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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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from typeddfs import TypedDfs |
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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 KeyPredObj: |
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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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key: str |
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@dataclass(frozen=True, repr=True, order=True) |
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class KeyPredObjSource: |
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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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key: str |
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source: str |
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@property |
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def to_key_pred_obj(self) -> KeyPredObj: |
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return KeyPredObj(self.pred, self.obj, self.key) |
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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. Also includes the search key, if meaningful. |
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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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key: Optional[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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Includes the key if it's present. |
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""" |
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s = self.sub |
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if self.key is None: |
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p = html.escape(self.pred, quote=True) |
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else: |
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p = html.escape(self.key + ":" + 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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object_id: str |
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object_name: str |
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weight: 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( |
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sub=self.origin_inchikey, pred=self.predicate, obj=self.object_name, key=self.search_key |
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) |
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@property |
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def to_key_pred_obj(self) -> KeyPredObj: |
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return KeyPredObj(pred=self.predicate, obj=self.object_name, key=self.search_key) |
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@property |
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def to_key_pred_obj_source(self) -> KeyPredObjSource: |
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return KeyPredObjSource( |
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pred=self.predicate, obj=self.object_name, key=self.search_key, source=self.data_source |
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) |
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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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# TODO: cache instead |
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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("origin_inchikey", "matched_inchikey", "compound_id", "compound_name", dtype=str) |
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.require("predicate", 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") |
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).build() |
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__all__ = ["AbstractHit", "HitFrame", "KeyPredObj", "KeyPredObjSource", "Triple", "HIT_FIELD_TYPE"] |
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dmyersturnbull /
mandos
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