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convert among citation formats

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

License: Other

Makefile 0.71% R 99.29%

citations doi digital-object-identifier metadata bibtex citeproc crosscite ris r r-package

handlr's Introduction

handlr

a tool for converting among citation formats.

heavily influenced by, and code ported from the Ruby gem bolognese

supported readers:

citeproc
ris
bibtex
codemeta
cff

supported writers:

citeproc
ris
bibtex
schemaorg
rdfxml
codemeta
cff

not supported yet, but plan to:

crosscite

Installation

stable version

install.packages("handlr")

dev version

remotes::install_github("ropensci/handlr")

library("handlr")

handlr's People

Contributors

Stargazers

Watchers

Forkers

kevcaz webteg aden2018 thierryo

handlr's Issues

fix author parsing in author_utils.R

basic parsing exists, but need to port remainder of logic

a feature request - make it possible to convert a handlr object to a data frame

I'd like to request a function to convert a handl object into a data frame. There are times when I'd would like to be able to scan through a large set of references. Or pull out a column like the DOIs. Thanks for considering this!

text format citations?

Seems like we don't support these yet. .e.g,

Arnaud, E., Castañeda-Álvarez, N. P., Cossi, J. G., Endresen, D. T. F., Jahanshiri, E., & Vigouroux, Y. (2016). Final Report of the Task Group on GBIF Data Fitness for Use in Agrobiodiversity. https://www.duo.uio.no/handle/10852/50041

woopsy: forgot to export print.handl

Give many more details on the `handl` internal object

move jsonld to suggests

HandlrClient$write(): run read() if not done yet

Would make write much nicer experience

change maintainer on cran

@bwiernik @ThierryO when you get a chance, could you submit a new version to cran changing the maintainer to whoever the new maintainer is? not urgent, but any correspondence from cran will go to me right now, so it'd be good to have it go to you instead. thanks!

make sure internal fxn `parse_attributes` is working

Change to new cran checks badge URL

👋🏽 I maintain the cran checks badges. Please change to the new cran checks badge URL (e.g., https://badges.cranchecks.info/worst/dplyr.svg). Old badges at (e.g. https://cranchecks.info/badges/worst/dplyr) will be unavailable as of Jan 1st 2023.

Blog post announcing the change: https://recology.info/2022/06/cran-checks-badges/
New badges repo: https://github.com/r-hub/cchecksbadges
Old badges repo: https://github.com/sckott/cchecksapi

fix: when reading from string/json some functions give file attribute as that string

z <- system.file('extdata/citeproc.json', package = "handlr")
x <- codemeta_writer(citeproc_reader(z))
out <- codemeta_reader(x)
attr(out, "file")

{
  "@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
  "@type": "BlogPosting",
  "@id": "https://doi.org/10.5438/4k3m-nyvg",
  "identifier": "https://doi.org/10.5438/4k3m-nyvg",
  "title": "Eating your own Dog Food",
  "agents": [
    {
      "@type": "Person",
      "name": "Martin Fenner",
      "givenName": "Martin",
      "familyName": "Fenner"
    }
  ],
  "description": "Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...",
  "tags": ["Phylogeny", "Malaria", "Parasites", "Taxonomy", "Mitochondrial genome", "Africa", "Plasmodium"],
  "datePublished": "2016-12-20",
  "publisher": "DataCite"
}

Support the Citation File Format

The Citation File Format is a human- and machine-readable and -writable format implemented in YAML to provide citation-relevant metadata for software. It has been conceived to make it possible for developers to provide the correct citation metadata for their software, and for users to gain access to the relevant information quickly. Its implementation takes into account the Software Citation Principles through requiring the necessary minimal information where feasible.

It would be great if handlr supported this format as well, most importantly as source, perhaps also as target format.

I'll be happy to put some work into this, but as I'm an R newbie may need some help.

If this is something that the project finds useful, I'd start with looking at the available readers and try my hand at implementing a reader for CFF. This could possibly be done as part of the CollabW19 hack day.

Please let me know your thoughts on this.

