GSRS 3 Main Deployment

GSRS 3.x is based on a Spring Boot microservice infrastructure and is highly flexible and configurable. Both the core substance modules as well as the modules for additional entities (e.g. products, applications, impurities, clinical trials, adverse events, etc) can be deployed in a variety of flexible configurations to suit the needs of the user and use-case. GSRS requires the use of an RDBMS database for data storage. The supported database flavors are: H2, PostGreSQL, MariaDB and MySQL.

GSRS 3.x works with Java 8, 11, 17; versions outside of these may result in build errors. Set JAVA_HOME to point to one of Java 8, 11, or 17 and verify with the terminal command: mvn --show-version. Note, however, that the pom.xml files still specify Java 8 or 11, and as of 3.1.1, the GSRS team writes code to conform with Java 8 or 11.

Important Notes:

For GSRS 3.1, there are database schema changes for the substances service. Before upgrading your system, please check the release notes for discussion. Also please check the README files in ./substances/database/sql/ for suggested steps.
In October 2024, we revised past Substances README files and database creation scripts to default to the use of sequences instead of auto_increment.
As of August 2022, an Oracle database instantiated by GSRS 3.x requires an extra script before data is stored. If you are creating a new database, see this script and its mention in the 3.1 database README. Please contact the GSRS team with any questions.

Get Started

To run a deployment of the GSRS you'll need a minimum of two backend services (gateway and substances) and one frontend service. The backend "gateway" coordinates traffic between different microservices including the frontend. The default "substances" backend service handles the REST API for substance information, controlled vocabulary, session information and other "core" entites. The frontend service loads an Angular frontend application.

This Main Deployment contains all the required and optional artifacts you need to deploy and run GSRS. Each artifact is contained in a subdirectory. Navigate to the documentation for each by following these links.

Beyond documentation of the parts, the rest of this README is meant to provide background on how to structure whole deployments of different types and to discuss ways of integrating the parts.

Your Deployment Type Depends on Your Goal

Developers will often want to deploy locally and be able to modify code on the fly. In this case, embedded Tomcat instances for each service make the most sense.

A production deployment may also use an embedded architecture in combination with other technologies such as Docker. A single Tomcat instance where all the microservices run under one Tomcat instance as individual "war" files is also an option.

Maven Central vs. Git

If you're evaluating GSRS or want to take the simplest path toward installation of a public release for production, it makes most sense to rely on Maven Central to download all the necessary dependencies. In this case, you only need to download gsrs3-main-deployment from the NCATS Github website. Next, when you run or package services, Maven will automatically locate and download the dependencies on Maven Central.

Developers who wish to peruse the code or make modifications to classes between releases can clone sources from the NCATS Github repository. If you do this, use mvn install on starter modules that you clone from the NCATS Github site.

Cloning/repositories from from Git

In order to launch a local maven run for testing GSRS 3.0, you will need to access to the following git repository:

https://github.com/ncats/gsrs3-main-deployment (GSRS 3 Main Deployment) this is the repository you are viewing now

This repository contains the small wrappers and basic configuration settings needed to build the WAR files and to launch all microservices in an embedded mode.
This repository also houses the raw compiled frontend artifacts which are needed to assemble the frontend.
This repository also houses a docs folder and README files which give additional information on installation, configuration and development.

The following additional git repositories are optional, and should be cloned by developers who wish to edit code in the dependencies of the GSRS 3 Main Deployment, for testing or other purposes.

https://github.com/ncats/gsrs-spring-starter (optional)

This is the core starter library which is a dependency for all other entity endpoints (it’s also in maven central so you don’t need to clone this repository unless you want the most up-to-date code or special feature branch)

https://github.com/ncats/gsrs-spring-module-substances (optional)

This is the core substance starter library and is the dependency where the majority of API logic is handled (it’s also in maven central so you don’t need to clone this repository unless you want the most up-to-date code or special feature branch)

https://github.com/ncats/GSRSFrontend/tree/development_3.0 (optional)

This is the raw angular/typescript/html codebase for the frontend. This is where the frontend static files are generated for use in the frontend microservice found in the gsrs3-main-deployment repository. At the time of this writing the process for doing that build into the gsrs3-main-deployment frontend module is fairly manual. There is some limited documentation about the process within the gsrs3-main-deployment frontend README. This is not needed unless you intend to make a real change to the frontend code. Many changes to the frontend code can be done by changing its config.json file instead of changing the source code.

