small update

Integration/MINERVA_access/get_identifiers.R

@@ -13,27 +13,33 @@ source("https://git-r3lab.uni.lu/covid/models/-/raw/master/Integration/MINERVA_a
 ### The address of the COVID-19 Disease Map in MINERVA
 map <- "https://covid19map.elixir-luxembourg.org/minerva/api/"
 
-components <- get_map_components(map)
+components <- get_map_components(map, project_id = "covid19_map_11Mar21")
 
 ### You may want to save components to JSON if you want to explore the structure of MINERVA's output
 
-get_annotations <- function(model_elements, annotation_type) {
-  ### For erroneous response, skip to next diagram
-  if(is.null(model_elements)) { return(NULL) }
-  ### Only elements that have annotations
-  these_refs <- model_elements$references[sapply(model_elements$references, length) > 0]
-  ### For empty list, skip to next diagram
-  if(length(these_refs) == 0) { return(NULL) }
-
-  ### Get all identifiers, for elements that have the requested annotation
-  identifiers <- sapply(these_refs,
-                        function(x) x[x$type == annotation_type, "resource"])
-  identifiers <- identifiers[sapply(identifiers,
-                                    function(x) ifelse(is.character(x) & length(x) > 0, TRUE, FALSE))]
-  return(identifiers)
+# get_annotations <- function(model_elements, annotation_type) {
+#   ### For erroneous response, skip to next diagram
+#   if(is.null(model_elements)) { return(NULL) }
+#   ### Only elements that have annotations
+#   these_refs <- model_elements$references[sapply(model_elements$references, length) > 0]
+#   ### For empty list, skip to next diagram
+#   if(length(these_refs) == 0) { return(NULL) }
+# 
+#   ### Get all identifiers, for elements that have the requested annotation
+#   identifiers <- sapply(these_refs,
+#                         function(x) x[x$type == annotation_type, "resource"])
+#   identifiers <- identifiers[sapply(identifiers,
+#                                     function(x) ifelse(is.character(x) & length(x) > 0, TRUE, FALSE))]
+#   return(identifiers)
+# }
+
+get_annotation <- function(references, selected_type) {
+  if(length(references) == 0) { return(NA) }
+  with(data.frame(references), resource[type == selected_type])
 }
 
 ### Get all HGNC symbols
-all_hgncs <- sapply(components$map_elements, get_annotations, "HGNC_SYMBOL")
+all_hgncs <- lapply(components$map_elements, 
+                    function(x) lapply(x$references, get_annotation, "HGNC_SYMBOL"))