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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 1363, Mon Apr 28 09:49:46 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 = reader(x), 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, reader(x))
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      tdl <- vector("list", length(x))
     tdl <- if (x$Length > 0)  
         vector("list", as.integer(x$Length))  
     else  
         list()  
   
23      counter <- 1      counter <- 1
24      while (!eoi(x)) {      while (!eoi(x)) {
25          x <- stepNext(x)          x <- stepNext(x)
26          elem <- getElem(x)          elem <- getElem(x)
27          doc <- readerControl$reader(elem, readerControl$language, if (is.null(x$Names)) as.character(counter) else x$Names[counter])          id <- if (is.null(names(x)))
28          filehash::dbInsert(db, ID(doc), doc)              as.character(counter)
29          if (x$Length > 0) tdl[[counter]] <- ID(doc)          else
30          else tdl <- c(tdl, ID(doc))              names(x)[counter]
31            doc <- readerControl$reader(elem, readerControl$language, id)
32            filehash::dbInsert(db, meta(doc, "id"), doc)
33            tdl[[counter]] <- meta(doc, "id")
34          counter <- counter + 1          counter <- counter + 1
35      }      }
36      names(tdl) <- x$Names      if (!is.null(names(x)))
37            names(tdl) <- names(x)
38    
39      df <- data.frame(MetaID = rep(0, length(tdl)), stringsAsFactors = FALSE)      structure(list(content = tdl,
40      filehash::dbInsert(db, "DMetaData", df)                     meta = CorpusMeta(),
41      dmeta.df <- data.frame(key = "DMetaData", subset = I(list(NA)))                     dmeta = data.frame(row.names = seq_along(tdl)),
42                       dbcontrol = dbControl),
43      .PCorpus(tdl, .MetaDataNode(), dmeta.df, dbControl)                class = c("PCorpus", "Corpus"))
44  }  }
45    
46  .VCorpus <- function(x, cmeta, dmeta) {  Corpus <-
47      attr(x, "CMetaData") <- cmeta  VCorpus <-
48      attr(x, "DMetaData") <- dmeta  function(x, readerControl = list(reader = reader(x), language = "en"))
49      class(x) <- c("VCorpus", "Corpus", "list")  {
50      x      stopifnot(inherits(x, "Source"))
 }  
51    
52  # Register S3 corpus classes to be recognized by S4 methods. This is      readerControl <- prepareReader(readerControl, reader(x))
53  # mainly a fix to be compatible with packages which were originally  
54  # developed to cooperate with corresponding S4 tm classes. Necessary      if (is.function(readerControl$init))
55  # since tm's class architecture was changed to S3 since tm version 0.5.          readerControl$init()
56  setOldClass(c("VCorpus", "Corpus", "list"))  
57        if (is.function(readerControl$exit))
58  # The "..." are additional arguments for the FunctionGenerator reader          on.exit(readerControl$exit())
 VCorpus <- Corpus <- function(x,  
                               readerControl = list(reader = x$DefaultReader, language = "en"),  
                               ...) {  
     readerControl <- prepareReader(readerControl, x$DefaultReader, ...)  
