lorebase-store 0.2.3__tar.gz → 0.3.1__tar.gz

lorebase_store-0.3.1/LICENSE

@@ -0,0 +1,201 @@
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lorebase_store-0.3.1/PKG-INFO

@@ -0,0 +1,44 @@
+Metadata-Version: 2.5
+Name: lorebase-store
+Version: 0.3.1
+Summary: Lorebase store: persistence, repositories, migrations and materializer
+Project-URL: Homepage, https://github.com/aantenore/lorebase
+Project-URL: Documentation, https://aantenore.github.io/lorebase/
+Project-URL: Repository, https://github.com/aantenore/lorebase
+Project-URL: Changelog, https://github.com/aantenore/lorebase/blob/main/CHANGELOG.md
+Project-URL: Issues, https://github.com/aantenore/lorebase/issues
+Author: Antonio Antenore
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: knowledge-graph,mcp,ontology,postgres,versioning
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Database
+Requires-Python: >=3.12
+Requires-Dist: alembic>=1.13
+Requires-Dist: asyncpg>=0.29
+Requires-Dist: cryptography>=42
+Requires-Dist: lorebase-core<0.4,>=0.3
+Requires-Dist: lorebase-platform<0.4,>=0.3
+Requires-Dist: opentelemetry-api>=1.25
+Requires-Dist: pgvector>=0.3
+Requires-Dist: sqlalchemy[asyncio]>=2.0.30
+Description-Content-Type: text/markdown
+
+# lorebase-store
+
+Part of [Lorebase](https://github.com/aantenore/lorebase), an open-source ontology platform: a versioned, governed knowledge graph on Postgres with git-like branching and three-way merge.
+
+The persistence layer of Lorebase on Postgres with pgvector: repositories, Alembic migrations (shipped in the wheel) and the materializer of branch heads.
+
+```sh
+pip install lorebase-store
+```
+
+It is a library of the other Lorebase packages and has no command of its own.
+
+Documentation: [Store schema notes](https://aantenore.github.io/lorebase/store-schema-notes/) and the [documentation site](https://aantenore.github.io/lorebase/). License: Apache-2.0.

lorebase_store-0.3.1/README.md

@@ -0,0 +1,13 @@
+# lorebase-store
+
+Part of [Lorebase](https://github.com/aantenore/lorebase), an open-source ontology platform: a versioned, governed knowledge graph on Postgres with git-like branching and three-way merge.
+
+The persistence layer of Lorebase on Postgres with pgvector: repositories, Alembic migrations (shipped in the wheel) and the materializer of branch heads.
+
+```sh
+pip install lorebase-store
+```
+
+It is a library of the other Lorebase packages and has no command of its own.
+
+Documentation: [Store schema notes](https://aantenore.github.io/lorebase/store-schema-notes/) and the [documentation site](https://aantenore.github.io/lorebase/). License: Apache-2.0.

{lorebase_store-0.2.3 → lorebase_store-0.3.1}/migrations/versions/0001_initial_schema.py

@@ -7,7 +7,8 @@ Besides the tables, this revision installs what model metadata cannot express:
 - native enum types, created once and shared by several tables;
 - `store.layout.hash_partitions` hash partitions on `domain_id`;
 - lz4 TOAST compression of `tree_nodes.body`;
-- the HNSW index of `embeddings` for `store.embeddings.dims`;
+- the HNSW index of `embeddings` for `store.embeddings.dims`, with the build parameters of
+  `store.storage` (`hnsw_m`, `hnsw_ef_construction`);
 - row-level security on `domain_id` keyed to the transaction setting `lorebase.domain_ids`
   (comma-separated Domain ids), bypassed when `lorebase.bypass_rls` is `on`.
 
@@ -100,6 +101,21 @@ def _settings() -> tuple[int, int]:
     return store.layout.hash_partitions, store.embeddings.dims
 
