PRISM Sample Data

Instructions on loading data into PRISM

Prereq

First you need to download the actual sample data and extract it into this directory.

wget https://github.com/UAMS-DBMI/PRISM_sample_data/releases/download/1.0/sample_data.tar.gz
tar xf sample_data.tar.gz

PathDB

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The pathology slides are in the images directory and need to be copied into the PVC that is shared between most of the PathDB containers.

POD=$(kubectl get pod -l prism=imageloader -o jsonpath="{.items[0].metadata.name}")
kubectl cp ./images/ $POD:/data/

After the images are in place the imageloader container is used to load the images into PathDB proper.

kubectl exec deployment/imageloader -- imageloader -src /data/images/example.csv -username admin -password bluecheese2018 -collectionname Public

Testing

You can now log into PathDB (default user: admin, password: bluecheese2018) and check to see if the images have appeared properly in the Public collection.

NBIA

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The radiology files are in the extracted radiology directory. These can either be loaded through Posda which is out of scope for this document, or directly with a small script.

First the files need to be copied into the NBIA containers dicom storage PVC.

POD=$(kubectl get pod -l prism=nbia -o jsonpath="{.items[0].metadata.name}")
kubectl cp ./radiology/ $POD:/opt/dicoms/

Then the included insert_dicom.py script can be used to load them into the NBIA database. To use the included script, the NBIA service needs to be directly accessable over 8080, so you may need to take down any other port forwards. Then run the following two commads in different terminals.

kubectl port-forward svc/nbia 8080:8080
python3 insert_dicom.py

This will walk the radiology directory and POST a request for each file to the nbia-api, which will parse the already copied dicom files into the NBIA database.

Testing

Before taking down the port-forwards, head to http://localhost:8080/nbia-search and log in as the nbiaAdmin user (default password admin).

• Click Data Admin->Perform Quality Control
• Select the Public collection from the filter on the left.
• Select all series on the right.
• Change the status to Visible and the Release to Yes.

Now when you return the nbia-search page, you should be able to select the Public collection from the left and see results.

Semantic RDF

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To populate the cohort builder with the sample data for these radiology/pathology subjects, the included rdf/statements.ttl needs to be loaded into the triplestore. Port forward directly into the triplestore.

kubectl port-forward svc/triplestore 7200:7200

Points your browser at http://localhost:7200 and ensure you have selected the PRISM repository from the top right, then click the "Import RDF Data". Then click "Upload RDF Files" and select the rdf/statements.ttl file to upload. After uploading click the orange "Import" button on the right, and accept all of the default options.

Testing

Take down the various port-forwards and go to the cohort builder from the main PRISM landing page. It should now not only load but when clicking "show collections" have a collection with iformation displayed.