Calculate overlay hits for a given user

R/API_calculate_overlay_hits.R

+##################################################
+## Script purpose: An example of MINERVA API call to retrieve overlays of a give user
+##                 and calculate "hits" of each element in the map
+## Date: 12/08/2020
+## Author: Marek Ostaszewski (marek.ostaszewski@uni.lu)
+## MINERVA API version: 15.0
+##################################################
+
+### A convenience function to handle GET and POST requests to MINERVA API
+library(httr)
+library(jsonlite)
+
+### Utility function using httr:POST to send queries to a given MINERVA Platform instance
+ask_POST <- function(mnv_base, query, body) {
+  resp <- httr::POST(url = paste0(mnv_base, query),
+                     body = body,
+                     httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"),
+                     httr::verbose())
+  if(httr::status_code(resp) == 200) {
+    return(httr::content(resp, as = "text"))
+  }
+  return(NULL)
+}
+
+### Base URL of this MINERVA instance
+base <- "https://pdmap.uni.lu/minerva/api/"
+
+### Provide the username and password of a given user - this is to access this user's overlays
+login <- "username"
+password <- "userpassword"
+
+### log in the user
+resp <- ask_POST(base, "doLogin", body = paste0("login=",login,"&password=",password))
+
+### Get the cookie token from the login response; if NULL the loogin was unsuccessfull
+token <- fromJSON(resp)$token
+
+map_base <- paste0(base, "projects/pd_map_autumn_19/")
+
+### Utility function using httr:GET to send queries to a given MINERVA Platform instance with the given token (logged user)
+ask_GET <- function(mnv_base, query) {
+  resp <- httr::GET(url = paste0(mnv_base, query),
+                    httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"),
+                    ### Currently ignoring SSL!
+                    httr::set_config(config(ssl_verifypeer = 0L)),
+                    httr::verbose())
+  if(httr::status_code(resp) == 200) {
+    return(httr::content(resp, as = "text"))
+  }
+  return(NULL)
+}
+
+### Utility function using httr:GET to send queries to a given MINERVA Platform instance with the given token (logged user)
+token_GET <- function(mnv_base, query, token) {
+  resp <- httr::GET(url = paste0(mnv_base, query),
+                    httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"),
+                    httr::set_cookies(MINERVA_AUTH_TOKEN = token),
+                    # ### Currently ignoring SSL!
+                    # httr::set_config(config(ssl_verifypeer = 0L)),
+                    httr::verbose())
+  if(httr::status_code(resp) == 200) {
+    return(httr::content(resp, as = "text"))
+  }
+  return(NULL)
+}
+
+### Retrieve all overlays
+overlays <- fromJSON(token_GET(map_base, "overlays/", token))
+
+### Select only overlays of this user (not public) that have data behind them
+selected_overlays <- overlays[!overlays$publicOverlay & overlays$inputDataAvailable, c("idObject", "name")]
+
+### Retrieve all elements' ids and names, for later resolution
+models <- fromJSON(token_GET(map_base, "models/", token), flatten = F)
+
+### Get elements of diagrams
+model_elements <- lapply(models$idObject, 
+                         function(x) fromJSON(token_GET(map_base, 
+                                                        paste0("models/",x,"/", "bioEntities/elements/?columns=id,name"),
+                                                        token),
+                                              flatten = F))
+### Name elements by id for easier referencing
+names(model_elements) <- models$idObject
+
+### Calculate hits for each overlay
+for(i in 1:nrow(selected_overlays)) {
+  ### GET all bioentities selected by this overlay
+  hits <- fromJSON(token_GET(base, 
+                             paste0("projects/pd_map_autumn_19/overlays/",selected_overlays[i,1],"/models/*/bioEntities/"), 
+                             token), flatten = T) #fromJSON() behaves strangely, forced 'flatten' because unflattened result gets coerced to a compound data.frame
+  
+  ### Create a column for element name
+  hits <- cbind(hits, element_name = "")
+  
+  ### From model_elements, take the element name and assig int to 'hits'
+  for(j in 1:nrow(hits)) {
+    res <- with(model_elements[[as.character(hits[j,2])]], name[id == hits[j,"overlayContent.idObject"]])
+    hits[j,"element_name"] <- res
+  }
+  
+  ### Combine with map/submap names for a detailed breakdown of hits
+  hits <- merge(hits, models[,c("name", "idObject")], by.x = "overlayContent.modelId", by.y = "idObject")
+  
+  ### Write down the table with the element hits by map/submap
+  ### A single element can have many instances, so there can be multiple hits
+  write.table(table(hits[,c("element_name","name")]),
+              file = paste0("hits_of_", selected_overlays[i,2],".txt"),
+              sep = "\t",
+              quote = F)
+}

R/API_find_drug_targets.R

@@ -2,7 +2,7 @@
 ## Script purpose: An example of MINERVA API call to retrieve 
 ##                 HGNC symbols of elements targetted by a given drug,
 ##                 and to retrieve drugs targetting elements with a given UniProt
-## Date: 17/03/2019
+## Date: 17/03/2020
 ## Author: Marek Ostaszewski (marek.ostaszewski@uni.lu)
 ## MINERVA API version: 14.0
 ##################################################

R/API_retrieve.R

 ##################################################
 ## Script purpose: An example of MINERVA API call to retrieve elements with a 
 ##                 given uniprot id and their interactions
-## Date: 17/03/2019
+## Date: 17/03/2020
 ## Author: Marek Ostaszewski (marek.ostaszewski@uni.lu)
 ## MINERVA API version: 14.0
 ##################################################

R/API_retrieve_neighbors_of_degs.R

@@ -2,7 +2,7 @@
 ## Script purpose: An example of MINERVA API call to retrieve 
 ##                 neighbors of 10 most differentially expressed molecules 
 ##                 in a given data overlay
-## Date: 17/03/2019
+## Date: 17/03/2020
 ## Author: Marek Ostaszewski (marek.ostaszewski@uni.lu)
 ## MINERVA API version: 14.0
 ##################################################