Nothing
R/htmlValue-methods.R
In biocViews: Categorized views of R package repositories
Defines functions
viewsHelper
cleanText
tableHelper
writeHtmlDoc
Documented in
writeHtmlDoc
writeHtmlDoc <- function(html, file)
{
## Temporary fix: we open and close 'file' here instead of passing it
## directly to saveXML because of a bug in current XML::saveXML
## (from XML 1.3-2). Bug reported to XML's author on 2006-12-14. Herve.
f <- file(file, open="w")
## another temp fix: write the DOCTYPE header here, perhaps we should
## use prefix for this in the call to saveXML?
writeLines(paste('<!DOCTYPE html PUBLIC',
'"-//W3C//DTD XHTML 1.0 Strict//EN"',
'"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">'),
con=f)
saveXML(html, f, prefix="")
close(f)
}
tableHelper <- function(tableData, table.attrs) {
dom <- xmlOutputDOM("table", attrs=table.attrs)
odd <- TRUE
for (fld in names(tableData)) {
rowClass <- if(odd) "row_odd" else "row_even"
odd <- !odd
dom$addTag("tr", attrs=c(class=rowClass), close=FALSE)
dom$addTag("th", fld)
dom$addTag("td", tableData[[fld]])
dom$closeTag()
}
dom$closeTag() ## end details table
dom$value()
}
cleanText <- function(text) {
text <- gsub("&([a-zA-Z0-9#]+;)", "@_@_@\\1", text)
text <- gsub("&", "&", text, fixed=TRUE)
text <- gsub("@_@_@([a-zA-Z0-9#]+;)", "&\\1", text)
text <- gsub("<", "<", text, fixed=TRUE)
text <- gsub(">", ">", text, fixed=TRUE)
text
}
setMethod("htmlValue", signature(object="rdPackageTable"),
function(object) {
dom <- xmlOutputDOM("table", attrs=c(class="repos_index"))
odd <- TRUE
alphaOrder <- order(tolower(names(object@packageList)))
dom$addTag("tr", close=FALSE)
dom$addTag("th", "Package")
dom$addTag("th", "Maintainer")
dom$addTag("th", "Title")
dom$closeTag()
for (pkg in object@packageList[alphaOrder]) {
rowClass <- if(odd) "row_odd" else "row_even"
odd <- !odd
dom$addTag("tr", attrs=c(class=rowClass), close=FALSE)
dom$addTag("td", attrs=c(class="package"), close=FALSE)
if (length(object@reposRoot) > 0)
root <- paste(object@reposRoot, object@htmlDir, sep="/")
else
root <- object@htmlDir
infoPage <- paste(root, htmlFilename(pkg), sep="/")
dom$addTag("a", attrs=c(href=infoPage), pkg@Package)
dom$closeTag()
dom$addTag("td", removeEmail(pkg@Maintainer),
attrs=c(class="maintainer"))
dom$addTag("td", pkg@Title, attrs=c(class="title"))
dom$closeTag() ## end tr
}
dom$value()
})
setMethod("htmlValue", signature(object="RepositoryDetail"),
function(object) {
dom <- xmlOutputDOM("div", attrs=c(class="RepositoryDetail"))
dom$addTag("h1", cleanText(object@Title))
## Package table
pkgTable <- as(object, "rdPackageTable")
dom$addNode(htmlValue(pkgTable))
dom$value()
})
setMethod("htmlValue", signature(object="pdAuthorMaintainerInfo"),
function(object) {
dom <- xmlOutputDOM("table", attrs=c(class="author_info"))
dom$addTag("tr", close=FALSE)
dom$addTag("td", "Author")
dom$addTag("td", cleanText(removeEmail(object@Author)))
dom$closeTag()
dom$addTag("tr", close=FALSE)
dom$addTag("td", "Maintainer")
dom$addTag("td", cleanText(removeEmail(object@Maintainer)))
dom$closeTag()
dom$value()
})
setMethod("htmlValue", signature(object="pdVignetteInfo"),
function(object) {
dom <- xmlOutputDOM("table", attrs=c(class="vignette"))
odd <- TRUE
rowClass <- "row_odd"
if (length(object@vignettes) > 0) {
vignetteTitles <-
ifelse(nzchar(object@vignetteTitles), object@vignetteTitles,