 
+def _hnsw_options() -> str:
+    """`WITH (...)` of the HNSW index from `store.storage.hnsw_m` and `hnsw_ef_construction`
+    (null: pgvector's default)."""
+    storage = op.get_context().config.attributes["store_settings"].storage
+    options = [
+        f"{name} = {value}"
+        for name, value in (
+            ("m", storage.hnsw_m),
+            ("ef_construction", storage.hnsw_ef_construction),
+        )
+        if value is not None
+    ]
+    return f" WITH ({', '.join(options)})" if options else ""
+
+
 def _create_partitions(partitions: int) -> None:
     for table in HASH_PARTITIONED:
         for remainder in range(partitions):
@@ -1024,7 +1040,8 @@ def upgrade() -> None:
     _compress(partitions)
     op.execute(
         f"CREATE INDEX embeddings_hnsw_{dims} ON embeddings "
-        f"USING hnsw ((embedding::vector({dims})) vector_cosine_ops) WHERE dims = {dims}"
+        f"USING hnsw ((embedding::vector({dims})) vector_cosine_ops){_hnsw_options()} "
+        f"WHERE dims = {dims}"
     )
     _enable_row_security(partitions)
 

lorebase_store-0.3.1/migrations/versions/0038_reconciliation_candidates.py

@@ -0,0 +1,131 @@
+"""Reconciliation candidates and validity periods on provenance (design 10.6).
+
+`provenance.valid_from` and `valid_to` hold the validity period of the values of a `valid_time`
+Attribute; existing entries read as "no period" (metadata-only change, no backfill).
+`reconciliation_candidates` holds contradictions between Sources awaiting a decision, one per
+`(domain_id, branch, fingerprint)`. Under the `domain_isolation` policy like every table with
+a `domain_id`.
+
+Revision ID: 0038
+Revises: 0037
+Create Date: 2026-10-29 09:00:00.000000
+"""
+
+from __future__ import annotations
+
+from collections.abc import Sequence
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+revision: str = "0038"
+down_revision: str | Sequence[str] | None = "0037"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+CANDIDATES = "reconciliation_candidates"
+
+DOMAIN_VISIBLE = (
+    "current_setting('lorebase.bypass_rls', true) = 'on' "
+    "OR domain_id = ANY (string_to_array(current_setting('lorebase.domain_ids', true), ','))"
+)
+
+
+def upgrade() -> None:
+    for column in ("valid_from", "valid_to"):
+        op.add_column("provenance", sa.Column(column, sa.DateTime(timezone=True), nullable=True))
+    op.create_table(
+        CANDIDATES,
+        sa.Column("domain_id", sa.Text(), nullable=False),
+        sa.Column("id", sa.Text(), nullable=False),
+        sa.Column("branch", sa.Text(), nullable=False),
+        sa.Column("type", sa.Text(), nullable=False),
+        sa.Column("status", sa.Text(), server_default=sa.text("'open'"), nullable=False),
+        sa.Column("fingerprint", sa.LargeBinary(), nullable=False),
+        sa.Column("kind_id", sa.Text(), nullable=False),
+        sa.Column("keys", postgresql.JSONB(astext_type=sa.Text()), nullable=False),
+        sa.Column("attribute_id", sa.Text(), nullable=True),
+        sa.Column(
+            "claims",
+            postgresql.JSONB(astext_type=sa.Text()),
+            server_default=sa.text("'[]'::jsonb"),
+            nullable=False,
+        ),
+        sa.Column(
+            "signals",
+            postgresql.JSONB(astext_type=sa.Text()),
+            server_default=sa.text("'{}'::jsonb"),
+            nullable=False,
+        ),
+        sa.Column("claim_count", sa.Integer(), server_default=sa.text("0"), nullable=False),
+        sa.Column("proposal_id", sa.Text(), nullable=True),
+        sa.Column("decision", postgresql.JSONB(astext_type=sa.Text()), nullable=True),
+        sa.Column("decided_by", sa.Text(), nullable=True),
+        sa.Column("decided_at", sa.DateTime(timezone=True), nullable=True),
+        sa.Column(
+            "created_at",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            nullable=False,
+        ),
+        sa.Column(
+            "updated_at",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            nullable=False,
+        ),
+        sa.CheckConstraint(
+            "octet_length(fingerprint) = 32",
+            name=op.f("ck_reconciliation_candidates_fingerprint_h32"),
+        ),
+        sa.CheckConstraint(
+            "type IN ('duplicate', 'contradiction', 'superseded', 'stale')",
+            name=op.f("ck_reconciliation_candidates_type"),
+        ),
+        sa.CheckConstraint(
+            "status IN ('open', 'resolved', 'dismissed', 'obsolete')",
+            name=op.f("ck_reconciliation_candidates_status"),
+        ),
+        sa.ForeignKeyConstraint(
+            ["domain_id"],
+            ["domains.id"],
+            name=op.f("fk_reconciliation_candidates_domain_id_domains"),
+            ondelete="CASCADE",
+        ),
+        sa.PrimaryKeyConstraint("domain_id", "id", name=op.f("pk_reconciliation_candidates")),
+        sa.UniqueConstraint(
+            "domain_id",
+            "branch",
+            "fingerprint",
+            name=op.f("uq_reconciliation_candidates_domain_id_branch_fingerprint"),
+        ),
+    )
+    op.create_index(
+        op.f("ix_reconciliation_candidates_domain_id_branch_status_type"),
+        CANDIDATES,
+        ["domain_id", "branch", "status", "type"],
+    )
+    op.create_index(
+        op.f("ix_reconciliation_candidates_domain_id_branch_kind_id_keys"),
+        CANDIDATES,
+        ["domain_id", "branch", "kind_id", "keys"],
+    )
+    op.execute(f"ALTER TABLE {CANDIDATES} ENABLE ROW LEVEL SECURITY")
+    op.execute(f"ALTER TABLE {CANDIDATES} FORCE ROW LEVEL SECURITY")
+    op.execute(
+        f"CREATE POLICY domain_isolation ON {CANDIDATES} "
+        f"USING ({DOMAIN_VISIBLE}) WITH CHECK ({DOMAIN_VISIBLE})"
+    )
+
+
+def downgrade() -> None:
+    op.drop_index(
+        op.f("ix_reconciliation_candidates_domain_id_branch_kind_id_keys"), table_name=CANDIDATES
+    )
+    op.drop_index(
+        op.f("ix_reconciliation_candidates_domain_id_branch_status_type"), table_name=CANDIDATES
+    )
+    op.drop_table(CANDIDATES)
+    for column in ("valid_to", "valid_from"):
+        op.drop_column("provenance", column)

