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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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4
src/submissions/__main__.py
View File

@@ -1,6 +1,5 @@
import sys, os import sys, os
from tools import ctx, setup_logger, check_if_app from tools import ctx, setup_logger, check_if_app
from backend import scripts
# environment variable must be set to enable qtwebengine in network path # environment variable must be set to enable qtwebengine in network path
if check_if_app(): if check_if_app():
@@ -9,6 +8,7 @@ if check_if_app():
# setup custom logger # setup custom logger
logger = setup_logger(verbosity=3) logger = setup_logger(verbosity=3)
from backend import scripts
from PyQt6.QtWidgets import QApplication from PyQt6.QtWidgets import QApplication
from frontend.widgets.app import App from frontend.widgets.app import App
@@ -25,6 +25,7 @@ def run_startup():
except AttributeError as e: except AttributeError as e:
logger.error(f"Couldn't run startup script {script} due to {e}") logger.error(f"Couldn't run startup script {script} due to {e}")
continue continue
logger.info(f"Running startup script: {func.__name__}")
func(ctx) func(ctx)
@@ -40,6 +41,7 @@ def run_teardown():
except AttributeError as e: except AttributeError as e:
logger.error(f"Couldn't run teardown script {script} due to {e}") logger.error(f"Couldn't run teardown script {script} due to {e}")
continue continue
logger.info(f"Running teardown script: {func.__name__}")
func(ctx) func(ctx)
if __name__ == '__main__': if __name__ == '__main__':

12
src/submissions/backend/db/__init__.py
View File

@@ -18,12 +18,8 @@ def set_sqlite_pragma(dbapi_connection, connection_record):
connection_record (_type_): _description_ connection_record (_type_): _description_
""" """
cursor = dbapi_connection.cursor() cursor = dbapi_connection.cursor()
# print(ctx.database_schema)
if ctx.database_schema == "sqlite": if ctx.database_schema == "sqlite":
execution_phrase = "PRAGMA foreign_keys=ON" execution_phrase = "PRAGMA foreign_keys=ON"
# cursor.execute(execution_phrase)
# elif ctx.database_schema == "mssql+pyodbc":
# execution_phrase = "SET IDENTITY_INSERT dbo._wastewater ON;"
else: else:
print("Nothing to execute, returning") print("Nothing to execute, returning")
cursor.close() cursor.close()
@@ -37,12 +33,9 @@ from .models import *
def update_log(mapper, connection, target): def update_log(mapper, connection, target):
# logger.debug("\n\nBefore update\n\n")
state = inspect(target) state = inspect(target)
# logger.debug(state)
object_name = state.object.truncated_name() object_name = state.object.truncated_name()
update = dict(user=getuser(), time=datetime.now(), object=object_name, changes=[]) update = dict(user=getuser(), time=datetime.now(), object=object_name, changes=[])
# logger.debug(update)
for attr in state.attrs: for attr in state.attrs:
hist = attr.load_history() hist = attr.load_history()
if not hist.has_changes(): if not hist.has_changes():
@@ -56,24 +49,19 @@ def update_log(mapper, connection, target):
continue continue
deleted = [str(item) for item in hist.deleted] deleted = [str(item) for item in hist.deleted]
change = dict(field=attr.key, added=added, deleted=deleted) change = dict(field=attr.key, added=added, deleted=deleted)
# logger.debug(f"Adding: {pformat(change)}")
if added != deleted: if added != deleted:
try: try:
update['changes'].append(change) update['changes'].append(change)
except Exception as e: except Exception as e:
logger.error(f"Something went wrong adding attr: {attr.key}: {e}") logger.error(f"Something went wrong adding attr: {attr.key}: {e}")
continue continue
# logger.debug(f"Adding to audit logs: {pformat(update)}")
if update['changes']: if update['changes']:
# Note: must use execute as the session will be busy at this point. # Note: must use execute as the session will be busy at this point.
# https://medium.com/@singh.surbhicse/creating-audit-table-to-log-insert-update-and-delete-changes-in-flask-sqlalchemy-f2ca53f7b02f # https://medium.com/@singh.surbhicse/creating-audit-table-to-log-insert-update-and-delete-changes-in-flask-sqlalchemy-f2ca53f7b02f
table = AuditLog.__table__ table = AuditLog.__table__
# logger.debug(f"Adding to {table}")
connection.execute(table.insert().values(**update)) connection.execute(table.insert().values(**update))
# logger.debug("Here is where I would insert values, if I was able.")
else: else:
logger.info(f"No changes detected, not updating logs.") logger.info(f"No changes detected, not updating logs.")
# if ctx.logging_enabled:
event.listen(LogMixin, 'after_update', update_log, propagate=True) event.listen(LogMixin, 'after_update', update_log, propagate=True)
event.listen(LogMixin, 'after_insert', update_log, propagate=True) event.listen(LogMixin, 'after_insert', update_log, propagate=True)

7
src/submissions/backend/db/models/__init__.py
View File

@@ -3,7 +3,6 @@ Contains all models for sqlalchemy
""" """
from __future__ import annotations from __future__ import annotations
import sys, logging import sys, logging
from pandas import DataFrame from pandas import DataFrame
from sqlalchemy import Column, INTEGER, String, JSON from sqlalchemy import Column, INTEGER, String, JSON
from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session
@@ -131,7 +130,6 @@ class BaseClass(Base):
search = name.title().replace(" ", "") search = name.title().replace(" ", "")
else: else:
search = name search = name
logger.debug(f"Searching for subclass: {search}")
return next((item for item in cls.__subclasses__() if item.__name__ == search), cls) return next((item for item in cls.__subclasses__() if item.__name__ == search), cls)
@classmethod @classmethod
@@ -146,9 +144,7 @@ class BaseClass(Base):
List[Any]: Results of sqlalchemy query. List[Any]: Results of sqlalchemy query.
""" """
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
# logger.debug(f"Queried model. Now running searches in {kwargs}")
for k, v in kwargs.items(): for k, v in kwargs.items():
# logger.debug(f"Running fuzzy search for attribute: {k} with value {v}")
# NOTE: Not sure why this is necessary, but it is. # NOTE: Not sure why this is necessary, but it is.
search = f"%{v}%" search = f"%{v}%"
try: try:
@@ -200,9 +196,7 @@ class BaseClass(Base):
model = cls model = cls
if query is None: if query is None:
query: Query = cls.__database_session__.query(model) query: Query = cls.__database_session__.query(model)
# logger.debug(f"Grabbing singles using {model.get_default_info}")
singles = model.get_default_info('singles') singles = model.get_default_info('singles')
# logger.info(f"Querying: {model}, with kwargs: {kwargs}")
for k, v in kwargs.items(): for k, v in kwargs.items():
logger.info(f"Using key: {k} with value: {v}") logger.info(f"Using key: {k} with value: {v}")
try: try:
@@ -227,7 +221,6 @@ class BaseClass(Base):
""" """
Add the object to the database and commit Add the object to the database and commit
""" """
# logger.debug(f"Saving object: {pformat(self.__dict__)}")
report = Report() report = Report()
try: try:
self.__database_session__.add(self) self.__database_session__.add(self)

9
src/submissions/backend/db/models/audit.py
View File

@@ -2,7 +2,6 @@
Contains the audit log class and functions. Contains the audit log class and functions.
""" """
from typing import List from typing import List
from dateutil.parser import parse from dateutil.parser import parse
from sqlalchemy.orm import declarative_base, DeclarativeMeta, Query from sqlalchemy.orm import declarative_base, DeclarativeMeta, Query
from . import BaseClass from . import BaseClass
@@ -48,32 +47,24 @@ class AuditLog(Base):
logger.warning(f"End date with no start date, using Jan 1, 2023") logger.warning(f"End date with no start date, using Jan 1, 2023")
start_date = session.query(cls, func.min(cls.time)).first()[1] start_date = session.query(cls, func.min(cls.time)).first()[1]
if start_date is not None: if start_date is not None:
# logger.debug(f"Querying with start date: {start_date} and end date: {end_date}")
match start_date: match start_date:
case date(): case date():
# logger.debug(f"Lookup BasicSubmission by start_date({start_date})")
start_date = start_date.strftime("%Y-%m-%d") start_date = start_date.strftime("%Y-%m-%d")
case int(): case int():
# logger.debug(f"Lookup BasicSubmission by ordinal start_date {start_date}")
start_date = datetime.fromordinal( start_date = datetime.fromordinal(
datetime(1900, 1, 1).toordinal() + start_date - 2).date().strftime("%Y-%m-%d") datetime(1900, 1, 1).toordinal() + start_date - 2).date().strftime("%Y-%m-%d")
case _: case _:
# logger.debug(f"Lookup BasicSubmission by parsed str start_date {start_date}")
start_date = parse(start_date).strftime("%Y-%m-%d") start_date = parse(start_date).strftime("%Y-%m-%d")
match end_date: match end_date:
case date() | datetime(): case date() | datetime():
# logger.debug(f"Lookup BasicSubmission by end_date({end_date})")
end_date = end_date + timedelta(days=1) end_date = end_date + timedelta(days=1)
end_date = end_date.strftime("%Y-%m-%d") end_date = end_date.strftime("%Y-%m-%d")
case int(): case int():
# logger.debug(f"Lookup BasicSubmission by ordinal end_date {end_date}")
end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date() + timedelta(days=1) end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date() + timedelta(days=1)
end_date = end_date.strftime("%Y-%m-%d") end_date = end_date.strftime("%Y-%m-%d")
case _: case _:
# logger.debug(f"Lookup BasicSubmission by parsed str end_date {end_date}")
end_date = parse(end_date) + timedelta(days=1) end_date = parse(end_date) + timedelta(days=1)
end_date = end_date.strftime("%Y-%m-%d") end_date = end_date.strftime("%Y-%m-%d")
# logger.debug(f"Compensating for same date by using time")
if start_date == end_date: if start_date == end_date:
start_date = datetime.strptime(start_date, "%Y-%m-%d").strftime("%Y-%m-%d %H:%M:%S.%f") start_date = datetime.strptime(start_date, "%Y-%m-%d").strftime("%Y-%m-%d %H:%M:%S.%f")
query = query.filter(cls.time == start_date) query = query.filter(cls.time == start_date)

