linkml-store 0.3.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- linkml_store/__init__.py +7 -0
- linkml_store/api/__init__.py +8 -0
- linkml_store/api/client.py +414 -0
- linkml_store/api/collection.py +1280 -0
- linkml_store/api/config.py +187 -0
- linkml_store/api/database.py +862 -0
- linkml_store/api/queries.py +69 -0
- linkml_store/api/stores/__init__.py +0 -0
- linkml_store/api/stores/chromadb/__init__.py +7 -0
- linkml_store/api/stores/chromadb/chromadb_collection.py +121 -0
- linkml_store/api/stores/chromadb/chromadb_database.py +89 -0
- linkml_store/api/stores/dremio/__init__.py +10 -0
- linkml_store/api/stores/dremio/dremio_collection.py +555 -0
- linkml_store/api/stores/dremio/dremio_database.py +1052 -0
- linkml_store/api/stores/dremio/mappings.py +105 -0
- linkml_store/api/stores/dremio_rest/__init__.py +11 -0
- linkml_store/api/stores/dremio_rest/dremio_rest_collection.py +502 -0
- linkml_store/api/stores/dremio_rest/dremio_rest_database.py +1023 -0
- linkml_store/api/stores/duckdb/__init__.py +16 -0
- linkml_store/api/stores/duckdb/duckdb_collection.py +339 -0
- linkml_store/api/stores/duckdb/duckdb_database.py +283 -0
- linkml_store/api/stores/duckdb/mappings.py +8 -0
- linkml_store/api/stores/filesystem/__init__.py +15 -0
- linkml_store/api/stores/filesystem/filesystem_collection.py +186 -0
- linkml_store/api/stores/filesystem/filesystem_database.py +81 -0
- linkml_store/api/stores/hdf5/__init__.py +7 -0
- linkml_store/api/stores/hdf5/hdf5_collection.py +104 -0
- linkml_store/api/stores/hdf5/hdf5_database.py +79 -0
- linkml_store/api/stores/ibis/__init__.py +5 -0
- linkml_store/api/stores/ibis/ibis_collection.py +488 -0
- linkml_store/api/stores/ibis/ibis_database.py +328 -0
- linkml_store/api/stores/mongodb/__init__.py +25 -0
- linkml_store/api/stores/mongodb/mongodb_collection.py +379 -0
- linkml_store/api/stores/mongodb/mongodb_database.py +114 -0
- linkml_store/api/stores/neo4j/__init__.py +0 -0
- linkml_store/api/stores/neo4j/neo4j_collection.py +429 -0
- linkml_store/api/stores/neo4j/neo4j_database.py +154 -0
- linkml_store/api/stores/solr/__init__.py +3 -0
- linkml_store/api/stores/solr/solr_collection.py +224 -0
- linkml_store/api/stores/solr/solr_database.py +83 -0
- linkml_store/api/stores/solr/solr_utils.py +0 -0
- linkml_store/api/types.py +4 -0
- linkml_store/cli.py +1147 -0
- linkml_store/constants.py +7 -0
- linkml_store/graphs/__init__.py +0 -0
- linkml_store/graphs/graph_map.py +24 -0
- linkml_store/index/__init__.py +53 -0
- linkml_store/index/implementations/__init__.py +0 -0
- linkml_store/index/implementations/llm_indexer.py +174 -0
- linkml_store/index/implementations/simple_indexer.py +43 -0
- linkml_store/index/indexer.py +211 -0
- linkml_store/inference/__init__.py +13 -0
- linkml_store/inference/evaluation.py +195 -0
- linkml_store/inference/implementations/__init__.py +0 -0
- linkml_store/inference/implementations/llm_inference_engine.py +154 -0
- linkml_store/inference/implementations/rag_inference_engine.py +276 -0
- linkml_store/inference/implementations/rule_based_inference_engine.py +169 -0
- linkml_store/inference/implementations/sklearn_inference_engine.py +314 -0
- linkml_store/inference/inference_config.py +66 -0
- linkml_store/inference/inference_engine.py +209 -0
- linkml_store/inference/inference_engine_registry.py +74 -0
- linkml_store/plotting/__init__.py +5 -0
- linkml_store/plotting/cli.py +826 -0
- linkml_store/plotting/dimensionality_reduction.py +453 -0
- linkml_store/plotting/embedding_plot.py +489 -0
