Merge pull request #6 from Open-EO/develop

DESCRIPTION

@@ -1,9 +1,12 @@
 Package: openEO.R.Backend
 Title: Reference backend implementation for openEO conformant backend with a local filesystem
-Version: 0.2.4
-Authors@R: person("Florian", "Lahn", email = "[email protected]", role = c("aut", "cre"))
+Version: 0.2.5
+Authors@R: c(person("Florian", "Lahn", email = "[email protected]", role = c("aut", "cre")),
+  person("Pramit","Ghosh",email = "[email protected]", role = c("aut","ctb")))
 Description: The package contains a backend solution in compliance with the openEO API. In this demonstration 
     the file backend solution is the local file system containing some raster data collections.
+URL: https://github.com/Open-EO/openeo-r-backend
+BugReports: https://github.com/Open-EO/openeo-r-backend/issues
 Depends: 
     R (>= 3.3),
     rgdal (>= 1.2-16),
@@ -27,7 +30,7 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.0.1
 VignetteBuilder: knitr
-License: Apache License
+License: Apache License 2.0
 Imports:
     plumber,
     jsonlite,

DOCKERFILE

@@ -1,11 +1,10 @@
-FROM openeo-baseserver:1.4
+FROM openeo-baseserver:1.5
 MAINTAINER Florian Lahn ([email protected])
-LABEL version="0.2.4"
+LABEL version="0.2.5"
 LABEL description="A simple openeo (almost) conformant backend for frontend development"
 
 # create the path for the user files
-RUN mkdir -p /opt/dockerfiles/
-RUN mkdir -p /var/openeo/workspace/
+RUN mkdir -p /opt/dockerfiles/ && mkdir -p /var/openeo/workspace/
 
 COPY ./ /opt/dockerfiles/
 

DOCKERFILE-base

@@ -1,11 +1,10 @@
-FROM r-base:3.4.4
+FROM r-base:3.5.0
 MAINTAINER Florian Lahn ([email protected])
-LABEL version="1.4"
+LABEL version="1.5"
 LABEL description="The basic configuration of the openeo r server image"
 
 # create the path for the user files
-RUN mkdir -p /opt/dockerfiles/
-RUN mkdir -p /var/openeo/workspace/
+RUN mkdir -p /opt/dockerfiles/ && mkdir -p /var/openeo/workspace/
 
 COPY ./ /opt/dockerfiles/
 

Dockerfiles/install_package.R

@@ -1,3 +1,7 @@
 library(devtools)
 
+# install the R UDF package from github
+install_github("pramitghosh/OpenEO.R.UDF",ref="v0.0.1",dependencies=TRUE)
+
+# install the R back-end package
 install("/opt/dockerfiles")

Dockerfiles/install_package_dependencies.R

@@ -5,4 +5,8 @@ library(devtools)
 
 install_deps("/opt/dockerfiles",repos=cran.mirror)
 installation = list.files("/opt/dockerfiles",recursive=TRUE,full.names = TRUE)
+
+# packages for the R UDFs
+install_github("r-spatial/stars", dependencies=TRUE)
+
 removed = file.remove(installation)

NAMESPACE

@@ -38,9 +38,13 @@ export(is.Process)
 export(is.Product)
 export(is.Service)
 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)
 import(DBI)
 import(plumber)

R/Collection-class.R

@@ -105,7 +105,6 @@ Collection <- R6Class(
     },
 
     addGranule = function(space=NULL,time=NULL, band=NULL, data, ..., meta_band = NULL) {
-
       dot_args = list(...)
 
       if (is.character(data)) {
@@ -188,15 +187,19 @@ Collection <- R6Class(
       } 
 
 
-      if (!is.null(band) && length(band) > 1) {
+      if (!is.null(band) && length(band) >= 1) { #unstack also one banded images
         # add multiple bands
-        bands = unstack(data)
         adding = tibble(band = band)
         if (self$dimensions$time) {
           adding = add_column(adding,time = time)
         }
 
-        layer = unstack(data)
+        if (class(data) != "RasterLayer") {
+          layer = unstack(data)
+        } else {
+          layer = list(data)
+        }
+
         adding = add_column(adding,data=layer)
 
         if (self$dimensions$space) {
@@ -326,9 +329,6 @@ Collection <- R6Class(
         if (self$dimensions$time) {
           # order by bands if present, stack single bands into one file
 
-          # space is fixed (for now)
-          # TODO rework the holding of spatial extents in a spatial* data.frame where we store the feature and
-          # state the IDs in the table
           if (self$dimensions$band) {
             private$data_table = private$data_table %>% 
             group_by(time,space) %>% 
@@ -433,7 +433,6 @@ Collection <- R6Class(
         }
 
         if (self$dimensions$time) {
-          # TODO group also by band! currently assuming that we have only one attribute--hmm maybe it doesn't matter
           out = private$data_table %>% dplyr::group_by(space) %>% dplyr::arrange(time) %>% dplyr::summarise(data=tibble(band,time,data) %>% (function(x, ...){
             values = unlist(x$data)
             names = paste(x$band,as.character(x$time), sep=".")
@@ -626,12 +625,10 @@ read_legend = function(legend.path,code, ...) {
   # prepareBands
   parentFolder = dirname(legend.path)
 
