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Add generic field extraction function #75

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katrinleinweber opened this issue May 2, 2018 · 0 comments
Open
3 tasks

Add generic field extraction function #75

katrinleinweber opened this issue May 2, 2018 · 0 comments

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@katrinleinweber
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katrinleinweber commented May 2, 2018

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

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