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Diff of /pkg/R/corpus.R

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revision 1108, Fri Oct 22 18:32:47 2010 UTC revision 1333, Fri Apr 18 10:38:46 2014 UTC
# Line 1  Line 1 
1  # Author: Ingo Feinerer  # Author: Ingo Feinerer
2    
3  .PCorpus <- function(x, cmeta, dmeta, dbcontrol) {  PCorpus <-
4      attr(x, "CMetaData") <- cmeta  function(x,
5      attr(x, "DMetaData") <- dmeta           readerControl = list(reader = x$defaultreader, language = "en"),
6      attr(x, "DBControl") <- dbcontrol           dbControl = list(dbName = "", dbType = "DB1"))
7      class(x) <- c("PCorpus", "Corpus", "list")  {
8      x      stopifnot(inherits(x, "Source"))
9  }  
10  DBControl <- function(x) attr(x, "DBControl")      readerControl <- prepareReader(readerControl, x$defaultreader)
11    
12        if (is.function(readerControl$init))
13            readerControl$init()
14    
15  PCorpus <- function(x,      if (is.function(readerControl$exit))
16                      readerControl = list(reader = x$DefaultReader, language = "en"),          on.exit(readerControl$exit())
                     dbControl = list(dbName = "", dbType = "DB1"),  
                     ...) {  
     readerControl <- prepareReader(readerControl, x$DefaultReader, ...)  
17    
18      if (!filehash::dbCreate(dbControl$dbName, dbControl$dbType))      if (!filehash::dbCreate(dbControl$dbName, dbControl$dbType))
19          stop("error in creating database")          stop("error in creating database")
20      db <- filehash::dbInit(dbControl$dbName, dbControl$dbType)      db <- filehash::dbInit(dbControl$dbName, dbControl$dbType)
21    
22      # Allocate memory in advance if length is known      # Allocate memory in advance if length is known
23      tdl <- if (x$Length > 0)      tdl <- if (x$length > 0) vector("list", as.integer(x$length)) else list()
         vector("list", as.integer(x$Length))  
     else  
         list()  
24    
25      counter <- 1      counter <- 1
26      while (!eoi(x)) {      while (!eoi(x)) {
27          x <- stepNext(x)          x <- stepNext(x)
28          elem <- getElem(x)          elem <- getElem(x)
29          doc <- readerControl$reader(elem, readerControl$language, if (is.null(x$Names)) as.character(counter) else x$Names[counter])          id <- if (is.null(x$names) || is.na(x$names))
30          filehash::dbInsert(db, ID(doc), doc)              as.character(counter)
31          if (x$Length > 0) tdl[[counter]] <- ID(doc)          else
32          else tdl <- c(tdl, ID(doc))              x$names[counter]
33            doc <- readerControl$reader(elem, readerControl$language, id)
34            filehash::dbInsert(db, meta(doc, "id"), doc)
35            if (x$length > 0) tdl[[counter]] <- meta(doc, "id")
36            else tdl <- c(tdl, meta(doc, "id"))
37          counter <- counter + 1          counter <- counter + 1
38      }      }
39      names(tdl) <- x$Names      if (!is.null(x$names) && !is.na(x$names))
40            names(tdl) <- x$names
     df <- data.frame(MetaID = rep(0, length(tdl)), stringsAsFactors = FALSE)  
     filehash::dbInsert(db, "DMetaData", df)  
     dmeta.df <- data.frame(key = "DMetaData", subset = I(list(NA)))  
41    
42      .PCorpus(tdl, .MetaDataNode(), dmeta.df, dbControl)      structure(list(content = tdl,
43                       meta = CorpusMeta(),
44                       dmeta = data.frame(row.names = seq_along(tdl)),
45                       dbcontrol = dbControl),
46                  class = c("PCorpus", "Corpus"))
47  }  }
48    
49  .VCorpus <- function(x, cmeta, dmeta) {  VCorpus <-
50      attr(x, "CMetaData") <- cmeta  function(x, readerControl = list(reader = x$defaultreader, language = "en"))
51      attr(x, "DMetaData") <- dmeta  {
52      class(x) <- c("VCorpus", "Corpus", "list")      stopifnot(inherits(x, "Source"))
53      x  
54  }      readerControl <- prepareReader(readerControl, x$defaultreader)
55    
56        if (is.function(readerControl$init))
57            readerControl$init()
58    
59  # Register S3 corpus classes to be recognized by S4 methods. This is      if (is.function(readerControl$exit))
60  # mainly a fix to be compatible with packages which were originally          on.exit(readerControl$exit())
 # developed to cooperate with corresponding S4 tm classes. Necessary  
 # since tm's class architecture was changed to S3 since tm version 0.5.  
 setOldClass(c("VCorpus", "Corpus", "list"))  
   
