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Second round of code cleanup.

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This commit is contained in:
lwark
2024-10-30 07:34:39 -05:00
parent 1f83b61c81
commit ba1b3e5cf3
19 changed files with 176 additions and 110 deletions
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41
src/submissions/backend/db/models/__init__.py
View File

@@ -28,6 +28,8 @@ class BaseClass(Base):
__table_args__ = {'extend_existing': True} #: Will only add new columns
singles = ['id']
@classmethod
@declared_attr
def __tablename__(cls) -> str:
@@ -92,17 +94,21 @@ class BaseClass(Base):
Returns:
dict | list | str: Output of key:value dict or single (list, str) desired variable
"""
dicto = dict(singles=['id'])
output = {}
for k, v in dicto.items():
if len(args) > 0 and k not in args:
# logger.debug(f"{k} not selected as being of interest.")
continue
else:
output[k] = v
if len(args) == 1:
return output[args[0]]
return output
# if issubclass(cls, BaseClass) and cls.__name__ != "BaseClass":
singles = list(set(cls.singles + BaseClass.singles))
# else:
# singles = cls.singles
# output = dict(singles=singles)
# output = {}
# for k, v in dicto.items():
# if len(args) > 0 and k not in args:
# # logger.debug(f"{k} not selected as being of interest.")
# continue
# else:
# output[k] = v
# if len(args) == 1:
# return output[args[0]]
return dict(singles=singles)
@classmethod
def query(cls, **kwargs) -> Any | List[Any]:
@@ -190,10 +196,15 @@ class ConfigItem(BaseClass):
Returns:
ConfigItem|List[ConfigItem]: Config item(s)
"""
config_items = cls.__database_session__.query(cls).all()
config_items = [item for item in config_items if item.key in args]
if len(args) == 1:
config_items = config_items[0]
query = cls.__database_session__.query(cls)
# config_items = [item for item in config_items if item.key in args]
match len(args):
case 0:
config_items = query.all()
case 1:
config_items = query.filter(cls.key == args[0]).first()
case _:
config_items = query.filter(cls.key.in_(args)).all()
return config_items

24
src/submissions/backend/db/models/controls.py
View File

@@ -131,10 +131,8 @@ class Control(BaseClass):
__mapper_args__ = {
"polymorphic_identity": "Basic Control",
"polymorphic_on": case(
(controltype_name == "PCR Control", "PCR Control"),
(controltype_name == "Irida Control", "Irida Control"),
else_="Basic Control"
),
"with_polymorphic": "*",
@@ -147,15 +145,15 @@ class Control(BaseClass):
def find_polymorphic_subclass(cls, polymorphic_identity: str | ControlType | None = None,
attrs: dict | None = None) -> Control:
"""
Find subclass based on polymorphic identity or relevant attributes.
Find subclass based on polymorphic identity or relevant attributes.
Args:
polymorphic_identity (str | None, optional): String representing polymorphic identity. Defaults to None.
attrs (str | SubmissionType | None, optional): Attributes of the relevant class. Defaults to None.
Args:
polymorphic_identity (str | None, optional): String representing polymorphic identity. Defaults to None.
attrs (str | SubmissionType | None, optional): Attributes of the relevant class. Defaults to None.
Returns:
Control: Subclass of interest.
"""
Returns:
Control: Subclass of interest.
"""
if isinstance(polymorphic_identity, dict):
# logger.debug(f"Controlling for dict value")
polymorphic_identity = polymorphic_identity['value']
@@ -189,14 +187,11 @@ class Control(BaseClass):
Args:
parent (QWidget): chart holding widget to add buttons to.
Returns:
"""
pass
return None
@classmethod
def make_chart(cls, parent, chart_settings: dict, ctx):
def make_chart(cls, parent, chart_settings: dict, ctx) -> Tuple[Report, "CustomFigure" | None]:
"""
Dummy operation to be overridden by child classes.
@@ -307,6 +302,7 @@ class PCRControl(Control):
return cls.execute_query(query=query, limit=limit)
@classmethod
@report_result
def make_chart(cls, parent, chart_settings: dict, ctx: Settings) -> Tuple[Report, "PCRFigure"]:
"""
Creates a PCRFigure. Overrides parent