Local Embedded Tomcat Instance Deployment

For the base level simple deployment, you can follow these steps:

Clone gsrs3-main-deployment repository
Clone gsrs-spring-starter git repo and install (optional)
Clone gsrs-module-substance-starter git repo and install (optional)
Within the gsrs3-main-deployment repository, modify the frontend/src/main/resources/application.properties file to have the port you’d like the frontend to run on. The default is port 8082 and that is typically sufficient for local deployments.
Within the gsrs3-main-deployment repository, modify the frontend/src/main/resources/static/assets/data/config.json file to have the "apiBaseUrl" property point to the correct REST API endpoint. In this case, that endpoint should be the full path you will use for the gateway, including a terminal slash ("/"). The JSON property "apiBaseUrl" might not be present in the JSON file. If not, add it as the first JSON property. Similarly add properties for "gsrsHomeBaseUrl" and optionally "apiSSG4mBaseUrl". add In the default configuration where the gateway is on localhost port 8081, you would write:
```
"apiBaseUrl": "http://localhost:8081/",
"gsrsHomeBaseUrl": "http://localhost:8081/ginas/app/ui/",
# optional
"apiSSG4mBaseUrl": "http://localhost:8081/",
```
Within the gsrs3-main-deployment repository, modify the substances/src/main/resources/application.conf file, assign a port number to server.port, tell it where the gateway is, and ensure the ix.home setting for the indexing/cache folder is properly configured, and any database connection strings are set as expected. In a default configuration which uses H2 and has substances running on port 8080, the following conf settings should be as shown below. NOTE: The above configuration will use an in-memory transient database if no datasource is specified. Every restart of the application will result in the data being lost in such a case, but this may lead to confusing results as the cache and index found in the ix.home directory will remain between restarts. If you wish to use a persistent database, please configure the JDBC connections accordingly. If using the in memory database, you may want to delete your ginas.ix folder between restarts.
```
# Use port 8080 for the substances API
server.port= 8080

# This says to use a local folder called ginas.ix 
ix.home="./ginas.ix"                     

# Set the gateway address (for use with returning proper url patterns from the API) 
application.host="http://localhost:8081"
```

Within the gsrs3-main-deployment repository, modify gateway/src/main/resources/application.yml, assign a port number to server.port, tell it where the other 2 microservices are. The default settings should typically be configured for substances on 8080 and the frontend on 8082, but this is subject to change. The following snippet would configure things for just the substances (running on 8080) and frontend (running on 8082):

zuul:
  #this sets sensitiveHeaders to empty list so cookies and auth headers are passed through both ways
  sensitiveHeaders:
  routes:
    ui:
      path: /ginas/app/ui/**
      url: http://localhost:8082
      serviceId: frontend
      stripPrefix: false
    #fallback anything else goes to substances
    legacy:
      path: /**
      url: http://localhost:8080
      serviceId: substances
  ignored-patterns:
      - "/actuator/health"

ribbon:
  eureka:
    enabled: false

server.port: 8081

Once the configuration above is performed, it's now possible to launch the serviced. Below we will describe how to launch each of the 3 services in 3 different terminals. Keep all terminals open (or have them run in the background via nohup or screen).

Running the gateway service: In a new terminal or screen session, in the gsrs3-main-deployment directory launch gateway with these commands:
```
cd gateway
./mvnw clean -U spring-boot:run
```
Running the substances service: Before running the substances service, it would be good to take note of the fork value in the substances/pom.xml file. As of GSRS 3.1.1, the default fork value is true. However, you can pass -Dwith.fork=false or -Dwith.fork=true to make an explicit choice. On windows, false may work better on the substances services. You may need this to avoid a 'filename too long' error common with spring boot. However, if you choose to run the service and add the test records on the command line, set the fork value to true.

