setGeneric("collocationAnalysis", function(kco, ...)  standardGeneric("collocationAnalysis") )

#' Collocation analysis
#'
#' @aliases collocationAnalysis
#'
#' @description
#'
#' Performs a collocation analysis for the given node (or query)
#' in the given virtual corpus.
#'
#' @details
#' The collocation analysis is currently implemented on the client side, as some of the
#' functionality is not yet provided by the KorAP backend. Mainly for this reason
#' it is very slow (several minutes, up to hours), but on the other hand very flexible.
#' You can, for example, perform the analysis in arbitrary virtual corpora, use complex node queries,
#' and look for expression-internal collocates using the focus function (see examples and demo).
#'
#' To increase speed at the cost of accuracy and possible false negatives,
#' you can decrease searchHitsSampleLimit and/or topCollocatesLimit and/or set exactFrequencies to FALSE.
#'
#' Note that some outdated non-DeReKo back-ends might not yet support returning tokenized matches (warning issued).
#' In this case, the client library will fall back to client-side tokenization which might be slightly less accurate.
#' This might lead to false negatives and to frequencies that differ from corresponding ones acquired via the web
#' user interface.
#'
#' @family collocation analysis functions
#'
#' @param lemmatizeNodeQuery     if TRUE, node query will be lemmatized, i.e. `x -> [tt/l=x]`
#' @param minOccur               minimum absolute number of observed co-occurrences to consider a collocate candidate
#' @param topCollocatesLimit     limit analysis to the n most frequent collocates in the search hits sample
#' @param searchHitsSampleLimit  limit the size of the search hits sample
#' @param stopwords              vector of stopwords not to be considered as collocates
#' @param withinSpan             KorAP span specification (see <https://korap.ids-mannheim.de/doc/ql/poliqarp-plus?embedded=true#spans>) for collocations to be searched within. Defaults to `base/s=s`.
#' @param exactFrequencies       if FALSE, extrapolate observed co-occurrence frequencies from frequencies in search hits sample, otherwise retrieve exact co-occurrence frequencies
#' @param seed                   seed for random page collecting order
#' @param expand                 if TRUE, `node` and `vc` parameters are expanded to all of their combinations
#' @param maxRecurse             apply collocation analysis recursively `maxRecurse` times
#' @param addExamples            If TRUE, examples for instances of collocations will be added in a column `example`. This makes a difference in particular if `node` is given as a lemma query.
#' @param thresholdScore         association score function (see \code{\link{association-score-functions}}) to use for computing the threshold that is applied for recursive collocation analysis calls
#' @param threshold              minimum value of `thresholdScore` function call to apply collocation analysis recursively
#' @param localStopwords         vector of stopwords that will not be considered as collocates in the current function call, but that will not be passed to recursive calls
#' @param collocateFilterRegex   allow only collocates matching the regular expression
#' @param ...                    more arguments will be passed to [collocationScoreQuery()]
#' @inheritParams collocationScoreQuery,KorAPConnection-method
#' @return Tibble with top collocates, association scores, corresponding URLs for web user interface queries, etc.
#'
#' @importFrom dplyr arrange desc slice_head bind_rows
#' @importFrom purrr pmap
#' @importFrom tidyr expand_grid
#'
#' @examples
#' \dontrun{
#'
#'  # Find top collocates of "Packung" inside and outside the sports domain.
#'  KorAPConnection(verbose = TRUE) |>
#'   collocationAnalysis("Packung", vc=c("textClass=sport", "textClass!=sport"),
#'                       leftContextSize=1, rightContextSize=1, topCollocatesLimit=20) |>
#'   dplyr::filter(logDice >= 5)
#' }
#'
#' \dontrun{
#'
#' # Identify the most prominent light verb construction with "in ... setzen".
#' # Note that, currently, the use of focus function disallows exactFrequencies.
#' KorAPConnection(verbose = TRUE) |>
#'   collocationAnalysis("focus(in [tt/p=NN] {[tt/l=setzen]})",
#'     leftContextSize=1, rightContextSize=0, exactFrequencies=FALSE, topCollocatesLimit=20)
#' }
#'
#' @export
setMethod("collocationAnalysis", "KorAPConnection",
          function(kco,
                   node,
                   vc = "",
                   lemmatizeNodeQuery = FALSE,
                   minOccur = 5,
                   leftContextSize = 5,
                   rightContextSize = 5,
                   topCollocatesLimit = 200,
                   searchHitsSampleLimit = 20000,
                   ignoreCollocateCase = FALSE,
                   withinSpan = ifelse(exactFrequencies, "base/s=s", ""),
                   exactFrequencies = TRUE,
                   stopwords = append(RKorAPClient::synsemanticStopwords(), node),
                   seed = 7,
                   expand = length(vc) != length(node),
                   maxRecurse = 0,
                   addExamples = FALSE,
                   thresholdScore = "logDice",
                   threshold = 2.0,
                   localStopwords = c(),
                   collocateFilterRegex = '^[:alnum:]+-?[:alnum:]*$',
                   ...) {
            # https://stackoverflow.com/questions/8096313/no-visible-binding-for-global-variable-note-in-r-cmd-check
            word <- frequency <- NULL

