Exporting query results to bibtex #20

zackbatist · 2019-02-28T17:34:46Z

Sorry to pester you with a feature request, but it would be fantastic if there could be built-in functionality that makes it easier to generate bibtex files based on the query results. My experience using R is somewhat limited, and I'm having trouble looping through the results and the entries of those results, to generate bibtex files containing records for each entry resulting from a given query. Any help with this would be very appreciated!

muschellij2 · 2019-02-28T19:06:57Z

I'm open to accepting a pull request if you want to implement it.

If not, I will get to it maybe around 3-4 months.
Does Scopus provide Bibtex outputs? Please indicate which API https://dev.elsevier.com/sc_apis.html and which endpoint https://dev.elsevier.com/api_docs.html provide that. What query are you using that are giving you results? Maybe also look at the raw JSON

muschellij2 · 2019-02-28T19:09:35Z

Also look at https://media.readthedocs.org/pdf/scopus/latest/scopus.pdf

muschellij2 · 2019-02-28T21:05:17Z

Looked at their code and adapted. Try bibtex_core_data after installing new rscopus from github.

See example

library(rscopus)
x = abstract_retrieval("S1053811915002700", identifier = "pii",
                       verbose = FALSE)
res2 = bibtex_core_data(x)
cat(res2)
#> @article{Muschelli2015Validatedimages,
#> author = {John Muschelli and Natalie L. Ullman and W. Andrew Mould and Paul Vespa and Daniel F. Hanley and Ciprian M. Crainiceanu},
#> title = {Validated automatic brain extraction of head CT images},
#> journal = {NeuroImage},
#> year = {2015},
#> volume = {114},
#> number = {},
#> pages = {379-385},
#> doi = {10.1016/j.neuroimage.2015.03.074}}

^{Created on 2019-02-28 by the reprex package (v0.2.1)}

zackbatist · 2019-02-28T21:53:03Z

Thank you so much! Will try it out once it gets pushed to github.

muschellij2 · 2019-02-28T23:06:04Z

Pushed.

CorradoLanera · 2019-12-28T14:06:22Z

I encounter some problem here:

library(rscopus)
api_key = get_api_key(NULL, error = FALSE)
if (!is.null(api_key)){
    x = abstract_retrieval("S1053811915002700", identifier = "pii",
                           verbose = FALSE)
    res = bibtex_core_data(x)
    cat(res)
    x = abstract_retrieval("S1053811915002700", identifier = "pii",
                           verbose = FALSE)
    res2 = bibtex_core_data(x)
    cat(res2)
}
#> @article{}@article{}

^{Created on 2019-12-28 by the reprex package (v0.3.0)}

Session info

devtools::session_info()
#> - Session info ---------------------------------------------------------------
#>  setting  value                       
#>  version  R version 3.6.2 (2019-12-12)
#>  os       Windows 10 x64              
#>  system   x86_64, mingw32             
#>  ui       RTerm                       
#>  language (EN)                        
#>  collate  English_United States.1252  
#>  ctype    English_United States.1252  
#>  tz       Europe/Berlin               
#>  date     2019-12-28                  
#> 
#> - 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         3.4.0      2019-12-09 [1] CRAN (R 3.6.1)            
#>  cli           2.0.0.9000 2019-12-21 [1] Github (r-lib/cli@0293ae7)
#>  crayon        1.3.4      2017-09-16 [1] CRAN (R 3.6.0)            
#>  curl          4.3        2019-12-02 [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        0.6.23     2019-11-23 [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)            
#>  evaluate      0.14       2019-05-28 [1] CRAN (R 3.6.0)            
#>  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)            
#>  glue          1.3.1      2019-03-12 [1] CRAN (R 3.6.0)            
#>  highr         0.8        2019-03-20 [1] CRAN (R 3.6.0)            
#>  htmltools     0.4.0      2019-10-04 [1] CRAN (R 3.6.1)            
#>  httr          1.4.1      2019-08-05 [1] CRAN (R 3.6.1)            
#>  jsonlite      1.6        2018-12-07 [1] CRAN (R 3.6.0)            
#>  knitr         1.26       2019-11-12 [1] CRAN (R 3.6.1)            
#>  lifecycle     0.1.0      2019-08-01 [1] CRAN (R 3.6.1)            
#>  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)            
#>  pillar        1.4.3      2019-12-20 [1] CRAN (R 3.6.2)            
#>  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)            
#>  pkgload       1.0.2      2018-10-29 [1] CRAN (R 3.6.0)            
#>  plyr          1.8.5      2019-12-10 [1] CRAN (R 3.6.1)            
#>  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            2.4.1      2019-11-12 [1] CRAN (R 3.6.1)            
#>  Rcpp          1.0.3      2019-11-08 [1] CRAN (R 3.6.1)            
#>  remotes       2.1.0      2019-06-24 [1] CRAN (R 3.6.0)            
#>  rlang         0.4.2      2019-11-23 [1] CRAN (R 3.6.1)            
#>  rmarkdown     2.0        2019-12-12 [1] CRAN (R 3.6.1)            
#>  rprojroot     1.3-2      2018-01-03 [1] CRAN (R 3.6.0)            
#>  rscopus     * 0.6.6      2019-09-17 [1] CRAN (R 3.6.1)            
#>  sessioninfo   1.1.1      2018-11-05 [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 3.6.1)            
#>  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)            
#>  usethis       1.5.1.9000 2019-12-21 [1] local                     
#>  vctrs         0.2.1      2019-12-17 [1] CRAN (R 3.6.2)            
#>  withr         2.1.2      2018-03-15 [1] CRAN (R 3.6.0)            
#>  xfun          0.11       2019-11-12 [1] CRAN (R 3.6.1)            
#>  yaml          2.2.0      2018-07-25 [1] CRAN (R 3.6.0)            
#>  zeallot       0.1.0      2018-01-28 [1] CRAN (R 3.6.0)            
#> 
#> [1] C:/Users/corra/Documents/R/win-library/3.6
#> [2] C:/Program Files/R/R-3.6.2/library

