test_that("bibConvert works ok", {
expect_error(bibConvert(tempfile(fileext = ".bib"), tempfile(fileext = ".bib")),
"input file .* doesn't exist")
bibConvert(tempfile(fileext = ".bib"), tempfile(fileext = ".bib"), options = c(h = ""))
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")
med_in_no_new_lines <- file.path(bibdir, "easyPubMedvig_no_new_lines.xml")
bibacc <- file.path(bibdir, "latin1accents_utf8.bib")
end_in <- file.path(bibdir, "Putnam1992.end")
litprog280_bib <- file.path(bibdir, "litprog280.bib")
tmp_xml <- tempfile(fileext = ".xml")
tmp_xml2 <- tempfile(fileext = ".xml")
tmp_bib <- tempfile(fileext = ".bib")
tmp_bib2 <- tempfile(fileext = ".bib")
tmp_bib3 <- tempfile(fileext = ".bib")
tmp_bibtex <- tempfile(fileext = ".bibtex")
tmp_biblatex <- tempfile(fileext = ".biblatex")
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")
tmp2_nbib <- tempfile(fileext = ".nbib")
tmp_ris <- tempfile(fileext = ".ris")
tmp_wordbib <- tempfile(fileext = ".wordbib")
tmp_word <- tempfile(fileext = ".word")
ex0_xml <- file.path(bibdir, "ex0.xml")
bibConvert(ex0_xml, tmp_bib, options = c(nb = ""))
expect_known_value(readLines(tmp_bib), "xml2bib.rds", update = FALSE)
bibConvert(tmp_bib, tmp_ads, options = c(nb = ""))
expect_known_value(readLines(tmp_ads), "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", options = c(nb = ""))
expect_known_value(readLines(tmp_bbl), "bib2biblatex.rds", update = FALSE)
bibConvert(tmp_bbl, tmp_bib2, informat = "biblatex", options = c(nb = ""))
expect_known_value(readLines(tmp_bib2), "biblatex2bib.rds", update = FALSE)
## TODO: need copac file to test for input from copac
## tmp2 <- bibConvert(tmp_copac, tmp_xml, options = c(h = ""))
## tmp2 <- bibConvert(tmp_copac, tmp_bib3, informat = "copac")
## export to copac is not implemented:
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")
## can't export to EBI, so using another file
bibConvert(system.file("bib", "ebi.xml", package = "rbibutils"), tmp_xml2,
informat = "ebi")
bibConvert(tmp_bib, tmp_end)
bibConvert(tmp_bib, tmp_end, outformat = "end", options = c(nb = ""))
expect_known_value(readLines(tmp_end), "bib2end.rds", update = FALSE)
bibConvert(tmp_end, tmp_bib3)
bibConvert(tmp_end, tmp_bib2, informat = "end", options = c(nb = ""))
## 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, options = c(nb = ""))
## 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")
## these raise valgrind erors abput uninitialised values:
## 2021-10-29 Note: restoring, maybe this was fixed when other valgroind
## errors were fixed?
bibConvert(endx_in, tmp_bib3, informat = "endx", options = c(nb = ""))
expect_known_value(readLines(tmp_bib3), "end2bib.rds", update = FALSE)
bibConvert(tmp_bib, tmp_isi, options = c(nb = ""))
expect_known_value(readLines(tmp_isi), "bib2isi.rds", update = FALSE)
bibConvert(tmp_isi, tmp_bib2, options = c(nb = ""))
expect_known_value(readLines(tmp_bib2), "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", options = c(nb = ""))
expect_known_value(readLines(tmp_bib), "med2bib.rds", update = FALSE)
## issue #4
tmp_meda <- tempfile()
tmp_medb <- tempfile()
bibConvert(infile = med_in, outfile = tmp_meda, informat = "med", outformat = "bib")
bibConvert(infile = med_in_no_new_lines, outfile = tmp_medb, informat = "med", outformat = "bib")
expect_identical(readLines(tmp_meda), readLines(tmp_medb))
unlink(tmp_meda)
unlink(tmp_medb)