            if(!exactFrequencies && (!is.na(withinSpan) && !is.null(withinSpan) && nchar(withinSpan)>0 )) {
              stop(sprintf("Not empty withinSpan (='%s') requires exactFrequencies=TRUE", withinSpan), call. = FALSE)
            }

            warnIfNotAuthorized(kco)

            if (lemmatizeNodeQuery) {
              node <- lemmatizeWordQuery(node)
            }

            result <- if (length(node) > 1 || length(vc) > 1) {
              grid <- if (expand) expand_grid(node=node, vc=vc) else tibble(node=node, vc=vc)
              purrr::pmap(grid, function(node, vc, ...)
                        collocationAnalysis(kco,
                                            node =node,
                                            vc = vc,
                                            minOccur = minOccur,
                                            leftContextSize = leftContextSize,
                                            rightContextSize = rightContextSize,
                                            topCollocatesLimit = topCollocatesLimit,
                                            searchHitsSampleLimit = searchHitsSampleLimit,
                                            ignoreCollocateCase = ignoreCollocateCase,
                                            withinSpan = withinSpan,
                                            exactFrequencies = exactFrequencies,
                                            stopwords = stopwords,
                                            addExamples = TRUE,
                                            localStopwords = localStopwords,
                                            seed = seed,
                                            expand = expand,
                                            ...) ) |>
                bind_rows()
            } else {
              set.seed(seed)
              candidates <- collocatesQuery(
                kco,
                node,
                vc = vc,
                minOccur = minOccur,
                leftContextSize = leftContextSize,
                rightContextSize = rightContextSize,
                searchHitsSampleLimit = searchHitsSampleLimit,
                ignoreCollocateCase = ignoreCollocateCase,
                stopwords = append(stopwords, localStopwords),
                ...
              )

              if (nrow(candidates) > 0) {
                candidates <- candidates |>
                  filter(frequency >= minOccur) |>
                  slice_head(n=topCollocatesLimit)
                collocationScoreQuery(
                  kco,
                  node = node,
                  collocate = candidates$word,
                  vc = vc,
                  leftContextSize = leftContextSize,
                  rightContextSize = rightContextSize,
                  observed = if (exactFrequencies) NA else candidates$frequency,
                  ignoreCollocateCase = ignoreCollocateCase,
                  withinSpan = withinSpan,
                  ...
                ) %>%
                  filter(.$O >= minOccur) %>%
                  dplyr::arrange(dplyr::desc(logDice))
              } else {
                tibble()
              }
            }
            if (maxRecurse > 0 & length(result) > 0 && any(!!thresholdScore >= threshold)) {
              recurseWith <- result |>
                filter(!!as.name(thresholdScore) >= threshold)
              result <- collocationAnalysis(
                kco,
                node = paste0("(", buildCollocationQuery(
                  removeWithinSpan(recurseWith$node, withinSpan),
                  recurseWith$collocate,
                  leftContextSize = leftContextSize,
                  rightContextSize = rightContextSize,
                  withinSpan = ""
                ), ")"),
                vc = vc,
                minOccur = minOccur,
                leftContextSize = leftContextSize,
                rightContextSize = rightContextSize,
                withinSpan = withinSpan,
                maxRecurse = maxRecurse - 1,
                stopwords = stopwords,
                localStopwords = recurseWith$collocate,
                exactFrequencies = exactFrequencies,
                searchHitsSampleLimit = searchHitsSampleLimit,
                topCollocatesLimit = topCollocatesLimit,
                addExamples = FALSE
              ) %>%
                bind_rows(result) %>%
                filter(logDice >= 2) %>%
                filter(.$O >= minOccur) %>%
                dplyr::arrange(dplyr::desc(logDice))
            }
            if (addExamples && length(result) > 0) {
              result$query <-buildCollocationQuery(
                result$node,
                result$collocate,
                leftContextSize = leftContextSize,
                rightContextSize = rightContextSize,
                withinSpan = withinSpan
              )
              result$example <- findExample(
                kco,
                query = result$query,
                vc = result$vc
              )
            }
            result
          }
)

