CU-869awpaf3: (chore): medcat-trainer: remove cdb_utils, fix vestigial medcat-v2 migration issues (#188)

Co-authored-by: Tom Searle <[email protected]>

Author: tomolopolis

medcat-trainer/webapp/api/api/medcat_utils.py

@@ -420,7 +420,7 @@ def meta_anns_concept_summary(self) -> List[Dict]:
             # Store results for this concept
             meta_performance[cui] = {
                 'cui': cui,
-                'concept_name': self.cat.cdb.cui2preferred_name[cui],
+                'concept_name': self.cat.cdb.cui2info[cui]['preferred_name'],
                 'meta_tasks': meta_task_results
             }
 

medcat-trainer/webapp/api/api/metrics.py

@@ -202,6 +202,7 @@ def clear_cached_medcat(project, cat_map: Dict[str, CAT]=CAT_MAP):
 
 
 def get_cached_cdb(cdb_id: str, cdb_map: Dict[str, CDB]=CDB_MAP) -> CDB:
+    from api.utils import clear_cdb_cnf_addons
     if cdb_id not in cdb_map:
         cdb_obj = ConceptDB.objects.get(id=cdb_id)
         cdb = CDB.load(cdb_obj.cdb_file.path)

medcat-trainer/webapp/api/api/model_cache.py

@@ -11,6 +11,7 @@
 from django.shortcuts import render
 from django.utils import timezone
 from django_filters import rest_framework as drf
+from medcat.utils.cdb_utils import ch2pt_from_pt2ch, get_all_ch, snomed_ct_concept_path
 from rest_framework import viewsets
 from rest_framework.decorators import api_view
 from rest_framework.response import Response
@@ -19,7 +20,6 @@
 from .admin import download_projects_with_text, download_projects_without_text, \
     import_concepts_from_cdb
 from .data_utils import upload_projects_export
-from .medcat_utils import ch2pt_from_pt2ch, get_all_ch, dedupe_preserve_order, snomed_ct_concept_path
 from .metrics import calculate_metrics
 from .model_cache import get_medcat, get_cached_cdb, VOCAB_MAP, clear_cached_medcat, CAT_MAP, CDB_MAP, is_model_loaded
 from .permissions import *
@@ -858,11 +858,11 @@ def cdb_cui_children(request, cdb_id):
 
     # currently assumes this is using the SNOMED CT terminology
     try:
-        root_term = {'cui': '138875005', 'pretty_name': cdb.cui2preferred_name['138875005']}
+        root_term = {'cui': '138875005', 'pretty_name': cdb.cui2info['138875005']['preferred_name']}
         if parent_cui is None:
             return Response({'results': [root_term]})
         else:
-            child_concepts = [{'cui': cui, 'pretty_name': cdb.cui2preferred_name[cui]}
+            child_concepts = [{'cui': cui, 'pretty_name': cdb.cui2info[cui]['preferred_name']}
                               for cui in cdb.addl_info.get('pt2ch')[parent_cui]]
             return Response({'results': child_concepts})
     except KeyError:
@@ -894,7 +894,7 @@ def generate_concept_filter_flat_json(request):
         for cui in cuis:
             ch_nodes = get_all_ch(cui, cdb)
             final_filter += [n for n in ch_nodes if n not in excluded_nodes]
-        final_filter = dedupe_preserve_order(final_filter)
+        final_filter = {cui:1 for cui in final_filter}.keys()
         filter_json = json.dumps(final_filter)
         response = HttpResponse(filter_json, content_type='application/json')
         response['Content-Disposition'] = 'attachment; filename=filter.json'
@@ -911,8 +911,8 @@ def generate_concept_filter(request):
         # get all children from 'parent' concepts above.
         final_filter = {}
         for cui in cuis:
-            final_filter[cui] = [{'cui': c, 'pretty_name': cdb.cui2preferred_name[c]} for c in get_all_ch(cui, cdb)
-                                 if c in cdb.cui2preferred_name and c != cui]
+            final_filter[cui] = [{'cui': c, 'pretty_name': cdb.cui2info[cui]['preferred_name']} for c in get_all_ch(cui, cdb)
+                                 if c in cdb.cui2info[cui]['preferred_name'] and c != cui]
         resp = {'filter_len': sum(len(f) for f in final_filter.values()) + len(final_filter.keys())}
         if resp['filter_len'] < 10000:
             # only send across concept filters that are small enough to render
@@ -928,12 +928,12 @@ def cuis_to_concepts(request):
     if cdb_id is not None:
         if cuis is not None:
             cdb = get_cached_cdb(cdb_id, CDB_MAP)
-            concept_list = [{'cui': cui, 'name': cdb.cui2preferred_name[cui]} for cui in cuis]
+            concept_list = [{'cui': cui, 'name': cdb.cui2info[cui]['preferred_name']} for cui in cuis]
             resp = {'concept_list': concept_list}
             return Response(resp)
         else:
             cdb = get_cached_cdb(cdb_id, CDB_MAP)
-            concept_list = [{'cui': cui, 'name': cdb.cui2preferred_name[cui]} for cui in cdb.cui2preferred_name.keys()]
+            concept_list = [{'cui': cui, 'name': cdb.cui2info[cui]['preferred_name']} for cui in cdb.cui2info.keys()]
             resp = {'concept_list': concept_list}
             return Response(resp)
     return HttpResponseBadRequest('Missing either cuis or cdb_id param. Cannot produce concept list.')