Dataverse data access module

[abearab]

Aim

Including a draft dataverse data collector as part of gget tool boxes.

e.g.

gget dataverse -t dataverse.tsv -o path-to-dir

import gget
# df table with `id`, `name`, and `type` columns
gget.dataverse(df = df,  path = 'path-to-dir')

Tasks

• make a python module and CLI for data collection from dataverse
• collect data for a list of datasets defined as a JSON
• build a JSON file for a list of datasets deposited in a given dataverse DOI at certain version
• collect data by providing a dataverse DOI and version
• collect data by providing a list of dataverse datafiles (i.e. id, name, and type) in dataframe or csv/tsv file
• collect data by providing a list of dataverse datafiles (i.e. id, name, and type) as arguments

History

As part of GilbertLabUCSF/CanDI#34, related to #121, I draft a module to collect data from dataverse. Then I thought data collection from dataverse can be a more general functionality here as part of gget.

I mostly borrowed codes from gears/utils.py or TDC/load.py. However, there are other efforts such as pyDataverse and easyDataverse.

References

• https://guides.dataverse.org/en/latest/api/dataaccess.html
• https://github.com/mims-harvard/TDC/blob/main/tdc/utils/load.py

[abearab]

@lauraluebbert – I simplified this feature as discussed here #124 (comment). It should be more straightforward now and it works smoothly on my end, let me know what you think!