update get_opentargets [skip ci]

R/filter_ontology.R

@@ -30,11 +30,8 @@ filter_ontology <- function(ont,
                                            to = "id") |> stats::na.omit()
     if(length(keep_descendants)>0){
       messager("Keeping descendants of",length(keep_descendants),"term(s).")
-      keep_descendants <- simona::dag_offspring(dag = ont,
-                                                include_self = include_self,
-                                                term = keep_descendants)
       ont <- simona::dag_filter(ont, 
-                                terms=keep_descendants, 
+                                root=as.character(keep_descendants),
                                 ...)
       messager(formatC(ont@n_terms,big.mark = ","),
                "terms remain after filtering.")
@@ -64,9 +61,12 @@ filter_ontology <- function(ont,
   }
   #### Use custom filtering methods ####
   if(!is.null(terms)){
+    terms <- map_ontology_terms(ont = ont,
+                                terms = terms,
+                                to = "id") |> stats::na.omit()
     ## Characters 
     if(is.character(terms)){
-      terms <- terms[terms %in% ont@terms] |> unique()
+      terms <- terms[simona::dag_has_terms(dag=ont, terms = unique(terms))]
       if(length(terms)==0) {
         stopper("None of the supplied terms found in the ontology.")
       } 

R/get_opentargets.R

@@ -1,6 +1,9 @@
 #' Get Open Targets
 #' 
 #' Get Open Targets disease-gene associations data
+#' NOTE: If you get an error like " Cannot call parquet...", 
+#' try running \code{arrow::install_arrow},
+#'  restarting the R session, and trying again.
 #' @source \href{https://community.opentargets.org/t/r-script-for-graphql-query-query-targetdiseaseevidence/662/5}{OpenTargets GraphQL queries in R}
 #' @param release Open Targets release version.
 #' @param data_type Type of data to download.
@@ -59,13 +62,12 @@ get_opentargets <- function(release="latest",
   d <- BiocParallel::bplapply(stats::setNames(tbl$Name,
                                               tbl$Name),
                               BPPARAM = BPPARAM,
-                              function(f){
-
+                              function(f){ 
                                 if(endsWith(f,".json")){
-                                  j <- jsonlite::fromJSON(file.path(ftp, f))
+                                  j <- jsonlite::fromJSON(paste0(ftp,"/",f))
                                   jsonlite::fromJSON(j$serialisedSchema) 
                                 } else if (endsWith(f,".parquet")){
-                                  arrow::read_parquet(file.path(ftp, f)) |>
+                                  arrow::read_parquet(paste0(ftp,f)) |>
                                     data.table::data.table()
                                 }
                               }) |> data.table::rbindlist(idcol = "file")