-  bandinfo = table %>% group_by(band_index) %>% summarise(band = first(band), data = first(filename)) %>% arrange(band_index)
+  bandinfo = table %>% group_by(band_index) %>% dplyr::summarise(band = first(band), data = first(filename)) %>% dplyr::arrange(band_index)
   # use band as band_index
   dots$band_id = bandinfo$band
 
-
-
   for (i in 1:nrow(table)) {
     row = table[i,]
     if (as.integer(row$whether_raster) == 1) {
@@ -645,3 +642,18 @@ read_legend = function(legend.path,code, ...) {
 
   return(collection)
 }
+
+#' @export
+setMethod("crs", signature="Collection", function(x, ...) {
+  return(crs.Collection(x,...))
+})
+
+crs.Collection = function(x, ...) {
+  if (x$dimensions$space) {
+    return(x$getGlobalSRS())
+  } else {
+    stop("Try to select a spatial reference system without a spatial dimension defined.")
+  }
+
+}
+

R/Server-class.R

@@ -31,8 +31,11 @@ OpenEOServer <- R6Class(
       workspaces.path = NULL,
       sqlite.path = NULL,
 
+      udf_transactions.path = NULL,
+
       api.port = NULL,
       host = NULL,
+      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,
@@ -195,13 +198,21 @@ OpenEOServer <- R6Class(
         if (is.null(self$workspaces.path)) {
           self$workspaces.path <- getwd()
         }
+
         if (is.null(self$data.path)) {
           self$data.path <- paste(self$workspaces.path,"data",sep="/")
-
-          if (!dir.exists(self$data.path)) {
-            dir.create(self$data.path,recursive = TRUE)
-          }
         }
+        if (!dir.exists(self$data.path)) {
+          dir.create(self$data.path,recursive = TRUE)
+        }
+
+        if (is.null(self$udf_transactions.path)) {
+          self$udf_transactions.path = paste(self$workspaces.path,"udf",sep="/")
+        }
+        if (!dir.exists(self$udf_transactions.path)) {
+          dir.create(self$udf_transactions.path, recursive = TRUE)
+        }
+
         if (is.null(self$secret.key)) {
           self$secret.key <- sha256(charToRaw("openEO-R"))
         }

R/api.R

@@ -41,6 +41,7 @@
     "/data/",
     "/data/{product_id}",
     "/jobs/",
+    "/jobs/{job_id}",
     "/jobs/{job_id}/download",
     "/jobs/{job_id}/queue",
     "/processes/",
@@ -112,7 +113,7 @@
       }
     },
     error=function(e) {
-      error(res,403,"Login failed.")
+      openEO.R.Backend:::error(res,403,"Login failed.")
     }
   )
 }
@@ -144,16 +145,19 @@
 
   }
 
-  job = Job$new(process_graph=process_graph,user_id = req$user$user_id)
-
-  job = job$run()
-
-  result = job$result
-  if (is.null(result)) {
-    openEO.R.Backend:::error(res,status = 500,msg = "The result was NULL due to an internal error during processing.")
-  }
-
-  return(.create_output(res = res,result = job$results, format = format))
+  tryCatch({
+    job = Job$new(process_graph=process_graph,user_id = req$user$user_id)
+
+    job = job$run()
+
+    if (is.null(job$results)) {
+      return(openEO.R.Backend:::error(res,status = 500,msg = "The result was NULL due to an internal error during processing."))
+    }
+
+    return(.create_output(res = res,result = job$results, format = format))
+  }, error= function(e) {
+    return(openEO.R.Backend:::error(res=res, status = 500, msg = e))
+  })
 }
 
 .ogrExtension = function(format) {
@@ -236,7 +240,7 @@
     }
   },
   error = function(e) {
-    error(res,401,"Unauthorized")
+    openEO.R.Backend:::error(res,401,"Unauthorized")
   }
   )
 }

R/api_job.R

@@ -155,7 +155,7 @@ createJobsEndpoint = function() {
   } else {
     job_results = paste(openeo.server$workspaces.path,"jobs",job_id,sep="/")
 
-    base_url = paste("http://",openeo.server$host,":",openeo.server$api.port,"/api/result/",job_id,sep="")
+    base_url = paste(openeo.server$baseserver.url,"result/",job_id,sep="")
 
     #get files in outputfolder but not the log file
     paste(base_url,list.files(job_results,pattern="[^process\\.log]"),sep="/")