Again in a new terminal or screen session, in the gsrs3-main-deployment directory launch substances by:

# To run substances as-is with no data load (fork should be set to false. This may only be a concern on Windows):
cd substances
./mvnw clean -U spring-boot:run -Dwith.fork=false

# If you’re using a blank database, you may want to add the test set of 18 records by doing the following instead
# to preload a small sample for testing (fork should be set to true):
cd substances 
./mvnw clean -U spring-boot:run -Dwith.fork=true -Dspring-boot.run.jvmArguments="-Dix.ginas.load.file=src/main/resources/rep18.gsrs"

Another reason to use '-Dwith.fork=true' or the default is if you wish to set jvmArguments for a specific service. This is more likely to be an issue if you're using embedded Tomcat in production with a large data set, rather than locally. The Substances service uses quite a bit of memory, whereas the other services don't need so much; so you'd use the defaults for other services, but apply specific values for substances. The effect of enabling fork is that the specific service will run in its own JVM instance. The POM configuration, with arguments, would like something like this:

    <plugin>
        <groupId>org.springframework.boot</groupId>
        <artifactId>spring-boot-maven-plugin</artifactId>
        ...
        <configuration>
            <fork>${with.fork}</fork>
            <jvmArguments>-Xmx16000m -Xms12000m</jvmArguments>
        </configuration>
    </plugin>

Running the frontend service: Again in a new terminal or screen session, in the gsrs3-main-deployment directory launch frontend by:
```
cd frontend
./mvnw clean -U spring-boot:run -Dfrontend.tag=$FRONTEND_TAG -Dwithout.visualizer -DskipTests 
```
As of GSRS 3.1.1, the Angular build is no longer included in the gsrs3-main-deployment repository. Instead, it is built automatically and included in the .jar' file or .war` file when you run or package the Frontend service. There is a bit of learning curve to get comfortable with the new approach. See the Frontend README.md and related resources for more information.
To confirm it’s working, navigate to http://localhost:8081/ginas/app/ui (or the equivalent for your configuration – note that "8081" in this case is the port for the gateway which will route to the frontend on another port). Note: if you deploy this application for others to use, please make sure to perform this step. Otherwise, the first user to hit the application will see an error message. If you deploy GSRS via script, include a GET (via curl or similar utilty) within the script.
You should be able to login on the Frontend. In the local development version, the username and password are admin, admin respectively.

Optionally use Development Mode for the Frontend in the Local Embedded Deployment

You can run the frontend in development mode.

Do that only if you want to make changes to the Angular code and compile on the fly while testing.

You will have to make some small modifications to the a) the gateway application.yml file and b) your own angular frontend code repository. First, stop the gateway service if it is running. Then, make the change below in the gsrs3-main-deployment/gateway/java/main/resources/application.yml file:

 # Change FROM
routes:
   ui:
      path: /ginas/app/ui/**    
      url: http://localhost:8082   
      serviceId: frontend
      stripPrefix: false

 # Change TO 
routes:    
  ui:
     path: /ginas/app/ui/**     
        url: http://localhost:4200/
        serviceId: frontend 
        # use default
        # stripPrefix: false

Save application.yml.
In your gateway terminal sesssion set API_BASE_PATH=''.
Restart the gateway.

Next, go to your own Angular code repo (typically GSRSFrontend) outside of the gsrs3-main-deployment folder. Temporarily edit the file, src/index.html, changing from <base href="/"> to <base href="/ginas/app/ui/">. Make sure you temporarily have following in src\app\fda\config\config.json and/or src\app\core\config\config.json

"apiBaseUrl": "http://localhost:8081/",
"gsrsHomeBaseUrl": "http://localhost:8081/ginas/app/ui/",
# optional
"apiSSG4mBaseUrl": "http://localhost:8081/",

Finally, recompile the angular code, as usual with the npm command. See Compile Requirements in the frontend README.

Now, hitting in your browser, http://localhost:8081/ginas/app/ui/home will run your own development Angular code, rather than the compiled version in the gsrs3-main-deployment repository. Please make sure not to commit the above changes if making a pull request to this repository.

Making an Additional Microservice

While the substance service is the core focus of GSRS, additional microservices can be built to relate another domains’ data to substances. Additional microservices currently implemented include Drug/Biologic Applications, Drug/Biologic Products and Clinical Trials. Each microservice works via two main elements: 1) a domain specific spring boot starter module, and 2) an executing implementation in gsrs3-main-deployment. The starter module builds on the core GSRS starter and defines domain specific models, controllers, indexers, services, etc. Next, the executing implementation in gsrs3-main-deployment contains a configuration file, and the "java main" application runner class that launches the microservice. Each domain starter module currently works with two datasources. The domain specific datasource holds the domain's own entity data. The other "default" datasource may or may not be the same as the substance core datasource. The default datasource stores all data records GSRS routinely keeps for all GSRS entities, such as backups and incremental edits of the entity. Currently, the default datasource also contains session and user data required for authentication. NOTE At present time, in order for the same authentication to work through the gateway and UI for each service, each service must point to the same default ("spring") core data source. Alternative authentication schemes which would lift this requirement are possible, but beyond the scope of this document.

