FHIR Shorthand ValidatorDocumentation

Release 0.2.2

Gregor Lichtner

Dec 10, 2021

CONTENTS:

1 FHIR Shorthand Validator 11.1 Quickstart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11.2 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21.3 Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21.4 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31.5 Credits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

2 Installation 52.1 Stable release . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52.2 From sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

3 fsh_validator 73.1 fsh_validator package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

4 Contributing 94.1 Types of Contributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94.2 Get Started! . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104.3 Pull Request Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114.4 Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114.5 Deploying . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

5 Credits 135.1 Development Lead . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135.2 Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

6 History 156.1 0.2.2 (2021-11-10) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156.2 0.2.1 (2021-11-11) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156.3 0.2.0 (2021-11-11) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156.4 0.1.9 (2021-11-09) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156.5 0.1.8 (2021-11-08) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156.6 0.1.7 (2021-11-05) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166.7 0.1.6 (2021-11-05) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166.8 0.1.5 (2021-11-03) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166.9 0.1.4 (2021-11-02) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166.10 0.1.3 (2021-10-25) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166.11 0.1.2 (2021-10-25) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166.12 0.1.1 (2021-10-25) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166.13 0.1.0 (2021-10-25) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

7 Indices and tables 17

i

Python Module Index 19

Index 21

ii

CHAPTER

ONE

FHIR SHORTHAND VALIDATOR

FHIR Shorthand Validator (fsh-validator) unshortens fsh input and validates all defined instances against their profiles.

fsh-validator is an interface to SUSHI and the HL7 FHIR Validator running the following workflow:

1. Run SUSHI to unshorten fsh files to structure definitions, instances, value sets etc.

2. Detect all defined profiles, valuesets and instances.

3. Validate all defined instances using the official HL7 FHIR Validator against their profiles.

For the full documentation see https://fsh-validator.readthedocs.io.

1.1 Quickstart

Install the latest fsh-validator:

pip install -U fsh-validator

Or directly from github repository:

pip install -U git+https://github.com/glichtner/fsh-validator

Run fsh-validator in your fsh project path:

$ fsh-validator --all

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1.2 Parameters

usage: fsh-validator [-h] [--all] [--subdir SUBDIR] [--validator-path PATH_VALIDATOR] [--→˓verbose] [--no-sushi] [--log-path LOG_PATH] [filename [filename ...]]

positional arguments:filename fsh file names (basename only - no path)

optional arguments:-h, --help show this help message and exit--all if set, all detected profiles will be validated--subdir SUBDIR Specifies the subdirectory (relative to input/fsh/) in which to␣

→˓search for profiles if --all is set--validator-path PATH_VALIDATOR

path to validator--verbose Be verbose--no-sushi Do not run sushi before validating--log-path LOG_PATH log file path - if supplied, log files will be written

1.3 Configuration

fsh-validator reads an optional configuration file .fsh-validator.yml in the base directory of the sushi project. Theconfiguration file currently supports the following parameters:

exclude_code_systems: A list of code systems to exclude from validation. If an instance contains a codefrom a code system in this list, the instance will be skipped. This is useful to exclude code systemsthat are not yet supported by the validator or that may cause problems when validating (e.g. ICD-10-gm) The code systems are specified by their canonical URI. The default is to not exclude any codesystems.

exclude_resource_types: A list of resource types to exclude from validation. If an instance implements aresource of a type in this list, the instance will be skipped. This is useful to exclude resources that arenot yet supported by the validator or that may cause problems when validating. The resource typesare specified by their canonical name (e.g. “Bundle”). The default is to not exclude any resourcetypes.

Example configuration file:

exclude_code_systems:- http://hl7.org/fhir/sid/icd-10-cm- http://fhir.de/CodeSystem/bfarm/icd-10-gm

exclude_resource_types:- Bundle- OperationOutcome

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1.4 Examples

Example call to validate a *single* profile

$ cd ExampleIG/$ fsh-validator input/fsh/p-thoracic-drainage.fsh

Example call to validate *all* profiles

The following call validates all profiles in the subdirectory “vaccination/” and writes the results of the validation logfiles in the directory logs/.

$ cd ExampleIG/$ fsh-validator --all --subdir vaccination/ --log-path logs/

This is equivalent to calling:

$ fsh-validator input/fsh/vaccination/*.fsh --log-path logs/

1.5 Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

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TWO

INSTALLATION

2.1 Stable release

To install FHIR Shorthand Validator, run this command in your terminal:

$ pip install fsh-validator

This is the preferred method to install FHIR Shorthand Validator, as it will always install the most recent stable release.

If you don’t have pip installed, this Python installation guide can guide you through the process.

2.2 From sources

The sources for FHIR Shorthand Validator can be downloaded from the Github repo.

You can either clone the public repository:

$ git clone git://github.com/glichtner/fsh-validator

Or download the tarball:

$ curl -OJL https://github.com/glichtner/fsh-validator/tarball/master

Once you have a copy of the source, you can install it with:

$ python setup.py install

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CHAPTER

THREE

FSH_VALIDATOR

3.1 fsh_validator package

3.1.1 Submodules

3.1.2 fsh_validator.cli module

3.1.3 fsh_validator.fsh_validator module

3.1.4 fsh_validator.fshpath module

FSH file paths representations.

class fsh_validator.fshpath.FshPath(filename)Bases: object

FSH file paths representations.

absolute()Resolve relative to absolute path.

Return type Path

Returns Absolute filename

exists()Return whether the file represented by this class exists.