GitHub version help files fail

With the GitHub version of handlr installed none of the help files are available. They all have the following error message
Error in fetch(key) : lazy-load database '/Users/gcn/Library/R/3.5/library/handlr/help/handlr.rdb' is corrupt

Session Info

devtools::session_info()
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.5.2 (2018-12-20)
 os       macOS Mojave 10.14.3        
 system   x86_64, darwin15.6.0        
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/Denver              
 date     2019-03-10                  

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version    date       lib source                              
 assertthat    0.2.0      2017-04-11 [2] CRAN (R 3.5.0)                      
 backports     1.1.3      2018-12-14 [2] CRAN (R 3.5.0)                      
 bibtex      * 0.4.2      2017-06-30 [1] CRAN (R 3.5.0)                      
 callr         3.1.1      2018-12-21 [2] CRAN (R 3.5.0)                      
 cli           1.0.1      2018-09-25 [2] CRAN (R 3.5.0)                      
 crayon        1.3.4      2017-09-16 [2] CRAN (R 3.5.0)                      
 crul          0.7.0      2019-01-04 [1] CRAN (R 3.5.2)                      
 curl          3.3        2019-01-10 [2] CRAN (R 3.5.2)                      
 data.table  * 1.12.0     2019-01-13 [2] CRAN (R 3.5.2)                      
 desc          1.2.0      2018-05-01 [2] CRAN (R 3.5.0)                      
 devtools    * 2.0.1      2018-10-26 [2] CRAN (R 3.5.1)                      
 digest        0.6.18     2018-10-10 [2] CRAN (R 3.5.0)                      
 fs            1.2.6      2018-08-23 [2] CRAN (R 3.5.0)                      
 glue          1.3.0      2018-07-17 [2] CRAN (R 3.5.0)                      
 handlr      * 0.1.0.9110 2019-03-10 [1] Github (ropensci/handlr@33bb39d)    
 hms           0.4.2      2018-03-10 [2] CRAN (R 3.5.0)                      
 httpcode      0.2.0      2016-11-14 [1] CRAN (R 3.5.0)                      
 httr          1.4.0      2018-12-11 [2] CRAN (R 3.5.0)                      
 jsonlite      1.6        2018-12-07 [2] CRAN (R 3.5.0)                      
 lubridate     1.7.4      2018-04-11 [1] CRAN (R 3.5.0)                      
 magrittr      1.5        2014-11-22 [2] CRAN (R 3.5.0)                      
 memoise       1.1.0      2017-04-21 [2] CRAN (R 3.5.0)                      
 mime          0.6        2018-10-05 [2] CRAN (R 3.5.1)                      
 packrat       0.5.0      2018-11-14 [2] CRAN (R 3.5.0)                      
 pillar        1.3.1      2018-12-15 [2] CRAN (R 3.5.0)                      
 pkgbuild      1.0.2      2018-10-16 [2] CRAN (R 3.5.1)                      
 pkgconfig     2.0.2      2018-08-16 [2] CRAN (R 3.5.1)                      
 pkgload       1.0.2      2018-10-29 [2] CRAN (R 3.5.1)                      
 plyr          1.8.4      2016-06-08 [2] CRAN (R 3.5.0)                      
 prettyunits   1.0.2      2015-07-13 [2] CRAN (R 3.5.0)                      
 processx      3.2.1      2018-12-05 [2] CRAN (R 3.5.0)                      
 ps            1.3.0      2018-12-21 [2] CRAN (R 3.5.0)                      
 R6            2.4.0      2019-02-14 [2] CRAN (R 3.5.2)                      
 Rcpp          1.0.0      2018-11-07 [2] CRAN (R 3.5.1)                      
 readr       * 1.3.1      2018-12-21 [2] CRAN (R 3.5.0)                      
 RefManageR  * 1.2.8      2019-03-02 [1] Github (ropensci/RefManageR@a1c9d05)
 remotes       2.0.2      2018-10-30 [2] CRAN (R 3.5.1)                      
 rlang         0.3.1      2019-01-08 [2] CRAN (R 3.5.2)                      
 rprojroot     1.3-2      2018-01-03 [2] CRAN (R 3.5.0)                      
 rstudioapi    0.9.0      2019-01-09 [2] CRAN (R 3.5.2)                      
 sessioninfo   1.1.1      2018-11-05 [2] CRAN (R 3.5.1)                      
 stringi       1.3.1      2019-02-13 [2] CRAN (R 3.5.2)                      
 stringr       1.4.0      2019-02-10 [2] CRAN (R 3.5.2)                      
 testthat      2.0.1      2018-10-13 [2] CRAN (R 3.5.1)                      
 tibble        2.0.1      2019-01-12 [2] CRAN (R 3.5.2)                      
 triebeard     0.3.0      2016-08-04 [2] CRAN (R 3.5.0)                      
 urltools      1.7.2      2019-02-04 [2] CRAN (R 3.5.2)                      
 usethis     * 1.4.0      2018-08-14 [2] CRAN (R 3.5.0)                      
 withr         2.1.2      2018-03-15 [2] CRAN (R 3.5.0)                      
 xml2          1.2.0      2018-01-24 [2] CRAN (R 3.5.0)                      

[1] /Users/gcn/Library/R/3.5/library
[2] /Library/Frameworks/R.framework/Versions/3.5/Resources/library

change internal data model to use "dates" as bolognese does

datacite/bolognese@8f31db8

Add Brenton M. Wiernik as maintainer to DESCRIPTION

@bwiernik could you please add yourself as maintainer to DESCRIPTION? Thanks for your work on this package!

drop RefManageR

read from all of: url, file, string (and DOI?)

i think bolognese does read from a DOI, maybe just a DOI as a URL though?

failure to read ris file

Dear authors
thanks for the useful package and I have the following error reporting:

> Embase <- ris_reader(
+   "/Users/zhangzhongheng/Downloads/records.ris"
+ )
Error: 'x' is not likely RIS format

this records.ris is exported from Embase; and I have tried several times by different number of citations, it reports the same error.

