Merge pull request #102 from dominikl/fix_object_loading

Fix object loading

CHANGELOG.md

@@ -1,3 +1,11 @@
+0.4.12 (April 2023)
+-------------------
+- fix IllegalAccessExceptions (PR #102)
+
+0.4.11 (October 2021)
+---------------------
+- fix variable exports (PRs #95, #96)
+
 0.4.10 (October 2020)
 ---------------------
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: romero.gateway
 Type: Package
-Version: 0.4.11-999
-Date: 2023-04-07
+Version: 0.4.12
+Date: 2023-04-10
 Title: OMERO R Gateway
 Description: R Wrapper around the OMERO Java Gateway, which
   enables access to an OMERO server within R.

R/Dataset.R

@@ -52,9 +52,8 @@ setMethod(
 
     jimgs <- fac$getImagesForDatasets(ctx, jlist)
     result <- c()
-    it <- jimgs$iterator()
-    while(it$hasNext()) {
-      jimg <- .jrcall(it, method = "next")
+    jimgslist <- as.list(jimgs)
+    for (jimg in jimgslist) {
       img <- Image(server=server, dataobject=jimg)
       result <- c(result, img)
     }

R/Image.R

@@ -193,9 +193,8 @@ setMethod(
     iid <- image@dataobject$getId()
     jchannels <- fac$getChannelData(ctx, .jlong(iid))
     channels <- c()
-    it <- jchannels$iterator()
-    while(it$hasNext()) {
-      jchannel <- .jrcall(it, method = "next")
+    jchannelslist <- as.list(jchannels)
+    for (jchannel in jchannelslist) {
       channels <- c(channels, jchannel$getName())
     }
     return(channels)
@@ -233,17 +232,14 @@ setMethod(
 
     roiresults <- fac$loadROIsByPlane(ctx, iid, z, t)
     rois <- data.frame(x = c(0), y = c(0), rx = c(0), ry = c(0), w = c(0), h = c(0), theta = c(0), text = c('remove'), stringsAsFactors = FALSE)
-    it <- roiresults$iterator()
-    while (it$hasNext()) {
-      roiresult <- .jrcall(it, method = "next")
+    roiresultslist <- as.list(roiresults)
+    for (roiresult in roiresultslist) {
       roidatas <- roiresult$getROIs()
-      it2 <- roidatas$iterator()
-      while (it2$hasNext()) {
-        roidata <- .jrcall(it2, method = "next")
+      roidataslist <- as.list(roidatas)
+      for (roidata in roidataslist) {
         shapes <- roidata$getShapes(z, t)
-        it3 <- shapes$iterator()
-        while (it3$hasNext()) {
-          shape <- .jrcall(it3, method = "next")
+        shapeslist <- as.list(shapes)
+        for (shape in shapeslist) {
           shape <- .jcast(shape, new.class = "omero.gateway.model.ShapeData")
           trans <- shape$getTransform()
           th <- NA

R/OMERO.R

@@ -436,9 +436,8 @@ setMethod(
     Name <- c()
     ID <- c()
     AnnotationID <- c()
-    it <- files$iterator()
-    while(it$hasNext()) {
-      file <- .jrcall(it, method = "next")
+    filelist <- as.list(files)
+    for (file in filelist) {
       Name <- c(Name, file$getFileName())
       ID <- c(ID, file$getFileID())
       AnnotationID <- c(AnnotationID, file$getId())
@@ -644,9 +643,8 @@ setMethod(f="getAnnotations",
 
             result <- data.frame(Type = character(), Namespace = character(), Name = character(), Content = character(), ID = numeric(), FileID = numeric())
 
-            it <- jannos$iterator()
-            while(it$hasNext()) {
-              anno <- .jrcall(it, method = "next")
+            jannoslist <- as.list(jannos)
+            for (anno in jannoslist) {
               javclass <- anno$getClass()
               annotype <- javclass$getName()
               annotype <- gsub("omero\\.gateway\\.model\\.", "", annotype)

