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Wrapper to DataCite metadata

Home Page: https://docs.ropensci.org/rdatacite

License: Other

R 97.75% Makefile 2.25%

datacite oai-pmh metadata api-wrapper rstats r solr identifier r-package

rdatacite's People

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Watchers

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shivam11 katrinleinweber ptagliolato

rdatacite's Issues

Feedback

@mfenner when you get a chance could you try out the pkg and let me know what could be better, no rush

Highligthing in Solr API

Asked question here https://groups.google.com/forum/?hl=en&fromgroups#!topic/datacite-metadata/q88TgSoy6yY

Seems it's not allowed

Maintenance status / help needed?

@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?

cran checks errors

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

Stats API

http://stats.datacite.org/

dpla_basic

dpla_basic error

I have installed the package successfully. When I run the function "dpla_basic" the R console declares- "could not find function "dpla_basic".

use publisher_facet for faceting

In your example for facets I would use publisher_facet instead of publisher. This avoids breaking up publisher names into single words.

new method for citation.crosscite.org

https://citation.crosscite.org/

Add datacite REST API methods

https://api.labs.datacite.org/ or https://api.datacite.org/ later perhaps

Is language as a filter, usable in dc_works() ?

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=

Register pkg with Zenodo

dc_search for relatedIdentifier possible?

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

- 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

Refractor to use DataCite REST API

The endpoint "https://search.datacite.org/api" is going to be deprecated in early 2019.

rdatacite/R/dc_search.R

Line 9 in c525d6d

#' url <- "https://search.datacite.org/api"

rdatacite should be using any of the other api.datacite.org endpoints. https://support.datacite.org/v1.2/reference

Pkg vignette using martins content

from https://github.com/datacite/metadata-reports

@mfenner

rows = 10000 should not convert to 1e+5

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!

Switch over to using new solrium interface

Error on `dc_oai_listsets()`

Error in result$children <- chunks : object 'result' not found

Error in readBin: How to find problematic metdataset at source?

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:

bisecting via the rows parameter combined with a given order,
skipping the problematic row and downloading a few more with offset = row+1
looking at the gap in date or DOI and trying to find the missing item on GBIF.org?

Session Info

─ 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

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

Add datacite doi resolver functionality?

http://data.datacite.org/static/index.html

cran email: undeclared package dependencies

$rdatacite
'library' or 'require' call not declared from: ‘httr’