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Diff of /pkg/R/corpus.R

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revision 988, Fri Sep 4 12:27:12 2009 UTC revision 1419, Sat May 2 17:23:47 2015 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"))
 }  
 DBControl <- function(x) attr(x, "DBControl")  
9    
10  PCorpus <- function(x,      readerControl <- prepareReader(readerControl, reader(x))
                     readerControl = list(reader = x$DefaultReader, language = "eng"),  
                     dbControl = list(dbName = "", dbType = "DB1"),  
                     ...) {  
     readerControl <- prepareReader(readerControl, x$DefaultReader, ...)  
11    
12      if (!filehash::dbCreate(dbControl$dbName, dbControl$dbType))      if (!filehash::dbCreate(dbControl$dbName, dbControl$dbType))
13          stop("error in creating database")          stop("error in creating database")
14      db <- filehash::dbInit(dbControl$dbName, dbControl$dbType)      db <- filehash::dbInit(dbControl$dbName, dbControl$dbType)
15    
16      # Allocate memory in advance if length is known      x <- open(x)
17      tdl <- if (x$Length > 0)      tdl <- vector("list", length(x))
         vector("list", as.integer(x$Length))  
     else  
         list()  
   
18      counter <- 1      counter <- 1
19      while (!eoi(x)) {      while (!eoi(x)) {
20          x <- stepNext(x)          x <- stepNext(x)
21          elem <- getElem(x)          elem <- getElem(x)
22          doc <- readerControl$reader(elem, readerControl$language, as.character(counter))          doc <- readerControl$reader(elem,
23          filehash::dbInsert(db, ID(doc), doc)                                      readerControl$language,
24          if (x$Length > 0) tdl[[counter]] <- ID(doc)                                      as.character(counter))
25          else tdl <- c(tdl, ID(doc))          filehash::dbInsert(db, meta(doc, "id"), doc)
26            tdl[[counter]] <- meta(doc, "id")
27          counter <- counter + 1          counter <- counter + 1
28      }      }
29        x <- close(x)
30    
31      df <- data.frame(MetaID = rep(0, length(tdl)), stringsAsFactors = FALSE)      p <- list(content = tdl,
32      filehash::dbInsert(db, "DMetaData", df)                meta = CorpusMeta(),
33      dmeta.df <- data.frame(key = "DMetaData", subset = I(list(NA)))                dmeta = data.frame(row.names = seq_along(tdl)),
34                  dbcontrol = dbControl)
35      .PCorpus(tdl, .MetaDataNode(), dmeta.df, dbControl)      class(p) <- c("PCorpus", "Corpus")
36        p
37  }  }
38    
39  .VCorpus <- function(x, cmeta, dmeta) {  Corpus <-
40      attr(x, "CMetaData") <- cmeta  VCorpus <-
41      attr(x, "DMetaData") <- dmeta  function(x, readerControl = list(reader = reader(x), language = "en"))
42      class(x) <- c("VCorpus", "Corpus", "list")  {
43      x      stopifnot(inherits(x, "Source"))
 }  
44    
45  # The "..." are additional arguments for the FunctionGenerator reader      readerControl <- prepareReader(readerControl, reader(x))
 VCorpus <- Corpus <- function(x,  
                     readerControl = list(reader = x$DefaultReader, language = "eng"),  
                     ...) {  
     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()  
46    
47      if (x$Vectorized)      x <- open(x)
48          tdl <- mapply(function(x, id) readerControl$reader(x, readerControl$language, id),      tdl <- vector("list", length(x))
49        # Check for parallel element access
50        if (is.function(getS3method("pGetElem", class(x), TRUE)))
51            tdl <- mapply(function(elem, id)
52                              readerControl$reader(elem, readerControl$language, id),
53                        pGetElem(x),                        pGetElem(x),
54                        id = as.character(seq_len(x$Length)),                        id = as.character(seq_along(x)),
55                        SIMPLIFY = FALSE)                        SIMPLIFY = FALSE)
56      else {      else {
57          counter <- 1          counter <- 1
58          while (!eoi(x)) {          while (!eoi(x)) {
59              x <- stepNext(x)              x <- stepNext(x)
60              elem <- getElem(x)              elem <- getElem(x)
61              doc <- readerControl$reader(elem, readerControl$language, as.character(counter))              doc <- readerControl$reader(elem,
62              if (x$Length > 0)                                          readerControl$language,
63                                            as.character(counter))
64                  tdl[[counter]] <- doc                  tdl[[counter]] <- doc
             else  
                 tdl <- c(tdl, list(doc))  
65              counter <- counter + 1              counter <- counter + 1
66          }          }
67      }      }
68        x <- close(x)
69    
70      df <- data.frame(MetaID = rep(0, length(tdl)), stringsAsFactors = FALSE)      as.VCorpus(tdl)
     .VCorpus(tdl, .MetaDataNode(), df)  
 }  
   
