Change order of the documentation parts to: 1. for users (user documentation), 2. for administrators (setup and config), 3. for developers (architecture)
This commit is contained in:
parent
777719df07
commit
8cd13bc6e8
94
README.md
94
README.md
@ -14,24 +14,46 @@ This bulk FHIR validation environment **aggregates/groups and presents validatio
|
||||
|
||||
|
||||
|
||||
## Based on open standards and powerfull and flexible Open Source Software
|
||||
## Usage
|
||||
|
||||
Therefore this validation environment uses following standards and Open Source Software by the Python Library [fhirvalidation.py](home/fhirvalidation.py):
|
||||
### Web UI
|
||||
|
||||
- Loading FHIR resources to be validated by [FHIR search](https://www.hl7.org/fhir/search.html) (for documentation see section "Select resources to be validated by FHIR Search parameters" below)
|
||||
|
||||
- [FHIR validation](https://www.hl7.org/fhir/validation.html#op) by [HAPI FHIR Validator](https://hapifhir.io/hapi-fhir/docs/validation/introduction.html) configured by Docker environment variables
|
||||
|
||||
- Aggregation by [Python Pandas](https://pandas.pydata.org/docs/user_guide/index.html) dataframe
|
||||
|
||||
- Presentation of validation results in web UI by [Jupyter Lab](https://jupyterlab.readthedocs.io/en/latest/)
|
||||
Access the [web user interface of Jupyter Lab](https://jupyterlab.readthedocs.io/en/latest/) on the configured (default: 80) port:
|
||||
http://yourserver/
|
||||
|
||||
|
||||
## Architecture
|
||||
#### Login
|
||||
|
||||
|
||||
Login with the initial password / token you configured in .env
|
||||
|
||||
## Installation and Configuration
|
||||
|
||||
#### Start validation
|
||||
|
||||
Now you can start the validation and aggregation of validation results.
|
||||
|
||||
Therefore run the Jupyter Notebook [fhir-validation.ipynb](home/fhir-validation.ipynb).
|
||||
|
||||
|
||||
#### Navigate validation results
|
||||
|
||||
You can navigate the validation results by "Table of Content" of Jupyter Lab. Therefore switch the left navigation bar from "File browser" to "Table of Contents".
|
||||
|
||||
|
||||
### User documentation
|
||||
|
||||
The further user documentation is embedded in the Jupyter Notebook:
|
||||
|
||||
The different outputs are described in markdown cells and used parameters are described in the code cells.
|
||||
|
||||
|
||||
### Select resources to be validated by FHIR Search parameters
|
||||
|
||||
You can select/filter the resources to be validated by [FHIR search](https://www.hl7.org/fhir/search.html) parameters.
|
||||
|
||||
For filter options you can set `search_parameters`, see [FHIR search common parameters for all resource types](https://www.hl7.org/fhir/search.html#standard), as well as additional FHIR search parameters for certain resource types like [Patient](https://www.hl7.org/fhir/patient.html#search), [Condition](https://www.hl7.org/fhir/condition.html#search), [Observation](https://www.hl7.org/fhir/observation.html#search), ...
|
||||
|
||||
|
||||
## Installation and configuration
|
||||
|
||||
### Setup FHIR Packages
|
||||
|
||||
@ -73,48 +95,30 @@ Start the validation environment by
|
||||
docker compose up -d
|
||||
``
|
||||
|
||||
## Usage
|
||||
## Software architecture
|
||||
|
||||
### Web UI
|
||||
### Based on open standards and powerful and flexible Open Source Software
|
||||
|
||||
Access the [web user interface of Jupyter Lab](https://jupyterlab.readthedocs.io/en/latest/) on the configured (default: 80) port:
|
||||
http://yourserver/
|
||||
The FHIR validation environment uses following standards and Open Source Software by the Python Library [fhirvalidation.py](home/fhirvalidation.py):
|
||||
|
||||
- Loading FHIR resources to be validated by [FHIR search](https://www.hl7.org/fhir/search.html) (for documentation see section "Select resources to be validated by FHIR Search parameters" below)
|
||||
|
||||
- [FHIR validation](https://www.hl7.org/fhir/validation.html#op) by [HAPI FHIR Validator](https://hapifhir.io/hapi-fhir/docs/validation/introduction.html) configured by Docker environment variables
|
||||
|
||||
- Aggregation by [Python Pandas](https://pandas.pydata.org/docs/user_guide/index.html) dataframe
|
||||
|
||||
- Presentation of validation results in web UI by [Jupyter Lab](https://jupyterlab.readthedocs.io/en/latest/)
|
||||
|
||||
|
||||
#### Login
|
||||
### Software architecture diagram
|
||||
|
||||
Login with the initial password / token you configured in .env
|
||||
Visualization of the components and the deployment:
|
||||
|
||||
|
||||
#### Start validation
|
||||
|
||||
Now you can start the validation and aggregation of validation results.
|
||||
|
||||
Therefore run the Jupyter Notebook [fhir-validation.ipynb](home/fhir-validation.ipynb).
|
||||
|
||||
|
||||
|
||||
#### Navigate validation results
|
||||
|
||||
You can navigate the validation results by "Table of Content" of Jupyter Lab. Therefore switch the left navigation bar from "File browser" to "Table of Contents".
|
||||
|
||||
|
||||
#### User documentation
|
||||
|
||||
The further user documentation is embedded in the Jupyter Notebook:
|
||||
|
||||
The different outputs are described in markdown cells and used parameters are described in the code cells.
|
||||
|
||||
|
||||
### Select resources to be validated by FHIR Search parameters
|
||||
|
||||
You can select/filter the resources to be validated by [FHIR search](https://www.hl7.org/fhir/search.html) parameters.
|
||||
|
||||
For filter options you can set `search_parameters`, see [FHIR search common parameters for all resource types](https://www.hl7.org/fhir/search.html#standard), as well as additional FHIR search parameters for certain resource types like [Patient](https://www.hl7.org/fhir/patient.html#search), [Condition](https://www.hl7.org/fhir/condition.html#search), [Observation](https://www.hl7.org/fhir/observation.html#search), ...
|
||||
|
||||
|
||||
|
||||
### Python library
|
||||
|
||||
If you dont want to use Jupyter Lab as a user interface (e.g. if you want to generate markdown for CI/CD reports), you can use the Python library [fhirvalidation.py](home/fhirvalidation.py) returning a [pandas](https://pandas.pydata.org/docs/user_guide/index.html) dataframe independent from Jupyter Lab.
|
||||
If you don't want to use Jupyter Lab as a user interface (e.g. if you want to generate markdown for CI/CD reports), you can use the Python library [fhirvalidation.py](home/fhirvalidation.py) returning a [pandas](https://pandas.pydata.org/docs/user_guide/index.html) dataframe independent from Jupyter Lab.
|
||||
|
||||
In the Jupyter Notebook, you can find documentation on how to use the library, including example with code snippets.
|
||||
Loading…
Reference in New Issue
Block a user