tablassert 7.4.9__tar.gz → 7.4.11__tar.gz

tablassert-7.4.11/AGENTS.md

@@ -0,0 +1,50 @@
+# AGENTS.md — Tablassert
+
+## Fast Start
+
+- Python package, not a monorepo. Main code lives in `src/tablassert/`; tests live in `tests/`.
+- Install with `uv sync`. QC is not available unless you install an extra: `uv sync --extra qc` or `uv sync --extra qc-cuda`.
+- CLI entrypoint is `tablassert.cli:APP`. Real user commands are:
+  - `uv run tablassert build <graph.yaml>`
+  - `uv run tablassert validate <table.yaml> <datassert>`
+
+## Verify Changes
+
+- Match the repo hooks before finishing: `uv run ruff check --fix .`, `uv run ruff format .`, `uv run pyright`, `uv run pytest`.
+- Full hook run: `uv run pre-commit run --all-files`.
+- Focused test runs:
+  - Single test: `uv run pytest tests/test_lib.py::test_name`
+  - By keyword: `uv run pytest -k "pattern"`
+  - With print output: `uv run pytest -s tests/test_lib.py`
+- Docs build: `uv run --group dev mkdocs build`
+
+## High-Value Structure
+
+- `src/tablassert/cli.py` is the wiring layer: `build()` calls `build_pipeline()`, `validate()` calls `validate_pipeline()`.
+- `src/tablassert/ingests.py` loads YAML and expands table configs into section dicts.
+- `src/tablassert/lib.py` is the core pipeline:
+  - `Tcode.collect()` builds the per-section operation list.
+  - `compile_subgraph()` executes that list into parquet.
+  - `compile_graph()` aggregates subgraph parquets into KGX NDJSON.
+  - `resolve_many()` is the direct library API for batch entity resolution.
+- Entity resolution uses DuckDB shard files under `<datassert>/data/`. `src/tablassert/fullmap.py` hardcodes `SHARDS = 10`.
+
+## Repo-Specific Gotchas
+
+- Heavy dependencies are lazy-loaded per module with `TYPE_CHECKING` + `lazy_loader`. Follow the existing pattern instead of importing heavy packages eagerly.
+- `tests/conftest.py` autouse-mocks `httpx.head`, so model URL validation tests do not hit the network unless a test is explicitly marked otherwise.
+- Network-dependent tests are marked `@pytest.mark.network`; GPU QC tests are marked with both `network` and `gpu` in `tests/test_qc.py`.
+- QC runtime selection is strict in `src/tablassert/qc.py`: if `onnxruntime-gpu` is installed but `CUDAExecutionProvider` is unavailable, the code raises instead of falling back to CPU.
+- Downloader behavior in `src/tablassert/downloader.py` is two-path: direct `httpx` fetch for known file URLs, headless-browser fallback for browser-only sources. Keep tests around payload validation and cleanup intact when changing it.
+
+## Conventions That Matter Here
+
+- Start every module with `from __future__ import annotations`.
+- Annotate locals, not just function signatures.
+- Use `Optional[T]` / `Union[...]`, not `T | None`.
+- Prefer `Path` over raw path strings.
+- Function docs are usually `# ?` comments above the code, not docstrings.
+
+## Side Effects
+
+- The package writes working artifacts to hidden directories in the repo root: `.storassert/`, `.logassert/`, `.cachassert/`, and `.onnxassert/`.

{tablassert-7.4.9 → tablassert-7.4.11}/CHANGELOG.md

@@ -2,6 +2,11 @@
 
 All notable changes to this project are documented in this file.
 
+## 7.4.10 - 2026-05-29
+
+### Changes
+- Enforced explicit `biolink:` namespace prefix on predicates and qualifiers emitted by `compile_subgraph()` in `lib.py`. Both `self.statement.predicate` and `x.qualifier` (in the qualifier loop) are now prefixed via `add("biolink:", ...)`, ensuring all output edges carry fully-qualified Biolink CURIEs rather than bare predicate/qualifier names.
+
 ## 7.4.9 - 2026-05-26
 
 ### Bug Fixes

{tablassert-7.4.9 → tablassert-7.4.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tablassert
-Version: 7.4.9
+Version: 7.4.11
 Summary: Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution and quality control built in.
 Project-URL: Homepage, https://github.com/SkyeAv/Tablassert
 Project-URL: Source, https://github.com/SkyeAv/Tablassert

tablassert-7.4.11/docs/changelog.md

@@ -0,0 +1,11 @@
+# Changelog
+
+The canonical release history lives in the repository root at [`CHANGELOG.md`](https://github.com/SkyeAv/Tablassert/blob/main/CHANGELOG.md).
+
+## Current Release Notes
+
+## 7.4.10 - 2026-05-29
+
+### Changes
+
+- Enforced explicit `biolink:` namespace prefix on predicates and qualifiers emitted by `compile_subgraph()` in `lib.py`. Both `self.statement.predicate` and `x.qualifier` (in the qualifier loop) are now prefixed via `add("biolink:", ...)`, ensuring all output edges carry fully-qualified Biolink CURIEs rather than bare predicate/qualifier names.

