tablassert 7.0.0__py3-none-any.whl

tablassert/models.py

@@ -0,0 +1,131 @@
+from tablassert.enums import EncodingMethods
+from tablassert.enums import Contributions
+from tablassert.enums import Repositories
+from tablassert.enums import Comparisons
+from tablassert.enums import FillMethods
+from tablassert.enums import Predicates
+from tablassert.enums import Qualifiers
+from tablassert.enums import Categories
+from tablassert.enums import Functions
+from tablassert.enums import Statuses
+from tablassert.enums import Syntaxes
+from tablassert.enums import Tokens
+from pydantic import NonNegativeInt
+from tablassert.enums import Files
+from pydantic import PositiveInt
+from pydantic import ConfigDict
+from pydantic import BaseModel
+from pydantic import HttpUrl
+from typing import Optional
+from pydantic import Field
+from typing import Literal
+from typing import Union
+from pathlib import Path
+
+
+class TablaBase(BaseModel):
+  model_config: ConfigDict = ConfigDict(  # pyright: ignore
+    str_strip_whitespace=False, validate_assignment=True, use_enum_values=True, extra="forbid", populate_by_name=True
+  )
+
+
+class Reindex(TablaBase):
+  column: str = Field(...)
+  comparison: Comparisons = Field(Comparisons.NE)
+  comparator: Union[str, int, float] = Field(...)
+
+
+class BaseSource(TablaBase):
+  local: Path = Field(...)
+  url: HttpUrl = Field(...)
+  rows: Optional[list[NonNegativeInt]] = Field(None)
+  row_slice: Optional[list[Union[NonNegativeInt, Literal[Tokens.AUTO]]]] = Field(None)
+  reindex: Optional[list[Reindex]] = Field(None)
+
+
+class Excel(BaseSource):
+  kind: Literal[Files.EXCEL] = Field(Files.EXCEL)
+  sheet: Optional[str] = Field("Sheet1")
+
+
+class Text(BaseSource):
+  kind: Literal[Files.TEXT] = Field(Files.TEXT)
+  delimiter: Optional[str] = Field(",")
+
+
+class Regex(TablaBase):
+  pattern: Union[int, float, str] = Field(...)
+  replacement: Union[int, float, str] = Field(...)
+
+
+class Math(TablaBase):
+  function: Functions = Field(...)
+  arguments: list[Union[Literal[Tokens.VALUES], float, int]] = Field(...)
+
+
+class Encoding(TablaBase):
+  method: EncodingMethods = Field(EncodingMethods.VALUE)
+  encoding: Union[str, int, float] = Field(...)
+  regex: Optional[list[Regex]] = Field(None)
+  fill: Optional[FillMethods] = Field(None)
+  remove: Optional[list[str]] = Field(None)
+  prefix: Optional[str] = Field(None)
+  suffix: Optional[str] = Field(None)
+  explode_by: Optional[str] = Field(None)
+  transformations: Optional[list[Math]] = Field(None)
+
+
+class NodeEncoding(Encoding):
+  taxon: Optional[PositiveInt] = Field(None)
+  prioritize: Optional[list[Categories]] = Field(None)
+  avoid: Optional[list[Categories]] = Field(None)
+
+
+class Qualifier(NodeEncoding):
+  qualifier: Qualifiers = Field(...)
+
+
+class Statement(TablaBase):
+  subject: NodeEncoding = Field(...)
+  object: NodeEncoding = Field(...)
+  predicate: Predicates = Field(Predicates.RELATED_TO)
+  qualifiers: Optional[list[Qualifier]] = Field(None)
+
+
+class Contributor(TablaBase):
+  kind: Contributions = Field(Contributions.CURATION)
+  name: str = Field(...)
+  date: str = Field(...)
+  organizations: Optional[list[str]] = Field(None)
+  comment: Optional[str] = Field(None)
+
+
+class Provenance(TablaBase):
+  repo: Repositories = Field(Repositories.PUBMED_CENTRAL)
+  publication: str = Field(...)
+  contributors: list[Contributor] = Field(...)
+
+
+class Annotation(Encoding):
+  annotation: str = Field(...)
+
+
+class Section(TablaBase):
+  # ? Pydantic "Section" Model And Coercion
+  syntax: Syntaxes = Field(Syntaxes.TC3)
+  status: Statuses = Field(Statuses.ALPHA)
+  source: Union[Excel, Text] = Field(...)
+  statement: Statement = Field(...)
+  provenance: Provenance = Field(...)
+  annotations: Optional[list[Annotation]] = Field(None)
+
+
+class Graph(TablaBase):
+  # ? Pydantic "Graph" Configuration
+  syntax: Syntaxes = Field(Syntaxes.GC2)
+  name: str = Field(...)
+  version: str = Field(...)
+  tables: list[Path] = Field(...)
+  dbssert: Path = Field(...)
+  pubmed_db: Optional[Path] = Field(None)
+  pmc_db: Optional[Path] = Field(None)