 `[.PCorpus` <- function(x, i) {  
     if (missing(i)) return(x)  
     cmeta <- CMetaData(x)  
     index <- attr(x, "DMetaData")[[1 , "subset"]]  
     attr(x, "DMetaData")[[1 , "subset"]] <- if (is.numeric(index)) index[i] else i  
     dmeta <- attr(x, "DMetaData")  
     dbcontrol <- DBControl(x)  
     class(x) <- "list"  
     .PCorpus(x[i, drop = FALSE], cmeta, dmeta, dbcontrol)  
 }  
   
 `[.VCorpus` <- function(x, i) {  
     if (missing(i)) return(x)  
     cmeta <- CMetaData(x)  
     dmeta <- DMetaData(x)[i, , drop = FALSE]  
     class(x) <- "list"  
     .VCorpus(x[i, drop = FALSE], cmeta, dmeta)  
71  }  }
72    
73  `[<-.PCorpus` <- function(x, i, value) {  `[.PCorpus` <-
74      db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])  function(x, i)
75      counter <- 1  {
76      for (id in unclass(x)[i]) {      if (!missing(i)) {
77          if (identical(length(value), 1)) db[[id]] <- value          x$content <- x$content[i]
78          else db[[id]] <- value[[counter]]          x$dmeta <- x$dmeta[i, , drop = FALSE]
         counter <- counter + 1  
79      }      }
80      x      x
81  }  }
82    
83  `[[.PCorpus` <-  function(x, i) {  `[.VCorpus` <-
84      db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])  function(x, i)
85      class(x) <- "list"  {
86      filehash::dbFetch(db, x[[i]])      if (!missing(i)) {
87  }          x$content <- x$content[i]
88  `[[.VCorpus` <-  function(x, i) {          x$dmeta <- x$dmeta[i, , drop = FALSE]
89      lazyTmMap <- meta(x, tag = "lazyTmMap", type = "corpus")          if (!is.null(x$lazy))
90      if (!is.null(lazyTmMap))              x$lazy$index <- x$lazy$index[i]
         .Call("copyCorpus", x, materialize(x, i))  
     class(x) <- "list"  
     x[[i]]  
 }  
   
 `[[<-.PCorpus` <-  function(x, i, value) {  
     db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])  
     index <- unclass(x)[[i]]  
     db[[index]] <- value  
     x  
91  }  }
 `[[<-.VCorpus` <-  function(x, i, value) {  
     # Mark new objects as not active for lazy mapping  
     lazyTmMap <- meta(x, tag = "lazyTmMap", type = "corpus")  
     if (!is.null(lazyTmMap)) {  
         lazyTmMap$index[i] <- FALSE  
         meta(x, tag = "lazyTmMap", type = "corpus") <- lazyTmMap  
     }  
     # Set the value  
     cl <- class(x)  
     class(x) <- "list"  
     x[[i]] <- value  
     class(x) <- cl  
92      x      x
93  }  }
94    
95  # Update \code{NodeID}s of a CMetaData tree  .map_name_index <-
96  update_id <- function(x, id = 0, mapping = NULL, left.mapping = NULL, level = 0) {  function(x, i)
97      # Traversal of (binary) CMetaData tree with setup of \code{NodeID}s  {
98      set_id <- function(x) {      if (is.character(i))
99          x$NodeID <- id          match(i, meta(x, "id", "local"))
100          id <<- id + 1      else
101          level <<- level + 1          i
         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  
102              }              }
             mapping <<- cbind(mapping, c(x$Children[[2]]$NodeID, id))  
             right <- set_id(x$Children[[2]])  
103    
104              x$Children <- list(left, right)  `[[.PCorpus` <-
105          }  function(x, i)
106          level <<- level - 1  {
107          x      i <- .map_name_index(x, i)
108      }      db <- filehash::dbInit(x$dbcontrol[["dbName"]], x$dbcontrol[["dbType"]])
109      list(root = set_id(x), left.mapping = left.mapping, right.mapping = mapping)      filehash::dbFetch(db, x$content[[i]])
110  }  }
111    `[[.VCorpus` <-
112  c2 <- function(x, y, ...) {  function(x, i)
113      # Update the CMetaData tree  {
114      cmeta <- .MetaDataNode(0, list(merge_date = as.POSIXlt(Sys.time(), tz = "GMT"), merger = Sys.getenv("LOGNAME")), list(CMetaData(x), CMetaData(y)))      i <- .map_name_index(x, i)
115      update.struct <- update_id(cmeta)      if (!is.null(x$lazy))
116            .Call(copyCorpus, x, materialize(x, i))
117      new <- .VCorpus(c(unclass(x), unclass(y)), update.struct$root, NULL)      x$content[[i]]
   