{tablassert-7.4.9 → tablassert-7.4.11}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "tablassert"
-version = "7.4.9"
+version = "7.4.11"
 description = "Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution and quality control built in."
 authors = [
     { name = "Skye Lane Goetz", email = "sgoetz@isbscience.org" }
@@ -100,7 +100,7 @@ dev = [
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
-markers = ["network: requires internet", "gpu: requires CUDAExecutionProvider"]
+markers = ["network: requires internet", "gpu: requires CUDAExecutionProvider", "datassert: requires the datassert DuckDB shards"]
 
 [tool.ruff]
 line-length = 120

{tablassert-7.4.9 → tablassert-7.4.11}/src/tablassert/cli.py

@@ -57,29 +57,30 @@ def build_pipeline(graph_configuration_file: Path, progress: "PipelineProgress")
     sections: list[dict[str, Any]] = list(chain.from_iterable(temp))
     n: int = len(sections)
 
-    # * Build TCode (3/6)
-    progress.stage(f"Building TCode | Sections: {n}")
-    advance = progress.section_loop(n, "TCode")
-    tcode: list[Tcode] = []
-    for idx, s in enumerate(sections, start=1):
-        try:
-            tcode.append(
-                Tcode.model_validate(
-                    {**s, "number": idx, "store": (STORE / f"{mkhash(s)}.parquet"), "log": g.log, "qc": g.qc}
-                )
-            )
-        except pydantic.ValidationError as e:
-            raise RuntimeError(
-                f"02 | FAILED VALIDATION | CONFIG: {graph_configuration_file} | IDX: {idx} | HASH: {mkhash(s)} | PYDANTIC: {flatten_pydantic_error(e)}"
-            ) from e
-        advance(format_section_oneline(tcode[-1]))
-
     with ExitStack() as stack:
         conns: list[object] = [
             stack.enter_context(duckdb.connect(g.datassert / "data" / f"{x}.duckdb", read_only=True))
             for x in range(SHARDS)
         ]
 
+        # * Build TCode (3/6)
+        progress.stage(f"Building TCode | Sections: {n}")
+        advance = progress.section_loop(n, "TCode")
+        tcode: list[Tcode] = []
+        for idx, s in enumerate(sections, start=1):
+            try:
+                tcode.append(
+                    Tcode.model_validate(
+                        {**s, "number": idx, "store": (STORE / f"{mkhash(s)}.parquet"), "log": g.log, "qc": g.qc},
+                        context={"conns": conns},
+                    )
+                )
+            except pydantic.ValidationError as e:
+                raise RuntimeError(
+                    f"02 | FAILED VALIDATION | CONFIG: {graph_configuration_file} | IDX: {idx} | HASH: {mkhash(s)} | PYDANTIC: {flatten_pydantic_error(e)}"
+                ) from e
+            advance(format_section_oneline(tcode[-1]))
+
         # * Collect Instructions (4/6)
         progress.stage(f"Collecting Instructions | Sections: {n}")
         advance = progress.section_loop(n, "Collect")
@@ -105,8 +106,9 @@ def build_pipeline(graph_configuration_file: Path, progress: "PipelineProgress")
     logger.info(f"BUILD DONE | SECTIONS: {n} | NAME: {g.name} | VERSION: {g.version}")
 
