linkml-store 0.1.6__py3-none-any.whl → 0.1.8__py3-none-any.whl

linkml_store/index/implementations/llm_indexer.py

@@ -1,20 +1,34 @@
+import logging
+from pathlib import Path
 from typing import TYPE_CHECKING, List
 
 import numpy as np
 
+from linkml_store.api.config import CollectionConfig
 from linkml_store.index.indexer import INDEX_ITEM, Indexer
 
 if TYPE_CHECKING:
     import llm
 
 
+logger = logging.getLogger(__name__)
+
+
 class LLMIndexer(Indexer):
     """
-    A implementations index wraps the llm library
+    An indexer that wraps the llm library.
+
+    This indexer is used to convert text to vectors using the llm library.
+
+    >>> indexer = LLMIndexer(cached_embeddings_database="tests/input/llm_cache.db")
+    >>> vector = indexer.text_to_vector("hello")
     """
 
     embedding_model_name: str = "ada-002"
     _embedding_model: "llm.EmbeddingModel" = None
+    cached_embeddings_database: str = None
+    cached_embeddings_collection: str = None
+    cache_queries: bool = False
 
     @property
     def embedding_model(self):
@@ -24,21 +38,85 @@ class LLMIndexer(Indexer):
             self._embedding_model = llm.get_embedding_model(self.embedding_model_name)
         return self._embedding_model
 
-    def text_to_vector(self, text: str) -> INDEX_ITEM:
+    def text_to_vector(self, text: str, cache: bool = None, **kwargs) -> INDEX_ITEM:
         """
         Convert a text to an indexable object
 
+        >>> indexer = LLMIndexer(cached_embeddings_database="tests/input/llm_cache.db")
+        >>> vector = indexer.text_to_vector("hello")
+
         :param text:
         :return:
         """
-        return self.texts_to_vectors([text])[0]
+        return self.texts_to_vectors([text], cache=cache, **kwargs)[0]
 
-    def texts_to_vectors(self, texts: List[str]) -> List[INDEX_ITEM]:
+    def texts_to_vectors(self, texts: List[str], cache: bool = None, **kwargs) -> List[INDEX_ITEM]:
         """
         Use LLM to embed
 
+        >>> indexer = LLMIndexer(cached_embeddings_database="tests/input/llm_cache.db")
+        >>> vectors = indexer.texts_to_vectors(["hello", "goodbye"])
+
         :param texts:
         :return:
         """
-        embeddings = self.embedding_model.embed_multi(texts)
+        logging.info(f"Converting {len(texts)} texts to vectors")
+        model = self.embedding_model
+        if self.cached_embeddings_database and (cache is None or cache or self.cache_queries):
+            model_id = model.model_id
+            if not model_id:
+                raise ValueError("Model ID is required to cache embeddings")
+            db_path = Path(self.cached_embeddings_database)
+            coll_name = self.cached_embeddings_collection
+            if not coll_name:
+                coll_name = "all_embeddings"
+            from linkml_store import Client
+
+            embeddings_client = Client()
+            config = CollectionConfig(
+                name=coll_name,
+                type="Embeddings",
+                attributes={
+                    "text": {"range": "string"},
+                    "model_id": {"range": "string"},
+                    "embedding": {"range": "float", "array": {}},
+                },
+            )
+            embeddings_db = embeddings_client.get_database(f"duckdb:///{db_path}")
+            if coll_name in embeddings_db.list_collection_names():
+                # Load existing collection and use its model
+                embeddings_collection = embeddings_db.create_collection(coll_name, metadata=config)
+            else:
+                embeddings_collection = embeddings_db.create_collection(coll_name, metadata=config)
+            texts = list(texts)
+            embeddings = list([None] * len(texts))
+            uncached_texts = []
+            n = 0
+            for i in range(len(texts)):
+                # TODO: optimize this
+                text = texts[i]
+                logger.info(f"Looking for cached embedding for {text}")
+                r = embeddings_collection.find({"text": text, "model_id": model_id})
+                if r.num_rows:
+                    embeddings[i] = r.rows[0]["embedding"]
+                    n += 1
+                    logger.info("Found")
+                else:
+                    uncached_texts.append((text, i))
+                    logger.info("NOT Found")
+            logger.info(f"Found {n} cached embeddings")
+            if uncached_texts:
+                logger.info(f"Embedding {len(uncached_texts)} uncached texts")
+                uncached_texts, uncached_indices = zip(*uncached_texts)
+                uncached_embeddings = list(model.embed_multi(uncached_texts))
+                # TODO: combine into a single insert with multiple rows
+                for i, index in enumerate(uncached_indices):
+                    logger.debug(f"Indexing text at {i}")
+                    embeddings[index] = uncached_embeddings[i]
+                    embeddings_collection.insert(
+                        {"text": uncached_texts[i], "embedding": embeddings[index], "model_id": model_id}
+                    )
+        else:
+            logger.info(f"Embedding {len(texts)} texts")
+            embeddings = model.embed_multi(texts)
         return [np.array(v, dtype=float) for v in embeddings]