     # Find indices to be updated for the left tree  
     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  
118      }      }
119    
120      # Update the DMetaData data frames for the left tree  `[[<-.PCorpus` <-
121      for (i in 1:ncol(update.struct$left.mapping)) {  function(x, i, value)
122          map <- update.struct$left.mapping[,i]  {
123          DMetaData(x)$MetaID <- replace(DMetaData(x)$MetaID, indices.mapping[[as.character(map[1])]], map[2])      i <- .map_name_index(x, i)
124        db <- filehash::dbInit(x$dbcontrol[["dbName"]], x$dbcontrol[["dbType"]])
125        db[[x$content[[i]]]] <- value
126        x
127      }      }
128    `[[<-.VCorpus` <-
129      # Find indices to be updated for the right tree  function(x, i, value)
130      indices.mapping <- NULL  {
131      for (m in levels(as.factor(DMetaData(y)$MetaID))) {      i <- .map_name_index(x, i)
132          indices <- (DMetaData(y)$MetaID == m)      # Mark new objects as inactive for lazy mapping
133          indices.mapping <- c(indices.mapping, list(m = indices))      if (!is.null(x$lazy))
134          names(indices.mapping)[length(indices.mapping)] <- m          x$lazy$index[i] <- FALSE
135        x$content[[i]] <- value
136        x
137      }      }
138    
139      # Update the DMetaData data frames for the right tree  as.list.PCorpus <- as.list.VCorpus <-
140      for (i in 1:ncol(update.struct$right.mapping)) {  function(x, ...)
141          map <- update.struct$right.mapping[,i]      setNames(content(x), as.character(lapply(content(x), meta, "id")))
142          DMetaData(y)$MetaID <- replace(DMetaData(y)$MetaID, indices.mapping[[as.character(map[1])]], map[2])  
143    as.VCorpus <-
144    function(x)
145        UseMethod("as.VCorpus")
146    as.VCorpus.VCorpus <- identity
147    as.VCorpus.list <-
148    function(x)
149    {
150        v <- list(content = x,
151                  meta = CorpusMeta(),
152                  dmeta = data.frame(row.names = seq_along(x)))
153        class(v) <- c("VCorpus", "Corpus")
154        v
155      }      }
156    
157      # Merge the DMetaData data frames  outer_union <-
158      labels <- setdiff(names(DMetaData(y)), names(DMetaData(x)))  function(x, y, ...)
159      na.matrix <- matrix(NA, nrow = nrow(DMetaData(x)), ncol = length(labels), dimnames = list(row.names(DMetaData(x)), labels))  {
160      x.dmeta.aug <- cbind(DMetaData(x), na.matrix)      if (nrow(x) > 0L)
161      labels <- setdiff(names(DMetaData(x)), names(DMetaData(y)))          x[, setdiff(names(y), names(x))] <- NA
162      na.matrix <- matrix(NA, nrow = nrow(DMetaData(y)), ncol = length(labels), dimnames = list(row.names(DMetaData(y)), labels))      if (nrow(y) > 0L)
163      y.dmeta.aug <- cbind(DMetaData(y), na.matrix)          y[, setdiff(names(x), names(y))] <- NA
164      DMetaData(new) <- rbind(x.dmeta.aug, y.dmeta.aug)      res <- rbind(x, y)
165        if (ncol(res) == 0L)
166      new          res <- data.frame(row.names = seq_len(nrow(x) + nrow(y)))
167        res
168  }  }
169    
170  c.Corpus <-  c.VCorpus <-
171  function(x, ..., recursive = FALSE)  function(..., recursive = FALSE)
172  {  {
173      args <- list(...)      args <- list(...)
174        x <- args[[1L]]
175    
176      if (identical(length(args), 0))      if (length(args) == 1L)
177          return(x)          return(x)
178    
179      if (!all(unlist(lapply(args, inherits, class(x)))))      if (!all(unlist(lapply(args, inherits, class(x)))))
180          stop("not all arguments are of the same corpus type")          stop("not all arguments are of the same corpus type")
181    
182      if (inherits(x, "PCorpus"))      v <- list(content = do.call("c", lapply(args, content)),
183          stop("concatenation of corpora with underlying databases is not supported")                meta = CorpusMeta(meta = do.call("c",
184                    lapply(args, function(a) meta(a, type = "corpus")))),
185      Reduce(c2, base::c(list(x), args))                dmeta = Reduce(outer_union, lapply(args, meta)))
