linkml-store 0.1.8__tar.gz → 0.1.10__tar.gz

linkml_store-0.1.10/PKG-INFO

@@ -0,0 +1,138 @@
+Metadata-Version: 2.1
+Name: linkml-store
+Version: 0.1.10
+Summary: linkml-store
+License: MIT
+Author: Author 1
+Author-email: author@org.org
+Requires-Python: >=3.9, !=2.7.*, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*, !=3.7.*, !=3.8.*
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Provides-Extra: analytics
+Provides-Extra: app
+Provides-Extra: chromadb
+Provides-Extra: fastapi
+Provides-Extra: h5py
+Provides-Extra: llm
+Provides-Extra: map
+Provides-Extra: mongodb
+Provides-Extra: pyarrow
+Provides-Extra: renderer
+Provides-Extra: tests
+Provides-Extra: validation
+Requires-Dist: black (>=24.0.0) ; extra == "tests"
+Requires-Dist: chromadb ; extra == "chromadb"
+Requires-Dist: click
+Requires-Dist: duckdb (>=0.10.1,<0.11.0)
+Requires-Dist: duckdb-engine (>=0.11.2)
+Requires-Dist: fastapi ; extra == "fastapi"
+Requires-Dist: h5py ; extra == "h5py"
+Requires-Dist: jinja2 (>=3.1.4,<4.0.0)
+Requires-Dist: jsonlines (>=4.0.0,<5.0.0)
+Requires-Dist: linkml ; extra == "validation"
+Requires-Dist: linkml-runtime (>=1.8.0rc2)
+Requires-Dist: linkml_map ; extra == "map"
+Requires-Dist: linkml_renderer ; extra == "renderer"
+Requires-Dist: llm ; extra == "llm"
+Requires-Dist: matplotlib ; extra == "analytics"
+Requires-Dist: pandas (>=2.2.1) ; extra == "analytics"
+Requires-Dist: plotly ; extra == "analytics"
+Requires-Dist: pyarrow ; extra == "pyarrow"
+Requires-Dist: pydantic (>=2.0.0,<3.0.0)
+Requires-Dist: pymongo ; extra == "mongodb"
+Requires-Dist: pystow (>=0.5.4,<0.6.0)
+Requires-Dist: seaborn ; extra == "analytics"
+Requires-Dist: sqlalchemy
+Requires-Dist: streamlit (>=1.32.2,<2.0.0) ; extra == "app"
+Requires-Dist: uvicorn ; extra == "fastapi"
+Description-Content-Type: text/markdown
+
+# linkml-store
+
+An AI-ready data management and integration platform. LinkML-Store
+provides an abstraction layer over multiple different backends
+(including DuckDB, MongoDB, and local filesystems), allowing for
+common query, index, and storage operations.
+
+For full documentation, see [https://linkml.io/linkml-store/](https://linkml.io/linkml-store/)
+
+__Warning__ LinkML-Store is still undergoing changes and refactoring,
+APIs and command line options are subject to change!
+
+## Quick Start
+
+Install, add data, query it:
+
+```
+pip install linkml-store[all]
+linkml-store -d duckdb:///db/my.db -c persons insert data/*.json
+linkml-store -d duckdb:///db/my.db -c persons query -w "occupation: Bricklayer"
+```
+
+Index it, search it:
+
+```
+linkml-store -d duckdb:///db/my.db -c persons index -t llm
+linkml-store -d duckdb:///db/my.db -c persons search "all persons employed in construction"
+```
+
+Validate it:
+
+```
+linkml-store -d duckdb:///db/my.db -c persons validate
+```
+
+## Basic usage
+
+* [Command Line](https://linkml.io/linkml-store/tutorials/Command-Line-Tutorial.html)
+* [Python](https://linkml.io/linkml-store/tutorials/Python-Tutorial.html)
+* API
+* Streamlit applications
+
+## Features
+
+### Multiple Adapters
+
+LinkML-Store is designed to work with multiple backends, giving a common abstraction layer
+
+* [MongoDB](https://linkml.io/linkml-store/how-to/Use-MongoDB.html)
+* [DuckDB](https://linkml.io/linkml-store/tutorials/Python-Tutorial.html)
+* [Solr](https://linkml.io/linkml-store/how-to/Query-Solr-using-CLI.html)
+* Filesystem
+
+Coming soon: any RDBMS, any triplestore, Neo4J, HDF5-based stores, ChromaDB/Vector dbs ...
+
+The intent is to give a union of all features of each backend. For
+example, analytic faceted queries are provided for *all* backends, not
+just Solr.
+
+### Composable indexes
+
+Many backends come with their own indexing and search
+schemes. Classically this was Lucene-based indexes, now it is semantic
+search using LLM embeddings.
+
+LinkML store treats indexing as an orthogonal concern - you can
+compose different indexing schemes with different backends. You don't
+need to have a vector database to run embedding search!
+
+See [How to Use-Semantic-Search](https://linkml.io/linkml-store/how-to/Use-Semantic-Search.html)
+
+### Validation
+
+LinkML-Store is backed by [LinkML](https://linkml.io), which allows
+for powerful expressive structural and semantic constraints.
+
+See [Indexing JSON](https://linkml.io/linkml-store/how-to/Index-Phenopackets.html)
+
+and [Referential Integrity](https://linkml.io/linkml-store/how-to/Check-Referential-Integrity.html)
+
+
+## Background
+
+See [these slides](https://docs.google.com/presentation/d/e/2PACX-1vSgtWUNUW0qNO_ZhMAGQ6fYhlXZJjBNMYT0OiZz8DDx8oj7iG9KofRs6SeaMXBBOICGknoyMG2zaHnm/embed?start=false&loop=false&delayms=3000) for more details
+

