test_that("bibConvert works ok", {
## TODO: on Windows tests containing
## expect_known_value(readLines(tmp_bib2), ... )
## fail since a BOM mark is added in that case. Changed these to drop the first line (the
## one containing BOM:
## expect_known_value(readLines(tmp_bib2)[-1], ...)
## This is not entirely satisfactory since the rds files created by 'expect_known_value'
## miss the first line.
bibdir <- system.file("bib", package = "rbibutils")
## file is from
## https://gist.github.com/low-decarie/3831049#file-endnote-xml
## downloaded on 2021-05-14
##
## This doesn't work under devtools since pkgload::system.file
## adds 'inst' again:
## endx_in <- system.file(bibdir, "endnote.xml", package = "rbibutils")
##
## file.path here is more logical anyway
endx_in <- file.path(bibdir, "endnote.xml")
med_in <- file.path(bibdir, "easyPubMedvig.xml")
bibacc <- file.path(bibdir, "latin1accents_utf8.bib")
end_in <- file.path(bibdir, "Putnam1992.end")
tmp_xml <- tempfile(fileext = ".xml")
tmp_bib <- tempfile(fileext = ".bib")
tmp_bib2 <- tempfile(fileext = ".bib")
tmp_bib3 <- tempfile(fileext = ".bib")
tmp_bbl <- tempfile(fileext = ".bbl")
tmp_bbl2 <- tempfile(fileext = ".bbl")
tmp_rds <- tempfile(fileext = ".rds")
tmp_R <- tempfile(fileext = ".R")
tmp_ads <- tempfile(fileext = ".ads")
tmp_copac <- tempfile(fileext = ".copac")
tmp_ebi <- tempfile(fileext = ".ebi")
tmp_end <- tempfile(fileext = ".end")
tmp_endx <- tempfile(fileext = ".endx")
tmp_isi <- tempfile(fileext = ".isi")
tmp_med <- tempfile(fileext = ".med")
tmp_nbib <- tempfile(fileext = ".nbib")
tmp_ris <- tempfile(fileext = ".ris")
tmp_wordbib <- tempfile(fileext = ".wordbib")
ex0_xml <- file.path(bibdir, "ex0.xml")
bibConvert(ex0_xml, tmp_bib)
expect_known_value(readLines(tmp_bib)[-1], "xml2bib.rds", update = FALSE)
bibConvert(tmp_bib, tmp_ads)
expect_known_value(readLines(tmp_ads)[-1], "bib2ads.rds", update = FALSE)
expect_error(bibConvert(tmp_ads, tmp_bib2),
"import from ADS abstracts format not implemented")
expect_error(bibConvert(tmp_ads, tmp_bib2, informat = "ads"),
"import from ADS abstracts format not implemented")
bibConvert(tmp_bib, tmp_bbl, outformat = "biblatex")
expect_known_value(readLines(tmp_bbl)[-1], "bib2biblatex.rds", update = FALSE)
bibConvert(tmp_bbl, tmp_bib2, informat = "biblatex")
expect_known_value(readLines(tmp_bib2)[-1], "biblatex2bib.rds", update = FALSE)
## TODO: need copac file to test for input from copac
expect_error(bibConvert(tmp_bib, tmp_copac),
"export to copac format not implemented")
expect_error(bibConvert(tmp_bib, tmp_ebi, outformat = "ebi"),
"export to EBI XML format not implemented")
## TODO: need EBI file to test for input from EBI
bibConvert(tmp_bib, tmp_end)
bibConvert(tmp_bib, tmp_end, outformat = "end")
expect_known_value(readLines(tmp_end)[-1], "bib2end.rds", update = FALSE)
bibConvert(tmp_end, tmp_bib3)
bibConvert(tmp_end, tmp_bib2, informat = "end")