   
     # Allocate memory in advance if length is known  
     tdl <- if (x$Length > 0)  
         vector("list", as.integer(x$Length))  
     else  
         list()  
59    
60      if (x$Vectorized)      tdl <- vector("list", length(x))
61          tdl <- mapply(function(x, id) readerControl$reader(x, readerControl$language, id),      # Check for parallel element access
62        if (is.function(getS3method("pGetElem", class(x), TRUE)))
63            tdl <- mapply(function(elem, id)
64                              readerControl$reader(elem, readerControl$language, id),
65                        pGetElem(x),                        pGetElem(x),
66                        id = if (is.null(x$Names)) as.character(seq_len(x$Length)) else x$Names,                        id = if (is.null(names(x)))
67                              as.character(seq_len(length(x)))
68                          else names(x),
69                        SIMPLIFY = FALSE)                        SIMPLIFY = FALSE)
70      else {      else {
71          counter <- 1          counter <- 1
72          while (!eoi(x)) {          while (!eoi(x)) {
73              x <- stepNext(x)              x <- stepNext(x)
74              elem <- getElem(x)              elem <- getElem(x)
75              doc <- readerControl$reader(elem, readerControl$language, if (is.null(x$Names)) as.character(counter) else x$Names[counter])              id <- if (is.null(names(x)))
76              if (x$Length > 0)                  as.character(counter)
                 tdl[[counter]] <- doc  
77              else              else
78                  tdl <- c(tdl, list(doc))                  names(x)[counter]
79                doc <- readerControl$reader(elem, readerControl$language, id)
80                tdl[[counter]] <- doc
81              counter <- counter + 1              counter <- counter + 1
82          }          }
83      }      }
84      names(tdl) <- x$Names      if (!is.null(names(x)))
85      df <- data.frame(MetaID = rep(0, length(tdl)), stringsAsFactors = FALSE)          names(tdl) <- names(x)
     .VCorpus(tdl, .MetaDataNode(), df)  
 }  
86    
87  `[.PCorpus` <- function(x, i) {      structure(list(content = tdl,
88      if (missing(i)) return(x)                     meta = CorpusMeta(),
89      index <- attr(x, "DMetaData")[[1 , "subset"]]                     dmeta = data.frame(row.names = seq_along(tdl))),
90      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))  
91  }  }
92    
93  `[.VCorpus` <- function(x, i) {  `[.PCorpus` <-
94      if (missing(i)) return(x)  function(x, i)
95      .VCorpus(NextMethod("["), CMetaData(x), DMetaData(x)[i, , drop = FALSE])  {
96        if (!missing(i)) {
97            x$content <- x$content[i]
98            x$dmeta <- x$dmeta[i, , drop = FALSE]
99        }
100        x
101  }  }
102    
103  `[<-.PCorpus` <- function(x, i, value) {  `[.VCorpus` <-
104      db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])  function(x, i)
105      counter <- 1  {
106      for (id in unclass(x)[i]) {      if (!missing(i)) {
107          if (identical(length(value), 1L)) db[[id]] <- value          x$content <- x$content[i]
108          else db[[id]] <- value[[counter]]          x$dmeta <- x$dmeta[i, , drop = FALSE]
109          counter <- counter + 1          if (!is.null(x$lazy))
110                x$lazy$index <- x$lazy$index[i]
111      }      }
112      x      x
113  }  }
114    
115  .map_name_index <- function(x, i) {  .map_name_index <-
116    function(x, i)
117    {
118      if (is.character(i)) {      if (is.character(i)) {
119          if (is.null(names(x)))          n <- names(x$content)
120              match(i, meta(x, "ID", type = "local"))          match(i, if (is.null(n)) meta(x, "id", "local") else n)
121          else      } else
             match(i, names(x))  
     }  
122      i      i
123  }  }
124    
125  `[[.PCorpus` <-  function(x, i) {  `[[.PCorpus` <-
126    function(x, i)
127    {
128      i <- .map_name_index(x, i)      i <- .map_name_index(x, i)
129      db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])      db <- filehash::dbInit(x$dbcontrol[["dbName"]], x$dbcontrol[["dbType"]])
130      filehash::dbFetch(db, NextMethod("[["))      filehash::dbFetch(db, x$content[[i]])
131  }  }
132  `[[.VCorpus` <-  function(x, i) {  `[[.VCorpus` <-
133    function(x, i)
134    {
135      i <- .map_name_index(x, i)      i <- .map_name_index(x, i)
136      lazyTmMap <- meta(x, tag = "lazyTmMap", type = "corpus")      if (!is.null(x$lazy))
137      if (!is.null(lazyTmMap))          .Call(copyCorpus, x, materialize(x, i))
138          .Call("copyCorpus", x, materialize(x, i))      x$content[[i]]
     NextMethod("[[")  
139  }  }
140    
141  `[[<-.PCorpus` <-  function(x, i, value) {  `[[<-.PCorpus` <-
142    function(x, i, value)
143    {
144      i <- .map_name_index(x, i)      i <- .map_name_index(x, i)
145      db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])      db <- filehash::dbInit(x$dbcontrol[["dbName"]], x$dbcontrol[["dbType"]])
146      index <- unclass(x)[[i]]      db[[x$content[[i]]]] <- value
     db[[index]] <- value  
147      x      x
148  }  }
149  `[[<-.VCorpus` <-  function(x, i, value) {  `[[<-.VCorpus` <-
150    function(x, i, value)
151    {
152      i <- .map_name_index(x, i)      i <- .map_name_index(x, i)
153      # Mark new objects as not active for lazy mapping      # Mark new objects as inactive for lazy mapping
154      lazyTmMap <- meta(x, tag = "lazyTmMap", type = "corpus")      if (!is.null(x$lazy))
155      if (!is.null(lazyTmMap)) {          x$lazy$index[i] <- FALSE
156          lazyTmMap$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  
157          x          x
158      }      }
     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  
 }  
159    
160  c2 <- function(x, y, ...) {  as.list.PCorpus <- as.list.VCorpus <-
161      # Update the CMetaData tree  function(x, ...)