basename(object@vignettes))
for (i in order(vignetteTitles)) {
rowClass <- if(odd) "row_odd" else "row_even"
dom$addTag("tr", attrs=c(class=rowClass), close=FALSE)
dom$addTag("th", vignetteTitles[i])
dom$addTag("td", close=FALSE)
pdflink <-
paste(object@reposRoot, object@vignettes[i], sep="/")
dom$addTag("a", "PDF", attrs=c(href=pdflink))
dom$closeTag()
if (nchar(object@vignetteScripts[i]) > 0) {
dom$addTag("td", close=FALSE)
Rlink <-
paste(object@reposRoot, object@vignetteScripts[i],
sep="/")
dom$addTag("a", "R Script", attrs=c(href=Rlink))
dom$closeTag()
}
dom$closeTag() ## end tr
odd <- !odd
}
} else {
dom$addTag("tr", attrs=c(class=rowClass), close=FALSE)
dom$addTag("td", "No vignettes available")
dom$closeTag()
odd <- !odd
}
rowClass <- if(odd) "row_odd" else "row_even"
if (length(object@manuals) > 0 && !is.na(object@manuals[1])) {
dom$addTag("tr", attrs=c(class=rowClass), close=FALSE)
dom$addTag("td", close=FALSE)
mlink <- paste(object@reposRoot, object@manuals[1], sep="/")
dom$addTag("a", "Reference Manual", attrs=c(href=mlink))
dom$closeTag()
dom$closeTag() ## end tr
odd <- !odd
} else {
dom$addTag("tr", attrs=c(class=rowClass), close=FALSE)
dom$addTag("td", "No reference manual available")
dom$closeTag()
odd <- !odd
}
dom$value()
})
setMethod("htmlValue", signature(object="pdDownloadInfo"),
function(object) {
flds <- c(source="source.ver",
win.binary="win.binary.ver",
mac.binary="mac.binary.ver",
mac.binary.mavericks="mac.binary.mavericks.ver",
`mac.binary.el-capitan`="mac.binary.el-capitan.ver")
fileTypes <- list(source="Package source",
win.binary="Windows 32-bit binary",
mac.binary="macOS 10.13 (High Sierra) binary",
mac.binary.mavericks="MacOS X 10.9 (Mavericks) binary",
`mac.binary.el-capitan`="MacOS X 10.11 (El Capitan) binary")
makeLinkHelper <- function(type) {
isAvailable = TRUE
archs <- slot(object, "Archs")
if (length(archs) > 0 && nchar(archs) > 0) {
if (type == "win.binary") {
if (length(grep("i386", archs, value=TRUE)) == 0) {
isAvailable = FALSE
}
}
}
pkgPath <- slot(object, flds[type])
if (isAvailable && !is.na(pkgPath) && length(pkgPath) > 0 && pkgPath != "") {
ref <- paste(object@reposRoot, pkgPath, sep="/")
aTag <- xmlNode("a", basename(pkgPath), attrs=c(href=ref))
} else {
aTag <- "Not Available"
}
aTag
}
fileLinks <- lapply(names(fileTypes), makeLinkHelper)
names(fileLinks) <- fileTypes
downloadStatsUrl <- slot(object, "downloadStatsUrl")
if ((length(downloadStatsUrl) == 1) &&
(nchar(downloadStatsUrl) > 0)) {
fileLinks <- c(fileLinks,
list("Package Downloads Report" =
xmlNode("a", "Downloads Stats",
attrs=c(href=paste(downloadStatsUrl, "/",
slot(object, "Package"),
".html", sep="")))))
}
domValue <- tableHelper(fileLinks,
table.attrs=list(class="downloads"))
domValue
})
setMethod("htmlValue", signature(object="pdDetailsInfo"),
function(object) {
## link generating functions
buildLinks <- function(x, root, class, check = FALSE) {
nodes <-
lapply(x,
function(y) {
urlError <- FALSE
if (nchar(y) == 0 || length(root) == 0) {
urlError <- TRUE
} else {
if (check) {
oldWarn <- options()[["warn"]]
options(warn = -1)
for (i in seq_len(length(root))) {
link <- paste(root[i], "/", y, ".html", sep="")
con <- try(url(link, "r"), silent = TRUE)
if (class(con)[[1]] != "try-error")
break;
}
options(warn = oldWarn)
if (class(con)[[1]] == "try-error") {
urlError <- TRUE
