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Diff of /pkg/R/corpus.R

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trunk/R/trunk/R/textdoccol.R revision 20, Tue Nov 8 16:40:52 2005 UTC pkg/R/corpus.R revision 1108, Fri Oct 22 18:32:47 2010 UTC
# Line 1  Line 1 
1  # Author: Ingo Feinerer  # Author: Ingo Feinerer
2    
3  # S4 class definition  .PCorpus <- function(x, cmeta, dmeta, dbcontrol) {
4  # Text document collection      attr(x, "CMetaData") <- cmeta
5  setClass("textdoccol", representation(docs = "list",      attr(x, "DMetaData") <- dmeta
6                                        tdm = "termdocmatrix"))      attr(x, "DBControl") <- dbcontrol
7        class(x) <- c("PCorpus", "Corpus", "list")
8  # Accessor function      x
9  if (!isGeneric("docs")) {  }
10      if (is.function("docs"))  DBControl <- function(x) attr(x, "DBControl")
11          fun <- docs  
12    PCorpus <- function(x,
13                        readerControl = list(reader = x$DefaultReader, language = "en"),
14                        dbControl = list(dbName = "", dbType = "DB1"),
15                        ...) {
16        readerControl <- prepareReader(readerControl, x$DefaultReader, ...)
17    
18        if (!filehash::dbCreate(dbControl$dbName, dbControl$dbType))
19            stop("error in creating database")
20        db <- filehash::dbInit(dbControl$dbName, dbControl$dbType)
21    
22        # Allocate memory in advance if length is known
23        tdl <- if (x$Length > 0)
24            vector("list", as.integer(x$Length))
25      else      else
26          fun <- function(object) standardGeneric("docs")          list()
27      setGeneric("docs", fun)  
28        counter <- 1
29        while (!eoi(x)) {
30            x <- stepNext(x)
31            elem <- getElem(x)
32            doc <- readerControl$reader(elem, readerControl$language, if (is.null(x$Names)) as.character(counter) else x$Names[counter])
33            filehash::dbInsert(db, ID(doc), doc)
34            if (x$Length > 0) tdl[[counter]] <- ID(doc)
35            else tdl <- c(tdl, ID(doc))
36            counter <- counter + 1
37        }
38        names(tdl) <- x$Names
39    
40        df <- data.frame(MetaID = rep(0, length(tdl)), stringsAsFactors = FALSE)
41        filehash::dbInsert(db, "DMetaData", df)
42        dmeta.df <- data.frame(key = "DMetaData", subset = I(list(NA)))
43    
44        .PCorpus(tdl, .MetaDataNode(), dmeta.df, dbControl)
45    }
46    
47    .VCorpus <- function(x, cmeta, dmeta) {
48        attr(x, "CMetaData") <- cmeta
49        attr(x, "DMetaData") <- dmeta
50        class(x) <- c("VCorpus", "Corpus", "list")
51        x
52    }
53    
54    # Register S3 corpus classes to be recognized by S4 methods. This is
55    # mainly a fix to be compatible with packages which were originally
56    # developed to cooperate with corresponding S4 tm classes. Necessary
57    # since tm's class architecture was changed to S3 since tm version 0.5.
58    setOldClass(c("VCorpus", "Corpus", "list"))
59    
60    # The "..." are additional arguments for the FunctionGenerator reader
61    VCorpus <- Corpus <- function(x,
62                                  readerControl = list(reader = x$DefaultReader, language = "en"),
63                                  ...) {
64        readerControl <- prepareReader(readerControl, x$DefaultReader, ...)