40
src/submissions/backend/db/models/controls.py
View File

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

90
src/submissions/backend/db/models/kits.py
View File

@@ -17,7 +17,6 @@ from io import BytesIO
logger = logging.getLogger(f'submissions.{__name__}') logger = logging.getLogger(f'submissions.{__name__}')
# logger.debug("Table for ReagentType/Reagent relations")
reagentroles_reagents = Table( reagentroles_reagents = Table(
"_reagentroles_reagents", "_reagentroles_reagents",
Base.metadata, Base.metadata,
@@ -26,7 +25,6 @@ reagentroles_reagents = Table(
extend_existing=True extend_existing=True
) )
# logger.debug("Table for EquipmentRole/Equipment relations")
equipmentroles_equipment = Table( equipmentroles_equipment = Table(
"_equipmentroles_equipment", "_equipmentroles_equipment",
Base.metadata, Base.metadata,
@@ -35,7 +33,6 @@ equipmentroles_equipment = Table(
extend_existing=True extend_existing=True
) )
# logger.debug("Table for Equipment/Process relations")
equipment_processes = Table( equipment_processes = Table(
"_equipment_processes", "_equipment_processes",
Base.metadata, Base.metadata,
@@ -44,7 +41,6 @@ equipment_processes = Table(
extend_existing=True extend_existing=True
) )
# logger.debug("Table for EquipmentRole/Process relations")
equipmentroles_processes = Table( equipmentroles_processes = Table(
"_equipmentroles_processes", "_equipmentroles_processes",
Base.metadata, Base.metadata,
@@ -53,7 +49,6 @@ equipmentroles_processes = Table(
extend_existing=True extend_existing=True
) )
# logger.debug("Table for SubmissionType/Process relations")
submissiontypes_processes = Table( submissiontypes_processes = Table(
"_submissiontypes_processes", "_submissiontypes_processes",
Base.metadata, Base.metadata,
@@ -62,7 +57,6 @@ submissiontypes_processes = Table(
extend_existing=True extend_existing=True
) )
# logger.debug("Table for KitType/Process relations")
kittypes_processes = Table( kittypes_processes = Table(
"_kittypes_processes", "_kittypes_processes",
Base.metadata, Base.metadata,
@@ -71,7 +65,6 @@ kittypes_processes = Table(
extend_existing=True extend_existing=True
) )
# logger.debug("Table for TipRole/Tips relations")
tiproles_tips = Table( tiproles_tips = Table(
"_tiproles_tips", "_tiproles_tips",
Base.metadata, Base.metadata,
@@ -80,7 +73,6 @@ tiproles_tips = Table(
extend_existing=True extend_existing=True
) )
# logger.debug("Table for Process/TipRole relations")
process_tiprole = Table( process_tiprole = Table(
"_process_tiprole", "_process_tiprole",
Base.metadata, Base.metadata,
@@ -89,7 +81,6 @@ process_tiprole = Table(
extend_existing=True extend_existing=True
) )
# logger.debug("Table for Equipment/Tips relations")
equipment_tips = Table( equipment_tips = Table(
"_equipment_tips", "_equipment_tips",
Base.metadata, Base.metadata,
@@ -116,7 +107,7 @@ class KitType(BaseClass):
cascade="all, delete-orphan", cascade="all, delete-orphan",
) )
# creator function: https://stackoverflow.com/questions/11091491/keyerror-when-adding-objects-to-sqlalchemy-association-object/11116291#11116291 # NOTE: creator function: https://stackoverflow.com/questions/11091491/keyerror-when-adding-objects-to-sqlalchemy-association-object/11116291#11116291
reagent_roles = association_proxy("kit_reagentrole_associations", "reagent_role", reagent_roles = association_proxy("kit_reagentrole_associations", "reagent_role",
creator=lambda RT: KitTypeReagentRoleAssociation( creator=lambda RT: KitTypeReagentRoleAssociation(
reagent_role=RT)) #: Association proxy to KitTypeReagentRoleAssociation reagent_role=RT)) #: Association proxy to KitTypeReagentRoleAssociation
@@ -152,18 +143,14 @@ class KitType(BaseClass):
""" """
match submission_type: match submission_type:
case SubmissionType(): case SubmissionType():
# logger.debug(f"Getting reagents by SubmissionType {submission_type}")
relevant_associations = [item for item in self.kit_reagentrole_associations if relevant_associations = [item for item in self.kit_reagentrole_associations if
item.submission_type == submission_type] item.submission_type == submission_type]
case str(): case str():
# logger.debug(f"Getting reagents by str {submission_type}")
relevant_associations = [item for item in self.kit_reagentrole_associations if relevant_associations = [item for item in self.kit_reagentrole_associations if
item.submission_type.name == submission_type] item.submission_type.name == submission_type]
case _: case _:
# logger.debug(f"Getting reagents")
relevant_associations = [item for item in self.kit_reagentrole_associations] relevant_associations = [item for item in self.kit_reagentrole_associations]
if required: if required:
# logger.debug(f"Filtering by required.")
return (item.reagent_role for item in relevant_associations if item.required == 1) return (item.reagent_role for item in relevant_associations if item.required == 1)
else: else:
return (item.reagent_role for item in relevant_associations) return (item.reagent_role for item in relevant_associations)
@@ -181,18 +168,14 @@ class KitType(BaseClass):
# NOTE: Account for submission_type variable type. # NOTE: Account for submission_type variable type.
match submission_type: match submission_type:
case str(): case str():
# logger.debug(f"Constructing xl map with str {submission_type}")
assocs = [item for item in self.kit_reagentrole_associations if assocs = [item for item in self.kit_reagentrole_associations if
item.submission_type.name == submission_type] item.submission_type.name == submission_type]
case SubmissionType(): case SubmissionType():
# logger.debug(f"Constructing xl map with SubmissionType {submission_type}")
assocs = [item for item in self.kit_reagentrole_associations if item.submission_type == submission_type] assocs = [item for item in self.kit_reagentrole_associations if item.submission_type == submission_type]
case _: case _:
raise ValueError(f"Wrong variable type: {type(submission_type)} used!") raise ValueError(f"Wrong variable type: {type(submission_type)} used!")
# logger.debug("Get all KitTypeReagentTypeAssociation for SubmissionType")
for assoc in assocs: for assoc in assocs:
try: try:
# logger.debug(f"Yielding: {assoc.reagent_role.name}, {assoc.uses}")
yield assoc.reagent_role.name, assoc.uses yield assoc.reagent_role.name, assoc.uses
except TypeError: except TypeError:
continue continue
@@ -220,27 +203,22 @@ class KitType(BaseClass):
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
match used_for: match used_for:
case str(): case str():
# logger.debug(f"Looking up kit type by used_for str: {used_for}")
query = query.filter(cls.used_for.any(name=used_for)) query = query.filter(cls.used_for.any(name=used_for))
case SubmissionType(): case SubmissionType():
# logger.debug(f"Looking up kit type by used_for SubmissionType: {used_for}")
query = query.filter(cls.used_for.contains(used_for)) query = query.filter(cls.used_for.contains(used_for))
case _: case _:
pass pass
match name: match name:
case str(): case str():
# logger.debug(f"Looking up kit type by name str: {name}")
query = query.filter(cls.name == name) query = query.filter(cls.name == name)
limit = 1 limit = 1
case _: case _:
pass pass
match id: match id:
case int(): case int():
# logger.debug(f"Looking up kit type by id int: {id}")
query = query.filter(cls.id == id) query = query.filter(cls.id == id)
limit = 1 limit = 1
case str(): case str():
# logger.debug(f"Looking up kit type by id str: {id}")
query = query.filter(cls.id == int(id)) query = query.filter(cls.id == int(id))
limit = 1 limit = 1
case _: case _:
@@ -262,10 +240,7 @@ class KitType(BaseClass):
dict: Dictionary containing relevant info for SubmissionType construction dict: Dictionary containing relevant info for SubmissionType construction
""" """
base_dict = dict(name=self.name, reagent_roles=[], equipment_roles=[]) base_dict = dict(name=self.name, reagent_roles=[], equipment_roles=[])
# base_dict['reagent roles'] = []
# base_dict['equipment roles'] = []
for k, v in self.construct_xl_map_for_use(submission_type=submission_type): for k, v in self.construct_xl_map_for_use(submission_type=submission_type):
# logger.debug(f"Value: {v}")
try: try:
assoc = next(item for item in self.kit_reagentrole_associations if item.reagent_role.name == k) assoc = next(item for item in self.kit_reagentrole_associations if item.reagent_role.name == k)
except StopIteration as e: except StopIteration as e:
@@ -280,10 +255,8 @@ class KitType(BaseClass):
except StopIteration: except StopIteration:
continue continue
for kk, vv in assoc.to_export_dict(extraction_kit=self).items(): for kk, vv in assoc.to_export_dict(extraction_kit=self).items():
# logger.debug(f"{kk}:{vv}")
v[kk] = vv v[kk] = vv
base_dict['equipment_roles'].append(v) base_dict['equipment_roles'].append(v)
# logger.debug(f"KT returning {base_dict}")
return base_dict return base_dict
@@ -347,28 +320,19 @@ class ReagentRole(BaseClass):
else: else:
match kit_type: match kit_type:
case str(): case str():
# logger.debug(f"Lookup ReagentType by kittype str {kit_type}")
kit_type = KitType.query(name=kit_type) kit_type = KitType.query(name=kit_type)
case _: case _:
pass pass
match reagent: match reagent:
case str(): case str():
# logger.debug(f"Lookup ReagentType by reagent str {reagent}")
reagent = Reagent.query(lot=reagent) reagent = Reagent.query(lot=reagent)
case _: case _:
pass pass
assert reagent.role assert reagent.role
# logger.debug(f"Looking up reagent type for {type(kit_type)} {kit_type} and {type(reagent)} {reagent}")
# logger.debug(f"Kit reagent types: {kit_type.reagent_types}")
result = set(kit_type.reagent_roles).intersection(reagent.role) result = set(kit_type.reagent_roles).intersection(reagent.role)
# logger.debug(f"Result: {result}")
# try:
return next((item for item in result), None) return next((item for item in result), None)
# except IndexError:
# return None
match name: match name:
case str(): case str():
# logger.debug(f"Looking up reagent type by name str: {name}")
query = query.filter(cls.name == name) query = query.filter(cls.name == name)
limit = 1 limit = 1
case _: case _:
@@ -457,7 +421,6 @@ class Reagent(BaseClass, LogMixin):
rtype = reagent_role.name.replace("_", " ") rtype = reagent_role.name.replace("_", " ")
except AttributeError: except AttributeError:
rtype = "Unknown" rtype = "Unknown"
# logger.debug(f"Role for {self.name}: {rtype}")
# NOTE: Calculate expiry with EOL from ReagentType # NOTE: Calculate expiry with EOL from ReagentType
try: try:
place_holder = self.expiry + reagent_role.eol_ext place_holder = self.expiry + reagent_role.eol_ext
@@ -493,14 +456,11 @@ class Reagent(BaseClass, LogMixin):
Report: Result of operation Report: Result of operation
""" """
report = Report() report = Report()
# logger.debug(f"Attempting update of last used reagent type at intersection of ({self}), ({kit})")
rt = ReagentRole.query(kit_type=kit, reagent=self, limit=1) rt = ReagentRole.query(kit_type=kit, reagent=self, limit=1)
if rt is not None: if rt is not None:
# logger.debug(f"got reagenttype {rt}")
assoc = KitTypeReagentRoleAssociation.query(kit_type=kit, reagent_role=rt) assoc = KitTypeReagentRoleAssociation.query(kit_type=kit, reagent_role=rt)
if assoc is not None: if assoc is not None:
if assoc.last_used != self.lot: if assoc.last_used != self.lot:
# logger.debug(f"Updating {assoc} last used to {self.lot}")
assoc.last_used = self.lot assoc.last_used = self.lot
result = assoc.save() result = assoc.save()
report.add_result(result) report.add_result(result)
@@ -539,23 +499,19 @@ class Reagent(BaseClass, LogMixin):
pass pass
match role: match role:
case str(): case str():
# logger.debug(f"Looking up reagents by reagent type str: {reagent_type}")
query = query.join(cls.role).filter(ReagentRole.name == role) query = query.join(cls.role).filter(ReagentRole.name == role)
case ReagentRole(): case ReagentRole():
# logger.debug(f"Looking up reagents by reagent type ReagentType: {reagent_type}")
query = query.filter(cls.role.contains(role)) query = query.filter(cls.role.contains(role))
case _: case _:
pass pass
match name: match name:
case str(): case str():
# logger.debug(f"Looking up reagent by name str: {name}")
# NOTE: Not limited due to multiple reagents having same name. # NOTE: Not limited due to multiple reagents having same name.
query = query.filter(cls.name == name) query = query.filter(cls.name == name)
case _: case _:
pass pass
match lot: match lot:
case str(): case str():
# logger.debug(f"Looking up reagent by lot number str: {lot}")
query = query.filter(cls.lot == lot) query = query.filter(cls.lot == lot)
# NOTE: In this case limit number returned. # NOTE: In this case limit number returned.
limit = 1 limit = 1
@@ -579,7 +535,6 @@ class Reagent(BaseClass, LogMixin):
case "expiry": case "expiry":
if isinstance(value, str): if isinstance(value, str):
field_value = datetime.strptime(value, "%Y-%m-%d") field_value = datetime.strptime(value, "%Y-%m-%d")
# field_value.replace(tzinfo=timezone)
elif isinstance(value, date): elif isinstance(value, date):
field_value = datetime.combine(value, datetime.min.time()) field_value = datetime.combine(value, datetime.min.time())
else: else:
@@ -589,7 +544,6 @@ class Reagent(BaseClass, LogMixin):
continue continue
case _: case _:
field_value = value field_value = value
# logger.debug(f"Setting reagent {key} to {field_value}")
self.__setattr__(key, field_value) self.__setattr__(key, field_value)
self.save() self.save()
@@ -634,25 +588,19 @@ class Discount(BaseClass):
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
match organization: match organization:
case Organization(): case Organization():
# logger.debug(f"Looking up discount with organization Organization: {organization}")
query = query.filter(cls.client == Organization) query = query.filter(cls.client == Organization)
case str(): case str():
# logger.debug(f"Looking up discount with organization str: {organization}")
query = query.join(Organization).filter(Organization.name == organization) query = query.join(Organization).filter(Organization.name == organization)
case int(): case int():
# logger.debug(f"Looking up discount with organization id: {organization}")
query = query.join(Organization).filter(Organization.id == organization) query = query.join(Organization).filter(Organization.id == organization)
case _: case _:
pass pass
match kit_type: match kit_type:
case KitType(): case KitType():
# logger.debug(f"Looking up discount with kit type KitType: {kit_type}")
query = query.filter(cls.kit == kit_type) query = query.filter(cls.kit == kit_type)
case str(): case str():
# logger.debug(f"Looking up discount with kit type str: {kit_type}")
query = query.join(KitType).filter(KitType.name == kit_type) query = query.join(KitType).filter(KitType.name == kit_type)
case int(): case int():
# logger.debug(f"Looking up discount with kit type id: {kit_type}")
query = query.join(KitType).filter(KitType.id == kit_type) query = query.join(KitType).filter(KitType.id == kit_type)
case _: case _:
pass pass
@@ -723,7 +671,6 @@ class SubmissionType(BaseClass):
return submission_type.template_file return submission_type.template_file
def get_template_file_sheets(self) -> List[str]: def get_template_file_sheets(self) -> List[str]:
logger.debug(f"Submission type to get sheets for: {self.name}")
""" """
Gets names of sheet in the stored blank form. Gets names of sheet in the stored blank form.
@@ -768,7 +715,6 @@ class SubmissionType(BaseClass):
dict: Map of locations dict: Map of locations
""" """
info = {k: v for k, v in self.info_map.items() if k != "custom"} info = {k: v for k, v in self.info_map.items() if k != "custom"}
logger.debug(f"Info map: {info}")
match mode: match mode:
case "read": case "read":
output = {k: v[mode] for k, v in info.items() if v[mode]} output = {k: v[mode] for k, v in info.items() if v[mode]}
@@ -844,11 +790,9 @@ class SubmissionType(BaseClass):
""" """
match equipment_role: match equipment_role:
case str(): case str():
# logger.debug(f"Getting processes for equipmentrole str {equipment_role}")
relevant = [item.get_all_processes(kit) for item in self.submissiontype_equipmentrole_associations if relevant = [item.get_all_processes(kit) for item in self.submissiontype_equipmentrole_associations if
item.equipment_role.name == equipment_role] item.equipment_role.name == equipment_role]
case EquipmentRole(): case EquipmentRole():
# logger.debug(f"Getting processes for equipmentrole EquipmentRole {equipment_role}")
relevant = [item.get_all_processes(kit) for item in self.submissiontype_equipmentrole_associations if relevant = [item.get_all_processes(kit) for item in self.submissiontype_equipmentrole_associations if
item.equipment_role == equipment_role] item.equipment_role == equipment_role]
case _: case _:
@@ -886,14 +830,12 @@ class SubmissionType(BaseClass):
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
match name: match name:
case str(): case str():
# logger.debug(f"Looking up submission type by name str: {name}")
query = query.filter(cls.name == name) query = query.filter(cls.name == name)
limit = 1 limit = 1
case _: case _:
pass pass
match key: match key:
case str(): case str():
# logger.debug(f"Looking up submission type by info-map key str: {key}")
query = query.filter(cls.info_map.op('->')(key) is not None) query = query.filter(cls.info_map.op('->')(key) is not None)
case _: case _:
pass pass
@@ -946,7 +888,6 @@ class SubmissionType(BaseClass):
import_dict = yaml.load(stream=f, Loader=yaml.Loader) import_dict = yaml.load(stream=f, Loader=yaml.Loader)
else: else:
raise Exception(f"Filetype {filepath.suffix} not supported.") raise Exception(f"Filetype {filepath.suffix} not supported.")
# logger.debug(pformat(import_dict))
try: try:
submission_type = cls.query(name=import_dict['name']) submission_type = cls.query(name=import_dict['name'])
except KeyError: except KeyError:
@@ -1076,23 +1017,17 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
match submission_type: match submission_type:
case SubmissionType(): case SubmissionType():
# logger.debug(f"Looking up {cls.__name__} by SubmissionType {submission_type}")
query = query.filter(cls.submission_type == submission_type) query = query.filter(cls.submission_type == submission_type)
case str(): case str():
# logger.debug(f"Looking up {cls.__name__} by name {submission_type}")
query = query.join(SubmissionType).filter(SubmissionType.name == submission_type) query = query.join(SubmissionType).filter(SubmissionType.name == submission_type)
case int(): case int():
# logger.debug(f"Looking up {cls.__name__} by id {submission_type}")
query = query.join(SubmissionType).filter(SubmissionType.id == submission_type) query = query.join(SubmissionType).filter(SubmissionType.id == submission_type)
match kit_type: match kit_type:
case KitType(): case KitType():
# logger.debug(f"Looking up {cls.__name__} by KitType {kit_type}")
query = query.filter(cls.kit_type == kit_type) query = query.filter(cls.kit_type == kit_type)
case str(): case str():
# logger.debug(f"Looking up {cls.__name__} by name {kit_type}")
query = query.join(KitType).filter(KitType.name == kit_type) query = query.join(KitType).filter(KitType.name == kit_type)
case int(): case int():
# logger.debug(f"Looking up {cls.__name__} by id {kit_type}")
query = query.join(KitType).filter(KitType.id == kit_type) query = query.join(KitType).filter(KitType.id == kit_type)
limit = query.count() limit = query.count()
return cls.execute_query(query=query, limit=limit) return cls.execute_query(query=query, limit=limit)
@@ -1107,7 +1042,6 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
exclude = ['_sa_instance_state', 'submission_types_id', 'kits_id', 'submission_type', 'kit_type'] exclude = ['_sa_instance_state', 'submission_types_id', 'kits_id', 'submission_type', 'kit_type']
base_dict = {k: v for k, v in self.__dict__.items() if k not in exclude} base_dict = {k: v for k, v in self.__dict__.items() if k not in exclude}
base_dict['kit_type'] = self.kit_type.to_export_dict(submission_type=self.submission_type) base_dict['kit_type'] = self.kit_type.to_export_dict(submission_type=self.submission_type)
# logger.debug(f"STKTA returning: {base_dict}")
return base_dict return base_dict
@@ -1128,10 +1062,11 @@ class KitTypeReagentRoleAssociation(BaseClass):
kit_type = relationship(KitType, kit_type = relationship(KitType,
back_populates="kit_reagentrole_associations") #: relationship to associated KitType back_populates="kit_reagentrole_associations") #: relationship to associated KitType
# reference to the "ReagentType" object # NOTE: reference to the "ReagentType" object
reagent_role = relationship(ReagentRole, reagent_role = relationship(ReagentRole,
back_populates="reagentrole_kit_associations") #: relationship to associated ReagentType back_populates="reagentrole_kit_associations") #: relationship to associated ReagentType
# NOTE: reference to the "SubmissionType" object
submission_type = relationship(SubmissionType, submission_type = relationship(SubmissionType,
back_populates="submissiontype_kit_rt_associations") #: relationship to associated SubmissionType back_populates="submissiontype_kit_rt_associations") #: relationship to associated SubmissionType
@@ -1203,19 +1138,15 @@ class KitTypeReagentRoleAssociation(BaseClass):
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
match kit_type: match kit_type:
case KitType(): case KitType():
# logger.debug(f"Lookup KitTypeReagentTypeAssociation by kit_type KitType {kit_type}")
query = query.filter(cls.kit_type == kit_type) query = query.filter(cls.kit_type == kit_type)
case str(): case str():
# logger.debug(f"Lookup KitTypeReagentTypeAssociation by kit_type str {kit_type}")
query = query.join(KitType).filter(KitType.name == kit_type) query = query.join(KitType).filter(KitType.name == kit_type)
case _: case _:
pass pass
match reagent_role: match reagent_role:
case ReagentRole(): case ReagentRole():
# logger.debug(f"Lookup KitTypeReagentTypeAssociation by reagent_type ReagentType {reagent_type}")
query = query.filter(cls.reagent_role == reagent_role) query = query.filter(cls.reagent_role == reagent_role)
case str(): case str():
# logger.debug(f"Lookup KitTypeReagentTypeAssociation by reagent_type ReagentType {reagent_type}")
query = query.join(ReagentRole).filter(ReagentRole.name == reagent_role) query = query.join(ReagentRole).filter(ReagentRole.name == reagent_role)
case _: case _:
pass pass
@@ -1242,7 +1173,6 @@ class KitTypeReagentRoleAssociation(BaseClass):
Returns: Returns:
Generator: Generates of reagents. Generator: Generates of reagents.
""" """
# logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
reagents = self.reagent_role.instances reagents = self.reagent_role.instances
try: try:
regex = self.uses['exclude_regex'] regex = self.uses['exclude_regex']
@@ -1309,7 +1239,6 @@ class SubmissionReagentAssociation(BaseClass):
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
match reagent: match reagent:
case Reagent() | str(): case Reagent() | str():
# logger.debug(f"Lookup SubmissionReagentAssociation by reagent Reagent {reagent}")
if isinstance(reagent, str): if isinstance(reagent, str):
reagent = Reagent.query(lot=reagent) reagent = Reagent.query(lot=reagent)
query = query.filter(cls.reagent == reagent) query = query.filter(cls.reagent == reagent)
@@ -1319,10 +1248,8 @@ class SubmissionReagentAssociation(BaseClass):
case BasicSubmission() | str(): case BasicSubmission() | str():
if isinstance(submission, str): if isinstance(submission, str):
submission = BasicSubmission.query(rsl_plate_num=submission) submission = BasicSubmission.query(rsl_plate_num=submission)
# logger.debug(f"Lookup SubmissionReagentAssociation by submission BasicSubmission {submission}")
query = query.filter(cls.submission == submission) query = query.filter(cls.submission == submission)
case int(): case int():
# logger.debug(f"Lookup SubmissionReagentAssociation by submission id {submission}")
submission = BasicSubmission.query(id=submission) submission = BasicSubmission.query(id=submission)
query = query.join(BasicSubmission).filter(BasicSubmission.id == submission) query = query.join(BasicSubmission).filter(BasicSubmission.id == submission)
case _: case _:
@@ -1439,21 +1366,18 @@ class Equipment(BaseClass, LogMixin):
query = cls.__database_session__.query(cls) query = cls.__database_session__.query(cls)
match name: match name:
case str(): case str():
# logger.debug(f"Lookup Equipment by name str {name}")
query = query.filter(cls.name == name) query = query.filter(cls.name == name)
limit = 1 limit = 1
case _: case _:
pass pass
match nickname: match nickname:
case str(): case str():
# logger.debug(f"Lookup Equipment by nickname str {nickname}")
query = query.filter(cls.nickname == nickname) query = query.filter(cls.nickname == nickname)
limit = 1 limit = 1
case _: case _:
pass pass
match asset_number: match asset_number:
case str(): case str():
# logger.debug(f"Lookup Equipment by asset_number str {asset_number}")
query = query.filter(cls.asset_number == asset_number) query = query.filter(cls.asset_number == asset_number)
limit = 1 limit = 1
case _: case _:
@@ -1569,11 +1493,9 @@ class EquipmentRole(BaseClass):
PydEquipmentRole: This EquipmentRole as PydEquipmentRole PydEquipmentRole: This EquipmentRole as PydEquipmentRole
""" """
from backend.validators.pydant import PydEquipmentRole from backend.validators.pydant import PydEquipmentRole
# logger.debug("Creating list of PydEquipment in this role")
equipment = [item.to_pydantic(submission_type=submission_type, extraction_kit=extraction_kit) for item in equipment = [item.to_pydantic(submission_type=submission_type, extraction_kit=extraction_kit) for item in
self.instances] self.instances]
pyd_dict = self.to_dict() pyd_dict = self.to_dict()
# logger.debug("Creating list of Processes in this role")
pyd_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=extraction_kit) pyd_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=extraction_kit)
return PydEquipmentRole(equipment=equipment, **pyd_dict) return PydEquipmentRole(equipment=equipment, **pyd_dict)
@@ -1595,14 +1517,12 @@ class EquipmentRole(BaseClass):
query = cls.__database_session__.query(cls) query = cls.__database_session__.query(cls)
match id: match id:
case int(): case int():
# logger.debug(f"Lookup EquipmentRole by id {id}")
query = query.filter(cls.id == id) query = query.filter(cls.id == id)
limit = 1 limit = 1
case _: case _:
pass pass
match name: match name:
case str(): case str():
# logger.debug(f"Lookup EquipmentRole by name str {name}")
query = query.filter(cls.name == name) query = query.filter(cls.name == name)
limit = 1 limit = 1
case _: case _:
@@ -1622,7 +1542,6 @@ class EquipmentRole(BaseClass):
List[Process]: List of processes List[Process]: List of processes
""" """
if isinstance(submission_type, str): if isinstance(submission_type, str):
# logger.debug(f"Checking if str {submission_type} exists")
submission_type = SubmissionType.query(name=submission_type) submission_type = SubmissionType.query(name=submission_type)
if isinstance(extraction_kit, str): if isinstance(extraction_kit, str):
extraction_kit = KitType.query(name=extraction_kit) extraction_kit = KitType.query(name=extraction_kit)
@@ -1808,7 +1727,6 @@ class Process(BaseClass):
query = cls.__database_session__.query(cls) query = cls.__database_session__.query(cls)
match name: match name:
case str(): case str():
# logger.debug(f"Lookup Process with name str {name}")
query = query.filter(cls.name == name) query = query.filter(cls.name == name)
limit = 1 limit = 1
case _: case _:
@@ -1892,13 +1810,11 @@ class Tips(BaseClass, LogMixin):
query = cls.__database_session__.query(cls) query = cls.__database_session__.query(cls)
match name: match name:
case str(): case str():
# logger.debug(f"Lookup Equipment by name str {name}")
query = query.filter(cls.name == name) query = query.filter(cls.name == name)
case _: case _:
pass pass
match lot: match lot:
case str(): case str():
# logger.debug(f"Lookup Equipment by nickname str {nickname}")
query = query.filter(cls.lot == lot) query = query.filter(cls.lot == lot)
limit = 1 limit = 1
case _: case _:

4
src/submissions/backend/db/models/organizations.py
View File

@@ -65,7 +65,6 @@ class Organization(BaseClass):
pass pass
match name: match name:
case str(): case str():
# logger.debug(f"Looking up organization with name starting with: {name}")
query = query.filter(cls.name.startswith(name)) query = query.filter(cls.name.startswith(name))
limit = 1 limit = 1
case _: case _:
@@ -159,21 +158,18 @@ class Contact(BaseClass):
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
match name: match name:
case str(): case str():
# logger.debug(f"Looking up contact with name: {name}")
query = query.filter(cls.name == name.title()) query = query.filter(cls.name == name.title())
limit = 1 limit = 1
case _: case _:
pass pass
match email: match email:
case str(): case str():
# logger.debug(f"Looking up contact with email: {name}")
query = query.filter(cls.email == email) query = query.filter(cls.email == email)
limit = 1 limit = 1
case _: case _:
pass pass
match phone: match phone:
case str(): case str():
# logger.debug(f"Looking up contact with phone: {name}")
query = query.filter(cls.phone == phone) query = query.filter(cls.phone == phone)
limit = 1 limit = 1
case _: case _:

