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:warning: ARCHIVED :warning: R interface to the Biodiversity Heritage Library (BHL) API

License: Other

Makefile 2.28% R 97.72%

web-api biodiversity-heritage-library data metadata api-wrapper r rstats r-package

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stevenysw nsm120 firefoxxy8 25280841

rbhl's Issues

Make it easy to get multiple pages of ocr text at one

E.g., using bhl_getpageocrtext, bhl_getpagemetadata and any others

They currently only allow one page at a time. STeps

Get page of the book
Iterate across pages to get all ocr for the book

Redo parameters, some missing in some fxns

API key

The README is wrong, the key has to be named bhl_key.
Could it become possible to put it as environment variable in .Renviron instead?

Remove pageid and names args from bhl_getpageocrtext

Somehow these args got into the fxn, but they aren't available in this method.

Remove them

Vignette missing title

See https://docs.ropensci.org/rbhl/articles/

this package needs an overhaul

redo stuff in httr instead of RCurl
move url out of arg params
get another api key for the package
maybe don't print the api call since the key is in the call, or just print the call without the key

importfrom any non-base R functions

move to markdown docs and tidy line width

Error message: SSL certificate expired

When trying to conduct searches using the rbhl package, I'm getting the following error message:
Error in curl::curl_fetch_memory(x$url$url, handle = x$url$handle) :
SSL certificate problem: certificate has expired

I've set my API key in .Renviron. This error message came up after using bhl_namesearch(). Is this a problem on my end? Thanks!

Session Info

─ Session info ────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.0 (2020-04-24)
 os       macOS Mojave 10.14.6        
 system   x86_64, darwin17.0          
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/New_York            
 date     2020-06-02                  

─ Packages ────────────────────────────────────────────────────────────────────────
 package     * version date       lib source        
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.0.0)
 backports     1.1.6   2020-04-05 [1] CRAN (R 4.0.0)
 callr         3.4.3   2020-03-28 [1] CRAN (R 4.0.0)
 cli           2.0.2   2020-02-28 [1] CRAN (R 4.0.0)
 colorspace    1.4-1   2019-03-18 [1] CRAN (R 4.0.0)
 crayon        1.3.4   2017-09-16 [1] CRAN (R 4.0.0)
 crul          0.9.0   2019-11-06 [1] CRAN (R 4.0.0)
 curl        * 4.3     2019-12-02 [1] CRAN (R 4.0.0)
 desc          1.2.0   2018-05-01 [1] CRAN (R 4.0.0)
 devtools      2.3.0   2020-04-10 [1] CRAN (R 4.0.0)
 digest        0.6.25  2020-02-23 [1] CRAN (R 4.0.0)
 dplyr         0.8.5   2020-03-07 [1] CRAN (R 4.0.0)
 ellipsis      0.3.0   2019-09-20 [1] CRAN (R 4.0.0)
 fansi         0.4.1   2020-01-08 [1] CRAN (R 4.0.0)
 fs            1.4.1   2020-04-04 [1] CRAN (R 4.0.0)
 ggplot2       3.3.0   2020-03-05 [1] CRAN (R 4.0.0)
 glue          1.4.1   2020-05-13 [1] CRAN (R 4.0.0)
 gtable        0.3.0   2019-03-25 [1] CRAN (R 4.0.0)
 httpcode      0.3.0   2020-04-10 [1] CRAN (R 4.0.0)
 jsonlite      1.6.1   2020-02-02 [1] CRAN (R 4.0.0)
 lattice       0.20-41 2020-04-02 [1] CRAN (R 4.0.0)
 lifecycle     0.2.0   2020-03-06 [1] CRAN (R 4.0.0)
 magrittr      1.5     2014-11-22 [1] CRAN (R 4.0.0)
 Matrix        1.2-18  2019-11-27 [1] CRAN (R 4.0.0)
 memoise       1.1.0   2017-04-21 [1] CRAN (R 4.0.0)
 munsell       0.5.0   2018-06-12 [1] CRAN (R 4.0.0)
 pillar        1.4.4   2020-05-05 [1] CRAN (R 4.0.0)
 pkgbuild      1.0.8   2020-05-07 [1] CRAN (R 4.0.0)
 pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.0.0)
 pkgload       1.0.2   2018-10-29 [1] CRAN (R 4.0.0)
 prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.0.0)
 processx      3.4.2   2020-02-09 [1] CRAN (R 4.0.0)
 ps            1.3.3   2020-05-08 [1] CRAN (R 4.0.0)
 purrr         0.3.4   2020-04-17 [1] CRAN (R 4.0.0)
 R6            2.4.1   2019-11-12 [1] CRAN (R 4.0.0)
 rbhl        * 0.9.0   2020-01-29 [1] CRAN (R 4.0.0)
 Rcpp          1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
 remotes       2.1.1   2020-02-15 [1] CRAN (R 4.0.0)
 rlang         0.4.6   2020-05-02 [1] CRAN (R 4.0.0)
 rprojroot     1.3-2   2018-01-03 [1] CRAN (R 4.0.0)
 rstudioapi    0.11    2020-02-07 [1] CRAN (R 4.0.0)
 scales        1.1.1   2020-05-11 [1] CRAN (R 4.0.0)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 4.0.0)
 testthat      2.3.2   2020-03-02 [1] CRAN (R 4.0.0)
 tibble        3.0.1   2020-04-20 [1] CRAN (R 4.0.0)
 tidyselect    1.1.0   2020-05-11 [1] CRAN (R 4.0.0)
 triebeard     0.3.0   2016-08-04 [1] CRAN (R 4.0.0)
 urltools      1.7.3   2019-04-14 [1] CRAN (R 4.0.0)
 usethis       1.6.1   2020-04-29 [1] CRAN (R 4.0.0)
 vctrs         0.3.0   2020-05-11 [1] CRAN (R 4.0.0)
 withr         2.2.0   2020-04-20 [1] CRAN (R 4.0.0)
 xml2          1.3.2   2020-04-23 [1] CRAN (R 4.0.0)