## github actions gives error on all platforms:
## incomplete final line found on '.../Rtmp770EIj/fileb7c68793fe6.bib'
## expect_known_value(readLines(tmp_bib2), "end2bib1.rds", update = FALSE)
bibConvert(end_in, tmp_bib3)
## see note above
## expect_known_value(readLines(tmp_bib3), "end2bib2.rds", update = FALSE)
expect_error(bibConvert(tmp_bib3, tmp_endx),
"export to Endnote XML format not implemented")
expect_error(bibConvert(tmp_bib3, tmp_endx, outformat = "endx"),
"export to Endnote XML format not implemented")
expect_message(bibConvert(endx_in, tmp_bib3), "no references to output")
bibConvert(endx_in, tmp_bib3, informat = "endx")
expect_known_value(readLines(tmp_bib3)[-1], "end2bib.rds", update = FALSE)
bibConvert(tmp_bib, tmp_isi)
expect_known_value(readLines(tmp_isi)[-1], "bib2isi.rds", update = FALSE)
bibConvert(tmp_isi, tmp_bib2)
expect_known_value(readLines(tmp_bib2)[-1], "isi2bib.rds", update = FALSE)
expect_error(bibConvert(tmp_bib, tmp_med),
"export to Medline XML format not implemented")
bibConvert(med_in, tmp_bib, informat = "med")
bibConvert(med_in, tmp_bib, informat = "med", outformat = "biblatex")
expect_known_value(readLines(tmp_bib)[-1], "med2bib.rds", update = FALSE)
## bibConvert(tmp_bib, tmp_nbib) # TODO: segfaults!
## bibConvert(tmp_nbib, tmp_bib2) # TODO: need nbib file for import!
## expect_known_value(readLines(tmp_bib2), "nbib2bib.rds", update = FALSE)
bibConvert(tmp_bib, tmp_ris)
expect_known_value(readLines(tmp_ris)[-1], "bib2ris.rds", update = FALSE)
bibConvert(tmp_ris, tmp_bib)
expect_known_value(readLines(tmp_bib)[-1], "ris2bib.rds", update = FALSE)
bibConvert(tmp_bib, tmp_xml)
expect_known_value(readLines(tmp_xml)[-1], "bib2xml2.rds", update = FALSE)
bibConvert(tmp_bib, tmp_rds)
expect_known_value(readRDS(tmp_rds)[-1], "bib2rds.rds", update = FALSE)
bib2R <- bibConvert(tmp_bib, tmp_R)
expect_known_value(bib2R$bib, "bib2R.rds", update = FALSE)
bibConvert(tmp_rds, tmp_xml) # rds to MODS XML intermediate
expect_known_value(readLines(tmp_xml)[-1], "rds2xml.rds", update = FALSE)
bibConvert(tmp_rds, tmp_bbl2, outformat = "biblatex")
expect_known_value(readLines(tmp_bbl2)[-1], "rds2bbl2.rds", update = FALSE)
bibConvert(tmp_bib, tmp_wordbib)
bibConvert(tmp_bib, tmp_wordbib, outformat = "wordbib")
expect_known_value(readLines(tmp_wordbib)[-1], "bib2wordbib.rds", update = FALSE)
## TODO: this currently misses the authors! Don't know if the culprit is
## the above conversion to wordbib.
bibConvert(tmp_wordbib, tmp_bib3)
bibConvert(tmp_wordbib, tmp_bib3, informat = "wordbib")
expect_known_value(readLines(tmp_bib3)[-1], "wordbib2bib.rds", update = FALSE)
## accept also 'word' since, due to a mixup, the C code was accepting that
bibConvert(tmp_bib, tmp_wordbib, outformat = "word")
bibConvert(tmp_wordbib, tmp_bib3, informat = "word")
cyr_utf8 <- file.path(bibdir, "cyr_utf8.bib")
bibConvert(cyr_utf8, tmp_bib, options = c(o = "cp1251"))
bibConvert(tmp_bib, tmp_xml, options = c(i = "cp1251"))
bibConvert(bibacc, tempfile(fileext = "bib"), outformat = "biblatex")
})
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