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

@@ -4,6 +4,7 @@ All kit and reagent related models
from __future__ import annotations
import datetime
import json
import sys
from pprint import pformat
import yaml
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
@@ -693,6 +694,9 @@ class SubmissionType(BaseClass):
Returns:
List[str]: List of sheet names
"""
# print(f"Getting template file from {self.__database_session__.get_bind()}")
if "pytest" in sys.modules:
return ExcelFile("C:\\Users\lwark\Documents\python\submissions\mytests\\test_assets\RSL-AR-20240513-1.xlsx").sheet_names
return ExcelFile(BytesIO(self.template_file), engine="openpyxl").sheet_names
def set_template_file(self, filepath: Path | str):

34
src/submissions/backend/db/models/submissions.py
View File

@@ -6,7 +6,7 @@ import sys
import types
from copy import deepcopy
from getpass import getuser
import logging, uuid, tempfile, re, yaml, base64
import logging, uuid, tempfile, re, base64
from zipfile import ZipFile
from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
@@ -167,28 +167,24 @@ class BasicSubmission(BaseClass):
"""
# NOTE: Create defaults for all submission_types
parent_defs = super().get_default_info()
# NOTE: Singles tells the query which fields to set limit to 1
dicto = super().get_default_info()
recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
dicto = dict(
dicto.update(dict(
details_ignore=['excluded', 'reagents', 'samples',
'extraction_info', 'comment', 'barcode',
'platemap', 'export_map', 'equipment', 'tips', 'custom'],
# NOTE: Fields not placed in ui form
form_ignore=['reagents', 'ctx', 'id', 'cost', 'extraction_info', 'signed_by', 'comment', 'namer',
'submission_object', "tips", 'contact_phone', 'custom'] + recover,
'submission_object', "tips", 'contact_phone', 'custom', 'cost_centre'] + recover,
# NOTE: Fields not placed in ui form to be moved to pydantic
form_recover=recover
)
# NOTE: Singles tells the query which fields to set limit to 1
dicto['singles'] = parent_defs['singles']
))
# NOTE: Grab mode_sub_type specific info.
output = {}
for k, v in dicto.items():
if len(args) > 0 and k not in args:
# logger.debug(f"Don't want {k}")
continue
else:
output[k] = v
if args:
output = {k: v for k, v in dicto.items() if k in args}
else:
output = {k: v for k, v in dicto.items()}
if isinstance(submission_type, SubmissionType):
st = submission_type
else:
@@ -198,7 +194,7 @@ class BasicSubmission(BaseClass):
else:
output['submission_type'] = st.name
for k, v in st.defaults.items():
if len(args) > 0 and k not in args:
if args and k not in args:
# logger.debug(f"Don't want {k}")
continue
else:
@@ -272,6 +268,7 @@ class BasicSubmission(BaseClass):
field = self.__getattribute__(name)
except AttributeError:
return None
# assert isinstance(field, list)
for item in field:
if extra:
yield item.to_sub_dict(extra)
@@ -1137,9 +1134,9 @@ class BasicSubmission(BaseClass):
limit = 1
case _:
pass
if chronologic:
logger.debug("Attempting sort by date descending")
query = query.order_by(cls.submitted_date.desc())
# if chronologic:
# logger.debug("Attempting sort by date descending")
query = query.order_by(cls.submitted_date.desc())
if page_size is not None:
query = query.limit(page_size)
page = page - 1
@@ -2980,7 +2977,6 @@ class WastewaterArticAssociation(SubmissionSampleAssociation):
Returns:
dict: Updated dictionary with row, column and well updated
"""
sample = super().to_sub_dict()
sample['ct'] = self.ct
sample['source_plate'] = self.source_plate