Content Comparison

UI Development

Prerequisite software to install

Set up the Maven Build

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• Java (Corretto JDK 11+ recommended)

• Maven 3

• Docker

• Yarn v1

Set up your GitHub fork and a local repository

1. Create a GitHub user account if you don't already have one.

2. Set up your local git environment according to Sage’s GitHub Security guidance

3. Fork the Sage-Bionetworks SynapseWebClient repository into your own GitHub account: https://help.github.com/articles/fork-a-repo

4. Clone

...

1. your fork of SynapseWebClient project

...

1. to your

...

1. local machine and enter the project root directory

   Code Block
   language bash
   git clone https://github.com/[YOUR

...

1. GITHUB NAME]/SynapseWebClient.git

...

Set up the Eclipse Build

1. Install Eclipse (Mars 4.5, Neon 4.6 GWT super dev mode does not start properly)
2. Install Google Web Toolkit, Google App Engine SDK, and Google plug-in for Eclipse using Eclipse new software from http://www.gwtproject.org/download.html.  Note: if you were using an older version of this plugin you will need to uninstall it and then re-install it to ensure it has  GWT 2.8 beta1 support. Another note: Installing the Google App Engine Maven Integration software made Eclipse error when building the SynapseWebClient. It would not work until I uninstalled it.
3. Install the Maven2Eclipse plugin: http://download.eclipse.org/technology/m2e/releases
4. Create a GitHub user account
   
   1. Contributors should fork the repository and submit GitHub Pull Requests for code inclusion.

5. Set up Git: https://help.github.com/articles/set-up-git

6. Import the project as a maven project
   
   1. File → Import → Maven → Existing Maven Projects
   2. Next, in Root Directory enter the local path to your repository clone
   3. Next, Finish 
7. You need to make sure the GWT xml files are on the classpath. All of these resources can be found in src/main/resources and src/test/resources directories. 
   
   1. Right-click on portal (project name) → Build Path → Configure Build Path...
   2. Remove the "Exclude" filter from the source tab on the src/main/resources and src/test/resources directories.
8. We need to tell the GWT Eclipse-plugin that this is a GWT project. Do this by Right-Clicking on the project in the package explorer and select: Google → Web Toolkit Settings...
   
   1. From the resulting dialog make sure the "Use Google Web Tookit" check box is selected.
   2. Also make sure you are using GWT 2.8 beta1
9. We need to tell the Google plugin where our web app directory can be found.  Right-click on the project in the package explorer and select Properties.
   
   1.  From the tree on the left of the dialog navigate to Google → Web Application
   2. Check the the check box: "This project has a WAR directory"
   3. With the "Browse" button, select "src/main/webapp"
   4. UN-CHECK the "Launch and deploy from this directory"  This is very important, if you keep this checked then Maven will not be able to generate a clean WAR file.  If you see "GWT needs to recompile" when you deploy your WAR then you probably have this box checked.
10. Now make sure GWT can compile your code
    
    1. Right-Click on the project from the package explorer.
    2. Select Google→GWT Compile...
    3. Under the "Entry Point Modules" you should see "PortalDebug - org.sagebionetworks.web",  if not, then add it with the add button.
    4. Remove the "Portal - org.sagebionetworks.web" entry.
    5. The first time you run this you will be asked to select the output directory where GWT will compile the code. You want this to match the Maven WAR output directory, so use "target/portal-<VERSION>-SNAPSHOT"
    6. If you get compilation errors from the JavaScript validator (i.e. NullPointerException), navigate to the project's properties → JavaScript → Include Path → Source, and exclude all files from the source. If an OutOfMemoryError was thrown while compiling, you can click the "Advanced" tab towards the bottom of the Google → GWT Compile window and add "-Xms512M -Xmx1524M" to the VM arguments to increase heap space.
11. If the GWT Compile successfully compiled, then you're ready to run the application.
    
