Merge pull request #75 from dominikl/add_ns

Set namespace of attached dataframe

R/OMERO.R

@@ -107,6 +107,7 @@ setGeneric(
 #' @param omero The OME object
 #' @param df The dataframe
 #' @param name An optional name
+#' @param ns An optional namespace for the file annotation
 #' @return The OME object
 #' @export attachDataframe
 #' @exportMethod attachDataframe
@@ -116,7 +117,7 @@ setGeneric(
 #' }
 setGeneric(
   name = "attachDataframe",
-  def = function(omero, df, name="R Dataframe")
+  def = function(omero, df, name="R Dataframe", ns=NA)
   {
     standardGeneric("attachDataframe")
   }
@@ -340,13 +341,14 @@ setMethod(
 #' @param omero The OME object
 #' @param df The dataframe
 #' @param name An optional name
+#' @param ns An optional namespace for the file annotation
 #' @return The OME object
 #' @export attachDataframe
 #' @exportMethod attachDataframe
 setMethod(
   f = "attachDataframe",
   signature = "OMERO",
-  definition = function(omero, df, name)
+  definition = function(omero, df, name, ns=NA)
   {
    if(!is.data.frame(df)) {
      return(FALSE)
@@ -402,7 +404,10 @@ setMethod(
     ctx <- getContext(server)
     fac <- gateway$getFacility(TablesFacility$class)
 
-    tabledata <- fac$addTable(ctx, omero@dataobject, name, table)
+    if (!is.na(ns))
+      tabledata <- fac$addTable(ctx, omero@dataobject, name, as.character(ns), table)
+    else
+      tabledata <- fac$addTable(ctx, omero@dataobject, name, table)
 
     return(omero)
   }

examples/AddTable.R

@@ -0,0 +1,41 @@
+###
+# Add a dataframe which is accessible to the OMERO.web client.
+#
+# This example uses the attachDataframe method again (like the AddData.R example),
+# but this time an 'Image' column with the image Ids is added and the dataframe 
+# gets attached to a dataset with the particular namespace 
+# 'openmicroscopy.org/omero/bulk_annotations'. This way the entries in the dataframe
+# will be picked up by the OMERO.web client and shown on the 'Tables' tab of the 
+# images.
+###
+
+library(romero.gateway)
+
+# Connect to server
+server <- OMEROServer(host = "localhost", username = "xx", password = "xx", port = as.integer(4064))server <- connect(server)
+server <- connect(server)
+
+# Load a dataset
+datasetId <- 1
+dataset <- loadObject(server, "DatasetData", datasetId)
+
+# Create a dataframe with one row per image, like:
+# Image, SomeValue, AnotherValue
+# 1, 'Some value', 'Another Value'
+# ...
+imgIds <- c()
+values1 <- c()
+values2 <- c()
+for (img in getImages(dataset)) {
+  imgIds <- c(imgIds, getOMEROID(img))
+  values1 <- c(values1, paste("Some value for image",img@dataobject$getName()))
+  values2 <- c(values2, paste("Another value for image",img@dataobject$getName()))
+}
+
+# Attach it as dataframe with namespace 'openmicroscopy.org/omero/bulk_annotations'
+# to make it available to OMERO.web
+df <- data.frame(Image = imgIds, SomeValue = values1, AnotherValue = values2)
+attachDataframe(dataset, df, "Example data", ns = "openmicroscopy.org/omero/bulk_annotations")
+
+# Go to OMERO.web client, select an image and you should see its values
+# in the 'Tables' tab.