- linkml_store/plotting/facet_chart.py +73 -0
- linkml_store/plotting/heatmap.py +383 -0
- linkml_store/utils/__init__.py +0 -0
- linkml_store/utils/change_utils.py +17 -0
- linkml_store/utils/dat_parser.py +95 -0
- linkml_store/utils/embedding_matcher.py +424 -0
- linkml_store/utils/embedding_utils.py +299 -0
- linkml_store/utils/enrichment_analyzer.py +217 -0
- linkml_store/utils/file_utils.py +37 -0
- linkml_store/utils/format_utils.py +550 -0
- linkml_store/utils/io.py +38 -0
- linkml_store/utils/llm_utils.py +122 -0
- linkml_store/utils/mongodb_utils.py +145 -0
- linkml_store/utils/neo4j_utils.py +42 -0
- linkml_store/utils/object_utils.py +190 -0
- linkml_store/utils/pandas_utils.py +93 -0
- linkml_store/utils/patch_utils.py +126 -0
- linkml_store/utils/query_utils.py +89 -0
- linkml_store/utils/schema_utils.py +23 -0
- linkml_store/utils/sklearn_utils.py +193 -0
- linkml_store/utils/sql_utils.py +177 -0
- linkml_store/utils/stats_utils.py +53 -0
- linkml_store/utils/vector_utils.py +158 -0
- linkml_store/webapi/__init__.py +0 -0
- linkml_store/webapi/html/__init__.py +3 -0
- linkml_store/webapi/html/base.html.j2 +24 -0
- linkml_store/webapi/html/collection_details.html.j2 +15 -0
- linkml_store/webapi/html/database_details.html.j2 +16 -0
- linkml_store/webapi/html/databases.html.j2 +14 -0
- linkml_store/webapi/html/generic.html.j2 +43 -0
- linkml_store/webapi/main.py +855 -0
- linkml_store-0.3.0.dist-info/METADATA +226 -0
- linkml_store-0.3.0.dist-info/RECORD +101 -0
- linkml_store-0.3.0.dist-info/WHEEL +4 -0
- linkml_store-0.3.0.dist-info/entry_points.txt +3 -0
- linkml_store-0.3.0.dist-info/licenses/LICENSE +22 -0
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Metadata-Version: 2.4
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Name: linkml-store
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Version: 0.3.0
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Summary: linkml-store
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Author-email: Author 1 <author@org.org>
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License-Expression: MIT
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License-File: LICENSE
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Requires-Python: <4.0,>=3.10
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Description-Content-Type: text/markdown
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# linkml-store
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An AI-ready data management and integration platform. LinkML-Store
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provides an abstraction layer over multiple different backends
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(including DuckDB, MongoDB, Neo4j, and local filesystems), allowing for
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common query, index, and storage operations.
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For full documentation, see [https://linkml.io/linkml-store/](https://linkml.io/linkml-store/)
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See [these slides](https://docs.google.com/presentation/d/e/2PACX-1vSgtWUNUW0qNO_ZhMAGQ6fYhlXZJjBNMYT0OiZz8DDx8oj7iG9KofRs6SeaMXBBOICGknoyMG2zaHnm/embed?start=false&loop=false&delayms=3000) for a high level overview.
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__Warning__ LinkML-Store is still undergoing changes and refactoring,
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APIs and command line options are subject to change!