linkml_store/index/implementations/simple_indexer.py

@@ -15,7 +15,7 @@ class SimpleIndexer(Indexer):
     This uses a naive method to generate an index from text. It is not suitable for production use.
     """
 
-    def text_to_vector(self, text: str) -> INDEX_ITEM:
+    def text_to_vector(self, text: str, cache: bool = None, **kwargs) -> INDEX_ITEM:
         """
         This is a naive method purely for testing
 
@@ -39,5 +39,5 @@ class SimpleIndexer(Indexer):
 
             # Increment the count at the computed index
             vector[index] += 1.0
-        logger.info(f"Indexed text: {text} as {vector}")
+        logger.debug(f"Indexed text: {text} as {vector}")
         return vector

linkml_store/index/indexer.py

@@ -1,3 +1,5 @@
+import logging
+from enum import Enum
 from typing import Any, Callable, Dict, List, Optional, Tuple
 
 import numpy as np
@@ -5,6 +7,13 @@ from pydantic import BaseModel
 
 INDEX_ITEM = np.ndarray
 
+logger = logging.getLogger(__name__)
+
+
+class TemplateSyntaxEnum(str, Enum):
+    jinja2 = "jinja2"
+    fstring = "fstring"
+
 
 def cosine_similarity(vector1, vector2):
     dot_product = np.dot(vector1, vector2)
@@ -21,8 +30,9 @@ class Indexer(BaseModel):
     name: Optional[str] = None
     index_function: Optional[Callable] = None
     distance_function: Optional[Callable] = None
-    index_attributes: Optional[str] = None
+    index_attributes: Optional[List[str]] = None
     text_template: Optional[str] = None
+    text_template_syntax: Optional[TemplateSyntaxEnum] = None
     filter_nulls: Optional[bool] = True
     vector_default_length: Optional[int] = 1000
     index_field: Optional[str] = "__index__"
@@ -41,24 +51,25 @@ class Indexer(BaseModel):
         Convert a list of objects to indexable objects
 
         :param objs:
-        :return:
+        :return: list of vectors
         """
-        return [self.object_to_vector(obj) for obj in objs]
+        return self.texts_to_vectors([self.object_to_text(obj) for obj in objs])
 
-    def texts_to_vectors(self, texts: List[str]) -> List[INDEX_ITEM]:
+    def texts_to_vectors(self, texts: List[str], cache: bool = None, **kwargs) -> List[INDEX_ITEM]:
         """
         Convert a list of texts to indexable objects
 
         :param texts:
         :return:
         """
-        return [self.text_to_vector(text) for text in texts]
+        return [self.text_to_vector(text, cache=cache, **kwargs) for text in texts]
 
-    def text_to_vector(self, text: str) -> INDEX_ITEM:
+    def text_to_vector(self, text: str, cache: bool = None, **kwargs) -> INDEX_ITEM:
         """
         Convert a text to an indexable object
 
         :param text:
+        :param cache:
         :return:
         """
         raise NotImplementedError
@@ -71,11 +82,24 @@ class Indexer(BaseModel):
         :return:
         """
         if self.index_attributes:
+            if len(self.index_attributes) == 1 and not self.text_template:
+                return str(obj[self.index_attributes[0]])
             obj = {k: v for k, v in obj.items() if k in self.index_attributes}
         if self.filter_nulls:
             obj = {k: v for k, v in obj.items() if v is not None}
         if self.text_template:
-            return self.text_template.format(**obj)
+            syntax = self.text_template_syntax
+            if not syntax:
+                if "{%" in self.text_template or "{{" in self.text_template:
+                    logger.info("Detected Jinja2 syntax in text template")
+                    syntax = TemplateSyntaxEnum.jinja2
+            if syntax and syntax == TemplateSyntaxEnum.jinja2:
+                from jinja2 import Template
+
+                template = Template(self.text_template)
+                return template.render(**obj)
+            else:
+                return self.text_template.format(**obj)
         return str(obj)
 
     def search(
@@ -91,7 +115,7 @@ class Indexer(BaseModel):
         """
 
