linkml-store 0.0.0__py3-none-any.whl → 0.1.6__py3-none-any.whl

linkml_store/utils/sql_utils.py

@@ -1,5 +1,5 @@
 import logging
-from typing import Optional, Tuple, Type, Union
+from typing import Any, Optional, Tuple, Type, Union
 
 import sqlalchemy
 import sqlalchemy.sql.sqltypes as sqlt
@@ -17,6 +17,12 @@ TYPE_MAP = {
     sqlt.FLOAT: "float",
 }
 
+OP_MAP = {
+    "eq": "=",
+    "in": "ARRAY_CONTAINS",
+    "$contains": "ARRAY_CONTAINS",
+}
+
 
 def _map_type(typ: Type) -> str:
     for k, v in TYPE_MAP.items():
@@ -33,13 +39,40 @@ def where_clause_to_sql(query: Query) -> str:
     elif isinstance(query.where_clause, list):
         where_clause_sql = " AND ".join(query.where_clause)
     elif isinstance(query.where_clause, dict):
-        # TODO: bobby tables
-        where_clause_sql = " AND ".join([f"{k} = '{v}'" for k, v in query.where_clause.items()])
+        conjs = []
+        for k, v in query.where_clause.items():
+            conjs.extend(col_val_constraints_to_conjs(k, v))
+        where_clause_sql = " AND ".join(conjs)
+
     else:
         raise ValueError(f"Invalid where_clause type: {type(query.where_clause)}")
     return "WHERE " + where_clause_sql
 
 
+def col_val_constraints_to_conjs(col_name: str, val_constraints: Any) -> list:
+    if val_constraints is None:
+        return []
+
+    def _quote(v: Any):
+        if isinstance(v, str):
+            # escape internal vs
+            v = v.replace("'", "''")
+            return f"'{v}'"
+        else:
+            return v
+
+    if isinstance(val_constraints, dict):
+        conjs = []
+        for k, v in val_constraints.items():
+            if k in OP_MAP:
+                conjs.append(f"{OP_MAP[k]}({col_name}, {_quote(v)})")
+            else:
+                conjs.append(f"{col_name} {k} {_quote(v)}")
+        return conjs
+    else:
+        return [f"{col_name} = {_quote(val_constraints)}"]
+
+
 def query_to_sql(query: Query, count=False, limit=None, offset: Optional[int] = None):
     select_cols = query.select_cols if query.select_cols else ["*"]
     if count:
@@ -67,7 +100,7 @@ def query_to_sql(query: Query, count=False, limit=None, offset: Optional[int] =
     return "\n".join(sql_str)
 
 
-def facet_count_sql(query: Query, facet_column: Union[str, Tuple[str, ...]], multivalued=False) -> str:
+def facet_count_sql(query: Query, facet_column: Union[str, Tuple[str, ...]], multivalued=False, limit=100) -> str:
     # Create a modified WHERE clause that excludes conditions directly related to facet_column
     modified_where = None
     if query.where_clause:
@@ -82,12 +115,18 @@ def facet_count_sql(query: Query, facet_column: Union[str, Tuple[str, ...]], mul
         facet_column = ", ".join(facet_column)
     from_table = query.from_table
     if multivalued:
-        from_table = f"(SELECT UNNEST({facet_column}) as {facet_column} FROM {query.from_table})"
+        from_table = f"(SELECT UNNEST({facet_column}) as {facet_column} FROM {query.from_table}"
+        from_table += f" {modified_where}" if modified_where else ""
+        from_table += ")"
+    else:
+        from_table += f" {modified_where}" if modified_where else ""
     sql_str = [f"SELECT {facet_column}, COUNT(*) as count", f"FROM {from_table}"]
-    if modified_where:
-        sql_str.append(f"{modified_where}")
+    # if modified_where:
+    #    sql_str.append(f"{modified_where}")
     sql_str.append(f"GROUP BY {facet_column}")
     sql_str.append("ORDER BY count DESC")  # Optional, order by count for convenience
+    if limit is not None:
+        sql_str.append(f"LIMIT {limit}")
     return "\n".join(sql_str)
 
 

{linkml_store-0.0.0.dist-info → linkml_store-0.1.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: linkml-store
-Version: 0.0.0
+Version: 0.1.6
 Summary: linkml-store
 License: MIT
 Author: Author 1
@@ -14,17 +14,25 @@ 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: 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,<0.12.0)
+Requires-Dist: duckdb-engine (>=0.11.2)
+Requires-Dist: h5py ; extra == "h5py"
+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,<3.0.0) ; extra == "analytics"
+Requires-Dist: pandas (>=2.2.1) ; extra == "analytics"
 Requires-Dist: plotly ; extra == "analytics"
 Requires-Dist: pydantic (>=2.0.0,<3.0.0)
 Requires-Dist: pymongo ; extra == "mongodb"
@@ -36,9 +44,12 @@ Description-Content-Type: text/markdown
 
 # linkml-store
 
-This is the project description.
+An integration layer for multiple database backends
 
-# Acknowledgements
+Currently this software is alpha, and has only been tested with DuckDB backends. See the Tutorial for more information.
 
