[REF] refactor marshmallow schema logic (#681)

* wip: refactoring of schema

* tmp commit neurovault away

* style fix

* import style fixes

* clean comments

* fix info endpoint

* remove comment

Author: jdkent

store/neurostore/resources/base.py

@@ -532,8 +532,12 @@ def post(self):
         if source_id:
             data = self._load_from_source(source, source_id)
         else:
-            data = parser.parse(self.__class__._schema, request)
+            unknown = self.__class__._schema.opts.unknown
+            data = parser.parse(
+                self.__class__._schema(exclude=("id",)), request, unknown=unknown
+            )
         args["nested"] = bool(args.get("nested") or request.args.get("source_id"))
+
         with db.session.no_autoflush:
             record = self.__class__.update_or_create(data)
 

store/neurostore/resources/data.py

@@ -1,7 +1,6 @@
 import string
 
 from flask import request
-from marshmallow import EXCLUDE
 from webargs.flaskparser import parser
 from webargs import fields
 import sqlalchemy.sql.expression as sae
@@ -207,14 +206,12 @@ def load_from_neurostore(cls, source_id):
             parent_source = parent.source
             parent_source_id = parent.source_id
 
-        schema = cls._schema(copy=True)
+        context = {
+            "clone": True,
+            "nested": True,
+        }
+        schema = cls._schema(context=context)
         tmp_data = schema.dump(annotation)
-        for note in tmp_data["notes"]:
-            note.pop("analysis_name")
-            note.pop("study_name")
-            note.pop("study_year")
-            note.pop("publication")
-            note.pop("authors")
         data = schema.load(tmp_data)
         data["source"] = "neurostore"
         data["source_id"] = source_id
@@ -266,12 +263,6 @@ def view_search(self, q, args):
 
         return q
 
-    def serialize_records(self, records, args, exclude=tuple()):
-        if args.get("flat"):
-            exclude = ("versions",)
-
-        return super().serialize_records(records, args, exclude)
-
     def join_tables(self, q):
         "join relevant tables to speed up query"
         q = q.options(joinedload("versions"))
@@ -382,8 +373,6 @@ class StudiesView(ObjectView, ListView):
         "pmid",
     )
 
-    # _default_exclude = ("has_coordinates", "has_images", "studysets")
-
     def view_search(self, q, args):
         # search studies for data_type
         if args.get("data_type"):
@@ -426,10 +415,6 @@ def serialize_records(self, records, args, exclude=tuple()):
                 study.studysets = study.studysets.filter(
                     Studyset.user_id == args.get("studyset_owner")
                 ).all()
-        if args.get("flat"):
-            exclude += ("analyses",)
-
-        exclude += ("studysets", "has_coordinates", "has_images")
         return super().serialize_records(records, args, exclude)
 
     @classmethod
@@ -452,8 +437,10 @@ def load_from_neurostore(cls, source_id):
             parent_source = parent.source
             parent_source_id = parent.source_id
 
-        schema = cls._schema(copy=True)
-        data = schema.load(schema.dump(study), unknown=EXCLUDE)
+        context = {"clone": True, "nested": True}
+        schema = cls._schema(context=context)
+        dump_study = schema.dump(study)
+        data = schema.load(dump_study)
         data["source"] = "neurostore"
         data["source_id"] = source_id
         data["source_updated_at"] = study.updated_at or study.created_at