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Description:

pfbfhir 0.0.8

Table of Contents

About The Project

Built With

Getting Started

Prerequisites
Installation

Usage
Roadmap
Contributing
License
Contact
Acknowledgments

pfb_fhir
About The Project
Render a PFB graph from FHIR data
Built With

pydantic
fastavro
pypfb[gen3]
flatten_json
fhirclientr4
synthea

Special thanks

Kyle Ellrott (OHSU)
NHGRI Genomic Data Science Analysis, Visualization and Informatics Lab-space AnVIL
NCPI FHIR Working Group, Robert Carroll (VUMC), Allison Heath (CHOP)
Center for Translational Data Science (UChicago) gen3
ncpi-fhir-pfb-prototype Brian O'Connor (Broad), Ann Van (Nimbus Informatics)
GA4GH cohort-rep-hackathon synthea

Getting Started
Installation:
# clone
git clone https://github.com/bmeg/pfb_fhir
cd pfb_fhir

To get a local copy up and running follow these simple example steps.
# use virtual env
python3 -m venv venv
source venv/bin/activate

# install dependencies
pip install -r requirements.txt

# install this package
pip install -e .

Usage
See help for a list of commands, examine configuration examples in fixtures:
$ pfb_fhir --help
Usage: pfb_fhir [OPTIONS] COMMAND [ARGS]...

Render FHIR Data in PFB.

Options:
-l, --log-level [NOTSET|DEBUG|INFO|WARNING|ERROR|CRITICAL]
--output_path TEXT Output path for working files and output.
Read from PFB_FHIR_OUTPUT_PATH [default:
./DATA]

--config_path TEXT Path to config file. Read from
PFB_FHIR_CONFIG_PATH [default:
./config.yaml]

--help Show this message and exit.

Commands:
version Print the version.
transform Transform FHIR resources from directory.
inspect Inspect a PFB.
visualize Create a simple visualization.
config Print the config.
demo Download Test data and create example PFB and figure.

Environmental variables and their defaults

PFB_FHIR_CONFIG_PATH ./config.yaml
PFB_FHIR_OUTPUT_PATH DATA/
PFB_FHIR_CACHE_PATH cache/

Demos
Several demonstration datasets are available:

anvil Read 1000G data from AnVIL.
dbgap Read open access data from dbGAP's FHIR service.
kf Read synthetic clinical data created by kids first.
ncpi Read examples from ncpi ImplementationGuide.
synthea Read synthetic clinical data created by synthea.
genomic-reporting Read oncology example from ImplementationGuide.

For example:
# run the demo
pfb_fhir demo dbgap

# view the image
open DEMO/dbgap/output/dbgap.pfb.avro.png

# inspect the pfb
pfb_fhir inspect --pfb_path DEMO/dbgap/output/dbgap.pfb.avro

# use gen3's pfb utility
cat DEMO/dbgap/output/dbgap.pfb.avro | pfb show stats

# or native avro tools
java -jar avro-tools-1.11.0.jar getschema DEMO/dbgap/output/dbgap.pfb.avro | \
jq '.fields[] | select(.name == "object") | .type[] | .name '

Using the PFB
Terra
# run the demo
pfb_fhir demo synthea

# upload that PFB to google storage
gsutil cp DEMO/synthea/output/synthea.pfb.avro $GOOGLE_BUCKET

# Sign the url so terra can read it.
gsutil signurl -u $GOOGLE_BUCKET/synthea.pfb.avro

# Or, grant access
# gsutil acl ch -u AllUsers:R $GOOGLE_BUCKET/synthea.pfb.avro

# url encode the signed url

open 'https://app.terra.bio/#import-data?format=PFB&url=https:....'

Gen3
The easiest way to see the resulting schema in gen3 is to use the Data Dictionary Development workflow
Use the intermediate file located at <PFB_FHIR_OUTPUT_PATH>//output/dump-ordered.json e.g. DEMO/ncpi/output/dump-ordered.json

Contributing
Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.
If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement".
Don't forget to give the project a star! Thanks again!

Fork the Project
Create your Feature Branch (git checkout -b feature/AmazingFeature)
Commit your Changes (git commit -m 'Add some AmazingFeature')
Push to the Branch (git push origin feature/AmazingFeature)
Open a Pull Request

Distribution
# update pypi

export TWINE_USERNAME= # the username to use for authentication to the repository.
export TWINE_PASSWORD= # the password to use for authentication to the repository.

rm -r dist/
python3 setup.py sdist bdist_wheel
twine upload dist/*

License
Distributed under the Apache License. See LICENSE for more information.
Contact
Brian Walsh - @bpwalsh - walsbr AT ohsu DOT edu
Acknowledgments

NIH-NCPI
AnVIL
ncpi-fhir-pfb-prototype
gen3

Roadmap

✅ config.yaml driven map of FHIR resource to PFB node,
✅ Parse FHIR resources, retrieve and cache FHIR profile (schema) elements,
✅ Recursively match with FHIR profiles (schemas)
✅ Flatten for export
✅ write to PFB
✅ test cases for protected/ resources - ResearchSubject, Patient, Specimen, Task, DocumentReference
✅ networkx based visualization
✅ pfb cli
✅ demo with public data
✅ update README with Terra import examples
✅ update README with gen3 import examples
✅ update to new release of pypfb 0.5.18
✅ include kids first
✅ simplify
✅ add genomic reporting examples
✅ pypi

Distribution
Test with docker
docker build -t pfb_fhir .

# typical run command
docker run -v $(pwd)/cache:/app/pfb_fhir/cache -v $(pwd)/DEMO:/app/pfb_fhir/DEMO pfb_fhir demo ncpi

Update pypi
export TWINE_USERNAME= # the username to use for authentication to the repository.
export TWINE_PASSWORD= # the password to use for authentication to the repository.

rm -r dist/
python3 setup.py sdist bdist_wheel
twine upload dist/*

Known Issues

simplify - could do a better job of making resulting nodes more "data frame friendly"
config.yaml - currently there is no way of expressing a reference found in a FHIR extension.