linkml_store-0.1.10/README.md

@@ -0,0 +1,84 @@
+# linkml-store
+
+An AI-ready data management and integration platform. LinkML-Store
+provides an abstraction layer over multiple different backends
+(including DuckDB, MongoDB, and local filesystems), allowing for
+common query, index, and storage operations.
+
+For full documentation, see [https://linkml.io/linkml-store/](https://linkml.io/linkml-store/)
+
+__Warning__ LinkML-Store is still undergoing changes and refactoring,
+APIs and command line options are subject to change!
+
+## Quick Start
+
+Install, add data, query it:
+
+```
+pip install linkml-store[all]
+linkml-store -d duckdb:///db/my.db -c persons insert data/*.json
+linkml-store -d duckdb:///db/my.db -c persons query -w "occupation: Bricklayer"
+```
+
+Index it, search it:
+
+```
+linkml-store -d duckdb:///db/my.db -c persons index -t llm
+linkml-store -d duckdb:///db/my.db -c persons search "all persons employed in construction"
+```
+
+Validate it:
+
+```
+linkml-store -d duckdb:///db/my.db -c persons validate
+```
+
+## Basic usage
+
+* [Command Line](https://linkml.io/linkml-store/tutorials/Command-Line-Tutorial.html)
+* [Python](https://linkml.io/linkml-store/tutorials/Python-Tutorial.html)
+* API
+* Streamlit applications
+
+## Features
+
+### Multiple Adapters
+
+LinkML-Store is designed to work with multiple backends, giving a common abstraction layer
+
+* [MongoDB](https://linkml.io/linkml-store/how-to/Use-MongoDB.html)
+* [DuckDB](https://linkml.io/linkml-store/tutorials/Python-Tutorial.html)
+* [Solr](https://linkml.io/linkml-store/how-to/Query-Solr-using-CLI.html)
+* Filesystem
+
+Coming soon: any RDBMS, any triplestore, Neo4J, HDF5-based stores, ChromaDB/Vector dbs ...
+
+The intent is to give a union of all features of each backend. For
+example, analytic faceted queries are provided for *all* backends, not
+just Solr.
+
+### Composable indexes
+
+Many backends come with their own indexing and search
+schemes. Classically this was Lucene-based indexes, now it is semantic
+search using LLM embeddings.
+
+LinkML store treats indexing as an orthogonal concern - you can
+compose different indexing schemes with different backends. You don't
+need to have a vector database to run embedding search!
+
+See [How to Use-Semantic-Search](https://linkml.io/linkml-store/how-to/Use-Semantic-Search.html)
+
+### Validation
+
+LinkML-Store is backed by [LinkML](https://linkml.io), which allows
+for powerful expressive structural and semantic constraints.
+
+See [Indexing JSON](https://linkml.io/linkml-store/how-to/Index-Phenopackets.html)
+
+and [Referential Integrity](https://linkml.io/linkml-store/how-to/Check-Referential-Integrity.html)
+
+
+## Background
+
+See [these slides](https://docs.google.com/presentation/d/e/2PACX-1vSgtWUNUW0qNO_ZhMAGQ6fYhlXZJjBNMYT0OiZz8DDx8oj7iG9KofRs6SeaMXBBOICGknoyMG2zaHnm/embed?start=false&loop=false&delayms=3000) for more details