    1. Option 1: start from within Eclipse.
       1. Right-Click on the project in the package explorer
       2. Select: Run As → Web Application (GWT Super Dev Mode)
       3. Set the run configuration VM Arguments to the following: "-XX:MaxPermSize=512m -Xms512m -Xmx2048m -XstartOnFirstThread".  Also look at your eclipse.ini file (if launching SDM from Eclipse).
       4. Double-click on the link provided in the Development Mode window to view the portal in your browser.  If you get asked what page to start on choose Portal.html.
    2. Option 2: build and run from the command line.
       1. Run 'mvn clean install'
       2. Run 'mvn gwt:run'

Eclipse Workspace Settings

Set file encoding to UTF-8 and the line-endings (for new files) to Unix, so that text files are saved in a format that is not specific to the Windows or Mac OS and most easily shared across heterogeneous developer desktops:

• Open Preferences
• Navigate to the Workspace preferences: General → Workspace
• Change the Text File Encoding to UTF-8
• Change the New Text File Line Delimiter to Other and select Unix from the drop-down

Troubleshooting

• Check your exclusion filters through configure build path in Eclipse to assure nothing is excluded, then refresh and clean the SWC project.
• "Could not deserialize" or similar problems in Super Dev Mode are most often fixed by re-building through the command line (running 'mvn clean install')
• (git) Pull the latest changes from the upstream repository.
• Try to rebuild your Eclipse's Portal project and keep your files in place.
• Perform a Maven update.  

1. Delete your project from Eclipse (leave "Delete project contents on disk" UNCHECKED)
2. Go to the project root on your file system and delete .classpath, .project and the .settings/ folder
3. Go to Step 6 in "UI Development above"

If this still doesn't work, or your dev mode is broken for another reason, there are some further steps you can take.
(Check out this site for more information: http://www.eclipsezone.com/eclipse/forums/t61566.html)

1. Use the '-clean' argument.
   1. One way to do this is to add -clean on its own line as the first line on the eclipse.ini file, and restart Eclipse.
2. Use a new workspace.
   1. I followed the instructions in the site linked above. The gist of it is:
      1. Export your preferences to somewhere outside your Eclipse environment environment (Export → General → Preferences. Make sure that 'Export All' is checked.)
      2. Switch to a new workspace. (Switch Workspace → Other, then name your new workspace.)
      3. Import your preferences into this new workspace (Import → General → Preferences, make sure 'Import All' is checked.)
      4. Import trunk as usual.

Technologies used

There are several technologies that we are currently utilizing in the portal. The following is a list of primers for each:

• Java!
• Google Web Toolkit
• For dependency injection, an example of Inversion of Control (IoC), we are using a combination of GIN and Guice.
  • Guice - is the base IoC technology but it is only fully functional in Server-side.
  • Gin - provides basic IoC for GWT client-side code.
  • Guice Servlet - This is a sub-project of Guice that allows dependency inject into Servelets.
• Http REST calls are currently made using Spring's RestTemplate. http://blog.springsource.com/2009/03/27/rest-in-spring-3-resttemplate/
• To create API REST stub-services we are using a combination of two technologies:
  • Jersey - provides a quick and easy method for transforming simple POJO's into RESTful web services using annotations. http://jersey.java.net/nonav/documentation/latest/user-guide.html
  • Grizzly - The GrizzlyWebContainerFactory makes it simple to start a local web container. http://blog.msbbc.co.uk/2008/11/java-using-jersey-and-grizzly-to-create.html
• Mockito testing framework - mock dependent classes/interfaces to isolate test.  Verify expected interactions (including async calls). 
• Bootstrap UI framework (including a number of extras widgets), wrapped for GWT.
• Markdown-it - for markdown processing .  Extended the library by adding a number of plugins, available on npm.  The Node.js plugin that's used to orchestrate the processing is called markdown-it-synapse
• AWS js sdk - direct browser upload/download from s3-like storage.
• jquery, moment js, font-awesome, mathjax, plot.ly, twitter, nodeca/pica (browser image resize), SparkMD5 (browser side md5 calculation), nchart and jsplumb (Dave's charting libraries for provenance), Google (analytics, search, closure-library, single sign on).

