dataquality/dataquier repository overview

⁠Data Quality in Epidemiological Research

Data quality assessments guided by a data quality framework introduced by Schmidt and colleagues, 2021⁠ target the data quality dimensions integrity, completeness, consistency, and accuracy. The scope of applicable functions rests on the availability of extensive metadata which can be provided in spreadsheet tables. Either standardized (e.g. as 'html5' reports) or individually tailored reports can be generated. For an introduction into the specification of corresponding metadata, please refer to the package website⁠.

This docker image provides a Shiny app to easily run data quality assessments. It uses the dataquieR R package available from CRAN⁠.

⁠Tags

The tags display the version of the dataquieR package and of its Shiny UI: dataquality/dataquier:<dataquieR version>_<dataquieRLauncher version>

⁠Usage

docker run --rm -p3838:3838 dataquality/dataquier

Then navigate your browser to

http://localhost:3838/⁠

The image does not use TLS and it uses the port 3838 internally. You can find the image sources at https://github.com/qihs-dataquality/dataquieRLauncher⁠ and the R package is hosted at https://gitlab.com/libreumg/dataquier⁠.

The RAM usage of the image depends on the size of the assessed data files, mostly. You should configure your Docker to allow at least 6 GBytes of RAM by the container to compute dataquieR's example reports.

The launcher underlies the same license conditions as the dataquieR package, i.e., the "BSD 2-clause license", see below⁠.

⁠License

BSD 2-Clause License, see LICENSE.

⁠Internal notes

For building, use the sh scripts in this folder, but adjust make.sh to your needs, so far.

For adding dataquieR 2.0.1 to a shinyproxy server, add something like below to application.yml:

    - id: dataquieR2
      display-name: dataquieR 2.0.1
      description: Run Data Quality Assessments
      container-cmd: ["R", "-e", "shiny::runApp('/opt/dataquieRLauncher')"]
      container-image: dataquality/dataquier:latest
      access-groups: [developers]

For bare-metal ShinyProxy installations with the Docker backend, the image already sets HOME=/home/dataquier and TMPDIR=/home/dataquier/tmp. ShinyProxy does not need to set these variables explicitly.

The image creates /home/dataquier/tmp for the unprivileged container user 10001:10001. Do not override TMPDIR with a read-only host mount or with a path that user 10001 cannot write to; otherwise R can fail at startup with Fatal error: cannot create 'R_TempDir'.