diff --git a/R/api.R b/R/api.R
index e1706cb743d87a16641aeb3dedd5c28c0470201d..d14964c7d4c7f3c42f6543747cbbd6e7931b09d7 100644
--- a/R/api.R
+++ b/R/api.R
@@ -127,10 +127,12 @@ load_compound_input <- function(m) {
                                         # nonexist <- setdiff(fnfields,fields)
         coll[[l]] <- dt #if (length(nonexist)==0) dt else dt[,(nonexist) := NULL]
         coll[[l]]$ORIG <- fn
-        
     }
     cmpds <- if (length(fns)>0) rbindlist(l=c(list(EMPTY_CMPD_LIST), coll), use.names = T, fill = T) else EMPTY_CMPD_LIST
 
+    ## Process sets.
+    cmpds = process_cmpd_sets(cmpds)
+    
     dups <- duplicated(cmpds$ID)
     dups <- dups | duplicated(cmpds$ID,fromLast = T)
     dupIDs <- cmpds$ID[dups]
diff --git a/R/base.R b/R/base.R
index 320d6b67e24aaf666374319b74f24f8ae7a87752..d64b4efa704835fbdcef04f8e622a081aa863c3d 100644
--- a/R/base.R
+++ b/R/base.R
@@ -143,3 +143,14 @@ uniqy_slugs <- function(slugs) {
     dt = data.table::data.table(slug=slugs)
     dt[,slug:=fifelse(rep(.N==1L,.N),slug,paste0(slug,"_",seq(1L,.N))),by="slug"]$slug
 }
+
+process_cmpd_sets <- function(cmpdlist) {
+    ## Process sets.
+    if (! ("set" %in% colnames(cmpdlist))) cmpdlist$set=NA_character_ else cmpdlist[,set:=as.character(set)]
+    ## Extract set names and fill out the empty ones.
+    slugs = cmpdlist[,.(slug=fifelse(is.na(set),gen_fname_slug(ORIG),set)),by=ORIG]
+    slugs[,slug:=uniqy_slugs(slug)]
+
+    cmpdlist[slugs,set:=i.slug,on="ORIG"]
+    cmpdlist
+}
diff --git a/tests/testthat/_snaps/base.md b/tests/testthat/_snaps/base.md
new file mode 100644
index 0000000000000000000000000000000000000000..3383291e685e5f54b5dd046143a9902abc811cba
--- /dev/null
+++ b/tests/testthat/_snaps/base.md
@@ -0,0 +1,24 @@
+# process_cmpd_sets
+
+    Code
+      x
+    Output
+         ID   ORIG  set
+      1:  1 f1.csv f1_2
+      2:  2 f1.csv f1_2
+      3:  3 f2.csv  aks
+      4:  4 f3.csv se32
+      5:  5 f3.csv se32
+
+---
+
+    Code
+      x
+    Output
+         ID         ORIG  set
+      1:  1     b/f2.csv   f2
+      2:  2     a/f1.csv   f1
+      3:  3 q/f/g/f2.csv  aks
+      4:  4 d/e/f/f3.csv se31
+      5:  5 m/n/q/f3.csv se32
+
diff --git a/tests/testthat/test-base.R b/tests/testthat/test-base.R
index ca5eb162da59f4f8a880246f767bd10527ca5594..60792b9d9c7972bcda0024ef3c771d9bbf649975 100644
--- a/tests/testthat/test-base.R
+++ b/tests/testthat/test-base.R
@@ -16,3 +16,17 @@ test_that("uniqy_slugs",{
     message(paste(out,coll=','))
     expect_true(1==1)
 })
+
+test_that("process_cmpd_sets",{
+
+    ## Test case when no base filename is the same.
+    cmpdl = data.table(ID=1:5,ORIG=c("f1.csv","f1.csv","f2.csv","f3.csv","f3.csv"),set=c(NA_character_,NA_character_,"aks","se31","se32"))
+    x = process_cmpd_sets(cmpdl)
+    expect_snapshot(x)
+
+    ## Test case with similar base filenames.
+    cmpdl = data.table(ID=1:5,ORIG=c("b/f2.csv","a/f1.csv","q/f/g/f2.csv","d/e/f/f3.csv","m/n/q/f3.csv"),set=c(NA_character_,NA_character_,"aks","se31","se32"))
+    x = process_cmpd_sets(cmpdl)
+    expect_snapshot(x)
+
+})