 
-def validate_pipeline(table_configuration_file: Path, progress: "PipelineProgress") -> None:
+def validate_pipeline(table_configuration_file: Path, datassert: Path, progress: "PipelineProgress") -> None:
     # ? Validate Section Syntax From A Configuration File
+    from tablassert.fullmap import SHARDS
     from tablassert.ingests import from_yaml, to_sections
     from tablassert.lib import Tcode
     from tablassert.progress import flatten_pydantic_error
@@ -124,27 +126,32 @@ def validate_pipeline(table_configuration_file: Path, progress: "PipelineProgres
     # * Validate Section Syntax (3/3)
     progress.stage(f"Validating Section Syntax | Sections: {n}")
     advance = progress.section_loop(n, "Validate")
-    for idx, s in enumerate(sections, start=1):
-        h: str = mkhash(s)
-        try:
-            Tcode.model_validate({**s, "number": idx, "store": (STORE / f"{h}.parquet")})
-        except pydantic.ValidationError as e:
-            raise RuntimeError(
-                f"02 | FAILED VALIDATION | CONFIG: {table_configuration_file} | IDX: {idx} | HASH: {h} | PYDANTIC: {flatten_pydantic_error(e)}"
-            ) from e
-        advance(f"#{idx} | HASH: {h}")
+    with ExitStack() as stack:
+        conns: list[object] = [
+            stack.enter_context(duckdb.connect(datassert / "data" / f"{x}.duckdb", read_only=True))
+            for x in range(SHARDS)
+        ]
+        for idx, s in enumerate(sections, start=1):
+            h: str = mkhash(s)
+            try:
+                Tcode.model_validate({**s, "number": idx, "store": (STORE / f"{h}.parquet")}, context={"conns": conns})
+            except pydantic.ValidationError as e:
+                raise RuntimeError(
+                    f"02 | FAILED VALIDATION | CONFIG: {table_configuration_file} | IDX: {idx} | HASH: {h} | PYDANTIC: {flatten_pydantic_error(e)}"
+                ) from e
+            advance(f"#{idx} | HASH: {h}")
 
     logger.info(f"VALIDATE DONE | SECTIONS: {n} | CONFIG: {table_configuration_file.name}")
 
 
-def run(stages: int, fn: Any, arg: Path) -> None:
+def run(stages: int, fn: Any, *args: Path) -> None:
     from tablassert.log import LOG_FORMAT, logger
     from tablassert.progress import PipelineProgress
 
     with PipelineProgress(total_stages=stages) as progress:
         sink_id: int = logger.add(progress.log_sink, level="INFO", format=LOG_FORMAT)
         try:
-            fn(arg, progress)
+            fn(*args, progress)
         finally:
             logger.remove(sink_id)
 
@@ -156,6 +163,6 @@ def build(graph_configuration_file: Path) -> None:
 
 
 @APP.command
-def validate(table_configuration_file: Path) -> None:
-    """Validate section syntax from a YAML configuration file."""
-    run(3, validate_pipeline, table_configuration_file)
+def validate(table_configuration_file: Path, datassert: Path) -> None:
+    """Validate section syntax from a YAML configuration file against a datassert directory."""
+    run(3, validate_pipeline, table_configuration_file, datassert)

{tablassert-7.4.9 → tablassert-7.4.11}/src/tablassert/fullmap.py

@@ -51,7 +51,9 @@ def distinct(lf: pl.LazyFrame, l1: str, l2: str, col: str = "term") -> pl.LazyFr
 
     terms: pl.LazyFrame = pl.concat([t1, t2]).unique(subset=[col], keep="first")
 
-    bad: str = r"^\d+$|^(none|nan|na|null|unknown)$|^$"
+    bad: str = (
+        r"^\d+$|^(none|nan|na|null|unknown|not applicable|p value|variable|result|exposure|expression|symbol)$|^$"
+    )
     terms = terms.filter(~pl.col(col).str.contains(bad))
     return terms.with_columns((plh.col(col).nchash.xxhash64() % SHARDS).alias("shard"))  # pyright: ignore
 
@@ -150,15 +152,15 @@ def log_unmatched(
 ) -> None:
     # * Log Unmatched Entities
     level_one: pl.LazyFrame = terms.filter(pl.col("nlp level") == 1)
-    antimatches: pl.LazyFrame = level_one.join(matches.lazy().select("term"), left_on="term", right_on="term", how="anti")
+    antimatches: pl.LazyFrame = level_one.join(
+        matches.lazy().select("term"), left_on="term", right_on="term", how="anti"
+    )
 
     # ! Collection Point: Requires Eager
     unnmatched: pl.DataFrame = antimatches.select("term").unique().collect()
     if unnmatched.height > 0:
         for term in unnmatched.get_column("term").to_list():
-            logger.info(
-                f"FAILED | STORE: {section_hash} | CONFIG: {config_file} | COL: {col} | VALUE: {term!r}"
-            )
+            logger.info(f"FAILED | STORE: {section_hash} | CONFIG: {config_file} | COL: {col} | VALUE: {term!r}")
 
 
 def resolve(

{tablassert-7.4.9 → tablassert-7.4.11}/src/tablassert/lib.py

@@ -342,8 +342,8 @@ class Tcode(Section):
                 [op for x in self.annotations for op in self.encoding(x, x.annotation)] if self.annotations else None,
                 self.node(self.statement.subject, "subject", conns),
                 self.node(self.statement.object, "object", conns),
-                (value, ("predicate", self.statement.predicate)),
-                [op for x in self.statement.qualifiers for op in self.node(x, x.qualifier, conns)]
+                (value, ("predicate", add("biolink:", self.statement.predicate))),
+                [op for x in self.statement.qualifiers for op in self.node(x, add("biolink:", x.qualifier), conns)]
                 if self.statement.qualifiers
                 else None,
                 (value, ("syntax", self.syntax)),