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## Quick Start
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Install, add data, query it:
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```
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pip install linkml-store[all]
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linkml-store -d duckdb:///db/my.db -c persons insert data/*.json
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linkml-store -d duckdb:///db/my.db -c persons query -w "occupation: Bricklayer"
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```
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Index it, search it:
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```
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linkml-store -d duckdb:///db/my.db -c persons index -t llm
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linkml-store -d duckdb:///db/my.db -c persons search "all persons employed in construction"
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```
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Validate it:
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```
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linkml-store -d duckdb:///db/my.db -c persons validate
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```
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## Basic usage
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* [Command Line](https://linkml.io/linkml-store/tutorials/Command-Line-Tutorial.html)
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* [Python](https://linkml.io/linkml-store/tutorials/Python-Tutorial.html)
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* API
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* Streamlit applications
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## The CRUDSI pattern
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Most database APIs implement the **CRUD** pattern: Create, Read, Update, Delete.
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LinkML-Store adds **Search** and **Inference** to this pattern, making it **CRUDSI**.
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The notion of "Search" and "Inference" is intended to be flexible and extensible,
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including:
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* Search
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* Traditional keyword search
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* Search using LLM Vector embeddings (*without* a dedicated vector database)
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* Pluggable specialized search, e.g. genomic sequence (not yet implemented)
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* Inference (encompassing *validation*, *repair*, and inference of missing data)
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* Classic rule-based inference
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* Inference using LLM Retrieval Augmented Generation (RAG)
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* Statistical/ML inference
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## Features
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### Multiple Adapters
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LinkML-Store is designed to work with multiple backends, giving a common abstraction layer
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* [MongoDB](https://linkml.io/linkml-store/how-to/Use-MongoDB.html)
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* [DuckDB](https://linkml.io/linkml-store/tutorials/Python-Tutorial.html)
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* [Solr](https://linkml.io/linkml-store/how-to/Query-Solr-using-CLI.html)
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* [Neo4j](https://linkml.io/linkml-store/how-to/Use-Neo4j.html)
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* **Ibis** - Universal database adapter supporting DuckDB, PostgreSQL, SQLite, BigQuery, Snowflake, and many more
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* Filesystem
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Coming soon: any RDBMS, any triplestore, HDF5-based stores, ChromaDB/Vector dbs ...
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The intent is to give a union of all features of each backend. For
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example, analytic faceted queries are provided for *all* backends, not
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just Solr.
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### Composable indexes
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Many backends come with their own indexing and search
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schemes. Classically this was Lucene-based indexes, now it is semantic
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search using LLM embeddings.
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LinkML store treats indexing as an orthogonal concern - you can
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compose different indexing schemes with different backends. You don't
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need to have a vector database to run embedding search!
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See [How to Use-Semantic-Search](https://linkml.io/linkml-store/how-to/Use-Semantic-Search.html)
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### Use with LLMs
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### Validation
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LinkML-Store is backed by [LinkML](https://linkml.io), which allows
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for powerful expressive structural and semantic constraints.
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See [Indexing JSON](https://linkml.io/linkml-store/how-to/Index-Phenopackets.html)
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and [Referential Integrity](https://linkml.io/linkml-store/how-to/Check-Referential-Integrity.html)
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## Web API
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There is a preliminary API following HATEOAS principles implemented using FastAPI.
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To start you should first create a config file, e.g. `db/conf.yaml`:
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Then run:
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```
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export LINKML_STORE_CONFIG=./db/conf.yaml
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make api
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```
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The API returns links as well as data objects, it's recommended to use a Chrome plugin for JSON viewing
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for exploring the API. TODO: add docs here.
