linkml-store 0.1.9__py3-none-any.whl → 0.1.10__py3-none-any.whl

linkml_store-0.1.10.dist-info/METADATA

@@ -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-0.1.9.dist-info → linkml_store-0.1.10.dist-info}/RECORD

@@ -1,8 +1,8 @@
 linkml_store/__init__.py,sha256=jlU6WOUAn8cKIhzbTULmBTWpW9gZdEt7q_RI6KZN1bY,118
 linkml_store/api/__init__.py,sha256=3CelcFEFz0y3MkQAzhQ9JxHIt1zFk6nYZxSmYTo8YZE,226
-linkml_store/api/client.py,sha256=YGji1WJp9j3W0yTqSbcPHmz7jjUXalnQXeWvJLyQNyE,8592
-linkml_store/api/collection.py,sha256=7ZPSs8LnmPI_-dYkZoTM87BE2gglRnU2p4XQhv4DYuU,27470
-linkml_store/api/config.py,sha256=VTtv42Vgnn3vKEERIOrtXjQDz4YHTJnm5pvvUnshqyA,3573
+linkml_store/api/client.py,sha256=dkcjZMx8V8a-zlD2Vm7QA8VVoKyk2wQQe0Ug1zcT-6o,9075
+linkml_store/api/collection.py,sha256=ZWVON3axSmvWQUrCNxPqVXthQ4VaeHmqprjwgNXYj9M,30357
+linkml_store/api/config.py,sha256=pgF9D_5buhChBIZXBkc84tNE0VQtP0iwCQ63Br1QR0c,3785
 linkml_store/api/database.py,sha256=9H-bj4_v_iJ5iQm_uaoR4_LefZknmbod--tOqD5mYmE,25730
 linkml_store/api/queries.py,sha256=w0qnNeCH6pC9WTGoEQYd300MF6o0G3atz2YxN3WecAs,2028
 linkml_store/api/stores/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -10,40 +10,49 @@ linkml_store/api/stores/chromadb/__init__.py,sha256=e9BkOPuPnVQKA5PRKDulag59yGNH
 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=PGzYdLx1bv5NK0TvEIKpNSQ7f6yiY3vylt_V_KFqqWo,6097
-linkml_store/api/stores/duckdb/duckdb_database.py,sha256=xk2bSeSWofGtPgp56168-4KIX4wJTtm9XgUtiBQOuNA,7194
+linkml_store/api/stores/duckdb/duckdb_collection.py,sha256=LTcrvPEuSaQP1riGytUCdmmbFb_zZFl1mDG6TqqXfto,6246
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 linkml_store/api/stores/duckdb/mappings.py,sha256=tDce3W1Apwammhf4LS6cRJ0m4NiJ0eB7vOI_4U5ETY8,148
 linkml_store/api/stores/filesystem/__init__.py,sha256=KjvCjdttwqMHNeGyL-gr59zRz0--HFEWWUNNCJ5hITs,347
-linkml_store/api/stores/filesystem/filesystem_collection.py,sha256=5WmWSIE22UnKm8UkfcpTinfnpgtv_FXcYTlT5vF2yKA,6321
+linkml_store/api/stores/filesystem/filesystem_collection.py,sha256=QPCuCHbxzbMPcsvxVp7kOAnT5_8m0kW60SZHtRo_87A,6403
 linkml_store/api/stores/filesystem/filesystem_database.py,sha256=HnHIv1aVtTiFSPY09s40QrMNhn_e-IKCYRXQk1S25Ak,2554
 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=CCsU1omeWXdb8Wzjt9DlmryBNgbfVbiTNtAJNrO-odI,4970
+linkml_store/api/stores/mongodb/mongodb_collection.py,sha256=R3zFca45V6_s8D_4f-tEhrFf_NH6z8UJj5suG7GshJc,6529
 linkml_store/api/stores/mongodb/mongodb_database.py,sha256=DKO-lMQzHyf-szVgH4tsP0UA68dlCFGv-oyVuXOIUd0,4003
 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/api/types.py,sha256=3aIQtDFMvsSmjuN5qrR2vNK5sHa6yzD_rEOPA6tHwvg,176
