R/AllOldClasses.R

Defines functions DataPackage CSVFile makeOldHTMLReport

Documented in CSVFile DataPackage makeOldHTMLReport

### The HTML based report classes in this file have been superceed by the referenceClass based ones in AllClasses.R The ones in this file will be officially depreciated eventually (probably next release) and are not intended to be used.
setClass("BaseReport",
    representation = representation(
        shortName           = "character",
        title               = "character",
        reportDirectory    = "character"
    ),
    prototype = list(
        shortName           = "coolProject",
        title               = "My cool project",
        reportDirectory    = "."
    )
)

setClass("HTMLReport", contains = "BaseReport",
    representation = representation(
        baseUrl = "character",
        basePath = "character",
        page    = "connection"
    )
)

makeOldHTMLReport <- function(shortName, title = NULL, reportDirectory = ".",
    baseUrl = "localhost", basePath = NULL, page = NULL,
    link.css = NULL, link.javascript = NULL, overwrite.js=TRUE)
{
    shortName <- sub(".html$", "", shortName)
    if(is.null(title))
        title <- shortName

    if(substr(reportDirectory,1,1) == "~"){
        reportDirectory <- path.expand(reportDirectory)
    }
    
    warning("HTMLReport has been superceded by htmlReportRef. It is still supported,
but will be deprecated in future releases of ReportingTools.")
    
    ## Not sure what to do here when basePath is set, but reportDirectory needs
    ## to be rewritten... Probably should just throw an execption    
    if(substr(reportDirectory, 1, 1) == "/"){
        if(is.null(basePath) || basePath == ""){
            basePath = "/"
        }
    } else {
        if(is.null(basePath)) basePath = "."
    }
    
    
    if(substr(basePath,1,1) == "~"){
        basePath <- path.expand(basePath)
    }
    
    pageDir <- file.path(basePath, reportDirectory)
    pageDir <- gsub("//+", "/", pageDir)
    
    jslibenv <- Sys.getenv("REPORTINGTOOLSJSLIB")
    csslibenv <- Sys.getenv("REPORTINGTOOLSCSSLIB")
    if(jslibenv != "" | csslibenv != "")
    {
        warning("Use of REPORTINGTOOLSJSLIB and REPORTINGTOOLSCSSLIB environment variables is 
deprecated. Please unset these in your environment.")
    }

    
    if(is.null(link.javascript)){
        js.libloc <- Sys.getenv("REPORTINGTOOLSJSLIB")
        if(js.libloc == ""){
            javascript.files <- c(system.file("extdata/jslib/jquery-1.8.0.min.js",
                package="ReportingTools"), 
                system.file("extdata/jslib/jquery.dataTables-1.9.3.js",
                    package="ReportingTools"),
                system.file("extdata/jslib/jquery.dataTables.columnFilter.js",
                    package="ReportingTools"),
                system.file("extdata/jslib/jquery.dataTables.plugins.js",
                    package="ReportingTools"),
                system.file("extdata/jslib/bootstrap.js",
                    package="ReportingTools"),
                system.file("extdata/jslib/jquery.dataTables.reprise.js",
                    package="ReportingTools")                                  
                                  )

            jsDir <- file.path(pageDir,"jslib")
            jsDir <- gsub("//+", "/", jsDir)

            if(!file.exists(jsDir))
                .safe.dir.create(jsDir, recursive=TRUE)
            
            file.copy(javascript.files, jsDir, overwrite=overwrite.js)
            javascript.files <- sub(".*extdata/","",javascript.files)
          } else {
            javascript.files <- paste(js.libloc, c("jquery-1.8.0.min.js",
                "jquery.dataTables-1.9.3.js","jquery.dataTables.columnFilter.js",
                "jquery.dataTables.plugins.js","jquery.dataTables.reprise.js",
                "bootstrap.js"), 
                sep="/")
        }
        link.javascript <- javascript.files
    }
    if(is.null(link.css)){
        css.libloc <- Sys.getenv("REPORTINGTOOLSCSSLIB")
        if(css.libloc == ""){
#            css.files <- c(system.file("extdata/csslib/reset-min.css", 
#                    package="ReportingTools"), 
#                system.file("extdata/csslib/reprise.table.css", 
#                    package="ReportingTools"),
          css.files <- c(
                         system.file("extdata/csslib/bootstrap.css",
                                     package="ReportingTools"),
                         system.file("extdata/csslib/reprise.table.bootstrap.css",
                                     package="ReportingTools")
                           )
            