238
src/submissions/backend/db/models/submissions.py
View File

File diff suppressed because it is too large Load Diff

57
src/submissions/backend/excel/parser.py
View File

@@ -1,6 +1,6 @@
''' """
contains parser objects for pulling values from client generated submission sheets. contains parser objects for pulling values from client generated submission sheets.
''' """
import logging import logging
from copy import copy from copy import copy
from getpass import getuser from getpass import getuser
@@ -53,7 +53,6 @@ class SheetParser(object):
self.parse_samples() self.parse_samples()
self.parse_equipment() self.parse_equipment()
self.parse_tips() self.parse_tips()
# logger.debug(f"Parser.sub after info scrape: {pformat(self.sub)}")
def parse_info(self): def parse_info(self):
""" """
@@ -71,7 +70,6 @@ class SheetParser(object):
logger.info( logger.info(
f"Checking for updated submission type: {self.submission_type.name} against new: {info['submission_type']['value']}") f"Checking for updated submission type: {self.submission_type.name} against new: {info['submission_type']['value']}")
if self.submission_type.name != info['submission_type']['value']: if self.submission_type.name != info['submission_type']['value']:
# logger.debug(f"info submission type: {info}")
if check: if check:
self.submission_type = SubmissionType.query(name=info['submission_type']['value']) self.submission_type = SubmissionType.query(name=info['submission_type']['value'])
logger.info(f"Updated self.submission_type to {self.submission_type}. Rerunning parse.") logger.info(f"Updated self.submission_type to {self.submission_type}. Rerunning parse.")
@@ -90,11 +88,9 @@ class SheetParser(object):
""" """
if extraction_kit is None: if extraction_kit is None:
extraction_kit = self.sub['extraction_kit'] extraction_kit = self.sub['extraction_kit']
# logger.debug(f"Parsing reagents for {extraction_kit}")
parser = ReagentParser(xl=self.xl, submission_type=self.submission_type, parser = ReagentParser(xl=self.xl, submission_type=self.submission_type,
extraction_kit=extraction_kit) extraction_kit=extraction_kit)
self.sub['reagents'] = parser.parse_reagents() self.sub['reagents'] = parser.parse_reagents()
# logger.debug(f"Reagents out of parser: {pformat(self.sub['reagents'])}")
def parse_samples(self): def parse_samples(self):
""" """
@@ -155,7 +151,6 @@ class InfoParser(object):
submission_type (str | SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.) submission_type (str | SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.)
sub_object (BasicSubmission | None, optional): Submission object holding methods. Defaults to None. sub_object (BasicSubmission | None, optional): Submission object holding methods. Defaults to None.
""" """
logger.info(f"\n\nHello from InfoParser!\n\n")
if isinstance(submission_type, str): if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type) submission_type = SubmissionType.query(name=submission_type)
if sub_object is None: if sub_object is None:
@@ -164,7 +159,6 @@ class InfoParser(object):
self.sub_object = sub_object self.sub_object = sub_object
self.map = self.fetch_submission_info_map() self.map = self.fetch_submission_info_map()
self.xl = xl self.xl = xl
# logger.debug(f"Info map for InfoParser: {pformat(self.map)}")
def fetch_submission_info_map(self) -> dict: def fetch_submission_info_map(self) -> dict:
""" """
@@ -174,7 +168,6 @@ class InfoParser(object):
dict: Location map of all info for this submission type dict: Location map of all info for this submission type
""" """
self.submission_type = dict(value=self.submission_type_obj.name, missing=True) self.submission_type = dict(value=self.submission_type_obj.name, missing=True)
# logger.debug(f"Looking up submission type: {self.submission_type['value']}")
info_map = self.sub_object.construct_info_map(submission_type=self.submission_type_obj, mode="read") info_map = self.sub_object.construct_info_map(submission_type=self.submission_type_obj, mode="read")
# NOTE: Get the parse_info method from the submission type specified # NOTE: Get the parse_info method from the submission type specified
return info_map return info_map
@@ -188,7 +181,6 @@ class InfoParser(object):
""" """
dicto = {} dicto = {}
# NOTE: This loop parses generic info # NOTE: This loop parses generic info
# logger.debug(f"Map: {self.map}")
for sheet in self.xl.sheetnames: for sheet in self.xl.sheetnames:
ws = self.xl[sheet] ws = self.xl[sheet]
relevant = [] relevant = []
@@ -197,11 +189,8 @@ class InfoParser(object):
if k == "custom": if k == "custom":
continue continue
if isinstance(v, str): if isinstance(v, str):
logger.debug(f"Found string for {k}, setting value to {v}")
dicto[k] = dict(value=v, missing=False) dicto[k] = dict(value=v, missing=False)
continue continue
# logger.debug(f"Looking for {k} in self.map")
# logger.debug(f"Locations: {v}")
for location in v: for location in v:
try: try:
check = location['sheet'] == sheet check = location['sheet'] == sheet
@@ -213,21 +202,18 @@ class InfoParser(object):
new = location new = location
new['name'] = k new['name'] = k
relevant.append(new) relevant.append(new)
# logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
# NOTE: make sure relevant is not an empty list. # NOTE: make sure relevant is not an empty list.
if not relevant: if not relevant:
continue continue
for item in relevant: for item in relevant:
# NOTE: Get cell contents at this location # NOTE: Get cell contents at this location
value = ws.cell(row=item['row'], column=item['column']).value value = ws.cell(row=item['row'], column=item['column']).value
# logger.debug(f"Value for {item['name']} = {value}")
match item['name']: match item['name']:
case "submission_type": case "submission_type":
value, missing = is_missing(value) value, missing = is_missing(value)
value = value.title() value = value.title()
case "submitted_date": case "submitted_date":
value, missing = is_missing(value) value, missing = is_missing(value)
logger.debug(f"Parsed submitted date: {value}")
# NOTE: is field a JSON? Includes: Extraction info, PCR info, comment, custom # NOTE: is field a JSON? Includes: Extraction info, PCR info, comment, custom
case thing if thing in self.sub_object.jsons(): case thing if thing in self.sub_object.jsons():
value, missing = is_missing(value) value, missing = is_missing(value)
@@ -240,7 +226,6 @@ class InfoParser(object):
logger.error(f"New value for {item['name']}") logger.error(f"New value for {item['name']}")
case _: case _:
value, missing = is_missing(value) value, missing = is_missing(value)
# logger.debug(f"Setting {item} on {sheet} to {value}")
if item['name'] not in dicto.keys(): if item['name'] not in dicto.keys():
try: try:
dicto[item['name']] = dict(value=value, missing=missing) dicto[item['name']] = dict(value=value, missing=missing)
@@ -264,7 +249,6 @@ class ReagentParser(object):
extraction_kit (str): Extraction kit used. extraction_kit (str): Extraction kit used.
sub_object (BasicSubmission | None, optional): Submission object holding methods. Defaults to None. sub_object (BasicSubmission | None, optional): Submission object holding methods. Defaults to None.
""" """
logger.info("\n\nHello from ReagentParser!\n\n")
if isinstance(submission_type, str): if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type) submission_type = SubmissionType.query(name=submission_type)
self.submission_type_obj = submission_type self.submission_type_obj = submission_type
@@ -272,9 +256,7 @@ class ReagentParser(object):
if isinstance(extraction_kit, dict): if isinstance(extraction_kit, dict):
extraction_kit = extraction_kit['value'] extraction_kit = extraction_kit['value']
self.kit_object = KitType.query(name=extraction_kit) self.kit_object = KitType.query(name=extraction_kit)
logger.debug(f"Got extraction kit object: {self.kit_object}")
self.map = self.fetch_kit_info_map(submission_type=submission_type) self.map = self.fetch_kit_info_map(submission_type=submission_type)
logger.debug(f"Reagent Parser map: {self.map}")
self.xl = xl self.xl = xl
@report_result @report_result
@@ -298,14 +280,11 @@ class ReagentParser(object):
del reagent_map['info'] del reagent_map['info']
except KeyError: except KeyError:
pass pass
# logger.debug(f"Reagent map: {pformat(reagent_map)}")
# NOTE: If reagent map is empty, maybe the wrong kit was given, check if there's only one kit for that submission type and use it if so. # NOTE: If reagent map is empty, maybe the wrong kit was given, check if there's only one kit for that submission type and use it if so.
if not reagent_map: if not reagent_map:
temp_kit_object = self.submission_type_obj.get_default_kit() temp_kit_object = self.submission_type_obj.get_default_kit()
# logger.debug(f"Temp kit: {temp_kit_object}")
if temp_kit_object: if temp_kit_object:
self.kit_object = temp_kit_object self.kit_object = temp_kit_object
# reagent_map = {k: v for k, v in self.kit_object.construct_xl_map_for_use(submission_type)}
logger.warning(f"Attempting to salvage with default kit {self.kit_object} and submission_type: {self.submission_type_obj}") logger.warning(f"Attempting to salvage with default kit {self.kit_object} and submission_type: {self.submission_type_obj}")
return self.fetch_kit_info_map(submission_type=self.submission_type_obj) return self.fetch_kit_info_map(submission_type=self.submission_type_obj)
else: else:
@@ -331,18 +310,15 @@ class ReagentParser(object):
for sheet in self.xl.sheetnames: for sheet in self.xl.sheetnames:
ws = self.xl[sheet] ws = self.xl[sheet]
relevant = {k.strip(): v for k, v in self.map.items() if sheet in self.map[k]['sheet']} relevant = {k.strip(): v for k, v in self.map.items() if sheet in self.map[k]['sheet']}
# logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
if relevant == {}: if relevant == {}:
continue continue
for item in relevant: for item in relevant:
# logger.debug(f"Attempting to scrape: {item}")
try: try:
reagent = relevant[item] reagent = relevant[item]
name = ws.cell(row=reagent['name']['row'], column=reagent['name']['column']).value name = ws.cell(row=reagent['name']['row'], column=reagent['name']['column']).value
lot = ws.cell(row=reagent['lot']['row'], column=reagent['lot']['column']).value lot = ws.cell(row=reagent['lot']['row'], column=reagent['lot']['column']).value
expiry = ws.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column']).value expiry = ws.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column']).value
if 'comment' in relevant[item].keys(): if 'comment' in relevant[item].keys():
# logger.debug(f"looking for {relevant[item]} comment.")
comment = ws.cell(row=reagent['comment']['row'], column=reagent['comment']['column']).value comment = ws.cell(row=reagent['comment']['row'], column=reagent['comment']['column']).value
else: else:
comment = "" comment = ""
@@ -353,10 +329,7 @@ class ReagentParser(object):
missing = False missing = False
else: else:
missing = True missing = True
# logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
lot = str(lot) lot = str(lot)
# logger.debug(
# f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
try: try:
check = name.lower() != "not applicable" check = name.lower() != "not applicable"
except AttributeError: except AttributeError:
@@ -381,12 +354,10 @@ class SampleParser(object):
sample_map (dict | None, optional): Locations in database where samples are found. Defaults to None. sample_map (dict | None, optional): Locations in database where samples are found. Defaults to None.
sub_object (BasicSubmission | None, optional): Submission object holding methods. Defaults to None. sub_object (BasicSubmission | None, optional): Submission object holding methods. Defaults to None.
""" """
logger.info("\n\nHello from SampleParser!\n\n")
self.samples = [] self.samples = []
self.xl = xl self.xl = xl
if isinstance(submission_type, str): if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type) submission_type = SubmissionType.query(name=submission_type)
# logger.debug(f"Sample parser is using submission type: {submission_type}")
self.submission_type = submission_type.name self.submission_type = submission_type.name
self.submission_type_obj = submission_type self.submission_type_obj = submission_type
if sub_object is None: if sub_object is None:
@@ -395,7 +366,6 @@ class SampleParser(object):
sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type) sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.sub_object = sub_object self.sub_object = sub_object
self.sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map) self.sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map)
# logger.debug(f"sample_info_map: {self.sample_info_map}")
self.plate_map_samples = self.parse_plate_map() self.plate_map_samples = self.parse_plate_map()
self.lookup_samples = self.parse_lookup_table() self.lookup_samples = self.parse_lookup_table()
@@ -409,11 +379,8 @@ class SampleParser(object):
Returns: Returns:
dict: Info locations. dict: Info locations.
""" """
# logger.debug(f"Looking up submission type: {submission_type}")
self.sample_type = self.sub_object.get_default_info("sample_type", submission_type=submission_type) self.sample_type = self.sub_object.get_default_info("sample_type", submission_type=submission_type)
self.samp_object = BasicSample.find_polymorphic_subclass(polymorphic_identity=self.sample_type) self.samp_object = BasicSample.find_polymorphic_subclass(polymorphic_identity=self.sample_type)
# logger.debug(f"Got sample class: {self.samp_object.__name__}")
# logger.debug(f"info_map: {pformat(se)}")
if sample_map is None: if sample_map is None:
sample_info_map = self.sub_object.construct_sample_map(submission_type=self.submission_type_obj) sample_info_map = self.sub_object.construct_sample_map(submission_type=self.submission_type_obj)
else: else:
@@ -432,9 +399,7 @@ class SampleParser(object):
ws = self.xl[smap['sheet']] ws = self.xl[smap['sheet']]
plate_map_samples = [] plate_map_samples = []
for ii, row in enumerate(range(smap['start_row'], smap['end_row'] + 1), start=1): for ii, row in enumerate(range(smap['start_row'], smap['end_row'] + 1), start=1):
# logger.debug(f"Parsing row: {row}")
for jj, column in enumerate(range(smap['start_column'], smap['end_column'] + 1), start=1): for jj, column in enumerate(range(smap['start_column'], smap['end_column'] + 1), start=1):
# logger.debug(f"Parsing column: {column}")
id = str(ws.cell(row=row, column=column).value) id = str(ws.cell(row=row, column=column).value)
if check_not_nan(id): if check_not_nan(id):
if id not in invalids: if id not in invalids:
@@ -442,10 +407,8 @@ class SampleParser(object):
sample_dict['sample_type'] = self.sample_type sample_dict['sample_type'] = self.sample_type
plate_map_samples.append(sample_dict) plate_map_samples.append(sample_dict)
else: else:
# logger.error(f"Sample cell ({row}, {column}) has invalid value: {id}.")
pass pass
else: else:
# logger.error(f"Sample cell ({row}, {column}) has no info: {id}.")
pass pass
return plate_map_samples return plate_map_samples
@@ -507,7 +470,6 @@ class SampleParser(object):
except (KeyError, IndexError): except (KeyError, IndexError):
check = False check = False
if check: if check:
# logger.debug(f"Direct match found for {psample['id']}")
new = lookup_samples[ii] | psample new = lookup_samples[ii] | psample
lookup_samples[ii] = {} lookup_samples[ii] = {}
else: else:
@@ -516,7 +478,6 @@ class SampleParser(object):
if merge_on_id in sample.keys()] if merge_on_id in sample.keys()]
jj, new = next(((jj, lsample | psample) for jj, lsample in searchables jj, new = next(((jj, lsample | psample) for jj, lsample in searchables
if lsample[merge_on_id] == psample['id']), (-1, psample)) if lsample[merge_on_id] == psample['id']), (-1, psample))
# logger.debug(f"Assigning from index {jj} - {new}")
if jj >= 0: if jj >= 0:
lookup_samples[jj] = {} lookup_samples[jj] = {}
if not check_key_or_attr(key='submitter_id', interest=new, check_none=True): if not check_key_or_attr(key='submitter_id', interest=new, check_none=True):
@@ -540,7 +501,6 @@ class EquipmentParser(object):
xl (Workbook): Openpyxl workbook from submitted excel file. xl (Workbook): Openpyxl workbook from submitted excel file.
submission_type (str | SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.) submission_type (str | SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.)
""" """
logger.info("\n\nHello from EquipmentParser!\n\n")
if isinstance(submission_type, str): if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type) submission_type = SubmissionType.query(name=submission_type)
self.submission_type = submission_type self.submission_type = submission_type
@@ -567,7 +527,6 @@ class EquipmentParser(object):
str: asset number str: asset number
""" """
regex = Equipment.get_regex() regex = Equipment.get_regex()
# logger.debug(f"Using equipment regex: {regex} on {input}")
try: try:
return regex.search(input).group().strip("-") return regex.search(input).group().strip("-")
except AttributeError as e: except AttributeError as e:
@@ -581,8 +540,6 @@ class EquipmentParser(object):
Returns: Returns:
List[dict]: list of equipment List[dict]: list of equipment
""" """
# logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}")
# logger.debug(f"Sheets: {sheets}")
for sheet in self.xl.sheetnames: for sheet in self.xl.sheetnames:
ws = self.xl[sheet] ws = self.xl[sheet]
try: try:
@@ -590,17 +547,14 @@ class EquipmentParser(object):
except (TypeError, KeyError) as e: except (TypeError, KeyError) as e:
logger.error(f"Error creating relevant equipment list: {e}") logger.error(f"Error creating relevant equipment list: {e}")
continue continue
# logger.debug(f"Relevant equipment: {pformat(relevant)}")
previous_asset = "" previous_asset = ""
for k, v in relevant.items(): for k, v in relevant.items():
# logger.debug(f"Checking: {v}")
asset = ws.cell(v['name']['row'], v['name']['column']).value asset = ws.cell(v['name']['row'], v['name']['column']).value
if not check_not_nan(asset): if not check_not_nan(asset):
asset = previous_asset asset = previous_asset
else: else:
previous_asset = asset previous_asset = asset
asset = self.get_asset_number(input=asset) asset = self.get_asset_number(input=asset)
# logger.debug(f"asset: {asset}")
eq = Equipment.query(asset_number=asset) eq = Equipment.query(asset_number=asset)
if eq is None: if eq is None:
eq = Equipment.query(name=asset) eq = Equipment.query(name=asset)
@@ -623,7 +577,6 @@ class TipParser(object):
xl (Workbook): Openpyxl workbook from submitted excel file. xl (Workbook): Openpyxl workbook from submitted excel file.
submission_type (str | SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.) submission_type (str | SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.)
""" """
logger.info("\n\nHello from TipParser!\n\n")
if isinstance(submission_type, str): if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type) submission_type = SubmissionType.query(name=submission_type)
self.submission_type = submission_type self.submission_type = submission_type
@@ -646,8 +599,6 @@ class TipParser(object):
Returns: Returns:
List[dict]: list of equipment List[dict]: list of equipment
""" """
# logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}")
# logger.debug(f"Sheets: {sheets}")
for sheet in self.xl.sheetnames: for sheet in self.xl.sheetnames:
ws = self.xl[sheet] ws = self.xl[sheet]
try: try:
@@ -655,7 +606,6 @@ class TipParser(object):
except (TypeError, KeyError) as e: except (TypeError, KeyError) as e:
logger.error(f"Error creating relevant equipment list: {e}") logger.error(f"Error creating relevant equipment list: {e}")
continue continue
# logger.debug(f"Relevant equipment: {pformat(relevant)}")
previous_asset = "" previous_asset = ""
for k, v in relevant.items(): for k, v in relevant.items():
asset = ws.cell(v['name']['row'], v['name']['column']).value asset = ws.cell(v['name']['row'], v['name']['column']).value
@@ -667,7 +617,6 @@ class TipParser(object):
asset = previous_asset asset = previous_asset
else: else:
previous_asset = asset previous_asset = asset
# logger.debug(f"asset: {asset}")
eq = Tips.query(lot=lot, name=asset, limit=1) eq = Tips.query(lot=lot, name=asset, limit=1)
try: try:
yield dict(name=eq.name, role=k, lot=lot) yield dict(name=eq.name, role=k, lot=lot)
@@ -684,7 +633,6 @@ class PCRParser(object):
filepath (Path | None, optional): file to parse. Defaults to None. filepath (Path | None, optional): file to parse. Defaults to None.
submission (BasicSubmission | None, optional): Submission parsed data to be added to. submission (BasicSubmission | None, optional): Submission parsed data to be added to.
""" """
# logger.debug(f'Parsing {filepath.__str__()}')
if filepath is None: if filepath is None:
logger.error('No filepath given.') logger.error('No filepath given.')
self.xl = None self.xl = None
@@ -727,5 +675,4 @@ class PCRParser(object):
value = row[1].value or "" value = row[1].value or ""
pcr[key] = value pcr[key] = value
pcr['imported_by'] = getuser() pcr['imported_by'] = getuser()
# logger.debug(f"PCR: {pformat(pcr)}")
return pcr return pcr

