Update API_retrieve.R

R/API_retrieve.R

@@ -23,53 +23,30 @@ ask_GET <- function(mnv_base, query) {
 ### Base URL of the map, we use Parkinson's disease map
 base_url <- "https://pdmap.uni.lu/minerva/api/projects/pd_map_autumn_19/"
 
-### Request identifiers of models for a given project (main map and submaps)
-models <- ask_GET(base_url, "models/")
-models <- fromJSON(models, flatten = F)
-
 ### For each model, retrieve elements with columns including references
-model_elements <- lapply(models$idObject, 
-                         function(x) fromJSON(ask_GET(paste0(base_url,"models/",x,"/"), 
-                                                      "bioEntities/elements/?columns=id,name,type,references"), 
-                                              flatten = F))
+model_elements <- fromJSON(ask_GET(paste0(base_url,"models/*/"), 
+                                   "bioEntities/elements/?columns=id,name,type,references"), 
+                           flatten = F)
+
 #Define UniProt identifiers to be matched in model elements
 uniprot_examples <- c("O43521", "P63167")
 
-### For each model, retrieve reactions
-model_reactions <- lapply(models$idObject, 
-                          function(x) fromJSON(ask_GET(paste0(base_url,"models/",x,"/"), 
-                                                       "bioEntities/reactions/?columns=id,type,reactionId,products,reactants,modifiers"), 
-                                               flatten = F))
-
 ### For results in each model, find element identifiers that have the selected uniprot id
 ### then find reactions having at least one of these elements, and append them to the output vector
 reaction_identifiers <- c()
 
-for (m in 1:length(model_elements)) {
-  ### In "resources" of each element, find those which have requested UniProt identifiers 
-  hits <- sapply(model_elements[[m]]$references,
-                 function(x) any(uniprot_examples %in% x$resource[x$type == "UNIPROT"]))
+### In "resources" of each element, find those which have requested UniProt identifiers 
+hits <- sapply(model_elements$references, 
+               function(x) any(uniprot_examples %in% x$resource[x$type == "UNIPROT"]))
   
-  ### Identifiers of the elements matching the search criteria
-  identifiers <- model_elements[[m]]$id[hits]
-  
-  ### Look for reaction identifiers only for non-zero results and models with existing reactions 
-  if(length(identifiers) > 0 && length(model_reactions[[m]]) > 0) {
-    
-    ### Which reactions have at least one modifier, product and reactant matching the list
-    hits <- which(sapply(model_reactions[[m]]$modifiers, 
-                      function(x) ifelse(length(x) == 0, F, any(x$aliasId %in% identifiers))))
-    hits <- c(hits, which(sapply(model_reactions[[m]]$products, 
-                      function(x) ifelse(length(x) == 0, F, any(x$aliasId %in% identifiers)))))
-    hits <- c(hits, which(sapply(model_reactions[[m]]$reactants, 
-                      function(x) ifelse(length(x) == 0, F, any(x$aliasId %in% identifiers)))))
-    
-    ### Append the data frame by these reaction identifiers
-    reaction_identifiers <- rbind(reaction_identifiers,
-                                  data.frame(reaction_id = model_reactions[[m]]$reactionId[unique(hits)],
-                                             model_id = models$idObject[m], stringsAsFactors = F))
-  }
-}
+### Identifiers of the elements matching the search criteria
+identifiers <- model_elements$id[hits]
+
+### Request for reactions that have one of the identifiers as a 'participantId' (reactant, product or modifier)
+model_reactions <- fromJSON(ask_GET(base_url, 
+                                    paste0("models/*/bioEntities/reactions/?participantId=", 
+                                           paste(identifiers, collapse = ","), 
+                                           "&columns=reactionId")))
 
 ### Create a validation URL for the disease map these identifiers come from
 visualize_reactions <- "https://pdmap.uni.lu/minerva/?search="