## this assignment was used when the above lines were commented out during memory leak tests.
## (but it causes check error on Windows due to BOM)
## tmp_bib <- file.path(bibdir, "bib_from_medin.bib")
bibConvert(tmp_bib, tmp_nbib)
## This
## bibConvert(tmp_nbib, tmp_bib2)
## fails to process the references with messages like:
##
## Warning. Tagged line not in properly started reference.
## Ignored: 'VI - 50'
##
## There is no error, just 0 output references. Apparently tmp_nbib created from
## bib-to-nbib doesn't contain crucial info for each reference.
##
## TODO: maybe exporting a dummy PMID field will resolve this when the input doesn't have
## it? Or give a more informative message?
##
## expect_known_value(readLines(tmp_bib2), "nbib2bib.rds", update = FALSE)
single_nbib <- system.file("bib", "single.nbib", package = "rbibutils")
bibConvert(single_nbib, tmp_bib2)
## when the input file contains PMID the nbib output is read back successfully:
bibConvert(tmp_bib2, tmp2_nbib)
bibConvert(tmp2_nbib, tmp_bib3 )
## use a shorter file in tests
## bibConvert(system.file("bib", "pubmed-balloongui-set.nbib", package = "rbibutils"), tmp_xml)
bibConvert(system.file("bib", "pubmed-balloongui-set_09_31542275.nbib", package = "rbibutils"), tmp_xml)
bibConvert(tmp_bib, tmp_ris, options = c(nb = ""))
expect_known_value(readLines(tmp_ris), "bib2ris.rds", update = FALSE)
bibConvert(tmp_ris, tmp_bib, options = c(nb = ""))
expect_known_value(readLines(tmp_bib), "ris2bib.rds", update = FALSE)
bibConvert(tmp_bib, tmp_xml, options = c(un = ""))
expect_known_value(readLines(tmp_xml), "bib2xml2.rds", update = FALSE)
bibConvert(tmp_bib, tmp_rds, options = c(nb = ""))
expect_known_value(readRDS(tmp_rds), "bib2rds.rds", update = FALSE)
bib2R <- bibConvert(tmp_bib, tmp_R)
expect_known_value(bib2R$bib, "bib2R.rds", update = FALSE)
bibConvert(tmp_rds, tmp_xml, options = c(un = "")) # rds to MODS XML intermediate
expect_known_value(readLines(tmp_xml), "rds2xml.rds", update = FALSE)
bibConvert(tmp_rds, tmp_bbl2, outformat = "biblatex", options = c(nb = ""))
expect_known_value(readLines(tmp_bbl2), "rds2bbl2.rds", update = FALSE)
bibConvert(tmp_bib, tmp_wordbib)
bibConvert(tmp_bib, tmp_wordbib, outformat = "wordbib", options = c(nb = ""))
expect_known_value(readLines(tmp_wordbib), "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", options = c(nb = ""))
expect_known_value(readLines(tmp_bib3), "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")
