[WIP] Add yields section to synthesis tables and models

pydatalab/schemas/sample.json

@@ -11,6 +11,14 @@
         "$ref": "#/definitions/Constituent"
       }
     },
+    "synthesis_products": {
+      "title": "Synthesis Products",
+      "default": [],
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/Constituent"
+      }
+    },
     "synthesis_description": {
       "title": "Synthesis Description",
       "type": "string"

pydatalab/schemas/startingmaterial.json

@@ -11,6 +11,14 @@
         "$ref": "#/definitions/Constituent"
       }
     },
+    "synthesis_products": {
+      "title": "Synthesis Products",
+      "default": [],
+      "type": "array",
+      "items": {
+        "$ref": "#/definitions/Constituent"
+      }
+    },
     "synthesis_description": {
       "title": "Synthesis Description",
       "type": "string"

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

@@ -3,7 +3,7 @@
 from pydantic import BaseModel, Field, root_validator
 
 from pydatalab.models.people import Person
-from pydatalab.models.utils import Constituent, InlineSubstance, PyObjectId
+from pydatalab.models.utils import Constituent, PyObjectId
 
 
 class HasOwner(BaseModel):
@@ -86,57 +86,25 @@ 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"],
+                        "item_id": values["item_id"],
+                    },
+                )
             )
-        ]
 
         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"]

webapp/src/components/CompactConstituentTable.vue

@@ -113,8 +113,8 @@ export default {
   },
   props: {
     modelValue: {
-      type: String,
-      default: "",
+      type: Array,
+      default: () => [],
     },
     typesToQuery: {
       type: Array,
@@ -132,7 +132,7 @@ export default {
   },
   computed: {
     newSelectIsShown() {
-      return this.constituents.length == 0 || this.addNewConstituentIsActive;
+      return this.addNewConstituentIsActive;
     },
     constituents: {
       get() {

webapp/src/components/SynthesisInformation.vue

@@ -15,16 +15,31 @@
       class="content-container"
       :style="{ 'max-height': contentMaxHeight }"
     >
+      <span id="synthesis-reactants-label" class="subheading mt-2 pb-2 ml-2">
+        <label for="synthesis-reactants-table">Reactants, reagents, inputs</label>
+      </span>
       <div class="card component-card">
         <div class="card-body pt-2 pb-0 mb-0 pl-5">
           <CompactConstituentTable
-            id="synthesis-table"
+            id="synthesis-reactants-table"
             v-model="constituents"
             :types-to-query="['samples', 'starting_materials']"
           />
         </div>
       </div>
-      <span id="synthesis-procedure-label" class="subheading ml-2">Procedure</span>
+      <span id="synthesis-products-label" class="subheading mt-2 pb-2 ml-2"
+        ><label for="synthesis-products-table">Products</label></span
+      >
+      <div class="card component-card">
+        <div class="card-body pt-2 pb-0 mb-0 pl-5">
+          <CompactConstituentTable
+            id="synthesis-products-table"
+            v-model="products"
+            :types-to-query="['samples', 'starting_materials']"
+          />
+        </div>
+      </div>
+      <span id="synthesis-procedure-label" class="subheading ml-2"><label>Procedure</label></span>
       <TinyMceInline
         v-model="SynthesisDescription"
         aria-labelledby="synthesis-procedure-label"
@@ -59,6 +74,7 @@ export default {
   },
   computed: {
     constituents: createComputedSetterForItemField("synthesis_constituents"),
+    products: createComputedSetterForItemField("synthesis_products"),
     SynthesisDescription: createComputedSetterForItemField("synthesis_description"),
   },
   watch: {
@@ -69,6 +85,12 @@ export default {
       },
       deep: true,
     },
+    products: {
+      handler() {
+        this.$store.commit("setItemSaved", { item_id: this.item_id, isSaved: false });
+      },
+      deep: true,
+    },
     SynthesisDescription: {
       handler() {
         this.$store.commit("setItemSaved", { item_id: this.item_id, isSaved: false });
@@ -80,6 +102,7 @@ export default {
     // Auto-collapsed when initialised empty
     this.isExpanded =
       (this.constituents && this.constituents.length > 0) ||
+      (this.products && this.products.length > 0) ||
       (this.SynthesisDescription && this.SynthesisDescription.trim() !== "");
     // If expanded set height to none, otherwise set to 0px
     if (this.isExpanded) {
@@ -122,6 +145,24 @@ export default {
       this.selectShown.push(false);
       this.isExpanded = true;
     },
+    addProduct(selectedItem) {
+      this.products.push({
+        item: selectedItem,
+        quantity: null,
+        unit: "g",
+      });
+      this.selectedNewProduct = null;
+      this.selectShown.push(false);
+      this.isExpanded = true;
+    },
+    turnOnRowProductSelect(index) {
+      this.selectProductShown[index] = true;
+      this.selectedChangedProduct = this.products[index].item;
+      this.$nextTick(function () {
+        // unfortunately this seems to be the "official" way to focus on the select element:
+        this.$refs[`select${index}`].$refs.selectComponent.$refs.search.focus();
+      });
+    },
     turnOnRowSelect(index) {
       this.selectShown[index] = true;
       this.selectedChangedConstituent = this.constituents[index].item;
@@ -134,6 +175,14 @@ export default {
       this.constituents[index].item = selectedItem;
       this.selectShown[index] = false;
     },
+    swapProduct(selectedItem, index) {
+      this.products[index].item = selectedItem;
+      this.selectShown[index] = false;
+    },
+    removeProduct(index) {
+      this.products.splice(index, 1);
+      this.selectShown.splice(index, 1);
+    },
     removeConstituent(index) {
       this.constituents.splice(index, 1);
       this.selectShown.splice(index, 1);
@@ -201,7 +250,6 @@ export default {
   font-size: small;
   font-weight: 600;
   text-transform: uppercase;
-  margin-bottom: 0px;
 }
 
 .content-container {