CU-8696ent8k: make prep_docs AnnotationEntity addition atomic.

webapp/api/api/data_utils.py

@@ -6,6 +6,7 @@
 from typing import Dict
 
 from django.contrib.auth.models import User
+from django.db import transaction
 from django.db.models import Q
 
 from core.settings import MEDIA_ROOT
@@ -42,14 +43,14 @@ def dataset_from_file(dataset: Dataset):
                         "The 'name' column are document IDs, and the 'text' column is the text you're "
                         "collecting annotations for")
 
-
-    for i, row in enumerate(df.iterrows()):
-        row = row[1]
-        document = Document()
-        document.name = row['name']
-        document.text = sanitise_input(row['text'])
-        document.dataset = dataset
-        document.save()
+    with transaction.atomic():
+        for i, row in enumerate(df.iterrows()):
+            row = row[1]
+            document = Document()
+            document.name = row['name']
+            document.text = sanitise_input(row['text'])
+            document.dataset = dataset
+            document.save()
 
 
 def sanitise_input(text: str):

webapp/api/api/utils.py

@@ -5,6 +5,7 @@
 
 from background_task import background
 from django.contrib.auth.models import User
+from django.db import transaction
 from django.db.models.signals import post_save
 from django.dispatch import receiver
 from medcat.cat import CAT
@@ -251,13 +252,14 @@ def prep_docs(project_id: List[int], doc_ids: List[int], user_id: int):
         logger.info(f'Running MedCAT model for project {project.id}:{project.name} over doc: {doc.id}')
         spacy_doc = cat(doc.text)
         anns = AnnotatedEntity.objects.filter(document=doc).filter(project=project)
-        add_annotations(spacy_doc=spacy_doc,
-                        user=user,
-                        project=project,
-                        document=doc,
-                        cat=cat,
-                        existing_annotations=anns)
-        # add doc to prepared_documents
+        with transaction.atomic():
+            add_annotations(spacy_doc=spacy_doc,
+                            user=user,
+                            project=project,
+                            document=doc,
+                            cat=cat,
+                            existing_annotations=anns)
+            # add doc to prepared_documents
         project.prepared_documents.add(doc)
     project.save()
     logger.info('Prepared all docs for project: %s, docs processed: %s',

webapp/api/api/views.py

@@ -5,6 +5,7 @@
 from background_task.models import Task, CompletedTask
 from django.contrib.auth.views import PasswordResetView
 from django.core.exceptions import ObjectDoesNotExist
+from django.db import transaction
 from django.http import HttpResponseBadRequest, HttpResponseServerError, HttpResponse
 from django.shortcuts import render
 from django.utils import timezone
@@ -248,7 +249,6 @@ def prepare_documents(request):
                                    'description': 'Missing CUI filter file, %s, cannot be found on the filesystem, '
                                                   'but is still set on the project. To fix remove and reset the '
                                                   'cui filter file' % project.cuis_file}, status=500)
-
     try:
         for d_id in d_ids:
             document = Document.objects.get(id=d_id)
@@ -264,26 +264,28 @@ def prepare_documents(request):
 
             is_validated = document in project.validated_documents.all()
 
-            # If the document is not already annotated, annotate it
-            if (len(anns) == 0 and not is_validated) or update:
-                # Based on the project id get the right medcat
-                cat = get_medcat(project=project)
-                logger.info('loaded medcat model for project: %s', project.id)
-
-                # Set CAT filters
-                cat.config.linking['filters']['cuis'] = cuis
-
-                spacy_doc = cat(document.text)
-                add_annotations(spacy_doc=spacy_doc,
-                                user=user,
-                                project=project,
-                                document=document,
-                                cat=cat,
-                                existing_annotations=anns)
-
-            # add doc to prepared_documents
-            project.prepared_documents.add(document)
-            project.save()
+            with transaction.atomic():
+                # If the document is not already annotated, annotate it
+                if (len(anns) == 0 and not is_validated) or update:
+                    # Based on the project id get the right medcat
+                    cat = get_medcat(project=project)
+                    logger.info('loaded medcat model for project: %s', project.id)
+
+                    # Set CAT filters
+                    cat.config.linking['filters']['cuis'] = cuis
+
+                    spacy_doc = cat(document.text)
+
+                    add_annotations(spacy_doc=spacy_doc,
+                                    user=user,
+                                    project=project,
+                                    document=document,
+                                    cat=cat,
+                                    existing_annotations=anns)
+
+                # add doc to prepared_documents
+                project.prepared_documents.add(document)
+                project.save()
 
     except Exception as e:
         stack = traceback.format_exc()