linkml-store 0.1.10__py3-none-any.whl → 0.1.11__py3-none-any.whl

linkml_store/utils/pandas_utils.py

@@ -0,0 +1,40 @@
+from typing import Dict, List, Tuple, Union
+
+import pandas as pd
+
+
+def facet_summary_to_dataframe_unmelted(
+    facet_summary: Dict[Union[str, Tuple[str, ...]], List[Tuple[Union[str, Tuple[str, ...]], int]]]
+) -> pd.DataFrame:
+    rows = []
+
+    for facet_type, facet_data in facet_summary.items():
+        if isinstance(facet_type, str):
+            # Single facet type
+            for category, value in facet_data:
+                rows.append({facet_type: category, "Value": value})
+        else:
+            # Multiple facet types
+            for cat_val_tuple in facet_data:
+                if len(cat_val_tuple) == 2:
+                    categories, value = cat_val_tuple
+                else:
+                    categories, value = cat_val_tuple[:-1], cat_val_tuple[-1]
+                row = {"Value": value}
+                for i, facet in enumerate(facet_type):
+                    row[facet] = categories[i]
+                rows.append(row)
+
+    df = pd.DataFrame(rows)
+
+    # Ensure all columns are present, fill with None if missing
+    all_columns = set(col for facet in facet_summary.keys() for col in (facet if isinstance(facet, tuple) else [facet]))
+    for col in all_columns:
+        if col not in df.columns:
+            df[col] = None
+
+    # Move 'Value' to the end
+    cols = [col for col in df.columns if col != "Value"] + ["Value"]
+    df = df[cols]
+
+    return df

linkml_store/utils/sql_utils.py

@@ -19,8 +19,9 @@ TYPE_MAP = {
 
 OP_MAP = {
     "eq": "=",
+    "$in": "ARRAY_CONTAINS",  ## mongodb
+    "$contains": "ARRAY_CONTAINS",  ## TODO: this is chromadb-specific
     "in": "ARRAY_CONTAINS",
-    "$contains": "ARRAY_CONTAINS",
 }
 
 

{linkml_store-0.1.10.dist-info → linkml_store-0.1.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml-store
-Version: 0.1.10
+Version: 0.1.11
 Summary: linkml-store
 License: MIT
 Author: Author 1
@@ -16,6 +16,7 @@ Provides-Extra: analytics
 Provides-Extra: app
 Provides-Extra: chromadb
 Provides-Extra: fastapi
+Provides-Extra: frictionless
 Provides-Extra: h5py
 Provides-Extra: llm
 Provides-Extra: map
@@ -30,11 +31,12 @@ 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 ; extra == "validation"
-Requires-Dist: linkml-runtime (>=1.8.0rc2)
+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"
@@ -122,6 +124,10 @@ 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
@@ -131,6 +137,33 @@ See [Indexing JSON](https://linkml.io/linkml-store/how-to/Index-Phenopackets.htm
 