## #########################
## -h and -v currently print to standard error and continue
## Without the assignment to tmp2 inside capture.output(..., type = "message")
## the results are printed by devtools::test() and friends.
## -h
## a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_bib, options = c(h = "")), type = "message")
## a <- capture.output(bibConvert(ex0_xml, tmp_bib, options = c(h = "")), type = "message")
## expect_match(a, "usage: xml2bib xml_file > bibtex_file", all = FALSE)
##
## The above catch the message by REprintf but then leak memory
## (discovered by valgrind with --leak-check=full --track-origins=yes --show-leak-kinds=all)
##
## The leak seems to come from capture.output() and its interference with testthat. Note
## that I put the above example in one of the Rd files and there was no problem there
## from the check (checks of examples are not run under testthat),
##
## For example in xml2any, help_xml2bibtex() has a bunch of print statements and
## starting from about the one with '-nl, --no-latex' (but not the previous ones)
## REprintf seem not to release some memory. testthat's caputure_output doesn't have
## argument 'type'. so doesn't capture stderr.
##
## So, for now just run the statement to make sure that they work (and similarly for the
## similar commands below. The downside is that the messages apppear in testthat.Rout and, if under devtools,
## on the console, which is unnerving. (:TODO: find a way to fix this)
tmp2 <- bibConvert(ex0_xml, tmp_bib, options = c(h = ""))
## a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_bib2, outformat = "biblatex", options = c(h = "")), type = "message")
## expect_match(a, "usage: xml2biblatex xml_file > biblatex_file", all = FALSE)
bibConvert(ex0_xml, tmp_bib2, outformat = "biblatex", options = c(h = ""))
## a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_ads, options = c(h = "")), type = "message")
## expect_match(a, "usage: xml2ads xml_file > adsabs_file", all = FALSE)
tmp2 <- bibConvert(ex0_xml, tmp_ads, options = c(h = ""))
## # a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_copac, options = c(h = "")), type = "message")
## # a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_ebi, options = c(h = "")), type = "message")
## a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_end, options = c(h = "")), type = "message")
## expect_match(a, "usage: xml2end xml_file > endnote_file", all = FALSE)
tmp2 <- bibConvert(ex0_xml, tmp_end, options = c(h = ""))
## # a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_endx, options = c(h = "")), type = "message")
## a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_isi, options = c(h = "")), type = "message")
## expect_match(a, "usage: xml2isi xml_file > isi_file", all = FALSE)
tmp2 <- bibConvert(ex0_xml, tmp_isi, options = c(h = ""))
# a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_med, options = c(h = "")), type = "message")
#a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_nbib, options = c(h = "")), type = "message")
#expect_match(a, "", all = FALSE)
## a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_ris, options = c(h = "")), type = "message")
## expect_match(a, "usage: xml2ris xml_file > ris_file", all = FALSE)
tmp2 <- bibConvert(ex0_xml, tmp_ris, options = c(h = ""))
## a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_wordbib, options = c(h = "")), type = "message")
## expect_match(a, "usage: xml2wordbib xml_file > word_file", all = FALSE)
tmp2 <- bibConvert(ex0_xml, tmp_wordbib, options = c(h = ""))
## a <- capture.output(tmp2 <- bibConvert(tmp_bib, tmp_xml, options = c(h = "")), type = "message")
## expect_match(a, "usage: bib2xml bibtex_file > xml_file", all = FALSE)
tmp2 <- bibConvert(tmp_bib, tmp_xml, options = c(h = ""))