lorebase_store-0.3.1/migrations/versions/0039_reconciliation_lookups.py

@@ -0,0 +1,42 @@
+"""Indexes of reconciliation candidate lookups (design 10.6).
+
+`(domain_id, proposal_id)` serves the `reconciliation` Proposal check and the settlement of a
+merged Proposal; a GIN index (`jsonb_path_ops`) on `keys` serves the containment test of the
+Record page (`keys @> '["key"]'`), which the btree index on `(domain_id, branch, kind_id,
+keys)` cannot answer.
+
+Revision ID: 0039
+Revises: 0038
+Create Date: 2026-10-29 18:00:00.000000
+"""
+
+from __future__ import annotations
+
+from collections.abc import Sequence
+
+from alembic import op
+
+revision: str = "0039"
+down_revision: str | Sequence[str] | None = "0038"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+CANDIDATES = "reconciliation_candidates"
+BY_PROPOSAL = "ix_reconciliation_candidates_domain_id_proposal_id"
+BY_KEY = "ix_reconciliation_candidates_keys"
+
+
+def upgrade() -> None:
+    op.create_index(BY_PROPOSAL, CANDIDATES, ["domain_id", "proposal_id"])
+    op.create_index(
+        BY_KEY,
+        CANDIDATES,
+        ["keys"],
+        postgresql_using="gin",
+        postgresql_ops={"keys": "jsonb_path_ops"},
+    )
+
+
+def downgrade() -> None:
+    op.drop_index(BY_KEY, table_name=CANDIDATES)
+    op.drop_index(BY_PROPOSAL, table_name=CANDIDATES)

