Improving location support

pydatalab/schemas/cell.json

@@ -1221,6 +1221,19 @@
       "title": "Display Order",
       "type": "array"
     },
+    "location": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "description": "The place where the item is located.",
+      "title": "Location"
+    },
     "collections": {
       "description": "Inlined info for the collections associated with this item.",
       "items": {

pydatalab/schemas/equipment.json

@@ -1057,6 +1057,19 @@
       "title": "Display Order",
       "type": "array"
     },
+    "location": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "description": "The place where the item is located.",
+      "title": "Location"
+    },
     "collections": {
       "description": "Inlined info for the collections associated with this item.",
       "items": {
@@ -1306,19 +1319,6 @@
       "description": "The manufacturer of this piece of equipment",
       "title": "Manufacturer"
     },
-    "location": {
-      "anyOf": [
-        {
-          "type": "string"
-        },
-        {
-          "type": "null"
-        }
-      ],
-      "default": null,
-      "description": "Place where the equipment is located",
-      "title": "Location"
-    },
     "contact": {
       "anyOf": [
         {

pydatalab/schemas/sample.json

@@ -1330,6 +1330,19 @@
       "title": "Display Order",
       "type": "array"
     },
+    "location": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "description": "The place where the item is located.",
+      "title": "Location"
+    },
     "collections": {
       "description": "Inlined info for the collections associated with this item.",
       "items": {

pydatalab/schemas/startingmaterial.json

@@ -1189,6 +1189,37 @@
   },
   "description": "A model for representing an experimental sample, based on the connection\nwith cheminventory.net, which mixes container-level and substance-level\ninformation.",
   "properties": {
+    "blocks_obj": {
+      "additionalProperties": {
+        "$ref": "#/$defs/DataBlockResponse"
+      },
+      "default": {},
+      "description": "A mapping from block ID to block data.",
+      "title": "Blocks Obj",
+      "type": "object"
+    },
+    "display_order": {
+      "default": [],
+      "description": "The order in which to display block data in the UI.",
+      "items": {
+        "type": "string"
+      },
+      "title": "Display Order",
+      "type": "array"
+    },
+    "location": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "description": "The place where the container is located.",
+      "title": "Location"
+    },
     "chemform": {
       "anyOf": [
         {
@@ -1313,24 +1344,6 @@
       "description": "Free-text details of the procedure applied to synthesise the sample",
       "title": "Synthesis Description"
     },
-    "blocks_obj": {
-      "additionalProperties": {
-        "$ref": "#/$defs/DataBlockResponse"
-      },
-      "default": {},
-      "description": "A mapping from block ID to block data.",
-      "title": "Blocks Obj",
-      "type": "object"
-    },
-    "display_order": {
-      "default": [],
-      "description": "The order in which to display block data in the UI.",
-      "items": {
-        "type": "string"
-      },
-      "title": "Display Order",
-      "type": "array"
-    },
     "collections": {
       "description": "Inlined info for the collections associated with this item.",
       "items": {
@@ -1646,19 +1659,6 @@
       "description": "Supplier or manufacturer of the chemical.",
       "title": "Supplier"
     },
-    "location": {
-      "anyOf": [
-        {
-          "type": "string"
-        },
-        {
-          "type": "null"
-        }
-      ],
-      "default": null,
-      "description": "The place where the container is located.",
-      "title": "Location"
-    },
     "comment": {
       "anyOf": [
         {

pydatalab/src/pydatalab/models/equipment.py

@@ -19,9 +19,6 @@ class Equipment(Item):
     manufacturer: str | None = None
     """The manufacturer of this piece of equipment"""
 
-    location: str | None = None
-    """Place where the equipment is located"""
-
     contact: str | None = None
     """Contact information for equipment (e.g., email address or phone number)."""
 

pydatalab/src/pydatalab/models/items.py

@@ -6,6 +6,7 @@
 from pydatalab.models.files import File
 from pydatalab.models.traits import (
     HasBlocks,
+    HasLocation,
     HasOwner,
     HasRevisionControl,
     IsCollectable,
@@ -18,7 +19,15 @@
 )
 