R/OMEROServer.R

@@ -608,31 +608,24 @@ setMethod(f="loadObject",
           {
             gateway <- getGateway(server)
             ctx <- getContext(server)
-            browse <- gateway$getFacility(J("omero.gateway.facility.BrowseFacility")$class)
+            lf <- gateway$getFacility(J("omero.gateway.facility.LoadFacility")$class)
             if (type == 'ImageData') {
-              object <- browse$getImage(ctx, .jlong(id))
+              object <- lf$getImage(ctx, .jlong(id))
+            }
+            else if (type == 'ProjectData') {
+              object <- lf$getProject(ctx, .jlong(id))
+            }
+            else if (type == 'ScreenData') {
+              object <- lf$getScreen(ctx, .jlong(id))
+            }
+            else if (type == 'DatasetData') {
+              object <- lf$getDataset(ctx, .jlong(id))
             }
-            else if (type == 'ProjectData' || type == 'DatasetData' || type == 'PlateData' || type == 'ScreenData') {
-              ids <- new (J("java.util.ArrayList"))
-              ids$add(new (J("java.lang.Long"), .jlong(id)))
-              if (type == 'ProjectData')
-                clazz <- J("omero.gateway.model.ProjectData")$class
-              if (type == 'DatasetData')
-                clazz <- J("omero.gateway.model.DatasetData")$class
-              if (type == 'ScreenData')
-                clazz <- J("omero.gateway.model.ScreenData")$class
-              if (type == 'PlateData')
-                clazz <- J("omero.gateway.model.PlateData")$class
-              tmp <- browse$getHierarchy(ctx, clazz, ids, .jnull(class = 'omero/sys/Parameters'))
-              it <- tmp$iterator()
-              object <- .jrcall(it, method = "next")
+            else if (type == 'PlateData') {
+              object <- lf$getPlate(ctx, .jlong(id))
             }
             else if(type == 'WellData') {
-              ids <- new (J("java.util.ArrayList"))
-              ids$add(new (J("java.lang.Long"), .jlong(id)))
-              tmp <- browse$getWells(ctx, ids)
-              it <- tmp$iterator()
-              object <- .jrcall(it, method = "next")
+              object <- lf$getWell(ctx, .jlong(id))
             }
             else { 
               object <- browse$findObject(ctx, type, .jlong(id))
@@ -768,9 +761,8 @@ setMethod(f="searchFor",
             jlist <- src$getDataObjects(as.integer(-1), .jnull(class = 'java/lang/Class'))
 
             result <- c()
-            it <- jlist$iterator()
-            while(it$hasNext()) {
-              dataobj <- .jrcall(it, method = "next")
+            jlistlist <- as.list(jlist)
+            for (dataobj in jlistlist) {
               obj <- OMERO(server=server, dataobject=dataobj)
               result <- c(result, cast(obj))
             }
@@ -797,9 +789,8 @@ setMethod(f="getScreens",
             jscreens <- browse$getHierarchy(ctx, J("omero.gateway.model.ScreenData")$class, .jlong(-1))
 
             screens <- c()
-            it <- jscreens$iterator()
-            while(it$hasNext()) {
-              jscreen <- .jrcall(it, method = "next")
+            jscreenslist <- as.list(jscreens)
+            for (jscreen in jscreenslist) {
               if(.jinstanceof(jscreen, J("omero.gateway.model.ScreenData"))) {
                 screen <- Screen(server=server, dataobject=jscreen)
                 screens <- c(screens, screen)
@@ -827,9 +818,8 @@ setMethod(f="getPlates",
             jplates <- browse$getHierarchy(ctx, J("omero.gateway.model.PlateData")$class, .jlong(-1))
 
             plates <- c()
-            it <- jplates$iterator()
-            while(it$hasNext()) {
-              jplate <- .jrcall(it, method = "next")
+            jplateslist <- as.list(jplates)
+            for (jplate in jplateslist) {
               if(.jinstanceof(jplate, J("omero.gateway.model.PlateData"))) {
                 jscreens <- jplate$getScreens()
                 if (is.jnull(jscreens)) {
@@ -861,9 +851,8 @@ setMethod(f="getProjects",
             jprojects <- browse$getHierarchy(ctx, J("omero.gateway.model.ProjectData")$class, .jlong(-1))
 
