Adding version control to samples, starting materials and cells

pydatalab/pyproject.toml

@@ -27,6 +27,7 @@ dependencies = [
     "pint ~= 0.24",
     "pandas[excel] ~= 2.2",
     "pymongo ~= 4.7",
+    "deepdiff ~= 8.1",
 ]
 
 [project.urls]

pydatalab/schemas/cell.json

@@ -36,6 +36,11 @@
       "title": "Revisions",
       "type": "object"
     },
+    "version": {
+      "title": "Version",
+      "default": 1,
+      "type": "integer"
+    },
     "creator_ids": {
       "title": "Creator Ids",
       "default": [],
@@ -525,6 +530,11 @@
           "title": "Revisions",
           "type": "object"
         },
+        "version": {
+          "title": "Version",
+          "default": 1,
+          "type": "integer"
+        },
         "creator_ids": {
           "title": "Creator Ids",
           "default": [],

pydatalab/schemas/equipment.json

@@ -36,6 +36,11 @@
       "title": "Revisions",
       "type": "object"
     },
+    "version": {
+      "title": "Version",
+      "default": 1,
+      "type": "integer"
+    },
     "creator_ids": {
       "title": "Creator Ids",
       "default": [],
@@ -489,6 +494,11 @@
           "title": "Revisions",
           "type": "object"
         },
+        "version": {
+          "title": "Version",
+          "default": 1,
+          "type": "integer"
+        },
         "creator_ids": {
           "title": "Creator Ids",
           "default": [],

pydatalab/schemas/sample.json

@@ -48,6 +48,11 @@
       "title": "Revisions",
       "type": "object"
     },
+    "version": {
+      "title": "Version",
+      "default": 1,
+      "type": "integer"
+    },
     "creator_ids": {
       "title": "Creator Ids",
       "default": [],
@@ -578,6 +583,11 @@
           "title": "Revisions",
           "type": "object"
         },
+        "version": {
+          "title": "Version",
+          "default": 1,
+          "type": "integer"
+        },
         "creator_ids": {
           "title": "Creator Ids",
           "default": [],

pydatalab/schemas/startingmaterial.json

@@ -48,6 +48,11 @@
       "title": "Revisions",
       "type": "object"
     },
+    "version": {
+      "title": "Version",
+      "default": 1,
+      "type": "integer"
+    },
     "creator_ids": {
       "title": "Creator Ids",
       "default": [],
@@ -631,6 +636,11 @@
           "title": "Revisions",
           "type": "object"
         },
+        "version": {
+          "title": "Version",
+          "default": 1,
+          "type": "integer"
+        },
         "creator_ids": {
           "title": "Creator Ids",
           "default": [],

pydatalab/src/pydatalab/models/traits.py

@@ -22,6 +22,9 @@ class HasRevisionControl(BaseModel):
     revisions: dict[int, Any] | None = None
     """An optional mapping from old revision numbers to the model state at that revision."""
 
+    version: int = 1
+    """The version number used by the version control system for tracking snapshots."""
+
 
 class HasBlocks(BaseModel):
     blocks_obj: dict[str, DataBlockResponse] = Field({})

pydatalab/src/pydatalab/mongo.py

@@ -117,6 +117,11 @@ def create_default_indices(
         - An index over item type,
         - A unique index over `item_id` and `refcode`.
         - A text index over user names and identities.
+        - Version control indexes:
+            - Index on item_versions.refcode for fast version history lookup
+            - Index on item_versions.user_id for fast user contribution queries
+            - Compound index on (refcode, version_number) for sorted version history
+            - Unique index on version_counters.refcode for atomic version numbering
 
     Parameters:
         background: If true, indexes will be created as background jobs.
@@ -208,4 +213,16 @@ def create_user_fts():
         db.users.drop_index(user_fts_name)
         ret += create_user_fts()
 
+    # Version control indexes
+    ret += db.item_versions.create_index("refcode", name="version refcode", background=background)
+    ret += db.item_versions.create_index("user_id", name="version user_id", background=background)
+    ret += db.item_versions.create_index(
+        [("refcode", pymongo.ASCENDING), ("version_number", pymongo.DESCENDING)],
+        name="refcode and version number",
+        background=background,
+    )
+    ret += db.version_counters.create_index(
+        "refcode", unique=True, name="unique refcode counter", background=background
+    )
+
     return ret