Nothing
R/OMEROServer.R
In romero.gateway: OMERO R Gateway
setClassUnion("jclassOrNULL", c("jobjRef", "NULL"))
#' OMEROServer class
#' Provides access to an OMERO server
#'
#' @slot host The host name
#' @slot port The port number
#' @slot username The username
#' @slot password The password
#' @slot credentialsFile Text file providing username and password
#' @slot gateway Reference to the Gateway
#' @slot user The logged in user
#' @slot ctx The current SecurityContext
#' @export OMEROServer
#' @exportClass OMEROServer
#' @import rJava
#' @importFrom utils read.csv read.table
#' @examples
#' \dontrun{
#' server <- OMEROServer(username = 'root', password = 'xyz', host = 'localhost')
#' }
OMEROServer <- setClass(
"OMEROServer",
slots = c(
host = "character",
port = "numeric",
username = "character",
password = "character",
credentialsFile = "character",
gateway = "jclassOrNULL",
user = "jclassOrNULL",
ctx = "jclassOrNULL"
),
prototype = list(
host = character(0),
port= 4064L,
username = character(0),
password = character(0),
credentialsFile = character(0),
gateway = NULL,
user = NULL,
ctx = NULL
)
)
#' Connect to an OMERO server
#'
#' @param server The server
#' @param group The group context (group name)
#' (optional, default: user's default group)
#' @return The server in "connected" state (if successful)
#' @export connect
#' @exportMethod connect
#' @examples
#' \dontrun{
#' server_connected <- connect(server)
#' }
setGeneric(name="connect",
def=function(server, group=NA)
{
standardGeneric("connect")
}
)
#' Disconnect from an OMERO server
#'
#' @param server The server
#' @return The server in "disconnected" state (if successful)
#' @export disconnect
#' @exportMethod disconnect
#' @examples
#' \dontrun{
#' disconnect(server)
#' }
setGeneric(name="disconnect",
def=function(server)
{
standardGeneric("disconnect")
}
)
#' Set a different group context
#'
#' @param server The server
#' @param group The name of the group
#' @return The server
#' @export setGroupContext
#' @exportMethod setGroupContext
#' @examples
#' \dontrun{
#' server <- setGroupContext(server, 'lab_2')
#' }
setGeneric(name="setGroupContext",
def=function(server, group)
{
standardGeneric("setGroupContext")
}
)
#' Get the current group context
#'
#' @param server The server
#' @return The name of the group
#' @export getGroupContext
#' @exportMethod getGroupContext
#' @examples
#' \dontrun{
#' current_group <- getGroupContext(server)
#' }
setGeneric(name="getGroupContext",
def=function(server)
{
standardGeneric("getGroupContext")
}
)
#' Get the reference to the Java Gatway
#'
#' @param server The server
#' @return The Java Gateway
#' @export getGateway
#' @exportMethod getGateway
#' @examples
#' \dontrun{
#' java_gw <- getGateway(server)
#' }
setGeneric(name="getGateway",
def=function(server)
{
standardGeneric("getGateway")
}
)
#' Get the current SecurityContext
#'
#' @param server The server
#' @return The SecurityContext
#' @export getContext
#' @exportMethod getContext
#' @examples
#' \dontrun{
#' sec_ctx <- getContext(server)
#' }
setGeneric(name="getContext",
def=function(server)
{
standardGeneric("getContext")
}
)
#' Load an object from the server
#'
#' @param server The server
#' @param type The object type
#' @param id The object ID
#' @return The OME remote object @seealso \linkS4class{OMERO}
#' @export loadObject
#' @exportMethod loadObject
#' @examples
#' \dontrun{
#' obj <- loadObject(server, "ImageData", 123)
#' image <- cast(obj)
#' }
setGeneric(name="loadObject",
def=function(server, type, id)
{
standardGeneric("loadObject")
}
)
#' Load a CSV file from the server
#'
#' @param server The server
#' @param id The original file ID
#' @param header Flag to indicate that the file starts with a header line
#' @param sep The separator character
#' @param quote The quote character
#' @param dec The decimal point character
#' @param fill Flag to indicate if blank fields should be added for rows with unequals length
#' @param comment.char The comment character
#' @return The dataframe constructed from the CSV file
#' @export loadCSV
#' @exportMethod loadCSV
#' @examples
#' \dontrun{
#' df <- loadCSV(server, file_annotation_id)
#' }
setGeneric(name="loadCSV",
def=function(server, id, header = TRUE, sep = ",", quote = "\"",
dec = ".", fill = TRUE, comment.char = "")
{
standardGeneric("loadCSV")
}
)
#' Get annotations attached to an OME object.
