Switch to crul from httr?

[maelle]

Out of loyalty to rOpenSci + bc crul has a cool helper for #68 it its dev version ☺

[cboettig]

👍 switch away!

[maelle]

I see httr use in this ORCID notebook that I will ignore.

For which functionality is ORCID needed? I'd be happy to add rorcid code if needed 😉

[cboettig]

Re ORCID / ORCID API, my thought was that it would be nice to have a utility to make it easier to look up a contributor's ORCID ID. I don't think this could be fully automated ever though, since something like 99% of ORCID users don't make their email address public, you basically have to search on full names to get a list of ORCID ids, and then leave it up to the user to match ID to the person; at which point you may as well just use the ORCID web search.

It seems the ORCID search always treats a query of givenName familyName as givenName OR familyName, which is super annoying. @sckott or maybe @mfenner might know if there's a way to do a less stupid search to look up orcid ids...

[sckott]

will have a look, i think they support solr dismax, so i think should be able to change to AND etc. 🤔

[sckott]

maybe

first_last <- function(..., rows = 10) {
  tt <- rorcid::orcid(..., rows = rows)
  dplyr::bind_rows(lapply(tt$`orcid-identifier.path`, function(w) {
    rr <- rorcid::orcid_id(w)
    data.frame(
      first = rr[[1]]$name$`given-names`$value,
      last = rr[[1]]$name$`family-name`$value,
      stringsAsFactors = FALSE
    )
  }))
}

#> first_last(query = "carl boettiger")
#>           first               last
#> 1          Carl          Boettiger
#> 2      Alistair          Boettiger
#> 3         David          Boettiger
#> 4        Camila Boettiger Philipps
#> 5          Carl              Kruse
#> 6           Ian               Carl
#> 7      Fr. Carl               Carl
#> 8     Carl Elie           Saroufim
#> 9  Carl-Fredrik             Westin
#> 10         Carl         Liebersohn


#> first_last(query = "given-names:carl AND family-name:boettiger")
#>   first      last
#> 1  Carl Boettiger

[maelle]

Closing in favor of a specific issue #90

[cboettig]

@sckott yes, that looks good! Though interface wise I think it we might tweak it a bit -- I'd prefer a function with a verb name like orcid_search() that takes arguments like given_name and family_name rather than having the user have to guess how to construct the query.

[sckott]

@cboettig okay, what about this:

field_match_list <- list(
  orcid = 'orcid',
  given_name = 'given-names',
  family_name = 'family-name',
  past_inst = 'past-institution-affiliation-name',
  current_prim_inst = 'current-primary-institution-affiliation-name',
  current_inst = 'current-institution-affiliation-name',
  credit_name = 'credit-name',
  other_name = 'other-names',
  email = 'email',
  digital_object_ids = 'digital-object-ids',
  work_title = 'work-titles',
  grant_number = 'grant-numbers',
  patent_number = 'patent-numbers',
  keywords = 'keywords',
  text = 'text'
)

ocom <- function(l) Filter(Negate(is.null), l)

orcid_search <- function(given_name = NULL, family_name = NULL, 
    past_inst = NULL, current_prim_inst = NULL, current_inst = NULL, 
    credit_name = NULL, other_name = NULL, email = NULL, 
    digital_object_ids = NULL, work_title = NULL, grant_number = NULL, 
    patent_number = NULL, keywords = NULL, text = NULL, rows = 10) {

  query <- ocom(list(given_name = given_name, family_name = family_name, 
    past_inst = past_inst, current_prim_inst = current_prim_inst, 
    current_inst = current_inst,
    credit_name = credit_name, other_name = other_name, email = email, 
    digital_object_ids = digital_object_ids, work_title = work_title, 
    grant_number = grant_number, patent_number = patent_number, 
    keywords = keywords, text = text))
  if (length(query) == 0) stop("must pass at least one param")
  names(query) <- vapply(names(query), function(z) field_match_list[[z]], "")

  # by default, combine with 'AND'
  query <- paste(names(query), unname(query), sep = ":", collapse = " AND ")

  tt <- rorcid::orcid(query = query, rows = rows)
  dplyr::bind_rows(lapply(tt$`orcid-identifier.path`, function(w) {
    rr <- rorcid::orcid_id(w)
    data.frame(
      first = rr[[1]]$name$`given-names`$value,
      last = rr[[1]]$name$`family-name`$value,
      orcid = w,
      stringsAsFactors = FALSE
    )
  }))
}

orcid_search(given_name = "carl", family_name = "boettiger")
#>   first      last               orcid
#> 1  Carl Boettiger 0000-0002-1642-628X

orcid_search(given_name = "carl")
#>    first       last               orcid
#> 1   Carl       Lind 0000-0001-5979-5504
#> 2   Carl       Mika 0000-0003-2348-4290
#> 3   Carl  Bergstrom 0000-0002-2070-385X
#> 4   Carl      Brown 0000-0002-1559-3238
#> 5   Carl      Death 0000-0002-1601-9473
#> 6   Carl   Puylaert 0000-0003-4269-8964
#> 7   Carl Wesolowski 0000-0003-0134-9346
#> 8   Carl  Shanholtz 0000-0003-3938-178X
#> 9   Carl     Snyder 0000-0002-3480-1354
#> 10  Carl     Wadell 0000-0002-2809-9386

---

The drawback here is that you don't have the flexibility of different SOLR combinators - AND vs. OR, etc. - so above I just by default combine multiple queries with AND

[cboettig]

@sckott Thanks! Yes, I think the above API makes sense. It might be worth providing a lower-level function allowing a more direct SOLR query, but IMO we do want to default to AND for an R-based API. (For instance, this matches familiar behavior to R users such as dplyr::filter.

In general I think an R user expects additional arguments to be a refinement of search, while in R it is natural to think of OR combinations as separate function calls, which is much more flexible anyway. For instance, if I had a list of researcher names for whom I wanted to look up ORCIDs for, I would not attempt this with some combination of OR, but rather make multiple calls.

It is very difficult to imagine a valid use case for search results such as given_name: Carl OR family_name: Boettiger.

[sckott]

well, the lower level function is already there: orcid() - we can change that one if you like?

right, okay, so we're good on the AND ✔️

yes hard to imagine wanting to do carl OR boetigger

[sckott]

okay function added to rorcid on master. see ropensci-archive/rorcid#54