-This [cookiecutter](https://cookiecutter.readthedocs.io/en/stable/README.html) project was developed from the [monarch-project-template](https://github.com/monarch-initiative/monarch-project-template) template and will be kept up-to-date using [cruft](https://cruft.github.io/cruft/).
+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.
 

linkml_store-0.1.6.dist-info/RECORD

@@ -0,0 +1,41 @@
+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
+linkml_store/api/stores/duckdb/duckdb_collection.py,sha256=CUfZAi2Z_uQ8DywXXEKu-Of3E_9i4GOvUVnq8qnhSew,5859
+linkml_store/api/stores/duckdb/duckdb_database.py,sha256=3Hz01lLm8-32blkITlTurF4fd4VHSAvyFKYA1v_9NfM,6591
+linkml_store/api/stores/duckdb/mappings.py,sha256=S4MWetLpQcxOwwedXrZTqazxdaHIQXXbq4VRq9Ok4B4,123
+linkml_store/api/stores/hdf5/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml_store/api/stores/hdf5/hdf5_collection.py,sha256=B7kjbb9oOgxfp9KLP42PJXIyRlVoTuscn_OR-vNxyGc,3806
+linkml_store/api/stores/hdf5/hdf5_database.py,sha256=EZbjrpaqiNDEFvoD5dZNcGBXA8z6HRNL81emueTZWNw,2714
+linkml_store/api/stores/mongodb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml_store/api/stores/mongodb/mongodb_collection.py,sha256=OW1IhDonKyG6jkb6Kyl0ZIBr1TYKw8iiXbx2dFrvQfk,3959
+linkml_store/api/stores/mongodb/mongodb_database.py,sha256=QAdTi8XYLsdrEvEUUKb9qolCPeEXgfecTQ1bz9GCWDg,3670
+linkml_store/api/stores/solr/solr_collection.py,sha256=pxT67C9OU6aaoshGZGU5ZZptLZStKOTLIBd5qGTpx2I,4723
+linkml_store/api/stores/solr/solr_database.py,sha256=7idTQL740r1wAvK21joUMz_ajM_qzLqdfPUADa7Fa7U,2876
+linkml_store/api/stores/solr/solr_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml_store/cli.py,sha256=r6UggDS2iFC5yIhBECwn-5aKmI38SHuYIJ5TEA0-CeM,13667
+linkml_store/constants.py,sha256=x4ZmDsfE9rZcL5WpA93uTKrRWzCD6GodYXviVzIvR38,112
+linkml_store/index/__init__.py,sha256=k3fq2gzhoBv3_QEu4zMbEEoc0tEOUOcrEjKQVvWfASs,881
+linkml_store/index/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml_store/index/implementations/llm_indexer.py,sha256=LymhrQIeik0Qe8P2b3y2Lg7Y0P0OJ8_WjFwv-hbULj8,1069
+linkml_store/index/implementations/simple_indexer.py,sha256=CwUBb_GO_JUd-f-KW6R4i26PUV251BNTZ2cE6Qo1fH4,1251
+linkml_store/index/indexer.py,sha256=d_QEwJ5qEx2pkNR-QJ9hAn0pyJbhZIIT83GBFKhJA6I,3462
+linkml_store/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+linkml_store/utils/format_utils.py,sha256=lTrNVEywRziCjcrEeUC3hpZZo8yDQYgG-qBanQhBYrI,3081
+linkml_store/utils/io.py,sha256=JHUrWDtlZC2jtN_PQZ4ypdGIyYlftZEN3JaCvEPs44w,884
+linkml_store/utils/object_utils.py,sha256=8rKboygmwlk7tGgd2TffR7lfGrXXJcQ_hEpduKP_v2A,2214
+linkml_store/utils/sql_utils.py,sha256=TeAhAHXi1GA0f2UVrxbzStwe49Q7fN0mu5WZyfDk-s8,5651
+linkml_store-0.1.6.dist-info/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
+linkml_store-0.1.6.dist-info/METADATA,sha256=NmD8dE9YlmNI6USIP1us-2sbc5yhtXRRYGjkhukScDQ,2064
+linkml_store-0.1.6.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+linkml_store-0.1.6.dist-info/entry_points.txt,sha256=6ema3OkAkUK0ux8roEeRPtSW_Tylend5BABf-xRsZiU,53
+linkml_store-0.1.6.dist-info/RECORD,,