#' Type, Namespace, Name, Content, ID, FileID (in case of file annotations)
#'
#' @param object The OME object
#' @param type The object type
#' @param id The object id
#' @param typeFilter Optional annotation type filter, e.g. FileAnnotation
#' @param nameFilter Optional name filter, e.g. file name of a FileAnnotation
#' @return The annotations
#' @export getAnnotations
#' @exportMethod getAnnotations
#' @examples
#' \dontrun{
#' annoations <- getAnnotations(image)
#' }
setGeneric(name="getAnnotations",
def=function(object, type, id, typeFilter, nameFilter)
{
standardGeneric("getAnnotations")
}
)
#' Search for OMERO objects
#'
#' @param server The server
#' @param type The type of the objects to search for, e.g. Image (default: Image)
#' @param scope Limit the scope to 'Name', 'Description' or 'Annotation' (optional)
#' @param query The search query
#' @return The search results (collection of OMERO objects) @seealso \linkS4class{OMERO}
#' @export searchFor
#' @exportMethod searchFor
#' @examples
#' \dontrun{
#' found <- searchFor(server, "Project", scope = "Name", "MyProject")
#' }
setGeneric(name="searchFor",
def=function(server, type, scope, query)
{
standardGeneric("searchFor")
}
)
#' Get all screens of the logged in user
#'
#' @param server The server
#' @return The screens @seealso \linkS4class{Screen}
#' @export getScreens
#' @exportMethod getScreens
#' @examples
#' \dontrun{
#' screens <- getScreens(server)
#' }
setGeneric(name="getScreens",
def=function(server)
{
standardGeneric("getScreens")
}
)
#' Get all plates of the logged in user
#'
#' @param object The server or screen
#' @return The plates @seealso \linkS4class{Plate}
#' @export getPlates
#' @exportMethod getPlates
#' @examples
#' \dontrun{
#' plates <- getPlates(server)
#' plates <- getPlates(screen)
#' }
setGeneric(name="getPlates",
def=function(object)
{
standardGeneric("getPlates")
}
)
#' Get all projects of the logged in user
#'
#' @param server The server
#' @return The projects @seealso \linkS4class{Project}
#' @export getProjects
#' @exportMethod getProjects
#' @examples
#' \dontrun{
#' projects <- getProjects(server)
#' }
setGeneric(name="getProjects",
def=function(server)
{
standardGeneric("getProjects")
}
)
#' Get all datasets of the logged in user
#'
#' @param object The server or project
#' @return The datasets @seealso \linkS4class{Dataset}
#' @export getDatasets
#' @exportMethod getDatasets
#' @examples
#' \dontrun{
#' datasets <- getDatasets(server)
#' datasets <- getDatasets(project)
#' }
setGeneric(name="getDatasets",
def=function(object)
{
standardGeneric("getDatasets")
}
)
#' Connect to an OMERO server
#'
#' @param server The server
#' @param group The group context (group name)
#' (optional, default: user's default group)
#' @return The server in "connected" state (if successful)
#' @export connect
#' @exportMethod connect
setMethod(f="connect",
signature="OMEROServer",
definition=function(server, group)
{
log <- new(SimpleLogger)
gateway <- new (Gateway, log)
if (length(server@credentialsFile)>0) {
cred <- read.table(server@credentialsFile, header=FALSE, sep="=", row.names=1, strip.white=TRUE, na.strings="NA", stringsAsFactors=FALSE)
username <- cred["omero.user", 1]
password <- cred["omero.pass", 1]
hostname <- cred["omero.host", 1]
portnumber <- cred["omero.port", 1]
}
if (length(server@username)>0)
username <- server@username
if (length(server@password)>0)
password <- server@password
if (length(server@host)>0)
hostname <- server@host
if (server@port>0)
portnumber <- server@port
lc <- new(LoginCredentials, username, password, hostname, as.integer(portnumber))
lc$setApplicationName("rOMERO")
user <- gateway$connect(lc)
server@gateway <- gateway
server@user <- user
if (!is.na(group)) {
for (g in as.list(user$getGroups())) {
if (g$getName() == group) {
server@ctx <- new (SecurityContext, .jlong(g$getId()))
break
}
}
if (is.null(server@ctx))
warning(paste("Group", group, "not found or user is not a member of this group. Using default group."))
}
if (is.null(server@ctx))
server@ctx <- new (SecurityContext, .jlong(user$getGroupId()))
return(server)
}
)
#' Disconnect from an OMERO server
#'
#' @param server The server
#' @return The server in "disconnected" state (if successful)
#' @export disconnect
#' @exportMethod disconnect
setMethod(f="disconnect",
signature="OMEROServer",
definition=function(server)
{
gateway <- getGateway(server)
gateway$disconnect()
return(invisible(server))
}
)
#' Set a different group context
#'
#' @param server The server
#' @param group The name of the group
#' @return The server
#' @export setGroupContext
#' @exportMethod setGroupContext
setMethod(f="setGroupContext",
signature="OMEROServer",
definition=function(server, group)
{
for (g in as.list(server@user$getGroups())) {
if (g$getName() == group) {
server@ctx <- new (SecurityContext, .jlong(g$getId()))
return(invisible(server))
}
}
warning(paste("Group", group, "not found or user is not a member of this group. Operation ignored."))