            cssDir <- (file.path(pageDir,"csslib"))
            cssDir <- gsub("//+", "/", cssDir)
            .safe.dir.create(cssDir, recursive=TRUE)
            
            file.copy(css.files, cssDir, overwrite=overwrite.js)
            css.files <- sub(".*extdata/","",css.files)

            css.png.package.dir <- c(system.file("extdata/csslib/images/", package="ReportingTools"))
            css.pngs <- list.files(path=css.png.package.dir)
            css.pngs <-  paste(css.png.package.dir,css.pngs, sep="/")

            cssPngsDir <- (file.path(pageDir,"csslib/images"))
            .safe.dir.create(cssPngsDir, recursive=TRUE)            
            file.copy(css.pngs,cssPngsDir)
           
          } else {
            css.files <- paste(css.libloc, 
                c("reset-min.css", "reprise.table.css"), sep="/")
        }
        link.css <- css.files
    }
    
    if(is.null(page)){
        pageDir <- file.path(basePath, reportDirectory)
        page <- openPage(paste(shortName, "html", sep="."), 
            dirname = pageDir, title = title, link.css = link.css,
            link.javascript = link.javascript)
    }
    hwrite(title, page = page, heading=2, br=TRUE)
    htmlRep <- new("HTMLReport", shortName = shortName,
        title = title, reportDirectory = reportDirectory, 
        baseUrl = baseUrl, basePath = basePath, page = page)
}

setClass("CSVFile", contains = "BaseReport")

CSVFile <- function(shortName, title = "", reportDirectory = ".")
{
    csvRep <- new("CSVFile", shortName = shortName, 
        reportDirectory = reportDirectory, title = title)
    return(csvRep)
}

setClass("DataPackage", contains = "BaseReport",
    representation = representation(
        version         = "character",
        dependencies    = "character",
        author          = "character",
        maintainer      = "character",
        license         = "character",
        description     = "character",
        package.Rd      = "character"
    ),
    prototype = list(
        version         = "0.0.1",
        dependencies    = "Biobase",
        author          = "nobody <[email protected]>",
        maintainer      = "nobody",
        license         = "No license specified",
        description     = "No description necessary",
        package.Rd      = ""
    )
)

DataPackage <- function(shortName, title = "", reportDirectory = ".",
    version = "0.0.1", dependencies = c("Biobase"), license = "",
    description = "", author = "nobody", 
    maintainer = "nobody <[email protected]>")
{
    dependencies <- unique(dependencies)
    dataPkg <- new("DataPackage", shortName = shortName, 
        reportDirectory = reportDirectory, title = title,
        version = version, dependencies = dependencies, license = license,
        description = description, author = author, maintainer = maintainer)
    ## Need to do some basic setup of the data package:
    ## Make directories, create the DESCRIPTION and NAMESPACE,
    ## add some documentation into the package.Rd file
    .safe.dir.create(reportDirectory)
    pkg.dir <- path(dataPkg)
    .safe.dir.create(pkg.dir)
    
    man.dir <- file.path(pkg.dir, "man")
    .safe.dir.create(man.dir)

    vignettes.dir <- file.path(pkg.dir, "vignettes")
    .safe.dir.create(vignettes.dir)
    
    data.dir <- file.path(pkg.dir, "data")
    .safe.dir.create(data.dir)
    
    ## I should move this to a finish method, just to make sure that
    ## any changes to the package are put into the description.
    ## Or add this to all accessor methods. Oy!
    description.str <- paste("Package: ", shortName, "\nVersion: ", version, 
        "\nTitle: ", title, "\nAuthor: ", author, "\nMaintainer: ", maintainer,
        "\nDepends: ", dependencies, "\nLicense: ", license, "\nType: Package",
        "\nLazyLoad: yes\nDescription: ", description, sep="")
    description.fn <- file.path(pkg.dir, "DESCRIPTION")
    
    namespace.str <- paste("#Export all variables that do not start with a period.", 
        "exportPattern(\"^[^\\\\.]+\")", sep = "\n")
    out <- file(file.path(pkg.dir, "NAMESPACE"), "wt") 
    writeLines(namespace.str, out)
    close(out)
    ## Also need to make a namespace file here.
    
    cat(description.str, file=description.fn)
    
    return(dataPkg)

}
Bioconductor-mirror/ReportingTools documentation built on July 28, 2017, 4:28 a.m.