R/zzz.R

In romero.gateway: OMERO R Gateway

#' @import methods
#' @importFrom utils packageVersion packageDescription download.file unzip
.onAttach <- function(libname, pkgname) {
  romeroVersion <- utils::packageVersion("romero.gateway")
  omeroVersion <- utils::packageDescription("romero.gateway", fields = "Description")
  reg <- regexec('OMERO[[:space:]]version:[[:space:]](?<version>[0-9]+\\.[0-9]+)', omeroVersion, perl=TRUE)
  omeroVersion <- regmatches(omeroVersion, reg)
  omeroVersion <- omeroVersion[[1]][[2]]
  
  omeroLibs <- find.package(package='romero.gateway')
  omeroLibs <- paste(omeroLibs, 'java', sep = '/')
  if (!dir.exists(omeroLibs)) {
    # java libs dir doesn't exist yet
    dir.create(omeroLibs, recursive = TRUE)
  }
  
  if (!file.exists(paste(omeroLibs, 'blitz.jar', sep = '/'))) {
    # OMERO java libraries haven't been downloaded yet.
    
    baseURL <- paste('http://downloads.openmicroscopy.org/latest/omero', omeroVersion, sep = '')
    zipFile <- 'OMERO.java.zip'
    packageStartupMessage(paste('Downloading OMERO Java libraries from', baseURL))
    packageStartupMessage(paste('Installing them in', omeroLibs))
    
    dest <- paste(omeroLibs, zipFile, sep = '/')
    download.file(paste(baseURL, zipFile, sep = '/'), destfile = dest)
    unzip(dest, exdir = omeroLibs)
    unzippedLibs <- NA
    for (dir in list.dirs(path = omeroLibs)) {
      x <- grep(paste(omeroLibs, "OMERO\\.java-.*", "libs", sep = '/'), dir)
      if (length(x)) {
        unzippedLibs <- dir
        break
      }
    }
    for (file in list.files(unzippedLibs)) {
      cpFrom <- paste(unzippedLibs, file, sep = '/')
      cpTo <-  paste(omeroLibs, file, sep = '/')
      file.copy(from = cpFrom, to = cpTo)
    }
    file.remove(dest)
    toDelete <- sub('/libs', '', unzippedLibs)
    if (startsWith(toDelete, omeroLibs)) {
      # make sure to not accidentely delete something else
      unlink(toDelete, recursive = TRUE, force = TRUE)
    }
  }
  
  .jinit(classpath = dir(omeroLibs, full.names=TRUE ))

  # Unfortunately have to add this stuff to base env
  # because romero.gateway env is locked
  env <- baseenv()
  
  # Genereal Java classes
  env$Collection <- J("java.util.Collection")
  env$Collections <- J("java.util.Collections")
  env$Iterator <- J("java.util.Iterator")
  env$ArrayList <- J("java.util.ArrayList")
  env$Set <- J("java.util.Set")
  env$HashSet <- J("java.util.HashSet")
  env$JFile <- J("java.io.File")
  env$Integer <- J("java.lang.Integer")
  env$Long <- J("java.lang.Long")
  env$Double <- J("java.lang.Double")
  env$String <- J("java.lang.String")
  env$Boolean <- J("java.lang.Boolean")
  env$Class <- J("java.lang.Class")
  
  # General Gateway classes
  env$rtypes <- J("omero.rtypes")
  env$SimpleLogger <- J("omero.log.SimpleLogger")
  env$LoginCredentials <- J("omero.gateway.LoginCredentials")
  env$SecurityContext <- J("omero.gateway.SecurityContext")
  env$Gateway <- J("omero.gateway.Gateway")
  env$BrowseFacility <- J("omero.gateway.facility.BrowseFacility")
  env$ROIFacility <- J("omero.gateway.facility.ROIFacility")
  env$MetadataFacility <- J("omero.gateway.facility.MetadataFacility")
  env$DataManagerFacility <- J("omero.gateway.facility.DataManagerFacility")
  env$TablesFacility <- J("omero.gateway.facility.TablesFacility")
  env$SearchFacility <- J("omero.gateway.facility.SearchFacility")
  env$RawDataFacility <- J("omero.gateway.facility.RawDataFacility")
  env$ROIFacility <- J("omero.gateway.facility.ROIFacility")
  
  # Gateway POJOs
  env$DataObject <- J("omero.gateway.model.DataObject")
  env$PlateData <- J("omero.gateway.model.PlateData")
  env$ScreenData <- J("omero.gateway.model.ScreenData")
  env$DatasetData <- J("omero.gateway.model.DatasetData")
  env$ProjectData <- J("omero.gateway.model.ProjectData")
  env$WellData <- J("omero.gateway.model.WellData")
  env$WellSampleData <- J("omero.gateway.model.WellSampleData")
  env$ExperimenterData <- J("omero.gateway.model.ExperimenterData")
  env$GroupData <- J("omero.gateway.model.GroupData")
  env$AnnotationData <- J("omero.gateway.model.AnnotationData")
  env$MapAnnotationData <- J("omero.gateway.model.MapAnnotationData")
  env$TagAnnotationData <- J("omero.gateway.model.TagAnnotationData")
  env$FileAnnotationData <- J("omero.gateway.model.FileAnnotationData")
  env$ImageData <- J("omero.gateway.model.ImageData")
  env$ChannelData <- J("omero.gateway.model.ChannelData")
  env$TableData <- J("omero.gateway.model.TableData")
  env$TableDataColumn <- J("omero.gateway.model.TableDataColumn")
  env$SearchParameters <- J("omero.gateway.model.SearchParameters")
  env$SearchScope <- J("omero.gateway.model.SearchScope")
  env$SearchResultCollection <- J("omero.gateway.model.SearchResultCollection")
  env$Plane2D <- J("omero.gateway.rnd.Plane2D")
  env$ROIData <- J("omero.gateway.model.ROIData")
  env$PointData <- J("omero.gateway.model.PointData")
  env$EllipseData <- J("omero.gateway.model.EllipseData")
  env$RectangleData <- J("omero.gateway.model.RectangleData")
  env$AffineTransform <- J("omero.model.AffineTransformI")
  
  msg <- paste("\n*** Welcome to rOMERO ", romeroVersion, " (~ OMERO ",omeroVersion,") ***\n", sep="")
  packageStartupMessage(msg)
}