1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
|
bibConvert <- function(infile, outfile, informat, outformat, ..., tex, encoding, options){
stopifnot(length(list(...)) == 0) # no ... arguments allowed
if(!is.character(infile))
stop("argument 'infile' must be a character string")
else if(!file.exists(infile) && (missing(options) || is.null(options["h"]))){
stop("input file \"", infile, "\" doesn't exist")
}
if(missing(informat)){
ext <- tools::file_ext(infile)
informat <- switch(ext,
xml = {
message("\n assuming input format is MOD XML intermediate.\n")
"xml"
},
bib = "bibtex",
bibtex = "bibtex",
biblatex = "biblatex",
copac = "copac",
end = "end",
endx = "endx",
isi = "isi",
med = "med",
nbib = "nbib",
ris = "ris",
wordbib = "wordbib",
"R" = ,
r = "r",
rds = "bibentry",
ads = "ads",
## default
stop("Can't infer input format, please use arg. informat")
)
}
if(missing(outformat)){
ext <- tools::file_ext(outfile)
outformat <- switch(ext,
xml = "xml",
bib = "bibtex",
bibtex = "bibtex",
biblatex = "biblatex",
ads = "ads",
copac = "copac",
end = "end",
endx = "endx", # is there to "endx"?
isi = "isi",
med = "med",
nbib = "nbib",
ris = "ris",
wordbib = "wordbib",
R = ,
r = "r",
rds = "bibentry",
## default
stop("Can't infer output format, please use arg. outformat")
)
}
if(informat == "xml")
xmlfile <- infile
else if(outformat == "xml")
xmlfile <- outfile
else{
xmlfile <- tempfile(fileext = ".xml")
on.exit(unlink(xmlfile))
}
#argv <- c("dummy", xmlfile)
#argv <- c("dummy", "-i", "cp1251", xmlfile)
#argv <- c("dummy", "-i", "cp1251", "-o", "utf8", xmlfile)
argv_2xml <- c("dummy")
argv_xml2 <- c("dummy")
if(!missing(encoding)){
if(length(encoding) == 1)
encoding <- rep(encoding, 2)
## todo: UTF-8 => utf8 ?
argv_2xml <- c(argv_2xml, "-i", encoding[1])
argv_xml2 <- c(argv_xml2, "-o", encoding[2])
}
if(!missing(tex)){
for(tex_op in tex){
switch(tex_op,
no_latex = { # accents to letters
argv_2xml <- c(argv_2xml, "-nl")
## TODO: this is relevant for xml2xxx only when xxx is a latex related format
## for now inserting a line in the C code to ignore it without warning
argv_xml2 <- c(argv_xml2, "-nl")
},
uppercase = {
argv_xml2 <- c(argv_xml2, "-U")
},
brackets = {
argv_xml2 <- c(argv_xml2, "-b")
},
dash = {
argv_xml2 <- c(argv_xml2, "-sd")
},
comma = {
argv_xml2 <- c(argv_xml2, "-fc")
},
## default
stop("unsupported 'tex' option")
)
}
}
if(!missing(options)){
nams <- names(options)
## options <- as.vector(options)
for(j in seq_along(options)){
switch(nams[j],
i = { argv_2xml <- c(argv_2xml, "-i", options[j])},
o = {
argv_xml2 <- c(argv_xml2, "-o", options[j])
## print(argv_xml2)
},
oxml = {argv_2xml <- c(argv_2xml, "-o", options[j])},
h = {
argv_2xml <- c(argv_2xml, "-h")
argv_xml2 <- c(argv_xml2, "-h")
},
v = {
argv_2xml <- c(argv_2xml, "-v")
argv_xml2 <- c(argv_xml2, "-v")
},
a = {argv_2xml <- c(argv_2xml, "-a")},
s = {argv_2xml <- c(argv_2xml, "-s")},
u = {argv_2xml <- c(argv_2xml, "-u")},
U = {argv_xml2 <- c(argv_xml2, "-U")},
un = {argv_2xml <- c(argv_2xml, "-un")},
x = {argv_2xml <- c(argv_2xml, "-x")},
nl = {
argv_2xml <- c(argv_2xml, "-nl")
argv_xml2 <- c(argv_xml2, "-nl")
},
d = { argv_2xml <- c(argv_2xml, "-d") },
c = {argv_2xml <- c(argv_2xml, "-c", options[j])},
## as = {argv_2xml <- c(argv_2xml, "-as", options[j])},
nt = {argv_2xml <- c(argv_2xml, "-nt")},
verbose = {
argv_2xml <- c(argv_2xml, "--verbose")
argv_xml2 <- c(argv_xml2, "--verbose")
