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Large scale frontend refactor

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This commit is contained in:
Landon Wark
2023-11-14 11:16:54 -06:00
parent bf4149b1b3
commit da714c355d
26 changed files with 2682 additions and 2447 deletions
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6
src/submissions/backend/validators/__init__.py
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@@ -10,7 +10,7 @@ class RSLNamer(object):
"""
Object that will enforce proper formatting on RSL plate names.
"""
def __init__(self, instr:str, sub_type:str|None=None):
def __init__(self, instr:str, sub_type:str|None=None, data:dict|None=None):
self.submission_type = sub_type
if self.submission_type == None:
@@ -19,7 +19,7 @@ class RSLNamer(object):
if self.submission_type != None:
enforcer = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.parsed_name = self.retrieve_rsl_number(instr=instr, regex=enforcer.get_regex())
self.parsed_name = enforcer.enforce_name(instr=self.parsed_name)
self.parsed_name = enforcer.enforce_name(instr=self.parsed_name, data=data)
@classmethod
def retrieve_submission_type(cls, instr:str|Path) -> str:
@@ -58,7 +58,7 @@ class RSLNamer(object):
except UnboundLocalError:
check = True
if check:
from frontend.custom_widgets import SubmissionTypeSelector
from frontend.widgets import SubmissionTypeSelector
dlg = SubmissionTypeSelector(title="Couldn't parse submission type.", message="Please select submission type from list below.")
if dlg.exec():
submission_type = dlg.parse_form()

28
src/submissions/backend/validators/pydant.py
View File

@@ -11,7 +11,7 @@ from . import RSLNamer
from pathlib import Path
import re
import logging
from tools import check_not_nan, convert_nans_to_nones, jinja_template_loading
from tools import check_not_nan, convert_nans_to_nones, jinja_template_loading, Report, Result
from backend.db.models import *
from sqlalchemy.exc import StatementError
from PyQt6.QtWidgets import QComboBox, QWidget
@@ -86,8 +86,8 @@ class PydReagent(BaseModel):
else:
return values.data['type']
def toSQL(self) -> Tuple[Reagent, dict]:
result = None
def toSQL(self) -> Tuple[Reagent, Report]:
report = Report()
logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}")
# reagent = lookup_reagents(ctx=self.ctx, lot_number=self.lot)
reagent = Reagent.query(lot_number=self.lot)
@@ -113,10 +113,10 @@ class PydReagent(BaseModel):
reagent.name = value
# add end-of-life extension from reagent type to expiry date
# NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
return reagent, result
return reagent, report
def toForm(self, parent:QWidget, extraction_kit:str) -> QComboBox:
from frontend.custom_widgets.misc import ReagentFormWidget
from frontend.widgets.submission_widget import ReagentFormWidget
return ReagentFormWidget(parent=parent, reagent=self, extraction_kit=extraction_kit)
class PydSample(BaseModel, extra='allow'):
@@ -180,8 +180,9 @@ class PydSubmission(BaseModel, extra='allow'):
submission_type: dict|None
# For defaults
submitter_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)
submitted_date: dict|None
rsl_plate_num: dict|None = Field(default=dict(value=None, missing=True), validate_default=True)
# submitted_date: dict|None
submitting_lab: dict|None
sample_count: dict|None
extraction_kit: dict|None
@@ -243,7 +244,7 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("rsl_plate_num")
@classmethod
def rsl_from_file(cls, value, values):
logger.debug(f"RSL-plate initial value: {value['value']}")
logger.debug(f"RSL-plate initial value: {value['value']} and other values: {values.data}")
sub_type = values.data['submission_type']['value']
if check_not_nan(value['value']):
# if lookup_submissions(ctx=values.data['ctx'], rsl_number=value['value']) == None:
@@ -256,7 +257,7 @@ class PydSubmission(BaseModel, extra='allow'):
# return dict(value=output, missing=True)
return value
else:
output = RSLNamer(instr=values.data['filepath'].__str__(), sub_type=sub_type).parsed_name
output = RSLNamer(instr=values.data['filepath'].__str__(), sub_type=sub_type, data=values.data).parsed_name
return dict(value=output, missing=True)
@field_validator("technician", mode="before")
@@ -346,12 +347,11 @@ class PydSubmission(BaseModel, extra='allow'):
missing_reagents = [reagent for reagent in self.reagents if reagent.missing]
return missing_info, missing_reagents
def toSQL(self):
code = 0
msg = None
status = None
def toSQL(self) -> Tuple[BasicSubmission, Result]:
self.__dict__.update(self.model_extra)
instance, code, msg = BasicSubmission.query_or_create(submission_type=self.submission_type['value'], rsl_plate_num=self.rsl_plate_num['value'])
result = Result(msg=msg, code=code)
self.handle_duplicate_samples()
logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
for key, value in self.__dict__.items():
@@ -389,10 +389,10 @@ class PydSubmission(BaseModel, extra='allow'):
except AttributeError as e:
logger.debug(f"Something went wrong constructing instance {self.rsl_plate_num}: {e}")
logger.debug(f"Constructed submissions message: {msg}")
return instance, {'code':code, 'message':msg, 'status':"Information"}
return instance, result
def toForm(self, parent:QWidget):
from frontend.custom_widgets.misc import SubmissionFormWidget
from frontend.widgets.submission_widget import SubmissionFormWidget
return SubmissionFormWidget(parent=parent, **self.improved_dict())
def autofill_excel(self, missing_only:bool=True):