ccda-to-omop 0.0.20

A package for converting HL7 CCDA documents to OHDSI OMOP

pypi: ccda_to_omop

foundry: CCDA_OMOP_Conversion_Package

This code is for converting HL7 CCDA documents to OHDSI OMOP. This is a python package with associated files to support publishing it in Palantir Foundry as well as PyPi. Currently a work in progess, adding PyPi.

PyPi Notes

• rm dist/*
• update the version number in the toml file
• build python3 -m build creates the packages and deposits them in the dist folder
• upload __python3 -m twine upload dist/*
  • for test: python3 -m twine upload --repository tstpypy dist/*
• specific files: __python3 -m twine upload dist/ccda_to_omop-0.0.11-py3-none-any.whl dist/ccda_to_omop-0.0.11.tar.gz
• check on pypi.org https://pypi.org/project/YOURPACKAGENAME

Sub Projects/Directories

This repositor has siblings that might be of interest.

• CCDA-tools is a collection of different file snoopers, scripts that find and show a XML elements with a certain tag, like id, code or section. https://github.com/chrisroederucdenver/CCDA-tools
• CCDA-data sample data is in it's own repo. The directory has been flattened compared to earlier work. https://github.com/chrisroederucdenver/CCDA-data
• CCDA_Private is a private repository for keeping and sharing the vocabularies used here. After dealing with licenses this data, the OMOP concepts can be dowloaded from athena.ohdsi.org. https://github.com/chrisroederucdenver/CCDA_OMOP_Private

Code here, prototype_2/value_transformations.py loads the concept map from a file map_to_standard.csv from the local top leve. It is not included in this repo however. It is in CCDA-tools. Running locally, for the moment, requires the file to be copied over (or linked). (now owned by cladteam)

Publishing Conda libraries (Foundry)

This repository template is set up to publish a Conda library into Foundry. The build.gradle file configures the publish task to only run when the repository is tagged. You can create a new tag from the "Branches" tab.

By default, the repository's name at creation time is used as the name for the Conda package. It is possible to change the name of the package by updating the condaPackageName variable in the gradle.properties file. Note that since this is a hidden file, you will need to enable "Show hidden files and folders".

#Important: underscores in the repository name are rewritten to dash. For example, if your repository is named my_library, then the library will be published as my-library.

Consuming Conda Libraries

Consumers will require read access on this repository to be able to consume the libraries it publishes. They can search for them in the Libraries section on the left-hand side in the consuming code repository. This will automatically add the dependency to meta.yaml and configure the appropriate Artifacts backing repositories.

Adding a library to your project will install packages from the source directory. The source directory defaults to src/ and we recommend not changing this. You still need to import packages before you can use them in your module. Be aware that you have to import package name and not library name (in this template, the package name is myproject).

Example

Let's say your library structure is:

conda_recipe/
src/
  examplepkg/
    __init__.py
    mymodule.py
  otherpkg/
    __init__.py
    utils.py
  setup.cfg
  setup.py

And in gradle.properties, the value of condaPackageName is mylibrary.

When consuming this library, the consuming repository's conda_recipe/meta.yaml file will contain:

requirements:
  run:
    - mylibrary

Then the packages, which in this example are examplepkg and otherpkg, can be imported as follows:

import examplepkg as E
from examplepkg import mymodule
from otherpkg.utils import some_function_in_utils

Note that the import will fail if the package does not include a file named __init__.py

Testing

Unit tests can be evaluated automatically as part of CI checks. You can enable this by uncommenting the following line in build.gradle:

// Apply the testing plugin
apply plugin: 'com.palantir.transforms.lang.pytest-defaults'

You can find an example unit test inside the src/test directory. Please refer to the documentation for more information.

CCDA_OMOP_by_Python

This is a project to convert CCDA documents to OMOP CDM format in Python. The bulk of the work is in the prototype_2 directory. Further instruction is in a README.md file there.

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