add functionaility to patch missing @ids on Person records. Uses Fuzz…

…y Wuzzy to match differences in names

.github/scripts/generate_identifier.py

@@ -14,6 +14,9 @@ def encode(name, i):
 	return result_str
 
 
+#Dan added the 'Moved Permanently' condition as a bandaid fix for repos that have been deleted
+#functionality here may need improvement/rethinking.
+
 def exists(model_id):
 	cmd = "curl https://api.github.com/repos/ModelAtlasofTheEarth/{0}".format(model_id)
 	output = json.loads(run_command_check_output(cmd))

.github/scripts/ro_crate_utils.py

@@ -5,6 +5,9 @@
 from config import MATE_DOI, NCI_RECORD, AUSCOPE_RECORD, MATE_THREDDS_BASE
 import re
 import glob
+from collections.abc import MutableMapping
+from fuzzywuzzy import fuzz, process
+
 
 def recursively_filter_key(obj, entity_template):
 
@@ -749,3 +752,57 @@ def replace_keys_recursive(obj):
         return set(replace_keys_recursive(list(obj)))
     else:
         return obj
+
+
+
+def collect_person_ids(data, person_records):
+    """
+    Recursively collects Person records with @id and stores them in person_records.
+
+    Args:
+        data: The input data structure (dict or list) to traverse.
+        person_records: A dictionary to store the collected Person records.
+    """
+    if isinstance(data, list):
+        for item in data:
+            collect_person_ids(item, person_records)
+    elif isinstance(data, MutableMapping):
+        if data.get('@type') == 'Person' and '@id' in data:
+            key = f"{data.get('givenName')} {data.get('familyName')}"
+            if key not in person_records:
+                person_records[key] = data.get('@id')
+        for value in data.values():
+            collect_person_ids(value, person_records)
+
+def assign_missing_ids(data, person_records, threshold=80):
+    """
+    Recursively assigns missing @id to Person records using fuzzy matching.
+
+    Args:
+        data: The input data structure (dict or list) to traverse.
+        person_records: A dictionary of collected Person records with their @id.
+        threshold: The minimum similarity score for fuzzy matching (default is 80).
+    """
+    if isinstance(data, list):
+        for item in data:
+            assign_missing_ids(item, person_records, threshold)
+    elif isinstance(data, MutableMapping):
+        if data.get('@type') == 'Person' and '@id' not in data:
+            key = f"{data.get('givenName')} {data.get('familyName')}"
+            best_match = process.extractOne(key, person_records.keys(), scorer=fuzz.token_sort_ratio)
+            if best_match and best_match[1] >= threshold:
+                data['@id'] = person_records[best_match[0]]
+        for value in data.values():
+            assign_missing_ids(value, person_records, threshold)
+
+def assign_ids(metadata, threshold=80):
+    """
+    Collects Person records with @id and assigns missing @id to Person records in metadata.
+
+    Args:
+        metadata: The input metadata dictionary to process.
+        threshold: The minimum similarity score for fuzzy matching (default is 80).
+    """
+    person_records = {}
+    collect_person_ids(metadata, person_records)
+    assign_missing_ids(metadata, person_records, threshold)

.github/scripts/write_repo_contents.py

@@ -3,7 +3,7 @@
 from github import Github, Auth
 from parse_issue import parse_issue
 from crosswalks import dict_to_metadata, dict_to_yaml, dict_to_report, metadata_to_nci
-from ro_crate_utils import replace_keys_recursive
+from ro_crate_utils import replace_keys_recursive, assign_ids
 from yaml_utils import format_yaml_string
 from request_utils import download_license_text
 from copy_files import copy_files
@@ -44,6 +44,8 @@
 rocratestr_nested = dict_to_metadata(data, flat_compact_crate=False, timestamp= timestamp)
 rocratedict = json.loads(rocratestr_nested)
 default_context_list = copy.deepcopy(rocratedict['@context'])
+#patch missign ids on Person Records
+assign_ids(rocratedict['@graph'])
 
 try:
 

requirements.txt

@@ -4,3 +4,4 @@ pygithub==2.2.0
 PyLD
 ruamel.yaml<0.18.0
 ruamel.yaml.string
+fuzzywuzzy