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import dataclasses |
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import html |
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from dataclasses import dataclass |
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from datetime import datetime |
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from typing import Optional, Sequence |
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import pandas as pd |
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from typeddfs import TypedDfs |
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from mandos.model import ReflectionUtils |
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HIT_FIELD_TYPE = frozenset([str, int, float, datetime]) |
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@dataclass(frozen=True, repr=True, order=True) |
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class Pair: |
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""" |
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Predicate, object pairs. |
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""" |
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pred: str |
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obj: str |
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@dataclass(frozen=True, repr=True, order=True) |
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class Triple: |
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""" |
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Usually compound, predicate, object. |
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""" |
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sub: str |
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pred: str |
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obj: str |
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@property |
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def n_triples(self) -> str: |
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""" |
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Returns a simple text statement in n-triples format. |
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""" |
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s = self.sub |
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p = html.escape(self.pred, quote=True) |
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o = html.escape(self.obj, quote=True) |
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return f'"{s}" "{p}" "{o}" .' |
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@dataclass(frozen=True, order=True, repr=True) |
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class AbstractHit: |
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""" |
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An abstract annotation (statement type), which may support additional fields. |
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""" |
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record_id: Optional[str] |
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origin_inchikey: str |
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matched_inchikey: str |
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compound_id: str |
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compound_name: str |
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predicate: str |
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statement: str |
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object_id: str |
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object_name: str |
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value: float |
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search_key: str |
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search_class: str |
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data_source: str |
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run_date: datetime |
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cache_date: Optional[datetime] |
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@property |
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def hit_class(self) -> str: |
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return self.__class__.__name__ |
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@property |
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def to_triple(self) -> Triple: |
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return Triple(sub=self.origin_inchikey, pred=self.predicate, obj=self.object_name) |
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@property |
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def to_pair(self) -> Pair: |
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return Pair(pred=self.predicate, obj=self.object_name) |
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def __hash__(self): |
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return hash(self.record_id) |
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@property |
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def universal_id(self) -> str: |
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""" |
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Gets an identifier (a hex key) that uniquely identifies the record by its unique attributes. |
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Does **NOT** distinguish between hits with duplicate information and does **NOT** |
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include ``record_id``. |
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Returns: |
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A 16-character hexadecimal string |
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""" |
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# excluding record_id only because it's not available for some hit types |
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# we'd rather immediately see duplicates if the exist |
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fields = { |
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field |
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for field in self.fields() |
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if field |
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not in {"record_id", "origin_inchikey", "compound_name", "search_key", "search_class"} |
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} |
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hexed = hex(hash(tuple([getattr(self, f) for f in fields]))) |
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# remove negative signs -- still unique |
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return hexed.replace("-", "").replace("0x", "") |
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@classmethod |
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def fields(cls) -> Sequence[str]: |
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""" |
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Finds the list of fields in this class by reflection. |
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""" |
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return [f.name for f in dataclasses.fields(cls)] |
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HitFrame = ( |
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TypedDfs.typed("HitFrame") |
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.require("record_id", dtype=str) |
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.require("inchikey", "compound_id", "compound_name", dtype=str) |
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.require("predicate", "statement", dtype=str) |
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.require("object_id", "object_name", dtype=str) |
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.require("search_key", "search_class", "data_source", dtype=str) |
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.require("hit_class", dtype=str) |
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.require("cache_date", "run_date", dtype=str) |
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.reserve("is_hit", dtype=bool) |
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.reserve("score", *[f"x_score_{i}" for i in range(1, 10)], dtype=float) |
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).build() |
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class HitUtils: |
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@classmethod |
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def hits_to_df(cls, hits: Sequence[AbstractHit]) -> HitFrame: |
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data = [] |
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for hit in hits: |
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x = {f: getattr(hit, f) for f in hit.__class__.fields()} |
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x["universal_id"] = hit.universal_id |
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x["hit_class"] = hit.hit_class |
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data.append(x) |
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return HitFrame([pd.Series(x) for x in data]) |
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@classmethod |
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def df_to_hits(cls, self: HitFrame) -> Sequence[AbstractHit]: |
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hits = [] |
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for row in self.iterrows(): |
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clazz = ReflectionUtils.injection(row.hit_class, AbstractHit) |
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# ignore extra columns |
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# if cols are missing, let it fail on clazz.__init__ |
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data = {f: getattr(row, f) for f in self.columns if f in row.__dict__} |
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# noinspection PyArgumentList |
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hit = clazz(**data) |
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hits.append(hit) |
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return hits |
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__all__ = ["AbstractHit", "HitFrame", "Pair", "Triple", "HIT_FIELD_TYPE", "HitUtils"] |
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dmyersturnbull /
mandos
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