# #' @export
removeWithinSpan <- function(query, withinSpan) {
  if (withinSpan == "") {
    return(query)
  }
  needle <- sprintf("^\\(contains\\(<%s>, ?(.*)\\){2}$", withinSpan)
  res <- gsub(needle, '\\1', query)
  needle <- sprintf("^contains\\(<%s>, ?(.*)\\)$", withinSpan)
  res <- gsub(needle, '\\1', res)
  return(res)
}

#' @importFrom magrittr debug_pipe
#' @importFrom stringr str_detect
#' @importFrom dplyr as_tibble tibble rename filter anti_join tibble bind_rows case_when
#'
matches2FreqTable <- function(matches,
                              index = 0,
                              minOccur = 5,
                              leftContextSize = 5,
                              rightContextSize = 5,
                              ignoreCollocateCase = FALSE,
                              stopwords = c(),
                              collocateFilterRegex =  '^[:alnum:]+-?[:alnum:]*$',
                              oldTable = data.frame(word = rep(NA, 1), frequency = rep(NA, 1)),
                              verbose = TRUE) {
  word <- NULL # https://stackoverflow.com/questions/8096313/no-visible-binding-for-global-variable-note-in-r-cmd-check
  frequency <- NULL

  if (nrow(matches) < 1) {
    dplyr::tibble(word=c(), frequency=c())
  } else if (index == 0) {
    if (! "tokens" %in% colnames(matches) || ! is.list(matches$tokens)) {
      log_info(verbose, "Outdated KorAP server: Falling back to client side tokenization.\n")
      return(snippet2FreqTable(matches$snippet, minOccur, leftContextSize, rightContextSize, ignoreCollocateCase = ignoreCollocateCase,
                        stopwords = stopwords, oldTable = oldTable, verbose = verbose))

    }
    log_info(verbose, paste("Joining", nrow(matches), "kwics\n"))
    for (i in 1:nrow(matches)) {
      oldTable <- matches2FreqTable(
        matches,
        i,
        leftContextSize = leftContextSize,
        rightContextSize = rightContextSize,
        collocateFilterRegex = collocateFilterRegex,
        oldTable = oldTable,
        stopwords = stopwords
      )
    }
    log_info(verbose, paste("Aggregating", length(oldTable$word), "tokens\n"))
    oldTable  |>
      group_by(word) |>
      mutate(word = dplyr::case_when(ignoreCollocateCase ~ tolower(word), TRUE ~ word)) |>
      summarise(frequency=sum(frequency), .groups = "drop") |>
      arrange(desc(frequency))
  } else {
    stopwordsTable <- dplyr::tibble(word=stopwords)

    left <- tail(unlist(matches$tokens$left[index]), leftContextSize)

#    cat(paste("left:", left, "\n", collapse=" "))

    right <- head(unlist(matches$tokens$right[index]), rightContextSize)

#    cat(paste("right:", right, "\n", collapse=" "))

    if(length(left) + length(right) == 0) {
      oldTable
    } else {
      table(c(left, right)) |>
        dplyr::as_tibble(.name_repair = "minimal") |>
        dplyr::rename(word = 1, frequency = 2) |>
        dplyr::filter(str_detect(word, collocateFilterRegex)) |>
        dplyr::anti_join(stopwordsTable, by="word")  |>
        dplyr::bind_rows(oldTable)
    }
  }
}

#' @importFrom magrittr debug_pipe
#' @importFrom stringr str_match str_split str_detect
#' @importFrom dplyr as_tibble tibble rename filter anti_join tibble bind_rows case_when
#'
snippet2FreqTable <- function(snippet,
                              minOccur = 5,
                              leftContextSize = 5,
                              rightContextSize = 5,
                              ignoreCollocateCase = FALSE,
                              stopwords = c(),
                              tokenizeRegex = "([! )(\uc2\uab,.:?\u201e\u201c\'\"]+|&quot;)",
                              collocateFilterRegex =  '^[:alnum:]+-?[:alnum:]*$',
                              oldTable = data.frame(word = rep(NA, 1), frequency = rep(NA, 1)),
                              verbose = TRUE) {
  word <- NULL # https://stackoverflow.com/questions/8096313/no-visible-binding-for-global-variable-note-in-r-cmd-check
  frequency <- NULL

