wcia-analytes-tool

Consumes OpenTHC Lab Metrics and WCIA Analytes, and produces diff objects and docs for use in WA State interop.

version 0.9.8

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Getting Started

Prep

1. Load the storage area with the OpenTHC Lab Metrics.
   Clone the https://github.com/openthc/api.git repository and copy its etc/lab-metric folder to this repository's storage/ folder (i.e., storage/lab-metric).

2. Load the storage area with the WCIA analytes json files. Clone the https://github.com/conflabs/wcia-analytes.git repository and copy its json/ folder to this repository's storage/ folder (i.e., storage/json).

3. From the CLI, run php makeOpenTHCResource.php to create the OpenTHC Json Resource.
   It is saved to the storage dir.

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Find Missing OpenTHC Lab Metrics

From the CLI, run php makeNotInWciaList.php to create a list of OpenTHC lab metrics that are not in the WCIA list.

Convert Missing OpenTHC Lab Metrics to WCIA Analytes

From the CLI, run php makeNewWciaAnalytes.php to create a list of new WCIA analytes from the OpenTHC lab metrics list.

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Find Missing WCIA Analytes

From the CLI, run php makeNotInOpenThcList.php to create a list of WCIA analytes that are not in the OpenTHC list.

Convert Missing WCIA Analytes to OpenTHC Lab Metrics

From the CLI, run php makeNewOpenThcLabMetrics.php to create a list of new OpenTHC stubs from the WCIA analytes list.

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Create Documents

From the CLI, run php makeMarkDown.php to create a series of mark down docs in the storage/docs folder.

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Unit Tests

The tests/ folder is a reflection of the src/ folder, but containing Unit Test classes. Run the unit tests from the CLI, like so: php vendor/bin/phpunit tests/.

Static Analysis

This project uses PHPStan for static analysis, and at a default level of 5. Run the analyser from the CLI like so, vendor/bin/phpstan analyse --level 5 src.

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Docker

For simple, reproducible server environments, I've included a Dockerfile for creating a quick CLI environment with which to run these scripts.

Docker Build

docker build -f Dockerfile -t wcia/analytes-generator:latest .

Docker Run CLI

docker run -it --rm -v $PWD:/srv wcia/analytes-generator:latest bash

Docker Run Unit Tests

docker run -it --rm -v $PWD:/srv wcia/analytes-generator:latest php vendor/bin/phpunit tests/

Docker Run Static Analysis

docker run -it --rm -v $PWD:/srv wcia/analytes-generator:latest vendor/bin/phpstan analyse --level 5 src