If the microservice to be added to gsrs3-main-deployment does not yet exist, the simplest path is to copy the substances folder to a new folder such as my-service. However, the following (and more) files will have to edited (E), renamed (R), deleted (D) and/or simplified (S) as appropriate:

pom.xml (E, S)
application.conf (E, S)
SubstancesApplication.java (R, S)
LoadGroupsAndUsersOnStartup.java (D)

If the microservice to be added already has an implementation in the gsrs3-main-deployment, then it’s likely that you just need to modify its application.conf file to meet your needs and then change the gateway’s application.yml file to include the associated paths. Either way, the application.conf file will have these important values, among others.

server.port = ####  
application.gateway = "http://localhost:8081"
ix.home= "ginas.ix/"

# Currently The GSRS FrontEnd requires that the export directory for your microservice be the same as that of substances in order
# for all exports to show in the user's download interface. This requirement will likely not be needed in future versions. 
ix.ginas.export.path=../substances/ginas.ix/gsrs_exports

# Default datasource #
spring.datasource.url="jdbc:h2:file:../substances/ginas.ix/h2/sprinxight;AUTO_SERVER=TRUE"
spring.datasource.driverClassName="org.h2.Driver"
spring.jpa.database-platform="org.hibernate.dialect.H2Dialect"
### !!!! CAREFUL !!!! ####
### Hibernate ddl auto (none, create, create-drop, validate, update) ###
spring.jpa.generate-ddl=false
spring.jpa.hibernate.ddl-auto=none
#spring.hibernate.show-sql=true

## Your microservice specific datasource ##
myservice.datasource.url="jdbc:h2:file:./ginas.ix/h2/myservicedb;AUTO_SERVER=TRUE"
myservice.datasource.driverClassName="org.h2.Driver"
myservice.datasource.username="sa"
myservice.datasource.password=""
myservice.jpa.database-platform="org.hibernate.dialect.H2Dialect"
### !!!! CAREFUL !!!! ####
### Hibernate ddl auto (none, create, create-drop, validate, update) ###
myservice.jpa.generate-ddl=false
myservice.jpa.hibernate.ddl-auto=none
#myservice.hibernate.show-sql=true

Note that your microservice datasource is configured in a spring starter module java configuration class. In this case, myservice in the datasource configuration corresponds to the PERSIST_UNIT value in your MyServiceDataSourceConfig class. That persist unit value should be all lower case. The spring value is the default PERSIST_UNIT. The default datasource is configured in the GSRS Spring Boot starter in the DefaultDataSourceConfig class.

To get your microservice running you also have to specify some paths in the gateway service application.yml. These paths tell the Gateway how to route traffic to your microservice's entity services. Let’s say your microservice has two entities, MyWidget and MyThingy; and your server.port defined above is 8999. Assuming an embedded tomcat context, your paths would look like this:

zuul:
  routes: 
    my_widgets:
      path: /api/v1/mywidgets/**
      url: http://localhost:8999/api/v1/mywidgets
      serviceId: my_widgets
    my_widgets_alt:
      path: /api/v1/mywidgets(**)/**
      url: http://localhost:8999/api/v1/mywidgets
      serviceId: my_widgets

    my_thingies:
      path: /api/v1/mythingies/**
      url: http://localhost:8999/api/v1/mythingies
      serviceId: my_thingies
    my_thingies_alt:
      path: /api/v1/mythingies(**)/**
      url: http://localhost:8999/api/v1/mythingies
      serviceId: my_thingies

While an entity class MyWidget is singular, the url uses the plural CONTEXT value as defined in something like MyWidgetEntityService.java. The _alt values are necessary to handle certain ODATA-like patterns not captured by the standard route.

Single Tomcat Deployment with WAR files for Core and Frontend

FDA currently uses the Single Tomcat WAR files deployment strategy in production for the GSRS core and additional microservices. The steps here have similarities to the local embedded testing deployment strategy as well as significant differences, so please review that section in this document before proceeding. FDA has also provided a detailed deployment guide in the docs folder which goes into some more specifics.

