Package 'certeapi'

Overview of API Endpoints

Description

This page provides an overview of all available API endpoints and their arguments. On the API server, this information is available at ⁠{host}/__docs__/⁠, where {host} is the API location, such as "localhost", an IP address, or DNS name.

Overview of endpoints

⁠[GET] /esbl_prediction⁠:

Description: Retrieve an ESBL ETEST prediction and reliability for a vector of MIC values.

Arguments:

• AMC Amoxicillin/clavulanic acid, can be left blank

• AMP Ampicillin, can be left blank

• TZP Piperacillin/tazobactam, can be left blank

• CXM Cefuroxime, can be left blank

• FOX Cefoxitin, can be left blank

• CTX Cefotaxime, can be left blank

• CAZ Ceftazidime, can be left blank

• GEN Gentamicin, can be left blank

• TOB Tobramycin, can be left blank

• TMP Trimethoprim, can be left blank

• NIT Nitrofurantoin, can be left blank

• FOS Fosfomycin, can be left blank

• CIP Ciprofloxacin, can be left blank

• IPM Imipenem, can be left blank

• MEM Meropenem, can be left blank

• COL Colistin, can be left blank

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Get File Locations

Description

Use get_model_path() to retrieve the prediction model path, which should be an RDS file.

Usage

get_api_file()

get_model_path(name, path = read_secret("api.modelpath"))

read_model(path)

Arguments

name	(file)name of the model
path	folder of where the models are stored

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Start API

Description

This function starts the API server.

Usage

startup(port = read_secret("api.port"))

Arguments

port	port number

Details

For cron on UNIX (Linux/macOS), use the following command:

⁠Rscript -e "certeapi::startup()" &>> /path/api.log &⁠

Use Rscript --vanilla -e to not load any user settings such as .Rprofile. The trailing & will make the script run in the background.

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