{linkml_store-0.1.8 → linkml_store-0.1.10}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "linkml-store"
-version = "0.1.8"
+version = "0.1.10"
 description = "linkml-store"
 authors = ["Author 1 <author@org.org>"]
 license = "MIT"
@@ -10,7 +10,7 @@ readme = "README.md"
 python = "^3.9, !=3.9.7"
 click = "*"
 pydantic = "^2.0.0"
-linkml-runtime = "^1.7.5"
+linkml-runtime = ">=1.8.0rc2"
 streamlit = { version = "^1.32.2", optional = true }
 sqlalchemy = "*"
 duckdb = "^0.10.1"
@@ -23,11 +23,16 @@ black = { version=">=24.0.0", optional = true }
 llm = { version="*", optional = true }
 pymongo = { version="*", optional = true }
 chromadb = { version="*", optional = true }
+pyarrow = { version="*", optional = true }
 h5py = { version="*", optional = true }
 linkml = { version="*", optional = true }
 linkml_map = { version="*", optional = true }
+linkml_renderer = { version="*", optional = true }
 pandas = ">=2.2.1"
 jinja2 = "^3.1.4"
+jsonlines = "^4.0.0"
+fastapi = { version="*", optional = true }
+uvicorn = { version="*", optional = true }
 
 [tool.poetry.group.dev.dependencies]
 pytest = {version = ">=7.1.2"}
@@ -43,6 +48,7 @@ furo = {version = "*"}
 nbsphinx = "*"
 jupyter = "*"
 jupysql = "*"
+papermill = "*"
 
 [tool.poetry.group.tests.dependencies]
 pytest = "^7.4.0"
@@ -60,11 +66,15 @@ llm = ["llm"]
 mongodb = ["pymongo"]
 chromadb = ["chromadb"]
 h5py = ["h5py"]
+pyarrow = ["pyarrow"]
 validation = ["linkml"]
 map = ["linkml_map"]
+renderer = ["linkml_renderer"]
+fastapi = ["fastapi", "uvicorn"]
 
 [tool.poetry.scripts]
 linkml-store = "linkml_store.cli:cli"
+linkml-store-api = "linkml_store.webapi.main:start"
 
 [tool.poetry-dynamic-versioning]
 enable = false
@@ -127,7 +137,7 @@ skip = '.git,*.pdf,*.svg,./tests,pyproject.toml,*.dill,poetry.lock,*.ipynb'
 # Ignore table where words could be split across rows
 # Ignore shortcut specifications like [Ff]alse
 ignore-regex = '(\|.*\|.*\|.*\||\[[A-Z][a-z]\][a-z][a-z])'
-ignore-words-list = 'mater,connexion,infarction'
+ignore-words-list = 'mater,connexion,infarction,nin'
 count = ""
 quiet-level = 3
 

{linkml_store-0.1.8 → linkml_store-0.1.10}/src/linkml_store/api/client.py

@@ -9,6 +9,7 @@ from linkml_store.api import Database
 from linkml_store.api.config import ClientConfig
 from linkml_store.api.stores.chromadb.chromadb_database import ChromaDBDatabase
 from linkml_store.api.stores.duckdb.duckdb_database import DuckDBDatabase
+from linkml_store.api.stores.filesystem.filesystem_database import FileSystemDatabase
 from linkml_store.api.stores.mongodb.mongodb_database import MongoDBDatabase
 from linkml_store.api.stores.solr.solr_database import SolrDatabase
 
@@ -20,6 +21,7 @@ HANDLE_MAP = {
     "solr": SolrDatabase,
     "mongodb": MongoDBDatabase,
     "chromadb": ChromaDBDatabase,
+    "file": FileSystemDatabase,
 }
 
 
@@ -96,7 +98,7 @@ class Client:
         """
         return self.metadata.base_dir
 
-    def from_config(self, config: Union[ClientConfig, str, Path], base_dir=None, **kwargs):
+    def from_config(self, config: Union[ClientConfig, dict, str, Path], base_dir=None, **kwargs):
         """
         Create a client from a configuration.
 
