Closed schifferl closed 3 years ago
I changed the columns. I also changed the dataset_name to study_name. I wouldn't add the dataset name to the tables: it would be a) the same name of the table without "_metadata.tsv" b) a different name, generating a relevant confusion, possibly
what do you think?
I'm making this note here since this issue is not yet closed, but I can create new issues.
"dataset_name" gets added when using makeCombinedMetadata to construct combined_metadata and checkCuration uses the /inst/extdata/template.csv. I used checkCuration in cMD's github action to update combined_metadata and determine if the curation is passing or failing, so we should also open an issue in cMD to change the dataset_name column to study_name.
Ok. It's not clear to me indeed if we can close this issue or not (as now the template.csv has study_name). Please, close if you think it can be closed
Thank you for making the changes @paolinomanghi, the reading in is now easier for me. From above, I am doing as you say in choice a)
, but it would be just the same to do it here. Go ahead, and do that if it is easy enough for you. The variable study_name
would be the table name without "_metadata.tsv". The issues raised by @jwokaty are good points too, but we don't need makeCombinedMetadata
anymore (this happens in cMD itself). So, ok to go ahead with the final change.
So, just to be clear: I don't modify the tables but I do switch from dataset_name to study_name in the grammar?
Hi @paolinomanghi, I think change the grammar and change the tables. This keeps one more step in the curation repo, where it seems to fit.
I've pushed the changes plus some other very little corrections to the tables. I'm closing this right now.
To improve consistency in naming of variables across all parts of the pipeline and APIs we should make the following changes to the template (and curated files).
Current Name -> New Name dataset_name -> study_name sampleID -> sample_id subjectID -> subject_id
Currently, study_name is not present in curated files and I generate it in the R package – it should be added to them.