## a <- capture.output(tmp2 <- bibConvert(tmp_bib2, tmp_xml, informat = "biblatex", options = c(h = "")), type = "message")
## expect_match(a, "usage: biblatex2xml bibtex_file > xml_file", all = FALSE)
tmp2 <- bibConvert(tmp_bib2, tmp_xml, informat = "biblatex", options = c(h = ""))
## a <- capture.output(tmp2 <- bibConvert(tmp_end, tmp_xml, options = c(h = "")), type = "message")
## expect_match(a, "usage: end2xml endnote_file > xml_file", all = FALSE)
tmp2 <- bibConvert(tmp_end, tmp_xml, options = c(h = ""))
## # a <- capture.output(tmp2 <- bibConvert(tmp_ads, tmp_xml, options = c(h = "")), type = "message")
## a <- capture.output(tmp2 <- bibConvert(tmp_copac, tmp_xml, options = c(h = "")), type = "message")
## expect_match(a, "usage: copac2xml copac_file > xml_file", all = FALSE)
## # a <- capture.output(tmp2 <- bibConvert(tmp_ebi, tmp_xml, options = c(h = "")), type = "message")
## a <- capture.output(tmp2 <- bibConvert(tmp_end, tmp_xml, options = c(h = "")), type = "message")
## expect_match(a, "usage: end2xml endnote_file > xml_file", all = FALSE)
tmp2 <- bibConvert(tmp_end, tmp_xml, options = c(h = ""))
## a <- capture.output(tmp2 <- bibConvert(tmp_endx, tmp_xml, options = c(h = "")), type = "message")
## expect_match(a, "usage: endx2xml endnotexml_file > xml_file", all = FALSE)
tmp2 <- bibConvert(tmp_endx, tmp_xml, options = c(h = ""))
## a <- capture.output(tmp2 <- bibConvert(tmp_isi, tmp_xml, options = c(h = "")), type = "message")
## expect_match(a, "usage: isi2xml isi_file > xml_file", all = FALSE)
tmp2 <- bibConvert(tmp_isi, tmp_xml, options = c(h = ""))
## a <- capture.output(tmp2 <- bibConvert(tmp_med, tmp_xml, options = c(h = "")), type = "message")
## expect_match(a, "usage: med2xml medline_file > xml_file", all = FALSE)
tmp2 <- bibConvert(tmp_med, tmp_xml, options = c(h = ""))
## a <- capture.output(tmp2 <- bibConvert(tmp_nbib, tmp_xml, options = c(h = "")), type = "message")
## expect_match(a, "usage: nbib2xml nbib_file > xml_file", all = FALSE)
tmp2 <- bibConvert(tmp_nbib, tmp_xml, options = c(h = ""))
## a <- capture.output(tmp2 <- bibConvert(tmp_ris, tmp_xml, options = c(h = "")), type = "message")
## expect_match(a, "ris_file can be replaced with file list or omitted to use as a filter", all = FALSE)
tmp2 <- bibConvert(tmp_ris, tmp_xml, options = c(h = ""))
## a <- capture.output(tmp2 <- bibConvert(tmp_wordbib, tmp_xml, options = c(h = "")), type = "message")
## expect_match(a, "usage: wordbib2xml word2007bib_file > xml_file", all = FALSE)
tmp2 <- bibConvert(tmp_wordbib, tmp_xml, options = c(h = ""))
## -v
## a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_bib, options = c(v = "")), type = "message")
## expect_match(a, ".*xml2bib, bibutils suite version", all = FALSE)
tmp2 <- bibConvert(ex0_xml, tmp_bib, options = c(v = ""))
## a <- capture.output(tmp2 <- bibConvert(tmp_bib, tmp_xml, options = c(v = "")), type = "message")
## expect_match(a, "bib2xml, bibutils suite version", all = FALSE)
tmp2 <- bibConvert(tmp_bib, tmp_xml, options = c(v = ""))
## --debug
## a <- capture.output(tmp2 <- bibConvert(ex0_xml, tmp_bib, options = c(debug = "")), type = "message")
## expect_match(a, "-------------------params start ", all = FALSE)
tmp2 <- bibConvert(ex0_xml, tmp_bib, options = c(debug = ""))
## a <- capture.output(tmp2 <- bibConvert(tmp_bib, tmp_xml, options = c(verbose = "")), type = "message")
## expect_match(a, "# NUM level = LEVEL 'TAG' = 'VALUE'", all = FALSE)
tmp2 <- bibConvert(tmp_bib, tmp_xml, options = c(verbose = ""))
