Merge pull request #51 from bhklab/development

small fixes

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: AnnotationGx
 Title: AnnotationGx: A package for building, updating and querying an
     annotation database for pharmaco-genomic data
-Version: 0.0.0.9096
+Version: 0.0.0.9097
 Authors@R: c(
     person("Jermiah", "Joseph", role = c("aut", "cre"),
         email = "[email protected]"),

R/chembl.R

@@ -135,9 +135,13 @@ queryChemblAPI <- function(resource, field, filter_type, value, format = "json")
 getChemblMechanism <- function(
     chembl.ID, resources = "mechanism", field = "molecule_chembl_id", filter_type = "in",
     returnURL = FALSE, raw = FALSE) {
+
+  funContext <- .funContext("getChemblMechanism")
   # constructChemblQuery(resource = "mechanism", field = "molecule_chembl_id", filter_type = "in", value = "CHEMBL1413")
   # urls <- constructChemblQuery(resource = resources, field = field, filter_type = filter_type, value = chembl.ID)
   # urls <- URLencode(urls)
+
+  .info(funContext, "Retrieving ChEMBL Mechanism information for ", length(chembl.ID), " ChEMBL IDs.")
   response_dts <- lapply(chembl.ID, function(chembl.ID) {
     request <- .build_chembl_request(resource = resources, field = field, filter_type = filter_type, value = chembl.ID)
 
@@ -165,8 +169,8 @@ getChemblMechanism <- function(
     }
     x
   })
-
-  data.table::rbindlist(response_dts)
+  
+  data.table::rbindlist(response_dts, fill = TRUE)
 }
 
 

R/unichem.R

@@ -106,7 +106,12 @@ queryUnichemCompound <- function(
     if(raw) return(response)
 
     if(response$response != "Success"){
-        .err("Unichem API request failed.")
+        msg <- paste(
+            "Unichem API request failed for compound", compound, "
+            with type", type, 
+            " . Error:", response$error
+        )
+        .err(.funContext("AnnotationGx::queryUnichemCompound"), msg)
     }
 
     # Mapping names to be consistent with other API calls