Cross-browser testing

We have a shared account to use BrowserStack to test the website for cross browser compatibility issues.
Alternatively, for testing IE on Mac I use VirtualBox with an image provided by Microsoft from modern.IE.  For this to work, in your Windows VM, you will need to map an ip to outer in order to access your local machine (note, Windows UAC requires you to do this as an admin).

How to limit GWT build permutations

To speed up build time, add the following property to your local maven settings.xml file:

<gwt.module.suffix>Debug</gwt.module.suffix>

How to point to the local stack

...

Build and launch a local backend stack.  From an up-to-date clone of Synapse-Repository-Services on your local box:

...

Build the local stack by running 'mvn clean install -Dorg.sagebionetworks.database.drop.schema=true'.

...

1. cd integration-test
2. mvn cargo:run

Verify the services are running correctly by visiting http://localhost:8080/services-repository-develop-SNAPSHOT/repo/v1/version you should see something like this:

{"version":"develop-SNAPSHOT"}

...

<org.sagebionetworks.authenticationservice.privateendpoint>http://localhost:8080/services-repository-develop-SNAPSHOT/auth/v1</org.sagebionetworks.authenticationservice.privateendpoint>
<org.sagebionetworks.authenticationservice.publicendpoint>http://localhost:8080/services-repository-develop-SNAPSHOT/auth/v1</org.sagebionetworks.authenticationservice.publicendpoint>
<org.sagebionetworks.repositoryservice.endpoint>http://localhost:8080/services-repository-develop-SNAPSHOT/repo/v1</org.sagebionetworks.repositoryservice.endpoint>
<org.sagebionetworks.fileservice.endpoint>http://localhost:8080/services-repository-develop-SNAPSHOT/file/v1</org.sagebionetworks.fileservice.endpoint>
<org.sagebionetworks.searchservice.endpoint>http://localhost:8080/services-repository-develop-SNAPSHOT/</org.sagebionetworks.searchservice.endpoint>
<org.sagebionetworks.portal.endpoint>http://127.0.0.1:8888/Portal.html</org.sagebionetworks.portal.endpoint>

Note that emails will not be sent when pointing to a local repo, the SynapseEmailService will instead write files to the devdata.sagebase.org s3 bucket in format <to_email_address>.json

Restart the Portal app to load these properties from settings.xml.

How to point to staging

Set the repository endpoints in your maven settings.xml file by adding the following properties:

<org.sagebionetworks.authenticationservice.privateendpoint>https://auth-staging.prod.sagebase.org/auth/v1</org.sagebionetworks.authenticationservice.privateendpoint>
<org.sagebionetworks.authenticationservice.publicendpoint>https://auth-staging.prod.sagebase.org/auth/v1</org.sagebionetworks.authenticationservice.publicendpoint>
<org.sagebionetworks.repositoryservice.endpoint>https://repo-staging.prod.sagebase.org/repo/v1</org.sagebionetworks.repositoryservice.endpoint>
<org.sagebionetworks.fileservice.endpoint>https://file-staging.prod.sagebase.org/file/v1</org.sagebionetworks.fileservice.endpoint>
<org.sagebionetworks.searchservice.endpoint>https://search-staging.prod.sagebase.org/</org.sagebionetworks.searchservice.endpoint>
<org.sagebionetworks.portal.endpoint>http://127.0.0.1:8888/Portal.html</org.sagebionetworks.portal.endpoint>

Restart the Portal app to load these properties from settings.xml.

How to point to prod

Set the repository endpoints in your maven settings.xml file by adding the following properties:

...

