ropensci-archive/fulltext

No results when using Crossref

santoshbs opened this issue · 4 comments

Session Info
 setting  value                       
 version  R version 4.0.2 (2020-06-22)
 os       Pop!_OS 20.10               
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language en_US:en                    
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Lyon                
 date     2021-04-28Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version  date       lib source        
 aRxiv         0.5.19   2019-08-08 [1] CRAN (R 4.0.2)
 assertthat    0.2.1    2019-03-21 [3] CRAN (R 4.0.1)
 backports     1.1.8    2020-06-17 [3] CRAN (R 4.0.2)
 blob          1.2.1    2020-01-20 [3] CRAN (R 4.0.1)
 cachem        1.0.4    2021-02-13 [1] CRAN (R 4.0.2)
 callr         3.6.0    2021-03-28 [1] CRAN (R 4.0.2)
 cli           2.4.0    2021-04-05 [1] CRAN (R 4.0.2)
 colorspace    1.4-1    2019-03-18 [3] CRAN (R 4.0.1)
 crayon        1.4.1    2021-02-08 [1] CRAN (R 4.0.2)
 crul          1.1.0    2021-02-15 [1] CRAN (R 4.0.2)
 curl          4.3      2019-12-02 [3] CRAN (R 4.0.1)
 DBI           1.1.0    2019-12-15 [3] CRAN (R 4.0.1)
 desc          1.3.0    2021-03-05 [1] CRAN (R 4.0.2)
 devtools      2.4.0    2021-04-07 [1] CRAN (R 4.0.2)
 digest        0.6.25   2020-02-23 [3] CRAN (R 4.0.1)
 dplyr         1.0.5    2021-03-05 [1] CRAN (R 4.0.2)
 DT            0.15     2020-08-05 [3] CRAN (R 4.0.2)
 ellipsis      0.3.1    2020-05-15 [3] CRAN (R 4.0.1)
 fansi         0.4.2    2021-01-15 [1] CRAN (R 4.0.2)
 fastmap       1.0.1    2019-10-08 [3] CRAN (R 4.0.1)
 fs            1.5.0    2020-07-31 [1] CRAN (R 4.0.2)
 fulltext    * 1.7.0    2021-02-13 [1] CRAN (R 4.0.2)
 generics      0.1.0    2020-10-31 [1] CRAN (R 4.0.2)
 ggplot2       3.3.2    2020-06-19 [3] CRAN (R 4.0.2)
 glue          1.4.2    2020-08-27 [1] CRAN (R 4.0.2)
 gtable        0.3.0    2019-03-25 [3] CRAN (R 4.0.1)
 hoardr        0.5.2    2018-12-02 [1] CRAN (R 4.0.2)
 htmltools     0.5.0    2020-06-16 [3] CRAN (R 4.0.2)
 htmlwidgets   1.5.1    2019-10-08 [3] CRAN (R 4.0.1)
 httpcode      0.3.0    2020-04-10 [1] CRAN (R 4.0.2)
 httpuv        1.5.4    2020-06-06 [3] CRAN (R 4.0.2)
 jsonlite      1.7.2    2020-12-09 [1] CRAN (R 4.0.2)
 later         1.1.0.1  2020-06-05 [3] CRAN (R 4.0.1)
 lifecycle     1.0.0    2021-02-15 [1] CRAN (R 4.0.2)
 lubridate     1.7.9    2020-06-08 [3] CRAN (R 4.0.1)
 magrittr      2.0.1    2020-11-17 [1] CRAN (R 4.0.2)
 memoise       2.0.0    2021-01-26 [1] CRAN (R 4.0.2)
 microdemic    0.6.0    2020-11-20 [1] CRAN (R 4.0.2)
 mime          0.10     2021-02-13 [1] CRAN (R 4.0.2)
 miniUI        0.1.1.1  2018-05-18 [3] CRAN (R 4.0.1)
 munsell       0.5.0    2018-06-12 [3] CRAN (R 4.0.1)
 pillar        1.6.0    2021-04-13 [1] CRAN (R 4.0.2)
 pkgbuild      1.2.0    2020-12-15 [1] CRAN (R 4.0.2)
 pkgconfig     2.0.3    2019-09-22 [3] CRAN (R 4.0.1)
 pkgload       1.2.1    2021-04-06 [1] CRAN (R 4.0.2)
 plyr          1.8.6    2020-03-03 [1] CRAN (R 4.0.2)
 prettyunits   1.1.1    2020-01-24 [3] CRAN (R 4.0.1)
 processx      3.5.1    2021-04-04 [1] CRAN (R 4.0.2)
 promises      1.1.0    2019-10-04 [3] CRAN (R 4.0.1)
 ps            1.6.0    2021-02-28 [1] CRAN (R 4.0.2)
 purrr         0.3.4    2020-04-17 [3] CRAN (R 4.0.1)
 R6            2.5.0    2020-10-28 [1] CRAN (R 4.0.2)
 rappdirs      0.3.3    2021-01-31 [1] CRAN (R 4.0.2)
 Rcpp          1.0.6    2021-01-15 [1] CRAN (R 4.0.2)
 rcrossref     1.1.0    2020-10-02 [1] CRAN (R 4.0.2)
 remotes       2.3.0    2021-04-01 [1] CRAN (R 4.0.2)
 rentrez       1.2.3    2020-11-10 [1] CRAN (R 4.0.2)
 reshape2      1.4.4    2020-04-09 [1] CRAN (R 4.0.2)
 rlang         0.4.10   2020-12-30 [1] CRAN (R 4.0.2)
 rplos         1.0.0    2021-02-23 [1] CRAN (R 4.0.2)
 rprojroot     1.3-2    2018-01-03 [3] CRAN (R 4.0.1)
 scales        1.1.1    2020-05-11 [3] CRAN (R 4.0.1)
 sessioninfo   1.1.1    2018-11-05 [3] CRAN (R 4.0.1)
 shiny         1.4.0.2  2020-03-13 [3] CRAN (R 4.0.1)
 solrium       1.1.4    2019-11-02 [1] CRAN (R 4.0.2)
 storr         1.2.5    2020-12-01 [1] CRAN (R 4.0.2)
 stringi       1.4.6    2020-02-17 [3] CRAN (R 4.0.2)
 stringr       1.4.0    2019-02-10 [3] CRAN (R 4.0.1)
 testthat      3.0.2    2021-02-14 [1] CRAN (R 4.0.2)
 tibble        3.1.1    2021-04-18 [1] CRAN (R 4.0.2)
 tidyselect    1.1.0    2020-05-11 [3] CRAN (R 4.0.1)
 triebeard     0.3.0    2016-08-04 [1] CRAN (R 4.0.2)
 urltools      1.7.3    2019-04-14 [1] CRAN (R 4.0.2)
 usethis       2.0.1    2021-02-10 [1] CRAN (R 4.0.2)
 utf8          1.2.1    2021-03-12 [1] CRAN (R 4.0.2)
 vctrs         0.3.7    2021-03-29 [1] CRAN (R 4.0.2)
 whisker       0.4      2019-08-28 [3] CRAN (R 4.0.1)
 withr         2.4.2    2021-04-18 [1] CRAN (R 4.0.2)
 XML           3.99-0.5 2020-07-23 [3] CRAN (R 4.0.2)
 xml2          1.3.2    2020-04-23 [3] CRAN (R 4.0.1)
 xtable        1.8-4    2019-04-21 [3] CRAN (R 4.0.1)