muschellij2 · 2019-12-30T15:15:30Z

Are you sure you're on the necessary IP?

What is the output of

res = rscopus::elsevier_authenticate()
res$auth_type

If this is "GUEST", then the bibtex_core_data may not work.

muschellij2 · 2019-12-30T15:31:20Z

Try updated GitHub package:

remotes::install_github("muschellij2/rscopus")

The issue is that if you're a guest, the authors data is not there:

library(rscopus)
x = abstract_retrieval("S1053811915002700", identifier = "pii",
                       verbose = FALSE)
res2 = bibtex_core_data(x)
#> Warning in bibtex_core_data(x): Most likely not fully authenticated, see
#> rscopus::elsevier_authenticate() to make sure not GUEST
cat(res2)
#> @article{Muschelli2015Validatedimages,
#> author = {},
#> address = {Johns Hopkins Bloomberg School of Public Health; David Geffen School of Medicine at UCLA; Johns Hopkins Medical Institutions},
#> title = {Validated automatic brain extraction of head CT images},
#> journal = {NeuroImage},
#> year = {2015},
#> volume = {114},
#> number = {},
#> pages = {379-385},
#> doi = {10.1016/j.neuroimage.2015.03.074}
#> abstract = {}}

^{Created on 2019-12-30 by the reprex package (v0.3.0.9000)}

CorradoLanera · 2020-01-01T12:56:20Z

Are you sure you're on the necessary IP?

What is the output of
res = rscopus::elsevier_authenticate()
res$auth_type
If this is "GUEST", then the bibtex_core_data may not work.

No, I didn't :-). Now, everything works well!

muschellij2 closed this as completed Feb 28, 2019

claell mentioned this issue Aug 17, 2023

Add proper export (to bibtex) pybliometrics-dev/pybliometrics#295

Open

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Exporting query results to bibtex #20

Exporting query results to bibtex #20

zackbatist commented Feb 28, 2019

muschellij2 commented Feb 28, 2019

muschellij2 commented Feb 28, 2019

muschellij2 commented Feb 28, 2019

zackbatist commented Feb 28, 2019

muschellij2 commented Feb 28, 2019

CorradoLanera commented Dec 28, 2019

muschellij2 commented Dec 30, 2019

muschellij2 commented Dec 30, 2019

CorradoLanera commented Jan 1, 2020

Exporting query results to bibtex #20

Exporting query results to bibtex #20

Comments

zackbatist commented Feb 28, 2019

muschellij2 commented Feb 28, 2019

muschellij2 commented Feb 28, 2019

muschellij2 commented Feb 28, 2019

zackbatist commented Feb 28, 2019

muschellij2 commented Feb 28, 2019

CorradoLanera commented Dec 28, 2019

muschellij2 commented Dec 30, 2019

muschellij2 commented Dec 30, 2019

CorradoLanera commented Jan 1, 2020