Merge branch 'main' into develop

.github/workflows/docker-compose-develop.yml

@@ -0,0 +1,15 @@
+name: docker-compose-workflow
+on:
+  push:
+    branches: [ "develop" ]
+  pull_request:
+    branches: [ "develop" ]
+
+jobs:
+  test:
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v2
+      - name: Run docker-compose
+        run: docker-compose up -d

.github/workflows/docker-compose-main.yml

@@ -0,0 +1,27 @@
+name: docker-compose-workflow
+on:
+  push:
+    branches: [ "main" ]
+
+jobs:
+  test:
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v2
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          push: true
+          tags: brianpondi/openeosits:latest
+
+      - name: Run docker-compose
+        run: docker-compose up -d

DESCRIPTION

@@ -45,7 +45,7 @@ Imports:
     rstac,
     caret,
     randomForest,
-    sits
+    sits (>= 1.4.1)
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Collate: 

Dockerfile

@@ -45,4 +45,4 @@ RUN Rscript -e "remotes::install_local('/opt/dockerfiles', dependencies=TRUE)"
 CMD ["R", "-q", "--no-save", "-f /opt/dockerfiles/Dockerfiles/start.R"]
 
 # Expose port
-EXPOSE 8000
+EXPOSE 8000

Dockerfiles/start.R

@@ -3,15 +3,13 @@ library(openeosits)
 
 aws.host <- Sys.getenv("AWSHOST")
 
-if (aws.host == "") {
-  aws.host <- NULL
-} else {
-  message("AWS host port id is:")
-  message(aws.host)
+if (aws.host == ""){
+  aws.host = NULL
+}else{
+  message("AWS host port id is:", aws.host)
 }
 
-
 config <- SessionConfig(api.port = 8000, host = "0.0.0.0", aws.ipv4 = aws.host)
 config$workspace.path <- "/var/openeo/workspace"
 createSessionInstance(config)
-Session$startSession()
+Session$startSession()

R/Collection-class.R

@@ -22,22 +22,21 @@ Collection <- R6Class(
     #' @param description Short description of the collection
     #'
     initialize = function(id = NA, title = NA, description = NA) {
-
-      self$id = id
-      self$title = title
-      self$description = description
+      self$id <- id
+      self$title <- title
+      self$description <- description
     },
 
     #' @description Add image collection to the collection class object
     #'
     #' @param ImageCollection Collection of class 'image collection'
     #'
     setCollection = function(ImageCollection) {
-      if (! gdalcubes:::is.image_collection(ImageCollection)) {
+      if (!gdalcubes:::is.image_collection(ImageCollection)) {
         stop("Assigned data is not an image collection")
       }
 
-      private$imageCollection = ImageCollection
+      private$imageCollection <- ImageCollection
       self$setMetadata()
     },
 
@@ -52,8 +51,7 @@ Collection <- R6Class(
     #' @description add extent and bands to the metadata of the collection object
     #'
     setMetadata = function() {
-
-      private$metadata = list(
+      private$metadata <- list(
         extent = extent(private$imageCollection),
         bands = gdalcubes:::libgdalcubes_image_collection_info(private$imageCollection)$bands$name
       )
@@ -72,12 +70,11 @@ Collection <- R6Class(
     #' @return converted bandlist
     #'
     getEoBands = function() {
-
-      list = list()
-      bands = as.list(self$getMetadata()$bands)
-      list = lapply(bands, function(x) {
-               append(list,  list(name = x))
-             })
+      list <- list()
+      bands <- as.list(self$getMetadata()$bands)
+      list <- lapply(bands, function(x) {
+        append(list, list(name = x))
+      })
       return(list)
     },
 
@@ -92,29 +89,31 @@ Collection <- R6Class(
         license = "proprietary",
         extent = list(
           spatial = list(
-            bbox = list(list(self$getMetadata()$extent$left, self$getMetadata()$extent$bottom,
-            self$getMetadata()$extent$right, self$getMetadata()$extent$top))
+            bbox = list(list(
+              self$getMetadata()$extent$left, self$getMetadata()$extent$bottom,
+              self$getMetadata()$extent$right, self$getMetadata()$extent$top
+            ))
           ),
           temporal = list(
             interval = list(list(self$getMetadata()$extent$t0, self$getMetadata()$extent$t1))
           )
         ),
-       links = list(
-         list(
-           rel = "self",
-           href = paste(Session$getConfig()$base_url, "collections", self$id, sep = "/")
-         ),
-         list(
-           rel = "parent",
-           href = paste(Session$getConfig()$base_url, "collections", sep = "/")
-         ))
+        links = list(
+          list(
+            rel = "self",
+            href = paste(Session$getConfig()$base_url, "collections", self$id, sep = "/")
+          ),
+          list(
+            rel = "parent",
+            href = paste(Session$getConfig()$base_url, "collections", sep = "/")
+          )
+        )
       )
     },
 