## --verbose
## a <- capture.output(tmp2 <- bibConvert(litprog280_bib, tmp_xml, options = c(verbose = "")), type = "message")
## expect_match(a, "bib2xml: Cannot find tag 'ISSN-L'", all = FALSE) # Note: there are other unknown tags
tmp2 <- bibConvert(litprog280_bib, tmp_xml, options = c(verbose = ""))
## #########################
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")
## #########################
tmpdir <- tempdir()
xampl_fn <- system.file("bib", "xampl_modified.bib", package = "rbibutils")
bibConvert(xampl_fn, tmp_ads, options = c(nb = ""))
expect_known_value(readLines(tmp_ads), "xampl_bib2ads.rds", update = FALSE)
bibConvert(xampl_fn, tmp_bbl, outformat = "biblatex", options = c(nb = ""))
expect_known_value(readLines(tmp_bbl), "xampl2biblatex.rds", update = FALSE)
xampl_fn2 <- file.path(tmpdir, "xampl_bbl2bib.bib")
bibConvert(tmp_bbl, xampl_fn2, informat = "biblatex", options = c(nb = ""))
expect_known_value(readLines(xampl_fn2), "xampl_bbl2bib.rds", update = FALSE)
bibConvert(xampl_fn, tmp_end)
bibConvert(xampl_fn, tmp_end, outformat = "end", options = c(nb = ""))
expect_known_value(readLines(tmp_end), "xampl_bib2end.rds", update = FALSE)
bibConvert(tmp_end, tmp_bib3)
bibConvert(tmp_end, tmp_bib2, informat = "end", options = c(nb = ""))
bibConvert(xampl_fn, tmp_isi, options = c(nb = ""))
expect_known_value(readLines(tmp_isi), "xampl_bib2isi.rds", update = FALSE)
bibConvert(tmp_isi, tmp_bib2, options = c(nb = ""))
expect_known_value(readLines(xampl_fn2), "xampl_isi2bib.rds", update = FALSE)
bibConvert(med_in, tmp_bib2, informat = "med")
bibConvert(med_in, tmp_bib3, informat = "med", outformat = "biblatex", options = c(nb = ""))
expect_known_value(readLines(tmp_bib3), "med2bib.rds", update = FALSE)
## tex.bib
tex_fn <- system.file("bib", "tex.bib", package = "rbibutils")
bibConvert(tex_fn, tmp_ads)
bibConvert(tex_fn, tmp_bibtex)
bibConvert(tex_fn, tmp_biblatex)
bibConvert(tex_fn, tmp_biblatex, informat = "biblatex") # it's bibtex but should work
## bibConvert(tex_fn, tmp_copac) # not supported
## bibConvert(tex_fn, tmp_ebi) # not supported
bibConvert(tex_fn, tmp_end)
## bibConvert(tex_fn, tmp_endx)
bibConvert(tex_fn, tmp_isi)
## bibConvert(tex_fn, tmp_med)
bibConvert(tex_fn, tmp_nbib)
bibConvert(tex_fn, tmp_ris)
bibConvert(tex_fn, tmp_R, outformat = "Rstyle")
bibConvert(tex_fn, tmp_rds)
bibConvert(tex_fn, tmp_xml)
bibConvert(tex_fn, tmp_wordbib)
bibConvert(tex_fn, tmp_word, outformat = "word")
bibConvert(tmp_bibtex , tmp_xml2)
bibConvert(tmp_biblatex, tmp_xml2)
bibConvert(tmp_word , tmp_xml2, informat = "word")
## bibConvert(tmp_ads , tmp_xml2) # not supported
## bibConvert(tmp_copac, tmp_xml2) # tmp_copac not available
## bibConvert(tmp_ebi , tmp_xml2) # tmp_ebi not available
bibConvert(tmp_end , tmp_xml2)
## bibConvert(tmp_endx , tmp_xml2) # tmp_endx not available
bibConvert(tmp_isi , tmp_xml2)
## bibConvert(tmp_med, , tmp_xml2) # tmp_med not available
bibConvert(tmp_nbib , tmp_xml2) # TODO: amend nbib output to output dummy PMID's
# when not present in input file?
bibConvert(tmp_ris , tmp_xml2)
bibConvert(tmp_R , tmp_xml2) # "bibentry"
bibConvert(tmp_rds , tmp_xml2)
bibConvert(tmp_xml , tmp_xml2)
bibConvert(tmp_wordbib , tmp_xml2)
readBib(tex_fn, direct = TRUE)
readBib(xampl_fn, direct = TRUE)
biblatex_fn <- system.file("bib", "biblatex-examples_sans_key_aksin.bib", package = "rbibutils")
tmp <- bibConvert(biblatex_fn, tmp_bib2, informat = "biblatex")
})
## TODO: 'tried to fix' is not followed by report if it was successful
##
## > tmp <- bibConvert(tex_fn, tmp_rds)
## Error in .bibentry_check_bibentry1(rval) :
## A bibentry of bibtype ‘Book’ has to specify the field: year
##
## Tried to fix above errors/warnings, see the warnings and messages below.
##
## key 'G-G'
## A bibentry of bibtype ‘Book’ has to specify the field: year
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