 # The "..." are additional arguments for the FunctionGenerator reader  
 VCorpus <- Corpus <- function(x,  
                               readerControl = list(reader = x$DefaultReader, language = "en"),  
                               ...) {  
     readerControl <- prepareReader(readerControl, x$DefaultReader, ...)  
61    
62      # Allocate memory in advance if length is known      # Allocate memory in advance if length is known
63      tdl <- if (x$Length > 0)      tdl <- if (x$length > 0) vector("list", as.integer(x$length)) else list()
         vector("list", as.integer(x$Length))  
     else  
         list()  
64    
65      if (x$Vectorized)      if (x$vectorized)
66          tdl <- mapply(function(x, id) readerControl$reader(x, readerControl$language, id),          tdl <- mapply(function(elem, id)
67                              readerControl$reader(elem, readerControl$language, id),
68                        pGetElem(x),                        pGetElem(x),
69                        id = if (is.null(x$Names)) as.character(seq_len(x$Length)) else x$Names,                        id = if (is.null(x$names) || is.na(x$names))
70                              as.character(seq_len(x$length))
71                          else x$names,
72                        SIMPLIFY = FALSE)                        SIMPLIFY = FALSE)
73      else {      else {
74          counter <- 1          counter <- 1
75          while (!eoi(x)) {          while (!eoi(x)) {
76              x <- stepNext(x)              x <- stepNext(x)
77              elem <- getElem(x)              elem <- getElem(x)
78              doc <- readerControl$reader(elem, readerControl$language, if (is.null(x$Names)) as.character(counter) else x$Names[counter])              id <- if (is.null(x$names) || is.na(x$names))
79              if (x$Length > 0)                  as.character(counter)
80                else
81                    x$names[counter]
82                doc <- readerControl$reader(elem, readerControl$language, id)
83                if (x$length > 0)
84                  tdl[[counter]] <- doc                  tdl[[counter]] <- doc
85              else              else
86                  tdl <- c(tdl, list(doc))                  tdl <- c(tdl, list(doc))
87              counter <- counter + 1              counter <- counter + 1
88          }          }
89      }      }
90      names(tdl) <- x$Names      if (!is.null(x$names) && !is.na(x$names))
91      df <- data.frame(MetaID = rep(0, length(tdl)), stringsAsFactors = FALSE)          names(tdl) <- x$names
     .VCorpus(tdl, .MetaDataNode(), df)  
 }  
92    
93  `[.PCorpus` <- function(x, i) {      structure(list(content = tdl,
94      if (missing(i)) return(x)                     meta = CorpusMeta(),
95      index <- attr(x, "DMetaData")[[1 , "subset"]]                     dmeta = data.frame(row.names = seq_along(tdl))),
96      attr(x, "DMetaData")[[1 , "subset"]] <- if (is.numeric(index)) index[i] else i                class = c("VCorpus", "Corpus"))
     dmeta <- attr(x, "DMetaData")  
     .PCorpus(NextMethod("["), CMetaData(x), dmeta, DBControl(x))  
97  }  }
98    
99  `[.VCorpus` <- function(x, i) {  `[.PCorpus` <-
100      if (missing(i)) return(x)  function(x, i)
