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https://github.com/lren-chuv/pfa-validator

Validation of the PFA model and its predictive algorithm
https://github.com/lren-chuv/pfa-validator

algorithm-factory docker-image pfa-standard testing

Last synced: about 2 months ago
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Validation of the PFA model and its predictive algorithm

Host: GitHub
URL: https://github.com/lren-chuv/pfa-validator
Owner: LREN-CHUV
License: apache-2.0
Created: 2017-09-21T12:28:31.000Z (over 7 years ago)
Default Branch: master
Last Pushed: 2023-02-15T02:08:18.000Z (almost 2 years ago)
Last Synced: 2024-04-17T06:13:25.879Z (9 months ago)
Topics: algorithm-factory, docker-image, pfa-standard, testing
Language: Python
Size: 80.1 KB
Stars: 2
Watchers: 5
Forks: 2
Open Issues: 11
Metadata Files:
- Readme: README.md
- License: LICENSE

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README

[![CHUV](https://img.shields.io/badge/CHUV-LREN-AF4C64.svg)](https://www.unil.ch/lren/en/home.html) [![License](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](https://github.com/LREN-CHUV/pfa-validator/blob/master/LICENSE) [![DockerHub](https://img.shields.io/badge/docker-hbpmip%2Fpfa--validator-008bb8.svg)](https://hub.docker.com/r/hbpmip/pfa-validator/) [![ImageVersion](https://images.microbadger.com/badges/version/hbpmip/pfa-validator.svg)](https://hub.docker.com/r/hbpmip/pfa-validator/tags "hbpmip/pfa-validator image tags") [![ImageLayers](https://images.microbadger.com/badges/image/hbpmip/pfa-validator.svg)](https://microbadger.com/#/images/hbpmip/pfa-validator "hbpmip/pfa-validator on microbadger") [![Codacy Badge](https://api.codacy.com/project/badge/Grade/96b3483a2345429fb9fc4918fa7d205b)](https://www.codacy.com/app/hbp-mip/pfa-validator?utm_source=github.com&utm_medium=referral&utm_content=HBPMedical/pfa-validator&utm_campaign=Badge_Grade) [![CircleCI](https://circleci.com/gh/HBPMedical/pfa-validator.svg?style=svg)](https://circleci.com/gh/HBPMedical/pfa-validator)

# pfa-validator

A small python program that validates that a PFA document is:
- Syntaxically correct JSON
- Syntaxically correct PFA
- Semantically correct PFA

This project does not perform cross-validation on the PFA document.

## Usage
The program can be run as a **Python program** or as a **Docker container**.

It may fetch the PFA document to validate from the file system or from a PostgreSQL database.

* **When fetching the PFA document from the file system**, the program expects a `PFA_PATH` environment
variable that contains the path to the PFA document to validate.

* **When fetching the PFA document from a PostgreSQL database**, the program expects the following environment variables:
* `INPUT_METHOD` that must be set to `POSTGRESQL`
* the database's credentials: `DB_HOST`, `DB_PORT`, `DB_NAME`, `DB_USER` and `DB_PASSWORD`
* the parameters of the query to perform: `DB_TABLE` `DB_COLUMN`
* the job ID (used to check the job_id column and get the right PFA document): `JOB_ID`

In addition, the program will also need the following environment variables to be set up in order to get some
validation data: `FEATURES_DB_HOST`, `FEATURES_DB_PORT`, `FEATURES_DB_NAME`, `FEATURES_DB_USER`, `FEATURES_DB_PASSWORD`
and `FEATURES_DB_TABLE`

### Examples

#### Validate a PFA file
1. Build the image: `docker build -t pfa-validator .`
2. Run a container based on that image:

```sh
docker run --volume $(pwd)/data:/data \
--env PFA_PATH="/data/example_01_valid/model.pfa" \
--env FEATURES_DB_HOST=db \
--env FEATURES_DB_PORT=5432 \
--env FEATURES_DB_NAME=sample \
--env FEATURES_DB_USER=sample \
--env FEATURES_DB_PASSWORD=... \
--env FEATURES_DB_TABLE=features \
hbpmip/pfa-validator:0.10.1-2
```

#### Validate a PFA PostgreSQL column
1. Build the image: `docker build -t pfa-validator .`
2. Run a container based on that image:

```sh
docker run \
--env INPUT_METHOD=POSTGRESQL \
--env JOB_ID=1
--env DB_HOST=172.20.0.2 \
--env DB_PORT=5432 \
--env DB_NAME=woken \
--env DB_USER=woken \
--env DB_PASSWORD=... \
--env DB_TABLE=job_result \
--env DB_COLUMN=data \
--env FEATURES_DB_HOST=db \
--env FEATURES_DB_PORT=5432 \
--env FEATURES_DB_NAME=sample \
--env FEATURES_DB_USER=sample \
--env FEATURES_DB_PASSWORD=... \
--env FEATURES_DB_TABLE=features \
hbpmip/pfa-validator:0.10.1-2
```

NOTE: If you don't want to use Docker, you can install the dependencies with: `pip install -r requirements.txt`
and run this program using Python2. The environment variables still have to be set up.

## TODO

* Allow validation of YAML formatted PFA document

# Acknowledgements

This work has been funded by the European Union Seventh Framework Program (FP7/20072013) under grant agreement no. 604102 (HBP)

This work is part of SP8 of the Human Brain Project (SGA1).