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get_document_structure.R
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library(dplyr)
library(tidyr)
library(stringr)
library(xml2)
docxfiles <- list.files("data/acrobat_docx_all/", full.names = TRUE)
manual_structure <- read.csv2("bookmartree_detail.csv")
doc_struct_list <- doc_struct_list[-which(names(doc_struct_list) == "data/acrobat_xml_all/Burrows 2016 Reducing the Risks from Rapid Demographic Change.xml")]
doc_struct_list <- doc_struct_list[-which(names(doc_struct_list) == "data/acrobat_xml_all/Cherp, 2012.xml")]
doc_struct_list <- doc_struct_list[-which(names(doc_struct_list) == "data/acrobat_xml_all/de Bruin et al. 2009 AD-DICE an implementation of adaptation in the DICE model.xml")]
doc_struct_list <- doc_struct_list[-which(names(doc_struct_list) == "data/acrobat_xml_all/Hanson et al. 2011 A global ranking of port cities with high exposure to climate extremes.xml")]
find_sections_in_text <- function(i_docxtxt, i_sections, DEBUG=FALSE) {
# Initialise
match_txtstruct <- list()
# Loop over sections
for (ksec in i_sections) {
if (DEBUG) cat(paste0("Processing section (", which(i_sections == ksec),"/", length(i_sections),"): ", ksec,"\n"))
# Initialise
flag_stringdist <- FALSE # Flag indicating the method used (i.e. grep or stringdist)
# Count number of words in current section title
nwords <- as.numeric(gregexpr("[[:alpha:]]+", ksec)[[1]]) %>% length()
if (DEBUG) cat(paste0("N-words: ", nwords,"\n"))
# Try to find best match
if (nwords == 1) {
# TODO: may want to switch that to a simple grep
id <- grep(tolower(paste0("^",ksec)), tolower(i_docxtxt))
if (length(id) == 0) {
dist <- sapply(i_docxtxt, function(t) {stringdist::stringdist(ksec,t,method = "jaccard",q=1)})
id <- as.numeric(which(dist == min(dist))[1])
flag_stringdist <- TRUE
if (DEBUG) cat(paste0("Method: string-distance jaccard 1-gram","\n"))
} else {
if (DEBUG) cat(paste0("Method: grep","\n"))
}
} else {
dist <- sapply(substr(i_docxtxt, 1, nchar(ksec)), function(t) {stringdist::stringdist(ksec,t,method = "jaccard",q=2)})
id <- as.numeric(which(dist == min(dist))[1])
flag_stringdist <- TRUE
if (DEBUG) cat(paste0("Method: string-distance jaccard 2-gram","\n"))
}
# Test validity of best match by checking line position
if (DEBUG) cat(paste0("Current position(s): ", paste(id, collapse=", "),"\n"))
if (flag_stringdist) {
if (which(i_sections == ksec) > 1) {
prev_pos <- as.numeric(match_txtstruct[[i_sections[which(i_sections == ksec)-1]]]$line)
if (DEBUG) cat(paste0("Previous position: ", prev_pos, " (", i_sections[which(i_sections == ksec)-1],")\n"))
#itr <- which(dist == min(dist))
if(id < prev_pos) print(paste0("===========> Warning! wrong sequence of sections <============ ", ksec))
# while(id < prev_pos) {
# itr <- itr+1
# id <- as.numeric(which(dist == min(dist))[itr])
# }
}
} else {
if (which(i_sections == ksec) > 1) {
prev_pos <- as.numeric(match_txtstruct[[i_sections[which(i_sections == ksec)-1]]]$line)
if (DEBUG) cat(paste0("Previous position: ", prev_pos, " (", i_sections[which(i_sections == ksec)-1],")\n"))
if (length(prev_pos) != 0) {
print(paste0("===========> Warning! could not find previous position <============ ", ksec))
} else {
if(id[1] < prev_pos) print(paste0("===========> Warning! wrong sequence of sections <============ ", ksec))
if (length(id) > 1) {
prev_pos <- as.numeric(match_txtstruct[[i_sections[which(i_sections == ksec)-1]]]$line)
ids <- id
itr <- 1
id <- ids[1]
while(id < prev_pos && itr <= length(ids)) {
