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getTVKQuery not finding some species #16

Closed fozy81 closed 10 years ago

fozy81 commented 10 years ago

Hi,

I'm looking for diatom: Eunotia pseudopectinalis

Here's the NBN page: https://data.nbn.org.uk/Taxa/NHMSYS0000602767

If I use:

tvk <- getTVKQuery(query = "Eunotia pseudopectinalis",species_only = FALSE, rec_only=F)

I get NULL. Am I missing something? If I search for the taxonomy I can find that:

tax <- getTaxonomy("NHMSYS0000602767") rank name ptaxonVersionKey 1 Kingdom Chromista NHMSYS0020787081 ...etc etc

Here's some other taxa with same issue:

Fistulifera / Mayamaea https://data.nbn.org.uk/Taxa/NHMSYS0020954993 Cyclotella pseudostelligera https://data.nbn.org.uk/Taxa/NHMSYS0000601856 Pseudostaurosira https://data.nbn.org.uk/Taxa/NHMSYS0000605811 Pseudostaurosira / Staurosira agg. https://data.nbn.org.uk/Taxa/NHMSYS0020955232 Pseudostaurosira brevistriata Pseudostaurosira medliniae Pseudostaurosira microstriata Pseudostaurosira pseudoconstruens Pseudostaurosira robusta

The NBN website search also does not find these taxa directly only after some digging. So if it is an issue, it may be with NBN to fix rather than this package. But wanted to check with you first.

Thank you

Tim

fozy81 commented 10 years ago

After contacting the NBN gateway directly, I'm informed of a 15 character limit on search terms. So that limits longer names from being queried. But if I truncate the query above it works:

tvktest <- getTVKQuery(query = "Eunotia pseud",species_only = FALSE, rec_only=F)

Possibly worth mentioning the 15 character limit in the rnbn documentation.

Tim

sckott commented 10 years ago

Hmm, that doesn't seem right, any way of increasing the 15 character limit @AugustT ?

AugustT commented 10 years ago

Hi Guys,

Tim - I guessed from your first message that this was an issue on the NBN side but did not think it would be a character limit issue. This does not seem ideal and I will have a chat with their technical team as to whether this can be adjusted.

Thanks for bring this to my attention,

Tom

AugustT commented 10 years ago

UPDATE:

I'm told the character limit has been upped to 30. And indeed the search now works:

library(rnbn)

tvk <- getTVKQuery(query = "Eunotia pseudopectinalis",species_only = FALSE, rec_only=F)

tvk$searchMatchTitle [1] "Eunotia pseudopectinalis"

Please note that rNBN's home on GitHub has now moved here: https://github.com/ropensci/rnbn