Merge pull request #7 from Open-EO/develop

Merging Develop

DESCRIPTION

@@ -60,12 +60,13 @@ Collate:
     'MapServerMap-class.R'
     'MapServerWeb-class.R'
     'ProcessGraph-class.R'
-    'Product-class.R'  
+    'Product-class.R'
     'R2Generic-class.R'
     'data.R'
     'processes.R'
     'Server-class.R'
     'Service-class.R'
+    'Udf-class.R'
     'User-class.R'
     'View-class.R'
     'api_processes.R'
@@ -75,5 +76,4 @@ Collate:
     'api_job.R'
     'api_data.R'
     'api.R'
-    'prepare_UDF.R'
     'serializer_proxy.R'

NAMESPACE

@@ -21,13 +21,15 @@ export(R2Generic)
 export(Service)
 export(SpaceView)
 export(TimeView)
+export(UdfTransaction)
 export(User)
 export(View)
 export(code)
 export(createServerInstance)
 export(create_dimensionality)
 export(create_dimensionality_modifier)
 export(exists.Service)
+export(exists.Udf)
 export(exists.User)
 export(getCollectionFromImageryStatement)
 export(is.MapServerConfig)
@@ -37,12 +39,11 @@ export(is.MapServerWeb)
 export(is.Process)
 export(is.Product)
 export(is.Service)
+export(is.Udf)
 export(is.User)
 export(loadSentinel2Data)
-export(raster_collection_export)
 export(read_legend)
 export(serializer_proxy)
-export(udf_export)
 export(write_generics)
 exportMethods(crs)
 exportMethods(extent)

R/Collection-class.R

@@ -4,6 +4,7 @@
 #' intermediate results from one process to an other (the result of a process is a Collection).
 #' 
 #' @field dimensions A dimensionality object containing information about the existence of dimensions
+#' @field space A tibble containing an index and the geometry
 #' @importFrom R6 R6Class
 #' @export
 Collection <- R6Class(
@@ -657,3 +658,33 @@ crs.Collection = function(x, ...) {
 
 }
 
+is.st_raster = function(x) {
+  dims = x$dimensions
+  return(dims$space && dims$time && dims$raster)
+}
+# what about multiband / attribute ?
+
+is.st_feature = function(x) {
+  dims = x$dimensions
+  return(dims$space && dims$time && dims$feature)
+}
+
+is.raster = function(x) {
+  dims = x$dimensions
+  return(dims$space && dims$raster && !dims$time)
+} 
+
+is.feature = function(x) {
+  dims = x$dimensions
+  return(dims$space && dims$feature && !dims$time)
+}
+
+is.timeseries = function(x) {
+  dims = x$dimensions
+  return(dims$time && !dims$space && !dims$raster && !dims$feature)
+}
+
+is.scalar = function(x) {
+  dims = x$dimensions
+  return(!dims$time && !dims$space && !dims$raster && !dims$feature)
+}

R/Job-class.R

@@ -6,12 +6,16 @@
 #' 
 #' @field job_id The unique identifier of the job
 #' @field status The current status in the job lifecycle
-#' @field process_graph graph of nested processes that is executable
-#' @field view Spatio-Temporal Extent to be used for the calculation
+#' @field process_graph graph of nested processes that is executable (ExecutableProcess)
+#' @field view Spatio-Temporal Extent to be used for the calculation (currently not in use)
 #' @field submitted Timestamp when the job was submitted to the server
 #' @field user_id The user who owns the job
 #' @field consumed_credits For accounting and billing the amount of credits consumed by this job
-#' @field filePath The system filepath that links to the stored JSON process graph
+#' @field last_update Timestamp when the job was last updated
+#' @field output output configuration like output$format copied from the process graph (pg)
+#' @field results Contains the result of the process_graph after execution (Collection)
+#' @field persistent Whether or not the job is stored in database
+#' @field output list containing the output configuration like format (or additional GDAL commands)
 #' 
 #' @include Process-class.R
 #' @importFrom R6 R6Class
@@ -31,9 +35,9 @@ Job <- R6Class(
     last_update=NULL,
     user_id=NULL,
     consumed_credits=NULL,
-    output=NULL,
-    results = NULL,
-    persistent = FALSE,
+    output=NULL, # output configuration like output$format copied from the process graph (pg)
+    results = NULL, # contains the results of the process_graph after execution
+    persistent = FALSE, # whether or not the job is stored in data base
 
     # functions ----
     initialize = function(job_id=NULL,process_graph=NULL,user_id = NULL) {
@@ -304,4 +308,16 @@ exists.Job = function(job_id) {
   } else {
     return(FALSE)
   }
+}
+
+syncJobId = function() {
+  randomString = paste("SYNC",createAlphaNumericId(n=1,length=11),sep="")
+
+
+  if (exists.Job(randomString)) {
+    # if id exists get a new one (recursive)
+    return(syncJobId())
+  } else {
+    return(randomString)
+  }
 }

R/R2Generic-class.R

@@ -85,3 +85,25 @@ R2Generic = R6Class(
 
   )
 )
+
+#' Write generics to disk
+#' 
+#' @description This function writes rasters in a consistent directory structure to disk in generic GeoTIFF formats. 
+#' It takes as input an object of class `Collection` and the path where the files are to be written to disk. Once the files 
+#' have been written to disk, it can be loaded into a `stars` object by the user after which custom functions could 
+#' be applied to it.
+#'
+#' @param collection_obj Object of class Collection as produced in the previous step while executing the process graph before encountering the UDF
+#' @param dir_name Path where the generics are to be written to disk. This could be obtained from the UDF process if it is defined by the user while registering it.
+#'
+#' @export
+#'
+write_generics = function(collection_obj, dir_name = "disk") #dir_name could be obtained if it is defined while registering the UDF
+{
+  scene_table = collection_obj$getData()
+  R2G_obj = R2Generic$new(scenes = scene_table)
+  R2G_obj$write_scenes(dir_name = dir_name)
+
+  R2G_obj$legend_to_disk(dir_name)
+
+}

R/Server-class.R

@@ -32,10 +32,11 @@ OpenEOServer <- R6Class(
       sqlite.path = NULL,
 
       udf_transactions.path = NULL,
+      udf_cleanup = TRUE,
 
       api.port = NULL,
       host = NULL,
-      baseserver.url = "http:localhost:8000/api/",
+      baseserver.url = "http://localhost:8000/api/",
       mapserver.url = NULL, #assuming here a url, if not specified the backend is probably started with docker-compose
 
       processes = NULL,
@@ -190,6 +191,16 @@ OpenEOServer <- R6Class(
           )")
         }
 
+        if (!dbExistsTable(con,"udf")) {
+          dbExecute(con, "create table udf (
+                    udf_id text,
+                    job_id text,
+                    start_date datetime default current_timestamp,
+                    end_date datetime,
+                    status text
+          )")
+        }
+
         dbDisconnect(con)
       },
 
@@ -264,6 +275,7 @@ OpenEOServer <- R6Class(
           }, error = function(e) {
             cat(str(e))
           }, finally={
+            removeJobsUdfData(job)
             logToConsole()
           })