{tablassert-7.4.9 → tablassert-7.4.11}/src/tablassert/models.py

@@ -25,6 +25,9 @@ from tablassert.enums import (
     Tokens,
 )
 
+from tablassert.fullmap import resolve
+from tablassert.nlp import level_one, level_two
+
 if TYPE_CHECKING:
     import httpx
     import polars as pl
@@ -315,6 +318,35 @@ class Annotation(Encoding):
         return annotation.replace("_", " ").strip()
 
 
+def resolves_value_encodings(statement: Statement, conns: list[object]) -> None:
+    # ? Resolve Every Value-Method Literal Against The Shared Datassert Shards
+    nodes: list[tuple[str, NodeEncoding]] = [("subject", statement.subject), ("object", statement.object)]
+    if statement.qualifiers:
+        nodes += [(q.qualifier, q) for q in statement.qualifiers]
+
+    for label, node in nodes:
+        if not eq(node.method, EncodingMethods.VALUE):
+            continue
+
+        term: str = str(node.encoding)
+        lf: pl.LazyFrame = pl.DataFrame({"term": [term]}).lazy()
+        lf = level_one(lf, "term")
+        lf = level_two(lf, "term")
+        resolved: pl.DataFrame = resolve(
+            lf,
+            "term",
+            conns,
+            taxon=str(node.taxon) if node.taxon else None,
+            prioritize=node.prioritize,
+            avoid=node.avoid,
+            log=False,
+            column_context=False,
+        ).collect()
+        if resolved.height == 0:
+            msg: str = f"21 | value encoding {term!r} in {label!r} did not resolve against datassert"
+            raise ValueError(msg)
+
+
 class Section(TablaBase):
     # ? Pydantic "Section" Model And Coercion
     syntax: Syntaxes = Field(Syntaxes.TC3, description="Section configuration syntax version.")
@@ -326,6 +358,16 @@ class Section(TablaBase):
         None, description="Optional extra encoded columns added to each row."
     )
 
+    @field_validator("statement", mode="after")
+    @classmethod
+    def value_encodings_resolve(cls, statement: Statement, info: Any) -> Statement:
+        # ? Ensure Value-Method Encodings Resolve Against The Shared Datassert Shards
+        conns: Optional[list[object]] = info.context.get("conns") if info.context else None
+        if conns is None:
+            return statement  # * skip without shared connections (contextless path)
+        resolves_value_encodings(statement, conns)
+        return statement
+
 
 class Graph(TablaBase):
     # ? Pydantic "Graph" Configuration

{tablassert-7.4.9 → tablassert-7.4.11}/src/tablassert/progress.py

@@ -35,8 +35,7 @@ def format_section_oneline(x: "Tcode") -> str:
     else:
         source_detail = f"TEXT({(x.source.delimiter or ',')!r})"  # pyright: ignore
     return (
-        f"#{x.number} | HASH: {x.store.stem} | SOURCE: {source_detail} "
-        f"| CONFIG: {x.config.name} | STATUS: {x.status}"
+        f"#{x.number} | HASH: {x.store.stem} | SOURCE: {source_detail} | CONFIG: {x.config.name} | STATUS: {x.status}"
     )
 
 

{tablassert-7.4.9 → tablassert-7.4.11}/tests/conftest.py

@@ -1,7 +1,8 @@
 from __future__ import annotations
 
+import os
 from pathlib import Path
-from typing import Any
+from typing import Any, Optional
 
 import httpx
 import pytest
@@ -26,3 +27,15 @@ def mockhttpxhead(monkeypatch: pytest.MonkeyPatch) -> None:
 @pytest.fixture
 def fixtures_path() -> Path:
     return Path(__file__).parent / "fixtures"
+
+
+@pytest.fixture
+def datassert_dir() -> Path:
+    # ? Shared Datassert Shard Directory (Skipped When Unavailable)
+    env: Optional[str] = os.environ.get("DATASSERT")
+    if not env:
+        pytest.skip("DATASSERT env var not set; skipping datassert-dependent test")
+    directory: Path = Path(env)
+    if not (directory / "data" / "0.duckdb").is_file():
+        pytest.skip(f"datassert shard data/0.duckdb not found under {directory}")
+    return directory

