

#####Generate WAR file

Run mvn package -Pprod And then you can find the WAR file under target directory.

##Profiles

fmu comes with three "profiles":

  • "dev" for development: it focuses on ease of development and productivity
  • "integration-test" for integration-test: ...
  • "prod" for production: it focuses on performance and scalability

Those profiles come in two different configurations:

  1. The Maven profiles are used at build time. For example mvn -Pprod package will package a production application.
  2. The Spring profiles work a run time. Some Spring beans will behave differently, depending on the profile.

Spring profiles are set by Maven, so we have a consistency between the two methods: of course, we have a "prod" profile on Maven and Spring at the same time.

####dev In default mode, fmu will use the "dev" profile If you run the application without Maven, launch the "Application" class (you can probably run it easily from your IDE by right-clicking on it).

  1. npm install to fetch all packages specified in the Package.json file
  2. bower install to fetch all packages specified in the bower.json file
  3. If you run the application with Maven, run mvn -Pdev spring-boot:run -Drun.jvmArguments="-XX:MaxPermSize=256M"

####prod In production, fmu has to run with the "prod" profile Use Maven to build the application with the "prod" profile: mvn -Pprod spring-boot:run -Drun.jvmArguments="-XX:MaxPermSize=256M"

####integration-test ...

##Testing

####Unit Tests (Java) We use the Surefire Maven plugin to run our unit tests. Run following command to run unit tests:

mvn clean test

During development unit test's can be run from within the IDE.

####Integration Tests (Java) The Failsafe Maven plugin is used to execute our integration tests. Run following command to run integration tests:

mvn clean verify -P integration-test

When running integration tests from within IntelliJ just ensure to write click the resources folder and select Mark Directory As Resources Root

####Unit Tests (JavaScript) Front end unit tests can be run directly using command line at the project folder. Use gulp test for unit testing

####Skipping Tests

Although its not safe but you can skip tests by appending this in the end of the command -Dmaven.test.skip=true

##Authentication Currently the “prod” and “dev” profiles uses fake login that doesn’t authenticate with the SSO server. A profile named “acctest” will authenticate with a test SSO server.

In order to login to the SSO-server the client needs a card reader and the NetID client installed.

http://www.e-identitet.se/index.php?page=net_id_download

A test card was issued to the fmu-team along with a paper containing credentials.

Regarding FMU integration with the SSO-service see: https://gist.github.com/knivmakkara/2443e6988a29b85f619f

##Endpoints

Spring-Boot Actuator endpoints allow you to monitor and interact with your application. Spring Boot includes a number of built-in endpoints and you can also add your own. For example the health endpoint provides basic application health information.

The way that endpoints are exposed will depend on the type of technology that you choose. Most applications choose HTTP monitoring, where the ID of the endpoint is mapped to a URL. For example, by default, the health endpoint will be mapped to /health.

Here you can see list of endpoints

##H2 Console

When running application in "dev" mode then H2 Console can be accessed through the URL: http://localhost:8080/console For database URL use: jdbc:h2:mem:fmu

##TroubleShooting

####PerGem or OutOfMemory Issue Please pass this JVM argument -Drun.jvmArguments="-XX:MaxPermSize=256M" if running through maven.

##Plugins

####EditorConfig EditorConfig helps developers define and maintain consistent coding styles between different editors and IDEs. Read more here

Add SSH key Follow this tutorial: https://help.github.com/articles/generating-ssh-keys If you run into issue like: ssh: connect to host github.com port 22: Connection refused Then follow advice here: http://stackoverflow.com/questions/7953806/github-ssh-via-public-wifi-port-22-blocked

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