1. cd SynapseWebClient

2. If you didn't set up the global pre-commit hook in step #2, set up a local pre-commit hook to detect secrets (do this for all repos that you clone in the future!):

   Code Block
   git secrets --install git secrets --register-aws

3. Set up upstream with

   Code Block
   git remote add upstream https://github.com/Sage-Bionetworks/SynapseWebClient

4. Fetch and merge changes from the Sage Bionetworks repo, which was named upstream: 

   Code Block
   git fetch upstream

5. Configure or update your Maven configuration settings.xml

   1. The file needs to placed in $HOME/.m2/settings.xml (e.g. jane/.m2/settings.xml)

   2. This should be the content of this file:

      settings.xml

      Code Block
      language xml
      <settings xmlns="http://maven.apache.org/SETTINGS/1.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0 http://maven.apache.org/xsd/settings-1.0.0.xsd"> <localRepository/> <interactiveMode/> <usePluginRegistry/> <offline/> <pluginGroups/> <servers/> <mirrors/> <proxies/> <profiles> <profile> <id>dev-environment</id> <activation> <activeByDefault>true</activeByDefault> </activation> <properties> <org.sagebionetworks.portal.endpoint>http://127.0.0.1:8888/Portal.html</org.sagebionetworks.portal.endpoint> <org.sagebionetworks.repositoryservice.endpoint>https://repo-prod.prod.sagebase.org/repo/v1</org.sagebionetworks.repositoryservice.endpoint> <!-- insert properties described below here --> <!-- <org.sagebionetworks.repositoryservice.endpoint>https://repo-staging.prod.sagebase.org/repo/v1</org.sagebionetworks.repositoryservice.endpoint> --> <!-- Uncomment the property below to limit GWT permutations and speed up build time --> <!-- <gwt.module.suffix>Debug</gwt.module.suffix> --> </properties> </profile> </profiles> <activeProfiles/> </settings>

6. Verify you can build the project and run the unit tests:

   Code Block
   mvn clean install

Development

You may use an IDE of your choice. Instructions for setting up IntelliJ IDEA and Eclipse can be found below.

To run the app in development mode, run yarn install then yarn dev. This will launch three processes:

• The GWT Codeserver, which watches for source changes

• A file watcher that monitors changes to static assets, and copies them to the deployed web application directory when they change

• An Apache Tomcat Docker container that will host the web application

As you make changes to the source code and static assets, changes will be picked up in the app when you refresh the page.

Running the accounts site to enable sign-in

SynapseWebClient delegates authentication and account management to a separate web application. In order to sign in to a local instance of SynapseWebClient, you must also start a local instance of the account management application. Set up the synapse-web-monorepo project and run the following command.

pnpm nx run SageAccountWeb:preview --port=3000 --host

If your portal instance is configured to use to a different backend stack, you will need to configure SageAccountWeb to also use the same stack.

We have an open ticket to improve this process: SWC-7230

JavaScript dependency development

If you have made changes to a JavaScript dependency (e.g. synapse-react-client), you can see those changes in your local development environment by “linking” the projects. As an example, we will link the synapse-react-client project.

1. In the synapse-react-client directory, run

   Code Block
   yarn link

2. In the SynapseWebClient directory, run

   Code Block
   yarn link synapse-react-client

   This will create a symlink on your machine so the node_modules/synapse-react-client directory points to your local synapse-react-client directory.

3. Make desired changes in the synapse-react-client project

4. Rebuild the JavaScript artifacts for synapse-react-client (pnpm nx run synapse-react-client:build)

5. If you’re running yarn dev, the changed JavaScript file should automatically be picked up. Refresh your browser window to see the changes (you will likely need to open your browser dev tools → Network → Disable Cache, and leave the browser devtools open)

When you want to unlink synapse-react-client, in the SynapseWebClient directory you can run yarn unlink synapse-react-client and then yarn install --force.

Known issues:

• Running yarn install in SynapseWebClient after linking synapse-react-client breaks the pnpm installation in the synapse-web-monorepo project. To fix this, run pnpm install --force in the synapse-web-monorepo project.

IDE Setup Instructions

This section contains instructions for setting up various IDEs to develop SynapseWebClient.