},
nb = {
## TODO: However, switch or no switch, on linux the BOM is not added.
## But BOM is inserted on windows without the switch.
## Currently I have no idea why linux is special in this respect.
argv_xml2 <- c(argv_xml2, "-nb")
## for 2xml the switch in bibutils is -un
argv_2xml <- c(argv_2xml, "-un")
},
debug = {
argv_2xml <- c(argv_2xml, "--debug")
argv_xml2 <- c(argv_xml2, "--debug")
},
##default
stop("unsupported option '", nams[j])
)
}
}
## print(argv_xml2)
argv_2xml <- c(argv_2xml, infile)
argv_xml2 <- c(argv_xml2, xmlfile)
argc_2xml <- as.integer(length(argv_2xml))
argc_xml2 <- as.integer(length(argv_xml2))
n_2xml <- as.double(0) # for the number of references (double
n_xml2 <- as.double(0)
## earlier versions accepted "word" (in the "C" code)
if(informat == "word")
informat <- "wordbib"
wrk <- switch(informat,
xml = {
wrk_in <- list(xmlfile)
},
bibtex = {
prg <- paste0("bib", "2xml")
argv_2xml[1] <- prg
wrk_in <- .C(C_any2xml_main, argc_2xml, argv_2xml, xmlfile, nref_in = n_2xml)
},
biblatex = ,
ads = ,
copac = ,
ebi = ,
end = ,
endx = ,
isi = ,
med = ,
nbib = ,
ris = ,
wordbib = {
#print("Hello!")
prg <- paste0(informat, "2xml")
argv_2xml[1] <- prg
wrk_in <- .C(C_any2xml_main, argc_2xml, argv_2xml, xmlfile, nref_in = n_2xml)
},
r = ,
bibentry = {
bibe <- if(informat == "bibentry")
readRDS(infile)
else
readBibentry(infile)
## convert to bibtex and save to file
bibfn <- tempfile(fileext = ".bib")
## krapka, check for keys
## krapka, bib2xml is not happy with empty keys
keys <- bibe$key
for(i in seq_along(bibe)){
if(is.null(keys[[i]]))
bibe$key[i] <- paste0("tmp", i)
}
writeLines(toBibtex(bibe), bibfn)
argv_2xml[length(argv_2xml)] <- bibfn
argv_2xml[1] <- "bib2xml"
wrk_in <- .C(C_any2xml_main, argc_2xml, argv_2xml, xmlfile, nref_in = n_2xml)
},
## default
stop("converting a file from format ", informat, " not available yet")
)
## output
argv_xml2 <- as.character(argv_xml2)
switch(outformat,
xml = {
wrk_out = list(xmlfile, nref_in = wrk_in$nref_in, nref_out = wrk_in$nref_in)
},
bibtex = ,
bib = {
# wrk_out <- .C(C_xml2bib_main, argc_xml2, argv_xml2, outfile, "xml2bib")
prg <- paste0("xml2", "bib")
argv_xml2[1] <- prg
wrk_out <- .C(C_xml2any_main, as.integer(argc_xml2), argv_xml2, outfile, nref_out = n_xml2)
},
# biblatex = {
#
# # wrk_out <- .C(C_xml2biblatex_main, argc_xml2, argv_xml2, outfile, "xml2biblatex")
# prg <- paste0("xml2", "biblatex")
# wrk_out <- .C(C_xml2any_main, argc_xml2, argv_xml2, outfile, prg)
# },
R = ,
r = ,
Rstyle = , # 2020-11-08 new:
# as print(be, style = "R"), currently this is returned by the C code
bibentry = {
## TODO: !!! the variants for bibentry should probably be specified by
## options, not different main level types.
# wrk_out <- .C(C_xml2bib_main, argc_xml2, argv_xml2, outfile, "xml2bib")
prg <- paste0("xml2", "bibentry") # "bibentryC"
argv_xml2[1] <- prg
wrk_out <- .C(C_xml2any_main, as.integer(argc_xml2), argv_xml2, outfile, nref_out = n_xml2)
#browser()
if(outformat != "Rstyle"){
# bibe <- source(outfile)$value # TODO: is the return value of source()
# # 'official'? (no, it isn't)
# names(bibe) <- unlist(bibe$key)
bibe <- readBibentry(outfile)
if(outformat == "bibentry"){
saveRDS(bibe, outfile)
}else{ # R TODO: (2020-11-07) now it could just return the outfile!!!
writeBibentry(bibe, outfile, style = "loose")
}
wrk_out <- list(bib = bibe, nref_out = length(bibe))
}# else - do nothing if outformat == "Rstyle")
},
{
## default
# stop("outformat ", outformat, " not supported by bibConvert yet")
## earlier versions accepted "word" (in the "C" code)
if(outformat == "word")
outformat <- "wordbib"
if(outformat == "ads"){
argv_xml2 <- c(argv_xml2, "--journals", adsout_journals)
argc_xml2 <- as.integer(length(argv_xml2))
}
prg <- paste0("xml2", outformat)
argv_xml2[1] <- prg
wrk_out <- .C(C_xml2any_main, argc_xml2, argv_xml2, outfile, nref_out = n_xml2)
}
)
if(is.numeric(wrk_out$nref_out) && wrk_out$nref_out == 0)
message("\nno references to output.\n",
"if this seems wrong, consider using argument 'informat'.\n")
wrk <- list("infile" = infile, "outfile" = outfile,
nref_in = wrk_in$nref_in,
nref_out = wrk_out$nref_out
)
if(!is.null(wrk_out$bib))
wrk <- c(wrk, list(bib = wrk_out$bib))
wrk
}
|