{tablassert-7.4.9 → tablassert-7.4.11}/tests/test_models.py

@@ -3,9 +3,11 @@ from __future__ import annotations
 from pathlib import Path
 from typing import Any
 
+import polars as pl
 import pytest
 from pydantic import ValidationError
 
+import tablassert.models as models
 from tablassert.enums import Categories
 from tablassert.ingests import from_yaml
 from tablassert.models import (
@@ -280,3 +282,193 @@ def test_section_with_annotations() -> None:
         ],
     )
     assert len(section.annotations) == 2  # pyright: ignore
+
+
+# ? Value Encoding Resolves Against Datassert (Context-Aware Pass)
+def test_value_encoding_resolves_pass(monkeypatch: pytest.MonkeyPatch) -> None:
+    def fake_resolve(_lf: Any, _col: str, _conns: list[object], **_kwargs: Any) -> Any:
+        return pl.DataFrame({"resolved": ["YES"]}).lazy()
+
+    monkeypatch.setattr(models, "resolve", fake_resolve)
+    section: Section = Section.model_validate(
+        {
+            "source": {"local": "./t.tsv", "url": "https://example.com/t.tsv", "kind": "text"},
+            "statement": {
+                "subject": {"method": "value", "encoding": "BRCA1"},
+                "object": {"method": "value", "encoding": "TP53"},
+            },
+            "provenance": {
+                "repo": "PMC",
+                "publication": "PMC000",
+                "contributors": [{"kind": "curation", "name": "T", "date": "2025"}],
+            },
+        },
+        context={"conns": [object()]},
+    )
+    assert section.statement.subject.encoding == "BRCA1"
+
+
+# ? Value Encoding Fails To Resolve Raises Code 21
+def test_value_encoding_resolves_fail(monkeypatch: pytest.MonkeyPatch) -> None:
+    def fake_resolve_empty(_lf: Any, _col: str, _conns: list[object], **_kwargs: Any) -> Any:
+        return pl.DataFrame({"resolved": []}).lazy()
+
+    monkeypatch.setattr(models, "resolve", fake_resolve_empty)
+    with pytest.raises(ValidationError) as exc_info:
+        Section.model_validate(
+            {
+                "source": {"local": "./t.tsv", "url": "https://example.com/t.tsv", "kind": "text"},
+                "statement": {
+                    "subject": {"method": "value", "encoding": "BRCA1"},
+                    "object": {"method": "value", "encoding": "TP53"},
+                },
+                "provenance": {
+                    "repo": "PMC",
+                    "publication": "PMC000",
+                    "contributors": [{"kind": "curation", "name": "T", "date": "2025"}],
+                },
+            },
+            context={"conns": [object()]},
+        )
+    assert "21 |" in str(exc_info.value)
+
+
+# ? Value Encoding Validator Skips Without Context
+def test_value_encoding_skips_without_context(monkeypatch: pytest.MonkeyPatch) -> None:
+    def fake_resolve_empty(_lf: Any, _col: str, _conns: list[object], **_kwargs: Any) -> Any:
+        return pl.DataFrame({"resolved": []}).lazy()
+
+    monkeypatch.setattr(models, "resolve", fake_resolve_empty)
+    section: Section = Section(  # pyright: ignore
+        source={"local": "./t.tsv", "url": "https://example.com/t.tsv", "kind": "text"},
+        statement={
+            "subject": {"method": "value", "encoding": "BRCA1"},
+            "object": {"method": "value", "encoding": "TP53"},
+        },
+        provenance={
+            "repo": "PMC",
+            "publication": "PMC000",
+            "contributors": [{"kind": "curation", "name": "T", "date": "2025"}],
+        },
+    )
+    assert section.statement.subject.encoding == "BRCA1"
+
+
+# ? Column Method Encodings Are Not Checked
+def test_column_encoding_not_checked(monkeypatch: pytest.MonkeyPatch) -> None:
+    def boom_resolve(_lf: Any, _col: str, _conns: list[object], **_kwargs: Any) -> Any:
+        raise AssertionError("resolve must not be called for column-method encodings")
+
+    monkeypatch.setattr(models, "resolve", boom_resolve)
+    section: Section = Section.model_validate(
+        {
+            "source": {"local": "./t.tsv", "url": "https://example.com/t.tsv", "kind": "text"},
+            "statement": {
+                "subject": {"method": "column", "encoding": "A"},
+                "object": {"method": "column", "encoding": "B"},
