https://github.com/Sage-Bionetworks/dccvalidator
Metadata Validation for Data Coordinating Centers
https://github.com/Sage-Bionetworks/dccvalidator
Last synced: 5 months ago
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Metadata Validation for Data Coordinating Centers
- Host: GitHub
- URL: https://github.com/Sage-Bionetworks/dccvalidator
- Owner: Sage-Bionetworks
- License: other
- Created: 2018-04-24T20:23:02.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2023-03-29T21:29:14.000Z (about 2 years ago)
- Last Synced: 2024-08-13T07:14:05.722Z (8 months ago)
- Language: R
- Homepage: https://sage-bionetworks.github.io/dccvalidator/
- Size: 9.07 MB
- Stars: 9
- Watchers: 11
- Forks: 12
- Open Issues: 58
-
Metadata Files:
- Readme: README.Rmd
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
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README
---
output:
md_document:
variant: gfm
---```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```# dccvalidator
[](https://CRAN.R-project.org/package=dccvalidator)
[](https://www.tidyverse.org/lifecycle/#maturing)dccvalidator is a package and Shiny app to perform data validation and QA/QC.
It's used in the [AMP-AD](https://ampadportal.org/) and
[PsychENCODE](http://www.psychencode.org) consortia to validate data prior to
data releases.## Installation
You can install dccvalidator from CRAN:
```{r installation-cran, eval = FALSE}
install.packages("dccvalidator")
```To install the development version from GitHub, run:
```{r installation-dev, eval = FALSE}
devtools::install_github("Sage-Bionetworks/dccvalidator")
```Many functions in dccvalidator use reticulate and the
[Synapse Python client](https://pypi.org/project/synapseclient/). See the
[reticulate documentation](https://rstudio.github.io/reticulate/#python-version)
for information on how to set R to use a specific version of Python if you don't
want to use the default Python installation on your machine. Whichever Python
installation you choose should have synapseclient installed.Because dccvalidator uses reticulate, it is not compatible with the
[synapser](https://r-docs.synapse.org/) package.## Check data
dccvalidator provides functions for checking the following common data quality
issues:- Annotation keys and values conform to a controlled vocabulary
- Column names match those of an associated metadata template
- Certain columns are not empty
- Certain columns are complete
- Identifiers match between two metadata files (e.g. all individuals in one file
are also present in another)
- Check that identifiers are unique within a file## Data submission validation
This package contains a Shiny app to validate manifests and metadata for AMP-AD
studies. It uses the dccvalidator package to check for common data quality
issues and gives realtime feedback to the data contributor on errors that need
to be fixed. The reporting UI is heavily inspired by the
[MetaDIG project's metadata quality reports](https://knb.ecoinformatics.org/quality/s=knb.suite.1/doi%3A10.5063%2FF12V2D1V).The application also allows users to submit documentation of their study, a
description of the methods used, etc.See the [customizing dccvalidator](https://sage-bionetworks.github.io/dccvalidator/articles/customizing-dccvalidator.html)
vignette for information on how to spin up a customized version of the
application## Requesting New Features or Bug Fixes
For new feature requests or bug fixes, please create an issue to let the maintainers know. If you’ve found a bug, create an associated issue and illustrate the bug with a minimal
[reprex](https://www.tidyverse.org/help/#reprex). If there is agreement that the problem exists or that a new feature is desired, then the issue will be triaged for future development based on priority.Please note that the dccvalidator project is released with a [Contributor Code of Conduct](https://sage-bionetworks.github.io/dccvalidator/CODE_OF_CONDUCT).
By contributing to this project via issue creation, comment, or pull request, you agree to abide by its terms.## Contributing
See the [Contributing Guide](https://github.com/Sage-Bionetworks/dccvalidator/blob/master/.github/CONTRIBUTING.md) to see how you can get involved in the development of this application.