         # Convert the query string to a vector
-        query_vector = self.text_to_vector(query)
+        query_vector = self.text_to_vector(query, cache=False)
 
         distances = []
 

linkml_store/utils/format_utils.py

@@ -4,13 +4,17 @@ import sys
 from enum import Enum
 from io import StringIO
 from pathlib import Path
-from typing import Any, Dict, List, Union
+from typing import Any, Dict, List, Optional, Union
 
 import yaml
 from pydantic import BaseModel
 
 
 class Format(Enum):
+    """
+    Supported generic file formats for loading and rendering objects.
+    """
+
     JSON = "json"
     JSONL = "jsonl"
     YAML = "yaml"
@@ -22,6 +26,10 @@ def load_objects(file_path: Union[str, Path], format: Union[Format, str] = None)
     """
     Load objects from a file in JSON, JSONLines, YAML, CSV, or TSV format.
 
+    >>> load_objects("tests/input/test_data/data.csv")
+    [{'id': '1', 'name': 'John', 'age': '30'},
+     {'id': '2', 'name': 'Alice', 'age': '25'}, {'id': '3', 'name': 'Bob', 'age': '35'}]
+
     :param file_path: The path to the file.
     :param format: The format of the file. Can be a Format enum or a string value.
     :return: A list of dictionaries representing the loaded objects.
@@ -57,10 +65,23 @@ def load_objects(file_path: Union[str, Path], format: Union[Format, str] = None)
     return objs
 
 
-def render_output(data: List[Dict[str, Any]], format: Union[Format, str] = Format.YAML) -> str:
+def render_output(data: Union[List[Dict[str, Any]], Dict[str, Any]], format: Union[Format, str] = Format.YAML) -> str:
     """
     Render output data in JSON, JSONLines, YAML, CSV, or TSV format.
 
+    >>> print(render_output([{"a": 1, "b": 2}, {"a": 3, "b": 4}], Format.JSON))
+    [
+      {
+        "a": 1,
+        "b": 2
+      },
+      {
+        "a": 3,
+        "b": 4
+      }
+    ]
+
+
     :param data: The data to be rendered.
     :param format: The desired output format. Can be a Format enum or a string value.
     :return: The rendered output as a string.
@@ -91,3 +112,32 @@ def render_output(data: List[Dict[str, Any]], format: Union[Format, str] = Forma
         return output.getvalue()
     else:
         raise ValueError(f"Unsupported output format: {format}")
+
+
+def guess_format(path: str) -> Optional[Format]:
+    """
+    Guess the format of a file based on its extension.
+
+    >>> guess_format("data.json")
+    <Format.JSON: 'json'>
+    >>> guess_format("data.jsonl")
+    <Format.JSONL: 'jsonl'>
+    >>> guess_format("data.yaml")
+    <Format.YAML: 'yaml'>
+    >>> assert not guess_format("data")
+
+    :param path: The path to the file.
+    :return: The guessed format.
+    """
+    if path.endswith(".json"):
+        return Format.JSON
+    elif path.endswith(".jsonl"):
+        return Format.JSONL
+    elif path.endswith(".yaml") or path.endswith(".yml"):
+        return Format.YAML
+    elif path.endswith(".tsv"):
+        return Format.TSV
+    elif path.endswith(".csv"):
+        return Format.CSV
+    else:
+        return None

linkml_store/utils/object_utils.py

@@ -1,6 +1,6 @@
 import json
 from copy import deepcopy
-from typing import Any, Dict, Union
+from typing import Any, Dict, List, Union
 
 from pydantic import BaseModel
 
@@ -71,3 +71,11 @@ def parse_update_expression(expr: str) -> Union[tuple[str, Any], None]:
     except ValueError:
         return None
     return path, val
+
+
+def clean_empties(value: Union[Dict, List]) -> Any:
+    if isinstance(value, dict):
+        value = {k: v for k, v in ((k, clean_empties(v)) for k, v in value.items()) if v is not None}
+    elif isinstance(value, list):
+        value = [v for v in (clean_empties(v) for v in value) if v is not None]
+    return value

{linkml_store-0.1.6.dist-info → linkml_store-0.1.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml-store
-Version: 0.1.6
+Version: 0.1.8
 Summary: linkml-store
 License: MIT
 Author: Author 1
@@ -27,6 +27,7 @@ Requires-Dist: click
 Requires-Dist: duckdb (>=0.10.1,<0.11.0)
 Requires-Dist: duckdb-engine (>=0.11.2)
 Requires-Dist: h5py ; extra == "h5py"
+Requires-Dist: jinja2 (>=3.1.4,<4.0.0)
 Requires-Dist: linkml ; extra == "validation"
 Requires-Dist: linkml-runtime (>=1.7.5,<2.0.0)
 Requires-Dist: linkml_map ; extra == "map"
@@ -53,3 +54,5 @@ There is also experimental support for vector-based indexing using OpenAI test e
 The goals of this project are to provide high level access to data stored in heterogeneous databases,
 with optional schema management using LinkML.
 