} else {
close(con)
}
} else {
link <- paste(root[1], "/", y, ".html", sep="")
}
}
if (urlError) {
node <- y
} else {
node <- xmlNode("a", y, attrs=c(href=link))
}
return(node)
})
if (length(nodes) == 0) {
args <- list()
} else if (length(nodes) == 1) {
args <- nodes
} else {
args <- vector("list", 2*length(nodes) - 1)
args[seq(1, 2*length(nodes) - 1, by = 2)] <- nodes
args[seq(2, 2*(length(nodes) - 1), by = 2)] <- list(", ")
}
args <- c(list(name = "div"), args, list(attrs = c(class=class)))
return(do.call(xmlNode, args))
}
buildViewLinks <- function(x) buildLinks(x, object@viewRoot, class="views")
buildPkgLinks <- function(x)
buildLinks(x, paste(object@reposFullUrl, "/html", sep=""),
class="packages", check=TRUE)
buildURLLink <- function(u) {
if (!length(u) || nchar(u) == 0)
node <- ""
else
node <- xmlNode("a", u, attrs=c(href=u))
return(node)
}
## create list elements for fields
flds <- c("biocViews"="biocViews", "Depends"="Depends",
"Imports"="Imports", "Suggests"="Suggests",
"System Requirements"="SystemRequirements",
"License"="License", "URL"="URL",
"Depends On Me"="dependsOnMe",
"Imports Me"="importsMe",
"Suggests Me"="suggestsMe",
"Development History"="devHistoryUrl")
tableDat <- vector("list", length = length(flds))
names(tableDat) <- flds
## add biocViews info
tableDat[["biocViews"]] <- buildViewLinks(object@biocViews)
## add Depends, Imports, Suggests, dependsOnMe, importsMe, suggestsMe
pkgFlds <-
c("Depends", "Imports", "Suggests",
"dependsOnMe", "importsMe", "suggestsMe")
tableDat[pkgFlds] <-
lapply(pkgFlds, function(x) buildPkgLinks(slot(object, x)))
## add SystemRequirements and License info
otherFlds <- c("SystemRequirements", "License")
tableDat[otherFlds] <-
lapply(otherFlds, function(x) paste(slot(object, x), collapse=", "))
## add URL info
tableDat[["URL"]] <- buildURLLink(object@URL)
## add development history
devHistoryUrl <- object@devHistoryUrl
if ((length(devHistoryUrl) == 1) &&
(nchar(devHistoryUrl) > 0)) {
tableDat[["devHistoryUrl"]] <-
xmlNode("a", "Bioconductor Changelog",
attrs=c(href=paste(devHistoryUrl, "/",
object@Package, sep="")))
} else {
flds <- flds[- match("devHistoryUrl", flds)]
tableDat[["devHistoryUrl"]] <- NULL
}
## rename rows
names(tableDat) <- names(flds)
domValue <- tableHelper(tableDat,
table.attrs=list(class="details"))
domValue
})
setMethod("htmlValue", signature(object="pdDescriptionInfo"),
function(object) {
node <- xmlNode("p", cleanText(object@Description),
attrs=c(class="description"))
node
})
setMethod("htmlValue", signature(object="PackageDetail"),
function(object) {
dom <- xmlOutputDOM("div", attrs=c(class="PackageDetail"))
## Heading
dom$addTag("h1", object@Package)
dom$addTag("h2", cleanText(object@Title))
## Description
descInfo <- as(object, "pdDescriptionInfo")
dom$addNode(htmlValue(descInfo))
## Author info
authorInfo <- as(object, "pdAuthorMaintainerInfo")
dom$addNode(htmlValue(authorInfo))
## Installation Instructions
dom$addTag("div", attrs=c(class="installInstruct"), close=FALSE)
dom$addTag("p", paste("To install this package,",
"start R and enter:"),
attrs=c(class="install"))
dom$addTag("pre",
paste(" if (!require(\"BiocManager\"))",
"\n install.packages(\"BiocManager\")",
"\n BiocManager::install(\"",
object@Package,
"\")", sep="")
)
dom$closeTag() # div
## Documentation
dom$addTag("h3", "Documentation")