One difference is that Tomcat (running on port 8080) routes traffic to executed war file instances, all running on the same port. In contrast, in the embedded case, the gateway routes traffic to executable jar files, and each jar contains its own webserver and runs on its own port.

Another difference is data written to disk, such as indexes and caches, are kept in folders separate from the code. In addition, a copy of each microservice configuration is also kept separate from the code. All edits to the configuration are made separately from the code. You will copy those edited files and use them to overwrite the ones that were generated (at packaging time) inside the WAR files.

Note, the following was elaborated on Tomcat 9, and should be adjusted for Tomcat 10. In version 10, Tomcat automatically makes a transformation of WAR files when they are copied to the folder: webapps-javaee. At FDA, even on version 10, the WAR files are copied to the webapps folder instead, and the transformation is made there explicitly. More on that later.

1. Start by cloning the gsrs3-main-deployment and other optional repositories

This gsrs3-main-deployment repository contains the small wrappers needed to build the WAR files needed for this deployment strategy. There are configurations in the repository for reference as well, but those configurations are usually made with the local testing deployment strategy in mind.

Note that gsrs3-main-deployment also houses the raw compiled frontend artifacts which are needed to assemble the frontend.

Clone gsrs3-main-deployment repository.

git clone https://github.com/ncats/gsrs3-main-deployment

Optionally, you can clone and install these repositories if you need the very latest code. If you do not, maven will download the published repositories as opposed to those on github.

At this time, you may also need to clone and install the applications (starter branch) and drug products repositories (starter branch). That is because the substance starter module has some dependendencies on applications and products.

2. Prepare your environment for this tutorial

On your server, create some helpful environment variables for this tutorial and then create folders where configurations and runtime time data can be written. These folders should be separate from the code so they can be reused without getting erased.

Run the following in your Linux terminal. Use can use git bash on windows.

# These export statements should be run each time you open a new terminal. 
export gsrs_ci_repo_dir=/path/to/your/gsrs3-main-deployment/repository
export webapps=/path/to/tomcat/webapps 
export config_dir=/path/to/gsrs_configs/ 
export data_dir=/path/to/data 

# The following need to be done once.
sudo mkdir $data_dir
sudo mkdir $data_dir/gsrs_substances.ix
sudo mkdir $data_dir/gsrs_substances.ix/h2
sudo mkdir $data_dir/gsrs_substances.ix/sequence
sudo mkdir $data_dir/gsrs_substances.ix/structure

mkdir -p $config_dir

3. Prepare your Frontend configs

Create a file $config_dir/frontend_application.conf and add the following.

# Set the gateway address
application.host="http://localhost:8080"

Create a file $config_dir/frontend_config.json and add the following.

Copy the contents of $webapps/frontend/src/main/resources/static/assets/data/config.json to this file. Modify it to have the "apiBaseUrl" and other properties point to the correct endpoints. In this case that endpoint should be the full path you will use for the gateway, including a terminal slash ("/"). The JSON property "apiBaseUrl" may not be present in the JSON file, if it is not, add it as the first JSON property. In the Single Tomcat configuration where the gateway is on localhost port 8080. Follow the same logic for "gsrsHomeBaseUrl" and optionally "apiSSG4mBaseUrl".

"apiBaseUrl": "http://localhost:8080/",
"gsrsHomeBaseUrl": "http://localhost:8080/ginas/app/ui/",
# optional
"apiSSG4mBaseUrl": "http://localhost:8080/",

4. Prepare your Substances configs

Create a file $config_dir/substances_application.conf and include the following.

include "substances-core.conf"

ix.home="$data_dir/gsrs_substances.ix"

# Set the gateway address 
application.host="http://localhost:8080" 

spring.application.name="substances"

ix.h2 {
        base = ${ix.home}/h2
      }
      
# Set the default Datasource, example H2 configuration

spring.datasource.url="jdbc:h2:file:${ix.h2.base}/sprinxight;AUTO_SERVER=TRUE" 
spring.datasource.driverClassName="org.h2.Driver"
spring.jpa.database-platform="org.hibernate.dialect.H2Dialect" 
### !!!! CAREFUL  !!!! ####
### Hibernate ddl auto (none, create, create-drop, validate, update) ### 
# if your db is not created automatically while testing set to true temporarily
spring.jpa.generate-ddl=false  
# if your db is not created automatically while testing set to create temporarily
spring.jpa.hibernate.ddl-auto=none
spring.hibernate.show-sql=true