12
src/submissions/backend/excel/reports.py
View File

@@ -32,7 +32,6 @@ class ReportArchetype(object):
filename = filename.absolute() filename = filename.absolute()
self.writer = ExcelWriter(filename.with_suffix(".xlsx"), engine='openpyxl') self.writer = ExcelWriter(filename.with_suffix(".xlsx"), engine='openpyxl')
self.df.to_excel(self.writer, sheet_name=self.sheet_name) self.df.to_excel(self.writer, sheet_name=self.sheet_name)
# logger.debug(f"Writing report to: {filename}")
self.writer.close() self.writer.close()
@@ -43,7 +42,6 @@ class ReportMaker(object):
self.end_date = end_date self.end_date = end_date
# NOTE: Set page size to zero to override limiting query size. # NOTE: Set page size to zero to override limiting query size.
self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date, page_size=0) self.subs = BasicSubmission.query(start_date=start_date, end_date=end_date, page_size=0)
# logger.debug(f"Number of subs returned: {len(self.subs)}")
if organizations is not None: if organizations is not None:
self.subs = [sub for sub in self.subs if sub.submitting_lab.name in organizations] self.subs = [sub for sub in self.subs if sub.submitting_lab.name in organizations]
self.detailed_df, self.summary_df = self.make_report_xlsx() self.detailed_df, self.summary_df = self.make_report_xlsx()
@@ -65,10 +63,8 @@ class ReportMaker(object):
df2 = df.groupby(["submitting_lab", "extraction_kit"]).agg( df2 = df.groupby(["submitting_lab", "extraction_kit"]).agg(
{'extraction_kit': 'count', 'cost': 'sum', 'sample_count': 'sum'}) {'extraction_kit': 'count', 'cost': 'sum', 'sample_count': 'sum'})
df2 = df2.rename(columns={"extraction_kit": 'run_count'}) df2 = df2.rename(columns={"extraction_kit": 'run_count'})
# logger.debug(f"Output daftaframe for xlsx: {df2.columns}")
df = df.drop('id', axis=1) df = df.drop('id', axis=1)
df = df.sort_values(['submitting_lab', "submitted_date"]) df = df.sort_values(['submitting_lab', "submitted_date"])
# logger.debug(f"Details dataframe:\n{df2}")
return df, df2 return df, df2
def make_report_html(self, df: DataFrame) -> str: def make_report_html(self, df: DataFrame) -> str:
@@ -86,12 +82,8 @@ class ReportMaker(object):
""" """
old_lab = "" old_lab = ""
output = [] output = []
# logger.debug(f"Report DataFrame: {df}")
for row in df.iterrows(): for row in df.iterrows():
# logger.debug(f"Row {ii}: {row}")
lab = row[0][0] lab = row[0][0]
# logger.debug(f"Old lab: {old_lab}, Current lab: {lab}")
# logger.debug(f"Name: {row[0][1]}")
data = [item for item in row[1]] data = [item for item in row[1]]
kit = dict(name=row[0][1], cost=data[1], run_count=int(data[0]), sample_count=int(data[2])) kit = dict(name=row[0][1], cost=data[1], run_count=int(data[0]), sample_count=int(data[2]))
# NOTE: if this is the same lab as before add together # NOTE: if this is the same lab as before add together
@@ -106,7 +98,6 @@ class ReportMaker(object):
total_runs=kit['run_count']) total_runs=kit['run_count'])
output.append(adder) output.append(adder)
old_lab = lab old_lab = lab
# logger.debug(output)
dicto = {'start_date': self.start_date, 'end_date': self.end_date, 'labs': output} dicto = {'start_date': self.start_date, 'end_date': self.end_date, 'labs': output}
temp = env.get_template('summary_report.html') temp = env.get_template('summary_report.html')
html = temp.render(input=dicto) html = temp.render(input=dicto)
@@ -127,14 +118,12 @@ class ReportMaker(object):
self.summary_df.to_excel(self.writer, sheet_name="Report") self.summary_df.to_excel(self.writer, sheet_name="Report")
self.detailed_df.to_excel(self.writer, sheet_name="Details", index=False) self.detailed_df.to_excel(self.writer, sheet_name="Details", index=False)
self.fix_up_xl() self.fix_up_xl()
# logger.debug(f"Writing report to: {filename}")
self.writer.close() self.writer.close()
def fix_up_xl(self): def fix_up_xl(self):
""" """
Handles formatting of xl file, mediocrely. Handles formatting of xl file, mediocrely.
""" """
# logger.debug(f"Updating worksheet")
worksheet: Worksheet = self.writer.sheets['Report'] worksheet: Worksheet = self.writer.sheets['Report']
for idx, col in enumerate(self.summary_df, start=1): # NOTE: loop through all columns for idx, col in enumerate(self.summary_df, start=1): # NOTE: loop through all columns
series = self.summary_df[col] series = self.summary_df[col]
@@ -149,7 +138,6 @@ class ReportMaker(object):
except ValueError as e: except ValueError as e:
logger.error(f"Couldn't resize column {col} due to {e}") logger.error(f"Couldn't resize column {col} due to {e}")
blank_row = get_first_blank_df_row(self.summary_df) + 1 blank_row = get_first_blank_df_row(self.summary_df) + 1
# logger.debug(f"Blank row index = {blank_row}")
for col in range(3, 6): for col in range(3, 6):
col_letter = row_map[col] col_letter = row_map[col]
worksheet.cell(row=blank_row, column=col, value=f"=SUM({col_letter}2:{col_letter}{str(blank_row - 1)})") worksheet.cell(row=blank_row, column=col, value=f"=SUM({col_letter}2:{col_letter}{str(blank_row - 1)})")

32
src/submissions/backend/excel/writer.py
View File

@@ -3,7 +3,6 @@ contains writer objects for pushing values to submission sheet templates.
""" """
import logging import logging
from copy import copy from copy import copy
from datetime import date
from operator import itemgetter from operator import itemgetter
from pprint import pformat from pprint import pformat
from typing import List, Generator, Tuple from typing import List, Generator, Tuple
@@ -111,7 +110,6 @@ class InfoWriter(object):
info_dict (dict): Dictionary of information to write. info_dict (dict): Dictionary of information to write.
sub_object (BasicSubmission | None, optional): Submission object containing methods. Defaults to None. sub_object (BasicSubmission | None, optional): Submission object containing methods. Defaults to None.
""" """
logger.debug(f"Info_dict coming into InfoWriter: {pformat(info_dict)}")
if isinstance(submission_type, str): if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type) submission_type = SubmissionType.query(name=submission_type)
if sub_object is None: if sub_object is None:
@@ -121,7 +119,6 @@ class InfoWriter(object):
self.xl = xl self.xl = xl
self.info_map = submission_type.construct_info_map(mode='write') self.info_map = submission_type.construct_info_map(mode='write')
self.info = self.reconcile_map(info_dict, self.info_map) self.info = self.reconcile_map(info_dict, self.info_map)
# logger.debug(pformat(self.info))
def reconcile_map(self, info_dict: dict, info_map: dict) -> Generator[(Tuple[str, dict]), None, None]: def reconcile_map(self, info_dict: dict, info_map: dict) -> Generator[(Tuple[str, dict]), None, None]:
""" """
@@ -170,7 +167,6 @@ class InfoWriter(object):
logger.error(f"No locations for {k}, skipping") logger.error(f"No locations for {k}, skipping")
continue continue
for loc in locations: for loc in locations:
logger.debug(f"Writing {k} to {loc['sheet']}, row: {loc['row']}, column: {loc['column']}")
sheet = self.xl[loc['sheet']] sheet = self.xl[loc['sheet']]
try: try:
sheet.cell(row=loc['row'], column=loc['column'], value=v['value']) sheet.cell(row=loc['row'], column=loc['column'], value=v['value'])
@@ -247,8 +243,6 @@ class ReagentWriter(object):
for v in reagent.values(): for v in reagent.values():
if not isinstance(v, dict): if not isinstance(v, dict):
continue continue
# logger.debug(
# f"Writing {reagent['type']} {k} to {reagent['sheet']}, row: {v['row']}, column: {v['column']}")
sheet.cell(row=v['row'], column=v['column'], value=v['value']) sheet.cell(row=v['row'], column=v['column'], value=v['value'])
return self.xl return self.xl
@@ -288,7 +282,6 @@ class SampleWriter(object):
multiples = ['row', 'column', 'assoc_id', 'submission_rank'] multiples = ['row', 'column', 'assoc_id', 'submission_rank']
for sample in sample_list: for sample in sample_list:
sample = self.submission_type.get_submission_class().custom_sample_writer(sample) sample = self.submission_type.get_submission_class().custom_sample_writer(sample)
logger.debug(f"Writing sample: {sample}")
for assoc in zip(sample['row'], sample['column'], sample['submission_rank']): for assoc in zip(sample['row'], sample['column'], sample['submission_rank']):
new = dict(row=assoc[0], column=assoc[1], submission_rank=assoc[2]) new = dict(row=assoc[0], column=assoc[1], submission_rank=assoc[2])
for k, v in sample.items(): for k, v in sample.items():
@@ -369,9 +362,8 @@ class EquipmentWriter(object):
mp_info = equipment_map[equipment['role']] mp_info = equipment_map[equipment['role']]
except KeyError: except KeyError:
logger.error(f"No {equipment['role']} in {pformat(equipment_map)}") logger.error(f"No {equipment['role']} in {pformat(equipment_map)}")
# logger.debug(f"{equipment['role']} map: {mp_info}") mp_info = None
placeholder = copy(equipment) placeholder = copy(equipment)
# if mp_info == {}:
if not mp_info: if not mp_info:
for jj, (k, v) in enumerate(equipment.items(), start=1): for jj, (k, v) in enumerate(equipment.items(), start=1):
dicto = dict(value=v, row=ii, column=jj) dicto = dict(value=v, row=ii, column=jj)
@@ -381,7 +373,6 @@ class EquipmentWriter(object):
try: try:
dicto = dict(value=v, row=mp_info[k]['row'], column=mp_info[k]['column']) dicto = dict(value=v, row=mp_info[k]['row'], column=mp_info[k]['column'])
except KeyError as e: except KeyError as e:
# logger.error(f"Keyerror: {e}")
continue continue
placeholder[k] = dicto placeholder[k] = dicto
if "asset_number" not in mp_info.keys(): if "asset_number" not in mp_info.keys():
@@ -400,17 +391,12 @@ class EquipmentWriter(object):
Workbook: Workbook with equipment written Workbook: Workbook with equipment written
""" """
for equipment in self.equipment: for equipment in self.equipment:
try: if not equipment['sheet'] in self.xl.sheetnames:
sheet = self.xl[equipment['sheet']]
except KeyError:
self.xl.create_sheet("Equipment") self.xl.create_sheet("Equipment")
finally: sheet = self.xl[equipment['sheet']]
sheet = self.xl[equipment['sheet']]
for k, v in equipment.items(): for k, v in equipment.items():
if not isinstance(v, dict): if not isinstance(v, dict):
continue continue
# logger.debug(
# f"Writing {k}: {v['value']} to {equipment['sheet']}, row: {v['row']}, column: {v['column']}")
if isinstance(v['value'], list): if isinstance(v['value'], list):
v['value'] = v['value'][0] v['value'] = v['value'][0]
try: try:
@@ -455,7 +441,6 @@ class TipWriter(object):
return return
for ii, tips in enumerate(tips_list, start=1): for ii, tips in enumerate(tips_list, start=1):
mp_info = tips_map[tips.role] mp_info = tips_map[tips.role]
# logger.debug(f"{tips['role']} map: {mp_info}")
placeholder = {} placeholder = {}
if mp_info == {}: if mp_info == {}:
for jj, (k, v) in enumerate(tips.__dict__.items(), start=1): for jj, (k, v) in enumerate(tips.__dict__.items(), start=1):
@@ -466,14 +451,12 @@ class TipWriter(object):
try: try:
dicto = dict(value=v, row=mp_info[k]['row'], column=mp_info[k]['column']) dicto = dict(value=v, row=mp_info[k]['row'], column=mp_info[k]['column'])
except KeyError as e: except KeyError as e:
# logger.error(f"Keyerror: {e}")
continue continue
placeholder[k] = dicto placeholder[k] = dicto
try: try:
placeholder['sheet'] = mp_info['sheet'] placeholder['sheet'] = mp_info['sheet']
except KeyError: except KeyError:
placeholder['sheet'] = "Tips" placeholder['sheet'] = "Tips"
# logger.debug(f"Final output of {tips['role']} : {placeholder}")
yield placeholder yield placeholder
def write_tips(self) -> Workbook: def write_tips(self) -> Workbook:
@@ -484,17 +467,12 @@ class TipWriter(object):
Workbook: Workbook with tips written Workbook: Workbook with tips written
""" """
for tips in self.tips: for tips in self.tips:
try: if not tips['sheet'] in self.xl.sheetnames:
sheet = self.xl[tips['sheet']]
except KeyError:
self.xl.create_sheet("Tips") self.xl.create_sheet("Tips")
finally: sheet = self.xl[tips['sheet']]
sheet = self.xl[tips['sheet']]
for k, v in tips.items(): for k, v in tips.items():
if not isinstance(v, dict): if not isinstance(v, dict):
continue continue
# logger.debug(
# f"Writing {k}: {v['value']} to {equipment['sheet']}, row: {v['row']}, column: {v['column']}")
if isinstance(v['value'], list): if isinstance(v['value'], list):
v['value'] = v['value'][0] v['value'] = v['value'][0]
try: try:

4
src/submissions/backend/scripts/__init__.py
View File

@@ -1,7 +1,7 @@
from .irida import import_irida from .irida import import_irida
def hello(ctx): def hello(ctx):
print("\n\nHello!\n\n") print("\n\nHello! Welcome to Robotics Submission Tracker.\n\n")
def goodbye(ctx): def goodbye(ctx):
print("\n\nGoodbye\n\n") print("\n\nGoodbye. Thank you for using Robotics Submission Tracker.\n\n")

6
src/submissions/backend/scripts/irida.py
View File

@@ -19,11 +19,10 @@ def import_irida(ctx:Settings):
existing_controls = [item.name for item in IridaControl.query()] existing_controls = [item.name for item in IridaControl.query()]
prm_list = ", ".join([f"'{thing}'" for thing in existing_controls]) prm_list = ", ".join([f"'{thing}'" for thing in existing_controls])
ctrl_db_path = ctx.directory_path.joinpath("submissions_parser_output", "submissions.db") ctrl_db_path = ctx.directory_path.joinpath("submissions_parser_output", "submissions.db")
# print(f"Incoming settings: {pformat(ctx)}")
try: try:
conn = sqlite3.connect(ctrl_db_path) conn = sqlite3.connect(ctrl_db_path)
except AttributeError as e: except AttributeError as e:
print(f"Error, could not import from irida due to {e}") logger.error(f"Error, could not import from irida due to {e}")
return return
sql = f"SELECT name, submitted_date, submission_id, contains, matches, kraken, subtype, refseq_version, " \ sql = f"SELECT name, submitted_date, submission_id, contains, matches, kraken, subtype, refseq_version, " \
f"kraken2_version, kraken2_db_version, sample_id FROM _iridacontrol INNER JOIN _control on _control.id " \ f"kraken2_version, kraken2_db_version, sample_id FROM _iridacontrol INNER JOIN _control on _control.id " \
@@ -32,8 +31,6 @@ def import_irida(ctx:Settings):
records = [dict(name=row[0], submitted_date=row[1], submission_id=row[2], contains=row[3], matches=row[4], kraken=row[5], records = [dict(name=row[0], submitted_date=row[1], submission_id=row[2], contains=row[3], matches=row[4], kraken=row[5],
subtype=row[6], refseq_version=row[7], kraken2_version=row[8], kraken2_db_version=row[9], subtype=row[6], refseq_version=row[7], kraken2_version=row[8], kraken2_db_version=row[9],
sample_id=row[10]) for row in cursor] sample_id=row[10]) for row in cursor]
# incoming_controls = set(item['name'] for item in records)
# relevant = list(incoming_controls - existing_controls)
for record in records: for record in records:
instance = IridaControl.query(name=record['name']) instance = IridaControl.query(name=record['name'])
if instance: if instance:
@@ -52,5 +49,4 @@ def import_irida(ctx:Settings):
if sample: if sample:
instance.sample = sample instance.sample = sample
instance.submission = sample.submissions[0] instance.submission = sample.submissions[0]
# pprint(instance.__dict__)
instance.save() instance.save()

14
src/submissions/backend/validators/__init__.py
View File

@@ -24,11 +24,9 @@ class RSLNamer(object):
filename = Path(filename) if Path(filename).exists() else filename filename = Path(filename) if Path(filename).exists() else filename
self.submission_type = sub_type self.submission_type = sub_type
if not self.submission_type: if not self.submission_type:
# logger.debug("Creating submission type because none exists")
self.submission_type = self.retrieve_submission_type(filename=filename) self.submission_type = self.retrieve_submission_type(filename=filename)
logger.info(f"got submission type: {self.submission_type}") logger.info(f"got submission type: {self.submission_type}")
if self.submission_type: if self.submission_type:
# logger.debug("Retrieving BasicSubmission subclass")
self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type) self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(submission_type=sub_type)) self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(submission_type=sub_type))
if not data: if not data:
@@ -52,7 +50,6 @@ class RSLNamer(object):
str: parsed submission type str: parsed submission type
""" """
def st_from_path(filename:Path) -> str: def st_from_path(filename:Path) -> str:
# logger.info(f"Using path method for {filename}.")
if filename.exists(): if filename.exists():
wb = load_workbook(filename) wb = load_workbook(filename)
try: try:
@@ -73,12 +70,9 @@ class RSLNamer(object):
if filename.startswith("tmp"): if filename.startswith("tmp"):
return "Bacterial Culture" return "Bacterial Culture"
regex = BasicSubmission.construct_regex() regex = BasicSubmission.construct_regex()
# logger.info(f"Using string method for {filename}.")
# logger.debug(f"Using regex: {regex}")
m = regex.search(filename) m = regex.search(filename)
try: try:
submission_type = m.lastgroup submission_type = m.lastgroup
# logger.debug(f"Got submission type: {submission_type}")
except AttributeError as e: except AttributeError as e:
submission_type = None submission_type = None
logger.critical(f"No submission type found or submission type found!: {e}") logger.critical(f"No submission type found or submission type found!: {e}")
@@ -98,7 +92,6 @@ class RSLNamer(object):
if check: if check:
if "pytest" in sys.modules: if "pytest" in sys.modules:
raise ValueError("Submission Type came back as None.") raise ValueError("Submission Type came back as None.")
# logger.debug("Final option, ask the user for submission type")
from frontend.widgets import ObjectSelector from frontend.widgets import ObjectSelector
dlg = ObjectSelector(title="Couldn't parse submission type.", dlg = ObjectSelector(title="Couldn't parse submission type.",
message="Please select submission type from list below.", obj_type=SubmissionType) message="Please select submission type from list below.", obj_type=SubmissionType)
@@ -116,21 +109,17 @@ class RSLNamer(object):
regex (str): string to construct pattern regex (str): string to construct pattern
filename (str): string to be parsed filename (str): string to be parsed
""" """
logger.info(f"Input string to be parsed: {filename}")
if regex is None: if regex is None:
regex = BasicSubmission.construct_regex() regex = BasicSubmission.construct_regex()
else: else:
# logger.debug(f"Incoming regex: {regex}")
try: try:
regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE) regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
except re.error as e: except re.error as e:
regex = BasicSubmission.construct_regex() regex = BasicSubmission.construct_regex()
logger.info(f"Using regex: {regex}")
match filename: match filename:
case Path(): case Path():
m = regex.search(filename.stem) m = regex.search(filename.stem)
case str(): case str():
# logger.debug(f"Using string method.")
m = regex.search(filename) m = regex.search(filename)
case _: case _:
m = None m = None
@@ -141,7 +130,6 @@ class RSLNamer(object):
parsed_name = None parsed_name = None
else: else:
parsed_name = None parsed_name = None
# logger.debug(f"Got parsed submission name: {parsed_name}")
return parsed_name return parsed_name
@classmethod @classmethod
@@ -187,8 +175,6 @@ class RSLNamer(object):
Returns: Returns:
str: output file name. str: output file name.
""" """
# logger.debug(f"Kwargs: {kwargs}")
# logger.debug(f"Template: {template}")
environment = jinja_template_loading() environment = jinja_template_loading()
template = environment.from_string(template) template = environment.from_string(template)
return template.render(**kwargs) return template.render(**kwargs)

