linkml-store 0.1.9__py3-none-any.whl → 0.1.11__py3-none-any.whl

linkml_store-0.1.11.dist-info/METADATA

@@ -0,0 +1,171 @@
+Metadata-Version: 2.1
+Name: linkml-store
+Version: 0.1.11
+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: frictionless
+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: frictionless ; extra == "frictionless"
+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 (>=1.8.0) ; extra == "validation"
+Requires-Dist: linkml-runtime (>=1.8.0)
+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)
+
+### Use with LLMs
+
+TODO - docs
+
+### 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)
+
+## Web API
+
+There is a preliminary API following HATEOAS principles implemented using FastAPI.
+
+To start you should first create a config file, e.g. `db/conf.yaml`:
+
+Then run:
+
+```
+export LINKML_STORE_CONFIG=./db/conf.yaml
+make api
+```
+
+The API returns links as well as data objects, it's recommended to use a Chrome plugin for JSON viewing
+for exploring the API. TODO: add docs here.
+
+The main endpoints are:
+
+* `http://localhost:8000/` - the root of the API
+* `http://localhost:8000/pages/` - browse the API via HTML
+* `http://localhost:8000/docs` - the Swagger UI
+
+## Streamlit app
+
+```
+make app
+```
+
+## 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-0.1.11.dist-info/RECORD

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{linkml_store-0.1.9.dist-info → linkml_store-0.1.11.dist-info}/entry_points.txt

@@ -1,3 +1,4 @@
 [console_scripts]
 linkml-store=linkml_store.cli:cli
+linkml-store-api=linkml_store.webapi.main:start
 

linkml_store-0.1.9.dist-info/METADATA

@@ -1,61 +0,0 @@
-Metadata-Version: 2.1
-Name: linkml-store
-Version: 0.1.9
-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: h5py
-Provides-Extra: llm
-Provides-Extra: map
-Provides-Extra: mongodb
-Provides-Extra: pyarrow
-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: 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 (>=1.7.5,<2.0.0)
-Requires-Dist: linkml_map ; extra == "map"
-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"
-Description-Content-Type: text/markdown
-
-# linkml-store
-
-An integration layer for multiple database backends
-
-Currently this software is alpha, and has only been tested with DuckDB backends. See the Tutorial for more information.
-
-There is also experimental support for vector-based indexing using OpenAI test embedding via the `llm` library.
-
-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-0.1.9.dist-info/RECORD

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