# NEED THIS for Applications-api and Products-api
gsrs.microservice.applications.api.baseURL="http://localhost:8080/"
gsrs.microservice.products.api.baseURL="http://localhost:8080/"

5. Prepare your Gateway configs

Create the file $config_dir/gateway_application.yml and add the following:

  spring:
    application:
      name: gateway

  debug: true

  zuul:
    # This sets sensitiveHeaders to empty list so cookies and auth headers are passed through both ways
    sensitiveHeaders:
    routes:
      ui:
        path: /ginas/app/ui/**
        url: http://localhost:8080/frontend/ginas/app/ui
        serviceId: frontend
      ginas_app:
        path: /ginas/app/**
        url: http://localhost:8080
        serviceId: ginas_app_route
      legacy:
        path: /**
        url: http://localhost:8080/substances
        serviceId: substances
    ignored-patterns:
        - "/actuator/health"

  ribbon:
    eureka:
      enabled: false

  # server.port: 8081
  # management.endpoints.web.exposure.include: *
  management.endpoints.web.exposure.include: 'routes,filters'

  eureka.client.enabled:  false

  zuul.host.socket-timeout-millis: 300000

6. Package your WAR files, then copy to Tomcat and rewrite configs

Next, do or run the following on command-line:

# Stop your tomcat, if not yet done

For the Frontend, run these commands in the command-line:  

cd $gsrs_ci_repo_dir/frontend

mvn package -DskipTests # to generate frontend.war

# Extract the war file into webapps folder

sudo unzip $gsrs_ci_repo_dir/frontend/target/frontend.war -d $webapps/frontend

sudo cp -rf ${config_dir}/frontend_config.json ${webapps}/frontend/WEB-INF/classes/static/assets/data/config.json

sudo chmod a+r  ${webapps}/frontend/WEB-INF/classes/static/assets/data/config.json

sudo chown tomcat:tomcat  ${webapps}/frontend/WEB-INF/classes/static/assets/data/config.json

sudo cp -rf ${config_dir}/frontend_application.conf ${webapps}/frontend/WEB-INF/classes/application.conf

sudo chmod a+r ${webapps}/frontend/WEB-INF/classes/application.conf

sudo chown tomcat:tomcat ${webapps}/frontend/WEB-INF/classes/application.conf

For Substances, run these commands on the command-line:

cd $gsrs_ci_repo_dir/substances

mvn package -DskipTests # to generate substances.war

sudo unzip $gsrs_ci_repo_dir/substances/target/substances.war -d $webapps/substances

sudo cp -rf ${config_dir}/substances_application.conf ${webapps}/substances/WEB-INF/classes/application.conf

sudo chmod a+r ${webapps}/substances/WEB-INF/classes/application.conf

sudo chown tomcat:tomcat ${webapps}/substances/WEB-INF/classes/application.conf

For the Gateway, run these commands on the command-line:

# Notice that the gateway is written to ROOT in the Tomcat webapps folder

cd $gsrs_ci_repo_dir/gateway

mvn package -DskipTests # to generate gateway.war

sudo unzip $gsrs_ci_repo_dir/gateway/target/gateway.war -d $webapps/ROOT

sudo cp -rf ${config_dir}/gateway_application.yml ${webapps}/ROOT/WEB-INF/classes/application.yml

sudo chmod a+r ${webapps}/ROOT/WEB-INF/classes/application.yml

sudo chown tomcat:tomcat ${webapps}/ROOT/WEB-INF/classes/application.yml

Now, you're ready to run the application in Tomcat. Do the following:

# Start your tomcat

# Check this log $webapps/../logs/catalina...log

# Try to hit these Urls
http://localhost:8080/api/v1/substances
http://localhost:8080/ginas/app/ui/

# Again, check this log $webapps/../logs/catalina...log

Turning on an Additional Entity Service in a Single Tomcat Instance

An additional microservice works with two main parts. First, a starter package that establishes microservice entities, repositories, controllers, indexers, etc. Next, there is an executing implementation in the gsrs3-main-deployment that imports the starter package and sets configuration properties. The gsrs3-main-deployment implementation for the microservice also has a main() method that runs the service.

