charcot

Putting brain images at the fingertips of scientists and researchers. Charcot allows interested parties to request Zips of brain image data by interactively building cohorts via a user-friendly graphical interface.

charcot
- Overview
- Install
  - Requirements
  - Steps
- Usage
- Architecture
- Developers

Install

The below steps assume MacOS or Unix-like systems only.

Requirements

nvm

curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.0/install.sh | bash

node 18, using nvm command that you installed above,
```
nvm install node@16
```
git
The aws cli. The steps on how to do this are beyond the scope of this document, but on mac you can do brew install aws
Admin level key id/key screte pair for both Mt Sinai ODP and paid accounts. The AWS in profiles respectively have to be named mssm and mssm-odp in your ~/.aws/credentials file. You can use aws configure from the command line to configure access to your AWS accounts.
zx
Java OpenJDK 17 or above
1. Install SDKMAN! as per here
2. Run command sdk use java 17.0.4-tem to activate Java 17 in your system (any Java version >= 17 will do)
Maven
Docker

Steps

In the steps below, replace <env> with the stage name. When running locally the default stage name will be your username, so use that as the value of <env>.

Git clone repo at https://github.com/NBTR-MSSM/charcot, git clone git@github.com:NBTR-MSSM/charcot.git
Install dependencies by running this command in the parent folder of the code cloned above, npm install
Build the fulfillment module Java code,
```
cd fulfillment/
mvn -U clean install
```
Deploy the app to the cloud, AWS_PROFILE=<your AWS profile> npx sst deploy:<env>
Populate image metadata in AWS: script/post-metadata.mjs -s <env>

Usage

Once deployment completes, open https://.mountsinaicarcot.org/.

Architecture

Refer to this document.

Developers

Take a look at the contributing and developer guides if you plan to develop for charcot.

NBTR-MSSM/charcot