Resolve taxonomic names from external APIs to PhyloPic #97
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willgearty
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(rebasing because of the updated snapshots on main) |
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Hi @willgearty, this works really well, great job! I've made some comments and suggestions - nothing major, but a few things to think about. Let me know if you want to chat about anything.
| name <- gsub("_", " ", name) | ||
| name <- URLencode(name) | ||
| # Query specified API for the name ------------------------------------- | ||
| if (api == "eol.org") { |
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It works really well but there is quite a bit of repeated code (e.g. L89–97). Could you perhaps start by making a list, subset the list to whatever API is requested and then run the code? I think this will help with managing any updates in future, including adding additional APIs? I get that there is some API specific code which is unavoidable.
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I've tried my best to reduce some of the repeated code, but the responses from these APIs are just sooooo different.
Co-authored-by: Lewis A. Jones <[email protected]>
| #' @return A `list` where each value is `n` (or fewer) PhyloPic image uuids (or | ||
| #' urls if `url = TRUE`) and each name is the taxonomic name as matched and | ||
| #' reported by the specified `api`. If `hierarchy` is `FALSE`, the list has | ||
| #' length 1. If `hierarchy` is `TRUE`, the list has maximum length |
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Ah you mean if you have a vector of more than length 1... well I guess if this is the case, does it even need to be named? I guess as long as get_phylopic and other functions can handle lists, it doesn't matter so much.
| #' | ||
| #' The following APIs are available for matching (`api`): | ||
| #' \itemize{ | ||
| #' \item{"eol.org": the \href{https://eol.org/}{Encyclopedia of Life}} |
This adds the
resolve_phylopic()function, which allows users to supply a taxonomic name that they expect to be matched in an external API (EOL, GBIF, PBDB, WoRMs, and OTOL atm) and then use that API to resolve the taxonomic name to PhyloPic. The function can return images (uuids/urls) for just the specified name or for a part of the taxonomic hierarchy (as reported by the API, except for EOL which doesn't supply taxonomic information).This basically accomplishes the asynchronous API searching that the PhyloPic website does, but with much lower overhead than calling all of those APIs within get_uuid (because it is user-driven).
Fixes #66.