Add alias-key-json CI test

tests/test_alias_json.py

@@ -0,0 +1,166 @@
+#! /usr/bin/env python3
+import json
+import re
+
+SKIP_VALID_ALIAS = {
+    "A",
+    "B",
+}
+
+SKIP_UNIQUE_VALUE_FOR_KEYS = {
+    "A",
+    "B",
+    "XD",
+    "XE",
+    "XF",
+    "XG",
+    "XH",
+    "XJ",
+    "XK",
+    "XL",
+    "XM",
+    "XM",
+    "XN",
+    "XP",
+    "XQ",
+    "XR",
+    "XT",
+    "XU",
+    "XV",
+    "XW",
+    "XY",
+    "XZ",
+    "XAA",
+    "XAB",
+    "XAC",
+    "XAD",
+    "XAD",
+    "XAE",
+    "XAE",
+    "XAF",
+    "XAG",
+    "XAH",
+    "XAH",
+    "XAK",
+    "XAL",
+    "XAP",
+    "XAP",
+    "XAQ",
+    "XAR",
+    "XAY",
+    "XBA",
+    "XBK",
+    "XBP",
+    "XBQ",
+    "XBR",
+    "XBS",
+    "XCA",
+}
+
+def are_keys_valid(json_data):
+    is_valid = True
+    for key in json_data.keys():
+        if not all(char.isupper() for char in key):
+            print(f"Key '{key}' is not in uppercase.")
+            is_valid = False
+        if 'O' in key or 'I' in key:
+            print(f"Key '{key}' contains illegal characters ('O' or 'I').")
+            is_valid = False
+    return is_valid
+
+
+def are_values_valid_pango_lineages(json_data):
+    is_valid = True  # Initialize to True
+
+    # Regex pattern for Pango lineage
+    pango_lineage_pattern = re.compile(r'^([A-Z]+)(\.[1-9]\d*\.[1-9]\d*\.[1-9]\d*)+$')
+    valid_keys = json_data.keys()
+
+    for key, value in json_data.items():
+        # Skip the check if the value is a list
+        if isinstance(value, list):
+            continue
+
+        if key in SKIP_VALID_ALIAS:
+            continue
+
+        # Check if the value matches the Pango lineage format
+        match = pango_lineage_pattern.match(value)
+        if not match:
+            print(f"Value '{value}' for key '{key}' is not a valid Pango lineage.")
+            is_valid = False
+            continue
+
+        # Check if the value starts with a key that's in valid_keys
+        starting_key = match.group(1)
+        if starting_key not in valid_keys:
+            print(f"Value '{value}' for key '{key}' does not start with a valid key.")
+            is_valid = False
+
+    return is_valid
+
+
+def dict_raise_on_duplicates(ordered_pairs):
+    d = {}
+    duplicate_keys = {}
+    for k, v in ordered_pairs:
+        if k in d:
+            duplicate_keys.setdefault(k, []).append(d[k])
+            duplicate_keys[k].append(v)
+        else:
+            d[k] = v
+    if duplicate_keys != {}:
+        raise ValueError(f"Duplicate keys found: `{duplicate_keys}`")
+    return d
+
+
+def test_json(json_str):
+    is_valid = True
+    try:
+        # Parse JSON string to dictionary
+        json_data = json.loads(json_str)
+    except json.JSONDecodeError as e:
+        print(f"Invalid JSON: {e}")
+        return False
+
+    # Test if keys are unique
+    try:
+        json.loads(json_str, object_pairs_hook=dict_raise_on_duplicates)
+    except ValueError as e:
+        print(e)
+        is_valid = False
+
+    # Initialize empty set for checking unique keys and values
+    values_set = set()
+
+    # Loop through each key-value pair
+    for key, value in json_data.items():
+        # Check if value is unique (converting lists to tuple for hashability)VAE
+        value_as_tuple = tuple(value) if isinstance(value, list) else value
+        if value_as_tuple in values_set:
+            if key in SKIP_UNIQUE_VALUE_FOR_KEYS:
+                continue
+            is_valid = False
+            all_keys = [k for k, v in json_data.items() if v == value]
+            print(
+                f"Duplicate value found: value `{value}` with keys `{all_keys}`"
+            )
+        else:
+            values_set.add(value_as_tuple)
+
+    # Check if keys are legal:
+    # - no O,I
+    # - capital letters only
+    is_valid &= are_keys_valid(json_data)
+    is_valid &= are_values_valid_pango_lineages(json_data)
+
+
+    return is_valid
+
+
+if __name__ == "__main__":
+    with open("pango_designation/alias_key.json", "r") as f:
+        json_str = f.read()
+        is_valid = test_json(json_str)
+        if is_valid is False:
+            exit(1)