return(invisible(server))
}
)
#' Get the current group context
#'
#' @param server The server
#' @return The name of the group
#' @export getGroupContext
#' @exportMethod getGroupContext
setMethod(f="getGroupContext",
signature="OMEROServer",
definition=function(server)
{
for (g in as.list(server@user$getGroups())) {
if (g$getId() == server@ctx$getGroupID()) {
return(g$getName())
}
}
return(NA)
}
)
#' Get the reference to the Java Gatway
#'
#' @param server The server
#' @return The Java Gateway
#' @export getGateway
#' @exportMethod getGateway
setMethod(f="getGateway",
signature="OMEROServer",
definition=function(server)
{
return(server@gateway)
}
)
#' Get the current SecurityContext
#'
#' @param server The server
#' @return The SecurityContext
#' @export getContext
#' @exportMethod getContext
setMethod(f="getContext",
signature="OMEROServer",
definition=function(server)
{
return(server@ctx)
}
)
#' Load an object from the server
#'
#' @param server The server
#' @param type The object type
#' @param id The object ID
#' @return The OME remote object @seealso \linkS4class{OMERO}
#' @export loadObject
#' @exportMethod loadObject
setMethod(f="loadObject",
signature="OMEROServer",
definition=function(server, type, id)
{
gateway <- getGateway(server)
ctx <- getContext(server)
browse <- gateway$getFacility(BrowseFacility$class)
if (type == 'ImageData') {
object <- browse$getImage(ctx, .jlong(id))
}
else if (type == 'ProjectData' || type == 'DatasetData' || type == 'PlateData' || type == 'ScreenData') {
ids <- new (ArrayList)
ids$add(new (Long, .jlong(id)))
if (type == 'ProjectData')
clazz <- ProjectData$class
if (type == 'DatasetData')
clazz <- DatasetData$class
if (type == 'ScreenData')
clazz <- ScreenData$class
if (type == 'PlateData')
clazz <- PlateData$class
tmp <- browse$getHierarchy(ctx, clazz, ids, .jnull(class = 'omero/sys/Parameters'))
it <- tmp$iterator()
object <- .jrcall(it, method = "next")
}
else if(type == 'WellData') {
ids <- new (ArrayList)
ids$add(new (Long, .jlong(id)))
tmp <- browse$getWells(ctx, ids)
it <- tmp$iterator()
object <- .jrcall(it, method = "next")
}
else {
object <- browse$findObject(ctx, type, .jlong(id))
}
ome <- OMERO(server=server, dataobject=object)
return(cast(ome))
}
)
#' Load a CSV file from the server
#'
#' @param server The server
#' @param id The original file ID
#' @param header Flag to indicate that the file starts with a header line
#' @param sep The separator character
#' @param quote The quote character
#' @param dec The decimal point character
#' @param fill Flag to indicate if blank fields should be added for rows with unequals length
#' @param comment.char The comment character
#' @return The dataframe constructed from the CSV file
#' @export loadCSV
#' @exportMethod loadCSV
setMethod(f="loadCSV",
signature="OMEROServer",
definition=function(server, id, header, sep, quote,
dec, fill, comment.char)
{
gateway <- getGateway(server)
ctx <- getContext(server)
browse <- gateway$getFacility(BrowseFacility$class)
orgFile <- browse$findIObject(ctx, "OriginalFile", .jlong(id))
store <- gateway$getRawFileService(ctx);
store$setFileId(.jlong(id))
file <- J("java.io.File")$createTempFile("attachment_", ".csv")
stream <- new(J("java.io.FileOutputStream"), file)
offset <- as.integer(0)
size <- as.integer(orgFile$getSize()$getValue())
INC <- as.integer(4096)
while ((offset+INC) < size) {
data <- store$read(.jlong(offset), INC)
stream$write(.jarray(data, "java/lang/Byte"))
offset <- offset + INC
}
data <- store$read(.jlong(offset), (size-offset))
stream$write(.jarray(data, contents.class = "java/lang/Byte"))
stream$close()
path <- file$getPath()
df <- utils::read.csv(path, header = header, sep = sep, quote = quote,
dec = dec, fill = fill, comment.char = comment.char)
file$delete()
return(df)
}
)
#' Get annotations attached to an OME object.
