[DRAFT] Add ability to tag items in any rich text field

.prettierrc

@@ -1 +1,2 @@
 printWidth: 100
+trailingComma: all

pydatalab/pydatalab/models/__init__.py

@@ -4,6 +4,7 @@
 
 from pydatalab.models.cells import Cell
 from pydatalab.models.collections import Collection
+from pydatalab.models.equipment import Equipment
 from pydatalab.models.files import File
 from pydatalab.models.people import Person
 from pydatalab.models.samples import Sample
@@ -13,6 +14,16 @@
     "samples": Sample,
     "starting_materials": StartingMaterial,
     "cells": Cell,
+    "equipment": Equipment,
 }
 
-__all__ = ("File", "Sample", "StartingMaterial", "Person", "Cell", "Collection", "ITEM_MODELS")
+__all__ = (
+    "File",
+    "Sample",
+    "StartingMaterial",
+    "Person",
+    "Cell",
+    "Collection",
+    "Equipment",
+    "ITEM_MODELS",
+)

pydatalab/pydatalab/models/equipment.py

@@ -0,0 +1,20 @@
+from typing import Optional
+
+from pydantic import Field
+
+from pydatalab.models.items import Item
+
+
+class Equipment(Item):
+    """A model for representing an experimental sample."""
+
+    type: str = Field("equipment", const="equipment", pattern="^equipment$")
+
+    serial_numbers: Optional[str]
+    """A string describing one or more serial numbers for the instrument."""
+
+    manufacturer: Optional[str]
+    """The manufacturer of this piece of equipment"""
+
+    location: Optional[str]
+    """Place where the equipment is located"""

pydatalab/pydatalab/routes/v0_1/items.py

@@ -74,6 +74,56 @@ def dereference_files(file_ids: List[Union[str, ObjectId]]) -> Dict[str, Dict]:
     return results
 
 
+def get_equipment_summary():
+    if not current_user.is_authenticated and not CONFIG.TESTING:
+        return (
+            jsonify(
+                status="error",
+                message="Authorization required to access chemical inventory.",
+            ),
+            401,
+        )
+
+    _project = {
+        "_id": 0,
+        "creators": {
+            "display_name": 1,
+            "contact_email": 1,
+        },
+        # "collections": {
+        #     "collection_id": 1,
+        #     "title": 1,
+        # },
+        "item_id": 1,
+        "name": 1,
+        "nblocks": {"$size": "$display_order"},
+        "characteristic_chemical_formula": 1,
+        "type": 1,
+        "date": 1,
+        "refcode": 1,
+        "location": 1,
+    }
+
+    items = [
+        doc
+        for doc in flask_mongo.db.items.aggregate(
+            [
+                {
+                    "$match": {
+                        "type": "equipment",
+                        **get_default_permissions(user_only=False),
+                    }
+                },
+                {"$project": _project},
+            ]
+        )
+    ]
+    return jsonify({"status": "success", "items": items})
+
+
+get_equipment_summary.methods = ("GET",)  # type: ignore
+
+
 def get_starting_materials():
     if not current_user.is_authenticated and not CONFIG.TESTING:
         return (
@@ -276,7 +326,10 @@ def search_items():
     if isinstance(types, str):
         types = types.split(",")  # should figure out how to parse as list automatically
 
-    match_obj = {"$text": {"$search": query}, **get_default_permissions(user_only=False)}
+    match_obj = {
+        "$text": {"$search": query},
+        **get_default_permissions(user_only=False),
+    }
     if types is not None:
         match_obj["type"] = {"$in": types}
 
@@ -360,7 +413,11 @@ def _create_sample(sample_dict: dict, copy_from_item_id: Optional[str] = None) -
             sample_dict = copied_doc
 
         elif copied_doc["type"] == "cells":
-            for component in ("positive_electrode", "negative_electrode", "electrolyte"):
+            for component in (
+                "positive_electrode",
+                "negative_electrode",
+                "electrolyte",
+            ):
                 if copied_doc.get(component):
                     existing_consituent_ids = [
                         constituent["item"].get("item_id", None)
@@ -402,7 +459,10 @@ def _create_sample(sample_dict: dict, copy_from_item_id: Optional[str] = None) -
         # locally for testing creator UI elements
         new_sample["creator_ids"] = [24 * "0"]
         new_sample["creators"] = [
-            {"display_name": "Public testing user", "contact_email": "[email protected]"}
+            {
+                "display_name": "Public testing user",
+                "contact_email": "[email protected]",
+            }
         ]
     else:
         new_sample["creator_ids"] = [current_user.person.immutable_id]
@@ -458,29 +518,36 @@ def _create_sample(sample_dict: dict, copy_from_item_id: Optional[str] = None) -
             400,
         )
 
