make catching InvalidBidsError configurable

khanlab · May 19, 2023 · 618b763 · 618b763
1 parent 65cfd1b
commit 618b763
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Showing 2 changed files with 21 additions and 4 deletions.
diff --git a/snakebids/plugins/validator.py b/snakebids/plugins/validator.py
@@ -24,8 +24,8 @@ class BidsValidator:
         Snakebids application to be run
     """
 
-    def __init__(self) -> None:
-        pass
+    def __init__(self, raise_invalid_bids: bool = True) -> None:
+        self.raise_invalid_bids = raise_invalid_bids
 
     def __call__(self, app: SnakeBidsApp) -> None:
         # Skip bids validation
@@ -54,4 +54,5 @@ def __call__(self, app: SnakeBidsApp) -> None:
             # Any other bids-validator error
             except subprocess.CalledProcessError as err:
                 app.config["plugins.validator.success"] = False
-                raise InvalidBidsError from err
+                if self.raise_invalid_bids:
+                    raise InvalidBidsError from err
diff --git a/snakebids/tests/test_validate_plugin.py b/snakebids/tests/test_validate_plugin.py
@@ -62,7 +62,7 @@ def test_missing_bids_validator(
         assert caplog.records[0].levelname == "WARNING"
         assert "Missing bids-validator installation" in caplog.records[0].message
 
-    def test_validation_error(self, app: SnakeBidsApp, mocker: MockerFixture):
+    def test_raise_validation_error(self, app: SnakeBidsApp, mocker: MockerFixture):
         # Test for any other bids-validation error
         mocker.patch(
             "subprocess.check_call", side_effect=subprocess.CalledProcessError(1, "")
@@ -78,3 +78,19 @@ def test_validation_error(self, app: SnakeBidsApp, mocker: MockerFixture):
 
         # Check validation failure
         assert not app.config["plugins.validator.success"]
+
+    def test_ignore_validation_error(self, app: SnakeBidsApp, mocker: MockerFixture):
+        # Test for any other bids-validation error
+        mocker.patch(
+            "subprocess.check_call", side_effect=subprocess.CalledProcessError(1, "")
+        )
+
+        app.config["bids_dirs"] = "path/to/bids/dir"
+        app.config["plugins.validator.skip"] = False
+
+        # Check if error is skipped on invalid
+        validator = BidsValidator(raise_invalid_bids=False)
+        validator(app)
+
+        # Check validation failure
+        assert not app.config["plugins.validator.success"]