#' Type, Namespace, Name, Content, ID, FileID (in case of file annotations)
#'
#' @param object The server
#' @param type The object type
#' @param id The object id
#' @param typeFilter Optional annotation type filter, e.g. FileAnnotation
#' @param nameFilter Optional name filter, e.g. file name of a FileAnnotation
#' @return The annotations
#' @export getAnnotations
#' @exportMethod getAnnotations
setMethod(f="getAnnotations",
signature=("OMEROServer"),
definition=function(object, type, id, typeFilter, nameFilter)
{
obj <- loadObject(object, type, id)
annos <- getAnnotations(obj, typeFilter = typeFilter, nameFilter = nameFilter)
return(annos)
}
)
#' Search for OMERO objects
#'
#' @param server The server
#' @param type The type of the objects to search for, e.g. Image (default: Image)
#' @param scope Limit the scope to 'Name', 'Description' or 'Annotation' (optional)
#' @param query The search query
#' @return The search results (collection of OMERO objects) @seealso \linkS4class{OMERO}
#' @export searchFor
#' @exportMethod searchFor
setMethod(f="searchFor",
signature=("OMEROServer"),
definition=function(server, type, scope, query)
{
gateway <- getGateway(server)
ctx <- getContext(server)
sf <- gateway$getFacility(SearchFacility$class)
types <- new(ArrayList)
scopes <- new(HashSet)
typeName <- attr(type, 'className')[1]
clazz <- ImageData$class
if(typeName == 'Project')
clazz <- ProjectData$class
else if(typeName == 'Dataset')
clazz <- DatasetData$class
else if(typeName == 'Screen')
clazz <- ScreenData$class
else if(typeName == 'Plate')
clazz <- PlateData$class
else if(typeName == 'Well')
clazz <- WellData$class
types$add(clazz)
sscope <- NA
if(!missing(scope)) {
if(scope == 'Name')
sscope <- SearchScope$NAME
else if(scope == 'Description')
sscope <- SearchScope$DESCRIPTION
else if(scope == 'Annotation')
sscope <- SearchScope$ANNOTATION
if(!missing(sscope))
scopes$add(sscope)
}
params <- new(SearchParameters, scopes, types, query)
src <- sf$search(ctx, params)
jlist <- src$getDataObjects(as.integer(-1), .jnull(class = 'java/lang/Class'))
result <- c()
it <- jlist$iterator()
while(it$hasNext()) {
dataobj <- .jrcall(it, method = "next")
obj <- OMERO(server=server, dataobject=dataobj)
result <- c(result, cast(obj))
}
return(result)
}
)
#' Get all screens of the logged in user
#'
#' @param server The server
#' @return The screens @seealso \linkS4class{Screen}
#' @export getScreens
#' @exportMethod getScreens
setMethod(f="getScreens",
signature=("OMEROServer"),
definition=function(server)
{
gateway <- getGateway(server)
ctx <- getContext(server)
browse <- gateway$getFacility(BrowseFacility$class)
jscreens <- browse$getHierarchy(ctx, ScreenData$class, .jlong(-1))
screens <- c()
it <- jscreens$iterator()
while(it$hasNext()) {
jscreen <- .jrcall(it, method = "next")
if(.jinstanceof(jscreen, ScreenData)) {
screen <- Screen(server=server, dataobject=jscreen)
screens <- c(screens, screen)
}
}
return(screens)
}
)
#' Get all plates of the logged in user
#'
#' @param object The server
#' @return The plates @seealso \linkS4class{Plate}
#' @export getPlates
#' @exportMethod getPlates
setMethod(f="getPlates",
signature=("OMEROServer"),
definition=function(object)
{
gateway <- getGateway(object)
ctx <- getContext(object)
browse <- gateway$getFacility(BrowseFacility$class)
jplates <- browse$getHierarchy(ctx, PlateData$class, .jlong(-1))
plates <- c()
it <- jplates$iterator()
while(it$hasNext()) {
jplate <- .jrcall(it, method = "next")
if(.jinstanceof(jplate, PlateData)) {
jscreens <- jplate$getScreens()
if (is.jnull(jscreens)) {
plate <- Plate(server=object, dataobject=jplate)
plates <- c(plates, plate)
}
}
}
return(plates)
}
)
#' Get all projects of the logged in user
#'
#' @param server The server
#' @return The projects @seealso \linkS4class{Project}
#' @export getProjects
#' @exportMethod getProjects
setMethod(f="getProjects",
signature=("OMEROServer"),
definition=function(server)
{
gateway <- getGateway(server)
ctx <- getContext(server)
browse <- gateway$getFacility(BrowseFacility$class)
jprojects <- browse$getHierarchy(ctx, ProjectData$class, .jlong(-1))
projects <- c()
it <- jprojects$iterator()
while(it$hasNext()) {
jproject <- .jrcall(it, method = "next")
if(.jinstanceof(jproject, ProjectData)) {
project <- Project(server=server, dataobject=jproject)
projects <- c(projects, project)
}
}
return(projects)
}
)
#' Get all datasets of the logged in user
#'
#' @param object The server
#' @return The datasets @seealso \linkS4class{Dataset}
#' @export getDatasets
#' @exportMethod getDatasets
setMethod(f="getDatasets",
signature=("OMEROServer"),
definition=function(object)
{
gateway <- getGateway(object)
ctx <- getContext(object)
browse <- gateway$getFacility(BrowseFacility$class)
jdatasets <- browse$getHierarchy(ctx, DatasetData$class, .jlong(-1))
datasets <- c()
it <- jdatasets$iterator()
while(it$hasNext()) {
jdataset <- .jrcall(it, method = "next")
if(.jinstanceof(jdataset, DatasetData)) {
dataset <- Dataset(server=object, dataobject=jdataset)
datasets <- c(datasets, dataset)
}
}
return(datasets)
}
)
Try the romero.gateway package in your browser
Any scripts or data that you put into this service are public.
