Kaelyn Long

Enable use_cache = FALSE for get_metadata()

2

ISSUE: metadata.R/`get_metadata(use_cache = FALSE)` was still using the cached file due to multiple `if (!file.exists())` bypasses ADJUSTED: - utils.R/`sync_remote_file()` adjusted to get user permission to overwrite if cached file exists...

I noticed an issue when trying to wrap the `cBioPortalData()` function within another function or the `mapply()` function. It seems that when multiple arguments to `cBioPortalData()` are being passed in...

Base metadata validator functions and vignette

1

Merging my work on metadata validation functions so we can start integrating it into the standard workflow. We have a few steps remaining, which I have created issues for: -...

We want to integrate the metadata validation functions (`metadataValidator.R`, `validate_metadata.qmd`) into a GH actions workflow to automatically run whenever the metadata schema is updated or a new study is curated.

Ontology validation based on external dictionary (OWL/CSV) files currently works with a local folder, I want to include a function/tooling to access the files stored in the curatedmetagenomicdata Google Cloud...

Functions in `R/metadataValidator.R` need roxygen2 documentation. Some of these functions are also demonstrated in `vignettes/validate_metadata.qmd`, but we need more prose to walk the user through the functions' main use cases...