mandos.analysis.distances.JPrimeMatrixCalculator._read_hits() - Code Metrics - Inspection of "fix: misc" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( 9ee5db...f62a2c )

by Douglas

created 2021-11-07 07:18 UTC

JPrimeMatrixCalculator._read_hits() A

↳ Parent: mandos.analysis.distances

Complexity

Conditions

Size

Total Lines	13
Code Lines	13

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	5
eloc	13
nop	2
dl	0
loc	13
rs	9.2833
c	0
b	0
f	0

"""
Calculations of overlap (similarity) between annotation sets.
"""
import abc
import math
import time
from collections import defaultdict
from pathlib import Path
from typing import Collection, Mapping, Optional, Sequence, Type, Union

import decorateme

import numpy as np

from pocketutils.core.chars import Chars

from pocketutils.core.enums import CleverEnum

from pocketutils.core.exceptions import XValueError

from pocketutils.tools.unit_tools import UnitTools

from typeddfs.df_errors import HashFileMissingError


from mandos.analysis import AnalysisUtils as Au
from mandos.analysis.io_defns import SimilarityDfLongForm, SimilarityDfShortForm
from mandos.model.hit_dfs import HitDf
from mandos.model.hits import AbstractHit
from mandos.model.utils import unlink

# note that most of these math functions are much faster than their numpy counterparts
# if we're not broadcasting, it's almost always better to use them
# some are more accurate, too
# e.g. we're using fsum rather than sum
from mandos.model.utils.setup import logger


class _Inf:
    def __init__(self, n: int):
        self.n = n

        self.used, self.t0, self.nonzeros = set(), time.monotonic(), 0


    def is_used(self, c1: str, c2: str) -> bool:

        return (c1, c2) in self.used or (c2, c1) in self.used

    def got(self, c1: str, c2: str, z: float) -> None:

        self.used.add((c1, c2))
        self.nonzeros += int(c1 != c2 and not np.isnan(z) and 0 < z < 1)
        if self.i % 1000 == 0:
            self.log("info")

    @property
    def i(self) -> int:

        return len(self.used)

    def log(self, level: str) -> None:

        delta = UnitTools.delta_time_to_str(time.monotonic() - self.t0, space=Chars.narrownbsp)
        logger.log(
            level.upper(),
            f"Processed {self.i:,}/{self.n:,} pairs in {delta};"
            + f" {self.nonzeros:,} ({self.nonzeros / self.i * 100:.1f}%) are nonzero",
        )

    def __repr__(self):
        return f"{self.__class__.__name__}({self.i}/{self.n})"

    def __str__(self):
        return repr(self)


@decorateme.auto_repr_str()

class MatrixCalculator(metaclass=abc.ABCMeta):
    def __init__(
        self,

        *,

        min_compounds: int,

        min_nonzero: int,

        min_hits: int,

        exclude: Optional[Collection[str]] = None,

    ):
        self.min_compounds = min_compounds
        self.min_nonzero = min_nonzero
        self.min_hits = min_hits
        self.exclude = set() if exclude is None else exclude

    def calc_all(self, hits: Path, to: Path, *, keep_temp: bool = False) -> SimilarityDfLongForm:
class Foo:
    def some_method(self, x, y):
        return x + y;
        raise NotImplemented()



class JPrimeMatrixCalculator(MatrixCalculator):

    def calc_all(self, path: Path, to: Path, *, keep_temp: bool = False) -> SimilarityDfLongForm:

        hits = self._read_hits(path)
        key_to_hit = Au.hit_multidict(hits, "search_key")
        logger.notice(f"Calculating J on {len(key_to_hit):,} keys from {len(hits):,} hits")
        good_keys = {}
        for key, key_hits in key_to_hit.items():
            key_hits: Sequence[AbstractHit] = key_hits
            n_compounds_0 = len({k.origin_inchikey for k in key_hits})
            part_path = self._path_of(path, key)
            df = None

            if part_path.exists():
                df = self._read_part(key, part_path)

            if df is None and n_compounds_0 >= self.min_compounds:
                df = self._calc_partial(key, key_hits)

                df.write_file(part_path, attrs=True, file_hash=True, mkdirs=True)
                logger.debug(f"Wrote results for {key} to {part_path}")
            if df is not None and self._should_include(df):
                good_keys[key] = part_path
            if df is not None:
                del df
        big_df = self._concat_parts(good_keys)
        big_df.write_file(to, attrs=True, file_hash=True, mkdirs=True)
        logger.notice(f"Wrote {len(big_df):,} rows to {to}")
        if not keep_temp:
            for k in good_keys:
                unlink(self._path_of(path, k))

