Introducing 'cwbtools

Using the 'cwbtools' package

The cwbtools package offers a toolset to create, modify and manage corpora to be used with the Corpus Workbench (CWB) from within R. It supports the transition from data formats established by well-known R packages such as tm, quanteda or tidytext to a CWB corpus, so that the efficiency of an query system using indexed corpora (i.e. CWB) can be used.

Moving to CWB indexed corpora is worth considering when working with large corpora. The cwbtools package is designed to be able to work with large data. The core tool of the cwbtools package is the CorpusData-Class. It offers a standard workflow to import and process data, and to generate an indexed corpus. It is implemented as a R6 class. The advantage of using the reference semantics of the R6 class system is that there is minimal copying of the data. Handling memory parsimoniously is necessary when working with large corpora.

Further functions of the package support the creation, modification and management of structural and positional attributes of a corpus, and of registry files. See the manual to learn more about these functions. To learn more about the data structure of the CWB and the CWB jargon, the IMS Open Corpus Workbench (CWB) Corpus Encoding Tutorial is recommended as a point of entry.

The focus of this vignette is the creation of CWB indexed corpora. We present three scenarios: Creating a corpus (a) from XML, (b) from a tibble and (c) from the VCorpus used by the tm package.

A few preliminary preparations are necessary, however.

Getting Started

The CWB stores each indexed corpora in an individual data directory. Registry files in a 'registry directory' (or 'registry' in short) describe the indexed corpora and include the path to the data directory.

For the following examples, we create a temporary directory structure for registry files, and indexed corpora, making sure that these directories exits and are empty.

tmpdir <- tempdir()
if (.Platform$OS.type == "windows") tmpdir <- normalizePath(tmpdir, winslash = "/")

registry_tmp <- file.path(tmpdir, "registry")
data_dir_tmp <- file.path(tmpdir, "data_dir")

if (!file.exists(registry_tmp)){
  dir.create (registry_tmp)
} else {
  file.remove(list.files(registry_tmp, full.names = TRUE))
}
if (!file.exists(data_dir_tmp)) dir.create(data_dir_tmp)

regdir_envvar <- Sys.getenv("CORPUS_REGISTRY")
Sys.setenv(CORPUS_REGISTRY = registry_tmp)

In addition to cwbtools, we rely extensively on the data.table package. It is a good companion to cwbtools because of its efficiency to handle large data. Apart from the processing speed, it supports in-place modifications of data. When corpora grow large, it is advisable to omit copying the data in memory if not absolutely necessary.

library(cwbtools)
library(data.table)

Core operations on structural and positional attributes are implemented in "pure R", but the CWB can be downloaded and stored within the package using the cwb_install() function. In the following examples, we will rely on the "pure R" approach.

Scenario 1: From XML to CWB - UN General Assembly Corpus

The first example is to turn a small sample corpus of debates in the UN General Assembly into an indexed corpus. The package includes some XML files that follow a standard suggested by the Text Encoding Initiative (TEI).

teidir <- system.file(package = "cwbtools", "xml", "UNGA")
teifiles <- list.files(teidir, full.names = TRUE)
list.files(teidir)

For our example, we need an (empty) data directory for the UNGA corpus.

unga_data_dir_tmp <- file.path(data_dir_tmp, "unga")
if (!file.exists(unga_data_dir_tmp)) dir.create(unga_data_dir_tmp)
file.remove(list.files(unga_data_dir_tmp, full.names = TRUE))

The point of departure then is to create a CorpusData object that will serve as a processor for these files and storage facility for the corpus data. The central fields of the class are named chunktable, tokenstream and metadata. When we inspect the new object at the outset, we will see that these fields are not filled initially.

UNGA <- CorpusData$new()
UNGA

To turn the XML files into the CorpusData object, we use the method$import_xml()`. To be able to add metadata from the header to the metadata table, the method requires a named vector of XPath expressions used to find the metadata within the XML document.

metadata <- c(
  lp = "//legislativePeriod", session = "//titleStmt/sessionNo",
  date = "//publicationStmt/date", url = "//sourceDesc/url",
  src = "//sourceDesc/filetype"
)
UNGA$import_xml(filenames = teifiles, meta = metadata)
UNGA

The input XML files are TEI files. Speaker information is included in the attributes of a tag named 'sp'. To maintain the original content, there is a element 'speaker' in the document that includes the information on the speaker call without having parsed it. It is not text spoken in the debate, so we consider it as noise to be removed.

to_keep <- which(is.na(UNGA$metadata[["speaker"]]))
UNGA$chunktable <- UNGA$chunktable[to_keep]
UNGA$metadata <- UNGA$metadata[to_keep][, speaker := NULL]

We assign more telling column names ...

setnames(UNGA$metadata, old = c("sp_who", "sp_state", "sp_role"), new = c("who", "state", "role"))

The CWB requires a tokenstream as input to generate positional attributes. NLP tools will offer lemmatization, part-of-speech-recognition and more. To keep things simple, we perform a very simple tokenization that relies on the tokenizers package.