162      cmeta <- .MetaDataNode(0, list(merge_date = as.POSIXlt(Sys.time(), tz = "GMT"), merger = Sys.getenv("LOGNAME")), list(CMetaData(x), CMetaData(y)))      content(x)
163      update.struct <- .update_id(cmeta)  
164    as.VCorpus <-
165    function(x)
166        UseMethod("as.VCorpus")
167    as.VCorpus.VCorpus <- identity
168    
169      new <- .VCorpus(c(unclass(x), unclass(y)), update.struct$root, NULL)  outer_union <-
170    function(x, y, ...)
171      # Find indices to be updated for the left tree  {
172      indices.mapping <- .find_indices(x)      if (nrow(x) > 0L)
173            x[, setdiff(names(y), names(x))] <- NA
174      # Update the DMetaData data frames for the left tree      if (nrow(y) > 0L)
175      for (i in 1:ncol(update.struct$left.mapping)) {          y[, setdiff(names(x), names(y))] <- NA
176          map <- update.struct$left.mapping[,i]      res <- rbind(x, y)
177          DMetaData(x)$MetaID <- replace(DMetaData(x)$MetaID, indices.mapping[[as.character(map[1])]], map[2])      if (ncol(res) == 0L)
178      }          res <- data.frame(row.names = seq_len(nrow(x) + nrow(y)))
179        res
     # Find indices to be updated for the right tree  
     indices.mapping <- .find_indices(y)  
   
     # 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  
180  }  }
181    
182  c.Corpus <-  c.VCorpus <-
183  function(x, ..., recursive = FALSE)  function(..., recursive = FALSE)
184  {  {
185      args <- list(...)      args <- list(...)
186        x <- args[[1L]]
187    
188      if (identical(length(args), 0L))      if (length(args) == 1L)
189          return(x)          return(x)
190    
191      if (!all(unlist(lapply(args, inherits, class(x)))))      if (!all(unlist(lapply(args, inherits, class(x)))))
192          stop("not all arguments are of the same corpus type")          stop("not all arguments are of the same corpus type")
193    
194      if (inherits(x, "PCorpus"))      structure(list(content = do.call("c", lapply(args, content)),
195          stop("concatenation of corpora with underlying databases is not supported")                     meta = structure(do.call("c",
196                         lapply(args, function(a) meta(a, type = "corpus"))),
197      l <- base::c(list(x), args)                                      class = "CorpusMeta"),
198      if (recursive)                     dmeta = Reduce(outer_union, lapply(args, meta))),
199          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))  
     }  
200  }  }
201    
202  c.TextDocument <- function(x, ..., recursive = FALSE) {  content.VCorpus <-
203      args <- list(...)  function(x)
204    {
205      if (identical(length(args), 0L))      if (!is.null(x$lazy))
206          return(x)          .Call(copyCorpus, x, materialize(x))
207        x$content
     if (!all(unlist(lapply(args, inherits, class(x)))))  
         stop("not all arguments are text documents")  
   
     dmeta <- data.frame(MetaID = rep(0, length(list(x, ...))), stringsAsFactors = FALSE)  
     .VCorpus(list(x, ...), .MetaDataNode(), dmeta)  
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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