 
-class Item(Entry, HasOwner, HasRevisionControl, IsCollectable, HasBlocks, abc.ABC):
+class Item(
+    Entry,
+    HasOwner,
+    HasRevisionControl,
+    IsCollectable,
+    HasLocation,
+    HasBlocks,
+    abc.ABC,
+):
     """The generic model for data types that will be exposed with their own named endpoints."""
 
     refcode: Refcode | None = None

pydatalab/src/pydatalab/models/starting_materials.py

@@ -3,11 +3,11 @@
 from pydantic import Field
 
 from pydatalab.models.items import Item
-from pydatalab.models.traits import HasSubstanceInfo, HasSynthesisInfo
+from pydatalab.models.traits import HasLocation, HasSubstanceInfo, HasSynthesisInfo
 from pydatalab.models.utils import IsoformatDateTime, StartingMaterialsStatus
 
 
-class StartingMaterial(Item, HasSynthesisInfo, HasSubstanceInfo):
+class StartingMaterial(Item, HasSynthesisInfo, HasSubstanceInfo, HasLocation):
     """A model for representing an experimental sample, based on the connection
     with cheminventory.net, which mixes container-level and substance-level
     information.

pydatalab/src/pydatalab/models/traits.py

@@ -13,6 +13,7 @@
     "IsCollectable",
     "HasSynthesisInfo",
     "HasSubstanceInfo",
+    "HasLocation",
 )
 
 
@@ -229,3 +230,8 @@ def add_molar_mass(cls, v, info):
                 return None
 
         return v
+
+
+class HasLocation(BaseModel):
+    location: str | None = Field(alias="Location")
+    """The place where the item is located."""

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

@@ -1809,3 +1809,26 @@ def get_access_token_info(refcode: str):
         ), 200
     else:
         return jsonify({"status": "success", "has_token": False}), 200
+
+
+@ITEMS.route("/locations", methods=["GET"])
+def get_locations_for_items():
+    items = flask_mongo.db.items.distinct(
+        "location",
+        {
+            "location": {"$ne": None},
+            **get_default_permissions(user_only=False),
+        },
+    )
+    flat_locations = list(items)
+    nested_locations = {}
+    for location_locators in flat_locations:
+        comprising_locations = location_locators.split(">")
+        curr_dict = nested_locations
+        for location in comprising_locations:
+            location = location.strip()
+            if location not in curr_dict:
+                curr_dict[location] = {}
+            curr_dict = curr_dict[location]
+
+    return jsonify({"flat_locations": flat_locations, "nested_locations": nested_locations}), 200

pydatalab/tests/server/conftest.py

@@ -7,6 +7,7 @@
 
 from pydatalab.models import Cell, Collection, Equipment, Sample, StartingMaterial
 from pydatalab.models.people import AccountStatus
+from pydatalab.mongo import flask_mongo
 
 TEST_DATABASE_NAME = "__datalab-testing__"
 
@@ -609,6 +610,24 @@ def _insert_and_cleanup_item_from_model(model):
     flask_mongo.db.items.delete_one({"refcode": model.refcode})
 
 
+@pytest.fixture(scope="function", name="item_creator")
+def fixture_item_creator():
+    ref_codes_to_remove = []
+
+    def _insert_item_from_model(model):
+        from pydatalab.models.utils import generate_unique_refcode
+        from pydatalab.mongo import flask_mongo
+
+        refcode = generate_unique_refcode()
+        model.refcode = refcode
+        flask_mongo.db.items.insert_one(model.model_dump(exclude_unset=False))
+        ref_codes_to_remove.append(refcode)
+        return model
+
+    yield _insert_item_from_model
+    flask_mongo.db.items.delete_many({"refcode": {"$in": ref_codes_to_remove}})
+
+
 @pytest.fixture(scope="module", name="insert_default_sample")
 def fixture_insert_default_sample(default_sample):
     yield from _insert_and_cleanup_item_from_model(default_sample)