An additional service like Clinical Trials already exists, for example. The entities present in the Clinical Trials starter package are ClinicalTrialUS and ClinicalTrialEurope. In the gsrs3-main-deployment, you'll see a folder gsrs3-main-deployment/clinical-trials. To make it work in the Single Tomcat instance scenario described above, take the following steps.

1. Prepare your environment for this additional microservice tutorial.

# These export statements should be run each time you open a new terminal. 

export gsrs_ci_repo_dir=/path/to/your/gsrs3-main-deployment/repository 	
export webapps=/path/to/tomcat/webapps 
export config_dir=/path/to/gsrs_configs/ 
export data_dir=/path/to/data

# The following need to be done once.
sudo mkdir -p $data_dir/gsrs_clinical-trials.ix/h2
sudo mkdir -p $data_dir/gsrs_substances.ix/h2

2. Prepare your Clinical Trials configs

Create a file $config_dir/clinical-trials_application.conf and include the following.

# This includes only the bare essentials. See gsrs3-main-deployment/clinical-trials

include "gsrs-core.conf"

ix.home="$data_dir/gsrs_clinical-trials.ix" 
ix.home_substances="$data_dir/gsrs_substances.ix" 

ix.ginas.export.path="$data_dir/gsrs_exports"

application.host= "http://localhost:8080"

# Leave commented out for Single Tomcat Instance
# server.port=8080

# H2 Database Connection
spring.datasource.url="jdbc:h2:file:${ix_home.substances}/h2/sprinxight;AUTO_SERVER=TRUE"
spring.datasource.driverClassName="org.h2.Driver"
spring.jpa.database-platform="org.hibernate.dialect.H2Dialect"
### !!!! CAREFUL  !!!! ####
spring.jpa.generate-ddl=false
# Hibernate ddl auto (none, create, create-drop, validate, update)
spring.jpa.hibernate.ddl-auto=none
spring.hibernate.show-sql=true

clinicaltrial.datasource.url="jdbc:h2:file:${ix.home}/h2/ctdb;AUTO_SERVER=TRUE"
clinicaltrial.datasource.driverClassName="org.h2.Driver"
clinicaltrial.datasource.username="sa"
clinicaltrial.datasource.password=""
clinicaltrial.jpa.database-platform="org.hibernate.dialect.H2Dialect"
### !!!! CAREFUL  !!!! ####
# clinicaltrial.jpa.generate-ddl=false
# For testing
# Hibernate ddl auto (none, create, create-drop, validate, update)
clinicaltrial.jpa.hibernate.ddl-auto=update
clinicaltrial.hibernate.show-sql=true
# For commit
# clinicaltrial.jpa.hibernate.ddl-auto=none
# clinicaltrial.hibernate.show-sql=true

3. Modify your Gateway configs

In $configs_dir/gateway_application.yml, add the following:

# Notice that In the Single Tomcat scenario, urls contain the gsrs3-main-deployment folder name of the microservice (e.g. clinical-trial) 

zuul:
  routes:
    # Put below already present routes
    clinical_trials_us:
      path: /api/v1/clinicaltrialsus/**
      url: http://localhost:8080/clinical-trials/api/v1/clinicaltrialsus
      serviceId: clinical_trials_us
    clinical_trials_us_alt:
      path: /api/v1/clinicaltrialsus(**)/**
      url: http://localhost:8080/clinical-trials/api/v1/clinicaltrialsus
      serviceId: clinical_trials_us
    clinical_trials_europe:
      path: /api/v1/clinicaltrialseurope/**
      url: http://localhost:8080/clinical-trials/api/v1/clinicaltrialseurope
      serviceId: clinical_trials_europe
    clinical_trials_europe_alt:
      path: /api/v1/clinicaltrialseurope(**)/**
      url: http://localhost:8080/clinical-trials/api/v1/clinicaltrialseurope
      serviceId: clinical_trials_europe

4. Package your WAR files, then copy to Tomcat and rewrite configs

Do or run the following on command-line:

# Stop your tomcat, if not yet done

For Clinical Trials, run these commands on the command-line:

cd $gsrs_ci_repo_dir/clinical-trials 

mvn package -DskipTests # to generate clinical-trials.war 

sudo unzip $gsrs_ci_repo_dir/clinical-trials/target/clinical-trials.war -d $webapps/clinical-trials 

sudo cp -rf ${config_dir}/clinical-trials_application.conf ${webapps}/clinical-trials/WEB-INF/classes/application.conf 

sudo chmod a+r ${webapps}/clinical-trials/WEB-INF/classes/application.conf 

sudo chown tomcat:tomcat ${webapps}/clinical-trials/WEB-INF/classes/application.conf

