Add generic field extraction function - Githubissues

TIBHannover / BacDiveR

Inofficial R client for the DSMZ's Bacterial Diversity Metadatabase (former contact: @katrinleinweber). https://api.bacdive.dsmz.de/client_examples seems to be the official alternatives.

https://TIBHannover.GitHub.io/BacDiveR/

MIT License

10 stars 12 forks source link

Add generic field extraction function #75

Open katrinleinweber opened 6 years ago

katrinleinweber commented 6 years ago

The BacDive example and my vignette have some demo code for a temp extraction. It would be neat to have a search function for specific "paths" within the returned (large) list of lists. For example: retrieve_field('geo') should return environment_sampling_isolation_source$origin$geo_loc_name

Similar example: extracting specific fields: https://github.com/EngqvistLab/fetch_microbial_growth_temperatures/blob/159c411ff12578a6ac7b45e95d661558caccc2ea/BacDive/1_BacDive_get_data.py#L204-L223

Things to check:

[ ] dumping str() into a file and extracting the path from there
[ ] something to extract a tree representation from the nested dataframes
[ ] or try jsonlite::flatten()

related to #95