tablassert/qc.py

@@ -0,0 +1,124 @@
+from sklearn.metrics.pairwise import cosine_similarity
+from sentence_transformers import SentenceTransformer
+from tablassert.utils import DISKCACHE
+from tablassert.log import logger
+from typing import Optional
+from typing import Literal
+from rapidfuzz import fuzz
+import onnxruntime as ort
+from pathlib import Path
+from operator import add
+from operator import ge
+from operator import eq
+import polars as pl
+
+SESSION_OPTS: object = ort.SessionOptions()
+SESSION_OPTS.graph_optimization_level = ort.GraphOptimizationLevel.ORT_ENABLE_ALL  # pyright: ignore
+
+MODEL: Path = Path("./.onnxassert/")
+MODEL_BACKEND: Literal["onnx"] = "onnx"
+MODEL_KWARGS: dict[str, object] = {"provider": "CPUExecutionProvider", "session_options": SESSION_OPTS}
+
+# TODO: Explore Best Model For QC
+BIOBERT: Optional[object] = None
+
+
+def get_biobert() -> object:
+  # ? Lazy-loads BioBERT once on first BERT_audit call, then caches globally
+  global BIOBERT
+  if BIOBERT:
+    return BIOBERT
+  elif not BIOBERT and MODEL.exists():
+    BIOBERT = SentenceTransformer(str(MODEL), backend=MODEL_BACKEND, model_kwargs=MODEL_KWARGS)  # pyright: ignore
+  else:
+    BIOBERT = SentenceTransformer(
+      "pritamdeka/BioBERT-mnli-snli-scinli-scitail-mednli-stsb", backend=MODEL_BACKEND, model_kwargs=MODEL_KWARGS
+    )  # pyright: ignore
+    MODEL.mkdir(parents=True, exist_ok=True)
+    BIOBERT.save(MODEL)  # pyright: ignore
+  return BIOBERT
+
+
+@DISKCACHE.memoize()  # pyright: ignore
+def fuzz_audit(x: object, original: str, preferred: str, min_fuzz: float = 20) -> bool:
+  # ? Decides Whether To Remove A Suspected Fullmap Error Based On Fuzzy Matching
+  o: str = x[original]  # pyright: ignore
+  p: str = x[preferred]  # pyright: ignore
+  return bool(ge(fuzz.ratio(o, p), min_fuzz) or ge(fuzz.partial_token_sort_ratio(o, p), min_fuzz))
+
+
+@DISKCACHE.memoize()  # pyright: ignore
+def BERT_audit(x: object, original: str, preferred: str, min_cos: float = 0.2) -> bool:
+  # ? Decides Whether To Remove A Suspected Fullmap Error Based On BERT EMBEDDINGS
+  o: str = x[original]  # pyright: ignore
+  p: str = x[preferred]  # pyright: ignore
+
+  embeddings: object = get_biobert().encode([o, p])  # pyright: ignore
+  similarity: float = cosine_similarity([embeddings[0]], [embeddings[1]])[0][0]  # pyright: ignore
+  return bool(ge(similarity, min_cos))
+
+
+def fullmap_audit(lf: pl.LazyFrame, col: str, section_hash: str, config_file: str, out: str = "passed") -> pl.LazyFrame:
+  # ? Ensures Fullmap Correct Processes Strings To CURIES
+  # * Deletes Suspected Errors
+  # ! Collection Points: map_elements With Custom Functions Require Eager
+  original: str = add("original ", col)
+  preferred: str = add(col, " name")
+  cols: list[str] = [col, original, preferred]
+
+  # * Stage 1: Exact String Matching Or Is Curie (Can Stay Lazy Until Filter)
+  df: pl.DataFrame = lf.collect()
+  pairs: pl.DataFrame = df.select(cols).unique()
+  pairs = pairs.with_columns(eq(pl.col(cols[1]), pl.col(cols[2])).alias(out))
+
+  passed: pl.DataFrame = pairs.filter(pl.col(out))
+  pending: pl.DataFrame = pairs.filter(~pl.col(out))
+
+  exempt_curies: str = r"^CHEBI|^PR|^UniProtKB"
+  is_exempt: pl.DataFrame = pending.with_columns(pl.col(cols[0]).str.contains(exempt_curies).alias(out))
+  pairs = pl.concat((passed, is_exempt))
+
+  passed = pairs.filter(pl.col(out))
+  pending = pairs.filter(~pl.col(out))
+
+  is_curie: pl.DataFrame = pending.with_columns(pl.col(cols[1]).str.contains(":").alias(out))
+  pairs = pl.concat((passed, is_curie))
+
+  passed = pairs.filter(pl.col(out))
+  pending = pairs.filter(~pl.col(out))
+
+  exceptions: str = r"^LOC|^si:"
+  is_exception: pl.DataFrame = pending.with_columns(pl.col(cols[2]).str.contains(exceptions).alias(out))
+  pairs = pl.concat((passed, is_exception))
+
+  passed = pairs.filter(pl.col(out))
+  pending = pairs.filter(~pl.col(out))
+
+  # * Stage 2: Fuzzy Matching Via RapidFuzz (Requires Eager)
+  masked_fuzz: pl.DataFrame = pending.with_columns(
+    pl.struct(cols[1:]).map_elements(lambda x: fuzz_audit(x, original, preferred), return_dtype=pl.Boolean).alias(out)
+  )
+  pairs = pl.concat((passed, masked_fuzz))
+
+  passed = pairs.filter(pl.col(out))
+  pending = pairs.filter(~pl.col(out))
+
+  # * Stage 3: BioBERT Embeddings (Requires Eager)
+  BERT_fuzz: pl.DataFrame = pending.with_columns(
+    pl.struct(cols[1:]).map_elements(lambda x: BERT_audit(x, original, preferred), return_dtype=pl.Boolean).alias(out)
+  )
+  pairs = pl.concat((passed, BERT_fuzz))
+
+  passed = pairs.filter(pl.col(out))
+  pending = pairs.filter(~pl.col(out))
+
+  # * Add Logging For Failed CURIES
+  if pending.height > 0:
+    for c, o, p in zip(
+      pending.get_column(col).to_list(), pending.get_column(original).to_list(), pending.get_column(preferred).to_list()
+    ):
+      logger.info(
+        f"FAILED QC | STORE: {section_hash} | CONFIG: {config_file} | COL: {col} | ORIGINAL: {o!r} | PREFERRED: {p!r} | CURIE: {c!r}"
+      )
+
+  return df.join(passed.select(col), on=col, how="semi").lazy()