Wrong author field

According to https://codemeta.github.io/terms/ there is no agents term. It should be author.

handlr/R/codemeta_reader.R

Line 33 in e019b85

author <- from_schema_org(meta$agents %||% NULL)

Data loss on citeproc import

cp_txt <- '[  {"id":"JolySilencetablemanners2008","accessed":{"date-parts":[[2019,10,27]]},"author":[{"family":"Joly","given":"Janneke F."},{"family":"Stapel","given":"Diederik A."},{"family":"Lindenberg","given":"Siegwart M."}],"container-title":"Personality and Social Psychology Bulletin","container-title-short":"Pers. Soc. Psychol. Bull.","DOI":"10.1177/0146167208318401","ISSN":"0146-1672, 1552-7433","issue":"8","issued":{"date-parts":[[2008,8]]},"language":"en","page":"1047-1056","references":"Retraction published 2012, <i>Personality and Social Psychology Bulletin, 38</i>[10], 1378, https://doi.org/10.1177/0146167212462821","source":"Crossref","title":"Silence and table manners: when environments activate norms","title-short":"Silence and table manners","type":"article-journal","URL":"http://journals.sagepub.com/doi/10.1177/0146167208318401","volume":"34"}]'
cp_parsed <- citeproc_reader(cp_txt)
names(cp_parsed)

When reading the Citeproc/CSL JSON format, handlr currently discards any valid CSL variables that are not part of its internal Crosscite format. This seems quite suboptimal, because it means that handlr can really only properly work with Citeproc data for a small number of item types (pretty much just article-journal and webpage). For example, the genre and medium variables that are used to indicate the category for a report or thesis are discarded. The variable editor is used for books and book chapters. In the example data I provide above, the variable references is discarded.

If I were to generate a reference for this item using the American Psychological Association CSL style, it would be:
Joly, J. F., Stapel, D. A., & Lindenberg, S. M. (2008). Silence and table manners: When environments activate norms. Personality and Social Psychology Bulletin, 34(8), 1047–1056. https://doi.org/10.1177/0146167208318401 (Retraction published 2012, Personality and Social Psychology Bulletin, 38[10], 1378, https://doi.org/10.1177/0146167212462821)

However, if I import the item to handlr, export to CSL JSON again, and render the citation, it's:
Joly, J. F., Stapel, D. A., & Lindenberg, S. M. (2008). Silence and table manners: When environments activate norms. Personality and Social Psychology Bulletin, 34(8), 1047–1056. https://doi.org/10.1177/0146167208318401

The retraction information has been lost.

Other variables, such as annote, , genre, note, medium, collection-title, number, and illustrator are also all discarded on import
For item types and fields that don't have a Crosscite analogue, it seems like it would be wise to store these in the item data (e.g., as csl_note, csl_medium) and map them to other formats at translation time as needed.

make sure each reader and writer works singular and plural

name participles dropped when reading from cff

See https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md#definitionspersonname-particle

authors:
  - family-names: Humboldt
    given-names: Alexander
    name-particle: von

will result in

[[1]]
[[1]]$type
[1] "Person"

[[1]]$name
[1] "Alexander Humboldt"

[[1]]$givenName
[1] "Alexander"

[[1]]$familyName
[1] "Humboldt"

instead of "Alexander von Humboldt".

Particularly problematic when working with Dutch names ;)

sanitize function

port over

large buffer overflows in bib

x <- handlr::HandlrClient$new(x = '~/Desktop/mrg.bib')
x$read("bibtex")
#> Error in do_read_bib(file, encoding = .Encoding, srcfile): lex fatal error:
#> input buffer overflow, can't enlarge buffer because scanner uses REJECT

Session Info

Session info --------------------------------------------------------------
 setting  value                       
 version  R version 3.5.1 (2018-07-02)
 system   x86_64, darwin15.6.0        
 ui       RStudio (1.2.1162)          
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/New_York            
 date     2018-12-18                  