UNGA$tokenize(lowercase = FALSE, strip_punct = FALSE)
UNGA

Let us see how it looks like now ...

UNGA$tokenstream

The CorpusData object now includes a table with the token stream, and we are ready to import the corpus into the CWB. We use the $encode() method for this purpose. Note that the workers are the p_attribute_encode function (to encode the token stream), and the s_attribute_encode function (to encode the structural attributes / the metadata).

s_attrs <- c("id", "who", "state", "role", "lp", "session", "date")
UNGA$encode(
  registry_dir = registry_tmp, data_dir = unga_data_dir_tmp,
  corpus = "UNGA", encoding = "utf8", method = "R",
  p_attributes = "word", s_attributes = character(),
  compress = FALSE
  )

In this example, the logical parameter compress is `TRUE. This triggers a so-called "huffcode"" compression, which will reduce corpus size and speed up queries. For big corpora, compression certainly makes sense, but it can be time-consuming. If you want to create a corpus experimentally and do not yet need optimization, performing the compression can be postponed or omitted.

The indexed corpus has now been prepared and can be used with CQP, CQPweb, or -- if you like R -- with a package such as polmineR. To see quickly whether everything has worked out as intended (and to keep installation requirements at a minimum), we use the low-level functionality of the RcppCWB package.

RcppCWB::cqp_initialize()
id_peace <- RcppCWB::cl_str2id(
  corpus = "UNGA", p_attribute = "word",
  str = "peace", registry = registry_tmp
)
cpos_peace <- RcppCWB::cl_id2cpos(
  corpus = "UNGA", p_attribute = "word",
  id = id_peace, registry = registry_tmp
)

tab <- data.frame(
  i = unlist(lapply(1:length(cpos_peace), function(x) rep(x, times = 11))),
  cpos = unlist(lapply(cpos_peace, function(x) (x - 5):(x + 5)))
  )
tab[["id"]] <- RcppCWB::cl_cpos2id(
  corpus = "UNGA", p_attribute = "word",
  cpos = tab[["cpos"]], registry = registry_tmp
)
tab[["str"]] <- RcppCWB::cl_id2str(
  corpus = "UNGA", p_attribute = "word",
  id = tab[["id"]], registry = registry_tmp
)

peace_context <- split(tab[["str"]], as.factor(tab[["i"]]))
peace_context <- unname(sapply(peace_context, function(x) paste(x, collapse = " ")))
head(peace_context)

Scenario 2: Tidytext to CWB

In a second scenario, we create a corpus of Jane Austen's books (included in the package janeaustenr). Again, we start by preparing an (empty) data directory ...

austen_data_dir_tmp <- file.path(data_dir_tmp, "austen")
if (!file.exists(austen_data_dir_tmp)) dir.create(austen_data_dir_tmp)
file.remove(list.files(austen_data_dir_tmp, full.names = TRUE))

... and instantiating a CorpusData object.

Austen <- CorpusData$new()

The tidytext package offers an efficient workflow to create the token stream we can assign to the CorpusData object.

books <- janeaustenr::austen_books()
tbl <- tidytext::unnest_tokens(books, word, text, to_lower = FALSE)
Austen$tokenstream <- as.data.table(tbl)

To demonstrate that we can use an additional positional attribute, we stem the tokens using the SnowballC package.

Austen$tokenstream[, stem := SnowballC::wordStem(tbl[["word"]], language = "english")]

In this case, (zero-based!) corpus positions need to be assigned explicitly.

Austen$tokenstream[, cpos := 0L:(nrow(tbl) - 1L)]

We can now create the table with the structural attributes.

cpos_max_min <- function(x) list(cpos_left = min(x[["cpos"]]), cpos_right = max(x[["cpos"]]))
Austen$metadata <- Austen$tokenstream[, cpos_max_min(.SD), by = book]
Austen$metadata[, book := as.character(book)]
setcolorder(Austen$metadata, c("cpos_left", "cpos_right", "book"))

A few finishing touches and we have the token stream ready to be encoded: We remove the metadata from the table in the tokenstream field and order the columns nicely.