romero.gateway documentation built on Dec. 23, 2018, 5:04 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
setClassUnion("jclassOrNULL", c("jobjRef", "NULL"))
#' OMEROServer class
#' Provides access to an OMERO server
#'
#' @slot host The host name
#' @slot port The port number
#' @slot username The username
#' @slot password The password
#' @slot credentialsFile Text file providing username and password
#' @slot gateway Reference to the Gateway
#' @slot user The logged in user
#' @slot ctx The current SecurityContext
#' @export OMEROServer
#' @exportClass OMEROServer
#' @import rJava
#' @importFrom utils read.csv read.table
#' @examples
#' \dontrun{
#' server <- OMEROServer(username = 'root', password = 'xyz', host = 'localhost')
#' }
OMEROServer <- setClass(
"OMEROServer",
slots = c(
host = "character",
port = "numeric",
username = "character",
password = "character",
credentialsFile = "character",
gateway = "jclassOrNULL",
user = "jclassOrNULL",
ctx = "jclassOrNULL"
),
prototype = list(
host = character(0),
port= 4064L,
username = character(0),
password = character(0),
credentialsFile = character(0),
gateway = NULL,
user = NULL,
ctx = NULL
)
)
#' Connect to an OMERO server
#'
#' @param server The server
#' @param group The group context (group name)
#' (optional, default: user's default group)
#' @return The server in "connected" state (if successful)
#' @export connect
#' @exportMethod connect
#' @examples
#' \dontrun{
#' server_connected <- connect(server)
#' }
setGeneric(name="connect",
def=function(server, group=NA)
{
standardGeneric("connect")
}
)
#' Disconnect from an OMERO server
#'
#' @param server The server
#' @return The server in "disconnected" state (if successful)
#' @export disconnect
#' @exportMethod disconnect
#' @examples
#' \dontrun{
#' disconnect(server)
#' }
setGeneric(name="disconnect",
def=function(server)
{
standardGeneric("disconnect")
}
)
#' Set a different group context
#'
#' @param server The server
#' @param group The name of the group
#' @return The server
#' @export setGroupContext
#' @exportMethod setGroupContext
#' @examples
#' \dontrun{
#' server <- setGroupContext(server, 'lab_2')
#' }
setGeneric(name="setGroupContext",
def=function(server, group)
{
standardGeneric("setGroupContext")
}
)
#' Get the current group context
#'
#' @param server The server
#' @return The name of the group
#' @export getGroupContext
#' @exportMethod getGroupContext
#' @examples
#' \dontrun{
#' current_group <- getGroupContext(server)
#' }
setGeneric(name="getGroupContext",
def=function(server)
{
standardGeneric("getGroupContext")
}
)
#' Get the reference to the Java Gatway
#'
#' @param server The server
#' @return The Java Gateway
#' @export getGateway
#' @exportMethod getGateway
#' @examples
#' \dontrun{
#' java_gw <- getGateway(server)
#' }
setGeneric(name="getGateway",
def=function(server)
{
standardGeneric("getGateway")
}
)
#' Get the current SecurityContext
#'
#' @param server The server
#' @return The SecurityContext
#' @export getContext
#' @exportMethod getContext
#' @examples
#' \dontrun{
#' sec_ctx <- getContext(server)
#' }
setGeneric(name="getContext",
def=function(server)
{
standardGeneric("getContext")
}
)
#' Load an object from the server
#'
#' @param server The server
#' @param type The object type
#' @param id The object ID
#' @return The OME remote object @seealso \linkS4class{OMERO}
#' @export loadObject
#' @exportMethod loadObject
#' @examples
#' \dontrun{
#' obj <- loadObject(server, "ImageData", 123)
#' image <- cast(obj)
#' }
setGeneric(name="loadObject",
def=function(server, type, id)
{
standardGeneric("loadObject")
}
)
#' Load a CSV file from the server
#'
#' @param server The server
#' @param id The original file ID
#' @param header Flag to indicate that the file starts with a header line
#' @param sep The separator character
#' @param quote The quote character
#' @param dec The decimal point character
#' @param fill Flag to indicate if blank fields should be added for rows with unequals length
#' @param comment.char The comment character
#' @return The dataframe constructed from the CSV file
#' @export loadCSV
#' @exportMethod loadCSV
#' @examples
#' \dontrun{
#' df <- loadCSV(server, file_annotation_id)
#' }
setGeneric(name="loadCSV",
def=function(server, id, header = TRUE, sep = ",", quote = "\"",
dec = ".", fill = TRUE, comment.char = "")
{
standardGeneric("loadCSV")
}
)
#' Get annotations attached to an OME object.