65    
66        # Allocate memory in advance if length is known
67        tdl <- if (x$Length > 0)
68            vector("list", as.integer(x$Length))
69        else
70            list()
71    
72        if (x$Vectorized)
73            tdl <- mapply(function(x, id) readerControl$reader(x, readerControl$language, id),
74                          pGetElem(x),
75                          id = if (is.null(x$Names)) as.character(seq_len(x$Length)) else x$Names,
76                          SIMPLIFY = FALSE)
77        else {
78            counter <- 1
79            while (!eoi(x)) {
80                x <- stepNext(x)
81                elem <- getElem(x)
82                doc <- readerControl$reader(elem, readerControl$language, if (is.null(x$Names)) as.character(counter) else x$Names[counter])
83                if (x$Length > 0)
84                    tdl[[counter]] <- doc
85                else
86                    tdl <- c(tdl, list(doc))
87                counter <- counter + 1
88            }
89        }
90        names(tdl) <- x$Names
91        df <- data.frame(MetaID = rep(0, length(tdl)), stringsAsFactors = FALSE)
92        .VCorpus(tdl, .MetaDataNode(), df)
93    }
94    
95    `[.PCorpus` <- function(x, i) {
96        if (missing(i)) return(x)
97        index <- attr(x, "DMetaData")[[1 , "subset"]]
98        attr(x, "DMetaData")[[1 , "subset"]] <- if (is.numeric(index)) index[i] else i
99        dmeta <- attr(x, "DMetaData")
100        .PCorpus(NextMethod("["), CMetaData(x), dmeta, DBControl(x))
101    }
102    
103    `[.VCorpus` <- function(x, i) {
104        if (missing(i)) return(x)
105        .VCorpus(NextMethod("["), CMetaData(x), DMetaData(x)[i, , drop = FALSE])
106    }
107    
108    `[<-.PCorpus` <- function(x, i, value) {
109        db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])
110        counter <- 1
111        for (id in unclass(x)[i]) {
112            if (identical(length(value), 1L)) db[[id]] <- value
113            else db[[id]] <- value[[counter]]
114            counter <- counter + 1
115        }
116        x
117    }
118    
119    .map_name_index <- function(x, i) {
120        if (is.character(i)) {
121            if (is.null(names(x)))
122                match(i, meta(x, "ID", type = "local"))
123            else
124                match(i, names(x))
125        }
126        i
127    }
128    
129    `[[.PCorpus` <-  function(x, i) {
130        i <- .map_name_index(x, i)
131        db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])
132        filehash::dbFetch(db, NextMethod("[["))
133    }
134    `[[.VCorpus` <-  function(x, i) {
135        i <- .map_name_index(x, i)
136        lazyTmMap <- meta(x, tag = "lazyTmMap", type = "corpus")
137        if (!is.null(lazyTmMap))
138            .Call("copyCorpus", x, materialize(x, i))
139        NextMethod("[[")
140    }
141    
142    `[[<-.PCorpus` <-  function(x, i, value) {
143        i <- .map_name_index(x, i)
144        db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])
145        index <- unclass(x)[[i]]
146        db[[index]] <- value
147        x
148    }
149    `[[<-.VCorpus` <-  function(x, i, value) {
150        i <- .map_name_index(x, i)
151        # Mark new objects as not active for lazy mapping
152        lazyTmMap <- meta(x, tag = "lazyTmMap", type = "corpus")
153        if (!is.null(lazyTmMap)) {
154            lazyTmMap$index[i] <- FALSE
155            meta(x, tag = "lazyTmMap", type = "corpus") <- lazyTmMap
156        }
157        # Set the value
158        cl <- class(x)
159        y <- NextMethod("[[<-")
160        class(y) <- cl
161        y
162    }
163    
164    # Update NodeIDs of a CMetaData tree
165    .update_id <- function(x, id = 0, mapping = NULL, left.mapping = NULL, level = 0) {
166        # Traversal of (binary) CMetaData tree with setup of NodeIDs
167        set_id <- function(x) {
168            x$NodeID <- id
169            id <<- id + 1
170            level <<- level + 1
171            if (length(x$Children) > 0) {
