fix error message and test for it

hail-is · Oct 23, 2023 · cae45a7 · cae45a7
1 parent 1ab9693
commit cae45a7
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/hail/python/test/hail/methods/test_impex.py b/hail/python/test/hail/methods/test_impex.py
@@ -1410,14 +1410,14 @@ def test_old_index_file_throws_error(self):
 
         with hl.TemporaryFilename() as f:
             hl.current_backend().fs.copy(bgen_file, f)
-            with pytest.raises(FatalError, match='have no .idx2 index file'):
+            with pytest.raises(FatalError, match=f'The following BGEN .idx2 index files do not exist.*{f}.idx2.*'):
                 hl.import_bgen(f, ['GT', 'GP'], sample_file, n_partitions=3)
 
             try:
                 with hl.current_backend().fs.open(f + '.idx', 'wb') as fobj:
                     fobj.write(b'')
 
-                with pytest.raises(FatalError, match='have no .idx2 index file'):
+                with pytest.raises(FatalError, match=f'The following BGEN .idx2 index files do not exist.*{f}.idx2.*'):
                     hl.import_bgen(f, ['GT', 'GP'], sample_file)
             finally:
                 hl.current_backend().fs.remove(f + '.idx')

diff --git a/hail/src/main/scala/is/hail/io/bgen/LoadBgen.scala b/hail/src/main/scala/is/hail/io/bgen/LoadBgen.scala
@@ -241,7 +241,7 @@ object LoadBgen {
 
   def getIndexFiles(fs: FS, files: Array[FileListEntry], indexFileMap: Map[String, String]): Array[String] = {
     val indexFiles = getIndexFileNames(fs, files, indexFileMap)
-    val missingIdxFiles = files.zip(indexFiles).filterNot { case (f, index) => fs.exists(index) && index.endsWith("idx2") }.map(_._1)
+    val missingIdxFiles = files.zip(indexFiles).filterNot { case (f, index) => fs.exists(index) && index.endsWith("idx2") }.map(_._1.getPath)
     if (missingIdxFiles.nonEmpty)
       fatal(
         s"""The following BGEN .idx2 index files do not exist. Use 'index_bgen' to create the index file once before calling 'import_bgen':