101      .VCorpus(NextMethod("["), CMetaData(x), DMetaData(x)[i, , drop = FALSE])  {
102        if (!missing(i)) {
103            x$content <- x$content[i]
104            x$dmeta <- x$dmeta[i, , drop = FALSE]
105        }
106        x
107  }  }
108    
109  `[<-.PCorpus` <- function(x, i, value) {  `[.VCorpus` <-
110      db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])  function(x, i)
111      counter <- 1  {
112      for (id in unclass(x)[i]) {      if (!missing(i)) {
113          if (identical(length(value), 1L)) db[[id]] <- value          x$content <- x$content[i]
114          else db[[id]] <- value[[counter]]          x$dmeta <- x$dmeta[i, , drop = FALSE]
115          counter <- counter + 1          if (!is.null(x$lazy))
116                x$lazy$index <- x$lazy$index[i]
117      }      }
118      x      x
119  }  }
120    
121  .map_name_index <- function(x, i) {  .map_name_index <-
122      if (is.character(i)) {  function(x, i)
123          if (is.null(names(x)))  {
124              match(i, meta(x, "ID", type = "local"))      if (is.character(i))
125            match(i, if (is.null(names(x))) meta(x, "id", "local") else names(x))
126          else          else
             match(i, names(x))  
     }  
127      i      i
128  }  }
129    
130  `[[.PCorpus` <-  function(x, i) {  `[[.PCorpus` <-
131    function(x, i)
132    {
133      i <- .map_name_index(x, i)      i <- .map_name_index(x, i)
134      db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])      db <- filehash::dbInit(x$dbcontrol[["dbName"]], x$dbcontrol[["dbType"]])
135      filehash::dbFetch(db, NextMethod("[["))      filehash::dbFetch(db, x$content[[i]])
136  }  }
137  `[[.VCorpus` <-  function(x, i) {  `[[.VCorpus` <-
138    function(x, i)
139    {
140      i <- .map_name_index(x, i)      i <- .map_name_index(x, i)
141      lazyTmMap <- meta(x, tag = "lazyTmMap", type = "corpus")      if (!is.null(x$lazy))
142      if (!is.null(lazyTmMap))          .Call(copyCorpus, x, materialize(x, i))
143          .Call("copyCorpus", x, materialize(x, i))      x$content[[i]]
     NextMethod("[[")  
144  }  }
145    
146  `[[<-.PCorpus` <-  function(x, i, value) {  `[[<-.PCorpus` <-
147    function(x, i, value)
148    {
149      i <- .map_name_index(x, i)      i <- .map_name_index(x, i)
150      db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])      db <- filehash::dbInit(x$dbcontrol[["dbName"]], x$dbcontrol[["dbType"]])
151      index <- unclass(x)[[i]]      db[[x$content[[i]]]] <- value
     db[[index]] <- value  
152      x      x
153  }  }
154  `[[<-.VCorpus` <-  function(x, i, value) {  `[[<-.VCorpus` <-
155    function(x, i, value)
156    {
157      i <- .map_name_index(x, i)      i <- .map_name_index(x, i)
158      # Mark new objects as not active for lazy mapping      # Mark new objects as inactive for lazy mapping
159      lazyTmMap <- meta(x, tag = "lazyTmMap", type = "corpus")      if (!is.null(x$lazy))
160      if (!is.null(lazyTmMap)) {          x$lazy$index[i] <- FALSE
161          lazyTmMap$index[i] <- FALSE      x$content[[i]] <- value
         meta(x, tag = "lazyTmMap", type = "corpus") <- lazyTmMap  
     }  
     # Set the value  
     cl <- class(x)  
     y <- NextMethod("[[<-")  
     class(y) <- cl  
     y  
 }  
   
