README.md

In ammaraziz/fuzee: R interface for fuzee database

Fuzee API

Interface to Fuzee API

Installation

install.packages("devtools")
devtools::install_github("ammaraziz/fuzee")

Usage

Hash your password

Generate a hash of your password. Type the following into your console:

 openssl::md5("mypassword")

Where mypassword is the password to log into fuzee. Output will look like:

% [1] "34819d7beeabb9260a5c854bc85b3e44"

Copy this hash, store it in a variable called password:

password = "34819d7beeabb9260a5c854bc85b3e44"

Do not store your password in plain text. Use the hashed string.

Download All Data

To download all data in a zip format, similar to the Export All button on Fuzee:

fuzee(username = '[e-mail]', 
      password = password,
      file = 'Desktop/all.zip')

Where file is the directory/filename to save the zip file.

To uncompress the zip file in R, run the following:

unzip(zipfile = "location/to/zipfile",
    exdir = "location/to/extract",
    overwrite = TRUE)

Download individual datasets

First authenticate using auth then download the dataset with export_dataset:

cookie = auth(username = email, password = password)
samples = export_dataset(dataset = "Samples - Received", cookie = cookie)

export_datasets() returns a dataframe directly in R.

Note: The dataset option must match one of the following:

Samples - Storage
Batches 
BXA 
Despatch 
Egg Culture
GA-PCRID
GA-Pyro
GA-Sequencing
HI
NAI
Samples - Received
Samples - Storage 
Seqirus
Shipments 
VirusCulture

Use get_codes() to see this list.

Future Improvments:

Support direct querying of:

• Worksheets > Genetic Analysis > Show All
• Shipments > Search Shipments
• Shipments > Search Samples

ammaraziz/fuzee documentation built on Aug. 4, 2022, 5:17 p.m.