tablassert/utils.py

@@ -0,0 +1,43 @@
+from diskcache import Cache
+from functools import cache
+from pathlib import Path
+from typing import Any
+from uuid import uuid3
+from uuid import UUID
+import polars as pl
+import xxhash
+
+STORE: Path = Path("./.storassert")
+STORE.mkdir(parents=True, exist_ok=True)
+
+DISKCACHE: object = Cache(
+  "./.cachassert",
+  size_limit=100_000_000,  # ~100MB
+  eviction_policy="least-recently-used",
+)
+
+
+def mkhash(x: Any) -> str:
+  b: bytes = str(x).encode("utf-8")
+  return xxhash.xxh64(b).hexdigest()
+
+
+def samphash(df: pl.DataFrame, n: int = 20) -> str:
+  # ? Hash Of Sampled DataFrame For Tempfile Naming
+  # ! Requires eager DataFrame input - call .collect() before passing LazyFrame
+  samp: pl.DataFrame = df.sample(min(n, df.height))
+  return mkhash(samp.to_init_repr())
+
+
+@cache
+def basespace(domain: str) -> UUID:
+  namespace: UUID = UUID("00000000-0000-0000-0000-000000000000")
+  return uuid3(namespace, domain)
+
+
+def namespace_uuid(domain: Any, *values: list[Any]) -> str:
+  domain = str(domain)
+  values = [str(x) for x in values if x]  # pyright: ignore
+  domainspace: UUID = basespace(domain)
+  joined: str = "\t".join(values)  # pyright: ignore
+  return str(uuid3(domainspace, joined))

tablassert-7.0.0.dist-info/METADATA

@@ -0,0 +1,141 @@
+Metadata-Version: 2.4
+Name: tablassert
+Version: 7.0.0
+Summary: Add your description here
+License-File: LICENSE
+Requires-Python: >=3.13
+Requires-Dist: diskcache>=5.6.3
+Requires-Dist: duckdb>=1.5.0
+Requires-Dist: fastexcel>=0.19.0
+Requires-Dist: loguru>=0.7.3
+Requires-Dist: mkdocs>=1.6.1
+Requires-Dist: onnxruntime>=1.24.3
+Requires-Dist: optimum-onnx>=0.1.0
+Requires-Dist: orjson>=3.11.7
+Requires-Dist: playwright>=1.58.0
+Requires-Dist: polars>=1.39.0
+Requires-Dist: pyarrow>=23.0.1
+Requires-Dist: pydantic>=2.12.5
+Requires-Dist: pyexcel>=0.7.4
+Requires-Dist: pyyaml>=6.0.3
+Requires-Dist: rapidfuzz>=3.14.3
+Requires-Dist: scikit-learn>=1.8.0
+Requires-Dist: sentence-transformers>=5.3.0
+Requires-Dist: sqlite-utils>=3.39
+Requires-Dist: typer>=0.24.1
+Requires-Dist: xxhash>=3.6.0
+Description-Content-Type: text/markdown
+
+# Tablassert
+
+### By Skye Lane Goetz, Gwênlyn Glusman, and Jared C. Roach
+
+Tablassert is a highly performant declarative knowledge graph backend designed to extract knowledge assertions from tabular data while exporting NCATS Translator-compliant Knowledge Graph Exchange (KGX) NDJSON.
+
+## Documentation
+
+**[Full Documentation](https://skyeav.github.io/Tablassert/)**
+
+Complete guides covering installation, configuration, tutorials, and API reference.
+
+## Quick Start
+
+```bash
+# Clone repository
+git clone https://github.com/SkyeAv/Tablassert.git
+cd Tablassert
+
+# Install with UV (requires Python 3.13+)
+uv sync
+
+# Run CLI
+uv run tablassert --help
+```
+
+Or install the CLI directly from PyPI:
+
+```bash
+# Option A: UV tool install
+uv tool install tablassert
+
+# Option B: pip install
+pip install tablassert
+
+tablassert --help
+```
+
+## Usage (With UV)
+
+### Prerequisites
+
+- Python 3.13 or higher
+- UV package manager
+
+### Method 1: Development Installation (Recommended)
+
+Best for exploring Tablassert or active development.
+
+```bash
+# Clone and install dependencies
+git clone https://github.com/SkyeAv/Tablassert.git
+cd Tablassert
+uv sync
+
+# Run CLI through UV
+uv run tablassert build-knowledge-graph /path/to/graph-config.yaml
+```
+
+### Method 2: Install from PyPI
+
+Recommended for most users.
+
+```bash
+# Option A: UV tool install
+uv tool install tablassert
+
+# Option B: pip install
+pip install tablassert
+
+tablassert build-knowledge-graph /path/to/graph-config.yaml
+```
+
+### Method 3: Install from GitHub main
+
+Use this when you want the latest main-branch build before a tagged release.
+
+```bash
+uv tool install git+https://github.com/SkyeAv/Tablassert.git@main
+tablassert build-knowledge-graph /path/to/graph-config.yaml
+```
+
+### Method 4: Local source install
+
+For contributors testing local changes.
+
+```bash
+# Clone repository
+git clone https://github.com/SkyeAv/Tablassert.git
+cd Tablassert
+
+# Install CLI tool from local source
+uv tool install .
+
+# CLI is now available
+tablassert build-knowledge-graph /path/to/graph-config.yaml
+```
+
+## Key Features
+
+- **Declarative Configuration:** YAML-based, no code required
+- **Entity Resolution:** Maps text to biological entities (genes, diseases, chemicals)
+- **Quality Control:** Three-stage validation (exact → fuzzy → BERT embeddings)
+- **KGX Compliance:** NCATS Translator-compatible NDJSON output
+- **Performance:** Parallel processing with disk caching
+
+## Contributors
+
+[Skye Lane Goetz](mailto:sgoetz@isbscience.org) - Institute for Systems Biology, CalPoly SLO
+
+[Gwênlyn Glusman](mailto:gglusman@isbscience.org) - Institute for Systems Biology
+
+Jared C. Roach - Institute for Systems Biology