Packages ------------------------------------------------------------------
 package    * version    date       source                          
 base       * 3.5.1      2018-07-05 local                           
 bibtex       0.4.2      2017-06-30 CRAN (R 3.5.0)                  
 compiler     3.5.1      2018-07-05 local                           
 crul         0.6.0      2018-07-10 CRAN (R 3.5.0)                  
 curl         3.2        2018-03-28 CRAN (R 3.5.0)                  
 datasets   * 3.5.1      2018-07-05 local                           
 devtools     1.13.6     2018-06-27 CRAN (R 3.5.0)                  
 digest       0.6.18     2018-10-10 CRAN (R 3.5.0)                  
 graphics   * 3.5.1      2018-07-05 local                           
 grDevices  * 3.5.1      2018-07-05 local                           
 handlr     * 0.0.4.9210 2018-12-19 Github (ropensci/handlr@0252efc)
 httpcode     0.2.0      2016-11-14 CRAN (R 3.5.0)                  
 httr         1.4.0      2018-12-11 CRAN (R 3.5.0)                  
 jsonlite     1.6        2018-12-07 CRAN (R 3.5.0)                  
 lubridate    1.7.4      2018-04-11 CRAN (R 3.5.0)                  
 magrittr     1.5        2014-11-22 CRAN (R 3.5.0)                  
 memoise      1.1.0      2017-04-21 CRAN (R 3.5.0)                  
 methods    * 3.5.1      2018-07-05 local                           
 packrat      0.4.9-3    2018-06-01 CRAN (R 3.5.0)                  
 plyr         1.8.4      2016-06-08 CRAN (R 3.5.0)                  
 R6           2.3.0      2018-10-04 CRAN (R 3.5.0)                  
 Rcpp         1.0.0      2018-11-07 CRAN (R 3.5.0)                  
 RefManageR   1.2.0      2018-04-25 CRAN (R 3.5.0)                  
 stats      * 3.5.1      2018-07-05 local                           
 stringi      1.2.4      2018-07-20 CRAN (R 3.5.0)                  
 stringr      1.3.1      2018-05-10 CRAN (R 3.5.0)                  
 tools        3.5.1      2018-07-05 local                           
 triebeard    0.3.0      2016-08-04 CRAN (R 3.5.0)                  
 urltools     1.7.1      2018-08-03 CRAN (R 3.5.0)                  
 utils      * 3.5.1      2018-07-05 local                           
 withr        2.1.2      2018-03-15 CRAN (R 3.5.0)                  
 xml2         1.2.0      2018-01-24 CRAN (R 3.5.0)

Support for CFF v1.2.0

Session Info

R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252    LC_MONETARY=Spanish_Spain.1252
[4] LC_NUMERIC=C                   LC_TIME=Spanish_Spain.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] handlr_0.3.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7        pillar_1.6.2      compiler_4.1.0    prettyunits_1.1.1 remotes_2.4.0    
 [6] tools_4.1.0       testthat_3.0.4    digest_0.6.27     pkgbuild_1.2.0    pkgload_1.2.1    
[11] tibble_3.1.4      lifecycle_1.0.0   jsonlite_1.7.2    evaluate_0.14     memoise_2.0.0    
[16] pkgconfig_2.0.3   rlang_0.4.11      rstudioapi_0.13   cli_3.0.1         crul_1.1.0       
[21] curl_4.3.2        yaml_2.2.1        xfun_0.25         fastmap_1.1.0     withr_2.4.2      
[26] xml2_1.3.2        knitr_1.33        vctrs_0.3.8       desc_1.3.0        fs_1.5.0         
[31] devtools_2.4.2    triebeard_0.3.0   rprojroot_2.0.2   glue_1.4.2        httpcode_0.3.0   
[36] R6_2.5.1          processx_3.5.2    fansi_0.5.0       rmarkdown_2.10    sessioninfo_1.1.1
[41] purrr_0.3.4       callr_3.7.0       magrittr_2.0.1    urltools_1.7.3    ps_1.6.0         
[46] ellipsis_0.3.2    htmltools_0.5.2   usethis_2.0.1     mime_0.11         utf8_1.2.2       
[51] cachem_1.0.6      crayon_1.4.1

Hi:

There is a new version of CFF (released on 31 May 2021) with some important changes (see changelog)

