Forbid fields other than those defined by each model class (#752)

Also adjust models and query methods to account for the new strict fields:

Ensure AssayTable.name is dropped on both sides of the conditional;
don't return audit_log_id, similarly to most other table classes;
remove author from SequencingGroupTable query fields as it is not present
in SequencingGroupFilter; remove outdated links/_links field alias.

Author: jmarshall

db/python/tables/assay.py

@@ -549,6 +549,7 @@ async def get_assays_for_sequencing_group_ids(
                 drow['external_ids'] = {drow.pop('name'): external_id}
             else:
                 drow['external_ids'] = {}
+                del drow['name']
 
             sequencing_group_id = drow.pop('sequencing_group_id')
             projects.add(drow.pop('project'))

db/python/tables/sample.py

@@ -49,7 +49,6 @@ class SampleTable(DbBase):
         'active',
         'type',
         'project',
-        'audit_log_id',
     ]
 
     # region GETS

db/python/tables/sequencing_group.py

@@ -59,7 +59,6 @@ class SequencingGroupTable(DbBase):
         'sg.technology',
         'sg.platform',
         'sg.meta',
-        'sg.author',
         'sg.archived',
     ]
     common_get_keys_str = ', '.join(common_get_keys)

models/base.py

@@ -1,4 +1,4 @@
-from pydantic.main import BaseModel
+from pydantic.main import BaseModel, Extra
 
 # annotate any external objects that must be instantiated with this
 # type to force openapi generator to allow for Nones (it will actually allow Any)
@@ -8,6 +8,10 @@
 class SMBase(BaseModel):
     """Base object for all models"""
 
+    class Config:
+        """Allow only the fields defined in each model class"""
+        extra = Extra.forbid
+
     @classmethod
     def from_dict(cls, d: dict):
         """Create an object from a dictionary"""

models/models/web.py

@@ -117,8 +117,3 @@ class ProjectSummary(SMBase):
     seqr_sync_types: list[str]
 
     links: PagingLinks | None
-
-    class Config:
-        """Config for ProjectSummaryResponse"""
-
-        fields = {'links': '_links'}