tablassert-7.0.0.dist-info/RECORD

@@ -0,0 +1,15 @@
+tablassert/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tablassert/downloader.py,sha256=UEMABrr2MBKLLfwU5L_qaaZz5FyIUhVLpED0G_ORhag,1071
+tablassert/enums.py,sha256=nptjto2Q1ajrOGZwpbA0DQZXtfabqMWTC1fvumYjlJA,20298
+tablassert/fullmap.py,sha256=XsVeD41DPX0BwnE2GuOUmXzF-fYSBwVm1CraiSgVIwE,6168
+tablassert/ingests.py,sha256=BhsiJfLLuB8wddx-yidOmetPmnqrFkWHQLVSsJTmJ48,1235
+tablassert/lib.py,sha256=fb6W-NAnJ_RuG9C_qGTFmWerfZJY5mHxD9_0jeu0mGI,21516
+tablassert/log.py,sha256=Vj6BjOZHUi3VXenDio02L76C0saaHIEUHPj1i0KtSYs,330
+tablassert/models.py,sha256=lgTW53aTIghIakFeIlqKZug1Zew1DTt2ez17xoZ-5Sk,3930
+tablassert/qc.py,sha256=kL93c4unMyy2_GsyyBUSqTjRsvsCgCJePkUjT8oJ6h0,4946
+tablassert/utils.py,sha256=cmnIKx9XlxrLCoRU__SCGNbCGmESLR8jI1jZ3X0FQC4,1187
+tablassert-7.0.0.dist-info/METADATA,sha256=75ZVWxKCghM75DK-V_xISii-udJ_v1V2EziggWJum24,3473
+tablassert-7.0.0.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
+tablassert-7.0.0.dist-info/entry_points.txt,sha256=-bQngz2RIsHPcYHcICE7GO6aB9CgVSkfI4Id_cRX_IQ,50
+tablassert-7.0.0.dist-info/licenses/LICENSE,sha256=OwLwApBpXalcfn9u_tsRU-hMA6aZ3apOuA2a136_aLs,11345
+tablassert-7.0.0.dist-info/RECORD,,

tablassert-7.0.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.29.0
+Root-Is-Purelib: true
+Tag: py3-none-any

tablassert-7.0.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+tablassert = tablassert.lib:CLI

tablassert-7.0.0.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
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+                        http://www.apache.org/licenses/
+
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