@@ -116,11 +118,13 @@ class Client:
         :return:
 
         """
+        if isinstance(config, dict):
+            config = ClientConfig(**config)
         if isinstance(config, Path):
             config = str(config)
         if isinstance(config, str):
-            if not base_dir:
-                base_dir = Path(config).parent
+            # if not base_dir:
+            #    base_dir = Path(config).parent
             parsed_obj = yaml.safe_load(open(config))
             config = ClientConfig(**parsed_obj)
         self.metadata = config
@@ -131,8 +135,15 @@ class Client:
 
     def _initialize_databases(self, **kwargs):
         for name, db_config in self.metadata.databases.items():
-            handle = db_config.handle.format(base_dir=self.base_dir)
+            base_dir = self.base_dir
+            logger.info(f"Initializing database: {name}, base_dir: {base_dir}")
+            if not base_dir:
+                base_dir = Path.cwd()
+                logger.info(f"Using current working directory: {base_dir}")
+            handle = db_config.handle.format(base_dir=base_dir)
             db_config.handle = handle
+            if db_config.schema_location:
+                db_config.schema_location = db_config.schema_location.format(base_dir=base_dir)
             db = self.attach_database(handle, alias=name, **kwargs)
             db.from_config(db_config)
 

{linkml_store-0.1.8 → linkml_store-0.1.10}/src/linkml_store/api/collection.py

@@ -4,16 +4,19 @@ import hashlib
 import logging
 from collections import defaultdict
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Dict, Iterator, List, Optional, TextIO, Type, Union
+from typing import TYPE_CHECKING, Any, ClassVar, Dict, Generic, Iterator, List, Optional, TextIO, Tuple, Type, Union
 
 import numpy as np
+from linkml_runtime import SchemaView
 from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition
 from linkml_runtime.linkml_model.meta import ArrayExpression
 from pydantic import BaseModel
 
+from linkml_store.api.types import DatabaseType
 from linkml_store.index import get_indexer
 from linkml_store.utils.format_utils import load_objects
 from linkml_store.utils.object_utils import clean_empties
+from linkml_store.utils.patch_utils import PatchDict, apply_patches_to_list, patches_from_objects_lists
 
 try:
     from linkml.validator.report import ValidationResult
@@ -36,7 +39,7 @@ IDENTIFIER = str
 FIELD_NAME = str
 
 
-class Collection:
+class Collection(Generic[DatabaseType]):
     """
     A collection is an organized set of objects of the same or similar type.
 
@@ -56,11 +59,12 @@ class Collection:
     """
 
     # name: str
-    parent: Optional["Database"] = None
+    parent: Optional[DatabaseType] = None
     _indexers: Optional[Dict[str, Indexer]] = None
     # hidden: Optional[bool] = False
 
     metadata: Optional[CollectionConfig] = None
+    default_index_name: ClassVar[str] = "simple"
 
     def __init__(
         self, name: str, parent: Optional["Database"] = None, metadata: Optional[CollectionConfig] = None, **kwargs
@@ -197,6 +201,10 @@ class Collection:
         """
         raise NotImplementedError
 
+    def _post_insert_hook(self, objs: List[OBJECT], **kwargs):
+        patches = [{"op": "add", "path": "/0", "value": obj} for obj in objs]
+        self._broadcast(patches, **kwargs)
+
     def delete(self, objs: Union[OBJECT, List[OBJECT]], **kwargs) -> Optional[int]:
         """
         Delete one or more objects from the collection.
@@ -301,7 +309,7 @@ class Collection:
 
     def query_facets(
         self, where: Optional[Dict] = None, facet_columns: List[str] = None, facet_limit=DEFAULT_FACET_LIMIT, **kwargs
-    ) -> Dict[str, Dict[str, int]]:
+    ) -> Dict[str, List[Tuple[Any, int]]]:
         """
         Run a query to get facet counts for one or more columns.
 