+            },
+            "provenance": {
+                "repo": "PMC",
+                "publication": "PMC000",
+                "contributors": [{"kind": "curation", "name": "T", "date": "2025"}],
+            },
+        },
+        context={"conns": [object()]},
+    )
+    assert section.statement.subject.encoding == "A"
+
+
+# ? Qualifier Value Encoding Is Checked Against Datassert
+def test_qualifier_value_encoding_checked(monkeypatch: pytest.MonkeyPatch) -> None:
+    def fake_resolve(lf: Any, col: str, _conns: list[object], **_kwargs: Any) -> Any:
+        term: str = str(lf.collect().get_column(col).to_list()[0])
+        if term in ("brca1", "tp53"):
+            return pl.DataFrame({"resolved": ["YES"]}).lazy()
+        return pl.DataFrame({"resolved": []}).lazy()
+
+    monkeypatch.setattr(models, "resolve", fake_resolve)
+    with pytest.raises(ValidationError) as exc_info:
+        Section.model_validate(
+            {
+                "source": {"local": "./t.tsv", "url": "https://example.com/t.tsv", "kind": "text"},
+                "statement": {
+                    "subject": {"method": "value", "encoding": "BRCA1"},
+                    "object": {"method": "value", "encoding": "TP53"},
+                    "qualifiers": [
+                        {"qualifier": "disease_context_qualifier", "method": "value", "encoding": "ZZZNOTAREALGENE123"}
+                    ],
+                },
+                "provenance": {
+                    "repo": "PMC",
+                    "publication": "PMC000",
+                    "contributors": [{"kind": "curation", "name": "T", "date": "2025"}],
+                },
+            },
+            context={"conns": [object()]},
+        )
+    assert "21 |" in str(exc_info.value)
+
+
+# ? Real Value Encoding Resolves Against The Datassert Shards
+@pytest.mark.datassert
+def test_real_value_encoding_resolves(datassert_dir: Path) -> None:
+    from contextlib import ExitStack
+
+    import duckdb
+
+    from tablassert.fullmap import SHARDS
+
+    with ExitStack() as stack:
+        conns: list[object] = [
+            stack.enter_context(duckdb.connect(datassert_dir / "data" / f"{x}.duckdb", read_only=True))
+            for x in range(SHARDS)
+        ]
+        section: Section = Section.model_validate(
+            {
+                "source": {"local": "./t.tsv", "url": "https://example.com/t.tsv", "kind": "text"},
+                "statement": {
+                    "subject": {"method": "value", "encoding": "BRCA1"},
+                    "object": {"method": "value", "encoding": "TP53"},
+                },
+                "provenance": {
+                    "repo": "PMC",
+                    "publication": "PMC000",
+                    "contributors": [{"kind": "curation", "name": "T", "date": "2025"}],
+                },
+            },
+            context={"conns": conns},
+        )
+        assert section.statement.subject.encoding == "BRCA1"
+
+
+# ? Real Value Encoding Failure Raises Code 21
+@pytest.mark.datassert
+def test_real_value_encoding_fails(datassert_dir: Path) -> None:
+    from contextlib import ExitStack
+
+    import duckdb
+
+    from tablassert.fullmap import SHARDS
+
+    with ExitStack() as stack:
+        conns: list[object] = [
+            stack.enter_context(duckdb.connect(datassert_dir / "data" / f"{x}.duckdb", read_only=True))
+            for x in range(SHARDS)
+        ]
+        with pytest.raises(ValidationError) as exc_info:
+            Section.model_validate(
+                {
+                    "source": {"local": "./t.tsv", "url": "https://example.com/t.tsv", "kind": "text"},
+                    "statement": {
+                        "subject": {"method": "value", "encoding": "ZZZNOTAREALGENE123"},
+                        "object": {"method": "value", "encoding": "TP53"},
+                    },
+                    "provenance": {
+                        "repo": "PMC",
+                        "publication": "PMC000",
+                        "contributors": [{"kind": "curation", "name": "T", "date": "2025"}],
+                    },
+                },
+                context={"conns": conns},
+            )
+        assert "21 |" in str(exc_info.value)