172                mapping <<- cbind(mapping, c(x$Children[[1]]$NodeID, id))
173                left <- set_id(x$Children[[1]])
174                if (level == 1) {
175                    left.mapping <<- mapping
176                    mapping <<- NULL
177                }
178                mapping <<- cbind(mapping, c(x$Children[[2]]$NodeID, id))
179                right <- set_id(x$Children[[2]])
180    
181                x$Children <- list(left, right)
182  }  }
183  setMethod("docs", "textdoccol", function(object) object@docs)          level <<- level - 1
184            x
185        }
186        list(root = set_id(x), left.mapping = left.mapping, right.mapping = mapping)
187    }
188    
189    # Find indices to be updated for a CMetaData tree
190    .find_indices <- function(x) {
191        indices.mapping <- NULL
192        for (m in levels(as.factor(DMetaData(x)$MetaID))) {
193            indices <- (DMetaData(x)$MetaID == m)
194            indices.mapping <- c(indices.mapping, list(m = indices))
195            names(indices.mapping)[length(indices.mapping)] <- m
196        }
197        indices.mapping
198    }
199    
200    c2 <- function(x, y, ...) {
201        # Update the CMetaData tree
202        cmeta <- .MetaDataNode(0, list(merge_date = as.POSIXlt(Sys.time(), tz = "GMT"), merger = Sys.getenv("LOGNAME")), list(CMetaData(x), CMetaData(y)))
203        update.struct <- .update_id(cmeta)
204    
205        new <- .VCorpus(c(unclass(x), unclass(y)), update.struct$root, NULL)
206    
207        # Find indices to be updated for the left tree
208        indices.mapping <- .find_indices(x)
209    
210        # Update the DMetaData data frames for the left tree
211        for (i in 1:ncol(update.struct$left.mapping)) {
212            map <- update.struct$left.mapping[,i]
213            DMetaData(x)$MetaID <- replace(DMetaData(x)$MetaID, indices.mapping[[as.character(map[1])]], map[2])
214        }
215    
216        # Find indices to be updated for the right tree
217        indices.mapping <- .find_indices(y)
218    
219  setGeneric("textdoccol", function(object) standardGeneric("textdoccol"))      # Update the DMetaData data frames for the right tree
220  # Read in text documents in XML Reuters Corpus Volume 1 (RCV1) format      for (i in 1:ncol(update.struct$right.mapping)) {
221  setMethod("textdoccol", "character", function(object) {          map <- update.struct$right.mapping[,i]
222      require(XML)          DMetaData(y)$MetaID <- replace(DMetaData(y)$MetaID, indices.mapping[[as.character(map[1])]], map[2])
223        }
224      tree <- xmlTreeParse(object)  
225      new("textdoccol", docs = xmlApply(xmlRoot(tree), parseNewsItem))      # Merge the DMetaData data frames
226  })      labels <- setdiff(names(DMetaData(y)), names(DMetaData(x)))
227        na.matrix <- matrix(NA, nrow = nrow(DMetaData(x)), ncol = length(labels), dimnames = list(row.names(DMetaData(x)), labels))
228  # TODO: Implement lacking fields.      x.dmeta.aug <- cbind(DMetaData(x), na.matrix)
229  # For this we need the full RCV1 XML set to know where to find those things      labels <- setdiff(names(DMetaData(x)), names(DMetaData(y)))
230  parseNewsItem <- function(node) {      na.matrix <- matrix(NA, nrow = nrow(DMetaData(y)), ncol = length(labels), dimnames = list(row.names(DMetaData(y)), labels))
231      author <- "Not yet implemented"      y.dmeta.aug <- cbind(DMetaData(y), na.matrix)
232      timestamp <- xmlAttrs(node)[["date"]]      DMetaData(new) <- rbind(x.dmeta.aug, y.dmeta.aug)
233      description <- "Not yet implemented"  
234      id <- as.integer(xmlAttrs(node)[["itemid"]])      new
235      origin <- "Not yet implemented"  }
236      # TODO: Concatenate list elements (= XML paragraphs) to a single string  
237      corpus <- unlist(xmlApply(node[["text"]], xmlValue), use.names = FALSE)  c.Corpus <-
238      heading <- xmlValue(node[["title"]])  function(x, ..., recursive = FALSE)
239    {
240      new("textdocument", author = author, timestamp = timestamp, description = description,      args <- list(...)