65
src/submissions/backend/validators/pydant.py
View File

@@ -1,6 +1,6 @@
''' """
Contains pydantic models and accompanying validators Contains pydantic models and accompanying validators
''' """
from __future__ import annotations from __future__ import annotations
import uuid, re, logging, csv, sys import uuid, re, logging, csv, sys
from pydantic import BaseModel, field_validator, Field, model_validator from pydantic import BaseModel, field_validator, Field, model_validator
@@ -123,18 +123,14 @@ class PydReagent(BaseModel):
Tuple[Reagent, Report]: Reagent instance and result of function Tuple[Reagent, Report]: Reagent instance and result of function
""" """
report = Report() report = Report()
# logger.debug("Adding extra fields.")
if self.model_extra is not None: if self.model_extra is not None:
self.__dict__.update(self.model_extra) self.__dict__.update(self.model_extra)
# logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}")
reagent = Reagent.query(lot=self.lot, name=self.name) reagent = Reagent.query(lot=self.lot, name=self.name)
# logger.debug(f"Result: {reagent}")
if reagent is None: if reagent is None:
reagent = Reagent() reagent = Reagent()
for key, value in self.__dict__.items(): for key, value in self.__dict__.items():
if isinstance(value, dict): if isinstance(value, dict):
value = value['value'] value = value['value']
# logger.debug(f"Reagent info item for {key}: {value}")
# NOTE: set fields based on keys in dictionary # NOTE: set fields based on keys in dictionary
match key: match key:
case "lot": case "lot":
@@ -149,7 +145,6 @@ class PydReagent(BaseModel):
if isinstance(value, str): if isinstance(value, str):
value = date(year=1970, month=1, day=1) value = date(year=1970, month=1, day=1)
value = datetime.combine(value, datetime.min.time()) value = datetime.combine(value, datetime.min.time())
logger.debug(f"Expiry date coming into sql: {value} with type {type(value)}")
reagent.expiry = value.replace(tzinfo=timezone) reagent.expiry = value.replace(tzinfo=timezone)
case _: case _:
try: try:
@@ -179,14 +174,12 @@ class PydSample(BaseModel, extra='allow'):
@model_validator(mode='after') @model_validator(mode='after')
@classmethod @classmethod
def validate_model(cls, data): def validate_model(cls, data):
# logger.debug(f"Data for pydsample: {data}")
model = BasicSample.find_polymorphic_subclass(polymorphic_identity=data.sample_type) model = BasicSample.find_polymorphic_subclass(polymorphic_identity=data.sample_type)
for k, v in data.model_extra.items(): for k, v in data.model_extra.items():
if k in model.timestamps(): if k in model.timestamps():
if isinstance(v, str): if isinstance(v, str):
v = datetime.strptime(v, "%Y-%m-%d") v = datetime.strptime(v, "%Y-%m-%d")
data.__setattr__(k, v) data.__setattr__(k, v)
# logger.debug(f"Data coming out of validation: {pformat(data)}")
return data return data
@field_validator("row", "column", "assoc_id", "submission_rank") @field_validator("row", "column", "assoc_id", "submission_rank")
@@ -238,7 +231,6 @@ class PydSample(BaseModel, extra='allow'):
""" """
report = None report = None
self.__dict__.update(self.model_extra) self.__dict__.update(self.model_extra)
# logger.debug(f"Here is the incoming sample dict: \n{self.__dict__}")
instance = BasicSample.query_or_create(sample_type=self.sample_type, submitter_id=self.submitter_id) instance = BasicSample.query_or_create(sample_type=self.sample_type, submitter_id=self.submitter_id)
for key, value in self.__dict__.items(): for key, value in self.__dict__.items():
match key: match key:
@@ -246,7 +238,6 @@ class PydSample(BaseModel, extra='allow'):
case "row" | "column": case "row" | "column":
continue continue
case _: case _:
# logger.debug(f"Setting sample field {key} to {value}")
instance.__setattr__(key, value) instance.__setattr__(key, value)
out_associations = [] out_associations = []
if submission is not None: if submission is not None:
@@ -254,15 +245,12 @@ class PydSample(BaseModel, extra='allow'):
submission = BasicSubmission.query(rsl_plate_num=submission) submission = BasicSubmission.query(rsl_plate_num=submission)
assoc_type = submission.submission_type_name assoc_type = submission.submission_type_name
for row, column, aid, submission_rank in zip(self.row, self.column, self.assoc_id, self.submission_rank): for row, column, aid, submission_rank in zip(self.row, self.column, self.assoc_id, self.submission_rank):
# logger.debug(f"Looking up association with identity: ({submission.submission_type_name} Association)")
# logger.debug(f"Looking up association with identity: ({assoc_type} Association)")
association = SubmissionSampleAssociation.query_or_create(association_type=f"{assoc_type} Association", association = SubmissionSampleAssociation.query_or_create(association_type=f"{assoc_type} Association",
submission=submission, submission=submission,
sample=instance, sample=instance,
row=row, column=column, id=aid, row=row, column=column, id=aid,
submission_rank=submission_rank, submission_rank=submission_rank,
**self.model_extra) **self.model_extra)
# logger.debug(f"Using submission_sample_association: {association}")
try: try:
out_associations.append(association) out_associations.append(association)
except IntegrityError as e: except IntegrityError as e:
@@ -332,7 +320,6 @@ class PydEquipment(BaseModel, extra='ignore'):
@field_validator('processes', mode='before') @field_validator('processes', mode='before')
@classmethod @classmethod
def make_empty_list(cls, value): def make_empty_list(cls, value):
# logger.debug(f"Pydantic value: {value}")
if isinstance(value, GeneratorType): if isinstance(value, GeneratorType):
value = [item.name for item in value] value = [item.name for item in value]
value = convert_nans_to_nones(value) value = convert_nans_to_nones(value)
@@ -355,7 +342,6 @@ class PydEquipment(BaseModel, extra='ignore'):
Tuple[Equipment, SubmissionEquipmentAssociation]: SQL objects Tuple[Equipment, SubmissionEquipmentAssociation]: SQL objects
""" """
if isinstance(submission, str): if isinstance(submission, str):
# logger.debug(f"Got string, querying {submission}")
submission = BasicSubmission.query(rsl_plate_num=submission) submission = BasicSubmission.query(rsl_plate_num=submission)
equipment = Equipment.query(asset_number=self.asset_number) equipment = Equipment.query(asset_number=self.asset_number)
if equipment is None: if equipment is None:
@@ -403,7 +389,6 @@ class PydEquipment(BaseModel, extra='ignore'):
class PydSubmission(BaseModel, extra='allow'): class PydSubmission(BaseModel, extra='allow'):
filepath: Path filepath: Path
submission_type: dict | None submission_type: dict | None
# For defaults
submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True) submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
submitted_date: dict | None submitted_date: dict | None
rsl_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True) rsl_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
@@ -427,7 +412,6 @@ class PydSubmission(BaseModel, extra='allow'):
if isinstance(value, dict): if isinstance(value, dict):
value = value['value'] value = value['value']
if isinstance(value, Generator): if isinstance(value, Generator):
# logger.debug("We have a generator")
return [PydTips(**tips) for tips in value] return [PydTips(**tips) for tips in value]
if not value: if not value:
return [] return []
@@ -436,9 +420,7 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator('equipment', mode='before') @field_validator('equipment', mode='before')
@classmethod @classmethod
def convert_equipment_dict(cls, value): def convert_equipment_dict(cls, value):
# logger.debug(f"Equipment: {value}")
if isinstance(value, Generator): if isinstance(value, Generator):
logger.debug("We have a generator")
return [PydEquipment(**equipment) for equipment in value] return [PydEquipment(**equipment) for equipment in value]
if isinstance(value, dict): if isinstance(value, dict):
return value['value'] return value['value']
@@ -454,7 +436,6 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("submitter_plate_num") @field_validator("submitter_plate_num")
@classmethod @classmethod
def enforce_with_uuid(cls, value): def enforce_with_uuid(cls, value):
# logger.debug(f"submitter_plate_num coming into pydantic: {value}")
if value['value'] in [None, "None"]: if value['value'] in [None, "None"]:
return dict(value=uuid.uuid4().hex.upper(), missing=True) return dict(value=uuid.uuid4().hex.upper(), missing=True)
else: else:
@@ -464,7 +445,6 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("submitted_date", mode="before") @field_validator("submitted_date", mode="before")
@classmethod @classmethod
def rescue_date(cls, value): def rescue_date(cls, value):
# logger.debug(f"\n\nDate coming into pydantic: {value}\n\n")
try: try:
check = value['value'] is None check = value['value'] is None
except TypeError: except TypeError:
@@ -509,7 +489,6 @@ class PydSubmission(BaseModel, extra='allow'):
@classmethod @classmethod
def lookup_submitting_lab(cls, value): def lookup_submitting_lab(cls, value):
if isinstance(value['value'], str): if isinstance(value['value'], str):
# logger.debug(f"Looking up organization {value['value']}")
try: try:
value['value'] = Organization.query(name=value['value']).name value['value'] = Organization.query(name=value['value']).name
except AttributeError: except AttributeError:
@@ -540,13 +519,11 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("rsl_plate_num") @field_validator("rsl_plate_num")
@classmethod @classmethod
def rsl_from_file(cls, value, values): def rsl_from_file(cls, value, values):
# logger.debug(f"RSL-plate initial value: {value['value']} and other values: {values.data}")
sub_type = values.data['submission_type']['value'] sub_type = values.data['submission_type']['value']
if check_not_nan(value['value']): if check_not_nan(value['value']):
value['value'] = value['value'].strip() value['value'] = value['value'].strip()
return value return value
else: else:
# logger.debug("Constructing plate sub_type.")
if "pytest" in sys.modules and sub_type.replace(" ", "") == "BasicSubmission": if "pytest" in sys.modules and sub_type.replace(" ", "") == "BasicSubmission":
output = "RSL-BS-Test001" output = "RSL-BS-Test001"
else: else:
@@ -623,7 +600,6 @@ class PydSubmission(BaseModel, extra='allow'):
@classmethod @classmethod
def expand_reagents(cls, value): def expand_reagents(cls, value):
if isinstance(value, Generator): if isinstance(value, Generator):
# logger.debug("We have a generator")
return [PydReagent(**reagent) for reagent in value] return [PydReagent(**reagent) for reagent in value]
return value return value
@@ -631,7 +607,6 @@ class PydSubmission(BaseModel, extra='allow'):
@classmethod @classmethod
def expand_samples(cls, value): def expand_samples(cls, value):
if isinstance(value, Generator): if isinstance(value, Generator):
# logger.debug("We have a generator")[
return [PydSample(**sample) for sample in value] return [PydSample(**sample) for sample in value]
return value return value
@@ -656,7 +631,6 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("cost_centre") @field_validator("cost_centre")
@classmethod @classmethod
def get_cost_centre(cls, value, values): def get_cost_centre(cls, value, values):
# logger.debug(f"Value coming in for cost_centre: {value}")
match value['value']: match value['value']:
case None: case None:
from backend.db.models import Organization from backend.db.models import Organization
@@ -671,7 +645,6 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("contact") @field_validator("contact")
@classmethod @classmethod
def get_contact_from_org(cls, value, values): def get_contact_from_org(cls, value, values):
# logger.debug(f"Checking on value: {value}")
match value: match value:
case dict(): case dict():
if isinstance(value['value'], tuple): if isinstance(value['value'], tuple):
@@ -684,7 +657,6 @@ class PydSubmission(BaseModel, extra='allow'):
if check is None: if check is None:
org = Organization.query(name=values.data['submitting_lab']['value']) org = Organization.query(name=values.data['submitting_lab']['value'])
contact = org.contacts[0].name contact = org.contacts[0].name
# logger.debug(f"Pulled: {contact}")
if isinstance(contact, tuple): if isinstance(contact, tuple):
contact = contact[0] contact = contact[0]
return dict(value=contact, missing=True) return dict(value=contact, missing=True)
@@ -692,7 +664,6 @@ class PydSubmission(BaseModel, extra='allow'):
return value return value
def __init__(self, run_custom: bool = False, **data): def __init__(self, run_custom: bool = False, **data):
logger.debug(f"{__name__} input data: {data}")
super().__init__(**data) super().__init__(**data)
# NOTE: this could also be done with default_factory # NOTE: this could also be done with default_factory
self.submission_object = BasicSubmission.find_polymorphic_subclass( self.submission_object = BasicSubmission.find_polymorphic_subclass(
@@ -755,13 +726,11 @@ class PydSubmission(BaseModel, extra='allow'):
except TypeError: except TypeError:
pass pass
else: else:
# logger.debug("Extracting 'value' from attributes")
output = {k: self.filter_field(k) for k in fields} output = {k: self.filter_field(k) for k in fields}
return output return output
def filter_field(self, key: str): def filter_field(self, key: str):
item = getattr(self, key) item = getattr(self, key)
# logger.debug(f"Attempting deconstruction of {key}: {item} with type {type(item)}")
match item: match item:
case dict(): case dict():
try: try:
@@ -793,13 +762,10 @@ class PydSubmission(BaseModel, extra='allow'):
""" """
report = Report() report = Report()
dicto = self.improved_dict() dicto = self.improved_dict()
# logger.warning(f"\n\nQuery or create: {self.submission_type['value']}, {self.rsl_plate_num['value']}")
instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'], instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
rsl_plate_num=self.rsl_plate_num['value']) rsl_plate_num=self.rsl_plate_num['value'])
logger.debug(f"Result of query or create: {instance}")
report.add_result(result) report.add_result(result)
self.handle_duplicate_samples() self.handle_duplicate_samples()
# logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
for key, value in dicto.items(): for key, value in dicto.items():
if isinstance(value, dict): if isinstance(value, dict):
try: try:
@@ -811,18 +777,13 @@ class PydSubmission(BaseModel, extra='allow'):
continue continue
if value is None: if value is None:
continue continue
# logger.debug(f"Setting {key} to {value}")
match key: match key:
case "reagents": case "reagents":
for reagent in self.reagents: for reagent in self.reagents:
logger.debug(f"Checking reagent {reagent.lot}")
reagent, _ = reagent.toSQL(submission=instance) reagent, _ = reagent.toSQL(submission=instance)
# logger.debug(f"Association: {assoc}")
case "samples": case "samples":
for sample in self.samples: for sample in self.samples:
sample, associations, _ = sample.toSQL(submission=instance) sample, associations, _ = sample.toSQL(submission=instance)
# logger.debug(f"Sample SQL object to be added to submission: {sample.__dict__}")
# logger.debug(associations)
for assoc in associations: for assoc in associations:
if assoc is not None: if assoc is not None:
if assoc not in instance.submission_sample_associations: if assoc not in instance.submission_sample_associations:
@@ -830,19 +791,16 @@ class PydSubmission(BaseModel, extra='allow'):
else: else:
logger.warning(f"Sample association {assoc} is already present in {instance}") logger.warning(f"Sample association {assoc} is already present in {instance}")
case "equipment": case "equipment":
# logger.debug(f"Equipment: {pformat(self.equipment)}")
for equip in self.equipment: for equip in self.equipment:
if equip is None: if equip is None:
continue continue
equip, association = equip.toSQL(submission=instance) equip, association = equip.toSQL(submission=instance)
if association is not None: if association is not None:
instance.submission_equipment_associations.append(association) instance.submission_equipment_associations.append(association)
logger.debug(f"Equipment associations: {instance.submission_equipment_associations}")
case "tips": case "tips":
for tips in self.tips: for tips in self.tips:
if tips is None: if tips is None:
continue continue
# logger.debug(f"Converting tips: {tips} to sql.")
try: try:
association = tips.to_sql(submission=instance) association = tips.to_sql(submission=instance)
except AttributeError: except AttributeError:
@@ -864,14 +822,11 @@ class PydSubmission(BaseModel, extra='allow'):
value = value value = value
instance.set_attribute(key=key, value=value) instance.set_attribute(key=key, value=value)
case item if item in instance.jsons(): case item if item in instance.jsons():
# logger.debug(f"{item} is a json.")
try: try:
ii = value.items() ii = value.items()
except AttributeError: except AttributeError:
ii = {} ii = {}
logger.debug(f"ii is {ii}, value is {value}")
for k, v in ii: for k, v in ii:
logger.debug(f"k is {k}, v is {v}")
if isinstance(v, datetime): if isinstance(v, datetime):
value[k] = v.strftime("%Y-%m-%d %H:%M:%S") value[k] = v.strftime("%Y-%m-%d %H:%M:%S")
else: else:
@@ -893,21 +848,17 @@ class PydSubmission(BaseModel, extra='allow'):
else: else:
logger.warning(f"{key} already == {value} so no updating.") logger.warning(f"{key} already == {value} so no updating.")
try: try:
# logger.debug(f"Calculating costs for procedure...")
instance.calculate_base_cost() instance.calculate_base_cost()
except (TypeError, AttributeError) as e: except (TypeError, AttributeError) as e:
logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using 0.") logger.error(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using 0.")
try: try:
instance.run_cost = instance.extraction_kit.cost_per_run instance.run_cost = instance.extraction_kit.cost_per_run
except AttributeError: except AttributeError:
instance.run_cost = 0 instance.run_cost = 0
# logger.debug(f"Calculated base run cost of: {instance.run_cost}")
# NOTE: Apply any discounts that are applicable for client and kit. # NOTE: Apply any discounts that are applicable for client and kit.
try: try:
# logger.debug("Checking and applying discounts...")
discounts = [item.amount for item in discounts = [item.amount for item in
Discount.query(kit_type=instance.extraction_kit, organization=instance.submitting_lab)] Discount.query(kit_type=instance.extraction_kit, organization=instance.submitting_lab)]
# logger.debug(f"We got discounts: {discounts}")
if len(discounts) > 0: if len(discounts) > 0:
instance.run_cost = instance.run_cost - sum(discounts) instance.run_cost = instance.run_cost - sum(discounts)
except Exception as e: except Exception as e:
@@ -925,7 +876,6 @@ class PydSubmission(BaseModel, extra='allow'):
SubmissionFormWidget: Submission form widget SubmissionFormWidget: Submission form widget
""" """
from frontend.widgets.submission_widget import SubmissionFormWidget from frontend.widgets.submission_widget import SubmissionFormWidget
# logger.debug(f"Disable: {disable}")
return SubmissionFormWidget(parent=parent, submission=self, disable=disable) return SubmissionFormWidget(parent=parent, submission=self, disable=disable)
def to_writer(self) -> "SheetWriter": def to_writer(self) -> "SheetWriter":
@@ -946,10 +896,8 @@ class PydSubmission(BaseModel, extra='allow'):
str: Output filename str: Output filename
""" """
template = self.submission_object.filename_template() template = self.submission_object.filename_template()
# logger.debug(f"Using template string: {template}")
render = self.namer.construct_export_name(template=template, **self.improved_dict(dictionaries=False)).replace( render = self.namer.construct_export_name(template=template, **self.improved_dict(dictionaries=False)).replace(
"/", "") "/", "")
# logger.debug(f"Template rendered as: {render}")
return render return render
# @report_result # @report_result
@@ -964,26 +912,20 @@ class PydSubmission(BaseModel, extra='allow'):
Report: Result object containing a message and any missing components. Report: Result object containing a message and any missing components.
""" """
report = Report() report = Report()
# logger.debug(f"Extraction kit: {extraction_kit}. Is it a string? {isinstance(extraction_kit, str)}")
if isinstance(extraction_kit, str): if isinstance(extraction_kit, str):
extraction_kit = dict(value=extraction_kit) extraction_kit = dict(value=extraction_kit)
if extraction_kit is not None and extraction_kit != self.extraction_kit['value']: if extraction_kit is not None and extraction_kit != self.extraction_kit['value']:
self.extraction_kit['value'] = extraction_kit['value'] self.extraction_kit['value'] = extraction_kit['value']
# logger.debug(f"Looking up {self.extraction_kit['value']}")
ext_kit = KitType.query(name=self.extraction_kit['value']) ext_kit = KitType.query(name=self.extraction_kit['value'])
ext_kit_rtypes = [item.to_pydantic() for item in ext_kit_rtypes = [item.to_pydantic() for item in
ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])] ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])]
# logger.debug(f"Kit reagents: {ext_kit_rtypes}")
# logger.debug(f"Submission reagents: {self.reagents}")
# NOTE: Exclude any reagenttype found in this pyd not expected in kit. # NOTE: Exclude any reagenttype found in this pyd not expected in kit.
expected_check = [item.role for item in ext_kit_rtypes] expected_check = [item.role for item in ext_kit_rtypes]
output_reagents = [rt for rt in self.reagents if rt.role in expected_check] output_reagents = [rt for rt in self.reagents if rt.role in expected_check]
logger.debug(f"Already have these reagent types: {output_reagents}")
missing_check = [item.role for item in output_reagents] missing_check = [item.role for item in output_reagents]
missing_reagents = [rt for rt in ext_kit_rtypes if rt.role not in missing_check] missing_reagents = [rt for rt in ext_kit_rtypes if rt.role not in missing_check]
missing_reagents += [rt for rt in output_reagents if rt.missing] missing_reagents += [rt for rt in output_reagents if rt.missing]
output_reagents += [rt for rt in missing_reagents if rt not in output_reagents] output_reagents += [rt for rt in missing_reagents if rt not in output_reagents]
# logger.debug(f"Missing reagents types: {missing_reagents}")
# NOTE: if lists are equal return no problem # NOTE: if lists are equal return no problem
if len(missing_reagents) == 0: if len(missing_reagents) == 0:
result = None result = None
@@ -1072,7 +1014,6 @@ class PydReagentRole(BaseModel):
instance: ReagentRole = ReagentRole.query(name=self.name) instance: ReagentRole = ReagentRole.query(name=self.name)
if instance is None: if instance is None:
instance = ReagentRole(name=self.name, eol_ext=self.eol_ext) instance = ReagentRole(name=self.name, eol_ext=self.eol_ext)
# logger.debug(f"This is the reagent type instance: {instance.__dict__}")
try: try:
assoc = KitTypeReagentRoleAssociation.query(reagent_role=instance, kit_type=kit) assoc = KitTypeReagentRoleAssociation.query(reagent_role=instance, kit_type=kit)
except StatementError: except StatementError:

20
src/submissions/frontend/visualizations/__init__.py
View File

@@ -41,7 +41,6 @@ class CustomFigure(Figure):
""" """
if modes: if modes:
ytitle = modes[0] ytitle = modes[0]
# logger.debug("Creating visibles list for each mode.")
self.update_layout( self.update_layout(
xaxis_title="Submitted Date (* - Date parsed from fastq file creation date)", xaxis_title="Submitted Date (* - Date parsed from fastq file creation date)",
yaxis_title=ytitle, yaxis_title=ytitle,
@@ -79,7 +78,6 @@ class CustomFigure(Figure):
rng = [1] rng = [1]
if months > 2: if months > 2:
rng += [iii for iii in range(3, months, 3)] rng += [iii for iii in range(3, months, 3)]
# logger.debug(f"Making buttons for months: {rng}")
buttons = [dict(count=iii, label=f"{iii}m", step="month", stepmode="backward") for iii in rng] buttons = [dict(count=iii, label=f"{iii}m", step="month", stepmode="backward") for iii in rng]
if months > date.today().month: if months > date.today().month:
buttons += [dict(count=1, label="YTD", step="year", stepmode="todate")] buttons += [dict(count=1, label="YTD", step="year", stepmode="todate")]
@@ -117,24 +115,6 @@ class CustomFigure(Figure):
{"yaxis.title.text": mode}, {"yaxis.title.text": mode},
]) ])
# def save_figure(self, group_name: str = "plotly_output", parent: QWidget | None = None):
# """
# Writes plotly figure to html file.
#
# Args:
# figs ():
# settings (dict): settings passed down from click
# fig (Figure): input figure object
# group_name (str): controltype
# """
#
# output = select_save_file(obj=parent, default_name=group_name, extension="png")
# self.write_image(output.absolute().__str__(), engine="kaleido")
#
# def save_data(self, group_name: str = "plotly_export", parent:QWidget|None=None):
# output = select_save_file(obj=parent, default_name=group_name, extension="xlsx")
# self.df.to_excel(output.absolute().__str__(), engine="openpyxl", index=False)
def to_html(self) -> str: def to_html(self) -> str:
""" """
Creates final html code from plotly Creates final html code from plotly