+    sample_list_entry = {
+        "refcode": data_model.refcode,
+        "item_id": data_model.item_id,
+        "nblocks": 0,
+        "date": data_model.date,
+        "name": data_model.name,
+        "creator_ids": data_model.creator_ids,
+        # TODO: This workaround for creators & collections is still gross, need to figure this out properly
+        "creators": [json.loads(c.json(exclude_unset=True)) for c in data_model.creators]
+        if data_model.creators
+        else [],
+        "collections": [
+            json.loads(c.json(exclude_unset=True, exclude_none=True))
+            for c in data_model.collections
+        ]
+        if data_model.collections
+        else [],
+        "type": data_model.type,
+    }
+
+    # hack to let us use _create_sample() for equipment too. We probably want to make
+    # a more general create_item() to more elegantly handle different returns.
+    if data_model.type == "equipment":
+        sample_list_entry["location"] = data_model.location
+
     data = (
         {
             "status": "success",
             "item_id": data_model.item_id,
-            "sample_list_entry": {
-                "refcode": data_model.refcode,
-                "item_id": data_model.item_id,
-                "nblocks": 0,
-                "date": data_model.date,
-                "name": data_model.name,
-                "creator_ids": data_model.creator_ids,
-                # TODO: This workaround for creators & collections is still gross, need to figure this out properly
-                "creators": [json.loads(c.json(exclude_unset=True)) for c in data_model.creators]
-                if data_model.creators
-                else [],
-                "collections": [
-                    json.loads(c.json(exclude_unset=True, exclude_none=True))
-                    for c in data_model.collections
-                ]
-                if data_model.collections
-                else [],
-                "type": data_model.type,
-            },
+            "sample_list_entry": sample_list_entry,
         },
         201,  # 201: Created
     )
@@ -585,7 +652,12 @@ def get_item_data(item_id, load_blocks: bool = False):
     # retrieve the entry from the database:
     cursor = flask_mongo.db.items.aggregate(
         [
-            {"$match": {"item_id": item_id, **get_default_permissions(user_only=False)}},
+            {
+                "$match": {
+                    "item_id": item_id,
+                    **get_default_permissions(user_only=False),
+                }
+            },
             {"$lookup": creators_lookup()},
             {"$lookup": collections_lookup()},
             {"$lookup": files_lookup()},
@@ -708,7 +780,14 @@ def save_item():
     updated_data = request_json["data"]
 
     # These keys should not be updated here and cannot be modified by the user through this endpoint
-    for k in ("_id", "file_ObjectIds", "creators", "creator_ids", "item_id", "relationships"):
+    for k in (
+        "_id",
+        "file_ObjectIds",
+        "creators",
+        "creator_ids",
+        "item_id",
+        "relationships",
+    ):
         if k in updated_data:
             del updated_data[k]
 
@@ -827,6 +906,7 @@ def search_users():
 ENDPOINTS: Dict[str, Callable] = {
     "/samples/": get_samples,
     "/starting-materials/": get_starting_materials,
+    "/equipment/": get_equipment_summary,
     "/search-items/": search_items,
     "/search-users/": search_users,
     "/new-sample/": create_sample,

webapp/package.json

@@ -63,9 +63,9 @@
     "cypress": "^13.6.1",
     "eslint": "^7.32.0",
     "eslint-config-prettier": "^8.3.0",
-    "eslint-plugin-prettier": "^4.0.0",
+    "eslint-plugin-prettier": "^5.0.0",
     "eslint-plugin-vue": "^8.0.3",
-    "prettier": "^2.4.1",
+    "prettier": "3.0.3",
     "typescript": "~3.9.3",
     "web-worker": "^1.2.0"
   }