vigInfo <- as(object, "pdVignetteInfo")
dom$addNode(htmlValue(vigInfo))
## Details
dom$addTag("h3", "Details")
detailsInfo <- as(object, "pdDetailsInfo")
dom$addNode(htmlValue(detailsInfo))
## Package Downloads
dom$addTag("h3", "Package Downloads")
downloadInfo <- as(object, "pdDownloadInfo")
dom$addNode(htmlValue(downloadInfo))
return(dom$value())
})
viewsHelper <- function(views) {
dom <- xmlOutputDOM("ul")
for (v in views) {
link <- htmlFilename(v)
dom$addTag("li", close=FALSE)
dom$addTag("a", v, attrs=c(href=link))
dom$closeTag()
}
dom$value()
}
setMethod("htmlValue", signature(object="bvSubViews"),
function(object) {
dom <- xmlOutputDOM("div", attrs=c(class="bv_subviews"))
dom$addTag("h2", "Subviews")
dom$addNode(viewsHelper(object@subViews))
dom$value()
})
setMethod("htmlValue", signature(object="bvParentViews"),
function(object) {
dom <- xmlOutputDOM("div", attrs=c(class="bv_parentviews"))
dom$addTag("h2", "Subview of")
dom$addNode(viewsHelper(object@parentViews))
dom$value()
})
setMethod("htmlValue", signature(object="BiocView"),
function(object) {
dom <- xmlOutputDOM("div", attrs=c(class="BiocView"))
## Heading
dom$addTag("h1", paste("Bioconductor Task View:", object@name))
## Parent Views
if (length(object@parentViews) > 0) {
parentViews <- as(object, "bvParentViews")
dom$addNode(htmlValue(parentViews))
}
## Subviews
if (length(object@subViews) > 0) {
subViews <- as(object, "bvSubViews")
dom$addNode(htmlValue(subViews))
}
dom$addTag("h2", "Packages in view")
if (length(object@packageList) > 0) {
pkgTable <- as(object, "rdPackageTable")
dom$addNode(htmlValue(pkgTable))
} else {
dom$addTag("p", "No packages in this view")
}
dom$value()
})
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Defines functions viewsHelper cleanText tableHelper writeHtmlDoc
Documented in writeHtmlDoc
writeHtmlDoc <- function(html, file)
{
## Temporary fix: we open and close 'file' here instead of passing it
## directly to saveXML because of a bug in current XML::saveXML
## (from XML 1.3-2). Bug reported to XML's author on 2006-12-14. Herve.
f <- file(file, open="w")
## another temp fix: write the DOCTYPE header here, perhaps we should
## use prefix for this in the call to saveXML?
writeLines(paste('<!DOCTYPE html PUBLIC',
'"-//W3C//DTD XHTML 1.0 Strict//EN"',
'"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">'),
con=f)
saveXML(html, f, prefix="")
close(f)
}
tableHelper <- function(tableData, table.attrs) {
dom <- xmlOutputDOM("table", attrs=table.attrs)
odd <- TRUE
for (fld in names(tableData)) {
rowClass <- if(odd) "row_odd" else "row_even"
odd <- !odd
dom$addTag("tr", attrs=c(class=rowClass), close=FALSE)
dom$addTag("th", fld)
dom$addTag("td", tableData[[fld]])
dom$closeTag()
}
dom$closeTag() ## end details table
dom$value()
}
cleanText <- function(text) {
text <- gsub("&([a-zA-Z0-9#]+;)", "@_@_@\\1", text)
text <- gsub("&", "&", text, fixed=TRUE)
text <- gsub("@_@_@([a-zA-Z0-9#]+;)", "&\\1", text)
text <- gsub("<", "<", text, fixed=TRUE)
text <- gsub(">", ">", text, fixed=TRUE)
text
}
setMethod("htmlValue", signature(object="rdPackageTable"),
function(object) {
dom <- xmlOutputDOM("table", attrs=c(class="repos_index"))
odd <- TRUE
alphaOrder <- order(tolower(names(object@packageList)))
dom$addTag("tr", close=FALSE)
dom$addTag("th", "Package")
dom$addTag("th", "Maintainer")
dom$addTag("th", "Title")