#' Type, Namespace, Name, Content, ID, FileID (in case of file annotations)
#'
#' @param object The OME object
#' @param type The object type
#' @param id The object id
#' @param typeFilter Optional annotation type filter, e.g. FileAnnotation
#' @param nameFilter Optional name filter, e.g. file name of a FileAnnotation
#' @return The annotations
#' @export getAnnotations
#' @exportMethod getAnnotations
#' @examples
#' \dontrun{
#' annoations <- getAnnotations(image)
#' }
setGeneric(name="getAnnotations",
def=function(object, type, id, typeFilter, nameFilter)
{
standardGeneric("getAnnotations")
}
)
#' Search for OMERO objects
#'
#' @param server The server
#' @param type The type of the objects to search for, e.g. Image (default: Image)
#' @param scope Limit the scope to 'Name', 'Description' or 'Annotation' (optional)
#' @param query The search query
#' @return The search results (collection of OMERO objects) @seealso \linkS4class{OMERO}
#' @export searchFor
#' @exportMethod searchFor
#' @examples
#' \dontrun{
#' found <- searchFor(server, "Project", scope = "Name", "MyProject")
#' }
setGeneric(name="searchFor",
def=function(server, type, scope, query)
{
standardGeneric("searchFor")
}
)
#' Get all screens of the logged in user
#'
#' @param server The server
#' @return The screens @seealso \linkS4class{Screen}
#' @export getScreens
#' @exportMethod getScreens
#' @examples
#' \dontrun{
#' screens <- getScreens(server)
#' }
setGeneric(name="getScreens",
def=function(server)
{
standardGeneric("getScreens")
}
)
#' Get all plates of the logged in user
#'
#' @param object The server or screen
#' @return The plates @seealso \linkS4class{Plate}
#' @export getPlates
#' @exportMethod getPlates
#' @examples
#' \dontrun{
#' plates <- getPlates(server)
#' plates <- getPlates(screen)
#' }
setGeneric(name="getPlates",
def=function(object)
{
standardGeneric("getPlates")
}
)
#' Get all projects of the logged in user
#'
#' @param server The server
#' @return The projects @seealso \linkS4class{Project}
#' @export getProjects
#' @exportMethod getProjects
#' @examples
#' \dontrun{
#' projects <- getProjects(server)
#' }
setGeneric(name="getProjects",
def=function(server)
{
standardGeneric("getProjects")
}
)
#' Get all datasets of the logged in user
#'
#' @param object The server or project
#' @return The datasets @seealso \linkS4class{Dataset}
#' @export getDatasets
#' @exportMethod getDatasets
#' @examples
#' \dontrun{
#' datasets <- getDatasets(server)
#' datasets <- getDatasets(project)
#' }
setGeneric(name="getDatasets",
def=function(object)
{
standardGeneric("getDatasets")
}
)
#' Connect to an OMERO server
#'
#' @param server The server
#' @param group The group context (group name)
#' (optional, default: user's default group)
#' @return The server in "connected" state (if successful)
#' @export connect
#' @exportMethod connect
setMethod(f="connect",
signature="OMEROServer",
definition=function(server, group)
{
log <- new(SimpleLogger)
gateway <- new (Gateway, log)
if (length(server@credentialsFile)>0) {
cred <- read.table(server@credentialsFile, header=FALSE, sep="=", row.names=1, strip.white=TRUE, na.strings="NA", stringsAsFactors=FALSE)
username <- cred["omero.user", 1]
password <- cred["omero.pass", 1]
hostname <- cred["omero.host", 1]
portnumber <- cred["omero.port", 1]
}
if (length(server@username)>0)
username <- server@username
if (length(server@password)>0)
password <- server@password
if (length(server@host)>0)
hostname <- server@host
if (server@port>0)
portnumber <- server@port
lc <- new(LoginCredentials, username, password, hostname, as.integer(portnumber))
lc$setApplicationName("rOMERO")
user <- gateway$connect(lc)
server@gateway <- gateway
server@user <- user
if (!is.na(group)) {
for (g in as.list(user$getGroups())) {
if (g$getName() == group) {
server@ctx <- new (SecurityContext, .jlong(g$getId()))
break
}
}
if (is.null(server@ctx))
warning(paste("Group", group, "not found or user is not a member of this group. Using default group."))
}
if (is.null(server@ctx))
server@ctx <- new (SecurityContext, .jlong(user$getGroupId()))
return(server)
}
)
#' Disconnect from an OMERO server
#'
#' @param server The server
#' @return The server in "disconnected" state (if successful)
#' @export disconnect
#' @exportMethod disconnect
setMethod(f="disconnect",
signature="OMEROServer",
definition=function(server)
{
gateway <- getGateway(server)
gateway$disconnect()
return(invisible(server))
}
)
#' Set a different group context
#'
#' @param server The server
#' @param group The name of the group
#' @return The server
#' @export setGroupContext
#' @exportMethod setGroupContext
setMethod(f="setGroupContext",
signature="OMEROServer",
definition=function(server, group)
{
for (g in as.list(server@user$getGroups())) {
if (g$getName() == group) {
server@ctx <- new (SecurityContext, .jlong(g$getId()))
return(invisible(server))
}
}
warning(paste("Group", group, "not found or user is not a member of this group. Operation ignored."))
