ensure there are notes for all analyses (#1161)

Author: jdkent

store/backend/neurostore/resources/base.py

@@ -2,6 +2,7 @@
 Base Classes/functions for constructing views
 """
 
+import json
 import re
 
 from connexion.context import context
@@ -11,6 +12,7 @@
     abort_permission,
     abort_validation,
     abort_not_found,
+    abort_unprocessable,
 )
 
 from psycopg2 import errors
@@ -45,6 +47,12 @@
 from . import data as viewdata
 
 
+@parser.error_handler
+def handle_parser_error(err, req, schema, *, error_status_code, error_headers):
+    detail = json.dumps(err.messages)
+    abort_unprocessable(f"input does not conform to specification: {detail}")
+
+
 def create_user():
     from auth0.v3.authentication.users import Users
 
@@ -128,10 +136,13 @@ def update_annotations(self, annotations):
         create_annotation_analyses = []
         for result in results:
             if result.analysis_id and not result.annotation_analysis_id:
+                note_payload = result.note or self._build_default_note(result.note_keys)
+                if note_payload is None:
+                    note_payload = {}
                 params = {
                     "analysis_id": result.analysis_id,
                     "annotation_id": result.id,
-                    "note": result.note or {},
+                    "note": note_payload,
                     "user_id": result.user_id,
                     "study_id": result.study_id,
                     "studyset_id": result.studyset_id,
@@ -215,6 +226,12 @@ def update_base_studies(self, base_studies):
     def eager_load(self, q, args):
         return q
 
+    @staticmethod
+    def _build_default_note(note_keys):
+        if not note_keys:
+            return None
+        return {key: None for key in note_keys.keys()}
+
     def db_validation(self, record, data):
         """
         Custom validation for database constraints.

store/backend/neurostore/schemas/data.py

@@ -6,6 +6,7 @@
     pre_dump,
     pre_load,
     post_load,
+    validates_schema,
     EXCLUDE,
     ValidationError,
 )
@@ -662,6 +663,19 @@ def add_id(self, data, **kwargs):
             data["studyset"] = {"id": data.pop("studyset_id")}
         return data
 
+    @validates_schema
+    def validate_notes(self, data, **kwargs):
+        notes = data.get("annotation_analyses") or []
+        invalid = {}
+
+        for idx, note in enumerate(notes):
+            note_payload = note.get("note") if isinstance(note, dict) else None
+            if not isinstance(note_payload, dict) or len(note_payload) == 0:
+                invalid[idx] = ["note must include at least one field"]
+
+        if invalid:
+            raise ValidationError({"notes": invalid})
+
 
 class BaseSnapshot(object):
     def __init__(self):

store/backend/neurostore/tests/api/test_annotations.py

@@ -18,6 +18,48 @@ def test_post_blank_annotation(auth_client, ingest_neurosynth, session):
     assert annot.annotation_analyses[0].user_id == annot.user_id
 
 
+def test_blank_annotation_populates_note_fields(auth_client, ingest_neurosynth, session):
+    dset = Studyset.query.first()
+    note_keys = {"included": "boolean", "quality": "string"}
+    payload = {
+        "studyset": dset.id,
+        "note_keys": note_keys,
+        "name": "with defaults",
+    }
+
+    resp = auth_client.post("/api/annotations/", data=payload)
+    assert resp.status_code == 200
+
+    for note in resp.json()["notes"]:
+        assert set(note["note"].keys()) == set(note_keys.keys())
+        assert all(value is None for value in note["note"].values())
+
+
+def test_annotation_rejects_empty_note(auth_client, ingest_neurosynth, session):
+    dset = Studyset.query.first()
+    study = dset.studies[0]
+    analysis = study.analyses[0]
+
+    payload = {
+        "studyset": dset.id,
+        "notes": [
+            {
+                "study": study.id,
+                "analysis": analysis.id,
+                "note": {},
+            }
+        ],
+        "note_keys": {"included": "boolean"},
+        "name": "invalid annotation",
+    }
+
+    resp = auth_client.post("/api/annotations/", data=payload)
+
+    assert resp.status_code == 422
+    error = resp.json()
+    assert "note must include at least one field" in error["detail"]
+
+
 def test_post_annotation(auth_client, ingest_neurosynth, session):
     dset = Studyset.query.first()
     # y for x in non_flat for y in x