Among other changes, CFF v1.2.0 does not require some fields:

version, date-released no longer required elements of a minimal CFF

This is causing an error when trying to convert CFF v1.2.0 to another format, see a minimal example:

``` r
#devtools::install_github("dieghernan/cffr")

library(cffr)

# Minimal cff structure as per v1.2.0

minimal <- cff()

minimal
#> authors:
#> - family-names: Druskat
#>   given-names: Stephan
#> cff-version: 1.2.0
#> message: If you use this software, please cite it using these metadata.
#> title: My Research Software

# Validate against the official schema.json v1.2.0 with {jsonvalidate}
# https://github.com/citation-file-format/citation-file-format/blob/main/schema.json

cff_validate(minimal)
#> 
#> cff_validate results-----
#> Congratulations! This cff object is valid

# Try to parse with handlr

library(handlr)
#> Warning: package 'handlr' was built under R version 4.1.1
library(yaml)

tohandlr <- cff_reader(as.yaml(minimal))
#> Error: 'date-released' is required

# Fix by forcing required arguments only in v1.1.0
# Force version and date-released
fix <- minimal
fix$`date-released` <- "2010-01-01"
fix$version <- "beta"

cff_validate(fix)
#> 
#> cff_validate results-----
#> Congratulations! This cff object is valid

tohandlr <- cff_reader(as.yaml(fix))
unclass(tohandlr)
#> $cff_version
#> [1] "1.2.0"
#> 
#> $message
#> [1] "If you use this software, please cite it using these metadata."
#> 
#> $id
#> NULL
#> 
#> $type
#> [1] "SoftwareSourceCode"
#> 
#> $citeproc_type
#> [1] "article-journal"
#> 
#> $bibtex_type
#> [1] "misc"
#> 
#> $ris_type
#> [1] "COMP"
#> 
#> $resource_type_general
#> [1] "Software"
#> 
#> $identifier
#> NULL
#> 
#> $doi
#> NULL
#> 
#> $b_url
#> NULL
#> 
#> $title
#> [1] "My Research Software"
#> 
#> $author
#> $author[[1]]
#> $author[[1]]$type
#> [1] "Person"
#> 
#> $author[[1]]$name
#> [1] "Stephan Druskat"
#> 
#> $author[[1]]$givenName
#> [1] "Stephan"
#> 
#> $author[[1]]$familyName
#> [1] "Druskat"
#> 
#> $author[[1]]$orcid
#> [1] ""
#> 
#> 
#> 
#> $date_published
#> [1] "2010-01-01"
#> 
#> $software_version
#> [1] "beta"
#> 
#> $description
#> $description$text
#> NULL
#> 
#> 
#> $license
#> $license$id
#> NULL
#> 
#> 
#> $keywords
#> NULL
#> 
#> $state
#> [1] "not_found"
#> 
#> $references
#> NULL
#> 
#> attr(,"from")
#> [1] "cff"
#> attr(,"source_type")
#> [1] "string"
#> attr(,"file")
#> [1] ""
#> attr(,"many")
#> [1] FALSE

^{Created on 2021-09-15 by the reprex package (v2.0.0)}

write handlr list with multiple citations to bibtex file

I have successfully used handlr to convert between bibilography file formats (yay!), and I can print my bibtex to teh console using bibtex_write. How do I write this to a text file external to R?

File: references.json.txt

library(handlr)
tmp <- citeproc_reader("references.json.txt")
bibtex_writer(tmp) # prints to console as a list

I tried an lapply approach and was unsuccesful:

lapply(tmp, function(x) write.table(x, 'test.bib', append= T, sep='\n', quote = F))

Session Info

``` > session_info() ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.0.2 (2020-06-22) os macOS Catalina 10.15.2 system x86_64, darwin17.0 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/Los_Angeles date 2020-10-30