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The main endpoints are:
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* `http://localhost:8000/` - the root of the API
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* `http://localhost:8000/pages/` - browse the API via HTML
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See [these slides](https://docs.google.com/presentation/d/e/2PACX-1vSgtWUNUW0qNO_ZhMAGQ6fYhlXZJjBNMYT0OiZz8DDx8oj7iG9KofRs6SeaMXBBOICGknoyMG2zaHnm/embed?start=false&loop=false&delayms=3000) for more details
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linkml_store/cli.py,sha256=dN1Nm4bECujbJSeDAEcm7ZveS6ffdQxSTk_pNexez3E,45542
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linkml_store/constants.py,sha256=x4ZmDsfE9rZcL5WpA93uTKrRWzCD6GodYXviVzIvR38,112
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linkml_store/api/__init__.py,sha256=3CelcFEFz0y3MkQAzhQ9JxHIt1zFk6nYZxSmYTo8YZE,226
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linkml_store/api/client.py,sha256=AXaGuvzuy1miW3-gm-0R5wkfuhfOlWYHKtzzjhY7Rmo,14054
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linkml_store/api/collection.py,sha256=XCedJbDLEYeH48PewkozCZz3f9hTzAKv2Dsaywi8Sp8,44761
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linkml_store/api/config.py,sha256=pOz210JIwkEEXtfjcsZBp1UEedkBu8RkH62Qa1b4exI,5777
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linkml_store/api/database.py,sha256=rcJ6FCWLZSUb8O0rcV1x99Em4t8BXfMs3KGXiMHWoIA,31964
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linkml_store/api/queries.py,sha256=pEABM3G-k52WVzbIVdkcOkVhgBDgMOGnmk50HliiXPE,2082
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linkml_store/api/types.py,sha256=3aIQtDFMvsSmjuN5qrR2vNK5sHa6yzD_rEOPA6tHwvg,176
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linkml_store/api/stores/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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linkml_store/api/stores/chromadb/__init__.py,sha256=e9BkOPuPnVQKA5PRKDulag59yGNHDP3U2_DnPSrFAKM,132
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linkml_store/api/stores/chromadb/chromadb_collection.py,sha256=RQUZx5oeotkzNihg-dlSevkiTiKY1d9x0bS63HF80W4,4270
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linkml_store/api/stores/chromadb/chromadb_database.py,sha256=dZA3LQE8-ZMhJQOzsUFyxehnKpFF7adR182aggfkaFY,3205
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linkml_store/api/stores/dremio/__init__.py,sha256=VP-i3xK-8bB9AFtQuYIieBUUUwYaDlo83epZcXeupZY,377
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linkml_store/api/stores/dremio/dremio_collection.py,sha256=ZBmjVBXTp-Xj-KppbT0d3pzh2JkxJxQFluft9MJBCeU,18106
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linkml_store/api/stores/dremio/dremio_database.py,sha256=5UJQM-0Kj0-KDapPr-lkICgR53aLC-u7Inzdp3O2y6M,38739
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linkml_store/api/stores/dremio/mappings.py,sha256=bf9mTNp062CQXRqakZye5XI49qQrK8A_W17p_OF2g-8,2867
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linkml_store/api/stores/dremio_rest/__init__.py,sha256=wm3jNFq-k9_rRsZXOlHyt4dhFU6b51RvZN4u43qK7aA,489
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linkml_store/api/stores/dremio_rest/dremio_rest_collection.py,sha256=8yxsNJlH82tGNb7g_qK3L79Ui8SJz04WogHKJlMWBtc,16266
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linkml_store/api/stores/dremio_rest/dremio_rest_database.py,sha256=Z_KVUpS5jj71CsQipH3fUEp-8c4MkUh6-XcVlI9vJ0o,37495
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linkml_store/api/stores/duckdb/__init__.py,sha256=rbQSDgNg-fdvi6-pHGYkJTST4p1qXUZBf9sFSsO3KPk,387
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linkml_store/api/stores/duckdb/duckdb_collection.py,sha256=AW7YhHdegHdbcAB1Lnr1WNI9VUAxRyMd3oHMnzfsLuQ,15057
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linkml_store/api/stores/duckdb/duckdb_database.py,sha256=L2tn8mKQWVjcssRpOODOOJHjIu2YRYN5xQJyaG8tBUA,11509