    def _read_hits(self, path: Path) -> Sequence[AbstractHit]:
        hits = HitDf.read_file(path)
        keys = hits["search_key"].unique()
        bad_excludes = [e for e in self.exclude if e not in keys]
        if len(bad_excludes) > 0:
            logger.error(f"Keys to exclude are not in the input file: {', '.join(bad_excludes)}")
        for key in keys:
            if key not in self.exclude:
                dfx = hits[hits["search_key"] == key]
                negatives = dfx[dfx["weight"] <= 0]
                if len(negatives) > 0:
                    logger.error(f"{len(negatives)} / {len(dfx):,} hits for {key} are nonpositive")
        return [h for h in hits.to_hits() if h.search_key not in self.exclude and h.weight > 0]

    def _calc_partial(self, key: str, key_hits: HitDf) -> SimilarityDfLongForm:
        df = self.calc_one(key, key_hits).to_long_form(kind="psi", key=key)

        return df.set_attrs(
            key=key,
            quartiles=[float(df["value"].quantile(x)) for x in [0, 0.25, 0.5, 0.75, 1]],
            n_hits=len(key_hits),
            n_values=len(df["value"].unique()),
            n_compounds=len(df["inchikey_1"].unique()),
            n_real=len(df[(df["value"] > 0) & (df["value"] < 1)]),
        )

    def _should_include(self, df: SimilarityDfLongForm) -> bool:

        key = df.attrs["key"]
        reqs = dict(n_compounds=self.min_compounds, n_hits=self.min_hits, n_real=self.min_nonzero)
        for a, mn in reqs.items():

            v = df.attrs[a]

            if v < mn:
                logger.warning(f"Key {key}: {a} = {v:,} < {mn:,}")
                return False
        return True

    def _read_part(self, key: str, part_path: Path) -> Optional[SimilarityDfLongForm]:
class Foo:
    def some_method(self, x, y):
        return x + y;
        try:
            df = SimilarityDfLongForm.read_file(part_path, file_hash=True, attrs=True)

            logger.warning(f"Results for key {key} already exist ({len(df):,} rows)")
            return df
        except HashFileMissingError:
            logger.error(f"Extant results for key {key} appear incomplete; restarting")
            logger.opt(exception=True).debug(f"Hash error for {key}")
            unlink(part_path)
        return None  #  calculate from scratch

    def _concat_parts(self, keys: Mapping[str, Path]):
class Foo:
    def some_method(self, x, y):
        return x + y;
        logger.notice(f"Included {len(keys):,} keys: {', '.join(keys)}")
        dfs = []
        for key, pp in keys.items():

            df = SimilarityDfLongForm.read_file(pp, attrs=True)

            n_values = df.attrs["n_values"]
            n_real = df.attrs["n_real"]
            quartiles = df.attrs["quartiles"]
            logger.info(f"Key {key}:")
            prefix = f"    {key} {Chars.fatright}"
            logger.info(f"{prefix} unique values = {n_values}")
            logger.info(f"{prefix} values in (0, 1) = {n_real:,}")
            logger.info(f"{prefix} quartiles: " + " | ".join([str(s) for s in quartiles]))
            dfs.append(df)
        return SimilarityDfLongForm.of(dfs, keys=keys)

    def calc_one(self, key: str, hits: Sequence[AbstractHit]) -> SimilarityDfShortForm:

        ik2hits = Au.hit_multidict(hits, "origin_inchikey")
        logger.info(f"Calculating J on {key} for {len(ik2hits):,} compounds and {len(hits):,} hits")
        data = defaultdict(dict)
        inf = _Inf(n=int(len(ik2hits) * (len(ik2hits) - 1) / 2))
        for (c1, hits1) in ik2hits.items():

            for (c2, hits2) in ik2hits.items():

                if inf.is_used(c1, c2):
                    continue
                z = 1 if c1 == c2 else self._j_prime(key, hits1, hits2)

                data[c1][c2] = z
                inf.got(c1, c2, z)
        inf.log("success")
        return SimilarityDfShortForm.from_dict(data)

    def _path_of(self, path: Path, key: str):
class Foo:
    def some_method(self, x, y):
        return x + y;
        return path.parent / f".{path.name}-{key}.tmp.feather"

    def _j_prime(
        self, key: str, hits1: Collection[AbstractHit], hits2: Collection[AbstractHit]

