Exporting collections to R (RDS) format

We are still unable to get Zotero items with their cached text into ITMS (Olga Scrivner's Interactive Text Mining Suite). Olga has written the following R-script to get exported csv-files (which contain the links to every folder where the pdf and the zotero-ft.cache are stored), but it doesn't work yet. If anybody with some coding knowledge would be willing to take a look and maybe help us out, that would be greatly appreciated. 

### Export CSV file (no text, no notes)
### Load libraries (make sure they are all installed first)

##select your csv file
mypath <- file.choose()

mydata <- read_csv(mypath)
shortdata <- mydata[,c("Key","Publication Year","Author","Title","Abstract Note","File Attachments")]

## loading text

id = vector()
lda.format <- vector()
terms <-list()
for (i in 1:nrow(shortdata)) {
path = shortdata['File Attachments'][[1]][i]
dotpath = strsplit(path, "/") # REPLACE by \ for PC - Let's hope there is not title with this symbol
paths = unlist(dotpath)[length(unlist(dotpath))]
uris.name = gsub(paths,".zotero-ft-cache", path) # replace pdf file name by cache file
text.scan <- scan(uris.name, what="character", sep="\n",blank.lines.skip = FALSE)
loc.a<- grep("References|REFERENCES", data)
if (length(data[loc.a])>1){
text <- data[1:(loc.a[length(loc.a)]-1)]
text <- data[1:(loc.a-1)]
text <- paste(text, collapse = " ")
text <-gsub("-\\s+", "", text)
text.punct <- rm_email(text)
text.punct <- rm_url(text.punct)
text.punct <- rm_twitter_url(text.punct)
text.punct <-rm_citation(text.punct)
text.punct <-rm_citation(text.punct, pattern="@rm_citation3")
text.punct <-rm_citation(text.punct, pattern="@rm_citation2")
text.punct <-rm_round(text.punct)
text.punct <-rm_curly(text.punct)
text.punct <-rm_square(text.punct)
text.punct <- rm_bracket(text.punct)
text.punct <- strip(text.punct, char.keep="-",digit.remove = TRUE, apostrophe.remove = FALSE,
lower.case = TRUE)
text.punct <- removePunctuation(text.punct,
preserve_intra_word_contractions = TRUE,
preserve_intra_word_dashes = TRUE)
text.punct <- removeWords(text.punct, stopwords("en"))
text.punct <- gsub("\\s\\s+"," ",text.punct)

lda.format[i] <- text.punct
id[i] <- i

d <- data_frame(txt = text.punct)
freq <- d %>% unnest_tokens(word, txt) %>%
count(word) %>%
terms[[i]] <- freq

### adding other fields
titles <- mydata$Title
abstracts <- mydata$`Abstract Note`
authors <- mydata$Author
datetimes <- mydata$`Publication Year`

collection <- list(id = id, titles=titles, abstracts=abstracts, authors=authors,datetimes=datetimes,
terms=terms, text = lda.format)

### save the file and share with Olga
save_collection <- saveRDS(collection, "collection.rds")
  • What exactly do you mean “doesn’t work”? Do you get an error somewhere? Where? What error message?
  • Brenton - thanks for getting back to me. Here you'll find the test csv file, the R console output and the rds file it created. I feel bad about posting so much code in here, hence the link. There are a couple of errors in the console as you'll see

  • Sorry, I don’t see any error messages in that text file, and I don’t have time to debug a script line by line. I need you to actually describe in detail what is happening and what isn’t working.
  • Thanks. And I understand. But let me try these two errors:

    > print(text.scan)
    [1] "%PDF-1.6"
    [2] "%âãÏÓ"
    [3] "48 0 obj <</Linearized 1/L 103414/O 50/E 57535/N 14/T 102407/H [ 796 361]>>"
    [4] "endobj"
    [41] "7ÿóððpó\004s·rßåqã~Æ“È\023&*ËPËxŸ\u0081¡GêÚ!Þæ¤\005,\b\003\030\u008f4.銌¹~Èh&˜\025Ïqâ‘Ã%W\u009dõ-)…"
    [42] "™JÓÂ\017\031YL0™è]ìõÃ-\030ÌÒž\005g=””ñ\u0090òX:õl\u008d²æ\0340ëCOŸ" [43] "¯JÐ\u009dÛ¢\037z–-îÌ\u0090Œç¸\003¶G©££\001H±¥AéŽ\016\u0090h\0062Ç%\003B§e H¢ê0v\003r\005…T:ðz\024\b4\031\030kÃ\u0081´\030\020K€E\f\030ø\030]8\027ä\035ôæ¨\001r\030Î2ëð8ð:\030\033qHM0g\022\\a:g_PâA¶¹×\034ä\031´ ¡£ÏÀØ{\024\024J@|\016 À"
    [44] "endstream"
    [45] "endobj"
  • edited November 10, 2018
    > text.scan <- scan(uris.name, what="character", sep="\n",blank.lines.skip = FALSE)
    Read 74 items
    Warning message:
    In scan(uris.name, what = "character", sep = "\n", blank.lines.skip = FALSE) :
    embedded nul(s) found in input

    Maybe seeing this may help you in putting us on the right track?
  • Okay, what you are encountering is that Windows R really just can’t handle Unicode characters. Any time you use print, writeLines, write.csv, etc. on Windows R, it is going to mangle the text. You should systematically go through your script and replace the string functions with ones from the stringr and stringi packages or else run the script on Mac or Linux (e.g., you could install Ubuntu on the Windows 10 Linux subsystem and then run R from there).
  • edited November 10, 2018
    I see. I do have a version of Ubuntu installed with the new hyper-v option. So guess I'll try there. Thanks!
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