             projects <- c()
-            it <- jprojects$iterator()
-            while(it$hasNext()) {
-              jproject <- .jrcall(it, method = "next")
+            jprojectslist <- as.list(jprojects)
+            for (jproject in jprojectslist) {
               if(.jinstanceof(jproject, J("omero.gateway.model.ProjectData"))) {
                 project <- Project(server=server, dataobject=jproject)
                 projects <- c(projects, project)
@@ -892,9 +881,8 @@ setMethod(f="getDatasets",
             jdatasets <- browse$getHierarchy(ctx, J("omero.gateway.model.DatasetData")$class, .jlong(-1))
 
             datasets <- c()
-            it <- jdatasets$iterator()
-            while(it$hasNext()) {
-              jdataset <- .jrcall(it, method = "next")
+            jdatasetslist <- as.list(jdatasets)
+            for (jdataset in jdatasetslist) {
               if(.jinstanceof(jdataset, J("omero.gateway.model.DatasetData"))) {
                 dataset <- Dataset(server=object, dataobject=jdataset)
                 datasets <- c(datasets, dataset)

R/Plate.R

@@ -65,9 +65,8 @@ setMethod(
     jwells <- browse$getWells(ctx, .jlong(getOMEROID(plate)))
 
     wells <- c()
-    it <- jwells$iterator()
-    while(it$hasNext()) {
-      jwell <- .jrcall(it, method = "next")
+    jwellslist <- as.list(jwells)
+    for (jwell in jwellslist) {
       if (jwell$asWell()$sizeOfWellSamples() > 0) {
         well <- Well(server=server, dataobject=jwell)
         wells <- c(wells, well)

R/Project.R

@@ -57,9 +57,8 @@ setMethod(
 
     jimgs <- fac$getImagesForProjects(ctx, jlist)
     result <- c()
-    it <- jimgs$iterator()
-    while(it$hasNext()) {
-      jimg <- .jrcall(it, method = "next")
+    jimgslist <- as.list(jimgs)
+    for (jimg in jimgslist) {
       img <- Image(server=server, dataobject=jimg)
       result <- c(result, img)
     }
@@ -89,12 +88,11 @@ setMethod(f="getDatasets",
             jlist <- J("java.util.Collections")$singletonList(id)
             jprojects <- fac$getHierarchy(ctx, J("omero.gateway.model.ProjectData")$class, jlist, .jnull())
 
-            it <- jprojects$iterator()
-            jproject <- .jrcall(it, method = "next")
+            tmplist <- as.list(jprojects)
+            jproject <- tmplist[[1]]
             datasets <- c()
-            it <- jproject$getDatasets()$iterator()
-            while(it$hasNext()) {
-              jdataset <- .jrcall(it, method = "next")
+            jdatasetlist <- as.list(jproject$getDatasets())
+            for (jdataset in jdatasetlist) {
               if(.jinstanceof(jdataset, J("omero.gateway.model.DatasetData"))) {
                 dataset <- Dataset(server=object@server, dataobject=jdataset)
                 datasets <- c(datasets, dataset)

R/Screen.R

@@ -52,17 +52,16 @@ setMethod(
       jlist$add(new(J("java.lang.Long"), .jlong(obj$getId())))
       set <- browse$loadHierarchy(ctx, J("omero.gateway.model.ScreenData")$class,
                                    jlist, .jnull())
-      it <- set$iterator()
-      loaded <- .jrcall(it, method = "next")
+      tmplist <- as.list(set)
+      loaded <- tmplist[[1]]
     }
     else
       loaded <- obj
 
     plates <- c()
     jplates <- loaded$getPlates()
-    it <- jplates$iterator()
-    while(it$hasNext()) {
-      jplate <- .jrcall(it, method = "next")
+    jplateslist <- as.list(jplates)
+    for (jplate in jplateslist) {
       plate <- Plate(server = server, dataobject = jplate)
       plates <- c(plates, plate)
     }

R/Well.R

@@ -91,10 +91,9 @@ setMethod(
     if (missing(fieldIndex)) {
       size <- as.integer(jfields$size())
       fields <- list(size)
-      it <- jfields$iterator()
+      jfieldslist = as.list(jfields)
       i <- 1
-      while(it$hasNext()) {
-        jfield <- .jrcall(it, method = "next")
+      for (jfield in jfieldslist) {
         jimg <- jfield$getImage()
         img <- Image(server=server, dataobject=jimg)
         fields[[i]] <-img