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.0)
ade4 1.7-15 2020-02-13 [1] CRAN (R 4.0.0)
AnnotationDbi * 1.50.3 2020-07-25 [1] Bioconductor
ape 5.4-1 2020-08-13 [1] CRAN (R 4.0.2)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2)
Biobase * 2.48.0 2020-04-27 [1] Bioconductor
BiocGenerics * 0.34.0 2020-04-27 [1] Bioconductor
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.0)
BiocParallel 1.22.0 2020-04-27 [1] Bioconductor
biomformat 1.16.0 2020-04-27 [1] Bioconductor
Biostrings 2.56.0 2020-04-27 [1] Bioconductor
bit 4.0.4 2020-08-04 [1] CRAN (R 4.0.2)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.0.2)
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0)
bookdown 0.20 2020-06-23 [1] CRAN (R 4.0.2)
boot 1.3-25 2020-04-26 [1] CRAN (R 4.0.2)
broom * 0.7.0 2020-07-09 [1] CRAN (R 4.0.2)
callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.2)
car 3.0-9 2020-08-11 [1] CRAN (R 4.0.2)
carData 3.0-4 2020-05-22 [1] CRAN (R 4.0.0)
caret * 6.0-86 2020-03-20 [1] CRAN (R 4.0.0)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.0)
class 7.3-17 2020-04-26 [1] CRAN (R 4.0.2)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.2)
clusterProfiler * 3.16.0 2020-04-27 [1] Bioconductor
codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.2)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
ComplexUpset * 0.5.15 2020-07-10 [1] Github (krassowski/complex-upset@f5dbafe)
cowplot * 1.1.0 2020-09-08 [1] CRAN (R 4.0.2)
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crosstalk 1.1.0.1 2020-03-13 [1] CRAN (R 4.0.0)
crul 1.0.0 2020-07-30 [1] CRAN (R 4.0.2)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
data.table 1.13.0 2020-07-24 [1] CRAN (R 4.0.2)
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0)
dbplyr 1.4.4 2020-05-27 [1] CRAN (R 4.0.0)
DelayedArray 0.14.1 2020-07-14 [1] Bioconductor
deldir 0.1-29 2020-09-13 [1] CRAN (R 4.0.2)
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desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
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devtools * 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
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DO.db 2.9 2020-06-08 [1] Bioconductor
DOSE 3.14.0 2020-04-27 [1] Bioconductor
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dplyr * 1.0.2 2020-08-18 [1] CRAN (R 4.0.2)
e1071 1.7-3 2019-11-26 [1] CRAN (R 4.0.0)
edgeR * 3.30.3 2020-06-02 [1] Bioconductor
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
enrichplot 1.8.1 2020-04-29 [1] Bioconductor
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farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0)
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fgsea 1.14.0 2020-04-27 [1] Bioconductor
forcats * 0.5.0 2020-03-01 [1] CRAN (R 4.0.0)
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fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.0)
GenomeInfoDb 1.24.2 2020-06-15 [1] Bioconductor
GenomeInfoDbData 1.2.3 2020-05-19 [1] Bioconductor
GenomicAlignments 1.24.0 2020-04-27 [1] Bioconductor
GenomicRanges 1.40.0 2020-04-27 [1] Bioconductor
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ggcorrplot * 0.1.3 2019-05-19 [1] CRAN (R 4.0.2)
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ggplot2 * 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
ggplotify * 0.0.5 2020-03-12 [1] CRAN (R 4.0.0)
ggpmisc * 0.3.6 2020-09-07 [1] CRAN (R 4.0.2)
ggpubr * 0.4.0 2020-06-27 [1] CRAN (R 4.0.2)
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ggsignif 0.6.0 2019-08-08 [1] CRAN (R 4.0.0)
ggthemes * 4.2.0 2019-05-13 [1] CRAN (R 4.0.0)
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GO.db 3.11.4 2020-06-08 [1] Bioconductor
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handlr * 0.3.0 2020-10-15 [1] CRAN (R 4.0.2)
haven 2.3.1 2020-06-01 [1] CRAN (R 4.0.0)
hexbin 1.28.1 2020-02-03 [1] CRAN (R 4.0.0)
highr 0.8 2019-03-20 [1] CRAN (R 4.0.0)
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0)
htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0)
httpcode 0.3.0 2020-04-10 [1] CRAN (R 4.0.0)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2)
igraph 1.2.5 2020-03-19 [1] CRAN (R 4.0.0)
ipred 0.9-9 2019-04-28 [1] CRAN (R 4.0.0)
IRanges * 2.22.2 2020-05-21 [1] Bioconductor
irlba 2.3.3 2019-02-05 [1] CRAN (R 4.0.0)
iterators 1.0.12 2019-07-26 [1] CRAN (R 4.0.0)
jsonlite 1.7.1 2020-09-07 [1] CRAN (R 4.0.2)
kableExtra * 1.2.1 2020-08-27 [1] CRAN (R 4.0.2)
knitr * 1.29 2020-06-23 [1] CRAN (R 4.0.2)
knn.covertree 1.0 2019-10-28 [1] CRAN (R 4.0.0)
labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0)
laeken 0.5.1 2020-02-05 [1] CRAN (R 4.0.0)
lattice * 0.20-41 2020-04-02 [1] CRAN (R 4.0.2)
lava 1.6.7 2020-03-05 [1] CRAN (R 4.0.0)
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limma * 3.44.3 2020-06-12 [1] Bioconductor
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magrittr * 1.5 2014-11-22 [1] CRAN (R 4.0.0)
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Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.2)
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microbiome * 1.10.0 2020-04-27 [1] Bioconductor
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mime 0.9 2020-02-04 [1] CRAN (R 4.0.0)
ModelMetrics 1.2.2.2 2020-03-17 [1] CRAN (R 4.0.0)
modelr 0.1.8 2020-05-19 [1] CRAN (R 4.0.0)
multtest 2.44.0 2020-04-27 [1] Bioconductor
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
nlme * 3.1-149 2020-08-23 [1] CRAN (R 4.0.2)
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org.Sc.sgd.db * 3.11.4 2020-06-13 [1] Bioconductor
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permute * 0.9-5 2019-03-12 [1] CRAN (R 4.0.0)
pheatmap 1.0.12 2019-01-04 [1] CRAN (R 4.0.0)
phyloseq * 1.32.0 2020-04-27 [1] Bioconductor
pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
plotly * 4.9.2.1 2020-04-04 [1] CRAN (R 4.0.0)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0)
polyclip 1.10-0 2019-03-14 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
pROC 1.16.2 2020-03-19 [1] CRAN (R 4.0.0)
processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2)
prodlim 2019.11.13 2019-11-17 [1] CRAN (R 4.0.0)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.0.0)
proxy 0.4-24 2020-04-25 [1] CRAN (R 4.0.0)
ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2)
purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
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R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
ranger * 0.12.1 2020-01-10 [1] CRAN (R 4.0.0)
rbibutils * 1.3 2020-10-05 [1] CRAN (R 4.0.2)
RColorBrewer * 1.1-2 2014-12-07 [1] CRAN (R 4.0.0)
Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
RcppEigen 0.3.3.7.0 2019-11-16 [1] CRAN (R 4.0.0)
RcppHNSW 0.3.0 2020-09-06 [1] CRAN (R 4.0.2)
RcppParallel 5.0.2 2020-06-24 [1] CRAN (R 4.0.2)
RCurl 1.98-1.2 2020-04-18 [1] CRAN (R 4.0.0)
readr * 1.3.1 2018-12-21 [1] CRAN (R 4.0.0)
readxl * 1.3.1 2019-03-13 [1] CRAN (R 4.0.0)
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remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
rentrez * 1.2.2 2019-05-02 [1] CRAN (R 4.0.2)
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reshape2 * 1.4.4 2020-04-09 [1] CRAN (R 4.0.0)
rhdf5 2.32.2 2020-07-03 [1] Bioconductor
Rhdf5lib 1.10.1 2020-07-09 [1] Bioconductor
rio 0.5.16 2018-11-26 [1] CRAN (R 4.0.0)
rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.2)
robustbase 0.93-6 2020-03-23 [1] CRAN (R 4.0.0)
rpart * 4.1-15 2019-04-12 [1] CRAN (R 4.0.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
Rsamtools 2.4.0 2020-04-27 [1] Bioconductor
RSpectra 0.16-0 2019-12-01 [1] CRAN (R 4.0.0)
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.0.0)
rstatix 0.6.0 2020-06-18 [1] CRAN (R 4.0.2)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
rtracklayer 1.48.0 2020-04-27 [1] Bioconductor
Rtsne 0.15 2018-11-10 [1] CRAN (R 4.0.0)
rvcheck 0.1.8 2020-03-01 [1] CRAN (R 4.0.0)
rvest 0.3.6 2020-07-25 [1] CRAN (R 4.0.2)
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scatterplot3d 0.3-41 2018-03-14 [1] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
SingleCellExperiment 1.10.1 2020-04-28 [1] Bioconductor
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spatstat * 1.64-1 2020-05-12 [1] CRAN (R 4.0.2)
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stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2)
stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
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tidyr * 1.1.2 2020-08-27 [1] CRAN (R 4.0.2)
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tweenr 1.0.1 2018-12-14 [1] CRAN (R 4.0.0)
UpSetR * 1.4.0 2019-05-22 [1] CRAN (R 4.0.0)
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vegan * 2.5-6 2019-09-01 [1] CRAN (R 4.0.0)
VIM 6.0.0 2020-05-08 [1] CRAN (R 4.0.0)
viridis * 0.5.1 2018-03-29 [1] CRAN (R 4.0.0)
viridisLite * 0.3.0 2018-02-01 [1] CRAN (R 4.0.0)
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withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
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[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