dom$closeTag()
for (pkg in object@packageList[alphaOrder]) {
rowClass <- if(odd) "row_odd" else "row_even"
odd <- !odd
dom$addTag("tr", attrs=c(class=rowClass), close=FALSE)
dom$addTag("td", attrs=c(class="package"), close=FALSE)
if (length(object@reposRoot) > 0)
root <- paste(object@reposRoot, object@htmlDir, sep="/")
else
root <- object@htmlDir
infoPage <- paste(root, htmlFilename(pkg), sep="/")
dom$addTag("a", attrs=c(href=infoPage), pkg@Package)
dom$closeTag()
dom$addTag("td", removeEmail(pkg@Maintainer),
attrs=c(class="maintainer"))
dom$addTag("td", pkg@Title, attrs=c(class="title"))
dom$closeTag() ## end tr
}
dom$value()
})
setMethod("htmlValue", signature(object="RepositoryDetail"),
function(object) {
dom <- xmlOutputDOM("div", attrs=c(class="RepositoryDetail"))
dom$addTag("h1", cleanText(object@Title))
## Package table
pkgTable <- as(object, "rdPackageTable")
dom$addNode(htmlValue(pkgTable))
dom$value()
})
setMethod("htmlValue", signature(object="pdAuthorMaintainerInfo"),
function(object) {
dom <- xmlOutputDOM("table", attrs=c(class="author_info"))
dom$addTag("tr", close=FALSE)
dom$addTag("td", "Author")
dom$addTag("td", cleanText(removeEmail(object@Author)))
dom$closeTag()
dom$addTag("tr", close=FALSE)
dom$addTag("td", "Maintainer")
dom$addTag("td", cleanText(removeEmail(object@Maintainer)))
dom$closeTag()
dom$value()
})
setMethod("htmlValue", signature(object="pdVignetteInfo"),
function(object) {
dom <- xmlOutputDOM("table", attrs=c(class="vignette"))
odd <- TRUE
rowClass <- "row_odd"
if (length(object@vignettes) > 0) {
vignetteTitles <-
ifelse(nzchar(object@vignetteTitles), object@vignetteTitles,
basename(object@vignettes))
for (i in order(vignetteTitles)) {
rowClass <- if(odd) "row_odd" else "row_even"
dom$addTag("tr", attrs=c(class=rowClass), close=FALSE)
dom$addTag("th", vignetteTitles[i])
dom$addTag("td", close=FALSE)
pdflink <-
paste(object@reposRoot, object@vignettes[i], sep="/")
dom$addTag("a", "PDF", attrs=c(href=pdflink))
dom$closeTag()
if (nchar(object@vignetteScripts[i]) > 0) {
dom$addTag("td", close=FALSE)
Rlink <-
paste(object@reposRoot, object@vignetteScripts[i],
sep="/")
dom$addTag("a", "R Script", attrs=c(href=Rlink))
dom$closeTag()
}
dom$closeTag() ## end tr
odd <- !odd
}
} else {
dom$addTag("tr", attrs=c(class=rowClass), close=FALSE)
dom$addTag("td", "No vignettes available")
dom$closeTag()
odd <- !odd
}
rowClass <- if(odd) "row_odd" else "row_even"
if (length(object@manuals) > 0 && !is.na(object@manuals[1])) {
dom$addTag("tr", attrs=c(class=rowClass), close=FALSE)
dom$addTag("td", close=FALSE)
mlink <- paste(object@reposRoot, object@manuals[1], sep="/")
dom$addTag("a", "Reference Manual", attrs=c(href=mlink))
dom$closeTag()
dom$closeTag() ## end tr
odd <- !odd
} else {
dom$addTag("tr", attrs=c(class=rowClass), close=FALSE)
dom$addTag("td", "No reference manual available")
dom$closeTag()
odd <- !odd
}
dom$value()
})
setMethod("htmlValue", signature(object="pdDownloadInfo"),
function(object) {
flds <- c(source="source.ver",
win.binary="win.binary.ver",
mac.binary="mac.binary.ver",
mac.binary.mavericks="mac.binary.mavericks.ver",
`mac.binary.el-capitan`="mac.binary.el-capitan.ver")
fileTypes <- list(source="Package source",
win.binary="Windows 32-bit binary",
mac.binary="macOS 10.13 (High Sierra) binary",
mac.binary.mavericks="MacOS X 10.9 (Mavericks) binary",
