add unit tests for keggCompounds

Author: LiNk-NY

NEWS

@@ -1,6 +1,11 @@
 CHANGES IN VERSION 1.42.0
 -----------------------
 
+SIGNIFICANT USER-VISIBLE CHANGES
+
+    o `keggCompounds` lists compound IDs for a given pathway (@KristinaRiemer,
+    #6).
+
 BUG FIXES
 
     o Update URL path in `.get.kegg.url` from `tmp` to `kegg` subfolder.
@@ -11,13 +16,13 @@ CHANGES IN VERSION 1.37.0
 BUG CORRECTION
 
     o 1.37.1 Fixes new endpoint
-    o 1.37.2 http to https fixes windows error 
+    o 1.37.2 http to https fixes windows error
 
 CHANGES IN VERSION 1.0.0
 -----------------------
 
 SIGNIFICANT USER-VISIBLE CHANGES
-    
+
     o Package introduced.
 
 NEW FEATURES

R/KEGGREST.R

@@ -66,9 +66,9 @@ keggGet <- function(dbentries,
     .getUrl(url, .flatFileParser)
 }
 
-keggCompounds <- function(pathway_id)
+keggCompounds <- function(pathwayID)
 {
-    url <- sprintf("%s/link/cpd/%s", .getRootUrl(), pathway_id)
+    url <- sprintf("%s/link/cpd/%s", .getRootUrl(), pathwayID)
     .getUrl(url, .compoundParser)
 }
 

inst/unitTests/test_KEGGREST.R

@@ -246,3 +246,26 @@ test_reference_parser <- function()
     refs <- res$REFERENCE[[1]]
     checkTrue(length(refs) > 0)
 }
+
+test_keggCompounds <- function() {
+    result <- c(
+        "C00011", "C00042", "C00090", "C00146", "C00160", "C00530",
+        "C00682", "C01407", "C02124", "C02222", "C02375", "C02575", "C02625",
+        "C02814", "C02933", "C03434", "C03572", "C03585", "C03664", "C03918",
+        "C04091", "C04431", "C04522", "C04706", "C04729", "C05618", "C06328",
+        "C06329", "C06594", "C06596", "C06597", "C06598", "C06599", "C06600",
+        "C06601", "C06602", "C06603", "C06755", "C06988", "C06989", "C06990",
+        "C07075", "C07088", "C07089", "C07090", "C07091", "C07092", "C07093",
+        "C07094", "C07095", "C07096", "C07097", "C07098", "C07099", "C07100",
+        "C07101", "C07102", "C07103", "C11352", "C12831", "C12832", "C12833",
+        "C12834", "C12835", "C12836", "C12837", "C12838", "C14419", "C14450",
+        "C16181", "C16182", "C16266", "C18236", "C18238", "C18240", "C18241",
+        "C18242", "C18243", "C18244", "C18933", "C21103", "C21104", "C21105"
+    )
+    checkTrue(
+        all(
+            result %in% keggCompounds("map00361")
+        )
+    )
+}
+

man/keggCompounds.Rd

@@ -7,10 +7,10 @@ Get list of compounds IDs for pathway
 Get list of compounds IDs for pathway.
 }
 \usage{
-keggCompounds(pathway_id)
+keggCompounds(pathwayID)
 }
 \arguments{
-  \item{target}{
+  \item{pathwayID}{
   A KEGG pathway identifier with the prefix \code{map} and 5 digit number.
 }
 
@@ -22,7 +22,7 @@ A list of KEGG compound identifiers
   \url{https://www.genome.jp/kegg/pathway.html}
 }
 \author{
-Dan Tenenbaum
+Dan Tenenbaum, Kristina Riemer
 }
 \examples{
 keggCompounds("map00361")