itr <- itr+1
id <- ids[itr]
}
}
}
}
}
# Special case for abstracts
if (tolower(ksec) == "abstract") {
id <- grep("^abstract", tolower(i_docxtxt))
}
# Special case for acknowledgments
if (flag_stringdist) {
if (tolower(ksec) == "acknowledgments") {
if (dist[id] >= 0.35) {
id <- grep("^acknowledgments", tolower(i_docxtxt))
}
}
if (tolower(ksec) == "acknowledgements") {
if (dist[id] >= 0.35) {
id <- grep("^acknowledgements", tolower(i_docxtxt))
}
}
}
# Save information in data frame
if (DEBUG) cat(paste0("flag_stringdist: ", flag_stringdist,"\n"))
if (DEBUG) cat(paste0("pattern: ", ksec,"\n"))
if (DEBUG) cat(paste0("line : ", id,"\n"))
if (DEBUG) cat(paste0("text : ", substr(i_docxtxt[id], 1, nchar(ksec)),"\n"))
if (DEBUG) cat(paste0("sdist : ", ifelse(flag_stringdist, dist[id], NA),"\n"))
match_txtstruct[[ksec]] <- data.frame(
pattern = ksec,
line = id,
text = substr(i_docxtxt[id], 1, nchar(ksec)),
sdist = ifelse(flag_stringdist, dist[id], NA),
stringsAsFactors = FALSE
)
if (DEBUG) cat(paste0("\n\n"))
}
# Bind data frames together
match_txtstruct <- do.call("rbind", match_txtstruct)
rownames(match_txtstruct) <- NULL
return(match_txtstruct)
}
processed_docs <- list()
for (k in docxfiles[177:384]) {
cat("-----------------------------------------------------\n")
cat(paste0(k ,"\n"))
cat("-----------------------------------------------------\n")
flag_case1 <- FALSE
flag_case2 <- FALSE
# Case 1: document structure has been extracted from the associated xml file using the bookmark-tree
if (any(basename(k) %in% paste0(substr(basename(names(doc_struct_list)), 1, nchar(basename(names(doc_struct_list)))-3), "docx"))) {
cat(paste0("> Case 1\n"))
id <- which(paste0(substr(basename(names(doc_struct_list)), 1, nchar(basename(names(doc_struct_list)))-3), "docx") == basename(k))
tmp_struct <- doc_struct_list[[id]]
if (min(tmp_struct$level) == 0) {
tmp_struct <- tmp_struct %>% filter(level == 1)
} else {
tmp_struct <- tmp_struct %>% filter(level %in% c(1,2))
}
# Exceptions
if (basename(k) %in% c("Buhl & Acosta (2016).docx")) tmp_struct <- tmp_struct %>% filter(level == 1)
tmp_struct <- tmp_struct %>%
filter(!title %in% c("Outline placeholder")) %>%
filter(!grepl("Tab[0-9]", title))
# Read in text
docxtxt <- textreadr::read_docx(k) %>% iconv(to='ASCII//TRANSLIT')
# Remove irrelevant text
docxtxt <- docxtxt[which(!grepl("e-mail", docxtxt))]
docxtxt <- docxtxt[which(!grepl("correspondance", docxtxt))]
# Remove citations (partial removal for now)
docxtxt <- gsub("[A-Z]([A-Za-z])+\\s\\([0-9]{4}\\) |
[A-Z]([A-Za-z])+\\sand\\s[A-Z]([A-Za-z])+\\s\\([0-9]{4}\\) |
[A-Z]([A-Za-z])+\\set\\sal\\.\\s\\([0-9]{4}\\) |
[A-Z]{1}([A-Za-z])+\\set\\sal\\.\\s[0-9]{4} |
[A-Z]{1}([a-z])+\\set\\sal\\. |
[A-Z]+\\s[0-9]{4}", "", docxtxt)
# Find sections in text
match_txtstruct <- find_sections_in_text(docxtxt, tmp_struct$title)
print(match_txtstruct)
structured_doc <- match_txtstruct %>%
rename(section = pattern) %>%
rename(match = text) %>%
mutate(file=basename(k)) %>%
select(file,section,line,match,sdist) %>%
mutate(text = "")
for (ksec in 1:(length(structured_doc$section)-1)) {
if (structured_doc$section[ksec] == "Abstract") {
id_start <- structured_doc$line[which(structured_doc$section == structured_doc$section[ksec])]
} else {
id_start <- structured_doc$line[which(structured_doc$section == structured_doc$section[ksec])] +1
}
id_end <- structured_doc$line[which(structured_doc$section == structured_doc$section[ksec+1])]-1