[1] /home/user1/R/x86_64-pc-linux-gnu-library/4.0
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library

When I execute this code, I get the message below. Nothing happens even after many minutes:

library(fulltext)
Sys.setenv(CROSSREF_EMAIL= 'myemail@gmail.com')
(res= ft_search(query= 'biology', 
                from = 'crossref', 
                limit= 25,
                verbose= TRUE,
                crossrefopts = list(filter = c(has_abstract = TRUE))))


*   Trying 208.254.38.72:443...
* TCP_NODELAY set
* Connected to api.crossref.org (208.254.38.72) port 443 (#1)
* ALPN, offering h2
* ALPN, offering http/1.1
* successfully set certificate verify locations:
*   CAfile: /etc/ssl/certs/ca-certificates.crt
  CApath: /etc/ssl/certs
* SSL connection using TLSv1.3 / TLS_AES_256_GCM_SHA384
* ALPN, server did not agree to a protocol
* Server certificate:
*  subject: CN=*.crossref.org
*  start date: Mar 13 00:00:00 2020 GMT
*  expire date: May 16 12:00:00 2022 GMT
*  subjectAltName: host "api.crossref.org" matched cert's "*.crossref.org"
*  issuer: C=US; O=DigiCert Inc; OU=www.digicert.com; CN=GeoTrust RSA CA 2018
*  SSL certificate verify ok.
> GET /works?query=biology&filter=has-license%3Atrue%2Chas-abstract%3Atrue&offset=0&rows=25 HTTP/1.1
Host: api.crossref.org
Accept-Encoding: gzip, deflate
Accept: application/json, text/xml, application/xml, */*
User-Agent: r-curl/4.3 crul/1.1.0 rOpenSci(rcrossref/1.1.0)
X-USER-AGENT: r-curl/4.3 crul/1.1.0 rOpenSci(rcrossref/1.1.0)

* old SSL session ID is stale, removing

I get the same problem, the request just hangs for a long time

I think it's the has-abstract filter that's the problem. Will have a look

@santoshbs they said it should get faster soon, in a few weeks https://gitlab.com/crossref/issues/-/issues/1254#note_590494898

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