@@ -319,7 +327,7 @@ class Collection:
         :param query: A Query object representing the base query.
         :param facet_columns: A list of column names to get facet counts for.
         :param facet_limit:
-        :return: A dictionary where keys are column names and values are pandas DataFrames
+        :return: A dictionary where keys are column names and values are tuples
                  containing the facet counts for each unique value in the respective column.
         """
         raise NotImplementedError
@@ -414,7 +422,30 @@ class Collection:
         **kwargs,
     ) -> QueryResult:
         """
-        Search the collection using a full-text search index.
+        Search the collection using a text-based index index.
+
+        Example:
+
+        >>> from linkml_store import Client
+        >>> from linkml_store.utils.format_utils import load_objects
+        >>> client = Client()
+        >>> db = client.attach_database("duckdb")
+        >>> collection = db.create_collection("Country")
+        >>> objs = load_objects("tests/input/countries/countries.jsonl")
+        >>> collection.insert(objs)
+
+        Now let's index, using the simple trigram-based index
+
+        >>> index = get_indexer("simple")
+        >>> collection.attach_indexer(index)
+
+        Now let's find all objects:
+
+        >>> qr = collection.search("France")
+        >>> score, top_obj = qr.ranked_rows[0]
+        >>> assert score > 0.1
+        >>> top_obj["code"]
+        'FR'
 
         :param query:
         :param where:
@@ -424,12 +455,18 @@ class Collection:
         :return:
         """
         if index_name is None:
-            if len(self._indexers) == 1:
-                index_name = list(self._indexers.keys())[0]
+            if len(self.indexers) == 1:
+                index_name = list(self.indexers.keys())[0]
             else:
-                raise ValueError("Multiple indexes found. Please specify an index name.")
+                logger.warning("Multiple indexes found. Using default index.")
+                index_name = self.default_index_name
         ix_coll = self.parent.get_collection(self._index_collection_name(index_name))
-        ix = self._indexers.get(index_name)
+        if index_name not in self.indexers:
+            ix = get_indexer(index_name)
+            if not self._indexers:
+                self._indexers = {}
+            self._indexers[index_name] = ix
+        ix = self.indexers.get(index_name)
         if not ix:
             raise ValueError(f"No index named {index_name}")
         qr = ix_coll.find(where=where, limit=-1, **kwargs)
@@ -446,7 +483,10 @@ class Collection:
     @property
     def is_internal(self) -> bool:
         """
-        Check if the collection is internal
+        Check if the collection is internal.
+
+        Internal collections are hidden by default. Examples of internal collections
+        include shadow "index" collections
 
         :return:
         """
@@ -462,6 +502,45 @@ class Collection:
         """
         Attach an index to the collection.
 
+        As an example, first let's create a collection in a database:
+
+        >>> from linkml_store import Client
+        >>> from linkml_store.utils.format_utils import load_objects
+        >>> client = Client()
+        >>> db = client.attach_database("duckdb")
+        >>> collection = db.create_collection("Country")
+        >>> objs = load_objects("tests/input/countries/countries.jsonl")
+        >>> collection.insert(objs)
+
+        We will create two indexes - one that indexes the whole object
+        (default behavior), the other one indexes the name only
+
+        >>> full_index = get_indexer("simple")
+        >>> full_index.name = "full"
+        >>> name_index = get_indexer("simple", text_template="{name}")
+        >>> name_index.name = "name"
+        >>> collection.attach_indexer(full_index)
+        >>> collection.attach_indexer(name_index)
+
+        Now let's find objects using the full index, using the string "France".
+        We expect the country France to be the top hit, but the score will
+        be less than zero because we did not match all fields in the object.
+
+        >>> qr = collection.search("France", index_name="full")
+        >>> score, top_obj = qr.ranked_rows[0]
+        >>> assert score > 0.1
+        >>> assert score < 0.5
+        >>> top_obj["code"]
+        'FR'
+
+        Now using the name index
+
+        >>> qr = collection.search("France", index_name="name")
+        >>> score, top_obj = qr.ranked_rows[0]
+        >>> assert score > 0.99
+        >>> top_obj["code"]
+        'FR'
+
         :param index:
         :param name:
         :param auto_index: Automatically index all objects in the collection
@@ -497,15 +576,18 @@ class Collection:
 
     def index_objects(self, objs: List[OBJECT], index_name: str, replace=False, **kwargs):
         """
-        Index a list of objects
+        Index a list of objects using a specified index.
+
+        By default, the indexed objects will be stored in a shadow
+        collection in the same database, with additional fields for the index vector
 