structured_doc$text[which(structured_doc$section == structured_doc$section[ksec])] <- paste(docxtxt[id_start:id_end], collapse=" ")
}
processed_docs[[k]] <- structured_doc %>%
filter(!tolower(section) %in% c("acknowledgments", "acknowledgements", "supplementary data", "references")) %>%
filter(!grepl("appendi", tolower(section)))
flag_case1 = TRUE
}
# Case 2: document structure has been manually extracted
id <- which(basename(substr(manual_structure$file,1 , nchar(paste(manual_structure$file))-4)) == substr(basename(k),1,nchar(basename(k))-5))
if (flag_case1 == FALSE & length(id) != 0) { # paste(manual_structure$manual[id]) != ""
print("Case 2")
# Read in text
docxtxt <- textreadr::read_docx(k) %>% iconv(to='ASCII//TRANSLIT')
# Remove irrelevant text
docxtxt <- docxtxt[which(!grepl("e-mail", docxtxt))]
docxtxt <- docxtxt[which(!grepl("correspondance", docxtxt))]
docxtxt <- docxtxt[which(!grepl("published", docxtxt))]
# Remove citations (partial removal for now)
docxtxt <- gsub("[A-Z]([A-Za-z])+\\s\\([0-9]{4}\\) |
[A-Z]([A-Za-z])+\\sand\\s[A-Z]([A-Za-z])+\\s\\([0-9]{4}\\) |
[A-Z]([A-Za-z])+\\set\\sal\\.\\s\\([0-9]{4}\\) |
[A-Z]{1}([A-Za-z])+\\set\\sal\\.\\s[0-9]{4} |
[A-Z]{1}([a-z])+\\set\\sal\\. |
[A-Z]+\\s[0-9]{4}", "", docxtxt)
# Find sections in text
tmp_manualstruct <- strsplit(paste(manual_structure$manual[id]), ";")[[1]] %>% trimws()
match_txtstruct <- find_sections_in_text(docxtxt, tmp_manualstruct)
print(match_txtstruct)
structured_doc <- match_txtstruct %>%
rename(section = pattern) %>%
rename(match = text) %>%
mutate(file=basename(k)) %>%
select(file,section,line,match,sdist) %>%
mutate(text = "")
for (ksec in 1:(length(structured_doc$section)-1)) {
if (structured_doc$section[ksec] == "Abstract") {
id_start <- structured_doc$line[which(structured_doc$section == structured_doc$section[ksec])]
} else {
id_start <- structured_doc$line[which(structured_doc$section == structured_doc$section[ksec])] +1
}
id_end <- structured_doc$line[which(structured_doc$section == structured_doc$section[ksec+1])]-1
structured_doc$text[which(structured_doc$section == structured_doc$section[ksec])] <- paste(docxtxt[id_start:id_end], collapse=" ")
}
processed_docs[[k]] <- structured_doc %>%
filter(!tolower(section) %in% c("acknowledgments", "acknowledgements", "Supplementary data", "references", "bibliography", "orcid ids", "notes")) %>%
filter(!grepl("appendix", tolower(section)))
flag_case2 = TRUE
}
# Case 3:
if (!flag_case1 & !flag_case2) {
print("Case 3")
docxtxt <- textreadr::read_docx(k) %>% iconv(to='ASCII//TRANSLIT')
# Remove irrelevant text
docxtxt <- docxtxt[which(!grepl("e-mail", docxtxt))]
docxtxt <- docxtxt[which(!grepl("correspondance", docxtxt))]
# Remove citations (partial removal for now)
docxtxt <- gsub("[A-Z]([A-Za-z])+\\s\\([0-9]{4}\\) |
[A-Z]([A-Za-z])+\\sand\\s[A-Z]([A-Za-z])+\\s\\([0-9]{4}\\) |
[A-Z]([A-Za-z])+\\set\\sal\\.\\s\\([0-9]{4}\\) |
[A-Z]{1}([A-Za-z])+\\set\\sal\\.\\s[0-9]{4} |
[A-Z]{1}([a-z])+\\set\\sal\\. |
[A-Z]+\\s[0-9]{4}", "", docxtxt)
match_txtstruct <- lapply(c("abstract", "introduction", "methods", "results", "discussion", "conclusion", "ackowledgments", "ackowledgements", "references", "bilbiography"), function(x) {
dist <- sapply(docxtxt, function(t) {stringdist::stringdist(tolower(x),tolower(t),method = "jaccard",q=1)})
id <- which(dist == min(dist))[1]
if (tolower(x) == "abstract") {
id <- grep("^abstract", tolower(docxtxt))
}
data.frame(
pattern = x,
line = id,
text = substr(docxtxt[id], 1, nchar(x)),
sdist = dist[id],
stringsAsFactors = FALSE
)
}) %>% do.call("rbind", .)