{tablassert-7.4.9 → tablassert-7.4.11}/uv.lock

@@ -2360,7 +2360,7 @@ wheels = [
 
 [[package]]
 name = "tablassert"
-version = "7.4.9"
+version = "7.4.11"
 source = { editable = "." }
 dependencies = [
     { name = "cyclopts" },

tablassert-7.4.9/AGENTS.md

@@ -1,168 +0,0 @@
-# AGENTS.md — Tablassert
-
-Guidance for AI coding agents working in this repository.
-
-## Project Overview
-
-Tablassert is a Python package (>=3.11) for tabular data assertion, normalization, and optional quality control. It builds declarative knowledge graphs from tabular data, exporting NCATS Translator-compliant KGX NDJSON. Uses **Polars** DataFrames, **DuckDB** for entity resolution, and **ONNX/BioBERT** for QC when enabled. CLI built with **cyclopts**. Models built with **Pydantic v2**.
-
-## Quick Reference
-
-| Task | Command |
-|---|---|
-| Install | `uv sync` |
-| Run CLI | `uv run tablassert` |
-| Lint | `uv run ruff check .` |
-| Lint (fix) | `uv run ruff check --fix .` |
-| Format | `uv run ruff format .` |
-| Format check | `uv run ruff format --check .` |
-| Type check | `uv run pyright` |
-| All checks | `uv run pre-commit run --all-files` |
-| Run all tests | `uv run pytest` |
-| Run single test | `uv run pytest tests/test_foo.py::test_name` |
-| Run by keyword | `uv run pytest -k "test_pattern"` |
-| Run with print | `uv run pytest -s tests/test_foo.py` |
-| Build | `uv build` |
-| Build docs | `uv run --group dev mkdocs build` |
-| Add dependency | `uv add <package>` |
-| Add dev dependency | `uv add --group dev <package>` |
-
-## Repository Structure
-
-```
-src/tablassert/
-  cli.py          # cyclopts CLI (entry point: tablassert.cli:APP)
-  lib.py          # Core logic: encodings, data loading, Tcode(Section) class
-  models.py       # Pydantic v2 models (TablaBase base class)
-  enums.py        # str, Enum subclasses (Tokens, Repositories, Comparisons, etc.)
-  fullmap.py      # NER / entity resolution (DuckDB, 10 shards)
-  qc.py           # Quality control (ONNX/BioBERT, sentence_transformers)
-  nlp.py          # Text normalization (level_one: strip+lowercase, level_two: regex)
-  ingests.py      # YAML ingestion: from_yaml(), to_sections(), fastmerge()
-  downloader.py   # httpx-based file downloads with retries
-  progress.py     # Rich progress bars for pipeline stages
-  utils.py        # Hashing (xxhash), STORE path, namespace UUIDs
-  log.py          # loguru logger → .logassert/tablassert.log; cat() helper for category tagging
-  __init__.py     # Empty file (lazy loading is per-module, not here)
-docs/             # MkDocs documentation source
-mkdocs.yml        # MkDocs configuration
-pyproject.toml    # Project config, dependencies, tool settings
-tests/            # Test directory (at repo root)
-```
-
-- `conftest.py` provides a `fixtures_path` fixture returning `Path(__file__).parent / "fixtures"`.
-- pytest configured via `pyproject.toml` `[tool.pytest.ini_options]` with `testpaths = ["tests"]`.
-- pytest markers: `network` requires internet; `gpu` requires `CUDAExecutionProvider`.
-- Test fixtures: `tests/fixtures/` contains YAML files for Section model tests.
-- Test modules: `test_downloader.py`, `test_enums.py`, `test_fullmap.py`, `test_ingests.py`, `test_lib.py`, `test_models.py`, `test_nlp.py`, `test_utils.py`.
-
-## Code Style
-
-### Imports
-
-- Every file starts with `from __future__ import annotations`
-- Heavy dependencies are loaded **lazily per-module** using this pattern:
-  ```python
-  from typing import TYPE_CHECKING
-  import lazy_loader as Lazy
-
-  if TYPE_CHECKING:
-      import polars as pl
-  else:
-      pl = Lazy.load("polars")
-  ```
-- Lazy-loaded deps: `polars`, `duckdb`, `orjson`, `xxhash`, `polars_hash`, `yaml`, `httpx`, `pyexcel`, `onnxruntime`, `sentence_transformers`
-- Direct (non-lazy) heavy deps: `sqlite_utils`, `rapidfuzz`, `pydantic`, `loguru`, `cyclopts`, `rich`, `yaml.CLoader`
-- Some modules mix direct and lazy imports for the same package (e.g., `ingests.py` does `from yaml import CLoader` directly, then lazy-loads `yaml` for `yaml.load()`)
-- Import order: standard library → blank line → third-party → blank line → local
-- Use `from __future__ import annotations` to enable deferred evaluation
-
-### Type Annotations
-
-- **Every variable** gets a type annotation, including locals: `col: str = "name"`, `df: pl.DataFrame = ...`
