Change order of the documentation parts to: 1. for users (user documentation), 2. for administrators (setup and config), 3. for developers (architecture)
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README.md
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README.md
@ -14,24 +14,46 @@ This bulk FHIR validation environment **aggregates/groups and presents validatio
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## Based on open standards and powerfull and flexible Open Source Software
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## Usage
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Therefore this validation environment uses following standards and Open Source Software by the Python Library [fhirvalidation.py](home/fhirvalidation.py):
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### Web UI
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- 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)
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- [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
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- Aggregation by [Python Pandas](https://pandas.pydata.org/docs/user_guide/index.html) dataframe
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- Presentation of validation results in web UI by [Jupyter Lab](https://jupyterlab.readthedocs.io/en/latest/)
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Access the [web user interface of Jupyter Lab](https://jupyterlab.readthedocs.io/en/latest/) on the configured (default: 80) port:
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http://yourserver/
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## Architecture
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#### Login
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Login with the initial password / token you configured in .env
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## Installation and Configuration
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#### Start validation
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Now you can start the validation and aggregation of validation results.
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Therefore run the Jupyter Notebook [fhir-validation.ipynb](home/fhir-validation.ipynb).
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#### Navigate validation results
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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".
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### User documentation
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The further user documentation is embedded in the Jupyter Notebook:
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The different outputs are described in markdown cells and used parameters are described in the code cells.
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### Select resources to be validated by FHIR Search parameters
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You can select/filter the resources to be validated by [FHIR search](https://www.hl7.org/fhir/search.html) parameters.
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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), ...
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## Installation and configuration
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### Setup FHIR Packages
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@ -73,48 +95,30 @@ Start the validation environment by
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docker compose up -d
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``
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## Usage
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## Software architecture
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### Web UI
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### Based on open standards and powerful and flexible Open Source Software
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Access the [web user interface of Jupyter Lab](https://jupyterlab.readthedocs.io/en/latest/) on the configured (default: 80) port:
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http://yourserver/
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The FHIR validation environment uses following standards and Open Source Software by the Python Library [fhirvalidation.py](home/fhirvalidation.py):
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- 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)
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- [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
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- Aggregation by [Python Pandas](https://pandas.pydata.org/docs/user_guide/index.html) dataframe
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- Presentation of validation results in web UI by [Jupyter Lab](https://jupyterlab.readthedocs.io/en/latest/)
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#### Login
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### Software architecture diagram
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Login with the initial password / token you configured in .env
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Visualization of the components and the deployment:
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#### Start validation
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Now you can start the validation and aggregation of validation results.
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Therefore run the Jupyter Notebook [fhir-validation.ipynb](home/fhir-validation.ipynb).
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#### Navigate validation results
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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".
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#### User documentation
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The further user documentation is embedded in the Jupyter Notebook:
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The different outputs are described in markdown cells and used parameters are described in the code cells.
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### Select resources to be validated by FHIR Search parameters
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You can select/filter the resources to be validated by [FHIR search](https://www.hl7.org/fhir/search.html) parameters.
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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), ...
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### Python library
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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.
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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.
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In the Jupyter Notebook, you can find documentation on how to use the library, including example with code snippets.
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In the Jupyter Notebook, you can find documentation on how to use the library, including example with code snippets.
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