`mac.binary.el-capitan`="MacOS X 10.11 (El Capitan) binary")
makeLinkHelper <- function(type) {
isAvailable = TRUE
archs <- slot(object, "Archs")
if (length(archs) > 0 && nchar(archs) > 0) {
if (type == "win.binary") {
if (length(grep("i386", archs, value=TRUE)) == 0) {
isAvailable = FALSE
}
}
}
pkgPath <- slot(object, flds[type])
if (isAvailable && !is.na(pkgPath) && length(pkgPath) > 0 && pkgPath != "") {
ref <- paste(object@reposRoot, pkgPath, sep="/")
aTag <- xmlNode("a", basename(pkgPath), attrs=c(href=ref))
} else {
aTag <- "Not Available"
}
aTag
}
fileLinks <- lapply(names(fileTypes), makeLinkHelper)
names(fileLinks) <- fileTypes
downloadStatsUrl <- slot(object, "downloadStatsUrl")
if ((length(downloadStatsUrl) == 1) &&
(nchar(downloadStatsUrl) > 0)) {
fileLinks <- c(fileLinks,
list("Package Downloads Report" =
xmlNode("a", "Downloads Stats",
attrs=c(href=paste(downloadStatsUrl, "/",
slot(object, "Package"),
".html", sep="")))))
}
domValue <- tableHelper(fileLinks,
table.attrs=list(class="downloads"))
domValue
})
setMethod("htmlValue", signature(object="pdDetailsInfo"),
function(object) {
## link generating functions
buildLinks <- function(x, root, class, check = FALSE) {
nodes <-
lapply(x,
function(y) {
urlError <- FALSE
if (nchar(y) == 0 || length(root) == 0) {
urlError <- TRUE
} else {
if (check) {
oldWarn <- options()[["warn"]]
options(warn = -1)
for (i in seq_len(length(root))) {
link <- paste(root[i], "/", y, ".html", sep="")
con <- try(url(link, "r"), silent = TRUE)
if (class(con)[[1]] != "try-error")
break;
}
options(warn = oldWarn)
if (class(con)[[1]] == "try-error") {
urlError <- TRUE
} else {
close(con)
}
} else {
link <- paste(root[1], "/", y, ".html", sep="")
}
}
if (urlError) {
node <- y
} else {
node <- xmlNode("a", y, attrs=c(href=link))
}
return(node)
})
if (length(nodes) == 0) {
args <- list()
} else if (length(nodes) == 1) {
args <- nodes
} else {
args <- vector("list", 2*length(nodes) - 1)
args[seq(1, 2*length(nodes) - 1, by = 2)] <- nodes
args[seq(2, 2*(length(nodes) - 1), by = 2)] <- list(", ")
}
args <- c(list(name = "div"), args, list(attrs = c(class=class)))
return(do.call(xmlNode, args))
}
buildViewLinks <- function(x) buildLinks(x, object@viewRoot, class="views")
buildPkgLinks <- function(x)
buildLinks(x, paste(object@reposFullUrl, "/html", sep=""),
class="packages", check=TRUE)
buildURLLink <- function(u) {
if (!length(u) || nchar(u) == 0)
node <- ""
else
node <- xmlNode("a", u, attrs=c(href=u))
return(node)
}
## create list elements for fields
flds <- c("biocViews"="biocViews", "Depends"="Depends",
"Imports"="Imports", "Suggests"="Suggests",
"System Requirements"="SystemRequirements",
"License"="License", "URL"="URL",
"Depends On Me"="dependsOnMe",
"Imports Me"="importsMe",
"Suggests Me"="suggestsMe",
"Development History"="devHistoryUrl")
tableDat <- vector("list", length = length(flds))
names(tableDat) <- flds
## add biocViews info
tableDat[["biocViews"]] <- buildViewLinks(object@biocViews)
## add Depends, Imports, Suggests, dependsOnMe, importsMe, suggestsMe
pkgFlds <-
c("Depends", "Imports", "Suggests",
"dependsOnMe", "importsMe", "suggestsMe")
tableDat[pkgFlds] <-
lapply(pkgFlds, function(x) buildPkgLinks(slot(object, x)))
## add SystemRequirements and License info
otherFlds <- c("SystemRequirements", "License")
tableDat[otherFlds] <-
