Merge branch 'main' into bc/components_test

.github/dependabot.yml

@@ -7,7 +7,6 @@ updates:
     day: monday
     time: "05:43"
   target-branch: main
-  versioning-strategy: lockfile-only
   labels:
   - dependency_updates
   groups:

.github/workflows/ci.yml

@@ -26,21 +26,21 @@ jobs:
         with:
           python-version: "3.10"
 
-      - name: Set up uv (latest)
-        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "0.4.x"
+          enable-cache: true
 
       - name: Install dependencies
         working-directory: ./pydatalab
         run: |
-          uv venv
-          uv pip install -r requirements/requirements-all-dev.txt
-          uv pip install -e '.[all, dev]'
+          uv sync --all-extras
 
       - name: Run pre-commit
         working-directory: ./pydatalab
         run: |
-          source .venv/bin/activate
-          pre-commit run --all-files --show-diff-on-failure
+          uv run pre-commit run --all-files --show-diff-on-failure
 
   pytest:
     name: Run Python unit tests
@@ -74,21 +74,21 @@ jobs:
         run: |
           wget https://fastdl.mongodb.org/tools/db/mongodb-database-tools-ubuntu2204-x86_64-100.9.0.deb && sudo apt install ./mongodb-database-tools-*-100.9.0.deb
 
-      - name: Set up uv (latest)
-        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "0.4.x"
+          enable-cache: true
 
       - name: Install locked versions of dependencies
         working-directory: ./pydatalab
         run: |
-          uv venv
-          uv pip install -r requirements/requirements-all-dev.txt
-          uv pip install -e '.[all, dev]'
+          uv sync --all-extras
 
       - name: Run all tests
         working-directory: ./pydatalab
         run: |
-          source .venv/bin/activate
-          pytest -rs -vvv --cov-report=term --cov-report=xml --cov ./pydatalab ./tests
+          uv run pytest -rs -vvv --cov-report=term --cov-report=xml --cov ./pydatalab ./tests
 
       - name: Upload coverage to Codecov
         if: matrix.python-version == '3.10' && github.repository == 'datalab-org/datalab'

INSTALL.md

@@ -178,11 +178,16 @@ Finally, recreate the lock files with:
 ```shell
 uv pip compile pyproject.toml -o requirements/requirements-all-dev.txt --extra all --extra dev
 uv pip compile pyproject.toml -o requirements/requirements-all.txt --extra all
+uv lock
 ```
 
 You should then inspect the changes to the requirements files (only your new
 package and its subdependencies should have been added) and commit the changes.
 
+> Regenerating the `Pipfile.lock` will not be necessary for long, but in this
+> case it can be synced with the requirements.txt files via `pipenv install -r requirements/requirements-all-dev.txt`,
+> and the resulting `Pipfile.lock` can be committed to the repository.
+
 ### Test server authentication/authorisation
 
 There are two approaches to authentication when developing *datalab* features locally.

pydatalab/pydatalab/routes/v0_1/collections.py

@@ -1,6 +1,7 @@
 import datetime
 import json
 
+from bson import ObjectId
 from flask import Blueprint, jsonify, request
 from flask_login import current_user
 from pydantic import ValidationError
@@ -325,3 +326,58 @@ def search_collections():
     ]
 
     return jsonify({"status": "success", "data": list(cursor)}), 200
+
+
+@COLLECTIONS.route("/collections/<collection_id>", methods=["POST"])
+def add_items_to_collection(collection_id):
+    data = request.get_json()
+    refcodes = data.get("data", {}).get("refcodes", [])
+
+    collection = flask_mongo.db.collections.find_one(
+        {"collection_id": collection_id, **get_default_permissions()}
+    )
+
+    if not collection:
+        return jsonify({"error": "Collection not found"}), 404
+
+    if not refcodes:
+        return jsonify({"error": "No item provided"}), 400
+
+    item_count = flask_mongo.db.items.count_documents(
+        {"refcode": {"$in": refcodes}, **get_default_permissions()}
+    )
+
+    if item_count == 0:
+        return jsonify({"error": "No matching items found"}), 404
+
+    update_result = flask_mongo.db.items.update_many(
+        {"refcode": {"$in": refcodes}, **get_default_permissions()},
+        {
+            "$addToSet": {
+                "relationships": {
+                    "description": "Is a member of",
+                    "relation": None,
+                    "type": "collections",
+                    "immutable_id": ObjectId(collection["_id"]),
+                    "item_id": None,
+                    "refcode": None,
+                }
+            }
+        },
+    )
+
+    if update_result.matched_count == 0:
+        return (jsonify({"status": "error", "message": "Unable to add to collection."}), 400)
+
+    if update_result.modified_count == 0:
+        return (
+            jsonify(
+                {
+                    "status": "success",
+                    "message": "No update was performed",
+                }
+            ),
+            200,
+        )
+
+    return (jsonify({"status": "success"}), 200)

pydatalab/pydatalab/routes/v0_1/items.py

@@ -129,6 +129,7 @@ def get_starting_materials():
                         "date": 1,
                         "chemform": 1,
                         "name": 1,
+                        "type": 1,
                         "chemical_purity": 1,
                         "supplier": 1,
                         "location": 1,
@@ -300,7 +301,8 @@ def search_items():
     nresults = request.args.get("nresults", default=100, type=int)
     types = request.args.get("types", default=None)
     if isinstance(types, str):
-        types = types.split(",")  # should figure out how to parse as list automatically
+        # should figure out how to parse as list automatically
+        types = types.split(",")
 
     match_obj = {
         "$text": {"$search": query},
@@ -428,10 +430,10 @@ def _create_sample(
         raise RuntimeError("Invalid type")
     model = ITEM_MODELS[type_]
 
-    ## the following code was used previously to explicitely check schema properties.
-    ## it doesn't seem to be necessary now, with extra = "ignore" turned on in the pydantic models,
-    ## and it breaks in instances where the models use aliases (e.g., in the starting_material model)
-    ## so we are taking it out now, but leaving this comment in case it needs to be reverted.
+    # the following code was used previously to explicitely check schema properties.
+    # it doesn't seem to be necessary now, with extra = "ignore" turned on in the pydantic models,
+    # and it breaks in instances where the models use aliases (e.g., in the starting_material model)
+    # so we are taking it out now, but leaving this comment in case it needs to be reverted.
     # schema = model.schema()
     # new_sample = {k: sample_dict[k] for k in schema["properties"] if k in sample_dict}
     new_sample = sample_dict