    ) -> float:
        if len(hits1) == 0 or len(hits2) == 0:
            return 0
        sources = {h.data_source for h in hits1}.intersection({h.data_source for h in hits2})
        if len(sources) == 0:
            return float("NaN")
        values = [
            self._jx(
                key,
                [h for h in hits1 if h.data_source == source],
                [h for h in hits2 if h.data_source == source],
            )
            for source in sources
        ]
        return float(math.fsum(values) / len(values))

    def _jx(
        self, key: str, hits1: Collection[AbstractHit], hits2: Collection[AbstractHit]

    ) -> float:
        if len(hits1) == len(hits2) == 0:

            return float("NaN")
        elif len(hits1) == 0 or len(hits2) == 0:
            return 0
        pair_to_weights = Au.weights_of_pairs(hits1, hits2)
        values = []
        for ca, cb in pair_to_weights.values():

            wedge = self._wedge(ca, cb)
            vee = self._vee(ca, cb)
            if vee > 0:
                values.append(wedge / vee)
        return float(math.fsum(values) / len(values))

    def _wedge(self, ca: float, cb: float) -> float:
class Foo:
    def some_method(self, x, y):
        return x + y;
        return math.sqrt(Au.elle(ca) * Au.elle(cb))

    def _vee(self, ca: float, cb: float) -> float:
class Foo:
    def some_method(self, x, y):
        return x + y;
        return Au.elle(ca) + Au.elle(cb) - math.sqrt(Au.elle(ca) * Au.elle(cb))


class MatrixAlg(CleverEnum):

    j = ()

    @property
    def clazz(self) -> Type[MatrixCalculator]:

        return {MatrixAlg.j: JPrimeMatrixCalculator}[self]


@decorateme.auto_utils()

class MatrixCalculation:
    @classmethod
    def create(

        cls,

        algorithm: Union[str, MatrixAlg],

        *,

        min_compounds: int,

        min_nonzero: int,

        min_hits: int,

        exclude: Optional[Collection[str]] = None,

    ) -> MatrixCalculator:
        return MatrixAlg.of(algorithm).clazz(
            min_compounds=min_compounds,
            min_nonzero=min_nonzero,
            min_hits=min_hits,
            exclude=exclude,
        )


__all__ = ["JPrimeMatrixCalculator", "MatrixAlg", "MatrixCalculation", "MatrixCalculator"]


1			"""
2			Calculations of overlap (similarity) between annotation sets.
3			"""
4			import abc
5			import math
6			import time
7			from collections import defaultdict
8			from pathlib import Path
9			from typing import Collection, Mapping, Optional, Sequence, Type, Union
10
11			import decorateme
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Unable to import 'decorateme' Loading history...
12			import numpy as np
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Unable to import 'numpy' Loading history...
13			from pocketutils.core.chars import Chars
			0 ignored issues – show introduced 2021-09-29 03:10 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core.chars' Loading history...
14			from pocketutils.core.enums import CleverEnum
			0 ignored issues – show introduced 2021-10-12 03:37 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core.enums' Loading history...
15			from pocketutils.core.exceptions import XValueError
			0 ignored issues – show introduced 2021-11-04 01:02 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.core.exceptions' Loading history... Unused Code introduced 2021-11-07 07:20 UTC by Report Bug Copy Issue Report Unused XValueError imported from pocketutils.core.exceptions Loading history...
16			from pocketutils.tools.unit_tools import UnitTools
			0 ignored issues – show introduced 2021-10-28 02:14 UTC by Report Bug Copy Issue Report Unable to import 'pocketutils.tools.unit_tools' Loading history...
17			from typeddfs.df_errors import HashFileMissingError
			0 ignored issues – show introduced 2021-11-05 00:32 UTC by Report Bug Copy Issue Report Unable to import 'typeddfs.df_errors' Loading history...
18
19			from mandos.analysis import AnalysisUtils as Au
20			from mandos.analysis.io_defns import SimilarityDfLongForm, SimilarityDfShortForm
21			from mandos.model.hit_dfs import HitDf
22			from mandos.model.hits import AbstractHit
23			from mandos.model.utils import unlink
24
25			# note that most of these math functions are much faster than their numpy counterparts
26			# if we're not broadcasting, it's almost always better to use them
27			# some are more accurate, too
28			# e.g. we're using fsum rather than sum
29			from mandos.model.utils.setup import logger
30
31
32			class _Inf:
33			def __init__(self, n: int):

dmyersturnbull / mandos

Push — main ( 9ee5db...f62a2c )

JPrimeMatrixCalculator._read_hits() A

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