Return type bool

Returns True if file exists, False otherwise

fsh_base_path()Get the FSH base path (without input/fsh/).

Return type Path

Returns FSH base path (without input/fsh/)

fsh_name()Get the FSH filename (relative to input/fsh/).

Return type Optional[Path]

Returns FSH filename (relative to input/fsh/)

fsh_parts()Process a filename into the fsh base path (without input/fsh/) and the fsh filename relative to input/fsh/.

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Return type Tuple[Path, Optional[Path]]

Returns Tuple of base path (without input/fsh/) and filename (relative to input/fsh/ folder)

3.1.5 Module contents

Top-level package for FHIR Shorthand Validator.

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CHAPTER

FOUR

CONTRIBUTING

Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.

You can contribute in many ways:

4.1 Types of Contributions

4.1.1 Report Bugs

Report bugs at https://github.com/glichtner/fsh-validator/issues.

If you are reporting a bug, please include:

• Your operating system name and version.

• Any details about your local setup that might be helpful in troubleshooting.

• Detailed steps to reproduce the bug.

4.1.2 Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants toimplement it.

4.1.3 Implement Features

Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open towhoever wants to implement it.

4.1.4 Write Documentation

FHIR Shorthand Validator could always use more documentation, whether as part of the official FHIR ShorthandValidator docs, in docstrings, or even on the web in blog posts, articles, and such.

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4.1.5 Submit Feedback

The best way to send feedback is to file an issue at https://github.com/glichtner/fsh-validator/issues.

If you are proposing a feature:

• Explain in detail how it would work.

• Keep the scope as narrow as possible, to make it easier to implement.

• Remember that this is a volunteer-driven project, and that contributions are welcome :)

4.2 Get Started!

Ready to contribute? Here’s how to set up fsh-validator for local development.

1. Fork the fsh-validator repo on GitHub.

2. Clone your fork locally:

$ git clone git@github.com:your_name_here/fsh-validator.git

3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set upyour fork for local development:

$ mkvirtualenv fsh-validator$ cd fsh-validator/$ python setup.py develop

4. Create a branch for local development:

$ git checkout -b name-of-your-bugfix-or-feature

Now you can make your changes locally.

5. When you’re done making changes, check that your changes pass flake8 and the tests, including testing otherPython versions with tox:

$ flake8 fsh-validator tests$ python setup.py test or pytest$ tox

To get flake8 and tox, just pip install them into your virtualenv.

6. Commit your changes and push your branch to GitHub:

$ git add .$ git commit -m "Your detailed description of your changes."$ git push origin name-of-your-bugfix-or-feature

7. Submit a pull request through the GitHub website.

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4.3 Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

1. The pull request should include tests.

2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function witha docstring, and add the feature to the list in README.rst.

3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check https://travis-ci.com/glichtner/fsh-validator/pull_requests and make sure that the tests pass for all supported Python versions.

4.4 Tips

To run a subset of tests:

$ python -m unittest tests.test_fsh-validator

4.5 Deploying

A reminder for the maintainers on how to deploy. Make sure all your changes are committed (including an entry inHISTORY.rst). Then run:

$ bump2version patch # possible: major / minor / patch$ git push$ git push --tags

Travis will then deploy to PyPI if tests pass.

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CHAPTER

FIVE

CREDITS

5.1 Development Lead

• Gregor Lichtner @glichtner

5.2 Contributors

None yet. Why not be the first?

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14 Chapter 5. Credits

CHAPTER

SIX

HISTORY

6.1 0.2.2 (2021-11-10)

• Fixed processing of bundle resources

• Fixed processing of profiles that have parent profiles defined in the same project

• Added possibility to exclude certain types of resources from validation (via .fsh-validator.yml file)

• Added exclusion of abstract profiles from validation

6.2 0.2.1 (2021-11-11)

• Improved output messages

6.3 0.2.0 (2021-11-11)

• Added possibility to excluding specific code systems from validation

6.4 0.1.9 (2021-11-09)

• Added workaround function for invalid SUSHI outputs (duplicated codings in MII Laboratory Observation Pro-file)

6.5 0.1.8 (2021-11-08)

• Added support for extensions

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6.6 0.1.7 (2021-11-05)

• Added requirements to setup.py

6.7 0.1.6 (2021-11-05)

• Reading FHIR version to use in validator from sushi-config.yaml

6.8 0.1.5 (2021-11-03)

• Fixed validation of questionnaires

6.9 0.1.4 (2021-11-02)

• Fixed instances/profiles regex for aliases

6.10 0.1.3 (2021-10-25)

• Fixed FshPath

6.11 0.1.2 (2021-10-25)

• Added requirements to setup.py

6.12 0.1.1 (2021-10-25)

• Fix python package

6.13 0.1.0 (2021-10-25)

• First release on PyPI.

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CHAPTER

SEVEN

INDICES AND TABLES

• genindex

• modindex

• search

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PYTHON MODULE INDEX

ffsh_validator, 8fsh_validator.fshpath, 7

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20 Python Module Index

INDEX

Aabsolute() (fsh_validator.fshpath.FshPath method), 7

Eexists() (fsh_validator.fshpath.FshPath method), 7

Ffsh_base_path() (fsh_validator.fshpath.FshPath

method), 7fsh_name() (fsh_validator.fshpath.FshPath method), 7fsh_parts() (fsh_validator.fshpath.FshPath method), 7fsh_validator

module, 8fsh_validator.fshpath

module, 7FshPath (class in fsh_validator.fshpath), 7

Mmodule

fsh_validator, 8fsh_validator.fshpath, 7

21