rownames(match_txtstruct) <- NULL
match_txtstruct <- match_txtstruct %>%
filter(sdist <= 0.35)
match_txtstruct <- find_sections_in_text(docxtxt, c("abstract", "introduction", "methods", "results", "discussion", "conclusion", "ackowledgments", "ackowledgements", "references", "bilbiography"), DEBUG=T)
print(match_txtstruct)
structured_doc <- match_txtstruct %>%
rename(section = pattern) %>%
rename(match = text) %>%
mutate(file=basename(k)) %>%
select(file,section,line,match,sdist) %>%
mutate(text = "")
for (ksec in 1:(length(structured_doc$section)-1)) {
if (tolower(structured_doc$section[ksec]) == "abstract") {
id_start <- structured_doc$line[which(structured_doc$section == structured_doc$section[ksec])]
} else {
id_start <- structured_doc$line[which(structured_doc$section == structured_doc$section[ksec])] +1
}
id_end <- structured_doc$line[which(structured_doc$section == structured_doc$section[ksec+1])]-1
structured_doc$text[which(structured_doc$section == structured_doc$section[ksec])] <- paste(docxtxt[id_start:id_end], collapse=" ")
}
processed_docs[[k]] <- structured_doc %>%
filter(!tolower(section) %in% c("acknowledgments", "acknowledgements", "references", "bibliography", "orcid ids", "notes")) %>%
filter(!grepl("appendi", tolower(section)))
}
# Export to txt file
nrow <- nrow(processed_docs[[k]])
if (nrow == 1) {
cat("======================================================\n", file = paste0("data/processed_docs/", substr(basename(k),1,nchar(basename(k))-4), "txt"), append=FALSE)
cat(paste0(processed_docs[[k]]$section[1], "\n"), file = paste0("data/processed_docs/", substr(basename(k),1,nchar(basename(k))-4), "txt"), append=TRUE)
cat("======================================================\n", file = paste0("data/processed_docs/", substr(basename(k),1,nchar(basename(k))-4), "txt"), append=TRUE)
cat(paste0(processed_docs[[k]]$text[1], "\n\n"), file = paste0("data/processed_docs/", substr(basename(k),1,nchar(basename(k))-4), "txt"), append=TRUE)
} else {
for (krow in 2:nrow) {
cat("======================================================\n", file = paste0("data/processed_docs/", substr(basename(k),1,nchar(basename(k))-4), "txt"), append=TRUE)
cat(paste0(processed_docs[[k]]$section[krow], "\n"), file = paste0("data/processed_docs/", substr(basename(k),1,nchar(basename(k))-4), "txt"), append=TRUE)
cat("======================================================\n", file = paste0("data/processed_docs/", substr(basename(k),1,nchar(basename(k))-4), "txt"), append=TRUE)
cat(paste0(processed_docs[[k]]$text[krow], "\n\n"), file = paste0("data/processed_docs/", substr(basename(k),1,nchar(basename(k))-4), "txt"), append=TRUE)
}
}
# # Tidy up
# file.remove(tmp_zip)
# unlink(tmp_dir, recursive = TRUE)
cat("\n\n")
}
# # Copy original docx file and transform into zip file
# tmp_copy <- paste0(substr(k, 1, nchar(k)-4), "_copy.docx")
# tmp_zip <- paste0(substr(k, 1, nchar(k)-4), "_copy.zip")
#
# file.copy(k, tmp_copy)
# file.rename(tmp_copy, tmp_zip)
#
# # Unzip file
# tmp_dir <- file.path(dirname(tmp_zip), "tmp_zipcontent")
# dir.create(tmp_dir, showWarnings = FALSE)
# unzip(tmp_zip,exdir=tmp_dir, overwrite = TRUE)
# if (file.exists(file.path(tmp_dir, "word", "header1.xml"))) {
# h1 <- xml_find_all(read_xml(file.path(tmp_dir, "word", "header1.xml")), "//w:t") %>% xml_contents() %>% paste() %>% paste(collapse="")
# dist <- sapply(docxtxt, function(t) {stringdist::stringdist(h1,docxtxt,method = "jaccard",q=1)})
# id <- which(dist == min(dist))[1]
# docxtxt <-
# }
# if (file.exists(file.path(tmp_dir, "word", "header2.xml"))) h2 <- xml_find_all(read_xml(file.path(tmp_dir, "word", "header2.xml")), "//w:t") %>% xml_contents() %>% paste() %>% paste(collapse="")
# if (file.exists(file.path(tmp_dir, "word", "footer1.xml"))) f1 <- xml_find_all(read_xml(file.path(tmp_dir, "word", "footer1.xml")), "//w:t") %>% xml_contents() %>% paste() %>% paste(collapse="")
# if (file.exists(file.path(tmp_dir, "word", "footer2.xml"))) f2 <- xml_find_all(read_xml(file.path(tmp_dir, "word", "footer2.xml")), "//w:t") %>% xml_contents() %>% paste() %>% paste(collapse="")