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linkml_store/api/stores/duckdb/mappings.py,sha256=tDce3W1Apwammhf4LS6cRJ0m4NiJ0eB7vOI_4U5ETY8,148
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linkml_store/api/stores/filesystem/__init__.py,sha256=rD6nsZLkMphS4EQSrGtjirYD32ENRIqv7Kllm5CLBMY,346
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linkml_store/api/stores/filesystem/filesystem_collection.py,sha256=9gqY2KRZsn_RWk4eKkxFd3_wcxs5YaXvcBI7GGJBMGE,6751
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linkml_store/api/stores/filesystem/filesystem_database.py,sha256=Ich707bWzgeq3tdv37wLLkM4Kb3lr4w3T1iftvbMqdw,2883
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linkml_store/api/stores/hdf5/__init__.py,sha256=l4cIh3v7P0nPbwGIsfuCMD_serQ8q8c7iuUA9W2Jb4o,97
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linkml_store/api/stores/hdf5/hdf5_collection.py,sha256=mnpLMYehn3PuaIjp2dXrIWu8jh-bdQ84X2Ku83jMdEY,3805
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linkml_store/api/stores/hdf5/hdf5_database.py,sha256=EZbjrpaqiNDEFvoD5dZNcGBXA8z6HRNL81emueTZWNw,2714
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linkml_store/api/stores/ibis/__init__.py,sha256=8Y80qhCEHCWO4JYhkGIKPSp3b60NBITYY5oGwaphhAk,134
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linkml_store/api/stores/ibis/ibis_collection.py,sha256=INlRfKL_le_UUJKZuljMGC6GtkhipXB5LoyA1z8-TAM,18952
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linkml_store/api/stores/ibis/ibis_database.py,sha256=RmlyKTUOjrot9SgePxAXQbzzD58BLETYyZ_vzzmp1-A,12436
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linkml_store/api/stores/mongodb/__init__.py,sha256=OSFCr7RQlDEe-O-Y0P_i912oAMK-L3pC7Cnj7sxlwAk,510
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linkml_store/api/stores/mongodb/mongodb_collection.py,sha256=lR18BdaVUbuJDIltuL42MnGJWyMa28XFi_x1PHb3u0M,14884
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linkml_store/api/stores/mongodb/mongodb_database.py,sha256=Lr47vVaJv_cgTCc2ArEma9R5T0agR_haaCJB6BageyI,4112
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linkml_store/api/stores/neo4j/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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linkml_store/api/stores/neo4j/neo4j_collection.py,sha256=a-Az5_ypdBMgeNyhrTW7q-ik-vYPCDDONIK7N_CDA9c,17449
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linkml_store/api/stores/neo4j/neo4j_database.py,sha256=QN6-iSshQwTk0GWDANmSCs8b_Oqd-KI5gI90nq82HWM,5574
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linkml_store/api/stores/solr/__init__.py,sha256=aAfnaN9mZOiIDj1NYz0Ll9fZF2gG7UU_vhP4SNCL2d8,36
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linkml_store/api/stores/solr/solr_collection.py,sha256=ZxRVs6q3tboqpWfuV2lUeaHmO178H8q3Hf8iEPAcwLE,8957
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linkml_store/api/stores/solr/solr_database.py,sha256=TFjqbY7jAkdrhAchbNg0E-mChSP7ogNwFExslbvX7Yo,2877
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linkml_store/api/stores/solr/solr_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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linkml_store/graphs/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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linkml_store/graphs/graph_map.py,sha256=bYRxv8n1YPnFqE9d6JKNmRawb8EAhsPlHhBue0gvtZE,712
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linkml_store/index/__init__.py,sha256=6SQzDe-WZSSqbGNsbCDfyPTyz0s9ISDKw1dm9xgQuT4,1396
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linkml_store/index/indexer.py,sha256=xzhkQvkl8LRjA3wBpIv9jrkLC6ATK81t__w04bm5Kb0,7711
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linkml_store/index/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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linkml_store/index/implementations/llm_indexer.py,sha256=8fBPSDjH_z5okJSqT5Pyy92IvHeX7hYVQrrKLTx5Kzc,7500