Austen$tokenstream[, book := NULL]
setcolorder(Austen$tokenstream, c("cpos", "word", "stem"))
Austen$tokenstream

Ready to encode the corpus!

Austen$encode(
   corpus = "AUSTEN", encoding = "utf8",
   p_attributes = c("word", "stem"), s_attributes = "book",
   registry_dir = registry_tmp, data_dir = austen_data_dir_tmp,
   method = "R", compress = FALSE
)

The new corpus will not be available unless we trigger that files in the registry directory are re-read.

RcppCWB::cqp_reset_registry(registry = registry_tmp)

This is a rudimentary check (using low-level RcppCWB functions) whether to corpus can be used. How often does the token "pride" occur?

corpus <- "AUSTEN"
token <- "pride"
p_attr <- "word"
id <- RcppCWB::cl_str2id(corpus = corpus, p_attribute = p_attr, str = token, registry = registry_tmp)
cpos <- RcppCWB::cl_id2cpos(corpus = corpus, p_attribute = p_attr, id = id, registry = registry_tmp)
count <- length(cpos)
count

Scenario 3: From tm-package VCorpus to CWB

In the third scenario, we will make the transition from a VCorpus (tm package) to a CWB indexed corpus. We use the Reuters corpus that is included as sample data in the tm package.

library(tm)
reut21578 <- system.file("texts", "crude", package = "tm")
reuters.tm <- VCorpus(DirSource(reut21578), list(reader = readReut21578XMLasPlain))

A quick way to attain the data format required for the CorpusData class is to coerce the VCorpus to a tibble, using respective functionality of the tidytext package.

library(tidytext)
reuters.tbl <- tidy(reuters.tm)
reuters.tbl

Columns with the metadata we may want to encode are still character vectors (length > 1). We turn the columns with the topic categorizations and the places into length-one character vectors.

reuters.tbl[["topics_cat"]] <- sapply(
  reuters.tbl[["topics_cat"]],
  function(x) paste(x, collapse = "|")
  )
reuters.tbl[["places"]] <- sapply(
  reuters.tbl[["places"]],
  function(x) paste(x, collapse = "|")
  )

This is the input we need. We instantiate a CorpusData object end make sure that a new data directory for the REUTERS corpus exists (and is empty) ...

Reuters <- CorpusData$new()
reuters_data_dir_tmp <- file.path(data_dir_tmp, "reuters")
if (!file.exists(reuters_data_dir_tmp)) dir.create(reuters_data_dir_tmp)
file.remove(list.files(reuters_data_dir_tmp, full.names = TRUE))

We assign the chunktable and the metadata, coerced to a data.table, to the object ...

Reuters$chunktable <- data.table(reuters.tbl[, c("id", "text")])
Reuters$metadata <- data.table(reuters.tbl[,c("id", "topics_cat", "places")])
Reuters

... we tokenize the text to gain the token stream table ...

Reuters$tokenize()

... we have a look at the token stream ...

Reuters$tokenstream

It seems that we can encode the corpus.

Reuters$encode(
   corpus = "REUTERS", encoding = "utf8",
   p_attributes = "word", s_attributes = c("topics_cat", "places"),
   registry_dir = registry_tmp,
   data_dir = data_dir_tmp,
   method = "R", compress = FALSE
)

The corpus will not be available unless we call cqp_reset_registry() so that files in the registry directory are reloaded.

RcppCWB::cqp_reset_registry(registry = registry_tmp)

The Reuters corpus is about oil production in the Middle East. To check quickly, whether it works, we count the number of occurrences of the word "oil".

id <- RcppCWB::cl_str2id(corpus = "REUTERS", p_attribute = "word", str = "oil", registry = registry_tmp)
cpos <- RcppCWB::cl_id2cpos(corpus = "REUTERS", p_attribute = "word", id = id, registry = registry_tmp)
count <- length(cpos)
count

Final Deeds and Words

As a matter of housekeeping, we remove the temporary directory.

unlink(registry_tmp, recursive = TRUE)
unlink(data_dir_tmp, recursive = TRUE)

Sys.setenv(CORPUS_REGISTRY = regdir_envvar)

Hope everything works! Enjoy! Feedback is welcome!



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cwbtools documentation built on June 11, 2021, 9:07 a.m.