186        class(v) <- c("VCorpus", "Corpus")
187        v
188  }  }
189    
190  c.TextDocument <- function(x, ..., recursive = FALSE) {  content.VCorpus <-
191      args <- list(...)  function(x)
192    {
193      if (identical(length(args), 0))      if (!is.null(x$lazy))
194          return(x)          .Call(copyCorpus, x, materialize(x))
195        x$content
196      if (!all(unlist(lapply(args, inherits, class(x)))))  }
         stop("not all arguments are text documents")  
197    
198      dmeta <- data.frame(MetaID = rep(0, length(list(x, ...))), stringsAsFactors = FALSE)  content.PCorpus <-
199      .VCorpus(list(x, ...), .MetaDataNode(), dmeta)  function(x)
200    {
201        db <- filehash::dbInit(x$dbcontrol[["dbName"]], x$dbcontrol[["dbType"]])
202        filehash::dbMultiFetch(db, unlist(x$content))
203  }  }
204    
205  print.Corpus <- function(x, ...) {  inspect <-
206      cat(sprintf(ngettext(length(x),  function(x)
207                           "A corpus with %d text document\n",      UseMethod("inspect", x)
208                           "A corpus with %d text documents\n"),  inspect.PCorpus <- inspect.VCorpus <-
209                  length(x)))  function(x)
210    {
211        print(x)
212        cat("\n")
213        print(noquote(content(x)))
214      invisible(x)      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$content)
220          cat(sprintf(ngettext(length(attr(CMetaData(object), "MetaData")),  
221                               "\nThe metadata consists of %d tag-value pair and a data frame\n",  names.PCorpus <- names.VCorpus <-
222                               "\nThe metadata consists of %d tag-value pairs and a data frame\n"),  function(x)
223                      length(CMetaData(object)$MetaData)))      as.character(meta(x, "id", "local"))
         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")  
     }  
 }  
224    
225  inspect <- function(x) UseMethod("inspect", x)  `names<-.PCorpus` <- `names<-.VCorpus` <-
226  inspect.PCorpus <- function(x) {  function(x, value)
227      summary(x)  {
228      cat("\n")      meta(x, "id", "local") <- as.character(value)
229      db <- filehash::dbInit(DBControl(x)[["dbName"]], DBControl(x)[["dbType"]])      x
     show(filehash::dbMultiFetch(db, unlist(x)))  
 }  
 inspect.VCorpus <- function(x) {  
     summary(x)  
     cat("\n")  
     print(noquote(lapply(x, identity)))  
230  }  }
231    
232  lapply.PCorpus <- function(X, FUN, ...) {  format.PCorpus <- format.VCorpus <-
233      db <- filehash::dbInit(DBControl(X)[["dbName"]], DBControl(X)[["dbType"]])  function(x, ...)
234      lapply(filehash::dbMultiFetch(db, unlist(X)), FUN, ...)  {
235  }      c(sprintf("<<%s>>", class(x)[1L]),
236  lapply.VCorpus <- function(X, FUN, ...) {        sprintf("Metadata:  corpus specific: %d, document level (indexed): %d",
237      lazyTmMap <- meta(X, tag = "lazyTmMap", type = "corpus")                length(meta(x, type = "corpus")),
238      if (!is.null(lazyTmMap))                ncol(meta(x, type = "indexed"))),
239          .Call("copyCorpus", X, materialize(X))        sprintf("Content:  documents: %d", length(x)))
     base::lapply(X, FUN, ...)  
240  }  }
241    
242  writeCorpus <-  function(x, path = ".", filenames = NULL) {  writeCorpus <-
243    function(x, path = ".", filenames = NULL)
244    {
245      filenames <- file.path(path,      filenames <- file.path(path,
246                             if (is.null(filenames)) unlist(lapply(x, function(x) sprintf("%s.txt", ID(x))))        if (is.null(filenames))
247              sprintf("%s.txt", as.character(meta(x, "id", "local")))
248                             else filenames)                             else filenames)
249      i <- 1  
250      for (o in x) {      stopifnot(length(x) == length(filenames))
251          writeLines(as.PlainTextDocument(o), filenames[i])  
252          i <- i + 1      mapply(function(doc, f) writeLines(as.character(doc), f), x, filenames)
253      }  
254        invisible(x)
255  }  }

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