#
# match_txtstruct <- lapply(tmp_struct$title, function(x) {
#
# dist <- sapply(docxtxt, function(t) {stringdist::stringdist(x,t,method = "jaccard",q=1)})
#
# id <- which(dist == min(dist))[1]
#
# if (tolower(x) == "abstract") {
# id <- grep("^abstract", tolower(docxtxt))
# }
#
# out <- data.frame(
# pattern = x,
# line = id,
# text = substr(docxtxt[id], 1, nchar(x)),
# sdist = dist[id],
# stringsAsFactors = FALSE
# )
#
# return(out)
# }) %>% do.call("rbind", .)
# rownames(match_txtstruct) <- NULL
# # Open xml file containing document content and styles
#
# tmp_stl <- file.path(tmp_dir, "word", "styles.xml")
# if (!file.exists(tmp_stl)) stop()
#
# tmp_xml <- file.path(tmp_dir, "word", "document.xml")
# if (!file.exists(tmp_xml)) stop()
#
# # xml <- x %>%
# # readLines() %>%
# # paste(collapse="") %>%
# # enc2utf8() %>%
# # iconv() %>%
# # read_xml()
#
# # Get styles
# stl <- read_xml(tmp_stl)
# ns_stl <- xml_ns(stl)
#
# # Get document content
# doc <- read_xml(tmp_xml)
# ns_doc <- xml_ns(doc)
#
# # w:document >
# # w:body >
# # w:p > paragraphs / sections in Word
# # w:r > runs (i.e. a series of text with the same font, color, etc)
# # w:t > text
#
# styles <- stl %>% xml_find_all("//w:style[@w:type='paragraph' or w:type='character']", ns=ns_stl) %>% xml_attr("w:styleId", ns=ns_stl)
# styles <- stl %>% xml_find_all("//w:style[@w:type='paragraph' or w:type='character']/w:name", ns=ns_stl) %>% xml_attr("w:val", ns=ns_stl)
#
# # Bookmarks are very helpful to quickly capture the structure of documents
# bookmarks <- xml_find_all(doc, paste0("//w:bookmarkStart"), ns_doc) %>%
# xml_attr("w:name", ns_doc)
# bookmarks <- bookmarks[which(!grepl("_bookmark", bookmarks) &
# !duplicated(bookmarks))]
#
# has_abstract <- grep("^abstract$", tolower(bookmarks))
# has_intro <- grep("^introduction$", tolower(bookmarks))
# has_result <- grep("result", tolower(bookmarks))
# has_discuss <- grep("discussion", tolower(bookmarks))
# has_conc <- grep("conclusion", tolower(bookmarks))
# has_ack <- grep("^ackowledgments$", tolower(bookmarks))
# has_refs <- grep("^references$", tolower(bookmarks))
#
# df_bookmark_style <- lapply(bookmarks, function(x) {
#
# res <- xml_find_all(doc, paste0("//w:p[./w:bookmarkStart/@w:name='", x, "']/w:pPr/w:pStyle"), ns_doc) %>%
# xml_attr("w:val", ns_doc)
#
# df <- data.frame(
# bookmark = x,
# style = ifelse(length(res) != 0, res, ""),
# stringsAsFactors = FALSE
# )
# return(df)
# }) %>% do.call("rbind", .)
#
# abstract <- xml_find_all(doc, paste0("//w:p[./w:bookmarkStart/@w:name='Abstract']/w:r/w:t"), ns_doc) %>%
# xml_contents() %>%
# paste(collapse="")
#
#
#
# for (ks in styles) {
# tmp <- xml_find_all(doc, paste0("//w:p[.//w:pStyle/@w:val=', ks,']"), ns=ns_doc)
#
# tmp <- tmp %>% xml_find_all("//w:t")
#
# print()
#
# }
#
# tmp <- xml_find_all(xml, "//w:p[.//w:pStyle/@w:val='Heading1']", ns=ns_doc)
#
#
#