+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.dist-info/RECORD

@@ -0,0 +1,45 @@
+linkml_store/__init__.py,sha256=jlU6WOUAn8cKIhzbTULmBTWpW9gZdEt7q_RI6KZN1bY,118
+linkml_store/api/__init__.py,sha256=3CelcFEFz0y3MkQAzhQ9JxHIt1zFk6nYZxSmYTo8YZE,226
+linkml_store/api/client.py,sha256=0Cs_0xW3NDUI6UJFtVvWd_XsGVLryMyh1SPrQhH4taU,8474
+linkml_store/api/collection.py,sha256=Nxauj22Vh38RaT6Hhwyn5j1_SXoHDf-EaoIy1osnIKo,24010
+linkml_store/api/config.py,sha256=VTtv42Vgnn3vKEERIOrtXjQDz4YHTJnm5pvvUnshqyA,3573
+linkml_store/api/database.py,sha256=OASaP8lbGIIJnrjTDDHq4ROzKrND8cizHauKMNFZaNo,24876
+linkml_store/api/queries.py,sha256=w0qnNeCH6pC9WTGoEQYd300MF6o0G3atz2YxN3WecAs,2028
+linkml_store/api/stores/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml_store/api/stores/chromadb/__init__.py,sha256=e9BkOPuPnVQKA5PRKDulag59yGNHDP3U2_DnPSrFAKM,132
+linkml_store/api/stores/chromadb/chromadb_collection.py,sha256=RQUZx5oeotkzNihg-dlSevkiTiKY1d9x0bS63HF80W4,4270
+linkml_store/api/stores/chromadb/chromadb_database.py,sha256=dZA3LQE8-ZMhJQOzsUFyxehnKpFF7adR182aggfkaFY,3205
+linkml_store/api/stores/duckdb/__init__.py,sha256=rbQSDgNg-fdvi6-pHGYkJTST4p1qXUZBf9sFSsO3KPk,387
+linkml_store/api/stores/duckdb/duckdb_collection.py,sha256=poKh6g9-sXA8Wl6B9-mxJqk9biJ0IK7_xz2iGG_U79g,6060
+linkml_store/api/stores/duckdb/duckdb_database.py,sha256=xk2bSeSWofGtPgp56168-4KIX4wJTtm9XgUtiBQOuNA,7194
+linkml_store/api/stores/duckdb/mappings.py,sha256=tDce3W1Apwammhf4LS6cRJ0m4NiJ0eB7vOI_4U5ETY8,148
+linkml_store/api/stores/filesystem/__init__.py,sha256=rbQSDgNg-fdvi6-pHGYkJTST4p1qXUZBf9sFSsO3KPk,387
+linkml_store/api/stores/filesystem/filesystem_collection.py,sha256=vIM8y71YNdjBsSUl02wXMdl6EY3QYjMCT5MzRI7pO04,5905
+linkml_store/api/stores/filesystem/filesystem_database.py,sha256=d-394QD565bHqJ2FzZjMZrFw8HY-v7k8bE2cxy24k-8,1098
+linkml_store/api/stores/hdf5/__init__.py,sha256=l4cIh3v7P0nPbwGIsfuCMD_serQ8q8c7iuUA9W2Jb4o,97
+linkml_store/api/stores/hdf5/hdf5_collection.py,sha256=mnpLMYehn3PuaIjp2dXrIWu8jh-bdQ84X2Ku83jMdEY,3805
+linkml_store/api/stores/hdf5/hdf5_database.py,sha256=EZbjrpaqiNDEFvoD5dZNcGBXA8z6HRNL81emueTZWNw,2714
+linkml_store/api/stores/mongodb/__init__.py,sha256=OSFCr7RQlDEe-O-Y0P_i912oAMK-L3pC7Cnj7sxlwAk,510
+linkml_store/api/stores/mongodb/mongodb_collection.py,sha256=wMaZb9B3PZ5lCDfj8kOrVnUJQ0O0lrP4PrcpEwAhEOI,4698
+linkml_store/api/stores/mongodb/mongodb_database.py,sha256=QAdTi8XYLsdrEvEUUKb9qolCPeEXgfecTQ1bz9GCWDg,3670
+linkml_store/api/stores/solr/__init__.py,sha256=aAfnaN9mZOiIDj1NYz0Ll9fZF2gG7UU_vhP4SNCL2d8,36
+linkml_store/api/stores/solr/solr_collection.py,sha256=8GmxErlWFOO0NnJiYo1Q7hegxCsfxaWc79eN7Jn02gA,4723
+linkml_store/api/stores/solr/solr_database.py,sha256=TFjqbY7jAkdrhAchbNg0E-mChSP7ogNwFExslbvX7Yo,2877
+linkml_store/api/stores/solr/solr_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml_store/cli.py,sha256=oMz13ndmFm3QCxg1ILPo0mlwtMgfd-tERXmW2LM7jzU,15871
+linkml_store/constants.py,sha256=x4ZmDsfE9rZcL5WpA93uTKrRWzCD6GodYXviVzIvR38,112
+linkml_store/index/__init__.py,sha256=dVrYtsFu7tEsMDaPMIc2LjsM76HoAKQz4uO8roR18Zw,993
+linkml_store/index/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml_store/index/implementations/llm_indexer.py,sha256=04cz-UaKlV7WTubHVr0v94XfqbN0N2Nnoud9Z7nETH4,4779
+linkml_store/index/implementations/simple_indexer.py,sha256=KnkFJtXTHnwjhD_D6ZK2rFhBID1dgCedcOVPEWAY2NU,1282
+linkml_store/index/indexer.py,sha256=C64J3-2oCqYXCouNQ4fxw4g7f7Nl2L0WwFf-zrcsogo,4491
+linkml_store/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml_store/utils/format_utils.py,sha256=18qmWVUr6ceOuvPROcNZ7mCBXpZyj3_cy1gNcpIqZC4,4352
+linkml_store/utils/io.py,sha256=JHUrWDtlZC2jtN_PQZ4ypdGIyYlftZEN3JaCvEPs44w,884
+linkml_store/utils/object_utils.py,sha256=is6T2gruvVKvWD5ZntcAl6Qi3L154FObEho_b_crTuE,2539
+linkml_store/utils/sql_utils.py,sha256=TeAhAHXi1GA0f2UVrxbzStwe49Q7fN0mu5WZyfDk-s8,5651
+linkml_store-0.1.8.dist-info/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
+linkml_store-0.1.8.dist-info/METADATA,sha256=EN8yT2duWya5DiUQKHx99XAjCqJfYOw2_XTQiltTLzo,2311
+linkml_store-0.1.8.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+linkml_store-0.1.8.dist-info/entry_points.txt,sha256=6ema3OkAkUK0ux8roEeRPtSW_Tylend5BABf-xRsZiU,53
+linkml_store-0.1.8.dist-info/RECORD,,