[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

new api version out, probably will need to rework pkg api

https://www.biodiversitylibrary.org/docs/api3.html

Finish off test suite

Some tests implemented, not all done yet.

Expand documentation in README to explain what BHL data contains

An opening exercise for our intern, Katie.

Reminder from Kurt Hornik to fix readme

on 2015-01-30

/data/Repositories/CRAN/web/packages/rbhl/README.html:
  Valid: FALSE (errors: 1, warnings: 0)
  Errors:
    line  col  message
     196   98  required attribute "alt" not specified

readme fixes

These packages contain README.md files with invalid HTML output created
by pandoc 1.12.4.2 according to W3C-validator.

I attach the HTML errors and warnings found below, and will put copies
of the corresponding HTML files up at
http://www.r-project.org/nosvn/pandoc.

Please investigate the problems and fix as needed.

Afaics, many of the problems are caused by adding "raw" HTML elements in
the README.md files and not realizing that the default output format
"html" is XHTML 1 (and not HTML 5). E.g., a raw
results in an

end tag for "br" omitted, but OMITTAG NO was specified

error.

Best
-k

rbhl.html:
  Valid: FALSE (errors: 1, warnings: 0)
  Errors:
    line  col  message
     195   98  required attribute "alt" not specified

These have README.md files which when converted to (X)HTML using a
current version of pandoc show problems when validated using W3C Markup
Validator, see below.

Most of these problems are caused by using images without giving a name
(so the required alt attribute for <img> is not provided), or using <br>
instead of <br/>.

Pls fix these problems in your README.md files for your next release: in
all cases I inspected, the fixes were obvious and confirmation using
pandoc and W3C markup validator seemed unnecessary.

Please also visit your package check web page at http://cran.r-project.org/web/checks/check_results_PACKAGENAME.html to see if other problems need to be addressed as well.