return(invisible(server))
}
)
#' Get the current group context
#'
#' @param server The server
#' @return The name of the group
#' @export getGroupContext
#' @exportMethod getGroupContext
setMethod(f="getGroupContext",
signature="OMEROServer",
definition=function(server)
{
for (g in as.list(server@user$getGroups())) {
if (g$getId() == server@ctx$getGroupID()) {
return(g$getName())
}
}
return(NA)
}
)
#' Get the reference to the Java Gatway
#'
#' @param server The server
#' @return The Java Gateway
#' @export getGateway
#' @exportMethod getGateway
setMethod(f="getGateway",
signature="OMEROServer",
definition=function(server)
{
return(server@gateway)
}
)
#' Get the current SecurityContext
#'
#' @param server The server
#' @return The SecurityContext
#' @export getContext
#' @exportMethod getContext
setMethod(f="getContext",
signature="OMEROServer",
definition=function(server)
{
return(server@ctx)
}
)
#' Load an object from the server
#'
#' @param server The server
#' @param type The object type
#' @param id The object ID
#' @return The OME remote object @seealso \linkS4class{OMERO}
#' @export loadObject
#' @exportMethod loadObject
setMethod(f="loadObject",
signature="OMEROServer",
definition=function(server, type, id)
{
gateway <- getGateway(server)
ctx <- getContext(server)
browse <- gateway$getFacility(BrowseFacility$class)
if (type == 'ImageData') {
object <- browse$getImage(ctx, .jlong(id))
}
else if (type == 'ProjectData' || type == 'DatasetData' || type == 'PlateData' || type == 'ScreenData') {
ids <- new (ArrayList)
ids$add(new (Long, .jlong(id)))
if (type == 'ProjectData')
clazz <- ProjectData$class
if (type == 'DatasetData')
clazz <- DatasetData$class
if (type == 'ScreenData')
clazz <- ScreenData$class
if (type == 'PlateData')
clazz <- PlateData$class
tmp <- browse$getHierarchy(ctx, clazz, ids, .jnull(class = 'omero/sys/Parameters'))
it <- tmp$iterator()
object <- .jrcall(it, method = "next")
}
else if(type == 'WellData') {
ids <- new (ArrayList)
ids$add(new (Long, .jlong(id)))
tmp <- browse$getWells(ctx, ids)
it <- tmp$iterator()
object <- .jrcall(it, method = "next")
}
else {
object <- browse$findObject(ctx, type, .jlong(id))
}
ome <- OMERO(server=server, dataobject=object)
return(cast(ome))
}
)
#' Load a CSV file from the server
#'
#' @param server The server
#' @param id The original file ID
#' @param header Flag to indicate that the file starts with a header line
#' @param sep The separator character
#' @param quote The quote character
#' @param dec The decimal point character
#' @param fill Flag to indicate if blank fields should be added for rows with unequals length
#' @param comment.char The comment character
#' @return The dataframe constructed from the CSV file
#' @export loadCSV
#' @exportMethod loadCSV
setMethod(f="loadCSV",
signature="OMEROServer",
definition=function(server, id, header, sep, quote,
dec, fill, comment.char)
{
gateway <- getGateway(server)
ctx <- getContext(server)
browse <- gateway$getFacility(BrowseFacility$class)
orgFile <- browse$findIObject(ctx, "OriginalFile", .jlong(id))
store <- gateway$getRawFileService(ctx);
store$setFileId(.jlong(id))
file <- J("java.io.File")$createTempFile("attachment_", ".csv")
stream <- new(J("java.io.FileOutputStream"), file)
offset <- as.integer(0)
size <- as.integer(orgFile$getSize()$getValue())
INC <- as.integer(4096)
while ((offset+INC) < size) {
data <- store$read(.jlong(offset), INC)
stream$write(.jarray(data, "java/lang/Byte"))
offset <- offset + INC
}
data <- store$read(.jlong(offset), (size-offset))
stream$write(.jarray(data, contents.class = "java/lang/Byte"))
stream$close()
path <- file$getPath()
df <- utils::read.csv(path, header = header, sep = sep, quote = quote,
dec = dec, fill = fill, comment.char = comment.char)
file$delete()
return(df)
}
)
#' Get annotations attached to an OME object.
