Try write_dwc() on non-Zenodo dataset

[peterdesmet]

@sarahcd do you have a good example dataset in the Movebank repository that I can use to test if the write_dwc() function handles it elegantly?

[peterdesmet]

@sarahcd in 2016 you suggested http://dx.doi.org/10.5441/001/1.sj8t3r11 (peterdesmet/movebank2gbif#4 (comment)). Maybe that is still a good one?

[sarahcd]

Yes that one still looks good! Once we confirm that our current examples are working, when I read through the vignette, I can try to think of studies with other variations we should try it on.

[peterdesmet]

Great, here's what I did:

library(frictionless)
library(movepub)
library(dplyr)

package <-
  create_package() %>%
  movepub::add_resource("reference-data", "https://www.datarepository.movebank.org/bitstream/handle/10255/move.488/Lesser%20Kestrels%20EBD-reference-data.csv?sequence=1") %>%
  movepub::add_resource("gps", "https://www.datarepository.movebank.org/bitstream/handle/10255/move.487/Lesser%20Kestrels%20EBD.csv?sequence=1")

write_package(package, "kestrels") # Save datapackage.json file
write_dwc(package, directory = "kestrels", doi = "https://doi.org/10.5441/001/1.sj8t3r11")
#> Creating EML metadata.
#> Reading data from `package`.
#> Creating database and transforming to Darwin Core.

^{Created on 2022-05-20 by the reprex package (v2.0.1)}

Works fine, but can you verify the resulting (meta)data:

• eml.xml.txt
• dwc_occurrence.csv

[sarahcd]

I also added rightsHolder and contact as described in the vignette. Noticed that in the eml, the contact seems to map to metadataProvider and contact. For the use case of publishing data from the Movebank Repository, these might differ, e.g., the corresponding researcher for the contact and the repository/curator as the metadataProvider. Otherwise everything looks good, I will try some more examples and update if I find other things to consider.

[peterdesmet]

Correct, the provided contact maps to metadataProvider and contact. I think it's a fair simplification over providing an extra argument in the function, and it is documented as such in the function https://inbo.github.io/movepub/reference/write_dwc.html#arguments

Any of the provided values can be changed in the IPT afterwards if need be.

[sarahcd]

One other comment: For datasets from the data repository, the link to the Movebank study is not in the DataCite metadata, so it is missing from the eml (it shows "deposit of Movebank study "). Until we get this added, is there a line of code I could use to define the link in R?

[peterdesmet]

Indeed, the study URL is pulled from the second alternativeIdentifier in the EML:

movepub/R/write_dwc.R

Line 96 in d9f1a2d

study_url <- eml$dataset$alternateIdentifier[[2]]

To allow users to define it, we could:

• Add a parameter study_id (from which the link can be build)
• Have users correct add this when they edit metadata in the IPT

Given that the link is used in the description and as external link, I think a parameter would be good?

[sarahcd]

I agree!

[peterdesmet]

Ok, recorded in separate issue. Any other remarks regarding trying write_dwc() on non-Zenodo datasets?

[sarahcd]

Everything else worked well on 3 GPS studies I tried it with.

[peterdesmet]

Excellent, will close this issue then.