hypothetical complexes via API

Resources/Hipathia/resolve_aliases.R

@@ -9,47 +9,30 @@ library(httr)
 library(jsonlite)
 
 ### A convenience function to handle API queries
-ask_GET <- function(furl, fask, unpack = T) {
-  print(URLencode(paste0(furl, fask)))
-  resp <- httr::GET(url = URLencode(paste0(furl, fask)), write_memory(),
-                    httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"),
-                    ### Currently ignoring SSL!
-                    httr::set_config(config(ssl_verifypeer = 0L)))
+ask_GET <- function(fask_url, verbose = F) {
+  if(verbose) {
+    message(URLencode(fask_url))
+  }
+  resp <- httr::GET(url = URLencode(fask_url),
+                    httr::add_headers('Content-Type' = "application/x-www-form-urlencoded"))
   if(httr::status_code(resp) == 200) {
-    ### when the content is sent as a zip file, it needs to be handled differently,
-    ### i.e. saved to a tmp file and unzipped
-    if(headers(resp)$`content-type` == "application/zip") {
-      tmp <- tempfile()
-      tmpc <- file(tmp, "wb")
-      writeBin(httr::content(resp, as = "raw"), con = tmpc)
-      close(tmpc)
-      unzipped <- unzip(tmp)
-      file.remove(tmp)
-      return(unzipped)
-    }
     return(httr::content(resp, as = "text"))
   }
   return(NULL)
 }
 
-### Define the source file (GitLab, raw link)
-diagram <- "https://git-r3lab.uni.lu/covid/models/-/raw/master/Curation/ER%20Stress/ER_Stress_stable.xml"
+### Define the source diagram name
+diag_name <- "Endoplasmatic Reticulum stress"
 
 ### Read in the raw SIF version (here straight from the github of Aurelien)
 raw_sif <- read.table(url("https://git-r3lab.uni.lu/covid/models/-/raw/master/Executable%20Modules/SBML_qual_build/sif/ER_Stress_stable_raw.sif"),
                       sep = " ", header = F, stringsAsFactors = F)
 
-### Read the list of resources to be integrated, from the MINERVA build scripts
-res <- read.csv(url("https://git-r3lab.uni.lu/covid/models/raw/master/Integration/MINERVA_build/resources.csv"),
-                header = T, stringsAsFactors = F)
-
-diag_name <- res[res$Resource == diagram, "Name"]
-
 ### Get MINERVA elements
 ### The address of the COVID-19 Disease Map in MINERVA
 map <- "https://covid19map.elixir-luxembourg.org/minerva/api/"
 ### Get configuration of the COVID-19 Disease Map, to obtain the latest (default) version
-cfg <- fromJSON(ask_GET(map, "configuration/"))
+cfg <- fromJSON(ask_GET(paste0(map, "configuration/")))
 project_id <- cfg$options[cfg$options$type == "DEFAULT_MAP","value"]
 ### The address of the latest (default) build 
 mnv_base <- paste0(map,"projects/",project_id,"/")
@@ -57,14 +40,13 @@ 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 <- ask_GET(paste0(mnv_base, "models/"))
 models <- fromJSON(models, flatten = F)
 
-this_refs <- models[models$name == diag_name]
-
+this_refs <- models[models$name == diag_name,]
 ### Get elements of the chosen diagram
-model_elements <- fromJSON(ask_GET(paste0(mnv_base,"models/",models$idObject[models$name == diag_name],"/"), 
-                                   "bioEntities/elements/?columns=id,name,type,references,elementId,complexId,bounds"),
+model_elements <- fromJSON(ask_GET(paste0(mnv_base,"models/",models$idObject[models$name == diag_name],"/", 
+                                   "bioEntities/elements/?columns=id,name,type,references,elementId,complexId,bounds,hypothetical")),
                            flatten = F)
 
 message("Fetching entrez ids...")
@@ -92,48 +74,25 @@ group_elements <- function(feid, felements, fentrez) {
   }
 }
 
-### A workaround function to get information about hypothetical complexes; 
-### currently MINERVA API does not support this, we need to get the entire CD file and parse it
-get_groups <- function(fname) {
-  message(paste0("Getting groups for ", fname, "..."))
-  library(xml2)
-  ## Currently comment out the MINERVA download, some content dlded as binary!
-  cd_map <- read_xml(ask_GET(mnv_base,
-                             paste0("models/",
-                                    models$idObject[models$name == fname],
-                                    ":downloadModel?handlerClass=lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser")))
-  ### CellDesigner namespace
-  ns_cd <- xml_ns_rename(xml_ns(read_xml("<root>
-                                            <sbml xmlns = \"http://www.sbml.org/sbml/level2/version4\"/>
-                                            <cd xmlns = \"http://www.sbml.org/2001/ns/celldesigner\"/>
-                                          </root>")), 
-                         d1 = "sbml", d2 = "cd")
-  ### Get complex ids
-  cids <- xml_attr(xml_find_all(cd_map, "//cd:complexSpeciesAlias", ns_cd), "species")
-  ### For each check, which is hypothetical
-  hypocs <- sapply(cids, 
-                   function(x) {
-                     tcid <- xml_find_first(cd_map, paste0("//sbml:species[@id='", x, "']"), ns_cd)
-                     ifelse(length(tcid) > 0, xml_text(xml_find_first(tcid, ".//cd:hypothetical", ns_cd)), NA)
-                   })
-  names(hypocs) <- gsub("s_id_", "",names(hypocs))
-  return(hypocs)
+### A function to get information about hypothetical complexes
+get_role <- function(feid, felements) {
+  fpos <- which(felements$elementId == feid)
+  if(length(fpos) == 0) return(NA)
+  
+  role <- ifelse(felements[fpos, "type"] == "Complex",
+                 ifelse(felements[fpos, "hypothetical"], "group", "complex"),
+                 "node")
+  return(role)
 }
 
-cgroups <- get_groups(diag_name)
-
 message("Translating...")
 ### Create a copy
 translated_sif <- raw_sif
 ### Retrieve Entrez and type for the entire columns of sources and targets
 s.entrez <- sapply(raw_sif[,1], group_elements, model_elements, entrez)
-s.type <- sapply(raw_sif[,1], function(x) { ifelse(x %in% names(cgroups),
-                                                   ifelse(is.na(cgroups[x]), "complex", "group"),
-                                                   "node") })
+s.type <- sapply(raw_sif[,1], get_role, model_elements)
 t.entrez <- sapply(raw_sif[,3], group_elements, model_elements, entrez)
-t.type <- sapply(raw_sif[,3], function(x) { ifelse(x %in% names(cgroups),
-                                                   ifelse(is.na(cgroups[x]), "complex", "group"),
-                                                   "node") })
+t.type <- sapply(raw_sif[,3], get_role, model_elements)
 ### Collect x.y information
 s.xy <- t(sapply(raw_sif[,1], function(x) unlist(model_elements$bounds[model_elements$elementId == x, c(3,4)])))
 colnames(s.xy) <- c("source.x", "source.y")