orion-data

Description: Repo for the KPMP upload tool back-end

Documentation

Visit kpmp.github.io/dlu

Removing packages

1. Connect to Mongo by opening ssh session to prod-upload

• ssh <username>@172.20.66.165 -L 27017:localhost:27017

2. Within mongo, delete package from package and file collection
3. Delete package off of the DLU
4. sudo rm /nfs/corenfs/kpmp-data/prod/dataLake/package_<package_id>
5. Navigate to clearCache URL to clear the old cache

• https://upload.kpmp.org/api/v1/clearCache

6. Navigate to upload and confirm packages no longer exist

Globus application registration

This application is registered in Globus here -- https://app.globus.org/ -- in the "KPMP Data Lake" project as "KPMP Data Lake Uploader". You need to grant the application's userID write access to the Guest Collection being used as the Data Lake INBOX.

Creating new credentials files for Globus

NOTE: You may have to do this when you deploy a newly-build image.

1. Go into the container and delete (if necessary) the StoredCredential file in the globus_tokens directory.
2. Bring the application down and then back up.
3. Spring will generate a URL and print it to stdout (follow the Docker logs), grab it and open it in a browser.
4. Authenticate.
5. The redirect to localhost will fail and produce a broken URL (since you're not running the app locally). Copy this URL.
6. Go into the orion-spring container and do a wget on the pasted URL. This will create the credentials file and the app will start running. NOTE: if "localhost" doesn't work for this URL, try "127.0.0.1".

Using REDCap Endpoint

1. Get your token: https://upload.kpmp.org/api/v1/token
2. POST REDCap data (in JSON format) to https://upload.kpmp.org:3030/v1/redcap?token=[token string]
3. Check for success response

Build

./gradlew build docker The default tag is the github branch name if no verison is provided To pass a version when building the docker image execute ./gradlew build docker -Ptag=<tagNumber>