Can't retreive all records using epmc_search --- Error in if (page_token == out$next_cursor) break : argument is zero length
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Hello,
First of all thanks for your package.
I think there are an error when the function epmc_search try to retrieve all records. For example the next query has 39 results and when I try to get back all of then the functions fails:
`epmc_search(query ="AUTHORID:0000-0003-1393-215X")
39 records found, returning 39
Error in if (page_token == out$next_cursor) break :
argument is zero length`
But If I set a limit lesst than the number of records the functions works:
`epmc_search(query ="AUTHORID:0000-0003-1393-215X", limit=1)
39 records found, returning 1
# A tibble: 1 × 27
id source pmid pmcid doi title authorString journalTitle issue journalVolume pubYear journalIssn pubType isOpenAccess inEPMC inPMC hasPDF hasBook hasSuppl
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 34207908 MED 34207908 PMC8… 10.3… Smar… Merazzo KJ,… Diagnostics… 6 11 2021 2075-4418 review… Y Y N Y N N
# … with 8 more variables: citedByCount <int>, hasReferences <chr>, hasTextMinedTerms <chr>, hasDbCrossReferences <chr>, hasLabsLinks <chr>,
# hasTMAccessionNumbers <chr>, firstIndexDate <chr>, firstPublicationDate <chr>`
This is my sessionInfo:
` sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8
[7] LC_PAPER=es_ES.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] europepmc_0.4 RMariaDB_1.1.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 rstudioapi_0.13 xml2_1.3.2 magrittr_2.0.1 progress_1.2.2 hms_1.1.0 tidyselect_1.1.1 bit_4.0.4 R6_2.5.1
[10] rlang_0.4.11 fansi_0.5.0 plyr_1.8.6 httr_1.4.2 dplyr_1.0.7 tools_4.1.1 utf8_1.2.2 cli_3.0.1 DBI_1.1.1
[19] ellipsis_0.3.2 bit64_4.0.5 assertthat_0.2.1 tibble_3.1.4 lifecycle_1.0.0 crayon_1.4.1 tidyr_1.1.3 purrr_0.3.4 vctrs_0.3.8
[28] curl_4.3.2 triebeard_0.3.0 glue_1.4.2 compiler_4.1.1 pillar_1.6.2 urltools_1.7.3 prettyunits_1.1.1 generics_0.1.0 jsonlite_1.7.2
[37] pkgconfig_2.0.3 `
Tell me if I can do something to help. =)
Hi @jcbailone thank you for your report. There has been an API change recently, which is implemented in the dev version on GitHub. Please update the {europepmc} package:
remotes::install_github("ropensci/europepmc")
I'll submit this version to CRAN soon.
Here's a reprex using your example with the current dev version on GitHub:
library(europepmc)
packageVersion("europepmc")
#> [1] '0.4.1'
epmc_search(query ="AUTHORID:0000-0003-1393-215X")
#> 39 records found, returning 39
#> # A tibble: 39 × 28
#> id source pmid pmcid doi title authorString journalTitle issue
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 34207908 MED 34207908 PMC82… 10.3… Smart… Merazzo KJ, … Diagnostics… 6
#> 2 33427446 MED 33427446 <NA> 10.1… Detec… Sánchez-Cano… ACS Sens 1
#> 3 29498271 MED 29498271 <NA> 10.1… NaNO<… López-Marzo … Anal Chem 6
#> 4 26155767 MED 26155767 <NA> 10.1… Rever… Herrasti Z, … Lab Chip 16
#> 5 24994664 MED 24994664 <NA> 10.1… Carbo… Herrasti Z, … Anal Bioana… 22
#> 6 31817657 MED 31817657 PMC69… 10.3… Compe… Montes-Cebri… Sensors (Ba… 24
#> 7 29254566 MED 29254566 <NA> 10.1… Using… Ben Ismail M… Anal Chim A… <NA>
#> 8 23601924 MED 23601924 PMC36… 10.1… Fast … Bedrina B, M… BMC Microbi… <NA>
#> 9 24482799 MED 24482799 <NA> 10.1… Elect… Herrasti Z, … Analyst 6
#> 10 26592620 MED 26592620 <NA> 10.1… Minia… Uria N, Abra… Talanta <NA>
#> # … with 29 more rows, and 19 more variables: journalVolume <chr>,
#> # pubYear <chr>, journalIssn <chr>, pubType <chr>, isOpenAccess <chr>,
#> # inEPMC <chr>, inPMC <chr>, hasPDF <chr>, hasBook <chr>, hasSuppl <chr>,
#> # citedByCount <int>, hasReferences <chr>, hasTextMinedTerms <chr>,
#> # hasDbCrossReferences <chr>, hasLabsLinks <chr>,
#> # hasTMAccessionNumbers <chr>, firstIndexDate <chr>,
#> # firstPublicationDate <chr>, pageInfo <chr>
Created on 2021-09-01 by the reprex package (v2.0.0)
Thank you for answering so quickly, now is working fine!!