3
src/submissions/frontend/visualizations/irida_charts.py
View File

@@ -3,13 +3,12 @@ Functions for constructing irida controls graphs using plotly.
""" """
from datetime import date from datetime import date
from pprint import pformat from pprint import pformat
from typing import Generator
import plotly.express as px import plotly.express as px
import pandas as pd import pandas as pd
from PyQt6.QtWidgets import QWidget from PyQt6.QtWidgets import QWidget
from . import CustomFigure from . import CustomFigure
import logging import logging
from tools import get_unique_values_in_df_column, divide_chunks from tools import get_unique_values_in_df_column
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")

2
src/submissions/frontend/visualizations/pcr_charts.py
View File

@@ -21,11 +21,9 @@ class PCRFigure(CustomFigure):
months = int(settings['months']) months = int(settings['months'])
except KeyError: except KeyError:
months = 6 months = 6
# logger.debug(f"DF: {self.df}")
self.construct_chart(df=df) self.construct_chart(df=df)
def construct_chart(self, df: pd.DataFrame): def construct_chart(self, df: pd.DataFrame):
# logger.debug(f"PCR df:\n {df}")
try: try:
scatter = px.scatter(data_frame=df, x='submitted_date', y="ct", scatter = px.scatter(data_frame=df, x='submitted_date', y="ct",
hover_data=["name", "target", "ct", "reagent_lot"], hover_data=["name", "target", "ct", "reagent_lot"],

3
src/submissions/frontend/visualizations/turnaround_chart.py
View File

@@ -23,7 +23,6 @@ class TurnaroundChart(CustomFigure):
months = int(settings['months']) months = int(settings['months'])
except KeyError: except KeyError:
months = 6 months = 6
# logger.debug(f"DF: {self.df}")
self.construct_chart() self.construct_chart()
if threshold: if threshold:
self.add_hline(y=threshold) self.add_hline(y=threshold)
@@ -32,11 +31,9 @@ class TurnaroundChart(CustomFigure):
def construct_chart(self, df: pd.DataFrame | None = None): def construct_chart(self, df: pd.DataFrame | None = None):
if df: if df:
self.df = df self.df = df
# logger.debug(f"PCR df:\n {df}")
self.df = self.df[self.df.days.notnull()] self.df = self.df[self.df.days.notnull()]
self.df = self.df.sort_values(['submitted_date', 'name'], ascending=[True, True]).reset_index(drop=True) self.df = self.df.sort_values(['submitted_date', 'name'], ascending=[True, True]).reset_index(drop=True)
self.df = self.df.reset_index().rename(columns={"index": "idx"}) self.df = self.df.reset_index().rename(columns={"index": "idx"})
# logger.debug(f"DF: {self.df}")
try: try:
scatter = px.scatter(data_frame=self.df, x='idx', y="days", scatter = px.scatter(data_frame=self.df, x='idx', y="days",
hover_data=["name", "submitted_date", "completed_date", "days"], hover_data=["name", "submitted_date", "completed_date", "days"],

20
src/submissions/frontend/widgets/app.py
View File

@@ -27,13 +27,11 @@ from .turnaround import TurnaroundTime
from .omni_search import SearchBox from .omni_search import SearchBox
logger = logging.getLogger(f'submissions.{__name__}') logger = logging.getLogger(f'submissions.{__name__}')
# logger.info("Hello, I am a logger")
class App(QMainWindow): class App(QMainWindow):
def __init__(self, ctx: Settings = None): def __init__(self, ctx: Settings = None):
# logger.debug(f"Initializing main window...")
super().__init__() super().__init__()
qInstallMessageHandler(lambda x, y, z: None) qInstallMessageHandler(lambda x, y, z: None)
self.ctx = ctx self.ctx = ctx
@@ -68,7 +66,6 @@ class App(QMainWindow):
""" """
adds items to menu bar adds items to menu bar
""" """
# logger.debug(f"Creating menu bar...")
menuBar = self.menuBar() menuBar = self.menuBar()
fileMenu = menuBar.addMenu("&File") fileMenu = menuBar.addMenu("&File")
editMenu = menuBar.addMenu("&Edit") editMenu = menuBar.addMenu("&Edit")
@@ -82,7 +79,6 @@ class App(QMainWindow):
fileMenu.addAction(self.importAction) fileMenu.addAction(self.importAction)
fileMenu.addAction(self.yamlExportAction) fileMenu.addAction(self.yamlExportAction)
fileMenu.addAction(self.yamlImportAction) fileMenu.addAction(self.yamlImportAction)
# methodsMenu.addAction(self.searchLog)
methodsMenu.addAction(self.searchSample) methodsMenu.addAction(self.searchSample)
maintenanceMenu.addAction(self.joinExtractionAction) maintenanceMenu.addAction(self.joinExtractionAction)
maintenanceMenu.addAction(self.joinPCRAction) maintenanceMenu.addAction(self.joinPCRAction)
@@ -92,27 +88,20 @@ class App(QMainWindow):
""" """
adds items to toolbar adds items to toolbar
""" """
# logger.debug(f"Creating toolbar...")
toolbar = QToolBar("My main toolbar") toolbar = QToolBar("My main toolbar")
self.addToolBar(toolbar) self.addToolBar(toolbar)
toolbar.addAction(self.addReagentAction) toolbar.addAction(self.addReagentAction)
# toolbar.addAction(self.addKitAction)
# toolbar.addAction(self.addOrgAction)
def _createActions(self): def _createActions(self):
""" """
creates actions creates actions
""" """
# logger.debug(f"Creating actions...")
self.importAction = QAction("&Import Submission", self) self.importAction = QAction("&Import Submission", self)
self.addReagentAction = QAction("Add Reagent", self) self.addReagentAction = QAction("Add Reagent", self)
# self.addKitAction = QAction("Import Kit", self)
# self.addOrgAction = QAction("Import Org", self)
self.joinExtractionAction = QAction("Link Extraction Logs") self.joinExtractionAction = QAction("Link Extraction Logs")
self.joinPCRAction = QAction("Link PCR Logs") self.joinPCRAction = QAction("Link PCR Logs")
self.helpAction = QAction("&About", self) self.helpAction = QAction("&About", self)
self.docsAction = QAction("&Docs", self) self.docsAction = QAction("&Docs", self)
# self.searchLog = QAction("Search Log", self)
self.searchSample = QAction("Search Sample", self) self.searchSample = QAction("Search Sample", self)
self.githubAction = QAction("Github", self) self.githubAction = QAction("Github", self)
self.yamlExportAction = QAction("Export Type Example", self) self.yamlExportAction = QAction("Export Type Example", self)
@@ -123,14 +112,12 @@ class App(QMainWindow):
""" """
connect menu and tool bar item to functions connect menu and tool bar item to functions
""" """
# logger.debug(f"Connecting actions...")
self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission) self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission)
self.addReagentAction.triggered.connect(self.table_widget.formwidget.add_reagent) self.addReagentAction.triggered.connect(self.table_widget.formwidget.add_reagent)
self.joinExtractionAction.triggered.connect(self.table_widget.sub_wid.link_extractions) self.joinExtractionAction.triggered.connect(self.table_widget.sub_wid.link_extractions)
self.joinPCRAction.triggered.connect(self.table_widget.sub_wid.link_pcr) self.joinPCRAction.triggered.connect(self.table_widget.sub_wid.link_pcr)
self.helpAction.triggered.connect(self.showAbout) self.helpAction.triggered.connect(self.showAbout)
self.docsAction.triggered.connect(self.openDocs) self.docsAction.triggered.connect(self.openDocs)
# self.searchLog.triggered.connect(self.runSearch)
self.searchSample.triggered.connect(self.runSampleSearch) self.searchSample.triggered.connect(self.runSampleSearch)
self.githubAction.triggered.connect(self.openGithub) self.githubAction.triggered.connect(self.openGithub)
self.yamlExportAction.triggered.connect(self.export_ST_yaml) self.yamlExportAction.triggered.connect(self.export_ST_yaml)
@@ -145,7 +132,6 @@ class App(QMainWindow):
j_env = jinja_template_loading() j_env = jinja_template_loading()
template = j_env.get_template("project.html") template = j_env.get_template("project.html")
html = template.render(info=self.ctx.package.__dict__) html = template.render(info=self.ctx.package.__dict__)
# logger.debug(html)
about = HTMLPop(html=html, title="About") about = HTMLPop(html=html, title="About")
about.exec() about.exec()
@@ -157,7 +143,6 @@ class App(QMainWindow):
url = Path(sys._MEIPASS).joinpath("files", "docs", "index.html") url = Path(sys._MEIPASS).joinpath("files", "docs", "index.html")
else: else:
url = Path("docs\\build\\index.html").absolute() url = Path("docs\\build\\index.html").absolute()
# logger.debug(f"Attempting to open {url}")
webbrowser.get('windows-default').open(f"file://{url.__str__()}") webbrowser.get('windows-default').open(f"file://{url.__str__()}")
def openGithub(self): def openGithub(self):
@@ -177,10 +162,6 @@ class App(QMainWindow):
instr = HTMLPop(html=html, title="Instructions") instr = HTMLPop(html=html, title="Instructions")
instr.exec() instr.exec()
# def runSearch(self):
# dlg = LogParser(self)
# dlg.exec()
def runSampleSearch(self): def runSampleSearch(self):
""" """
Create a search for samples. Create a search for samples.
@@ -253,7 +234,6 @@ class App(QMainWindow):
class AddSubForm(QWidget): class AddSubForm(QWidget):
def __init__(self, parent: QWidget): def __init__(self, parent: QWidget):
# logger.debug(f"Initializating subform...")
super(QWidget, self).__init__(parent) super(QWidget, self).__init__(parent)
self.layout = QVBoxLayout(self) self.layout = QVBoxLayout(self)
# NOTE: Initialize tab screen # NOTE: Initialize tab screen

31
src/submissions/frontend/widgets/controls_chart.py
View File

@@ -6,7 +6,6 @@ from PyQt6.QtWidgets import (
QWidget, QComboBox, QPushButton QWidget, QComboBox, QPushButton
) )
from PyQt6.QtCore import QSignalBlocker from PyQt6.QtCore import QSignalBlocker
from backend import ChartReportMaker from backend import ChartReportMaker
from backend.db import ControlType, IridaControl from backend.db import ControlType, IridaControl
import logging import logging
@@ -21,12 +20,9 @@ class ControlsViewer(InfoPane):
def __init__(self, parent: QWidget, archetype: str) -> None: def __init__(self, parent: QWidget, archetype: str) -> None:
super().__init__(parent) super().__init__(parent)
logger.debug(f"Incoming Archetype: {archetype}")
self.archetype = ControlType.query(name=archetype) self.archetype = ControlType.query(name=archetype)
if not self.archetype: if not self.archetype:
return return
logger.debug(f"Archetype set as: {self.archetype}")
# logger.debug(f"\n\n{self.app}\n\n")
# NOTE: set tab2 layout # NOTE: set tab2 layout
self.control_sub_typer = QComboBox() self.control_sub_typer = QComboBox()
# NOTE: fetch types of controls # NOTE: fetch types of controls
@@ -54,12 +50,6 @@ class ControlsViewer(InfoPane):
self.save_button.pressed.connect(self.save_png) self.save_button.pressed.connect(self.save_png)
self.export_button.pressed.connect(self.save_excel) self.export_button.pressed.connect(self.save_excel)
# def save_chart_function(self):
# self.fig.save_figure(parent=self)
#
# def save_data_function(self):
# self.fig.save_data(parent=self)
@report_result @report_result
def update_data(self, *args, **kwargs): def update_data(self, *args, **kwargs):
""" """
@@ -71,20 +61,6 @@ class ControlsViewer(InfoPane):
self.mode_sub_typer.disconnect() self.mode_sub_typer.disconnect()
except TypeError: except TypeError:
pass pass
# NOTE: correct start date being more recent than end date and rerun
# if self.datepicker.start_date.date() > self.datepicker.end_date.date():
# threemonthsago = self.datepicker.end_date.date().addDays(-60)
# msg = f"Start date after end date is not allowed! Setting to {threemonthsago.toString()}."
# logger.warning(msg)
# # NOTE: block signal that will rerun controls getter and set start date Without triggering this function again
# with QSignalBlocker(self.datepicker.start_date) as blocker:
# self.datepicker.start_date.setDate(threemonthsago)
# self.update_data()
# report.add_result(Result(owner=self.__str__(), msg=msg, status="Warning"))
# return report
# # NOTE: convert to python useable date objects
# self.start_date = self.datepicker.start_date.date().toPyDate()
# self.end_date = self.datepicker.end_date.date().toPyDate()
self.con_sub_type = self.control_sub_typer.currentText() self.con_sub_type = self.control_sub_typer.currentText()
self.mode = self.mode_typer.currentText() self.mode = self.mode_typer.currentText()
self.mode_sub_typer.clear() self.mode_sub_typer.clear()
@@ -104,7 +80,6 @@ class ControlsViewer(InfoPane):
self.mode_sub_typer.clear() self.mode_sub_typer.clear()
self.mode_sub_typer.setEnabled(False) self.mode_sub_typer.setEnabled(False)
self.chart_maker_function() self.chart_maker_function()
# return report
@report_result @report_result
def chart_maker_function(self, *args, **kwargs): def chart_maker_function(self, *args, **kwargs):
@@ -119,14 +94,11 @@ class ControlsViewer(InfoPane):
Tuple[QMainWindow, dict]: Collection of new main app window and result dict Tuple[QMainWindow, dict]: Collection of new main app window and result dict
""" """
report = Report() report = Report()
# logger.debug(f"Control getter context: \n\tControl type: {self.con_sub_type}\n\tMode: {self.mode}\n\tStart \
# Date: {self.start_date}\n\tEnd Date: {self.end_date}")
# NOTE: set the mode_sub_type for kraken # NOTE: set the mode_sub_type for kraken
if self.mode_sub_typer.currentText() == "": if self.mode_sub_typer.currentText() == "":
self.mode_sub_type = None self.mode_sub_type = None
else: else:
self.mode_sub_type = self.mode_sub_typer.currentText() self.mode_sub_type = self.mode_sub_typer.currentText()
logger.debug(f"Subtype: {self.mode_sub_type}")
months = self.diff_month(self.start_date, self.end_date) months = self.diff_month(self.start_date, self.end_date)
# NOTE: query all controls using the type/start and end dates from the gui # NOTE: query all controls using the type/start and end dates from the gui
chart_settings = dict(sub_type=self.con_sub_type, start_date=self.start_date, end_date=self.end_date, chart_settings = dict(sub_type=self.con_sub_type, start_date=self.start_date, end_date=self.end_date,
@@ -136,14 +108,11 @@ class ControlsViewer(InfoPane):
self.report_obj = ChartReportMaker(df=self.fig.df, sheet_name=self.archetype.name) self.report_obj = ChartReportMaker(df=self.fig.df, sheet_name=self.archetype.name)
if issubclass(self.fig.__class__, CustomFigure): if issubclass(self.fig.__class__, CustomFigure):
self.save_button.setEnabled(True) self.save_button.setEnabled(True)
# logger.debug(f"Updating figure...")
# NOTE: construct html for webview # NOTE: construct html for webview
try: try:
html = self.fig.to_html() html = self.fig.to_html()
except AttributeError: except AttributeError:
html = "" html = ""
# logger.debug(f"The length of html code is: {len(html)}")
self.webview.setHtml(html) self.webview.setHtml(html)
self.webview.update() self.webview.update()
# logger.debug("Figure updated... I hope.")
return report return report

8
src/submissions/frontend/widgets/equipment_usage.py
View File

@@ -21,9 +21,7 @@ class EquipmentUsage(QDialog):
self.setWindowTitle(f"Equipment Checklist - {submission.rsl_plate_num}") self.setWindowTitle(f"Equipment Checklist - {submission.rsl_plate_num}")
self.used_equipment = self.submission.get_used_equipment() self.used_equipment = self.submission.get_used_equipment()
self.kit = self.submission.extraction_kit self.kit = self.submission.extraction_kit
# logger.debug(f"Existing equipment: {self.used_equipment}")
self.opt_equipment = submission.submission_type.get_equipment() self.opt_equipment = submission.submission_type.get_equipment()
# logger.debug(f"EquipmentRoles: {self.opt_equipment}")
self.layout = QVBoxLayout() self.layout = QVBoxLayout()
self.setLayout(self.layout) self.setLayout(self.layout)
self.populate_form() self.populate_form()
@@ -38,7 +36,6 @@ class EquipmentUsage(QDialog):
self.buttonBox.rejected.connect(self.reject) self.buttonBox.rejected.connect(self.reject)
label = self.LabelRow(parent=self) label = self.LabelRow(parent=self)
self.layout.addWidget(label) self.layout.addWidget(label)
# logger.debug("Creating widgets for equipment")
for eq in self.opt_equipment: for eq in self.opt_equipment:
widg = eq.to_form(parent=self, used=self.used_equipment) widg = eq.to_form(parent=self, used=self.used_equipment)
self.layout.addWidget(widg) self.layout.addWidget(widg)
@@ -124,9 +121,7 @@ class RoleComboBox(QWidget):
Changes processes when equipment is changed Changes processes when equipment is changed
""" """
equip = self.box.currentText() equip = self.box.currentText()
# logger.debug(f"Updating equipment: {equip}")
equip2 = next((item for item in self.role.equipment if item.name == equip), self.role.equipment[0]) equip2 = next((item for item in self.role.equipment if item.name == equip), self.role.equipment[0])
# logger.debug(f"Using: {equip2}")
with QSignalBlocker(self.process) as blocker: with QSignalBlocker(self.process) as blocker:
self.process.clear() self.process.clear()
self.process.addItems([item for item in equip2.processes if item in self.role.processes]) self.process.addItems([item for item in equip2.processes if item in self.role.processes])
@@ -136,7 +131,6 @@ class RoleComboBox(QWidget):
Changes what tips are available when process is changed Changes what tips are available when process is changed
""" """
process = self.process.currentText().strip() process = self.process.currentText().strip()
# logger.debug(f"Checking process: {process} for equipment {self.role.name}")
process = Process.query(name=process) process = Process.query(name=process)
if process.tip_roles: if process.tip_roles:
for iii, tip_role in enumerate(process.tip_roles): for iii, tip_role in enumerate(process.tip_roles):
@@ -144,7 +138,6 @@ class RoleComboBox(QWidget):
tip_choices = [item.name for item in tip_role.instances] tip_choices = [item.name for item in tip_role.instances]
widget.setEditable(False) widget.setEditable(False)
widget.addItems(tip_choices) widget.addItems(tip_choices)
# logger.debug(f"Tiprole: {tip_role.__dict__}")
widget.setObjectName(f"tips_{tip_role.name}") widget.setObjectName(f"tips_{tip_role.name}")
widget.setMinimumWidth(200) widget.setMinimumWidth(200)
widget.setMaximumWidth(200) widget.setMaximumWidth(200)
@@ -169,7 +162,6 @@ class RoleComboBox(QWidget):
eq = Equipment.query(name=self.box.currentText()) eq = Equipment.query(name=self.box.currentText())
tips = [PydTips(name=item.currentText(), role=item.objectName().lstrip("tips").lstrip("_")) for item in tips = [PydTips(name=item.currentText(), role=item.objectName().lstrip("tips").lstrip("_")) for item in
self.findChildren(QComboBox) if item.objectName().startswith("tips")] self.findChildren(QComboBox) if item.objectName().startswith("tips")]
# logger.debug(tips)
try: try:
return PydEquipment( return PydEquipment(
name=eq.name, name=eq.name,

1
src/submissions/frontend/widgets/gel_checker.py
View File

@@ -148,5 +148,4 @@ class ControlsForm(QWidget):
dicto['values'].append(dict(name=label[1], value=le.currentText())) dicto['values'].append(dict(name=label[1], value=le.currentText()))
if label[0] not in [item['name'] for item in output]: if label[0] not in [item['name'] for item in output]:
output.append(dicto) output.append(dicto)
# logger.debug(pformat(output))
return output, self.comment_field.toPlainText() return output, self.comment_field.toPlainText()

