Research Hub

Overview

The Research Hub is an extendable application for loading entities and providing a UI for searching and viewing the data for them. It uses DataHub and Entity Services for ingesting and harmonizing, and Grove React for the front end.

Getting Started

There are two main steps to use this application:

1. Install Research Hub
2. Install the domain you want to use (found in the examples directory or create your own)

1. Install Research Hub

Prerequites

1. MarkLogic 9.0-11 or 10.0-3
2. Java 8+ (used for running QuickStart and gradle-wrapper)
3. Node 10 or 12
4. Optionally Docker Desktop if you want/need to run MarkLogic inside a container

1.1 Prepare local environment

It is recommended to use the default ports, DB names, and App Server names defined in the gradle.properties file. Use our pre-configured Docker setup if you have conflicts with your local MarkLogic instance.

1.2 Deploy DHF

First, generate Data Hub source files:

`./gradlew hubInit`

Second, deploy the database components (including Data Hub) to MarkLogic:

`./gradlew mlDeploy`

1.3 Install UI

`cd ui`
`npm install`

2. Install One of the Included Examples

Two examples are included in this code base. By copying these example files into the main code area, and modifying some core files, you will be installing a fully-functional Research Hub. These are included to provide sample code and patterns for building your own research hubs.

A gradle "install" task is included in each example sub-directory to automate much of this process. The manual steps are documented in the README.md in each example sub-directory.

These two example domains are pharma-research and person-position. They include different datasets, models, flows, and UI components.

To install one of the example domains, follow the README.md file in that example sub-directory, which are included in this codebase.

Building your own entity

You can create your own entity by running a gradle command to scaffold the files you need.

run ./gradlew createEntity -PentityName=YourEntityName

The task will create the necessary files and print out their locations for you to go edit.

Deleting a scaffolded entity

If for some reason you need to delete an entity that you scaffolded, simply run this command. run

./gradlew deleteEntity -PentityName=YourEntityName

Building your own concept

You can create your own concept by running a gradle command to scaffold the files you need.

run ./gradlew createConcept -PconceptName=YourConceptName

The task will create the necessary files and print out their locations for you to go edit.

Deleting a scaffolded concept

If for some reason you need to delete a concept that you scaffolded, simply run this command. run

./gradlew deleteConcept -PconceptName=YourConceptName

The task will create the necessary files and print out their locations for you to go edit.

Running the UI

After installing Research Hub and a domain, you can start the ui using:

`cd ui`
`npm start`

If the start fails, it may be necessary to install the nodemon (Node Monitor), cross-env, and concurrently packages with npm install nodemon, npm install cross-env, and npm install concurrently respectively from the ui directory. Typically, these are installed with -g option which makes the packages globally available across all projects.

Running Tests

After installing Research Hub and a domain, you can run any tests that were created by going to http://localhost:8015/test/ (or http://localhost:8115/test/ if using our Docker setup), and using the UI there to run tests.