lapply(otherFlds, function(x) paste(slot(object, x), collapse=", "))
## add URL info
tableDat[["URL"]] <- buildURLLink(object@URL)
## add development history
devHistoryUrl <- object@devHistoryUrl
if ((length(devHistoryUrl) == 1) &&
(nchar(devHistoryUrl) > 0)) {
tableDat[["devHistoryUrl"]] <-
xmlNode("a", "Bioconductor Changelog",
attrs=c(href=paste(devHistoryUrl, "/",
object@Package, sep="")))
} else {
flds <- flds[- match("devHistoryUrl", flds)]
tableDat[["devHistoryUrl"]] <- NULL
}
## rename rows
names(tableDat) <- names(flds)
domValue <- tableHelper(tableDat,
table.attrs=list(class="details"))
domValue
})
setMethod("htmlValue", signature(object="pdDescriptionInfo"),
function(object) {
node <- xmlNode("p", cleanText(object@Description),
attrs=c(class="description"))
node
})
setMethod("htmlValue", signature(object="PackageDetail"),
function(object) {
dom <- xmlOutputDOM("div", attrs=c(class="PackageDetail"))
## Heading
dom$addTag("h1", object@Package)
dom$addTag("h2", cleanText(object@Title))
## Description
descInfo <- as(object, "pdDescriptionInfo")
dom$addNode(htmlValue(descInfo))
## Author info
authorInfo <- as(object, "pdAuthorMaintainerInfo")
dom$addNode(htmlValue(authorInfo))
## Installation Instructions
dom$addTag("div", attrs=c(class="installInstruct"), close=FALSE)
dom$addTag("p", paste("To install this package,",
"start R and enter:"),
attrs=c(class="install"))
dom$addTag("pre",
paste(" if (!require(\"BiocManager\"))",
"\n install.packages(\"BiocManager\")",
"\n BiocManager::install(\"",
object@Package,
"\")", sep="")
)
dom$closeTag() # div
## Documentation
dom$addTag("h3", "Documentation")
vigInfo <- as(object, "pdVignetteInfo")
dom$addNode(htmlValue(vigInfo))
## Details
dom$addTag("h3", "Details")
detailsInfo <- as(object, "pdDetailsInfo")
dom$addNode(htmlValue(detailsInfo))
## Package Downloads
dom$addTag("h3", "Package Downloads")
downloadInfo <- as(object, "pdDownloadInfo")
dom$addNode(htmlValue(downloadInfo))
return(dom$value())
})
viewsHelper <- function(views) {
dom <- xmlOutputDOM("ul")
for (v in views) {
link <- htmlFilename(v)
dom$addTag("li", close=FALSE)
dom$addTag("a", v, attrs=c(href=link))
dom$closeTag()
}
dom$value()
}
setMethod("htmlValue", signature(object="bvSubViews"),
function(object) {
dom <- xmlOutputDOM("div", attrs=c(class="bv_subviews"))
dom$addTag("h2", "Subviews")
dom$addNode(viewsHelper(object@subViews))
dom$value()
})
setMethod("htmlValue", signature(object="bvParentViews"),
function(object) {
dom <- xmlOutputDOM("div", attrs=c(class="bv_parentviews"))
dom$addTag("h2", "Subview of")
dom$addNode(viewsHelper(object@parentViews))
dom$value()
})
setMethod("htmlValue", signature(object="BiocView"),
function(object) {
dom <- xmlOutputDOM("div", attrs=c(class="BiocView"))
## Heading
dom$addTag("h1", paste("Bioconductor Task View:", object@name))
## Parent Views
if (length(object@parentViews) > 0) {
parentViews <- as(object, "bvParentViews")
dom$addNode(htmlValue(parentViews))
}
## Subviews
if (length(object@subViews) > 0) {
subViews <- as(object, "bvSubViews")
dom$addNode(htmlValue(subViews))
}
dom$addTag("h2", "Packages in view")
if (length(object@packageList) > 0) {
pkgTable <- as(object, "rdPackageTable")
dom$addNode(htmlValue(pkgTable))
} else {
dom$addTag("p", "No packages in this view")
}
dom$value()
})
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