 # Update NodeIDs of a CMetaData tree  
 .update_id <- function(x, id = 0, mapping = NULL, left.mapping = NULL, level = 0) {  
     # Traversal of (binary) CMetaData tree with setup of NodeIDs  
     set_id <- function(x) {  
         x$NodeID <- id  
         id <<- id + 1  
         level <<- level + 1  
         if (length(x$Children) > 0) {  
             mapping <<- cbind(mapping, c(x$Children[[1]]$NodeID, id))  
             left <- set_id(x$Children[[1]])  
             if (level == 1) {  
                 left.mapping <<- mapping  
                 mapping <<- NULL  
             }  
             mapping <<- cbind(mapping, c(x$Children[[2]]$NodeID, id))  
             right <- set_id(x$Children[[2]])  
   
             x$Children <- list(left, right)  
         }  
         level <<- level - 1  
162          x          x
163      }      }
     list(root = set_id(x), left.mapping = left.mapping, right.mapping = mapping)  
 }  
   
 # Find indices to be updated for a CMetaData tree  
 .find_indices <- function(x) {  
     indices.mapping <- NULL  
     for (m in levels(as.factor(DMetaData(x)$MetaID))) {  
         indices <- (DMetaData(x)$MetaID == m)  
         indices.mapping <- c(indices.mapping, list(m = indices))  
         names(indices.mapping)[length(indices.mapping)] <- m  
     }  
     indices.mapping  
 }  
   
 c2 <- function(x, y, ...) {  
     # Update the CMetaData tree  
     cmeta <- .MetaDataNode(0, list(merge_date = as.POSIXlt(Sys.time(), tz = "GMT"), merger = Sys.getenv("LOGNAME")), list(CMetaData(x), CMetaData(y)))  
     update.struct <- .update_id(cmeta)  
   
     new <- .VCorpus(c(unclass(x), unclass(y)), update.struct$root, NULL)  
164    
165      # Find indices to be updated for the left tree  outer_union <-
166      indices.mapping <- .find_indices(x)  function(x, y, ...)
167    {
168      # Update the DMetaData data frames for the left tree      if (nrow(x) > 0L)
169      for (i in 1:ncol(update.struct$left.mapping)) {          x[, setdiff(names(y), names(x))] <- NA
170          map <- update.struct$left.mapping[,i]      if (nrow(y) > 0L)
171          DMetaData(x)$MetaID <- replace(DMetaData(x)$MetaID, indices.mapping[[as.character(map[1])]], map[2])          y[, setdiff(names(x), names(y))] <- NA
172      }      res <- rbind(x, y)
173        if (ncol(res) == 0L)
174      # Find indices to be updated for the right tree          res <- data.frame(row.names = seq_len(nrow(x) + nrow(y)))
175      indices.mapping <- .find_indices(y)      res
   
     # Update the DMetaData data frames for the right tree  
     for (i in 1:ncol(update.struct$right.mapping)) {  
         map <- update.struct$right.mapping[,i]  
         DMetaData(y)$MetaID <- replace(DMetaData(y)$MetaID, indices.mapping[[as.character(map[1])]], map[2])  
     }  
   
     # Merge the DMetaData data frames  
     labels <- setdiff(names(DMetaData(y)), names(DMetaData(x)))  
     na.matrix <- matrix(NA, nrow = nrow(DMetaData(x)), ncol = length(labels), dimnames = list(row.names(DMetaData(x)), labels))  
     x.dmeta.aug <- cbind(DMetaData(x), na.matrix)  
     labels <- setdiff(names(DMetaData(x)), names(DMetaData(y)))  
     na.matrix <- matrix(NA, nrow = nrow(DMetaData(y)), ncol = length(labels), dimnames = list(row.names(DMetaData(y)), labels))  
     y.dmeta.aug <- cbind(DMetaData(y), na.matrix)  
     DMetaData(new) <- rbind(x.dmeta.aug, y.dmeta.aug)  
   