         :param objs:
-        :param index_name:
+        :param index_name: e.g. simple, llm
         :param replace:
         :param kwargs:
         :return:
         """
-        ix = self._indexers.get(index_name)
+        ix = self._indexers.get(index_name, None)
         if not ix:
             raise ValueError(f"No index named {index_name}")
         ix_coll_name = self._index_collection_name(index_name)
@@ -523,6 +605,7 @@ class Collection:
                 ix_coll.delete_where()
 
         ix_coll.insert(objects_with_ix, **kwargs)
+        ix_coll.commit()
 
     def list_index_names(self) -> List[str]:
         """
@@ -557,12 +640,22 @@ class Collection:
 
         :return:
         """
-        sv = self.parent.schema_view
+        sv: SchemaView = self.parent.schema_view
         if sv:
             cls = sv.get_class(self.target_class_name)
+            if cls and not cls.attributes:
+                if not sv.class_induced_slots(cls.name):
+                    for att in self._induce_attributes():
+                        cls.attributes[att.name] = att
+                    sv.set_modified()
             return cls
         return None
 
+    def _induce_attributes(self) -> List[SlotDefinition]:
+        result = self.find({}, limit=-1)
+        cd = self.induce_class_definition_from_objects(result.rows, max_sample_size=None)
+        return list(cd.attributes.values())
+
     @property
     def identifier_attribute_name(self) -> Optional[str]:
         """
@@ -579,6 +672,37 @@ class Collection:
                     return att.name
         return None
 
+    def set_identifier_attribute_name(self, name: str):
+        """
+        Set the name of the identifier attribute for the collection.
+
+        AKA the primary key.
+
+        :param name: The name of the identifier attribute.
+        """
+        cd = self.class_definition()
+        if not cd:
+            raise ValueError(f"Cannot find class definition for {self.target_class_name}")
+        id_att = None
+        candidates = []
+        sv: SchemaView = self.parent.schema_view
+        cls = sv.get_class(cd.name)
+        existing_id_slot = sv.get_identifier_slot(cls.name)
+        if existing_id_slot:
+            if existing_id_slot.name == name:
+                return
+            existing_id_slot.identifier = False
+        for att in cls.attributes.values():
+            candidates.append(att.name)
+            if att.name == name:
+                att.identifier = True
+                id_att = att
+            else:
+                att.identifier = False
+        if not id_att:
+            raise ValueError(f"No attribute found with name {name} in {candidates}")
+        sv.set_modified()
+
     def object_identifier(self, obj: OBJECT, auto=True) -> Optional[IDENTIFIER]:
         """
         Return the identifier for an object.
@@ -622,6 +746,8 @@ class Collection:
             for k, v in obj.items():
                 keys[k].append(v)
         for k, vs in keys.items():
+            if k == "_id":
+                continue
             multivalueds = []
             inlineds = []
             rngs = []
@@ -698,6 +824,39 @@ class Collection:
         """
         raise NotImplementedError
 
+    def apply_patches(self, patches: List[PatchDict], **kwargs):
+        """
+        Apply a patch to the collection.
+
+        Patches conform to the JSON Patch format,
+
+        :param patches:
+        :param kwargs:
+        :return:
+        """
+        all_objs = self.find(limit=-1).rows
+        primary_key = self.identifier_attribute_name
+        if not primary_key:
+            raise ValueError(f"No primary key for {self.target_class_name}")
+        new_objs = apply_patches_to_list(all_objs, patches, primary_key=primary_key, **kwargs)
+        self.replace(new_objs)
+
+    def diff(self, other: "Collection", **kwargs):
+        """
+        Diff two collections.
+
+        :param other:
+        :param kwargs:
+        :return:
+        """
+        src_objs = self.find(limit=-1).rows
+        tgt_objs = other.find(limit=-1).rows
+        primary_key = self.identifier_attribute_name
+        if not primary_key:
+            raise ValueError(f"No primary key for {self.target_class_name}")
+        patches_from_objects_lists(src_objs, tgt_objs, primary_key=primary_key)
+        return patches_from_objects_lists(src_objs, tgt_objs, primary_key=primary_key)
+
     def iter_validate_collection(self, **kwargs) -> Iterator["ValidationResult"]:
         """
         Validate the contents of the collection
@@ -717,3 +876,14 @@ class Collection:
         for obj in result.rows:
             obj = clean_empties(obj)
             yield from validator.iter_results(obj, class_name)
+
+    def commit(self):
+        """
+        Commit changes to the collection.
+
+        :return:
+        """
+        pass
+
+    def _broadcast(self, *args, **kwargs):
+        self.parent.broadcast(self, *args, **kwargs)