5. For the Gateway, update application.yml

sudo cp -rf ${config_dir}/gateway_application.yml ${webapps}/ROOT/WEB-INF/classes/application.yml 

sudo chmod a+r ${webapps}/ROOT/WEB-INF/classes/application.yml 

sudo chown tomcat:tomcat ${webapps}/ROOT/WEB-INF/classes/application.yml

Now, you're ready to run the application in tomcat. Do the following:

# Start your tomcat 

# Check this log $webapps/../logs/catalina...log 

# Try to hit these Urls 

http://localhost:8080/api/v1/clinical-trials 

http://localhost:8080/ginas/app/ui/browse-clinical-trials 

# Again, check this log $webapps/../logs/catalina...log

Adding a New Frontend Submodule for a New microservice

When developers add a new microservice to the GSRS, they may also want to create a frontend module to interact with the backend service. The frontend code is all separate from the backend and currently in a single Angular project. Typically, each entity service has its own folder where Angular code and templates are stored. To date, all non-core folders are located in the folder: src/app/fda

Critical files affecting non-substance modules are:

src/app/fda/config/config.json
src/app/fda/fda.module.ts

Projects can be selectively defined as loaded components. This makes it easy to display content in templates only when the entity component is configured to be on. For example:

<div *ngIf = "loadedComponents.clinicaltrialsus">
  your content
</div>

In this example, "clinicaltrialsus" is the name of the loaded component. The following shows several files that you will likely have to modify if you add a frontend for a new entity service.

# src/app/fda/config.json 
# Add:
"loadedComponents": {
  ...
  "clinicaltrialsus": true
  },
"navItems": [
  ...
  {
    "component": "clinicaltrialsus",
    "display": "Browse Clinical Trials",
    "path": "browse-clinical-trials-us",
    "order": 999
  }
 ]

# src/app/core/config/config.model.ts
# Add: 
export interface LoadedComponents {
  ...
  clinicaltrialsus?: boolean;
}

# src/app/fda/fda.module.ts
# Add Module and Service declarations, varying approaches used.

# src/app/core/facets-manager/facets-manager.component.ts
# Modify this method to add your entity group to the `if` statement so that facets will be collected. 
set configName(configName: string) {
     ... 
     if (configName === '...' || configName === 'clinicaltrialsus' ...

# src/app/core/base/base.component.html
# Add: 
  <span *ngIf = "loadedComponents.clinicaltrialsus">
  <a mat-menu-item routerLink="/browse-clinical-trials-us">
    Browse US Clinical Trials
  </a>
  <mat-divider></mat-divider>
  </span>

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GSRS 3 Main Deployment

Important Notes:

Get Started

Your Deployment Type Depends on Your Goal

Maven Central vs. Git

Cloning/repositories from from Git

Local Embedded Tomcat Instance Deployment

Optionally use Development Mode for the Frontend in the Local Embedded Deployment

Making an Additional Microservice

Single Tomcat Deployment with WAR files for Core and Frontend

Turning on an Additional Entity Service in a Single Tomcat Instance

Adding a New Frontend Submodule for a New microservice

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Name		Name	Last commit message	Last commit date
Latest commit History 54 Commits
.github/workflows		.github/workflows
adverse-events		adverse-events
applications		applications
clinical-trials		clinical-trials
deployment-extras		deployment-extras
docs		docs
frontend		frontend
gateway		gateway
impurities		impurities
invitro-pharmacology		invitro-pharmacology
products		products
ssg4m		ssg4m
substances		substances
README.md		README.md

ncats/gsrs3-main-deployment

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GSRS 3 Main Deployment

Important Notes:

Get Started

Your Deployment Type Depends on Your Goal

Maven Central vs. Git

Cloning/repositories from from Git

Local Embedded Tomcat Instance Deployment

Optionally use Development Mode for the Frontend in the Local Embedded Deployment

Making an Additional Microservice

Single Tomcat Deployment with WAR files for Core and Frontend

Turning on an Additional Entity Service in a Single Tomcat Instance

Adding a New Frontend Submodule for a New microservice

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