simplify checking/parsing of results

R/api-gol.R

@@ -2,11 +2,7 @@
 ## Summary information about the Graph of Life
 .gol_about <- function(...) {
     res <- otl_POST(path="graph/about", body=list(), ...)
-    cont <- otl_parse(res)
-    if (length(cont) < 1) {
-        warning("Nothing returned")
-    }
-    return(cont)
+    res
 }
 
 
@@ -33,8 +29,7 @@
     q <- list(study_id=jsonlite::unbox(study_id), tree_id=jsonlite::unbox(tree_id),
         git_sha=jsonlite::unbox(git_sha))
     res <- otl_POST(path="graph/source_tree", body=q, ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }
 
 ##' @importFrom jsonlite unbox
@@ -53,6 +48,5 @@
         q <- list(ott_id=jsonlite::unbox(ott_id), include_lineage=jsonlite::unbox(include_lineage))
     }
     res <- otl_POST(path="graph/node_info", body=q, ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }

R/api-studies.R

@@ -28,8 +28,7 @@
     res <- otl_POST(path="studies/find_studies/",
                     body=req_body,
                     ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }
 
 ##' @importFrom jsonlite unbox
@@ -65,17 +64,15 @@
                     body=c(req_body,
                            jsonlite::unbox(verbose),
                            jsonlite::unbox(exact)), ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }
 
 
 ##' @importFrom httr content
 ## Return a list of properties that can be used to search studies and trees
 .studies_properties <- function() {
     res <- otl_POST(path="studies/properties/", body=list())
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }
 
 
@@ -92,8 +89,7 @@
     res <- otl_GET(path=paste("study",
                               paste0(study_id, otl_formats(format)), sep="/"),
                    ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }
 
 
@@ -117,13 +113,12 @@
     tip_label <- paste0("/?tip_label=", tip_label)
     tree_file <- paste0(tree_id, otl_formats(format), tip_label)
     res <- otl_GET(path=paste("study", study_id, "tree", tree_file, sep="/"), ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }
 
 ##' @importFrom httr content
 .get_study_meta <- function(study_id, ...) {
-    otl_parse(otl_GET(path= paste("study", study_id, "meta", sep="/"), ...))
+    otl_GET(path= paste("study", study_id, "meta", sep="/"), ...)
 }
 
 
@@ -149,7 +144,7 @@
     format <- otl_formats(format)
     url_stem <- paste("study", study_id, "tree", paste0(tree_id, format), sep="/")
     res <- otl_GET(path=paste(url_stem, "?subtree_id=", subtree_id, sep=""), ...)
-    otl_parse(res)
+    res
 }
 
 ### Let's not worry about those for now, as their results could be

R/api-taxonomy.R

@@ -2,9 +2,7 @@
 ## Summary information about the OpenTree Taxaonomy (OTT)
 .taxonomy_about <- function(...) {
     res <- otl_POST(path="/taxonomy/about", body=list(), ...)
-    cont <- otl_parse(res)
-
-    return(cont)
+    res
 }
 
 
@@ -28,8 +26,7 @@
               include_lineage = jsonlite::unbox(include_lineage),
               list_terminal_descendants = jsonlite::unbox(list_terminal_descendants))
     res <- otl_POST(path="/taxonomy/taxon", body=q, ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }
 
 
@@ -46,8 +43,7 @@
     }
     q <- list(ott_id=jsonlite::unbox(ott_id))
     res <- otl_POST(path="/taxonomy/subtree", body=q, ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }
 
 
@@ -61,6 +57,5 @@
     }
     q <- list(ott_ids=ott_ids)
     res <- otl_POST(path="/taxonomy/lica", body=q, ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }

R/api-tnrs.R

@@ -40,17 +40,15 @@
     q <- q[!toKeep]
 
     res <- otl_POST("tnrs/match_names", body=q, ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }
 
 
 ##' @importFrom httr content
 ## Get OpenTree TNRS contexts
 .tnrs_contexts <- function(...) {
     res <- otl_POST("tnrs/contexts", body=list(), ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }
 
 
@@ -63,6 +61,5 @@
     }
     q <- list(names=names)
     res <- otl_POST("tnrs/infer_context", body=q, ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }

R/api-tol.R

@@ -7,8 +7,7 @@
     }
     q <- list(study_list=jsonlite::unbox(study_list))
     res <- otl_POST(path="tree_of_life/about", body=q, ...)
-    cont <- otl_parse(res)
-    return(invisible(cont))
+    res
 }
 
 
@@ -26,8 +25,7 @@
         q <- list(ott_ids = ott_ids)
     }
     res <- otl_POST(path="tree_of_life/mrca", body=q, ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }
 
 
@@ -47,8 +45,7 @@
         q <- list(ott_id = jsonlite::unbox(ott_id))
     }
     res <- otl_POST(path="tree_of_life/subtree", body=q, ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }
 
 
@@ -71,6 +68,5 @@
     q <- list(ott_ids  = ott_ids)
 
     res <- otl_POST("tree_of_life/induced_subtree", body=q, ...)
-    cont <- otl_parse(res)
-    return(cont)
+    res
 }

R/base.R

@@ -42,20 +42,21 @@ otl_check_error <- function(cont) {
     }
 }
 
+## Check and parse result of query
 otl_check <- function(req) {
     if (!req$status_code <  400) {
         msg <- otl_parse(req)
         stop("HTTP failure: ", req$status_code, "\n", msg, call. = FALSE)
     }
     desc <- otl_parse(req)
     otl_check_error(desc)
+    desc
 }
 
 ##' @importFrom httr GET
 otl_GET <- function(path, dev_url = FALSE, otl_v = otl_version(), ...) {
     req <- httr::GET(otl_url(), path=paste(otl_v, path, sep="/"), ...)
     otl_check(req)
-    req
 }
 
 ##' @importFrom jsonlite toJSON
@@ -69,7 +70,6 @@ otl_POST <- function(path, body, dev_url = FALSE, otl_v = otl_version(), ...) {
                       path=paste(otl_v, path, sep="/"),
                       body=body_json, ...)
     otl_check(req)
-    req
 }