FINDtestdirData

Data in the data/ directory is organized by the apps that use them.

Available Datasets

covid19

• testdir.csv: test directory
• selftests.csv: directory of selftests
• eqa_covid_testdir: EQA test directory

moneypox

• mpx_testdir.csv: monkeypox test directory

ntd

• chagas_testdir.csv: Chagas test directory

Preview and Main Data

There are two versions of each data set: A regularly refreshed 'preview' version and an approved 'main' version. Each refresh of 'preview' automatically triggers an update of a pull request.

Main (Production)

https://raw.githubusercontent.com/dsbbfinddx/FINDtestdirData/main/data/covid19/testdir.csv

Preview

https://raw.githubusercontent.com/dsbbfinddx/FINDtestdirData/preview-testdir/data/covid19/testdir.csv

Use in R

With latest shinyfind, the 'main' set can read into R, using:

shinyfind::get_data("testdir", app = "covid19")
shinyfind::get_data("mpx_testdir", app = "monkeypox")

The 'preview' dataset:

shinyfind::get_data("testdir", app = "covid19", version = "preview")

where covid19 is the name of the folder in this repo and also the name of the app's folder in shinytestdir

Alternatively, use options() to set the version. This is useful in shiny apps, if you want to maintain a main and a preview version of an app.

options(find.data.version = "preview")
shinyfind::get_data("testdir", "covid19")

These functions are memoised. By default, they download the data once a day, at 7am UTC.

Same use for other dataset:

shinyfind::get_data("selftests", "covid19")
shinyfind::get_data("selftests", "covid19", "preview")

Updates

Data is updated locally by running:

source("script/update-all.R")

This processes all downloads and pushes the data to the preview branch. GHA will automatically open an PR afterwards.

Review

If the updated data (on the preview- branch) differs from main, an automated pull request is generated. This PR can be assigned to any colaborator of this repo.

How to add a new data set myname

1. Add an R script, updata-myname.R, to prepare the data. The script writes data/myname.csv.

2. Copy .github/workflows/testdir-pull-request.yml and rename to .github/workflows/myname-pull-request.yml. Substitute all testdir by myname.

3. Update update-all.R

TODO

data/testdir_data.csv is there because a production app is using it. Remove once the app switches to using shinyfind::get_data("testdir").