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Removed logger.debugs for proven functions.

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This commit is contained in:
lwark
2024-12-12 12:17:21 -06:00
parent b174eb1221
commit 67520cb784
32 changed files with 80 additions and 758 deletions
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40
src/submissions/backend/db/models/controls.py
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@@ -171,11 +171,9 @@ class Control(BaseClass):
match submission_type:
case str():
from backend import BasicSubmission, SubmissionType
# logger.debug(f"Lookup controls by SubmissionType str: {submission_type}")
query = query.join(BasicSubmission).join(SubmissionType).filter(SubmissionType.name == submission_type)
case SubmissionType():
from backend import BasicSubmission
# logger.debug(f"Lookup controls by SubmissionType: {submission_type}")
query = query.join(BasicSubmission).filter(BasicSubmission.submission_type_name == submission_type.name)
case _:
pass
@@ -203,31 +201,23 @@ class Control(BaseClass):
if start_date is not None:
match start_date:
case date():
# logger.debug(f"Lookup control by start date({start_date})")
start_date = start_date.strftime("%Y-%m-%d")
case int():
# logger.debug(f"Lookup control by ordinal start date {start_date}")
start_date = datetime.fromordinal(
datetime(1900, 1, 1).toordinal() + start_date - 2).date().strftime("%Y-%m-%d")
case _:
# logger.debug(f"Lookup control with parsed start date {start_date}")
start_date = parse(start_date).strftime("%Y-%m-%d")
match end_date:
case date():
# logger.debug(f"Lookup control by end date({end_date})")
end_date = end_date.strftime("%Y-%m-%d")
case int():
# logger.debug(f"Lookup control by ordinal end date {end_date}")
end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date().strftime(
"%Y-%m-%d")
case _:
# logger.debug(f"Lookup control with parsed end date {end_date}")
end_date = parse(end_date).strftime("%Y-%m-%d")
# logger.debug(f"Looking up BasicSubmissions from start date: {start_date} and end date: {end_date}")
query = query.filter(cls.submitted_date.between(start_date, end_date))
match name:
case str():
# logger.debug(f"Lookup control by name {control_name}")
query = query.filter(cls.name.startswith(name))
limit = 1
case _:
@@ -273,7 +263,6 @@ class Control(BaseClass):
except StopIteration as e:
raise AttributeError(
f"Couldn't find existing class/subclass of {cls} with all attributes:\n{pformat(attrs.keys())}")
# logger.info(f"Recruiting model: {model}")
return model
@classmethod
@@ -343,7 +332,6 @@ class PCRControl(Control):
parent.mode_typer.clear()
parent.mode_typer.setEnabled(False)
report = Report()
# logger.debug(f"Chart settings: {pformat(chart_settings)}")
controls = cls.query(submission_type=chart_settings['sub_type'], start_date=chart_settings['start_date'],
end_date=chart_settings['end_date'])
data = [control.to_sub_dict() for control in controls]
@@ -411,21 +399,16 @@ class IridaControl(Control):
kraken = self.kraken
except TypeError:
kraken = {}
# logger.debug("calculating kraken count total to use in percentage")
kraken_cnt_total = sum([kraken[item]['kraken_count'] for item in kraken])
# logger.debug("Creating new kraken.")
new_kraken = [dict(name=item, kraken_count=kraken[item]['kraken_count'],
kraken_percent="{0:.0%}".format(kraken[item]['kraken_count'] / kraken_cnt_total),
target=item in self.controltype.targets)
for item in kraken]
# logger.debug(f"New kraken before sort: {new_kraken}")
new_kraken = sorted(new_kraken, key=itemgetter('kraken_count'), reverse=True)
# logger.debug("setting targets")
if self.controltype.targets:
targets = self.controltype.targets
else:
targets = ["None"]
# logger.debug("constructing output dictionary")
output = dict(
name=self.name,
type=self.controltype.name,
@@ -447,7 +430,6 @@ class IridaControl(Control):
Returns:
List[dict]: list of records
"""
# logger.debug("load json string for mode (i.e. contains, matches, kraken2)")
try:
data = self.__getattribute__(mode)
except TypeError:
@@ -460,12 +442,10 @@ class IridaControl(Control):
else:
if consolidate:
on_tar = {k: v for k, v in data.items() if k.strip("*") in self.controltype.targets[control_sub_type]}
# logger.debug(f"Consolidating off-targets to: {self.controltype.targets[control_sub_type]}")
off_tar = sum(v[f'{mode}_ratio'] for k, v in data.items() if
k.strip("*") not in self.controltype.targets[control_sub_type])
on_tar['Off-target'] = {f"{mode}_ratio": off_tar}
data = on_tar
# logger.debug("dict keys are genera of bacteria, e.g. 'Streptococcus'")
for genus in data:
_dict = dict(
name=self.name,
@@ -473,7 +453,6 @@ class IridaControl(Control):
genus=genus,
target='Target' if genus.strip("*") in self.controltype.targets[control_sub_type] else "Off-target"
)
# logger.debug("get Target or Off-target of genus")
for key in data[genus]:
_dict[key] = data[genus][key]
yield _dict
@@ -487,7 +466,6 @@ class IridaControl(Control):
List[str]: List of control mode names.