linkml_store-0.1.6.dist-info/RECORD

@@ -1,41 +0,0 @@
-linkml_store/__init__.py,sha256=jlU6WOUAn8cKIhzbTULmBTWpW9gZdEt7q_RI6KZN1bY,118
-linkml_store/api/__init__.py,sha256=3CelcFEFz0y3MkQAzhQ9JxHIt1zFk6nYZxSmYTo8YZE,226
-linkml_store/api/client.py,sha256=hoiEE3FnNvCpvJ8LrEoTjOWg_jUolbbZEVIBef0Xv7c,7551
-linkml_store/api/collection.py,sha256=QKmiBTb9YjpRFgon1A2nurWQnIxU8uz9EPtvJT-paT8,17203
-linkml_store/api/config.py,sha256=qXB41OrPP3dh96XnigkJiTbAH12aPcKycSUH0MV8BHM,3269
-linkml_store/api/database.py,sha256=dXKImuXLOaBx4JiTDSuhCL6B4rOnIzY57Rg052Odupc,13701
-linkml_store/api/queries.py,sha256=w0qnNeCH6pC9WTGoEQYd300MF6o0G3atz2YxN3WecAs,2028
-linkml_store/api/stores/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml_store/api/stores/chromadb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml_store/api/stores/chromadb/chromadb_collection.py,sha256=hiNhnUNKrsgjYZynXCkAbLssh38Xu9D59OX8ZARnWIU,4186
-linkml_store/api/stores/chromadb/chromadb_database.py,sha256=dZA3LQE8-ZMhJQOzsUFyxehnKpFF7adR182aggfkaFY,3205
-linkml_store/api/stores/duckdb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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