  if (length(snippet) < 1) {
    dplyr::tibble(word=c(), frequency=c())
  } else if (length(snippet) > 1) {
    log_info(verbose, paste("Joining", length(snippet), "kwics\n"))
    for (s in snippet) {
      oldTable <- snippet2FreqTable(
        s,
        leftContextSize = leftContextSize,
        rightContextSize = rightContextSize,
        collocateFilterRegex = collocateFilterRegex,
        oldTable = oldTable,
        stopwords = stopwords
      )
    }
    log_info(verbose, paste("Aggregating", length(oldTable$word), "tokens\n"))
    oldTable  |>
      group_by(word) |>
      mutate(word = dplyr::case_when(ignoreCollocateCase ~ tolower(word), TRUE ~ word)) |>
      summarise(frequency=sum(frequency), .groups = "drop") |>
      arrange(desc(frequency))
  } else {
    stopwordsTable <- dplyr::tibble(word=stopwords)
    match <-
      str_match(
        snippet,
        '<span class="context-left">(<span class="more"></span>)?(.*[^ ]) *</span><span class="match"><mark>.*</mark></span><span class="context-right"> *([^<]*)'
      )

    left <- if(leftContextSize > 0)
      tail(unlist(str_split(match[1, 3], tokenizeRegex)), leftContextSize)
    else
      ""
#    cat(paste("left:", left, "\n", collapse=" "))

    right <- if(rightContextSize > 0)
      head(unlist(str_split(match[1, 4], tokenizeRegex)), rightContextSize)
    else
        ""
#    cat(paste("right:", right, "\n", collapse=" "))

    if(is.na(left[1]) || is.na(right[1]) || length(left) + length(right) == 0) {
      oldTable
    } else {
      table(c(left, right)) |>
        dplyr::as_tibble(.name_repair = "minimal") |>
        dplyr::rename(word = 1, frequency = 2) |>
        dplyr::filter(str_detect(word, collocateFilterRegex)) |>
        dplyr::anti_join(stopwordsTable, by="word")  |>
        dplyr::bind_rows(oldTable)
    }
  }
}

#' Preliminary synsemantic stopwords function
#'
#' @description
#' `r lifecycle::badge("experimental")`
#'
#' Preliminary synsemantic stopwords function to be used in collocation analysis.
#'
#' @details
#' Currently only suitable for German. See stopwords package for other languages.
#'
#' @param ... future arguments for language detection
#'
#' @family collocation analysis functions
#' @return Vector of synsemantic stopwords.
#' @export
synsemanticStopwords <- function(...) {
  res <- c(
    "der",
    "die",
    "und",
    "in",
    "den",
    "von",
    "mit",
    "das",
    "zu",
    "im",
    "ist",
    "auf",
    "sich",
    "Die",
    "des",
    "dem",
    "nicht",
    "ein",
    "Ein",
    "eine",
    "Eine",
    "es",
    "auch",
    "an",
    "als",
    "am",
    "aus",
    "Der",
    "bei",
    "er",
    "dass",
    "sie",
    "nach",
    "um",
    "Das",
    "zum",
    "noch",
    "war",
    "einen",
    "einer",
    "wie",
    "einem",
    "vor",
    "bis",
    "\u00fcber",
    "so",
    "aber",
    "Eine",
    "diese",
    "Diese",
    "oder"
  )
  return(res)
}


# #' @export
findExample <-
  function(kco,
           query,
           vc = "",
           matchOnly = TRUE) {
    out <- character(length = length(query))

    if (length(vc) < length(query))
      vc <- rep(vc, length(query))

    for (i in seq_along(query)) {
      q <- corpusQuery(kco, paste0("(", query[i], ")"), vc = vc[i], metadataOnly = FALSE)
      if (q@totalResults > 0) {
        q <- fetchNext(q, maxFetch=50, randomizePageOrder=F)
        example <- as.character((q@collectedMatches)$snippet[1])
        out[i] <- if(matchOnly) {
          gsub('.*<mark>(.+)</mark>.*', '\\1', example)
        } else {
          stringr::str_replace(example, '<[^>]*>', '')
        }
      } else {
        out[i] = ""
      }
    }
    out
  }

collocatesQuery <-
  function(kco,
           query,
           vc = "",
           minOccur = 5,
           leftContextSize = 5,
           rightContextSize = 5,
           searchHitsSampleLimit = 20000,
           ignoreCollocateCase = FALSE,
           stopwords = c(),
           ...) {
    frequency <- NULL
    q <- corpusQuery(kco, query, vc, metadataOnly = F, ...)
    if(q@totalResults == 0) {
      tibble(word=c(), frequency=c())
    } else {
      q <- fetchNext(q, maxFetch=searchHitsSampleLimit, randomizePageOrder=TRUE)
      matches2FreqTable (q@collectedMatches,
                         0,
                        minOccur = minOccur,
                        leftContextSize = leftContextSize,
                        rightContextSize = rightContextSize,
                        ignoreCollocateCase = ignoreCollocateCase,
                        stopwords = stopwords,
                        ...,
                        verbose = kco@verbose) |>
        mutate(frequency = frequency * q@totalResults / min(q@totalResults, searchHitsSampleLimit)) |>
        filter(frequency >= minOccur)
    }
  }