ropensci / bold

Interface to the Bold Systems barcode webservice
https://docs.ropensci.org/bold
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Typo in dataTypes 'depository' prevents fetching related data #83

Closed salix-d closed 2 years ago

salix-d commented 2 years ago

When querying taxon data with bold_tax_id(), if dataTypes is 'depository', the query returns empty even thought there is depository data as can be seen when setting dataTypes to 'all'.

The problem is with their API. Example : https://v4.boldsystems.org/index.php/API_Tax/TaxonData?taxId=88899&dataTypes=depository returns [] https://v4.boldsystems.org/index.php/API_Tax/TaxonData?taxId=88899&dataTypes=all

{
   [...],
  "depositry": {
    "Mined from GenBank, NCBI": 26,
    "Smithsonian Tropical Research Institute": 10,
    "Royal Ontario Museum": 1,
    "Centro de Ornitologia y Biodiversidad": 9,
    "Museo Nacional de Ciencias Naturales": 3,
    "Coleccion Boliviana de Fauna": 3,
    "Universidad de San Carlos de Guatemala, Escuela de Biologia": 1,
    "Universidad Nacional Mayor de San Marcos, Museo de Historia Natural": 8,
    "Museo Argentino de Ciencias Naturales, Bernardino Rivadavia": 3,
    "Universidad Nacional Autonoma de Mexico, Instituto de Biologia": 2,
    "Universidade Federal de Minas Gerais": 1,
    "Instituto Nacional de Pesquisas da Amazonia": 1,
    "Museum National d'Histoire Naturelle, Paris": 5,
    "Museo Nacional de Brasil": 2,
    "Universidad EAFIT": 2,
    "Instituto de Investigacion de Recursos Biologicos Alexander von Humboldt": 2
  },
  [...]
}

So to get that info, dataTypes need to be switched to 'all' and then filtered out.

Will inform BOLD's support.

salix-d commented 2 years ago

Just saw the typo in the JSON so I tried https://v4.boldsystems.org/index.php/API_Tax/TaxonData?taxId=88899&dataTypes=depositry and it still returns []

But for good measure I tried plural of the typo and plural of supposed key word and : https://v4.boldsystems.org/index.php/API_Tax/TaxonData?taxId=88899&dataTypes=depositories

{
  "depositry": {
    "Mined from GenBank, NCBI": 26,
    "Smithsonian Tropical Research Institute": 10,
    "Royal Ontario Museum": 1,
    "Centro de Ornitologia y Biodiversidad": 9,
    "Museo Nacional de Ciencias Naturales": 3,
    "Coleccion Boliviana de Fauna": 3,
    "Universidad de San Carlos de Guatemala, Escuela de Biologia": 1,
    "Universidad Nacional Mayor de San Marcos, Museo de Historia Natural": 8,
    "Museo Argentino de Ciencias Naturales, Bernardino Rivadavia": 3,
    "Universidad Nacional Autonoma de Mexico, Instituto de Biologia": 2,
    "Universidade Federal de Minas Gerais": 1,
    "Instituto Nacional de Pesquisas da Amazonia": 1,
    "Museum National d'Histoire Naturelle, Paris": 5,
    "Museo Nacional de Brasil": 2,
    "Universidad EAFIT": 2,
    "Instituto de Investigacion de Recursos Biologicos Alexander von Humboldt": 2
  }
}

So I can just switch the keyword to that!

salix-d commented 2 years ago

Following my report, BOLD did fix this issue. Both words ('depository' and 'depositories') will return results and they also corrected the typo in the return JSON.