yaml validation

environment.yml

@@ -14,6 +14,7 @@ dependencies:
 - pytest-cov
 - pip
 - pyyaml
+- jsonschema
 - pip:
     - ndx-franklab-novela
-    - neo
+    - neo

src/spikegadgets_to_nwb/convert_yaml.py

@@ -1,5 +1,6 @@
 import yaml
 from xml.etree import ElementTree
+from spikegadgets_to_nwb import metadata_validation
 
 from pynwb import NWBFile, TimeSeries
 from pynwb.file import Subject, ProcessingModule
@@ -37,8 +38,12 @@ def load_metadata(
     tuple[dict, list[dict]]
         the yaml generator metadata and list of probe metadatas
     """
+    metadata = None
     with open(metadata_path, "r") as stream:
         metadata = yaml.safe_load(stream)
+    is_metadata_valid, metadata_errors = metadata_validation.validate(metadata)
+    if not is_metadata_valid:
+        raise ValueError("".join(metadata_errors))
     probe_metadata = []
     for path in probe_metadata_paths:
         with open(path, "r") as stream:

src/spikegadgets_to_nwb/metadata_validation.py

@@ -0,0 +1,74 @@
+import jsonschema
+import os
+import yaml
+import copy
+import datetime
+
+
+def _get_nwb_json_schema_path() -> str:
+    """Get the NWB JSON Schema file path
+
+    Returns
+    -------
+    str
+        NWB Schema file Path
+    """
+    current_path = os.path.dirname(os.path.abspath(__file__))
+    json_schema_file = "/./nwb_schema.json"
+    return f"{current_path}{os.path.normpath(json_schema_file)}"
+
+
+def _get_json_schema() -> str:
+    """Get JSON Schema
+
+    Returns
+    -------
+    str
+        JSON Schema content
+    """
+    json_schema = None
+    json_schema_path = _get_nwb_json_schema_path()
+    with open(json_schema_path, "r") as stream:
+        json_schema = yaml.safe_load(stream)
+    return json_schema
+
+
+def validate(metadata: dict) -> tuple:
+    """Validates metadata
+
+    Parameters
+    ----------
+    metadata : dict
+        metadata documenting the particulars of a session
+
+    Returns
+    -------
+    tuple
+        information of the validity of the metadata data and any errors
+    """
+    assert metadata is not None  # metadata cannot be null
+    assert isinstance(metadata, dict)  # cannot proceed if metadata is not a dictionary
+
+    # date_of_birth is set to a datetime by the YAML-to-dict converter.
+    # This code converts date_of_birth  to string
+    metadata_content = copy.deepcopy(metadata) or {}
+    if (
+        metadata_content["subject"]
+        and metadata_content["subject"]["date_of_birth"]
+        and type(metadata_content["subject"]["date_of_birth"]) is datetime.datetime
+    ):
+        metadata_content["subject"]["date_of_birth"] = (
+            metadata_content["subject"]["date_of_birth"].utcnow().isoformat()
+        )
+
+    schema = _get_json_schema()
+    validator = jsonschema.Draft202012Validator(schema)
+    metadata_validation_errors = validator.iter_errors(metadata_content)
+    errors = []
+
+    for metadata_validation_error in metadata_validation_errors:
+        errors.append(metadata_validation_error.message)
+
+    is_valid = len(errors) == 0
+
+    return is_valid, errors