Merging validation functions

dandi/cli/cmd_validate.py

@@ -11,11 +11,7 @@
 
 @click.command()
 @click.option(
-    "--schema", help="Validate against new BIDS schema version.", metavar="VERSION"
-)
-@click.option(
-    "--report-path",
-    help="Write report under path, this option implies `--report/-r`.",
+    "--bids-schema", help="Validate against new BIDS schema version.", metavar="VERSION"
 )
 @click.option(
     "--report",
@@ -24,42 +20,9 @@
     help="Whether to write a report under a unique path in the DANDI log directory.",
 )
 @click.option(
-    "--grouping",
-    "-g",
-    help="How to group error/warning reporting.",
-    type=click.Choice(["none", "path"], case_sensitive=False),
-    default="none",
+    "--report-path",
+    help="Write report under path, this option implies `--report/-r`.",
 )
-@click.argument("paths", nargs=-1, type=click.Path(exists=True, dir_okay=True))
-@map_to_click_exceptions
-def validate_bids(
-    paths,
-    schema,
-    report,
-    report_path,
-    grouping="none",
-):
-    """Validate BIDS paths.
-
-    Notes
-    -----
-    Used from bash, eg:
-        dandi validate-bids /my/path
-    """
-
-    from ..validate import validate_bids as validate_bids_
-
-    validator_result = validate_bids_(  # Controller
-        *paths,
-        report=report,
-        report_path=report_path,
-        schema_version=schema,
-    )
-
-    _process_issues(validator_result, grouping)
-
-
-@click.command()
 @devel_option("--schema", help="Validate against new schema version", metavar="VERSION")
 @devel_option(
     "--allow-any-path",
@@ -79,6 +42,9 @@ def validate_bids(
 @map_to_click_exceptions
 def validate(
     paths,
+    bids_schema,
+    report,
+    report_path,
     schema=None,
     devel_debug=False,
     allow_any_path=False,
@@ -108,9 +74,16 @@ def validate(
     validator_result = validate_(
         *paths,
         schema_version=schema,
+        bids_schema_version=bids_schema,
         devel_debug=devel_debug,
         allow_any_path=allow_any_path,
     )
+    from collections import Counter
+
+    # for some reason we get the same error repeated over and over again, probably related
+    # to different behaviour of yield and return
+    print(Counter([i.id for i in validator_result]))
+    raise
 
     _process_issues(validator_result, grouping)
 

dandi/cli/command.py

@@ -148,7 +148,7 @@ def main(ctx, log_level, pdb=False):
 from .cmd_service_scripts import service_scripts  # noqa: E402
 from .cmd_shell_completion import shell_completion  # noqa: E402
 from .cmd_upload import upload  # noqa: E402
-from .cmd_validate import validate, validate_bids  # noqa: E402
+from .cmd_validate import validate  # noqa: E402
 
 __all_commands__ = (
     delete,
@@ -162,7 +162,6 @@ def main(ctx, log_level, pdb=False):
     shell_completion,
     upload,
     validate,
-    validate_bids,
 )
 
 for cmd in __all_commands__:

dandi/files/bids.py

@@ -54,7 +54,7 @@ def bids_root(self) -> Path:
         """
         The directory on the filesystem in which the BIDS dataset is located
         """
-        return self.filepath.parent
+        return self.filepath.parent.resolve()
 
     def _validate(self) -> None:
         with self._lock:
@@ -71,19 +71,36 @@ def _validate(self) -> None:
                     list
                 )
                 self._asset_metadata = defaultdict(dict)
+                print("..")
                 for result in results:
+                    print(result)
                     if result.id in BIDS_ASSET_ERRORS:
+                        print("jj")
+                        print(result)
+                        print("jj")
                         assert result.path
                         self._asset_errors[str(result.path)].append(result)
                     elif result.id in BIDS_DATASET_ERRORS:
+                        print("ii")
+                        print(result)
                         self._dataset_errors.append(result)
+                        print("ii")
                     elif result.id == "BIDS.MATCH":
+                        print("kk")
+                        print(result)
+                        print("kk")
                         assert result.path
+                        print(result.path)
+                        print("kk1")
                         bids_path = result.path.relative_to(self.bids_root).as_posix()
+                        print("kk2")
                         assert result.metadata is not None
+                        print("kk3")
                         self._asset_metadata[bids_path] = prepare_metadata(
                             result.metadata
                         )
+                        print("kk4")
+                print("..")
 
     def get_asset_errors(self, asset: BIDSAsset) -> list[ValidationResult]:
         """:meta private:"""
@@ -154,7 +171,7 @@ def bids_path(self) -> str:
         """
         ``/``-separated path to the asset from the root of the BIDS dataset
         """
-        return self.filepath.relative_to(self.bids_root).as_posix()
+        return self.filepath.resolve().relative_to(self.bids_root).as_posix()
 
     def get_validation_errors(
         self,

dandi/validate.py

@@ -145,6 +145,7 @@ def validate_bids(
 
 def validate(
     *paths: str,
+    bids_schema_version: Optional[str] = None,
     schema_version: Optional[str] = None,
     devel_debug: bool = False,
     allow_any_path: bool = False,