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linkml_store/index/implementations/simple_indexer.py,sha256=KnkFJtXTHnwjhD_D6ZK2rFhBID1dgCedcOVPEWAY2NU,1282
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linkml_store/inference/__init__.py,sha256=b8NAFNZjOYU_8gOvxdyCyoiHOOl5Ai2ckKs1tv7ZkkY,342
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linkml_store/inference/evaluation.py,sha256=YDFYaEu2QLSfFq4oyARrnKfTiPLtNF8irhhspgVDfdY,6013
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linkml_store/inference/inference_config.py,sha256=bbYiWf9eYdjEDzpMK-k5AfrhyzZlotVxPLZtjnVsA5Q,2283
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linkml_store/inference/inference_engine.py,sha256=r5Adx1ZOfe4eJ9XgMEYgXb9XhSDCzq7t4Sdvn4EXOUQ,7191
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linkml_store/inference/implementations/llm_inference_engine.py,sha256=qoMrzsEE5zDTHc6Y1nBQcSOYDjJETRqsZL7Zl7p3hLg,5407
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linkml_store/inference/implementations/rule_based_inference_engine.py,sha256=0IEY_fsHJPJy6QKbYQU_qE87RRnPOXQxPuJKXCQG8jU,6250
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linkml_store/utils/change_utils.py,sha256=O2rvSvgTKB60reLLz9mX5OWykAA_m93bwnUh5ZWa0EY,471
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linkml_store/utils/format_utils.py,sha256=FTJzl9Owzoe4FRK5dD5uXgPdgLWN6ydYDdOQN-_JHIw,17711
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linkml_store/utils/io.py,sha256=JHUrWDtlZC2jtN_PQZ4ypdGIyYlftZEN3JaCvEPs44w,884
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linkml_store/utils/mongodb_utils.py,sha256=Rl1YmMKs1IXwSsJIViSDChbi0Oer5cBnMmjka2TeQS8,4665
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linkml_store/utils/neo4j_utils.py,sha256=y3KPmDZ8mQmePgg0lUeKkeKqzEr2rV226xxEtHc5pRg,1266
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linkml_store/utils/object_utils.py,sha256=s6GIcfEODI8oALL_-ohtTlW_jwCRL48KaP1FGp4YS9M,6596
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linkml_store/utils/pandas_utils.py,sha256=ttkXGCJZcNhmy72SkY4ZfKbC-lyscpI74YLKznJ8AfM,3183
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linkml_store/utils/schema_utils.py,sha256=iJiZxo5NGr7v87h4DV6V9DrDOZHSswMRuf0N4V2rVtg,646
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linkml_store/utils/sql_utils.py,sha256=GF4s51BP3WmnYuBgtUiwo3uXvYX_ypyrknk4a6tIoSE,6210
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linkml_store/utils/stats_utils.py,sha256=4KqBb1bqDgAmq-1fJLLu5B2paPgoZZc3A-gnyVam4bI,1799
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linkml_store/webapi/html/base.html.j2,sha256=hoiV2uaSxxrQp7VuAZBOHueH7czyJMYcPBRN6dZFYhk,693
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linkml_store/webapi/html/collection_details.html.j2,sha256=FcCnkgtJAhfW84tVXQfAXP8eiq4BcrTeudZXQGL1Slg,385
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linkml_store/webapi/html/database_details.html.j2,sha256=qtXdavbZb0mohiObI9dvJtkifAS16LAOcgv8qwtQz70,451
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linkml_store/webapi/html/generic.html.j2,sha256=KtLaO2HUEF2Opq-OwHKgRKetNWe8IWc6JuIkxRPsywk,1018
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linkml_store-0.3.0.dist-info/METADATA,sha256=X-GO67m-w-KOIihCTrNxNyNCwHsyGENlkTp89FW3zWI,7550
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linkml_store-0.3.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
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linkml_store-0.3.0.dist-info/entry_points.txt,sha256=JdjSqGpOUBmbDaPFfLkqWi1hzSwlPxkkZxadllGlEsI,104
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linkml_store-0.3.0.dist-info/licenses/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
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The MIT License (MIT)
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THE SOFTWARE.
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