Fix init check and add path2rxn workaround

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: enviPathR
 Title: Client for the 'enviPath' 'RESTful' API
-Version: 1.0.1
+Version: 1.0.2
 Authors@R:
     c(person(given = "Giulio", family = "Benedetti",
           role = c("aut", "cre", "cph"),

NEWS

@@ -1,5 +1,5 @@
-Changes in version 0.99.x
-* Introduced epTypes, epLogin, epLogout, epList, epLink, epGet and epModel
-
 Changes in version 1.0.x
-* Submitted to CRAN
+* Submitted to CRAN
+
+Changes in version 0.99.x
+* Introduced epTypes, epLogin, epLogout, epList, epLink, epGet and epModel

R/get.R

@@ -30,7 +30,7 @@
 #'   not serial. (Default: \code{5})
 #' 
 #' @returns
-#' A list of objects
+#' A list of objects.
 #' 
 #' @examples
 #' \dontshow{
@@ -76,8 +76,6 @@ epGet <- function(type, init = NULL, pkg = NULL, property = NULL,
         SIMPLIFY = FALSE,
         BPPARAM = BPPARAM
     )
-    # Reduce list to single object
-    if( length(out) == 1L ) out <- out[[1L]]
     return(out)
 } 
 

R/link.R

@@ -110,6 +110,10 @@ epLink <- function(from, to, init = NULL, pkg = NULL, BPPARAM = bpparam(), rate
     if( by == "pathway2compound" ){
         linkmap[to] <- str_remove(linkmap[[to]], "/structure/.*")
     }
+    if( by == "pathway2reaction" ){
+        rxn_df <- epList("reaction", pkg = pkg)
+        linkmap[to] <- rxn_df$id[rxn_df$name %in% linkmap[[to]]]
+    }
     # Remove id prefix
     linkmap[to] <- str_remove(linkmap[[to]], ".*/")
     return(linkmap)
@@ -142,7 +146,7 @@ epLink <- function(from, to, init = NULL, pkg = NULL, BPPARAM = bpparam(), rate
     # Check if pkg exists
     is_init <- !is.null(init)
     # Check pkg format
-    if( is_init && !all(is.character(init) & nzchar(init)) ){
+    if( is_init && (!is.character(init) || !all(nzchar(init))) ){
         stop(
             "'init' must be a character vector specifying the unique ",
             "identifiers of type 'from' that should be mapped on 'to'.",

R/login.R

@@ -3,8 +3,8 @@
 #' @name epLogin
 #' 
 #' @description
-#' epLogin lets you perform login to enviPath. An account is required to use the
-#' enviPath API.
+#' epLogin and epLogout let you log in and out of enviPath, respectively. An
+#' account is required to use the enviPath API.
 #' 
 #' @param username \code{Character scalar}. String specifying the username
 #' used to log into an enviPath personal account.
@@ -13,7 +13,7 @@
 #' used to log into an enviPath personal account.
 #' 
 #' @returns
-#' A message upon successful login.
+#' A message upon successful login or logout.
 #' 
 #' @examples
 #' \dontshow{

R/zzz.R

@@ -13,7 +13,8 @@
         pathway2compound = c(item = "nodes", var = "idcomp"),
         pathway2edge = c(item = "links", var = "id"),
         pathway2node = c(item = "nodes", var = "id"),
-        pathway2reaction = c(item = "links", var = "idreaction"),
+        # pathway2reaction = c(item = "links", var = "idreaction"),
+        pathway2reaction = c(item = "links", var = "name"),
         pathway2structure = c(item = "nodes", var = "idcomp"),
         reaction2compound = list(item = c("educts", "products"), var = "id"),
         reaction2ec = c(item = "ecNumbers", var = "id"),

tests/httptest/model/util-e1f28b-POST.R

@@ -1,11 +1,11 @@
 structure(list(method = "POST", url = "https://util", status_code = 403L, 
     headers = structure(list(Server = "nginx/1.24.0 (Ubuntu)", 
-        Date = "Fri, 16 Oct 2026 03:48:10 GMT", `Content-Type` = "application/json; charset=utf-8", 
+        Date = "Sat, 24 Oct 2026 03:32:47 GMT", `Content-Type` = "application/json; charset=utf-8", 
         `Content-Length` = "139", Connection = "keep-alive", 
         Vary = "Authorization, Cookie", `X-Frame-Options` = "DENY", 
         `X-Content-Type-Options` = "nosniff", `Referrer-Policy` = "same-origin", 
         `Cross-Origin-Opener-Policy` = "same-origin"), class = "httr2_headers"), 
     body = charToRaw("{\"message\": \"Getting Setting with id https://envipath.org/setting/1d915a48-286a-4394-9693-bfaa187326a5 failed due to insufficient rights!\"}"), 
-    timing = c(redirect = 0, namelookup = 3.2e-05, connect = 0, 
-    pretransfer = 0.000166, starttransfer = 0.347267, total = 0.347304
+    timing = c(redirect = 0, namelookup = 3.3e-05, connect = 0, 
+    pretransfer = 0.000128, starttransfer = 0.412069, total = 0.412121
     ), cache = new.env(parent = emptyenv())), class = "httr2_response")

tests/testthat/test-get.R

@@ -20,6 +20,6 @@ with_mock_dir("../httptest/get", {
         rxn <- epGet("reaction", rxn_id, BPPARAM = BPPARAM)
 
         expect_type(rxn, "list")
-        expect_length(rxn, 15L)
+        expect_length(rxn[[1L]], 15L)
     })
 })

tests/testthat/test-link.R

@@ -18,6 +18,12 @@ with_mock_dir("../httptest/link", {
             fixed = TRUE
         )
 
+        expect_error(
+            epLink(types[1], types[2], factor(cpd_id), BPPARAM = BPPARAM),
+            "'init' must be a character vector specifying the unique identifiers of type 'from' that should be mapped on 'to'.",
+            fixed = TRUE
+        )
+
         cpd2inchikey <- epLink(types[1], types[2], cpd_id, BPPARAM = BPPARAM)
 
         expect_named(cpd2inchikey, types)