#! /usr/bin/env python
# -*- coding: utf-8 -*-
import json
from collections import namedtuple
from typing import Dict, Union, Sequence
import numpy as np
import pandas as pd
import pytest
from dios import DictOfSeries
from saqc.constants import UNFLAGGED, BAD, DOUBTFUL
from saqc.core.translator import PositionalTranslator, Translator, DmpTranslator
from saqc.core.flags import Flags
from saqc.core.core import SaQC
from tests.common import initData
def _genTranslators():
for dtype in (str, float, int):
flags = {
dtype(-2): UNFLAGGED,
dtype(-1): BAD,
**{dtype(f * 10): float(f) for f in range(10)},
}
translator = Translator(flags)
yield flags, translator
def _genFlags(data: Dict[str, Union[Sequence, pd.Series]]) -> Flags:
flags = DictOfSeries()
for k, v in data.items():
if not isinstance(v, pd.Series):
v = pd.Series(
v, index=pd.date_range("2012-01-01", freq="1D", periods=len(v))
)
flags[k] = v
return Flags(flags)
def test_forwardTranslation():
for flags, translator in _genTranslators():
for k, expected in flags.items():
got = translator(k)
assert expected == got or np.isnan([got, expected]).all()
for k in ["bad", 3.14, max]:
with pytest.raises(ValueError):
translator(k)
def test_backwardTranslation():
field = "var1"
for _, translator in _genTranslators():
keys = tuple(translator._backward.keys())
flags = _genFlags({field: np.array(keys)})
translated = translator.backward(flags, None)
expected = set(translator._backward.values())
assert not (set(translated[field]) - expected)
def test_backwardTranslationFail():
field = "var1"
for _, translator in _genTranslators():
keys = tuple(translator._backward.keys())
# add an scheme invalid value to the flags
flags = _genFlags({field: np.array(keys + (max(keys) + 1,))})
with pytest.raises(ValueError):
translator.backward(flags, None)
def test_dmpTranslator():
Selector = namedtuple("Selector", ["field"])
Function = namedtuple("Function", ["name"])
translator = DmpTranslator()
keys = np.array(tuple(translator._backward.keys()) * 50)
flags = _genFlags({"var1": keys, "var2": keys, "var3": keys})
flags[:, "var1"] = BAD
flags[:, "var1"] = DOUBTFUL
flags[:, "var2"] = BAD
to_call = [
(Selector("var1"), Function("flagFoo")),
(Selector("var1"), Function("flagBar")),
(Selector("var2"), Function("flagFoo")),
]
tflags = translator.backward(flags, to_call)
assert set(tflags.columns.get_level_values(1)) == {
"quality_flag",
"quality_comment",
"quality_cause",
}
assert (tflags.loc[:, ("var1", "quality_flag")] == "DOUBTFUL").all(axis=None)
assert (tflags.loc[:, ("var1", "quality_comment")] == '{"test": "flagBar"}').all(
axis=None
)
assert (tflags.loc[:, ("var2", "quality_flag")] == "BAD").all(axis=None)
assert (tflags.loc[:, ("var2", "quality_comment")] == '{"test": "flagFoo"}').all(
axis=None
)
assert (tflags.loc[:, ("var3", "quality_comment")] == '{"test": ""}').all(axis=None)
def test_positionalTranslator():
translator = PositionalTranslator()
flags = _genFlags({"var1": np.zeros(100), "var2": np.zeros(50)})
flags[1::3, "var1"] = BAD
flags[1::3, "var1"] = DOUBTFUL
flags[2::3, "var1"] = BAD
tflags = translator.backward(flags, None) # type: ignore
assert (tflags["var2"].replace(-9999, np.nan).dropna() == 9).all(axis=None)
assert (tflags["var1"].iloc[1::3] == 9210).all(axis=None)
assert (tflags["var1"].iloc[2::3] == 9002).all(axis=None)
def test_positionalTranslatorIntegration():
data = initData(3)
col: str = data.columns[0]
translator = PositionalTranslator()
saqc = SaQC(data=data, translator=translator)
saqc = saqc.breaks.flagMissing(col).outliers.flagRange(col, min=3, max=10)
data, flags = saqc.getResult()
for field in flags.columns:
assert flags[field].astype(str).str.match("^9[012]*$").all()
round_trip = translator.backward(translator.forward(flags), saqc._computed)
assert (flags.values == round_trip.values).all()
assert (flags.index == round_trip.index).all()
assert (flags.columns == round_trip.columns).all()
def test_dmpTranslatorIntegration():
data = initData(3)
col = data.columns[0]
translator = DmpTranslator()
saqc = SaQC(data=data, translator=translator)
saqc = saqc.breaks.flagMissing(col).outliers.flagRange(col, min=3, max=10)
data, flags = saqc.getResult()
qflags = flags.xs("quality_flag", axis="columns", level=1)
qfunc = flags.xs("quality_comment", axis="columns", level=1).applymap(
lambda v: json.loads(v)["test"]
)
qcause = flags.xs("quality_cause", axis="columns", level=1)
assert qflags.isin(translator._forward.keys()).all(axis=None)
assert qfunc.isin({"", "breaks.flagMissing", "outliers.flagRange"}).all(axis=None)
assert (qcause == "").all(axis=None)
round_trip = translator.backward(translator.forward(flags), saqc._computed)
assert round_trip.xs("quality_flag", axis="columns", level=1).equals(qflags)
assert (
round_trip.xs("quality_comment", axis="columns", level=1)
.applymap(lambda v: json.loads(v)["test"] == "")
.all(axis=None)
)
def _buildupSaQCObjects():
"""
return two saqc object, whereas the flags from the previous run
are reused
"""
data = initData(3)
col = data.columns[0]
flags = None
out = []
for _ in range(2):
saqc = SaQC(data=data, flags=flags)
saqc = saqc.breaks.flagMissing(col, to_mask=False).outliers.flagRange(
col, min=3, max=10, to_mask=False
)
saqc = saqc.evaluate()
flags = saqc._flags
out.append(saqc)
return out
def test_translationPreservesFlags():
saqc1, saqc2 = _buildupSaQCObjects()
_, flags1 = saqc1.getResult(raw=True)
_, flags2 = saqc2.getResult(raw=True)
for k in flags2.columns:
got = flags2.history[k].hist.iloc[:, 1:]
f1hist = flags1.history[k].hist.iloc[:, 1:]
expected = pd.concat([f1hist, f1hist], axis="columns")
expected.columns = got.columns
assert expected.equals(got)
def test_positionalTranslationPreservesFlags():
saqc1, saqc2 = _buildupSaQCObjects()
translator = PositionalTranslator()
_, flags1 = saqc1.getResult(raw=True)
_, flags2 = saqc2.getResult(raw=True)
tflags1 = translator.backward(flags1, saqc1._computed).astype(str)
tflags2 = translator.backward(flags2, saqc2._computed).astype(str)
for k in flags2.columns:
expected = tflags1[k].str.slice(start=1) * 2
got = tflags2[k].str.slice(start=1)
assert expected.equals(got)
def test_dmpTranslationPreservesFlags():
saqc1, saqc2 = _buildupSaQCObjects()
_, flags1 = saqc1.getResult(raw=True)
_, flags2 = saqc2.getResult(raw=True)
translator = DmpTranslator()
tflags1 = translator.backward(flags1, saqc1._computed)
tflags2 = translator.backward(flags2, saqc2._computed)
assert tflags1.equals(tflags2)