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View Code? Open in Web Editor NEWWrapper to DataCite metadata
Home Page: https://docs.ropensci.org/rdatacite
License: Other
Wrapper to DataCite metadata
Home Page: https://docs.ropensci.org/rdatacite
License: Other
I'll work through it to see why, but the call:
neotoma_dois <- dc_facet(q = "publisher:[Neotoma]", fl = c('doi','publicationYear'))
Error in vapply(elements, encode, character(1)) :
values must be length 1,
but FUN(X[[5]]) result is length 2
The endpoint "https://search.datacite.org/api" is going to be deprecated in early 2019.
Line 9 in c525d6d
rdatacite should be using any of the other api.datacite.org endpoints. https://support.datacite.org/v1.2/reference
@bmkramer
Do you still intend to become this package's maintainer?
If so do you need any help? For instance an aspect where you'd appreciate some tips, contributions, a PR review? Do you need an invitation to our friendly Slack workspace?
https://api.labs.datacite.org/ or https://api.datacite.org/ later perhaps
https://api.datacite.org/clients
or add new method for
I couldn't work out how to do it.
Would like to recreate this search (for English language theses) with rdatacite:
https://search.datacite.org/ui?q=resourceType%3AThesis&fq=&fq=&fq=&fq=&fq=language_facet%3A%22English%22&fq=
Can a web-based search for arelatedIdentifier=$doi
be ported to dc_search
? I tried these syntaxes:
rdatacite::dc_search("relatedIdentifier%3D%2210.1002%2Fbimj.201700219%22")
rdatacite::dc_search("relatedIdentifier='10.1002%2Fbimj.201700219'")
rdatacite::dc_search("relatedIdentifier:'10.1002%2Fbimj.201700219'")
rdatacite::dc_search("relatedIdentifier='10.1002/bimj.201700219'")
rdatacite::dc_search("relatedIdentifier:[10.1002/bimj.201700219]")
rdatacite::dc_search("relatedIdentifier:10.1002/bimj.201700219")
rdatacite::dc_search('relatedIdentifier:"10.1002/bimj.201700219"')
rdatacite::dc_search('relatedIdentifier%3A%5B10.1002%2Fbimj.201700219%5D')
but am always getting only
# A tibble: 0 x 0
I'm not sure whether I'm missing something, or what else to try. Thanks for any hints here :-)
- Session info -----------------------------------------------------------------------------------------------------------
setting value
version R version 3.6.1 (2019-07-05)
os Windows 8.1 x64
system x86_64, mingw32
ui RStudio
language en
collate German_Germany.1252
ctype German_Germany.1252
tz Europe/Berlin
date 2019-10-22
- Packages ---------------------------------------------------------------------------------------------------------------
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.1)
callr 3.3.2 2019-09-22 [1] CRAN (R 3.6.1)
cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
crul 0.8.4 2019-08-02 [1] CRAN (R 3.6.1)
curl 4.2 2019-09-24 [1] CRAN (R 3.6.1)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
devtools * 2.2.1 2019-09-24 [1] CRAN (R 3.6.1)
digest 0.6.21 2019-09-20 [1] CRAN (R 3.6.1)
dplyr * 0.8.3 2019-07-04 [1] CRAN (R 3.6.1)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.1)
fansi 0.4.0 2018-10-05 [1] CRAN (R 3.6.0)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
ggplot2 * 3.2.1 2019-08-10 [1] CRAN (R 3.6.1)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.1)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0)
hms 0.5.1 2019-08-23 [1] CRAN (R 3.6.1)
httpcode 0.2.0 2016-11-14 [1] CRAN (R 3.6.0)
httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.1)
inline 0.3.15 2018-05-18 [1] CRAN (R 3.6.1)
jsonlite 1.6 2018-12-07 [1] CRAN (R 3.6.0)
knitr 1.25 2019-09-18 [1] CRAN (R 3.6.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0)
lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.6.1)
lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.6.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
MASS 7.3-51.4 2019-03-31 [2] CRAN (R 3.6.1)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0)
oai * 0.3.0 2019-09-07 [1] CRAN (R 3.6.1)
packrat 0.5.0 2018-11-14 [1] CRAN (R 3.6.1)
pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.0)
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
pkgdown * 1.4.1 2019-09-15 [1] CRAN (R 3.6.1)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.6.0)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.1)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
purrr * 0.3.3 2019-10-18 [1] CRAN (R 3.6.1)
R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0)
Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.1)
rdatacite 0.4.2 2019-05-07 [1] CRAN (R 3.6.1)
readr * 1.3.1 2018-12-21 [1] CRAN (R 3.6.0)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.1)
rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
rstudioapi 0.10 2019-03-19 [1] CRAN (R 3.6.0)
scales 1.0.0 2018-08-09 [1] CRAN (R 3.6.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
skimr 1.0.7 2019-06-20 [1] CRAN (R 3.6.1)
solrium 1.0.2 2018-12-13 [1] CRAN (R 3.6.1)
StanHeaders 2.19.0 2019-09-07 [1] CRAN (R 3.6.1)
stringi * 1.4.3 2019-03-12 [1] CRAN (R 3.6.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0)
testthat * 2.2.1 2019-07-25 [1] CRAN (R 3.6.1)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0)
tidyr 1.0.0 2019-09-11 [1] CRAN (R 3.6.1)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.0)
triebeard 0.3.0 2016-08-04 [1] CRAN (R 3.6.0)
urltools 1.7.3 2019-04-14 [1] CRAN (R 3.6.0)
usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.1)
utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.0)
vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.1)
ViewPipeSteps 0.1.0 2019-10-09 [1] Github (daranzolin/ViewPipeSteps@0772271)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
writexl 1.1 2018-12-02 [1] CRAN (R 3.6.1)
xfun 0.10 2019-10-01 [1] CRAN (R 3.6.1)
xml2 1.2.2 2019-08-09 [1] CRAN (R 3.6.1)
zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.0)
[1] C:/USERNAME/R/win-library/3.6
[2] C:/Program Files/R/R-3.6.1/library
It would useful for teams of bibliometricians to be able to share/sync a cache of their DataCite queries. Analogous to pybliometrics Python package for example.