 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
 

{linkml_store-0.1.10.dist-info → linkml_store-0.1.11.dist-info}/RECORD

@@ -1,48 +1,50 @@
 linkml_store/__init__.py,sha256=jlU6WOUAn8cKIhzbTULmBTWpW9gZdEt7q_RI6KZN1bY,118
 linkml_store/api/__init__.py,sha256=3CelcFEFz0y3MkQAzhQ9JxHIt1zFk6nYZxSmYTo8YZE,226
-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/client.py,sha256=8hfO7loCxGbqcmbKXqheRRh5AUbhHvFJxk1WDiYIYik,10890
+linkml_store/api/collection.py,sha256=Z5LoBitii7C8jKN6fGcajaxq63n8ktEh2Da9sAs1UIk,34674
+linkml_store/api/config.py,sha256=wgXmDhViayUOiAlFgu81G3fPlhMNBATfO4GUQ-TcIjk,4665
+linkml_store/api/database.py,sha256=mWF0pAoGZsk0A9WZP-4lUjbB7xs2nCwJYjH7r4rtBNE,26624
 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=LTcrvPEuSaQP1riGytUCdmmbFb_zZFl1mDG6TqqXfto,6246
-linkml_store/api/stores/duckdb/duckdb_database.py,sha256=O3hKEMLT5sn4JLL6te-xcUz2UT6zSQeqv6YwRUGZWK8,8175
+linkml_store/api/stores/duckdb/duckdb_collection.py,sha256=d9aYNFt9t8itNmhb6H2PdsxHL1dkYiW0N9wF8SATk1g,6767
+linkml_store/api/stores/duckdb/duckdb_database.py,sha256=WT7fBp2So9ht-JN2D4oFYoy4k_AfSGVgWKA9MTISFTQ,8664
 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=QPCuCHbxzbMPcsvxVp7kOAnT5_8m0kW60SZHtRo_87A,6403
-linkml_store/api/stores/filesystem/filesystem_database.py,sha256=HnHIv1aVtTiFSPY09s40QrMNhn_e-IKCYRXQk1S25Ak,2554
+linkml_store/api/stores/filesystem/filesystem_collection.py,sha256=9gqY2KRZsn_RWk4eKkxFd3_wcxs5YaXvcBI7GGJBMGE,6751
+linkml_store/api/stores/filesystem/filesystem_database.py,sha256=sV-lueyrh3R6edyWkwN6qKa7yjPc8PIcF1rxgox6oA4,2875
 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=R3zFca45V6_s8D_4f-tEhrFf_NH6z8UJj5suG7GshJc,6529
-linkml_store/api/stores/mongodb/mongodb_database.py,sha256=DKO-lMQzHyf-szVgH4tsP0UA68dlCFGv-oyVuXOIUd0,4003
+linkml_store/api/stores/mongodb/mongodb_collection.py,sha256=W-j1tkk8h1-zzjIRe-IYAnAOwlFSwr4fnDtgiu7RsVI,6695
+linkml_store/api/stores/mongodb/mongodb_database.py,sha256=LQ1Tb70pzLPx1HAvc8CGD7affyCJfOtXZnXJceTY97A,2450
 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_collection.py,sha256=ZlxC3JbVaHfSA4HuTeJTsp6qe48tHS6Fgel5jsqXcsM,4727
 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=Y8QUPMCRY5jkwwvz-78k5A1dM-nOj1lavZsBR2gGTMw,19325
+linkml_store/cli.py,sha256=4pxdrmN5hlKalNGLQgfkIIjWXfNENpqHoDu0SzJZuLY,20296
 linkml_store/constants.py,sha256=x4ZmDsfE9rZcL5WpA93uTKrRWzCD6GodYXviVzIvR38,112
-linkml_store/index/__init__.py,sha256=n5omzpf9nuQ8Dl2vjTVE4ATBXI0Lrs3HNmB25ZsPB1w,1076
+linkml_store/index/__init__.py,sha256=6SQzDe-WZSSqbGNsbCDfyPTyz0s9ISDKw1dm9xgQuT4,1396
 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/llm_indexer.py,sha256=LI5f8SLF_rJY5W6wZPLaUqpyoq-VDW_KqlCBNDNm_po,4827
 linkml_store/index/implementations/simple_indexer.py,sha256=KnkFJtXTHnwjhD_D6ZK2rFhBID1dgCedcOVPEWAY2NU,1282
-linkml_store/index/indexer.py,sha256=F130IKT6xZ9tTeH6D32sCcZkkLTTha8CETgZz_ksXyY,4737
+linkml_store/index/indexer.py,sha256=K-TDPzdTyGFo6iG4XI_A_3IpwDbKeiTIbdr85NIL5r8,4918
 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=kG-mTE9bZXfYvXsrShQN5Tz_Nxj-DFW_ykgJKVJlLQE,6581
+linkml_store/utils/file_utils.py,sha256=rQ7-XpmI6_Kx_dhEnI98muFRr0MmgI_kZ_9cgJBf_0I,1411
+linkml_store/utils/format_utils.py,sha256=m9jBeytym1xkuST1iWbvvdEQn0wPu2ODjYDDHF-WfeA,8608
 linkml_store/utils/io.py,sha256=JHUrWDtlZC2jtN_PQZ4ypdGIyYlftZEN3JaCvEPs44w,884
 linkml_store/utils/object_utils.py,sha256=is6T2gruvVKvWD5ZntcAl6Qi3L154FObEho_b_crTuE,2539
+linkml_store/utils/pandas_utils.py,sha256=INL8aZ5v2OeLg-Uzfa8P1cpnMMKA1DumiTB0q175tw8,1389
 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/utils/sql_utils.py,sha256=ecnc8GjeGK41AA-aA1dl7Gy9OBpr_xJ7Gbk-V8VKGCM,5728
 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
@@ -51,8 +53,8 @@ linkml_store/webapi/html/database_details.html.j2,sha256=qtXdavbZb0mohiObI9dvJtk
 linkml_store/webapi/html/databases.html.j2,sha256=a9BCWQYfPeFhdUd31CWhB0yWhTIFXQayO08JgjyqKoc,294
 linkml_store/webapi/html/generic.html.j2,sha256=1P5BKExQX5ZI94tUlMHK9BtTIXkP2ZnLAS014bPOgZM,1001
 linkml_store/webapi/main.py,sha256=VurUh7iAFB0pgdevguRgVcsOgFfKZecOLLkDeLUEGIc,20306
-linkml_store-0.1.10.dist-info/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
-linkml_store-0.1.10.dist-info/METADATA,sha256=Sgmk0smejNvDqBKqhVO-yF7H1YzMkdrZnA-0HNmLjxo,4746
-linkml_store-0.1.10.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-linkml_store-0.1.10.dist-info/entry_points.txt,sha256=gWxVsHqx-t-UKWFHFzawQTvs4is4vC1rCF5AeKyqWWk,101
-linkml_store-0.1.10.dist-info/RECORD,,
+linkml_store-0.1.11.dist-info/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
+linkml_store-0.1.11.dist-info/METADATA,sha256=Ax6ogNmpPOy5OQy2b4T1eGohOJYmDG15gk441ZVUYEM,5471
+linkml_store-0.1.11.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+linkml_store-0.1.11.dist-info/entry_points.txt,sha256=gWxVsHqx-t-UKWFHFzawQTvs4is4vC1rCF5AeKyqWWk,101
+linkml_store-0.1.11.dist-info/RECORD,,