tool to validate yaml

Author: samuelbray32

src/trodes_to_nwb/database_validation.py

@@ -0,0 +1,73 @@
+import yaml
+
+spyglass_error = (
+    "This functional is optional and requires the spyglass package. It is only relevant"
+    + " for those using spyglass for data management and requires spyglass be installed."
+)
+
+
+def check_for_brain_region(data: dict):
+    from spyglass.common import BrainRegion
+
+    missing_regions = []
+    for k, v in data.items():
+        if isinstance(v, dict):
+            missing_regions.extend(check_for_brain_region(v))
+            continue
+        if isinstance(v, list):
+            for item in v:
+                if isinstance(item, dict):
+                    missing_regions.extend(check_for_brain_region(item))
+            continue
+        if "location" in k:
+            key = {"region_name": v}
+            if not (BrainRegion & key):
+                missing_regions.append(v)
+    return list(set(missing_regions))
+
+
+def yaml_database_validation(yaml_path: str):
+    """Validate the YAML file against the database tables to reduce duplication and errors.
+
+    Parameters
+    ----------
+    yaml_path : str
+        Path to the YAML file.
+    """
+
+    yaml_data = yaml.safe_load(open(yaml_path))
+    try:
+        from spyglass.common import CameraDevice, Task
+    except ImportError:
+        raise ImportError(spyglass_error)
+
+    # check entries for tables in the database for consistency with the yaml file
+    yaml_to_table = {
+        "tasks": Task(),
+        "cameras": CameraDevice(),
+    }
+    for yaml_key, table in yaml_to_table.items():
+        if yaml_key not in yaml_data:
+            continue
+        print(f"Checking table `{table.camel_name}` against yaml key `{yaml_key}`")
+        for key in yaml_data[yaml_key]:
+            _primary = {k: v for k, v in key.items() if k in table.primary_key}
+            if not (query := (table & _primary)):
+                continue
+
+            table_entry = query.fetch1()
+            for k, v in key.items():
+                if k not in table_entry:
+                    continue
+                if table_entry[k] != v:
+                    print(
+                        f"\tFor entry {_primary} in table {table.camel_name} \n"
+                        + f"\t\t Mismatch in {k}: {table_entry[k]} != {v}"
+                    )
+    if new_regions := check_for_brain_region(yaml_data):
+        print(
+            "The following brain regions are missing from the BrainRegion table.\n"
+            + " Consider using existing BrainRegion entries:"
+        )
+        for region in new_regions:
+            print(f"\t{region}")