1
src/submissions/frontend/widgets/info_tab.py
View File

@@ -18,7 +18,6 @@ class InfoPane(QWidget):
def __init__(self, parent: QWidget) -> None: def __init__(self, parent: QWidget) -> None:
super().__init__(parent) super().__init__(parent)
self.app = self.parent().parent() self.app = self.parent().parent()
# logger.debug(f"\n\n{self.app}\n\n")
self.report = Report() self.report = Report()
self.datepicker = StartEndDatePicker(default_start=-180) self.datepicker = StartEndDatePicker(default_start=-180)
self.webview = QWebEngineView() self.webview = QWebEngineView()

12
src/submissions/frontend/widgets/misc.py
View File

@@ -1,6 +1,6 @@
''' """
Contains miscellaneous widgets for frontend functions Contains miscellaneous widgets for frontend functions
''' """
import math import math
from datetime import date from datetime import date
from PyQt6.QtGui import QPageLayout, QPageSize, QStandardItem, QIcon from PyQt6.QtGui import QPageLayout, QPageSize, QStandardItem, QIcon
@@ -8,7 +8,7 @@ from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtWidgets import ( from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QLabel, QVBoxLayout,
QLineEdit, QComboBox, QDialog, QLineEdit, QComboBox, QDialog,
QDialogButtonBox, QDateEdit, QPushButton, QFormLayout, QWidget, QHBoxLayout, QSizePolicy QDialogButtonBox, QDateEdit, QPushButton, QWidget, QHBoxLayout, QSizePolicy
) )
from PyQt6.QtCore import Qt, QDate, QSize, QMarginsF from PyQt6.QtCore import Qt, QDate, QSize, QMarginsF
from tools import jinja_template_loading from tools import jinja_template_loading
@@ -66,7 +66,6 @@ class AddReagentForm(QDialog):
self.type_input.addItems([item.name for item in ReagentRole.query() if kit in item.kit_types]) self.type_input.addItems([item.name for item in ReagentRole.query() if kit in item.kit_types])
else: else:
self.type_input.addItems([item.name for item in ReagentRole.query()]) self.type_input.addItems([item.name for item in ReagentRole.query()])
# logger.debug(f"Trying to find index of {reagent_type}")
# NOTE: convert input to user-friendly string? # NOTE: convert input to user-friendly string?
try: try:
reagent_role = reagent_role.replace("_", " ").title() reagent_role = reagent_role.replace("_", " ").title()
@@ -106,7 +105,6 @@ class AddReagentForm(QDialog):
""" """
Updates reagent names form field with examples from reagent type Updates reagent names form field with examples from reagent type
""" """
# logger.debug(self.type_input.currentText())
self.name_input.clear() self.name_input.clear()
lookup = Reagent.query(role=self.type_input.currentText()) lookup = Reagent.query(role=self.type_input.currentText())
self.name_input.addItems(list(set([item.name for item in lookup]))) self.name_input.addItems(list(set([item.name for item in lookup])))
@@ -145,7 +143,8 @@ def save_pdf(obj: QWebEngineView, filename: Path):
obj.page().printToPdf(filename.absolute().__str__(), page_layout) obj.page().printToPdf(filename.absolute().__str__(), page_layout)
# subclass # NOTE: subclass
class CheckableComboBox(QComboBox): class CheckableComboBox(QComboBox):
# once there is a checkState set, it is rendered # once there is a checkState set, it is rendered
# here we assume default Unchecked # here we assume default Unchecked
@@ -162,7 +161,6 @@ class CheckableComboBox(QComboBox):
return item.checkState() == Qt.CheckState.Checked return item.checkState() == Qt.CheckState.Checked
def changed(self): def changed(self):
logger.debug("emitting updated")
self.updated.emit() self.updated.emit()

11
src/submissions/frontend/widgets/omni_search.py
View File

@@ -1,6 +1,6 @@
''' """
Search box that performs fuzzy search for samples Search box that performs fuzzy search for samples
''' """
from pprint import pformat from pprint import pformat
from typing import Tuple, Any, List from typing import Tuple, Any, List
from pandas import DataFrame from pandas import DataFrame
@@ -39,7 +39,6 @@ class SearchBox(QDialog):
else: else:
self.sub_class = None self.sub_class = None
self.results = SearchResults(parent=self, object_type=self.object_type, extras=self.extras, **kwargs) self.results = SearchResults(parent=self, object_type=self.object_type, extras=self.extras, **kwargs)
# logger.debug(f"results: {self.results}")
self.layout.addWidget(self.results, 5, 0) self.layout.addWidget(self.results, 5, 0)
self.setLayout(self.layout) self.setLayout(self.layout)
self.setWindowTitle(f"Search {self.object_type.__name__}") self.setWindowTitle(f"Search {self.object_type.__name__}")
@@ -51,7 +50,6 @@ class SearchBox(QDialog):
Changes form inputs based on sample type Changes form inputs based on sample type
""" """
deletes = [item for item in self.findChildren(FieldSearch)] deletes = [item for item in self.findChildren(FieldSearch)]
# logger.debug(deletes)
for item in deletes: for item in deletes:
item.setParent(None) item.setParent(None)
# NOTE: Handle any subclasses # NOTE: Handle any subclasses
@@ -62,7 +60,6 @@ class SearchBox(QDialog):
self.object_type = self.original_type self.object_type = self.original_type
else: else:
self.object_type = self.original_type.find_regular_subclass(self.sub_class.currentText()) self.object_type = self.original_type.find_regular_subclass(self.sub_class.currentText())
logger.debug(f"{self.object_type} searchables: {self.object_type.searchables}")
for iii, searchable in enumerate(self.object_type.searchables): for iii, searchable in enumerate(self.object_type.searchables):
widget = FieldSearch(parent=self, label=searchable, field_name=searchable) widget = FieldSearch(parent=self, label=searchable, field_name=searchable)
widget.setObjectName(searchable) widget.setObjectName(searchable)
@@ -85,10 +82,9 @@ class SearchBox(QDialog):
Shows dataframe of relevant samples. Shows dataframe of relevant samples.
""" """
fields = self.parse_form() fields = self.parse_form()
# logger.debug(f"Got fields: {fields}")
sample_list_creator = self.object_type.fuzzy_search(**fields) sample_list_creator = self.object_type.fuzzy_search(**fields)
data = self.object_type.results_to_df(objects=sample_list_creator) data = self.object_type.results_to_df(objects=sample_list_creator)
# Setting results moved to here from __init__ 202411118 # NOTE: Setting results moved to here from __init__ 202411118
self.results.setData(df=data) self.results.setData(df=data)
@@ -154,7 +150,6 @@ class SearchResults(QTableView):
def parse_row(self, x): def parse_row(self, x):
context = {item['name']: x.sibling(x.row(), item['column']).data() for item in self.columns_of_interest} context = {item['name']: x.sibling(x.row(), item['column']).data() for item in self.columns_of_interest}
logger.debug(f"Context: {context}")
try: try:
object = self.object_type.query(**context) object = self.object_type.query(**context)
except KeyError: except KeyError:

2
src/submissions/frontend/widgets/pop_ups.py
View File

@@ -9,7 +9,7 @@ from PyQt6.QtWebEngineWidgets import QWebEngineView
from tools import jinja_template_loading from tools import jinja_template_loading
import logging import logging
from backend.db import models from backend.db import models
from typing import Any, Literal from typing import Literal
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")

15
src/submissions/frontend/widgets/submission_details.py
View File

@@ -45,7 +45,6 @@ class SubmissionDetails(QDialog):
self.btn.clicked.connect(self.save_pdf) self.btn.clicked.connect(self.save_pdf)
self.back = QPushButton("Back") self.back = QPushButton("Back")
self.back.setFixedWidth(100) self.back.setFixedWidth(100)
# self.back.clicked.connect(self.back_function)
self.back.clicked.connect(self.webview.back) self.back.clicked.connect(self.webview.back)
self.layout.addWidget(self.back, 0, 0, 1, 1) self.layout.addWidget(self.back, 0, 0, 1, 1)
self.layout.addWidget(self.btn, 0, 1, 1, 9) self.layout.addWidget(self.btn, 0, 1, 1, 9)
@@ -70,7 +69,6 @@ class SubmissionDetails(QDialog):
if "Submission" in title: if "Submission" in title:
self.btn.setEnabled(True) self.btn.setEnabled(True)
self.export_plate = title.split(" ")[-1] self.export_plate = title.split(" ")[-1]
# logger.debug(f"Updating export plate to: {self.export_plate}")
else: else:
self.btn.setEnabled(False) self.btn.setEnabled(False)
try: try:
@@ -78,7 +76,6 @@ class SubmissionDetails(QDialog):
except IndexError as e: except IndexError as e:
check = title check = title
if title == check: if title == check:
# logger.debug("Disabling back button")
self.back.setEnabled(False) self.back.setEnabled(False)
else: else:
self.back.setEnabled(True) self.back.setEnabled(True)
@@ -91,7 +88,6 @@ class SubmissionDetails(QDialog):
Args: Args:
sample (str): Submitter Id of the sample. sample (str): Submitter Id of the sample.
""" """
# logger.debug(f"Details: {sample}")
if isinstance(sample, str): if isinstance(sample, str):
sample = BasicSample.query(submitter_id=sample) sample = BasicSample.query(submitter_id=sample)
base_dict = sample.to_sub_dict(full_data=True) base_dict = sample.to_sub_dict(full_data=True)
@@ -114,7 +110,6 @@ class SubmissionDetails(QDialog):
base_dict = reagent.to_sub_dict(extraction_kit=self.kit, full_data=True) base_dict = reagent.to_sub_dict(extraction_kit=self.kit, full_data=True)
env = jinja_template_loading() env = jinja_template_loading()
temp_name = "reagent_details.html" temp_name = "reagent_details.html"
# logger.debug(f"Returning template: {temp_name}")
try: try:
template = env.get_template(temp_name) template = env.get_template(temp_name)
except TemplateNotFound as e: except TemplateNotFound as e:
@@ -147,29 +142,23 @@ class SubmissionDetails(QDialog):
Args: Args:
submission (str | BasicSubmission): Submission of interest. submission (str | BasicSubmission): Submission of interest.
""" """
# logger.debug(f"Details for: {submission}")
if isinstance(submission, str): if isinstance(submission, str):
submission = BasicSubmission.query(rsl_plate_num=submission) submission = BasicSubmission.query(rsl_plate_num=submission)
self.rsl_plate_num = submission.rsl_plate_num self.rsl_plate_num = submission.rsl_plate_num
self.base_dict = submission.to_dict(full_data=True) self.base_dict = submission.to_dict(full_data=True)
# logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k == 'reagents'})}")
# NOTE: don't want id # NOTE: don't want id
# logger.debug(f"Creating barcode.")
# logger.debug(f"Making platemap...")
self.base_dict['platemap'] = submission.make_plate_map(sample_list=submission.hitpick_plate()) self.base_dict['platemap'] = submission.make_plate_map(sample_list=submission.hitpick_plate())
self.base_dict['excluded'] = submission.get_default_info("details_ignore") self.base_dict['excluded'] = submission.get_default_info("details_ignore")
self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict) self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
template_path = Path(self.template.environment.loader.__getattribute__("searchpath")[0]) template_path = Path(self.template.environment.loader.__getattribute__("searchpath")[0])
with open(template_path.joinpath("css", "styles.css"), "r") as f: with open(template_path.joinpath("css", "styles.css"), "r") as f:
css = f.read() css = f.read()
# logger.debug(f"Submission_details: {pformat(self.base_dict)}")
# logger.debug(f"User is power user: {is_power_user()}")
self.html = self.template.render(sub=self.base_dict, permission=is_power_user(), css=css) self.html = self.template.render(sub=self.base_dict, permission=is_power_user(), css=css)
self.webview.setHtml(self.html) self.webview.setHtml(self.html)
@pyqtSlot(str) @pyqtSlot(str)
def sign_off(self, submission: str | BasicSubmission): def sign_off(self, submission: str | BasicSubmission):
logger.debug(f"Signing off on {submission} - ({getuser()})") logger.info(f"Signing off on {submission} - ({getuser()})")
if isinstance(submission, str): if isinstance(submission, str):
submission = BasicSubmission.query(rsl_plate_num=submission) submission = BasicSubmission.query(rsl_plate_num=submission)
submission.signed_by = getuser() submission.signed_by = getuser()
@@ -195,7 +184,6 @@ class SubmissionComment(QDialog):
super().__init__(parent) super().__init__(parent)
try: try:
self.app = parent.parent().parent().parent().parent().parent().parent self.app = parent.parent().parent().parent().parent().parent().parent
# logger.debug(f"App: {self.app}")
except AttributeError: except AttributeError:
pass pass
self.submission = submission self.submission = submission
@@ -225,5 +213,4 @@ class SubmissionComment(QDialog):
return None return None
dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S") dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
full_comment = {"name": commenter, "time": dt, "text": comment} full_comment = {"name": commenter, "time": dt, "text": comment}
# logger.debug(f"Full comment: {full_comment}")
return full_comment return full_comment

13
src/submissions/frontend/widgets/submission_table.py
View File

@@ -1,6 +1,6 @@
''' """
Contains widgets specific to the submission summary and submission details. Contains widgets specific to the submission summary and submission details.
''' """
import logging import logging
from pprint import pformat from pprint import pformat
from PyQt6.QtWidgets import QTableView, QMenu from PyQt6.QtWidgets import QTableView, QMenu
@@ -107,20 +107,16 @@ class SubmissionsSheet(QTableView):
Args: Args:
event (_type_): the item of interest event (_type_): the item of interest
""" """
# logger.debug(event.__dict__)
id = self.selectionModel().currentIndex() id = self.selectionModel().currentIndex()
id = id.sibling(id.row(), 0).data() id = id.sibling(id.row(), 0).data()
submission = BasicSubmission.query(id=id) submission = BasicSubmission.query(id=id)
# logger.debug(f"Event submission: {submission}")
self.menu = QMenu(self) self.menu = QMenu(self)
self.con_actions = submission.custom_context_events() self.con_actions = submission.custom_context_events()
# logger.debug(f"Menu options: {self.con_actions}")
for k in self.con_actions.keys(): for k in self.con_actions.keys():
# logger.debug(f"Adding {k}")
action = QAction(k, self) action = QAction(k, self)
action.triggered.connect(lambda _, action_name=k: self.triggered_action(action_name=action_name)) action.triggered.connect(lambda _, action_name=k: self.triggered_action(action_name=action_name))
self.menu.addAction(action) self.menu.addAction(action)
# add other required actions # NOTE: add other required actions
self.menu.popup(QCursor.pos()) self.menu.popup(QCursor.pos())
def triggered_action(self, action_name: str): def triggered_action(self, action_name: str):
@@ -130,8 +126,6 @@ class SubmissionsSheet(QTableView):
Args: Args:
action_name (str): name of the action from the menu action_name (str): name of the action from the menu
""" """
# logger.debug(f"Action: {action_name}")
# logger.debug(f"Responding with {self.con_actions[action_name]}")
func = self.con_actions[action_name] func = self.con_actions[action_name]
func(obj=self) func(obj=self)
@@ -179,7 +173,6 @@ class SubmissionsSheet(QTableView):
if sub is None: if sub is None:
continue continue
try: try:
# logger.debug(f"Found submission: {sub.rsl_plate_num}")
count += 1 count += 1
except AttributeError: except AttributeError:
continue continue