-- Use `Optional[T]` and `Union[...]` (not `T | None` or `X | Y`)
-- Use `Self` for class methods returning the class type
-- Use `Path` (not `str`) for filesystem paths
-- Use `# pyright: ignore` comments to suppress false positives from lazy-loaded modules
-
-### Pydantic Models
-
-- All models inherit from `TablaBase(BaseModel)` which sets:
-  ```python
-  model_config: ConfigDict = ConfigDict(  # pyright: ignore
-      str_strip_whitespace=False,
-      validate_assignment=True,
-      use_enum_values=True,
-      extra="forbid",
-      populate_by_name=True,
-  )
-  ```
-- Required fields: `Field(...)` (ellipsis sentinel)
-- Optional fields: `Optional[T] = Field(None)`
-- All enums are `str, Enum` subclasses (defined in `enums.py`)
-
-### Enums
-
-All enums live in `enums.py` and extend `str, Enum`. Key enums: `Tokens`, `Repositories`, `Contributions`, `Comparisons`, `Functions`, `Files`, `EncodingMethods`, `FillMethods`, `Syntaxes`, `Statuses`, `Categories`, `Predicates`, `Qualifiers`.
-
-### Naming
-
-- Functions/variables: `snake_case`
-- Classes: `PascalCase`
-- Module-level constants: `UPPER_CASE`
-
-### Comments
-
-- `# ?` — descriptions / clarifications
-- `# !` — warnings / important notes
-- `# *` — stage markers (pipeline steps)
-- `# TODO:` — todos
-- No docstrings on functions; use `# ?` comment on the line above instead
-
-### Formatting (enforced by ruff)
-
-- Line length: **120**
-- Quote style: **double quotes**
-- Indent: **4 spaces**
-- `skip-magic-trailing-comma = true`
-- Target: Python >=3.11
-
-### Error Handling
-
-- Use `RuntimeError` for exceptional cases (no custom exception classes currently)
-- Use `logger.warning()` for non-fatal issues (e.g., empty subgraphs)
-- Logger: `from tablassert.log import logger` (or `cat()` for category-tagged logger)
-
-### Other Conventions
-
-- `operator.add` for Polars string concatenation on columns (not `+` directly)
-- CLI entry point: `tablassert.cli:APP` (cyclopts app)
-- Use `rich.progress` for progress tracking in CLI (via `progress.py` which wraps Rich Live/Progress)
-- Data side-effects stored in hidden directories: `.logassert/`, `.storassert/`, `.onnxassert/`
-
-## Tools
-
-- **ruff** — linting (`ruff check`) and formatting (`ruff format`)
-- **pyright** — type checking (no pyrightconfig.json; uses defaults)
-- **pre-commit** — runs ruff fix, ruff-format, pyright, and pytest on all Python files
-- **pytest** — testing (>=9.0.2)
-- **uv** — package manager (use `uv run` for all commands, `uv add` for deps)
-- **hatchling** — build backend
-
-## Optional Dependency Groups
-
-Defined in `pyproject.toml` `[project.optional-dependencies]`:
-- `rt` — `polars[rtcompat]` (runtime-compatible Polars build for CPUs without required instructions)
-- `qc` — `onnxruntime` (CPU QC runtime)
-- `qc-cuda` — `onnxruntime-gpu` (CUDA QC runtime; single GPU on device 0)
-
-All other ML, web, and Excel dependencies are in core `dependencies`; the ONNX Runtime choice is extra-driven.
-
-Install with: `uv sync`, `uv sync --extra qc`, `uv sync --extra qc-cuda`, or `pip install tablassert[...]`
-
-## CI Workflows
-
-- **PyPI publish** (`.github/workflows/pipy.yml`): builds and publishes on push to `main`
-- **MkDocs deploy** (`.github/workflows/docs.yml`): builds docs and deploys to GitHub Pages on push to `main`
-- **Docker publish** (`.github/workflows/docker.yml`): builds and pushes image to GHCR on tag push (`v*`)
-- **Autotag** (`.github/workflows/autotag.yml`): automatic version tagging

tablassert-7.4.9/docs/changelog.md

@@ -1,11 +0,0 @@
-# Changelog
-
-The canonical release history lives in the repository root at [`CHANGELOG.md`](https://github.com/SkyeAv/Tablassert/blob/main/CHANGELOG.md).
-
-## Current Release Notes
-
-## 7.4.9 - 2026-05-26
-
-### Bug Fixes
-
-- Fixed `OSError: Too many open files` during subgraph build at large scales (700+ sections). `with_mesh()` and `with_captions()` in `lib.py` opened a `sqlite_utils.Database` per section but never closed the underlying SQLite connection, leaving FD release to GC. In the tight sequential `compile_subgraph` loop the leaked FDs accumulated past the OS soft limit, causing the next `to_store()` → `df.write_parquet()` (which polars 1.39 routes through `sink_parquet`) to fail opening its target `.storassert/*.parquet`. Both functions now wrap their query bodies in `try:` / `finally: db.conn.close()`.