Import into cBioPortal database from Kubernetes

[inodb]

One way to do it semi-manually now is:

1. First download a study from datahub on your local machine following https://github.com/cbioportal/datahub#how-to-download-data

2. Update a local portal.properties to have the correct import credentials

3. Start a cbioportal-importer container:

kubectl run --rm -i --tty cbioportal-importer --image=cbioportal/cbioportal:release-3.3.0 --restart=Never -- sh

You can exit it for now after starting

4. Copy the properties & study into the container

kubectl cp portal.properties cbioportal-importer:/cbioportal/
kubectl cp ucec_tcga_pub cbioportal-importer:/cbioportal/ucec_tcga_pub

5. Attach to the cbioportal-importer pod again and import (this tries to import into beta database):

kubectl attach -it cbioportal-importer
# once inside
metaImport.py -s /cbioportal/ucec_tcga_pub -o -u https://beta.cbioportal.org

Now you can detach again with Ctrl + P followed by Ctrl + Q

6. Check logs with kubectl logs -f cbioportal-importer

7. Delete the pod again with kubectl delete pod cbioportal-importer

We should find some way to this in a more automated fashion. Some options:

• Spin up a pod with multiple containers. First container downloads the datahub study of interest set with some env variable. Second container is the cBioPortal importer that actually imports it

• Have an "always on" import container. Whenever we copy files into a particular folder it starts importing