Add synthesis_products field with self-loop by default

Author: ml-evs

pydatalab/src/pydatalab/models/samples.py

@@ -11,3 +11,4 @@ class Sample(Item, HasSynthesisInfo):
 
     chemform: str | None = Field(example=["Na3P", "LiNiO2@C"])
     """A string representation of the chemical formula or composition associated with this sample."""
+

pydatalab/src/pydatalab/models/traits.py

@@ -86,57 +86,20 @@ class HasSynthesisInfo(BaseModel):
     synthesis_constituents: list[Constituent] = Field([])
     """A list of references to constituent materials giving the amount and relevant inlined details of consituent items."""
 
+    synthesis_products: list[Constituent] = Field([])
+    """A list of references to constituent materials giving the amount and relevant inlined details of relevant sythesis products."""
+
     synthesis_description: str | None = None
     """Free-text details of the procedure applied to synthesise the sample"""
 
     @root_validator
-    def add_missing_synthesis_relationships(cls, values):
-        """Add any missing sample synthesis constituents to parent relationships"""
-        from pydatalab.models.relationships import RelationshipType, TypedRelationship
-
-        constituents_set = set()
-        if values.get("synthesis_constituents") is not None:
-            existing_parent_relationship_ids = set()
-            if values.get("relationships") is not None:
-                existing_parent_relationship_ids = {
-                    relationship.refcode or relationship.item_id
-                    for relationship in values["relationships"]
-                    if relationship.relation == RelationshipType.PARENT
-                }
-            else:
-                values["relationships"] = []
-
-            for constituent in values.get("synthesis_constituents", []):
-                # If this is an inline relationship, just skip it
-                if isinstance(constituent.item, InlineSubstance):
-                    continue
-
-                constituent_id = constituent.item.refcode or constituent.item.item_id
-
-                if constituent_id not in existing_parent_relationship_ids:
-                    relationship = TypedRelationship(
-                        relation=RelationshipType.PARENT,
-                        refcode=constituent.item.refcode,
-                        item_id=constituent.item.item_id,
-                        type=constituent.item.type,
-                        description="Is a constituent of",
-                    )
-                    values["relationships"].append(relationship)
-
-                # Accumulate all constituent IDs in a set to filter those that have been deleted
-                constituents_set.add(constituent_id)
-
-        # Finally, filter out any parent relationships with item that were removed
-        # from the synthesis constituents
-        values["relationships"] = [
-            rel
-            for rel in values["relationships"]
-            if not (
-                (rel.refcode or rel.item_id) not in constituents_set
-                and rel.relation == RelationshipType.PARENT
-                and rel.type in ("samples", "starting_materials")
+    def add_self_product(cls, values):
+        if not values.get("synthesis_products"):
+            values["synthesis_products"].append(
+                Constituent(
+                    quantity=None, item={"type": values["type"], "refcode": values["refcode"]}
+                )
             )
-        ]
 
         return values
 

pydatalab/src/pydatalab/routes/v0_1/items.py

@@ -966,7 +966,7 @@ def get_item_data(
     )
 
     # Must be exported to JSON first to apply the custom pydantic JSON encoders
-    return_dict = json.loads(doc.json(exclude_unset=True))
+    return_dict = json.loads(doc.json())
 
     if item_id is None:
         item_id = return_dict["item_id"]