Which of the "cache"-related CRAN packages seems most usable to ensure that? I tried it with r-lib/memoise#106 but that approach seems to have failed.
Error in result$children <- chunks : object 'result' not found
In your example for facets I would use publisher_facet
instead of publisher
. This avoids breaking up publisher names into single words.
When I run:
dc_arch <- dc_search(q = "archaeology", rows = 100000)
I get:
https://search.datacite.org/api?q=archaeology&rows=1e+05&wt=json
Error: 500 - For input string: "1e+05"
But when I use this URL in my browser: https://search.datacite.org/api?q=archaeology&rows=100000&wt=json I appear to get a valid response.
So is it possible to protect large numbers to prevent the dc_*
functions from getting a URL with exponential notation? I'm currently doing this, which seems to work:
dc_arch <- dc_search(q = "archaeology", rows = pretty(100000)[2])
But maybe there's a better way? Thanks!
$rdatacite
'library' or 'require' call not declared from: ‘httr’
https://cran.r-project.org/web/checks/check_results_rdatacite.html
i guess examples didn't get dontrun maybe, not sure
need to resubmit asap
http://search.datacite.org/help.html
I swear I already wrote wrapper functions for this API, but I guess I didn't, can't find code anywhere,
I'm running into a problem when downloading GBIF's metadata records:
> dc_works("prefix:10.15468", rows = 99999L)
Error in readBin(x, character()) :
R character strings are limited to 2^31-1 bytes
I'm guessing that's because they submitted a very large file encoded in their JSON/XML upload to DataCite. Is there a more elegant way of finding out which DOI is the problematic one, than:
rows
parameter combined with a given order,offset = row+1
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 3.6.2 (2019-12-12)
os macOS Catalina 10.15.2
system x86_64, darwin15.6.0
ui RStudio
language en
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Copenhagen
date 2019-12-15
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
! package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)
backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.0)
callr 3.4.0 2019-12-09 [1] CRAN (R 3.6.0)
cli 2.0.0 2019-12-09 [1] CRAN (R 3.6.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
crul 0.9.0 2019-11-06 [1] CRAN (R 3.6.0)
curl 4.3 2019-12-02 [1] CRAN (R 3.6.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
devtools * 2.2.1 2019-09-24 [1] CRAN (R 3.6.0)
digest 0.6.23 2019-11-23 [1] CRAN (R 3.6.0)
dplyr * 0.8.3 2019-07-04 [1] CRAN (R 3.6.0)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.0)
fansi 0.4.0 2018-10-05 [1] CRAN (R 3.6.0)
R fd * 0.1.0 <NA> [?] <NA>
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.0)
ggplot2 * 3.2.1 2019-08-10 [1] CRAN (R 3.6.0)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0)
hms 0.5.2 2019-10-30 [1] CRAN (R 3.6.0)
httpcode 0.2.0 2016-11-14 [1] CRAN (R 3.6.0)
httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.0)
jsonlite 1.6 2018-12-07 [1] CRAN (R 3.6.0)
knitr 1.26 2019-11-12 [1] CRAN (R 3.6.0)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0)
lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.6.0)
lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.6.0)
magrittr * 1.5 2014-11-22 [1] CRAN (R 3.6.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0)
oai 0.3.0 2019-09-07 [1] CRAN (R 3.6.0)
pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.0)
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
plyr 1.8.5 2019-12-10 [1] CRAN (R 3.6.0)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.0)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.0)
purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.0)
Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.6.0)
rdatacite 0.4.2 2019-05-07 [1] CRAN (R 3.6.0)
readr * 1.3.1 2018-12-21 [1] CRAN (R 3.6.0)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.0)
rlang 0.4.2 2019-11-23 [1] CRAN (R 3.6.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
rstudioapi 0.10 2019-03-19 [1] CRAN (R 3.6.0)
scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
solrium 1.1.4 2019-11-02 [1] CRAN (R 3.6.0)
stringi * 1.4.3 2019-03-12 [1] CRAN (R 3.6.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0)
testthat * 2.3.1 2019-12-01 [1] CRAN (R 3.6.0)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.0)
triebeard 0.3.0 2016-08-04 [1] CRAN (R 3.6.0)
urltools 1.7.3 2019-04-14 [1] CRAN (R 3.6.0)
usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.0)
vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
xfun 0.11 2019-11-12 [1] CRAN (R 3.6.0)
xml2 1.2.2 2019-08-09 [1] CRAN (R 3.6.0)
zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.0)
[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
R ── Package was removed from disk
@mfenner when you get a chance could you try out the pkg and let me know what could be better, no rush
I have installed the package successfully. When I run the function "dpla_basic" the R console declares- "could not find function "dpla_basic".
Asked question here https://groups.google.com/forum/?hl=en&fromgroups#!topic/datacite-metadata/q88TgSoy6yY
Seems it's not allowed
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