     #' @description List extended metadata for the collection handler
     #'
     collectionInfoExtended = function() {
-
       list(
         stac_version = Session$getConfig()$stac_version,
         stac_extensions = list(Session$getConfig()$stac_extensions),
@@ -124,29 +123,29 @@ Collection <- R6Class(
         license = "proprietary",
         extent = list(
           spatial = list(
-            bbox = list(list(self$getMetadata()$extent$left, self$getMetadata()$extent$bottom,
-                             self$getMetadata()$extent$right, self$getMetadata()$extent$top))
+            bbox = list(list(
+              self$getMetadata()$extent$left, self$getMetadata()$extent$bottom,
+              self$getMetadata()$extent$right, self$getMetadata()$extent$top
+            ))
           ),
           temporal = list(
             interval = list(list(self$getMetadata()$extent$t0, self$getMetadata()$extent$t1))
           )
         ),
         links = list(list(
           rel = "root",
-          href = paste(Session$getConfig()$base_url, "collections", sep = "/"))
-        ),
+          href = paste(Session$getConfig()$base_url, "collections", sep = "/")
+        )),
         "cube:dimensions" = list(
           x = list(
             type = "spatial",
             axis = "x",
-            extent = list(self$getMetadata()$extent$left, self$getMetadata()$extent$right
-            )
+            extent = list(self$getMetadata()$extent$left, self$getMetadata()$extent$right)
           ),
           y = list(
             type = "spatial",
             axis = "y",
-            extent = list(self$getMetadata()$extent$bottom, self$getMetadata()$extent$top
-            )
+            extent = list(self$getMetadata()$extent$bottom, self$getMetadata()$extent$top)
           ),
           t = list(
             type = "temporal",
@@ -157,7 +156,7 @@ Collection <- R6Class(
             values = list(self$getMetadata()$bands)
           )
         ),
-        summaries = list(constellation = list(""), 'eo:bands' = self$getEoBands())
+        summaries = list(constellation = list(""), "eo:bands" = self$getEoBands())
       )
     }
   ),
@@ -168,12 +167,13 @@ Collection <- R6Class(
 )
 
 #' @export
-is.Collection = function(obj) {
+is.Collection <- function(obj) {
   return("Collection" %in% class(obj))
 }
 
+
 #' collections:
-#'sentinel-s2-l2a
+#' sentinel-2-l2a
 SENTINEL_2_L2A <- Collection$new(
   id = "SENTINEL-2-L2A",
   title = "Sentinel 2 L2A",

R/api.R

@@ -280,6 +280,8 @@ addEndpoint = function() {
   Session$assignProcess(load_collection)
   Session$assignProcess(ml_regularize_data_cube)
   Session$assignProcess(ml_fit_class_random_forest)
+  Session$assignProcess(ml_predict)
+  Session$assignProcess(save_ml_model)
   Session$assignProcess(save_result)
 
  # assign math processes

R/processes.R

@@ -30,7 +30,6 @@ schema_format <- function(type, subtype = NULL, items = NULL) {
 }
 
 
-
 #' datacube_schema
 #' @description Return a list with data cube description and schema
 #'
@@ -46,6 +45,21 @@ datacube_schema <- function() {
 #' return object for the processes
 eo_datacube <- datacube_schema()
 
+#' ml datacube_schema
+#' @description Return a list with ml data cube description and schema
+#'
+#' @return datacube list
+ml_datacube_schema <- function() {
+  info <- list(
+    description = "A data cube with the predicted values. It removes the specified dimensions and adds new dimension for the predicted values. It has the name `predictions` and is of type `other`. If a single value is returned, the dimension has a single label with name `0`.",
+    schema = list(type = "object", subtype = "datacube")
+  )
+  return(info)
+}
+
+#' return object from ml pedict process
+eo_ml_datacube <- ml_datacube_schema()
+
 
 #' load collection
 load_collection <- Process$new(
@@ -258,7 +272,7 @@ ml_fit_class_random_forest <- Process$new(
       name = "seed",
       description = "A randomization seed to use for the random sampling in training. If not given or `null`, no seed is used and results may differ on subsequent use.",
       schema = list(
-        type = list("integer", NULL)
+        type = list("integer", "null")
       ),
       optional = TRUE
     )
@@ -277,6 +291,81 @@ ml_fit_class_random_forest <- Process$new(
   }
 )
 
+
+#' ml predict
+ml_predict <- Process$new(
+  id = "ml_predict",
+  description = "Applies a machine learning model to a data cube of input features and returns the predicted values.",
+  categories = as.array("machine learning"),
+  summary = "Predict using ML",
+  parameters = list(
+    Parameter$new(
+      name = "data",
+      description = "The data cube containing the input features.",
+      schema = list(
+        type = "object",
+        subtype = "datacube"
+      )
+    ),
+    Parameter$new(
+      name = "model",
+      description = "A ML model that was trained with one of the ML training processes such as ``ml_fit_class_random_forest()``.",
+      schema = list(
+        type = "object",
+        subtype = "ml-model"
+      )
+    ),
+    Parameter$new(
+      name = "dimensions",
+      description = "Zero or more dimensions that will be reduced by the model. Fails with a `DimensionNotAvailable` exception if one of the specified dimensions does not exist.",
+      schema = list(
+        type = "array"
+      )
+    )
+  ),
+  returns = eo_ml_datacube,
+  operation = function(data, model, dimensions = c("bands", "time"), job) {
+
+    #if (dimensions != "bands"){
+    #  stop("The dimensions specified is not supported, only bands dimensions are supported currently.")
+    #}
+    # TO DO
+  }
+)
+
+#' save ml model
+save_ml_model <- Process$new(
+  id = "save_ml_model",
+  description = "Saves a machine learning model as part of a batch job.The model will be accompanied by a separate STAC Item that implements the [ml-model extension](https://github.com/stac-extensions/ml-model).",
+  categories = as.array("machine learning", "import"),
+  summary = "Save a ML model",
+  parameters = list(
+    Parameter$new(
+      name = "data",
+      description = "The data to save.",
+      schema = list(
+        type = "object",
+        subtype = "ml-model"
+      )
+    ),
+    Parameter$new(
+      name = "options",
+      description = "Additional parameters to create the file(s).",
+      schema = list(
+        type = "object"
+      ),
+      optional = TRUE
+    )
+  ),
+  returns = list(
+    description = "false if saving failed, true otherwise.",
+    schema = list(type = "boolean")
+  ),
+  operation = function(data, format, options = NULL, job) {
+    # TO DO
+  }
+)
+
 #' save result
 save_result <- Process$new(
   id = "save_result",