77
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -1,9 +1,9 @@
''' """
Contains all submission related frontend functions Contains all submission related frontend functions
''' """
from PyQt6.QtWidgets import ( from PyQt6.QtWidgets import (
QWidget, QPushButton, QVBoxLayout, QWidget, QPushButton, QVBoxLayout,
QComboBox, QDateEdit, QLineEdit, QLabel, QCheckBox, QBoxLayout, QHBoxLayout, QGridLayout QComboBox, QDateEdit, QLineEdit, QLabel, QCheckBox, QHBoxLayout, QGridLayout
) )
from PyQt6.QtCore import pyqtSignal, Qt, QSignalBlocker from PyQt6.QtCore import pyqtSignal, Qt, QSignalBlocker
from . import select_open_file, select_save_file from . import select_open_file, select_save_file
@@ -34,7 +34,6 @@ class MyQComboBox(QComboBox):
super(MyQComboBox, self).__init__(*args, **kwargs) super(MyQComboBox, self).__init__(*args, **kwargs)
self.scrollWidget = scrollWidget self.scrollWidget = scrollWidget
self.setFocusPolicy(Qt.FocusPolicy.StrongFocus) self.setFocusPolicy(Qt.FocusPolicy.StrongFocus)
logger.debug(f"Scrollwidget: {scrollWidget}")
def wheelEvent(self, *args, **kwargs): def wheelEvent(self, *args, **kwargs):
if self.hasFocus(): if self.hasFocus():
@@ -61,14 +60,12 @@ class MyQDateEdit(QDateEdit):
class SubmissionFormContainer(QWidget): class SubmissionFormContainer(QWidget):
# A signal carrying a path # NOTE: A signal carrying a path
import_drag = pyqtSignal(Path) import_drag = pyqtSignal(Path)
def __init__(self, parent: QWidget) -> None: def __init__(self, parent: QWidget) -> None:
# logger.debug(f"Setting form widget...")
super().__init__(parent) super().__init__(parent)
self.app = self.parent().parent() self.app = self.parent().parent()
# logger.debug(f"App: {self.app}")
self.report = Report() self.report = Report()
self.setStyleSheet('background-color: light grey;') self.setStyleSheet('background-color: light grey;')
self.setAcceptDrops(True) self.setAcceptDrops(True)
@@ -89,7 +86,6 @@ class SubmissionFormContainer(QWidget):
Sets filename when file dropped Sets filename when file dropped
""" """
fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0]) fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0])
# logger.debug(f"App: {self.app}")
self.app.last_dir = fname.parent self.app.last_dir = fname.parent
self.import_drag.emit(fname) self.import_drag.emit(fname)
@@ -127,7 +123,6 @@ class SubmissionFormContainer(QWidget):
# NOTE: set file dialog # NOTE: set file dialog
if isinstance(fname, bool) or fname is None: if isinstance(fname, bool) or fname is None:
fname = select_open_file(self, file_extension="xlsx") fname = select_open_file(self, file_extension="xlsx")
# logger.debug(f"Attempting to parse file: {fname}")
if not fname: if not fname:
report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical")) report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
return report return report
@@ -139,14 +134,10 @@ class SubmissionFormContainer(QWidget):
return return
except AttributeError: except AttributeError:
self.prsr = SheetParser(filepath=fname) self.prsr = SheetParser(filepath=fname)
# logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
self.pyd = self.prsr.to_pydantic() self.pyd = self.prsr.to_pydantic()
# logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
self.form = self.pyd.to_form(parent=self) self.form = self.pyd.to_form(parent=self)
self.layout().addWidget(self.form) self.layout().addWidget(self.form)
return report return report
# logger.debug(f"Outgoing report: {self.report.results}")
# logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
@report_result @report_result
def add_reagent(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None, def add_reagent(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
@@ -172,14 +163,12 @@ class SubmissionFormContainer(QWidget):
if dlg.exec(): if dlg.exec():
# NOTE: extract form info # NOTE: extract form info
info = dlg.parse_form() info = dlg.parse_form()
# logger.debug(f"Reagent info: {info}")
# NOTE: create reagent object # NOTE: create reagent object
reagent = PydReagent(ctx=self.app.ctx, **info, missing=False) reagent = PydReagent(ctx=self.app.ctx, **info, missing=False)
# NOTE: send reagent to db # NOTE: send reagent to db
sqlobj, result = reagent.toSQL() sqlobj, result = reagent.toSQL()
sqlobj.save() sqlobj.save()
report.add_result(result) report.add_result(result)
# logger.debug(f"Reagent: {reagent}, Report: {report}")
return reagent, report return reagent, report
@@ -189,7 +178,6 @@ class SubmissionFormWidget(QWidget):
def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None: def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None:
super().__init__(parent) super().__init__(parent)
# logger.debug(f"Disable: {disable}")
if disable is None: if disable is None:
disable = [] disable = []
self.app = parent.app self.app = parent.app
@@ -200,17 +188,13 @@ class SubmissionFormWidget(QWidget):
defaults = st.get_default_info("form_recover", "form_ignore", submission_type=self.pyd.submission_type['value']) defaults = st.get_default_info("form_recover", "form_ignore", submission_type=self.pyd.submission_type['value'])
self.recover = defaults['form_recover'] self.recover = defaults['form_recover']
self.ignore = defaults['form_ignore'] self.ignore = defaults['form_ignore']
# logger.debug(f"Attempting to extend ignore list with {self.pyd.submission_type['value']}")
self.layout = QVBoxLayout() self.layout = QVBoxLayout()
for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()): for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()):
# logger.debug(f"Creating widget: {k}")
if k in self.ignore: if k in self.ignore:
logger.warning(f"{k} in form_ignore {self.ignore}, not creating widget") logger.warning(f"{k} in form_ignore {self.ignore}, not creating widget")
continue continue
try: try:
# logger.debug(f"Key: {k}, Disable: {disable}")
check = k in disable check = k in disable
# logger.debug(f"Check: {check}")
except TypeError: except TypeError:
check = False check = False
try: try:
@@ -225,7 +209,6 @@ class SubmissionFormWidget(QWidget):
sub_obj=st, disable=check) sub_obj=st, disable=check)
if add_widget is not None: if add_widget is not None:
self.layout.addWidget(add_widget) self.layout.addWidget(add_widget)
# if k == "extraction_kit":
if k in self.__class__.update_reagent_fields: if k in self.__class__.update_reagent_fields:
add_widget.input.currentTextChanged.connect(self.scrape_reagents) add_widget.input.currentTextChanged.connect(self.scrape_reagents)
self.disabler = self.DisableReagents(self) self.disabler = self.DisableReagents(self)
@@ -236,15 +219,10 @@ class SubmissionFormWidget(QWidget):
self.scrape_reagents(self.extraction_kit) self.scrape_reagents(self.extraction_kit)
def disable_reagents(self): def disable_reagents(self):
"""
Disables all ReagentFormWidgets in this form/
"""
for reagent in self.findChildren(self.ReagentFormWidget): for reagent in self.findChildren(self.ReagentFormWidget):
# if self.disabler.checkbox.isChecked():
# # reagent.setVisible(True)
# # with QSignalBlocker(self.disabler.checkbox) as b:
# reagent.flip_check()
# else:
# # reagent.setVisible(False)
# # with QSignalBlocker(self.disabler.checkbox) as b:
# reagent.check.setChecked(False)
reagent.flip_check(self.disabler.checkbox.isChecked()) reagent.flip_check(self.disabler.checkbox.isChecked())
@@ -263,7 +241,6 @@ class SubmissionFormWidget(QWidget):
Returns: Returns:
self.InfoItem: Form widget to hold name:value self.InfoItem: Form widget to hold name:value
""" """
# logger.debug(f"Key: {key}, Disable: {disable}")
if isinstance(submission_type, str): if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type) submission_type = SubmissionType.query(name=submission_type)
if key not in self.ignore: if key not in self.ignore:
@@ -276,7 +253,6 @@ class SubmissionFormWidget(QWidget):
case _: case _:
widget = self.InfoItem(parent=self, key=key, value=value, submission_type=submission_type, widget = self.InfoItem(parent=self, key=key, value=value, submission_type=submission_type,
sub_obj=sub_obj) sub_obj=sub_obj)
# logger.debug(f"Setting widget enabled to: {not disable}")
if disable: if disable:
widget.input.setEnabled(False) widget.input.setEnabled(False)
widget.input.setToolTip("Widget disabled to protect database integrity.") widget.input.setToolTip("Widget disabled to protect database integrity.")
@@ -298,24 +274,20 @@ class SubmissionFormWidget(QWidget):
""" """
self.extraction_kit = args[0] self.extraction_kit = args[0]
report = Report() report = Report()
logger.debug(f"Extraction kit: {self.extraction_kit}")
# NOTE: Remove previous reagent widgets # NOTE: Remove previous reagent widgets
try: try:
old_reagents = self.find_widgets() old_reagents = self.find_widgets()
except AttributeError: except AttributeError:
logger.error(f"Couldn't find old reagents.") logger.error(f"Couldn't find old reagents.")
old_reagents = [] old_reagents = []
# logger.debug(f"\n\nAttempting to clear: {old_reagents}\n\n")
for reagent in old_reagents: for reagent in old_reagents:
if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton): if isinstance(reagent, self.ReagentFormWidget) or isinstance(reagent, QPushButton):
reagent.setParent(None) reagent.setParent(None)
reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=self.extraction_kit) reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=self.extraction_kit)
# logger.debug(f"Got reagents: {pformat(reagents)}")
for reagent in reagents: for reagent in reagents:
add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.extraction_kit) add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.extraction_kit)
self.layout.addWidget(add_widget) self.layout.addWidget(add_widget)
report.add_result(integrity_report) report.add_result(integrity_report)
# logger.debug(f"Outgoing report: {report.results}")
if hasattr(self.pyd, "csv"): if hasattr(self.pyd, "csv"):
export_csv_btn = QPushButton("Export CSV") export_csv_btn = QPushButton("Export CSV")
export_csv_btn.setObjectName("export_csv_btn") export_csv_btn.setObjectName("export_csv_btn")
@@ -326,6 +298,7 @@ class SubmissionFormWidget(QWidget):
self.layout.addWidget(submit_btn) self.layout.addWidget(submit_btn)
submit_btn.clicked.connect(self.submit_new_sample_function) submit_btn.clicked.connect(self.submit_new_sample_function)
self.setLayout(self.layout) self.setLayout(self.layout)
self.disabler.checkbox.setChecked(True)
return report return report
def clear_form(self): def clear_form(self):
@@ -365,23 +338,16 @@ class SubmissionFormWidget(QWidget):
report = Report() report = Report()
result = self.parse_form() result = self.parse_form()
report.add_result(result) report.add_result(result)
# logger.debug(f"Submission: {pformat(self.pyd)}")
# logger.debug("Checking kit integrity...")
if self.disabler.checkbox.isChecked(): if self.disabler.checkbox.isChecked():
_, result = self.pyd.check_kit_integrity() _, result = self.pyd.check_kit_integrity()
report.add_result(result) report.add_result(result)
if len(result.results) > 0: if len(result.results) > 0:
return return
# logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n")
base_submission, result = self.pyd.to_sql() base_submission, result = self.pyd.to_sql()
# logger.debug(f"SQL object: {pformat(base_submission.__dict__)}")
# logger.debug(f"Base submission: {base_submission.to_dict()}")
# NOTE: check output message for issues # NOTE: check output message for issues
# logger.debug(f"Result of to_sql: {result}")
try: try:
trigger = result.results[-1] trigger = result.results[-1]
code = trigger.code code = trigger.code
# logger.debug(f"Code from return: {code}")
except IndexError as e: except IndexError as e:
logger.error(result.results) logger.error(result.results)
logger.error(f"Problem getting error code: {e}") logger.error(f"Problem getting error code: {e}")
@@ -408,11 +374,8 @@ class SubmissionFormWidget(QWidget):
pass pass
# NOTE: add reagents to submission object # NOTE: add reagents to submission object
for reagent in base_submission.reagents: for reagent in base_submission.reagents:
# logger.debug(f"Updating: {reagent} with {reagent.lot}")
reagent.update_last_used(kit=base_submission.extraction_kit) reagent.update_last_used(kit=base_submission.extraction_kit)
# logger.debug(f"Final reagents: {pformat(base_submission.reagents)}")
save_output = base_submission.save() save_output = base_submission.save()
# logger.debug(f"Save output: {save_output}")
# NOTE: update summary sheet # NOTE: update summary sheet
self.app.table_widget.sub_wid.setData() self.app.table_widget.sub_wid.setData()
# NOTE: reset form # NOTE: reset form
@@ -423,7 +386,6 @@ class SubmissionFormWidget(QWidget):
check = True check = True
if check: if check:
self.setParent(None) self.setParent(None)
# logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
return report return report
def export_csv_function(self, fname: Path | None = None): def export_csv_function(self, fname: Path | None = None):
@@ -454,7 +416,6 @@ class SubmissionFormWidget(QWidget):
info = {} info = {}
reagents = [] reagents = []
for widget in self.findChildren(QWidget): for widget in self.findChildren(QWidget):
# logger.debug(f"Parsed widget of type {type(widget)}")
match widget: match widget:
case self.ReagentFormWidget(): case self.ReagentFormWidget():
reagent, _ = widget.parse_form() reagent, _ = widget.parse_form()
@@ -464,16 +425,10 @@ class SubmissionFormWidget(QWidget):
field, value = widget.parse_form() field, value = widget.parse_form()
if field is not None: if field is not None:
info[field] = value info[field] = value
# logger.debug(f"Info: {pformat(info)}")
logger.debug(f"Reagents going into pyd: {pformat(reagents)}")
self.pyd.reagents = reagents self.pyd.reagents = reagents
logger.debug(f"Reagents after insertion in pyd: {pformat(self.pyd.reagents)}")
# logger.debug(f"Attrs not in info: {[k for k, v in self.__dict__.items() if k not in info.keys()]}")
for item in self.recover: for item in self.recover:
# logger.debug(f"Attempting to recover: {item}")
if hasattr(self, item): if hasattr(self, item):
value = getattr(self, item) value = getattr(self, item)
# logger.debug(f"Setting {item}")
info[item] = value info[item] = value
for k, v in info.items(): for k, v in info.items():
self.pyd.set_attribute(key=k, value=v) self.pyd.set_attribute(key=k, value=v)
@@ -551,9 +506,6 @@ class SubmissionFormWidget(QWidget):
except (TypeError, KeyError): except (TypeError, KeyError):
pass pass
obj = parent.parent().parent() obj = parent.parent().parent()
# logger.debug(f"Object: {obj}")
# logger.debug(f"Parent: {parent.parent()}")
# logger.debug(f"Creating widget for: {key}")
match key: match key:
case 'submitting_lab': case 'submitting_lab':
add_widget = MyQComboBox(scrollWidget=parent) add_widget = MyQComboBox(scrollWidget=parent)
@@ -567,7 +519,6 @@ class SubmissionFormWidget(QWidget):
looked_up_lab = Organization.query(name=value, limit=1) looked_up_lab = Organization.query(name=value, limit=1)
except AttributeError: except AttributeError:
looked_up_lab = None looked_up_lab = None
# logger.debug(f"\n\nLooked up lab: {looked_up_lab}")
if looked_up_lab: if looked_up_lab:
try: try:
labs.remove(str(looked_up_lab.name)) labs.remove(str(looked_up_lab.name))
@@ -586,12 +537,9 @@ class SubmissionFormWidget(QWidget):
# NOTE: create combobox to hold looked up kits # NOTE: create combobox to hold looked up kits
add_widget = MyQComboBox(scrollWidget=parent) add_widget = MyQComboBox(scrollWidget=parent)
# NOTE: lookup existing kits by 'submission_type' decided on by sheetparser # NOTE: lookup existing kits by 'submission_type' decided on by sheetparser
# logger.debug(f"Looking up kits used for {submission_type}")
uses = [item.name for item in submission_type.kit_types] uses = [item.name for item in submission_type.kit_types]
obj.uses = uses obj.uses = uses
# logger.debug(f"Kits received for {submission_type}: {uses}")
if check_not_nan(value): if check_not_nan(value):
# logger.debug(f"The extraction kit in parser was: {value}")
try: try:
uses.insert(0, uses.pop(uses.index(value))) uses.insert(0, uses.pop(uses.index(value)))
except ValueError: except ValueError:
@@ -626,7 +574,6 @@ class SubmissionFormWidget(QWidget):
else: else:
# NOTE: anything else gets added in as a line edit # NOTE: anything else gets added in as a line edit
add_widget = QLineEdit() add_widget = QLineEdit()
# logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
add_widget.setText(str(value).replace("_", " ")) add_widget.setText(str(value).replace("_", " "))
add_widget.setToolTip(f"Enter value for {key}") add_widget.setToolTip(f"Enter value for {key}")
if add_widget is not None: if add_widget is not None:
@@ -725,7 +672,6 @@ class SubmissionFormWidget(QWidget):
if not self.lot.isEnabled(): if not self.lot.isEnabled():
return None, report return None, report
lot = self.lot.currentText() lot = self.lot.currentText()
# logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
wanted_reagent = Reagent.query(lot=lot, role=self.reagent.role) wanted_reagent = Reagent.query(lot=lot, role=self.reagent.role)
# NOTE: if reagent doesn't exist in database, offer to add it (uses App.add_reagent) # NOTE: if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
if wanted_reagent is None: if wanted_reagent is None:
@@ -741,7 +687,6 @@ class SubmissionFormWidget(QWidget):
return wanted_reagent, report return wanted_reagent, report
else: else:
# NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check # NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check
# logger.debug("Will not add reagent.")
report.add_result(Result(msg="Failed integrity check", status="Critical")) report.add_result(Result(msg="Failed integrity check", status="Critical"))
return None, report return None, report
else: else:
@@ -791,7 +736,6 @@ class SubmissionFormWidget(QWidget):
looked_up_rt = KitTypeReagentRoleAssociation.query(reagent_role=reagent.role, looked_up_rt = KitTypeReagentRoleAssociation.query(reagent_role=reagent.role,
kit_type=extraction_kit) kit_type=extraction_kit)
relevant_reagents = [str(item.lot) for item in looked_up_rt.get_all_relevant_reagents()] relevant_reagents = [str(item.lot) for item in looked_up_rt.get_all_relevant_reagents()]
logger.debug(f"Relevant reagents for {reagent}: {relevant_reagents}")
# NOTE: if reagent in sheet is not found insert it into the front of relevant reagents so it shows # NOTE: if reagent in sheet is not found insert it into the front of relevant reagents so it shows
if str(reagent.lot) not in relevant_reagents: if str(reagent.lot) not in relevant_reagents:
if check_not_nan(reagent.lot): if check_not_nan(reagent.lot):
@@ -803,7 +747,6 @@ class SubmissionFormWidget(QWidget):
looked_up_reg = None looked_up_reg = None
if isinstance(looked_up_reg, list): if isinstance(looked_up_reg, list):
looked_up_reg = None looked_up_reg = None
# logger.debug(f"Because there was no reagent listed for {reagent.lot}, we will insert the last lot used: {looked_up_reg}")
if looked_up_reg: if looked_up_reg:
try: try:
relevant_reagents.remove(str(looked_up_reg.lot)) relevant_reagents.remove(str(looked_up_reg.lot))
@@ -812,15 +755,11 @@ class SubmissionFormWidget(QWidget):
relevant_reagents.insert(0, str(looked_up_reg.lot)) relevant_reagents.insert(0, str(looked_up_reg.lot))
else: else:
if len(relevant_reagents) > 1: if len(relevant_reagents) > 1:
# logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. Moving to front of list.")
idx = relevant_reagents.index(str(reagent.lot)) idx = relevant_reagents.index(str(reagent.lot))
# logger.debug(f"The index we got for {reagent.lot} in {relevant_reagents} was {idx}")
moved_reag = relevant_reagents.pop(idx) moved_reag = relevant_reagents.pop(idx)
relevant_reagents.insert(0, moved_reag) relevant_reagents.insert(0, moved_reag)
else: else:
# logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. But no need to move due to short list.")
pass pass
logger.debug(f"New relevant reagents: {relevant_reagents}")
self.setObjectName(f"lot_{reagent.role}") self.setObjectName(f"lot_{reagent.role}")
self.addItems(relevant_reagents) self.addItems(relevant_reagents)
self.setToolTip(f"Enter lot number for the reagent used for {reagent.role}") self.setToolTip(f"Enter lot number for the reagent used for {reagent.role}")

1
src/submissions/frontend/widgets/summary.py
View File

@@ -35,7 +35,6 @@ class Summary(InfoPane):
def update_data(self): def update_data(self):
super().update_data() super().update_data()
orgs = [self.org_select.itemText(i) for i in range(self.org_select.count()) if self.org_select.itemChecked(i)] orgs = [self.org_select.itemText(i) for i in range(self.org_select.count()) if self.org_select.itemChecked(i)]
# logger.debug(f"Getting report from {self.start_date} to {self.end_date} using {orgs}")
self.report_obj = ReportMaker(start_date=self.start_date, end_date=self.end_date, organizations=orgs) self.report_obj = ReportMaker(start_date=self.start_date, end_date=self.end_date, organizations=orgs)
self.webview.setHtml(self.report_obj.html) self.webview.setHtml(self.report_obj.html)
if self.report_obj.subs: if self.report_obj.subs:

20
src/submissions/tools/__init__.py
View File

@@ -27,14 +27,14 @@ timezone = tz("America/Winnipeg")
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")
logger.debug(f"Package dir: {project_path}") logger.info(f"Package dir: {project_path}")
if platform.system() == "Windows": if platform.system() == "Windows":
os_config_dir = "AppData/local" os_config_dir = "AppData/local"
print(f"Got platform Windows, config_dir: {os_config_dir}") logger.info(f"Got platform Windows, config_dir: {os_config_dir}")
else: else:
os_config_dir = ".config" os_config_dir = ".config"
print(f"Got platform other, config_dir: {os_config_dir}") logger.info(f"Got platform other, config_dir: {os_config_dir}")
main_aux_dir = Path.home().joinpath(f"{os_config_dir}/submissions") main_aux_dir = Path.home().joinpath(f"{os_config_dir}/submissions")
@@ -184,7 +184,6 @@ def convert_nans_to_nones(input_str) -> str | None:
Returns: Returns:
str: _description_ str: _description_
""" """
# logger.debug(f"Input value of: {input_str}")
if check_not_nan(input_str): if check_not_nan(input_str):
return input_str return input_str
return None return None
@@ -512,7 +511,6 @@ def get_config(settings_path: Path | str | None = None) -> Settings:
Returns: Returns:
Settings: Pydantic settings object Settings: Pydantic settings object
""" """
# logger.debug(f"Creating settings...")
if isinstance(settings_path, str): if isinstance(settings_path, str):
settings_path = Path(settings_path) settings_path = Path(settings_path)
@@ -566,7 +564,6 @@ def get_config(settings_path: Path | str | None = None) -> Settings:
default_settings = yaml.load(dset, Loader=yaml.Loader) default_settings = yaml.load(dset, Loader=yaml.Loader)
settings = Settings(**default_settings) settings = Settings(**default_settings)
settings.save(settings_path=settings_path) settings.save(settings_path=settings_path)
# logger.debug(f"Using {settings_path} for config file.")
with open(settings_path, "r") as stream: with open(settings_path, "r") as stream:
settings = yaml.load(stream, Loader=yaml.Loader) settings = yaml.load(stream, Loader=yaml.Loader)
return Settings(**settings) return Settings(**settings)
@@ -755,7 +752,6 @@ def setup_lookup(func):
raise ValueError("Could not sanitize dictionary in query. Make sure you parse it first.") raise ValueError("Could not sanitize dictionary in query. Make sure you parse it first.")
elif v is not None: elif v is not None:
sanitized_kwargs[k] = v sanitized_kwargs[k] = v
# logger.debug(f"sanitized kwargs: {sanitized_kwargs}")
return func(*args, **sanitized_kwargs) return func(*args, **sanitized_kwargs)
return wrapper return wrapper
@@ -800,7 +796,6 @@ class Result(BaseModel, arbitrary_types_allowed=True):
logger.error(f"Exception origin: {origin}") logger.error(f"Exception origin: {origin}")
if "unique constraint failed:" in origin: if "unique constraint failed:" in origin:
field = " ".join(origin.split(".")[1:]).replace("_", " ").upper() field = " ".join(origin.split(".")[1:]).replace("_", " ").upper()
# logger.debug(field)
value = f"{field} doesn't have a unique value.\nIt must be changed." value = f"{field} doesn't have a unique value.\nIt must be changed."
else: else:
value = f"Got unknown integrity error: {value}" value = f"Got unknown integrity error: {value}"
@@ -844,7 +839,6 @@ class Report(BaseModel):
except AttributeError: except AttributeError:
logger.error(f"Problem adding result.") logger.error(f"Problem adding result.")
case Report(): case Report():
# logger.debug(f"Adding all results in report to new report")
for res in result.results: for res in result.results:
logger.info(f"Adding {res} from {result} to results.") logger.info(f"Adding {res} from {result} to results.")
self.results.append(res) self.results.append(res)
@@ -934,7 +928,7 @@ def check_authorization(func):
""" """
def wrapper(*args, **kwargs): def wrapper(*args, **kwargs):
logger.debug(f"Checking authorization") logger.info(f"Checking authorization")
if is_power_user(): if is_power_user():
return func(*args, **kwargs) return func(*args, **kwargs)
else: else:
@@ -957,7 +951,7 @@ def report_result(func):
""" """
def wrapper(*args, **kwargs): def wrapper(*args, **kwargs):
logger.debug(f"Report result being called by {func.__name__}") logger.info(f"Report result being called by {func.__name__}")
output = func(*args, **kwargs) output = func(*args, **kwargs)
match output: match output:
case Report(): case Report():
@@ -970,14 +964,13 @@ def report_result(func):
case _: case _:
report = None report = None
return report return report
logger.debug(f"Got report: {report}") logger.info(f"Got report: {report}")
try: try:
results = report.results results = report.results
except AttributeError: except AttributeError:
logger.error("No results available") logger.error("No results available")
results = [] results = []
for iii, result in enumerate(results): for iii, result in enumerate(results):
logger.debug(f"Result {iii}: {result}")
try: try:
dlg = result.report() dlg = result.report()
dlg.exec() dlg.exec()
@@ -990,7 +983,6 @@ def report_result(func):
true_output = true_output[0] true_output = true_output[0]
else: else:
true_output = None true_output = None
# logger.debug(f"Returning true output: {true_output}")
return true_output return true_output
return wrapper return wrapper