241          id = id, origin = origin, corpus = corpus, heading = heading)  
242  }      if (identical(length(args), 0L))
243            return(x)
244  # If necessary build the term-document matrix for a given text document collection  
245  setGeneric("buildTDM", function(object) standardGeneric("buildTDM"))      if (!all(unlist(lapply(args, inherits, class(x)))))
246  setMethod("buildTDM", "textdoccol", function(object) {          stop("not all arguments are of the same corpus type")
247      termdocmatrix(docs(object))  
248  })      if (inherits(x, "PCorpus"))
249            stop("concatenation of corpora with underlying databases is not supported")
250    
251        l <- base::c(list(x), args)
252        if (recursive)
253            Reduce(c2, l)
254        else {
255            l <- do.call("c", lapply(l, unclass))
256            .VCorpus(l,
257                     cmeta = .MetaDataNode(),
258                     dmeta = data.frame(MetaID = rep(0, length(l)), stringsAsFactors = FALSE))
259        }
260    }
261    
262    c.TextDocument <- function(x, ..., recursive = FALSE) {
263        args <- list(...)
264    
265        if (identical(length(args), 0L))
266            return(x)
267    
268        if (!all(unlist(lapply(args, inherits, class(x)))))
269            stop("not all arguments are text documents")
270    
271        dmeta <- data.frame(MetaID = rep(0, length(list(x, ...))), stringsAsFactors = FALSE)
272        .VCorpus(list(x, ...), .MetaDataNode(), dmeta)
273    }
274    
275    print.Corpus <- function(x, ...) {
276        cat(sprintf(ngettext(length(x),
277                             "A corpus with %d text document\n",
278                             "A corpus with %d text documents\n"),
279                    length(x)))
280        invisible(x)
281    }
282    
283    summary.Corpus <- function(object, ...) {
284        print(object)
285        if (length(DMetaData(object)) > 0) {
286            cat(sprintf(ngettext(length(attr(CMetaData(object), "MetaData")),
287                                 "\nThe metadata consists of %d tag-value pair and a data frame\n",
288                                 "\nThe metadata consists of %d tag-value pairs and a data frame\n"),
289                        length(CMetaData(object)$MetaData)))
290            cat("Available tags are:\n")
291            cat(strwrap(paste(names(CMetaData(object)$MetaData), collapse = " "), indent = 2, exdent = 2), "\n")
292            cat("Available variables in the data frame are:\n")
293            cat(strwrap(paste(names(DMetaData(object)), collapse = " "), indent = 2, exdent = 2), "\n")
294        }
295    }
296    
297    inspect <- function(x) UseMethod("inspect", x)
298    inspect.PCorpus <- function(x) {
299        summary(x)
300        cat("\n")
301        db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])
302        show(filehash::dbMultiFetch(db, unlist(x)))
303    }
304    inspect.VCorpus <- function(x) {
305        summary(x)
306        cat("\n")
307        print(noquote(lapply(x, identity)))
308    }
309    
310    lapply.PCorpus <- function(X, FUN, ...) {
311        db <- filehash::dbInit(DBControl(X)[["dbName"]], DBControl(X)[["dbType"]])
312        lapply(filehash::dbMultiFetch(db, unlist(X)), FUN, ...)
313    }
314    lapply.VCorpus <- function(X, FUN, ...) {
315        lazyTmMap <- meta(X, tag = "lazyTmMap", type = "corpus")
316        if (!is.null(lazyTmMap))
317            .Call("copyCorpus", X, materialize(X))
318        base::lapply(X, FUN, ...)
319    }
320    
321    writeCorpus <-  function(x, path = ".", filenames = NULL) {
322        filenames <- file.path(path,
323                               if (is.null(filenames)) unlist(lapply(x, function(x) sprintf("%s.txt", ID(x))))
324                               else filenames)
325        i <- 1
326        for (o in x) {
327            writeLines(as.PlainTextDocument(o), filenames[i])
328            i <- i + 1
329        }
330    }

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