"""
try:
# logger.debug("Creating a list of JSON columns in _controls table")
cols = [item.name for item in list(cls.__table__.columns) if isinstance(item.type, JSON)]
except AttributeError as e:
logger.error(f"Failed to get available modes from db: {e}")
@@ -504,7 +482,6 @@ class IridaControl(Control):
"""
super().make_parent_buttons(parent=parent)
rows = parent.layout.rowCount() - 2
# logger.debug(f"Parent rows: {rows}")
checker = QCheckBox(parent)
checker.setChecked(True)
checker.setObjectName("irida_check")
@@ -539,10 +516,8 @@ class IridaControl(Control):
except AttributeError:
consolidate = False
report = Report()
# logger.debug(f"settings: {pformat(chart_settings)}")
controls = cls.query(subtype=chart_settings['sub_type'], start_date=chart_settings['start_date'],
end_date=chart_settings['end_date'])
# logger.debug(f"Controls found: {controls}")
if not controls:
report.add_result(Result(status="Critical", msg="No controls found in given date range."))
return report, None
@@ -552,19 +527,16 @@ class IridaControl(Control):
control in controls]
# NOTE: flatten data to one dimensional list
data = [item for sublist in data for item in sublist]
# logger.debug(f"Control objects going into df conversion: {pformat(data)}")
if not data:
report.add_result(Result(status="Critical", msg="No data found for controls in given date range."))
return report, None
df = cls.convert_data_list_to_df(input_df=data, sub_mode=chart_settings['sub_mode'])
# logger.debug(f"Chart df: \n {df}")
if chart_settings['sub_mode'] is None:
title = chart_settings['sub_mode']
else:
title = f"{chart_settings['mode']} - {chart_settings['sub_mode']}"
# NOTE: send dataframe to chart maker
df, modes = cls.prep_df(ctx=ctx, df=df)
# logger.debug(f"prepped df: \n {df}")
fig = IridaFigure(df=df, ytitle=title, modes=modes, parent=parent,
settings=chart_settings)
return report, fig
@@ -581,9 +553,7 @@ class IridaControl(Control):
Returns:
DataFrame: dataframe of controls
"""
# logger.debug(f"Subtype: {sub_mode}")
df = DataFrame.from_records(input_df)
# logger.debug(f"DF from records: {df}")
safe = ['name', 'submitted_date', 'genus', 'target']
for column in df.columns:
if column not in safe:
@@ -636,7 +606,6 @@ class IridaControl(Control):
Returns:
DataFrame: output dataframe with dates incremented.
"""
# logger.debug(f"Unique items: {df['name'].unique()}")
# NOTE: get submitted dates for each control
dict_list = [dict(name=item, date=df[df.name == item].iloc[0]['submitted_date']) for item in
sorted(df['name'].unique())]
@@ -664,7 +633,6 @@ class IridaControl(Control):
check = False
previous_dates.add(item['date'])
if check:
# logger.debug(f"We found one! Increment date!\n\t{item['date']} to {item['date'] + timedelta(days=1)}")
# NOTE: get df locations where name == item name
mask = df['name'] == item['name']
# NOTE: increment date in dataframe
@@ -673,15 +641,12 @@ class IridaControl(Control):
passed = False
else:
passed = True
# logger.debug(f"\n\tCurrent date: {item['date']}\n\tPrevious dates:{previous_dates}")
# logger.debug(f"DF: {type(df)}, previous_dates: {type(previous_dates)}")
# NOTE: if run didn't lead to changed date, return values
if passed:
# logger.debug(f"Date check passed, returning.")
return df, previous_dates
# NOTE: if date was changed, rerun with new date
else:
# logger.warning(f"Date check failed, running recursion")
logger.warning(f"Date check failed, running recursion")
df, previous_dates = cls.check_date(df, item, previous_dates)
return df, previous_dates
@@ -708,13 +673,10 @@ class IridaControl(Control):
# NOTE: sort by and exclude from
sorts = ['submitted_date', "target", "genus"]
exclude = ['name', 'genera']
# logger.debug(df.columns)
modes = [item for item in df.columns if item not in sorts and item not in exclude]
# logger.debug(f"Modes coming out: {modes}")
# NOTE: Set descending for any columns that have "{mode}" in the header.
ascending = [False if item == "target" else True for item in sorts]
df = df.sort_values(by=sorts, ascending=ascending)
# logger.debug(df[df.isna().any(axis=1)])
# NOTE: actual chart construction is done by
return df, modes