Technologies used

There are several technologies that we are currently utilizing in the portal. The following is a list of primers for each:

• Java!

• Google Web Toolkit

• React and the Synapse React Client

  • Further reading: How to create and render a React component in SynapseWebClient

• For dependency injection, an example of Inversion of Control (IoC), we are using a combination of GIN and Guice.

  • Guice - is the base IoC technology but it is only fully functional in Server-side.

  • Gin - provides basic IoC for GWT client-side code.

  • Guice Servlet - This is a sub-project of Guice that allows dependency inject into servlets.

• HTTP REST calls are currently made using Spring's RestTemplate. http://blog.springsource.com/2009/03/27/rest-in-spring-3-resttemplate/

• Mockito testing framework - mock dependent classes/interfaces to isolate test.  Verify expected interactions (including async calls). 

• Bootstrap 3 UI framework (including a number of extras widgets), wrapped for GWT (deprecated).

• Markdown-it - for markdown processing .  Extended the library by adding a number of plugins, available on npm.  The Node.js plugin that's used to orchestrate the processing is called markdown-it-synapse. The source code for many of these plugins is in the synapse-web-monorepo project.

• AWS js sdk - direct browser upload/download from s3-like storage.

• jquery, moment js, font-awesome, mathjax, plot.ly, twitter, nodeca/pica (browser image resize), SparkMD5 (browser side md5 calculation), nchart and jsplumb (Dave's charting libraries for provenance), Google (analytics, search, closure-library, single sign on).

• frontend-maven-plugin to install Node and Yarn at build-time, which provides numerous JavaScript dependencies via NPM.

End-to-end testing

Instructions on running end-to-end tests are included in this README.

How to point to a local instance of the Synapse backend

1. Follow the instructions on the Platform Bootstrap to set up a local backend stack. 

2. Build and launch a local backend stack.  From an up-to-date clone of Synapse-Repository-Services on your local box:

   1. Build the local stack by running mvn clean install -Dorg.sagebionetworks.database.drop.schema=true.

   2. Now launch it:

      Code Block
      cd integration-test mvn cargo:run

   3. Verify the services are running correctly by visiting http://localhost:8080/services-repository-develop-SNAPSHOT/repo/v1/version. You should see something like this:

      Code Block
      {"version":"develop-SNAPSHOT"}

3. In the SWC project root pom.xml, change the synapse.version tag to develop-SNAPSHOT, so that Maven utilizes artifacts that were built by running on your local stack.

4. Update the repository endpoint property in your maven settings.xml file:

   Code Block
   <org.sagebionetworks.repositoryservice.endpoint>http://localhost:8080/services-repository-develop-SNAPSHOT/repo/v1</org.sagebionetworks.repositoryservice.endpoint>

5. Restart the Portal app to load these properties from settings.xml.

How to point to a remote stack

Set the repository endpoint parameters in your maven settings.xml file. 

To point to the development stack set:

<org.sagebionetworks.repositoryservice.endpoint>https://repo-dev.dev.sagebase.org/repo/v1</org.sagebionetworks.repositoryservice.

...

endpoint>

To point to staging set:

<org.sagebionetworks.

...

repositoryservice.

...

endpoint>https://

...

repo-

...

staging.prod.sagebase.org/

...

repo/v1</org.sagebionetworks.

...

repositoryservice.endpoint>

To point to production set:

<org.sagebionetworks.

...

repositoryservice.

...

endpoint>https://

...

repo-prod.prod.sagebase.org/repo/v1</org.sagebionetworks.

...

repositoryservice.

...

Pointing to prod is especially useful at transitions between releases, so that there is a stack that you can point at. 

endpoint>

Restart the Portal app to load these properties this property from settings.xml.

Documenting complicated UI in the code

To get the big picture of widget relationships, sometimes it is helpful to have a picture.  We are testing the use of tools like httphttps://asciiflowmermaid.js.comorg/ to help in these situations.

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