#' Type, Namespace, Name, Content, ID, FileID (in case of file annotations)
#'
#' @param object The server
#' @param type The object type
#' @param id The object id
#' @param typeFilter Optional annotation type filter, e.g. FileAnnotation
#' @param nameFilter Optional name filter, e.g. file name of a FileAnnotation
#' @return The annotations
#' @export getAnnotations
#' @exportMethod getAnnotations
setMethod(f="getAnnotations",
signature=("OMEROServer"),
definition=function(object, type, id, typeFilter, nameFilter)
{
obj <- loadObject(object, type, id)
annos <- getAnnotations(obj, typeFilter = typeFilter, nameFilter = nameFilter)
return(annos)
}
)
#' Search for OMERO objects
#'
#' @param server The server
#' @param type The type of the objects to search for, e.g. Image (default: Image)
#' @param scope Limit the scope to 'Name', 'Description' or 'Annotation' (optional)
#' @param query The search query
#' @return The search results (collection of OMERO objects) @seealso \linkS4class{OMERO}
#' @export searchFor
#' @exportMethod searchFor
setMethod(f="searchFor",
signature=("OMEROServer"),
definition=function(server, type, scope, query)
{
gateway <- getGateway(server)
ctx <- getContext(server)
sf <- gateway$getFacility(SearchFacility$class)
types <- new(ArrayList)
scopes <- new(HashSet)
typeName <- attr(type, 'className')[1]
clazz <- ImageData$class
if(typeName == 'Project')
clazz <- ProjectData$class
else if(typeName == 'Dataset')
clazz <- DatasetData$class
else if(typeName == 'Screen')
clazz <- ScreenData$class
else if(typeName == 'Plate')
clazz <- PlateData$class
else if(typeName == 'Well')
clazz <- WellData$class
types$add(clazz)
sscope <- NA
if(!missing(scope)) {
if(scope == 'Name')
sscope <- SearchScope$NAME
else if(scope == 'Description')
sscope <- SearchScope$DESCRIPTION
else if(scope == 'Annotation')
sscope <- SearchScope$ANNOTATION
if(!missing(sscope))
scopes$add(sscope)
}
params <- new(SearchParameters, scopes, types, query)
src <- sf$search(ctx, params)
jlist <- src$getDataObjects(as.integer(-1), .jnull(class = 'java/lang/Class'))
result <- c()
it <- jlist$iterator()
while(it$hasNext()) {
dataobj <- .jrcall(it, method = "next")
obj <- OMERO(server=server, dataobject=dataobj)
result <- c(result, cast(obj))
}
return(result)
}
)
#' Get all screens of the logged in user
#'
#' @param server The server
#' @return The screens @seealso \linkS4class{Screen}
#' @export getScreens
#' @exportMethod getScreens
setMethod(f="getScreens",
signature=("OMEROServer"),
definition=function(server)
{
gateway <- getGateway(server)
ctx <- getContext(server)
browse <- gateway$getFacility(BrowseFacility$class)
jscreens <- browse$getHierarchy(ctx, ScreenData$class, .jlong(-1))
screens <- c()
it <- jscreens$iterator()
while(it$hasNext()) {
jscreen <- .jrcall(it, method = "next")
if(.jinstanceof(jscreen, ScreenData)) {
screen <- Screen(server=server, dataobject=jscreen)
screens <- c(screens, screen)
}
}
return(screens)
}
)
#' Get all plates of the logged in user
#'
#' @param object The server
#' @return The plates @seealso \linkS4class{Plate}
#' @export getPlates
#' @exportMethod getPlates
setMethod(f="getPlates",
signature=("OMEROServer"),
definition=function(object)
{
gateway <- getGateway(object)
ctx <- getContext(object)
browse <- gateway$getFacility(BrowseFacility$class)
jplates <- browse$getHierarchy(ctx, PlateData$class, .jlong(-1))
plates <- c()
it <- jplates$iterator()
while(it$hasNext()) {
jplate <- .jrcall(it, method = "next")
if(.jinstanceof(jplate, PlateData)) {
jscreens <- jplate$getScreens()
if (is.jnull(jscreens)) {
plate <- Plate(server=object, dataobject=jplate)
plates <- c(plates, plate)
}
}
}
return(plates)
}
)
#' Get all projects of the logged in user
#'
#' @param server The server
#' @return The projects @seealso \linkS4class{Project}
#' @export getProjects
#' @exportMethod getProjects
setMethod(f="getProjects",
signature=("OMEROServer"),
definition=function(server)
{
gateway <- getGateway(server)
ctx <- getContext(server)
browse <- gateway$getFacility(BrowseFacility$class)
jprojects <- browse$getHierarchy(ctx, ProjectData$class, .jlong(-1))
projects <- c()
it <- jprojects$iterator()
while(it$hasNext()) {
jproject <- .jrcall(it, method = "next")
if(.jinstanceof(jproject, ProjectData)) {
project <- Project(server=server, dataobject=jproject)
projects <- c(projects, project)
}
}
return(projects)
}
)
#' Get all datasets of the logged in user
#'
#' @param object The server
#' @return The datasets @seealso \linkS4class{Dataset}
#' @export getDatasets
#' @exportMethod getDatasets
setMethod(f="getDatasets",
signature=("OMEROServer"),
definition=function(object)
{
gateway <- getGateway(object)
ctx <- getContext(object)
browse <- gateway$getFacility(BrowseFacility$class)
jdatasets <- browse$getHierarchy(ctx, DatasetData$class, .jlong(-1))
datasets <- c()
it <- jdatasets$iterator()
while(it$hasNext()) {
jdataset <- .jrcall(it, method = "next")
if(.jinstanceof(jdataset, DatasetData)) {
dataset <- Dataset(server=object, dataobject=jdataset)
datasets <- c(datasets, dataset)
}
}
return(datasets)
}
)
Try the romero.gateway package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.