</details>

[feature request] Default action on `could not figure out the mime type`

Hello,

I wonder if there could be a default action specified on mime type exception.

Despite I have octet-stream in a application list and handlr should've not fail.

 $ cat ~/.config/mimeapps.list | grep octet-stream
application/octet-stream=nvim.desktop;
 $ handlr open user
could not figure out the mime type of 'user'
 $ file user                                    
user: GVariant Database file, version 0
 $ file --mime user        
user: application/octet-stream; charset=binary

p.s. If you acknowledge that it's a bug I can create a new ticket.

I can even upload the file, it's basically default dconf registry

Add `.zenodo.json` writer

It's often useful to add a .zenodo.json file before uploading the package to zenodo to customise metadata.

Unfortunately, I don't know any tool to assist you in producing such a file. And even though zenodo allows you to export a CFF file, it doesn't look like it can read from one to create the deposit metadata.

I believe handlr would be the perfect place to help users create a .zenodo.json file from any existing file. What do you think?

codemeta: `@context` item should be changed I think

right now codemeta_writer is assigning https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld to @context, but I think it should be the below:

"@context": [
    "http://purl.org/codemeta/2.0",
    "http://schema.org"
  ]

linting for standalone functions

e.g., bibtex_writer - you can pass in any list, so not great experience when the appropriate list elements are not present

Error in `ris_reader()` for files with more than one abstract

For RIS files with multiple abstracts the ris_reader() function aborts with the following error message:

> handlr::ris_reader("example.ris")
Error in if (!nchar(grep("^AB|^N2", x, value = TRUE)) > 200) { : 
  the condition has length > 1

My example RIS looks like this (as exported by Zotero):

TY  - JOUR
TI  - Energy Poverty in Europe: A Multidimensional Approach
AU  - Bollino, Carlo Andrea
AU  - Botti, Fabrizio
T2  - PSL Quarterly Review
AB  - With the European Commission’s “Third Energy Package”, the challenges posed by energy poverty have been recently acknowledged by European legislation.  The paper develops a synthetic indicator of energy poverty for the purpose of assessing households’ well-being across different domains of inequality in access to energy services and to a healthy domestic environment. These dimensions are broadly defined in terms of energy affordability and thermal efficiency, two of the main manifestations of energy poverty. The analysis focuses on Europe and expands on existing economic literature by employing a fuzzy analysis for the definition of a multidimensional energy poverty index, which is then used to investigate the role of individual and household characteristics in shaping energy poverty. We find that during the European crisis energy poverty has been more stable than monetary poverty, and that thermal efficiency plays a crucial role in shaping individual and countries’ average degrees of energy poverty. 

 
JEL codes: I32; Q41; D10; D63
DA  - 2017/12/04/
PY  - 2017
DO  - 10.13133/2037-3643_70.283_4
DP  - DOI.org (Datacite)
VL  - V. 70
SP  - 473
EP  - 507 Paginazione
LA  - en
ST  - Energy Poverty in Europe
UR  - https://ojs.uniroma1.it/index.php/PSLQuarterlyReview/article/view/14155
Y2  - 2023/05/09/13:08:44
KW  - Energy Poverty, Fuel Poverty, Multidimensional Poverty, Fuzzy Analysis
KW  - I32; Q41; D10; D63
ER  - 

TY  - JOUR
TI  - The energy divide: Integrating energy transitions, regional inequalities and poverty trends in the European Union
AU  - Bouzarovski, Stefan
AU  - Tirado Herrero, Sergio
T2  - European Urban and Regional Studies
AB  - Energy poverty can be understood as the inability of a household to secure a socially and materially necessitated level of energy services in the home. While the condition is widespread across Europe, its spatial and social distribution is highly uneven. In this paper, the existence of a geographical energy poverty divide in the European Union (EU) provides a starting point for conceptualizing and exploring the relationship between energy transitions – commonly described as wide-ranging processes of socio-technical change – and existing patterns of regional economic inequality. We have undertaken a comprehensive analysis of spatial and temporal trends in the national-scale patterns of energy poverty, as well as gas and electricity prices. The results of our work indicate that the classic economic development distinction between the core and periphery also holds true in the case of energy poverty, as the incidence of this phenomenon is significantly higher in Southern and Eastern European EU Member States. The paper thus aims to provide the building blocks for a novel theoretical integration of questions of path-dependency, uneven development and material deprivation in existing interpretations of energy transitions.
DA  - 2017/01//
PY  - 2017
DO  - 10.1177/0969776415596449
DP  - DOI.org (Crossref)
VL  - 24
IS  - 1
SP  - 69
EP  - 86
J2  - European Urban and Regional Studies
LA  - en
SN  - 0969-7764, 1461-7145
ST  - The energy divide
UR  - http://journals.sagepub.com/doi/10.1177/0969776415596449
Y2  - 2023/05/09/13:08:56
L1  - https://europepmc.org/articles/pmc5477826?pdf=render
ER  -

If I remove abstracts beforehand, the error does not occur:

clean_ris <- function(file) {
  ris <- readLines(file, encoding = "UTF-8")
  ris <- paste(ris[!grepl("^AB|^N2", ris)], collapse = "\n")
  cat(ris, "\n", file = file)
  file
}

handlr::ris_reader(clean_ris("example.ris"))

It seems like this issue relates to the fact that when multiple abstracts are found, the if condition to determine abstract length (Line 113 in ris_reader.R) is not valid. My workaround is to add a call to any() to ensure that a single logical value is passed to if:

if (!any(nchar(grep("^AB|^N2", x, value = TRUE)) > 200))

I don't know if this is a reliable fix or if it introduces issues down the line, but in the case of my example RIS, it seems to work.

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