linkml_store-0.1.6.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+linkml-store=linkml_store.cli:cli
+

linkml_store/api/metadata.py

@@ -1,5 +0,0 @@
-from pydantic import BaseModel
-
-
-class MetaData(BaseModel):
-    pass

linkml_store-0.0.0.dist-info/RECORD

@@ -1,29 +0,0 @@
-linkml_store/__init__.py,sha256=jlU6WOUAn8cKIhzbTULmBTWpW9gZdEt7q_RI6KZN1bY,118
-linkml_store/api/__init__.py,sha256=Il3wGkN6evgc3OOWQYL7q3J-tRBs_0yQ3Nj-s6eo-0Y,284
-linkml_store/api/client.py,sha256=6zGzhTd6zJ-V5fzLbgljI6onq_XVvaxoeyXK5d1U9wM,4353
-linkml_store/api/collection.py,sha256=zr9iMXCJPsBOYLwO8I0dLIl01sVG4sgXtpgVdHJIVNo,11334
-linkml_store/api/database.py,sha256=oulUxyUGfq6dMQge___dYcevunDOIlLUBGTeewRZqDs,6682
-linkml_store/api/metadata.py,sha256=k9F6D_nuIZ0wWocj0ew2FYSKOc06CJWvwoUpHcrs7JA,69
-linkml_store/api/queries.py,sha256=5WgI_od_Qlpiza-u-XCrxL0F3Etf6mdeCCSSxeHT0PI,1698
-linkml_store/api/stores/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml_store/api/stores/duckdb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml_store/api/stores/duckdb/duckdb_collection.py,sha256=3hxwnRoY8pIZuW09yi4BSRDUT_pzTo9Mj82SBTT1aNw,4194
-linkml_store/api/stores/duckdb/duckdb_database.py,sha256=efTwzAoAc4YugBqNl9aQhlBzcPU4GDLwGQC5UPk_Uuw,6104
-linkml_store/api/stores/duckdb/mappings.py,sha256=S4MWetLpQcxOwwedXrZTqazxdaHIQXXbq4VRq9Ok4B4,123
-linkml_store/api/stores/mongodb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml_store/api/stores/mongodb/mongodb_collection.py,sha256=atFpJWTENwCBmRjtC5iWkwwV-3XnVr16A_nuXDS76Ig,2094
-linkml_store/api/stores/mongodb/mongodb_database.py,sha256=EpiTUftXlmOC8V4lPcrGOX2xq0leqWpmPVaZGsUMESI,3984
-linkml_store/constants.py,sha256=x4ZmDsfE9rZcL5WpA93uTKrRWzCD6GodYXviVzIvR38,112
-linkml_store/index/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml_store/index/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml_store/index/implementations/llm_index.py,sha256=JAxg1dIuU7W8ZtnsGcogbBUvyrPTZCbKhEFv-0lEKrk,1061
-linkml_store/index/implementations/simple_index.py,sha256=ep73dg86QqV7B7t_VoOK1weVx5RD0xvJ7uJPsszd5I0,1134
-linkml_store/index/index.py,sha256=uwgKtw76ch0qe5CbSj2Ft_WAhY94Qm5qLBJucl-VPWA,3420
-linkml_store/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml_store/utils/io.py,sha256=JHUrWDtlZC2jtN_PQZ4ypdGIyYlftZEN3JaCvEPs44w,884
-linkml_store/utils/sql_utils.py,sha256=sCM9GqEW6zZ3-2n5tsW7gzi0DerP6TXx3AJDY_0kCJ4,4557
-linkml_store-0.0.0.dist-info/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
-linkml_store-0.0.0.dist-info/METADATA,sha256=Ignb5ab4IwjIfm60g2yciUqYBb0IstFvABlOMFTygPk,1717
-linkml_store-0.0.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-linkml_store-0.0.0.dist-info/entry_points.txt,sha256=YdXo7B96u7fP8WX9cirGelqH0kjx7vGjT-w8hq8HFSE,54
-linkml_store-0.0.0.dist-info/RECORD,,

linkml_store-0.0.0.dist-info/entry_points.txt

@@ -1,3 +0,0 @@
-[console_scripts]
-linkml-store=linkml_store.cli:main
-