#! /usr/bin/env python
# -*- coding: utf-8 -*-
import json
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 (
FloatTranslator,
PositionalTranslator,
Translator,
DmpTranslator,
)
from saqc.core.flags import Flags
from saqc.core.core import SaQC
from saqc.core.lib import APIController, SaQCFunction, ColumnSelector
from saqc.funcs.flagtools import flagDummy
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():
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 = [
# the initial columns
(ColumnSelector("var1"), SaQCFunction("flagInit", flagDummy)),
(ColumnSelector("var2"), SaQCFunction("flagInit", flagDummy)),
(
ColumnSelector("var3"),
SaQCFunction("flagInit", flagDummy, comment="initial flags"),
),
(ColumnSelector("var1"), SaQCFunction("flagFoo", flagDummy)),
(
ColumnSelector("var1"),
SaQCFunction("flagBar", flagDummy, comment="I did it"),
),
(ColumnSelector("var2"), SaQCFunction("flagFoo", flagDummy)),
]
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", "comment": "I did it"}'
).all(axis=None)
assert (tflags.loc[:, ("var2", "quality_flag")] == "BAD").all(axis=None)
assert (
tflags.loc[:, ("var2", "quality_comment")]
== '{"test": "flagFoo", "comment": ""}'
).all(axis=None)
assert (
tflags.loc[flags["var3"] == BAD, ("var3", "quality_comment")]
== '{"test": "flagInit", "comment": "initial flags"}'
).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() == 90).all(axis=None)
assert (tflags["var1"].iloc[1::3] == 90210).all(axis=None)
assert (tflags["var1"].iloc[2::3] == 90002).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, flag=DOUBTFUL
)
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))
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))
assert round_trip.xs("quality_flag", axis="columns", level=1).equals(qflags)
assert round_trip.xs("quality_comment", axis="columns", level=1).equals(
flags.xs("quality_comment", axis="columns", level=1)
)
assert round_trip.xs("quality_cause", axis="columns", level=1).equals(
flags.xs("quality_cause", axis="columns", level=1)
)
def _buildupSaQCObjects():
"""
return two evaluated saqc objects calling the same functions,
whereas the flags from the evaluetion of the first objetc are
used as input flags of the second
"""
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_callHistoryYieldsSameResults():
# a simple SaQC run
data = initData(3)
col = data.columns[0]
saqc1 = SaQC(data=data)
saqc1 = saqc1.breaks.flagMissing(col, to_mask=False).outliers.flagRange(
col, min=3, max=10, to_mask=False
)
_, flags1 = saqc1.getResult(raw=True)
# generate a dummy call history from flags
translator = FloatTranslator()
graph = translator.buildGraph(flags1)
saqc2 = SaQC(data=data)
# convert the call history into an excution plan and inject into a blank SaQC object
saqc2._planned = [(s, APIController(plot=False), f) for s, f in graph]
# replay the functions
_, flags2 = saqc2.getResult()
assert flags2.equals(flags1.toFrame())
def test_multicallsPreserveHistory():
saqc1, saqc2 = _buildupSaQCObjects()
_, flags1 = saqc1.getResult(raw=True)
_, flags2 = saqc2.getResult(raw=True)
# check, that the `History` is duplicated
for col in flags2.columns:
hist1 = flags1.history[col].hist.loc[:, 1:]
hist2 = flags2.history[col].hist.loc[:, 1:]
hist21 = hist2.iloc[:, : len(hist1.columns)]
hist22 = hist2.iloc[:, len(hist1.columns) :]
hist21.columns = hist1.columns
hist22.columns = hist1.columns
assert hist1.equals(hist21)
assert hist1.equals(hist22)
assert hist21.equals(hist22)
assert len(saqc2._computed) == len(saqc1._computed) * 2
def test_positionalMulitcallsPreserveState():
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)