Merge pull request #2331 from bpinsard/fix/bids-filter-file_pathexist

FIX: non-existing path or JSON syntax error for `--bids-filter-file` should raise on error.

Author: effigies

fmriprep/cli/parser.py

@@ -55,11 +55,17 @@ def _filter_pybids_none_any(dct):
             for k, v in dct.items()
         }
 
-    def _bids_filter(value):
-        from json import loads
-
-        if value and Path(value).exists():
-            return loads(Path(value).read_text(), object_hook=_filter_pybids_none_any)
+    def _bids_filter(value, parser):
+        from json import loads, JSONDecodeError
+
+        if value:
+            if Path(value).exists():
+                try:
+                    return loads(Path(value).read_text(), object_hook=_filter_pybids_none_any)
+                except JSONDecodeError as e:
+                    raise parser.error(f"JSON syntax error in: <{value}>.")
+            else:
+                raise parser.error(f"Path does not exist: <{value}>.")
 
     verstr = f"fMRIPrep v{config.environment.version}"
     currentv = Version(config.environment.version)
@@ -76,6 +82,7 @@ def _bids_filter(value):
     PathExists = partial(_path_exists, parser=parser)
     IsFile = partial(_is_file, parser=parser)
     PositiveInt = partial(_min_one, parser=parser)
+    BIDSFilter = partial(_bids_filter, parser=parser)
 
     # Arguments as specified by BIDS-Apps
     # required, positional arguments
@@ -139,7 +146,7 @@ def _bids_filter(value):
         "--bids-filter-file",
         dest="bids_filters",
         action="store",
-        type=_bids_filter,
+        type=BIDSFilter,
         metavar="FILE",
         help="a JSON file describing custom BIDS input filters using PyBIDS. "
         "For further details, please check out "

fmriprep/cli/tests/test_parser.py

@@ -114,3 +114,28 @@ def _mock_is_bl(*args, **kwargs):
     assert ("FLAGGED" in captured) is flagged[0]
     if flagged[0]:
         assert (flagged[1] or "reason: unknown") in captured
+
+
+def test_bids_filter_file(tmp_path, capsys):
+    bids_path = tmp_path / "data"
+    out_path = tmp_path / "out"
+    bff = tmp_path / "filter.json"
+    args = [str(bids_path), str(out_path), "participant",
+            "--bids-filter-file", str(bff)]
+    bids_path.mkdir()
+
+    parser = _build_parser()
+
+    with pytest.raises(SystemExit) as error:
+        parser.parse_args(args)
+
+    err = capsys.readouterr().err
+    assert "Path does not exist:" in err
+
+    bff.write_text('{"invalid json": }')
+
+    with pytest.raises(SystemExit) as error:
+        parser.parse_args(args)
+
+    err = capsys.readouterr().err
+    assert "JSON syntax error in:" in err