lorebase_store-0.3.1/migrations/versions/0040_source_written.py

@@ -0,0 +1,148 @@
+"""Last-written state of Sources (design 9.1 "Corrections that stick").
+
+`source_written` holds, per Source, target branch, Kind or Relation and key, the hashes of the
+values the Source last wrote and the Source branch Revision that holds them;
+`source_written_pending` the state a run carries in its open Proposal, moved to
+`source_written` when the Proposal merges. Both are empty at first: Sources seed their state
+on their next run. Under the `domain_isolation` policy like every table with a `domain_id`.
+
+Revision ID: 0040
+Revises: 0039
+Create Date: 2026-10-29 20:00:00.000000
+"""
+
+from __future__ import annotations
+
+from collections.abc import Sequence
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+revision: str = "0040"
+down_revision: str | Sequence[str] | None = "0039"
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
+
+WRITTEN = "source_written"
+PENDING = "source_written_pending"
+
+DOMAIN_VISIBLE = (
+    "current_setting('lorebase.bypass_rls', true) = 'on' "
+    "OR domain_id = ANY (string_to_array(current_setting('lorebase.domain_ids', true), ','))"
+)
+
+
+def _state_columns() -> list[sa.Column[object]]:
+    return [
+        sa.Column(
+            "written",
+            postgresql.JSONB(astext_type=sa.Text()),
+            server_default=sa.text("'{}'::jsonb"),
+            nullable=False,
+        ),
+        sa.Column("revision_id", sa.LargeBinary(), nullable=True),
+        sa.Column(
+            "value_revisions",
+            postgresql.JSONB(astext_type=sa.Text()),
+            server_default=sa.text("'{}'::jsonb"),
+            nullable=False,
+        ),
+        sa.Column("deleted", sa.Boolean(), server_default=sa.text("false"), nullable=False),
+    ]
+
+
+def _tail_columns() -> list[sa.Column[object]]:
+    return [
+        sa.Column("run_id", sa.Text(), nullable=False),
+        sa.Column(
+            "updated_at",
+            sa.DateTime(timezone=True),
+            server_default=sa.text("now()"),
+            nullable=False,
+        ),
+    ]
+
+
+def _isolate(table: str) -> None:
+    op.execute(f"ALTER TABLE {table} ENABLE ROW LEVEL SECURITY")
+    op.execute(f"ALTER TABLE {table} FORCE ROW LEVEL SECURITY")
+    op.execute(
+        f"CREATE POLICY domain_isolation ON {table} "
+        f"USING ({DOMAIN_VISIBLE}) WITH CHECK ({DOMAIN_VISIBLE})"
+    )
+
+
+def upgrade() -> None:
+    op.create_table(
+        WRITTEN,
+        sa.Column("domain_id", sa.Text(), nullable=False),
+        sa.Column("source_id", sa.Text(), nullable=False),
+        sa.Column("target_branch", sa.Text(), nullable=False),
+        sa.Column("element", sa.Text(), nullable=False),
+        sa.Column("key", sa.Text(), nullable=False),
+        *_state_columns(),
+        *_tail_columns(),
+        sa.CheckConstraint(
+            "octet_length(revision_id) = 32", name=op.f("ck_source_written_revision_id_h32")
+        ),
+        sa.ForeignKeyConstraint(
+            ["domain_id"],
+            ["domains.id"],
+            name=op.f("fk_source_written_domain_id_domains"),
+            ondelete="CASCADE",
+        ),
+        sa.PrimaryKeyConstraint(
+            "domain_id",
+            "source_id",
+            "target_branch",
+            "element",
+            "key",
+            name=op.f("pk_source_written"),
+        ),
+    )
+    op.create_table(
+        PENDING,
+        sa.Column("domain_id", sa.Text(), nullable=False),
+        sa.Column("proposal_id", sa.Text(), nullable=False),
+        sa.Column("element", sa.Text(), nullable=False),
+        sa.Column("key", sa.Text(), nullable=False),
+        sa.Column("source_id", sa.Text(), nullable=False),
+        sa.Column("target_branch", sa.Text(), nullable=False),
+        *_state_columns(),
+        sa.Column(
+            "preserve",
+            postgresql.JSONB(astext_type=sa.Text()),
+            server_default=sa.text("'[]'::jsonb"),
+            nullable=False,
+        ),
+        *_tail_columns(),
+        sa.CheckConstraint(
+            "octet_length(revision_id) = 32",
+            name=op.f("ck_source_written_pending_revision_id_h32"),
+        ),
+        sa.ForeignKeyConstraint(
+            ["domain_id"],
+            ["domains.id"],
+            name=op.f("fk_source_written_pending_domain_id_domains"),
+            ondelete="CASCADE",
+        ),
+        sa.PrimaryKeyConstraint(
+            "domain_id", "proposal_id", "element", "key", name=op.f("pk_source_written_pending")
+        ),
+    )
+    op.create_index(
+        op.f("ix_source_written_pending_domain_id_source_id_target_branch"),
+        PENDING,
+        ["domain_id", "source_id", "target_branch"],
+    )
+    _isolate(WRITTEN)
+    _isolate(PENDING)
+
+
+def downgrade() -> None:
+    op.drop_index(
+        op.f("ix_source_written_pending_domain_id_source_id_target_branch"), table_name=PENDING
+    )
+    op.drop_table(PENDING)
+    op.drop_table(WRITTEN)