Study Tracker Setup

These instructions assume that you have a working VM with a current LTS version of Ubuntu:

Created a PostgreSQL database that can be used by Study Tracker.
Have a configured Benchling tenant. This is optional to run Study Tracker, but the configuration described below includes Benchling references.
Have a configured Egnyte tenant. This is also optional.
Have Okta configured for your organization and have created an app in your SSO dashboard for Study Tracker.
- Configure your app with the single-sign-on URL ending in /saml/SSO and the audience URI/SP Entity ID ending in /saml/metadata.
- So for example, if your Study Tracker app was being hosted at https://mystudytracker:8443, the SSO URL value would be https://mystudytracker:8443/saml/SSO. These URLs are case-sensitive.

Setting up the server

Install Java, Maven, Git, and NPM

 sudo apt-get install openjdk-11-jdk
 sudo apt-get install maven
 sudo apt-get install npm
 sudo apt-get install git

Update NPM and dependencies

 sudo npm install -g npm less less-watch-compiler webpack webpack-cli

Downloading Study Tracker

Generate an RSA key for cloning the repository. Don't use a password.
```
 ssh-keygen -t rsa -b 4096
 
```
Associate the generated public key with your GitHub account so that you can clone the repository.
Clone the repository into a directory of your choice.
```
 git clone [email protected]:Decibel-Therapeutics/Study-Tracker.git
 
```
Enter the directory you cloned the repository to.
For now, checkout and use the development branch:
```
 git checkout development
 
```

Configure Study Tracker

Create a flyway.conf file with the following info:

 flyway.user=studytracker
 flyway.password=studytracker
 flyway.url=jdbc:postgresql://localhost:5432/study-tracker

Run Flyway to clean and populate the database with initial state

 mvn -Dflyway.configFiles=flyway.conf flyway:clean
 mvn -Dflyway.configFiles=flyway.conf flyway:migrate

Create a P12 keystore and self-signed certificate for SSL in the directory src/main/resources

 keytool -genkeypair -alias stsslstore -keyalg RSA -keysize 2048 -storetype PKCS12 -keystore stssl.p12 -validity 3650

Create a JKS keystore for SAML authentication in the directory src/main/resources

 keytool -genkeypair -alias stsaml -keypass mypassword -keystore saml-keystore.jks

Create a application.properties file in the directory src/main/resources. Sample contents:

 # Application
 application.host-name=myhost.com
 
 # Admin
 [email protected]
 admin.password=xxxxxx

 # Data Source
 db.username=studytracker
 db.password=xxxxx
 db.host=localhost
 db.port=5432
 db.name=study-tracker

 # JPA
 spring.jpa.show-sql=true
 spring.jpa.hibernate.ddl-auto=validate

 # AWS
 aws.region=us-east-1
 aws.access-key-id=xxxxxx
 aws.secret-access-key=xxxxxx
 
 # Events
 events.mode=eventbridge
 aws.eventbridge.bus-name=research-data-dev

 # Email
 spring.mail.host=xxxxx
 spring.mail.port=xxxxx
 spring.mail.username=xxxxx
 spring.mail.password=xxxxx
 spring.mail.properties.mail.smtp.auth=true
 spring.mail.properties.mail.smtp.starttls.enable=true
 email.outgoing-email-address=${spring.mail.username}

 ### Notebook
 # Options: none, idbs, benchling
 notebook.mode=benchling
 benchling.eln.api.token=xxxxx
 benchling.eln.api.root-url=https://mytenant.benchling.com
 benchling.eln.api.root-entity=
 benchling.eln.api.root-folder-url=${benchling.eln.api.root-url}/decibeltest/f_

 ### Storage
 # Options: local, egnyte
 storage.mode=egnyte
 storage.use-existing=true
 storage.max-folder-read-depth=3
 
 # Local
 storage.temp-dir=/tmp
 storage.local-dir=${storage.temp-dir}
 
 # Egnyte
 egnyte.root-url=https://mytenant.egnyte.com
 egnyte.api-token=xxxxx
 egnyte.root-path=Shared/General/StudyTracker
 egnyte.qps=3
 
 ### Studies
 study.default-code-prefix=ST
 study.default-external-code-prefix=EX
 study.code-counter-start=10001

 ## SSL (optional)
 server.port=8443
 server.ssl.enabled=true
 server.ssl.key-store-type=PKCS12
 server.ssl.key-alias=stsslstore
 server.ssl.key-store=classpath:stssl.p12
 server.ssl.key-store-password=xxxxx

 ## Okta
 sso.url=xxxxx
 security.sso=okta-saml
 saml.audience=xxxxx
 saml.idp=xxxxx
 saml.metadata-url=xxxx
 saml.keystore.location=classpath:saml-keystore.jks
 saml.keystore.alias=stsaml
 saml.keystore.password=xxxx

Adding a company logo

Create a folder named images within the directory src/main/resources/static.
Copy a PNG image file to this directory and name it logo.png.

Running Study Tracker

Build the application:

 npm install
 npm run build
 mvn clean package -DskipTests

Run the app:
```
 java -jar /path/to/study-tracker.war
```

The first time you run Study Tracker, no users will be registered in the app. Upon initialization, the application will create an admin user with a temporary password. Look for this line in the output log:

2021-08-10 18:25:09.106  INFO 732669 --- [           main] c.d.s.c.i.AdminUserInitializer           : Created admin user with username 'admin' and password 'xxxxxx'. You should change this password from the login page as soon as possible.

Make a note of this password and use it to login to the application. You should change this password as soon as possible in the login screen.

Running as a service

In the directory /etc/systemd/system/ create a file named study-tracker.service and give it the following contents:

 [Unit]
 Description=Study Tracker

 [Service]
 WorkingDirectory=/path/to/app
 ExecStart=/usr/bin/java -jar study-tracker.war
 Restart=always
 StandardOutput=syslog
 StandardError=syslog
 SyslogIdentifier=study-tracker

 [Install]
 WantedBy=multi-user.target

Start the service:
```
 sudo systemctl start study-tracker
```
Enable auto-start of the application on server restart:
```
 sudo systemctl enable study-tracker
```

Updating Study Tracker

Stop the application server:
```
 sudo systemctl stop study-tracker
```

Pull the latest commit:

 git reset --hard HEAD
 git pull --force

Update the database:

 mvn -Dflyway.configFiles=flyway.conf flyway:migrate

Build the application:

 npm install
 npm run build
 mvn clean package -DskipTests

Copy the artifacts to the appropriate location and restart the service:
```
 sudo systemctl start study-tracker
```

Signing in the first time

Production Deployment Changes

When deploying in a production environment, there are a few things you should do differently.

Run the server on port 443. You can configure this in the application.properties file.
```
 server.port=443
```

woemler/Elasticsearch-setup.md

Elasticsearch Setup