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write handlr list with multiple citations to bibtex file #23

Closed taylorreiter closed 3 years ago

taylorreiter commented 3 years ago

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) crayon 1.3.4 2017-09-16 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sckott commented 3 years ago

thanks @taylorreiter for the question

If there's more than 1 citation we use lapply, see https://github.com/ropensci/handlr/blob/master/R/bibtex_writer.R#L36

Problem with that is it returns a list, but a list is best to keep each citation distinct from one another. That is, we could output a character vector but there's no way then for the user to easily separate citations if they wanted to inside of R. A character vector would be easier to then write to disk, but I think the below example is easy enough. What do you think?

library(handlr)
tmp <- citeproc_reader("~/Downloads/references.json.txt")
x <- bibtex_writer(tmp)
lapply(x, cat, file="test.bib", sep="\n", append=TRUE)

an alternative is using the R6 class like:

library(handlr)
x <- HandlrClient$new("~/Downloads/references.json.txt")
x$read()
x$write("bibtex", file="test4.bib")

which does handle multiple citations automatically for you

taylorreiter commented 3 years ago

Thank you @sckott!! These are wonderful examples.