     new  
176  }  }
177    
178  c.Corpus <-  c.VCorpus <-
179  function(x, ..., recursive = FALSE)  function(..., recursive = FALSE)
180  {  {
181      args <- list(...)      args <- list(...)
182        x <- args[[1L]]
183    
184      if (identical(length(args), 0L))      if (length(args) == 1L)
185          return(x)          return(x)
186    
187      if (!all(unlist(lapply(args, inherits, class(x)))))      if (!all(unlist(lapply(args, inherits, class(x)))))
188          stop("not all arguments are of the same corpus type")          stop("not all arguments are of the same corpus type")
189    
190      if (inherits(x, "PCorpus"))      structure(list(content = do.call("c", lapply(args, content)),
191          stop("concatenation of corpora with underlying databases is not supported")                     meta = structure(do.call("c",
192                         lapply(args, function(a) meta(a, type = "corpus"))),
193      l <- base::c(list(x), args)                                      class = "CorpusMeta"),
194      if (recursive)                     dmeta = Reduce(outer_union, lapply(args, meta))),
195          Reduce(c2, l)                class = c("VCorpus", "Corpus"))
     else {  
         l <- do.call("c", lapply(l, unclass))  
         .VCorpus(l,  
                  cmeta = .MetaDataNode(),  
                  dmeta = data.frame(MetaID = rep(0, length(l)), stringsAsFactors = FALSE))  
     }  
196  }  }
197    
198  c.TextDocument <- function(x, ..., recursive = FALSE) {  as.list.PCorpus <- as.list.VCorpus <-
199      args <- list(...)  function(x, ...)
200        content(x)
     if (identical(length(args), 0L))  
         return(x)  
201    
202      if (!all(unlist(lapply(args, inherits, class(x)))))  content.VCorpus <-
203          stop("not all arguments are text documents")  function(x)
204    {
205      dmeta <- data.frame(MetaID = rep(0, length(list(x, ...))), stringsAsFactors = FALSE)      if (!is.null(x$lazy))
206      .VCorpus(list(x, ...), .MetaDataNode(), dmeta)          .Call(copyCorpus, x, materialize(x))
207        x$content
208  }  }
209    
210  print.Corpus <- function(x, ...) {  content.PCorpus <-
211      cat(sprintf(ngettext(length(x),  function(x)
212                           "A corpus with %d text document\n",  {
213                           "A corpus with %d text documents\n"),      db <- filehash::dbInit(x$dbcontrol[["dbName"]], x$dbcontrol[["dbType"]])
214                  length(x)))      filehash::dbMultiFetch(db, unlist(x$content))
     invisible(x)  
215  }  }
216    
217  summary.Corpus <- function(object, ...) {  length.PCorpus <- length.VCorpus <-
218      print(object)  function(x)
219      if (length(DMetaData(object)) > 0) {      length(x$content)
         cat(sprintf(ngettext(length(attr(CMetaData(object), "MetaData")),  
                              "\nThe metadata consists of %d tag-value pair and a data frame\n",  
                              "\nThe metadata consists of %d tag-value pairs and a data frame\n"),  
                     length(CMetaData(object)$MetaData)))  
         cat("Available tags are:\n")  
         cat(strwrap(paste(names(CMetaData(object)$MetaData), collapse = " "), indent = 2, exdent = 2), "\n")  
         cat("Available variables in the data frame are:\n")  
         cat(strwrap(paste(names(DMetaData(object)), collapse = " "), indent = 2, exdent = 2), "\n")  
     }  
 }  
220    
221  inspect <- function(x) UseMethod("inspect", x)  print.PCorpus <- print.VCorpus <-
222  inspect.PCorpus <- function(x) {  function(x, ...)
223      summary(x)  {
224      cat("\n")      writeLines(sprintf("<<%s (documents: %d, metadata (corpus/indexed): %d/%d)>>",
225      db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])                         class(x)[1],
226      show(filehash::dbMultiFetch(db, unlist(x)))                         length(x),
227  }                         length(meta(x, type = "corpus")),
228  inspect.VCorpus <- function(x) {                         ncol(meta(x, type = "indexed"))))
229      summary(x)      invisible(x)
     cat("\n")  
     print(noquote(lapply(x, identity)))  
230  }  }
231    
232  lapply.PCorpus <- function(X, FUN, ...) {  inspect <-
233      db <- filehash::dbInit(DBControl(X)[["dbName"]], DBControl(X)[["dbType"]])  function(x)
234      lapply(filehash::dbMultiFetch(db, unlist(X)), FUN, ...)      UseMethod("inspect", x)
235  }  inspect.PCorpus <- inspect.VCorpus <-
236  lapply.VCorpus <- function(X, FUN, ...) {  function(x)
237      lazyTmMap <- meta(X, tag = "lazyTmMap", type = "corpus")  {
238      if (!is.null(lazyTmMap))      print(x)
239          .Call("copyCorpus", X, materialize(X))      cat("\n")
240      base::lapply(X, FUN, ...)      print(noquote(content(x)))
241        invisible(x)
242  }  }
243    
244  writeCorpus <-  function(x, path = ".", filenames = NULL) {  writeCorpus <-
245    function(x, path = ".", filenames = NULL)
246    {
247      filenames <- file.path(path,      filenames <- file.path(path,
248                             if (is.null(filenames)) unlist(lapply(x, function(x) sprintf("%s.txt", ID(x))))        if (is.null(filenames))
249              sprintf("%s.txt", as.character(meta(x, "id", "local")))
250                             else filenames)                             else filenames)
251      i <- 1  
252      for (o in x) {      stopifnot(length(x) == length(filenames))
253          writeLines(as.PlainTextDocument(o), filenames[i])  
254          i <- i + 1      mapply(function(doc, f) writeLines(as.character(doc), f), x, filenames)
255      }  
256        invisible(x)
257  }  }

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