daxkellie
commented
4 months ago Hi @T-LeB, Thanks for reaching out about this issue. This is some serious super-sleuthing and I was able to replicate the issue that you described, so there is definitely something weird going on here.
We'll have to investigate this further to know exactly what's going on, but I suspect there is something weird happening when parsing the 3 fields you omitted between steps 4 and 5 (datasetName, catalogNumber, recordedBy) when they come first in galah_select(). When I moved those three fields to the end of the list, things seemed to work correctly. What's weird is that (like you mentioned) moving other fields before scientificName didn't result in the same issue.
This isn't a solution to the underlying problem, but to get you up and running again, shifting those fields to the end should allow you to get all the columns you requested.
# Add datasetName, catalogNumber, recordedBy at the end of `galah_select()`
sp_rec <- galah_call() |>
identify("Swainsona viridis") |>
select(scientificName, eventDate,
decimalLatitude,decimalLongitude,coordinateUncertaintyInMeters,
verbatimLocality,occurrenceRemarks, habitat,eventRemarks,
fieldNotes,basisOfRecord, datasetName, catalogNumber, recordedBy) |>
atlas_occurrences()
#> Request for 96 occurrences placed in queue
#> Current queue length: 1
#> Downloading
sp_rec
#> # A tibble: 96 × 14
#> scientificName eventDate decimalLatitude decimalLongitude
#> <chr> <dttm> <dbl> <dbl>
#> 1 Swainsona viridis 2010-04-01 00:00:00 -31.6 140.
#> 2 Swainsona viridis 1925-10-24 00:00:00 NA NA
#> 3 Swainsona viridis NA -31.9 141.
#> 4 Swainsona viridis 1967-08-15 00:00:00 -32.6 140.
#> 5 Swainsona viridis NA -31.9 141.
#> 6 Swainsona viridis 2010-03-30 00:00:00 -31.7 140.
#> 7 Swainsona viridis NA -31.2 140.
#> 8 Swainsona viridis 1938-04-06 00:00:00 -30.7 139.
#> 9 Swainsona viridis 1923-08-22 00:00:00 -31.7 140.
#> 10 Swainsona viridis 1973-09-24 00:00:00 NA NA
#> # ℹ 86 more rows
#> # ℹ 10 more variables: coordinateUncertaintyInMeters <dbl>,
#> # verbatimLocality <chr>, occurrenceRemarks <chr>, habitat <chr>,
#> # eventRemarks <chr>, fieldNotes <chr>, basisOfRecord <chr>,
#> # datasetName <chr>, catalogNumber <chr>, recordedBy <chr>
T-LeB
Acanthiza
ZacPentecost
Describe the bug I have a brief code chunk (step 3) for downloading species occurrence data in full Darwin Core format, i wrote this and was using it without issue about 6 weeks ago and in that time have not updated R or made any other meaningful changes.
When I run it now it returns a tibble with just 8 columns (recordID, scientificName,taxonConceptID, decimalLat,decimalLong,eventDate,occurrenceStatus,dataResourceName). I figured the default output of atlas_occurrences must've changed and checked the documentation but couldnt find any info on it.
I tried again specifying the columns i was after in atlas_occurrences (see step 4).
This returns an empty tibble. I tried tweaking the galah_select() request and found it would work if I excluded the first three column headers (step 5) (datasetName, catalogNumber, recordedBy), it would also come back empty if any combination of those three was used together (e.g step 6). But if I run it on any of those three headers individually it would work fine (e.g step 7).
No errors or warnings get thrown either.
I can work around this by running the different functional combinations and joining the data, but I cant wrap my head around this behaviour.
galah version Initially in 2.0.1 continued once i updated to 2.0.2
To Reproduce Steps to reproduce
library(galah)
galah_config(email = "", verbose = FALSE)
sp_rec <- galah_call() |> galah_identify("Swainsona viridis") |> atlas_occurrences()
sp_rec <- galah_call() |> galah_identify("Swainsona viridis") |> atlas_occurrences(select = galah_select(datasetName, catalogNumber, recordedBy, scientificName, eventDate, decimalLatitude,decimalLongitude,coordinateUncertaintyInMeters, verbatimLocality,occurrenceRemarks, habitat,eventRemarks, fieldNotes,basisOfRecord))
sp_rec <- galah_call() |> galah_identify("Swainsona viridis") |> atlas_occurrences(select = galah_select(scientificName, eventDate, decimalLatitude,decimalLongitude,coordinateUncertaintyInMeters, verbatimLocality,occurrenceRemarks, habitat,eventRemarks, fieldNotes,basisOfRecord))
sp_rec <- galah_call() |> galah_identify("Swainsona viridis") |> atlas_occurrences(select = galah_select(datasetName,catalogNumber))
sp_rec <- galah_call() |> galah_identify("Swainsona viridis") |> atlas_occurrences(select = galah_select(datasetName))
Expected behaviour I expect the initial call to return the full darwin core format data for the species or i expect galah_select() to return a full tibble with all the columns requested.
Additional context I have tried to double and triple check i've not missed anything and its not covered by existing issues, so sorry if i have missed something basic.