-linkml_store/cli.py,sha256=HIPG-LZDB9Mgue6_KKDiaUpNO90chUCnYOnLbUdFogk,19098
+linkml_store/cli.py,sha256=Y8QUPMCRY5jkwwvz-78k5A1dM-nOj1lavZsBR2gGTMw,19325
 linkml_store/constants.py,sha256=x4ZmDsfE9rZcL5WpA93uTKrRWzCD6GodYXviVzIvR38,112
-linkml_store/index/__init__.py,sha256=dVrYtsFu7tEsMDaPMIc2LjsM76HoAKQz4uO8roR18Zw,993
+linkml_store/index/__init__.py,sha256=n5omzpf9nuQ8Dl2vjTVE4ATBXI0Lrs3HNmB25ZsPB1w,1076
 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/index/indexer.py,sha256=F130IKT6xZ9tTeH6D32sCcZkkLTTha8CETgZz_ksXyY,4737
 linkml_store/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml_store/utils/change_utils.py,sha256=O2rvSvgTKB60reLLz9mX5OWykAA_m93bwnUh5ZWa0EY,471
-linkml_store/utils/format_utils.py,sha256=I6rYInqdrOSWK_ydtlgYJ8ArPGP-Q8iQoD4nzrp-ajM,6568
+linkml_store/utils/format_utils.py,sha256=kG-mTE9bZXfYvXsrShQN5Tz_Nxj-DFW_ykgJKVJlLQE,6581
 linkml_store/utils/io.py,sha256=JHUrWDtlZC2jtN_PQZ4ypdGIyYlftZEN3JaCvEPs44w,884
 linkml_store/utils/object_utils.py,sha256=is6T2gruvVKvWD5ZntcAl6Qi3L154FObEho_b_crTuE,2539
 linkml_store/utils/patch_utils.py,sha256=q-h_v68okyruzdPTEHCe0WubbQHKpi1qy5bJ9vFWDo8,4823
 linkml_store/utils/query_utils.py,sha256=HWt46BsGWoIGiNBTtvpXGY6onPRWsQky6eu_9cYqbvo,3440
+linkml_store/utils/schema_utils.py,sha256=iJiZxo5NGr7v87h4DV6V9DrDOZHSswMRuf0N4V2rVtg,646
 linkml_store/utils/sql_utils.py,sha256=TeAhAHXi1GA0f2UVrxbzStwe49Q7fN0mu5WZyfDk-s8,5651
-linkml_store-0.1.9.dist-info/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
-linkml_store-0.1.9.dist-info/METADATA,sha256=6TNxC0HDbb4CGFH1GhDfU1BryD2uGFCi5cRJUj4MZQ8,2421
-linkml_store-0.1.9.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-linkml_store-0.1.9.dist-info/entry_points.txt,sha256=6ema3OkAkUK0ux8roEeRPtSW_Tylend5BABf-xRsZiU,53
-linkml_store-0.1.9.dist-info/RECORD,,
+linkml_store/webapi/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml_store/webapi/html/__init__.py,sha256=hwp5eeBJKH65Bvv1x9Z4vsT1tLSYtb9Dq4I9r1kL1q0,69
+linkml_store/webapi/html/base.html.j2,sha256=hoiV2uaSxxrQp7VuAZBOHueH7czyJMYcPBRN6dZFYhk,693
+linkml_store/webapi/html/collection_details.html.j2,sha256=FcCnkgtJAhfW84tVXQfAXP8eiq4BcrTeudZXQGL1Slg,385
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+linkml_store/webapi/html/generic.html.j2,sha256=1P5BKExQX5ZI94tUlMHK9BtTIXkP2ZnLAS014bPOgZM,1001
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+linkml_store-0.1.10.dist-info/RECORD,,

{linkml_store-0.1.9.dist-info → linkml_store-0.1.10.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
-