Merge branch 'repo_update' into 'master'

an improvement in the access script and a small diagram correction

See merge request !282

Integration/MINERVA_access/get_identifiers.R

@@ -7,66 +7,33 @@
 
 options(stringsAsFactors = F)
 
-library(httr)
-library(jsonlite)
-library(here)
-
-setwd(paste0(here(),"/Integration/MINERVA_build/"))
-
-### Map and pathway enrichment analysis.
-### Requires commandline input or file "input.txt" to be present in the script directory.
-
-### A convenience function to handle API queries
-ask_GET <- function(furl, fask) {
-  resp <- httr::GET(url = paste0(furl, fask),
-                    httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"))
-  if(httr::status_code(resp) == 200) {
-    return(httr::content(resp, as = "text"))
-  }
-  return(NULL)
-}
+### Helper functions to access and retrieve content from MINERVA-hosted diagrams
+source("https://git-r3lab.uni.lu/covid/models/-/raw/master/Integration/MINERVA_access/minerva_access_functions.R")
 
 ### The address of the COVID-19 Disease Map in MINERVA
 map <- "https://covid19map.elixir-luxembourg.org/minerva/api/"
 
-### Get configuration of the COVID-19 Disease Map, to obtain the latest (default) version
-cfg <- ask_GET(map, "configuration/")
-cfg <- fromJSON(cfg)
-project_id <- cfg$options[cfg$options$type == "DEFAULT_MAP","value"]
-
-### The address of the latest (default) build 
-mnv_base <- paste0(map,"projects/",project_id,"/")
-
-message(paste0("Asking for diagrams in: ", mnv_base, "models/"))
-
-### Get diagrams
-models <- ask_GET(mnv_base, "models/")
-models <- fromJSON(models, flatten = F)
+components <- get_map_components(map)
 
-### Get elements of diagrams
-model_elements <- lapply(models$idObject, 
-                         function(x) fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/"), 
-                                                      "bioEntities/elements/?columns=id,name,type,references"), 
-                                              flatten = F))
+### You may want to save components to JSON if you want to explore the structure of MINERVA's output
 
-all_hgncs <- c()
-### Go through all diagram elements and:
-for(me in model_elements) {
+get_annotations <- function(model_elements, annotation_type) {
   ### For erroneous response, skip to next diagram
-  if(is.null(me)) { next }
+  if(is.null(model_elements)) { return(NULL) }
   ### Only elements that have annotations
-  these_refs <- me$references[sapply(me$references, length) > 0]
+  these_refs <- model_elements$references[sapply(model_elements$references, length) > 0]
   ### For empty list, skip to next diagram
-  if(length(these_refs) == 0) { next }
-  
-  ### Get all HGNC symbols, for elements that have annotations
-  all_hgncs <- c(all_hgncs, sapply(these_refs,
-                                   function(x) x[x$type == "HGNC_SYMBOL", "resource"]))
-  all_hgncs <- all_hgncs[sapply(all_hgncs,
-                                function(x) ifelse(is.character(x) & length(x) > 0, TRUE, FALSE))]
+  if(length(these_refs) == 0) { return(NULL) }
+
+  ### Get all identifiers, for elements that have the requested annotation
+  identifiers <- sapply(these_refs,
+                        function(x) x[x$type == annotation_type, "resource"])
+  identifiers <- identifiers[sapply(identifiers,
+                                    function(x) ifelse(is.character(x) & length(x) > 0, TRUE, FALSE))]
+  return(identifiers)
 }
 
-### Get unique HGNC symbols
-all_hgncs <- unique(all_hgncs)
+### Get all HGNC symbols
+all_hgncs <- sapply(components$map_elements, get_annotations, "HGNC_SYMBOL")