Merge pull request #1646: index: Allow FileNotFoundError to be handle…

…d at the top level

CHANGES.md

@@ -2,6 +2,11 @@
 
 ## __NEXT__
 
+### Bug Fixes
+
+* index: Previously specifying a directory that does not exist in the path to `--output` would result in an incorrect error stating that the input file does not exist. It now shows the correct path responsible for the error. [#1644][] (@victorlin)
+
+[#1644]: https://github.com/nextstrain/augur/issues/1644
 
 ## 26.0.0 (17 September 2024)
 

augur/index.py

@@ -2,7 +2,6 @@
 """
 
 from itertools import combinations
-import sys
 import csv
 
 from .io.file import open_file
@@ -209,15 +208,11 @@ def run(args):
     ("?" and "-"), and other invalid characters in a set of sequences and write
     the composition as a data frame to the given sequence index path.
     '''
-    try:
-        if is_vcf(args.sequences):
-            num_of_seqs = index_vcf(args.sequences, args.output)
-            tot_length = None
-        else:
-            num_of_seqs, tot_length = index_sequences(args.sequences, args.output)
-    except FileNotFoundError:
-        print(f"ERROR: Could not open sequences file '{args.sequences}'.", file=sys.stderr)
-        return 1
+    if is_vcf(args.sequences):
+        num_of_seqs = index_vcf(args.sequences, args.output)
+        tot_length = None
+    else:
+        num_of_seqs, tot_length = index_sequences(args.sequences, args.output)
 
     if args.verbose:
         if tot_length:

tests/functional/index.t

@@ -18,7 +18,16 @@ This should fail.
   $ ${AUGUR} index \
   >   --sequences index/missing_sequences.fasta \
   >   --output "$TMP/sequence_index.tsv"
-  ERROR: Could not open sequences file 'index/missing_sequences.fasta'.
-  [1]
+  ERROR: No such file or directory: 'index/missing_sequences.fasta'
+  [2]
+
+Try writing output to a directory that does not exist.
+This should fail.
+
+  $ ${AUGUR} index \
+  >   --sequences index/sequences.fasta \
+  >   --output "results/sequence_index.tsv"
+  ERROR: No such file or directory: 'results/sequence_index.tsv'
+  [2]
 
   $ popd > /dev/null