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Renaming ReagentType to ReagentRole

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This commit is contained in:
lwark
2024-06-07 14:15:19 -05:00
parent a355c5bb76
commit c7b6c90eac
8 changed files with 197 additions and 129 deletions
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6
src/submissions/frontend/widgets/gel_checker.py
View File

@@ -55,6 +55,9 @@ class GelBox(QDialog):
layout.addWidget(QLabel("DNA Core Submission Number"),0,1)
self.core_number = QLineEdit()
layout.addWidget(self.core_number, 0,2)
layout.addWidget(QLabel("Gel Barcode"),0,3)
self.gel_barcode = QLineEdit()
layout.addWidget(self.gel_barcode, 0, 4)
# setting this layout to the widget
# plot window goes on right side, spanning 3 rows
layout.addWidget(self.imv, 1, 1,20,20)
@@ -80,8 +83,9 @@ class GelBox(QDialog):
Tuple[str, str|Path, list]: output values
"""
dna_core_submission_number = self.core_number.text()
gel_barcode = self.gel_barcode.text()
values, comment = self.form.parse_form()
return dna_core_submission_number, self.img_path, values, comment
return dna_core_submission_number, gel_barcode, self.img_path, values, comment
class ControlsForm(QWidget):

64
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -9,12 +9,12 @@ from pathlib import Path
from . import select_open_file, select_save_file
import logging, difflib, inspect
from pathlib import Path
from tools import Report, Result, check_not_nan, workbook_2_csv
from tools import Report, Result, check_not_nan, workbook_2_csv, main_form_style
from backend.excel.parser import SheetParser
from backend.validators import PydSubmission, PydReagent
from backend.db import (
KitType, Organization, SubmissionType, Reagent,
ReagentRole, KitTypeReagentRoleAssociation
ReagentRole, KitTypeReagentRoleAssociation, BasicSubmission
)
from pprint import pformat
from .pop_ups import QuestionAsker, AlertPop
@@ -149,6 +149,8 @@ class SubmissionFormContainer(QWidget):
class SubmissionFormWidget(QWidget):
def __init__(self, parent: QWidget, submission: PydSubmission) -> None:
super().__init__(parent)
# self.report = Report()
@@ -169,15 +171,16 @@ class SubmissionFormWidget(QWidget):
except AttributeError:
logger.error(f"Couldn't get attribute from pyd: {k}")
value = dict(value=None, missing=True)
add_widget = self.create_widget(key=k, value=value, submission_type=self.pyd.submission_type['value'])
add_widget = self.create_widget(key=k, value=value, submission_type=self.pyd.submission_type['value'], sub_obj=st)
if add_widget != None:
self.layout.addWidget(add_widget)
if k == "extraction_kit":
add_widget.input.currentTextChanged.connect(self.scrape_reagents)
self.setStyleSheet(main_form_style)
self.scrape_reagents(self.pyd.extraction_kit)
def create_widget(self, key: str, value: dict | PydReagent, submission_type: str | None = None,
extraction_kit: str | None = None) -> "self.InfoItem":
extraction_kit: str | None = None, sub_obj:BasicSubmission|None=None) -> "self.InfoItem":
"""
Make an InfoItem widget to hold a field
@@ -197,13 +200,13 @@ class SubmissionFormWidget(QWidget):
else:
widget = None
case _:
widget = self.InfoItem(self, key=key, value=value, submission_type=submission_type)
widget = self.InfoItem(self, key=key, value=value, submission_type=submission_type, sub_obj=sub_obj)
return widget
return None
def scrape_reagents(self, *args, **kwargs): #extraction_kit:str, caller:str|None=None):
"""
Extracted scrape reagents function that will run when
Extracted scrape reagents function that will run when
form 'extraction_kit' widget is updated.
Args:
@@ -395,11 +398,11 @@ class SubmissionFormWidget(QWidget):
class InfoItem(QWidget):
def __init__(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None) -> None:
def __init__(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None, sub_obj:BasicSubmission|None=None) -> None:
super().__init__(parent)
layout = QVBoxLayout()
self.label = self.ParsedQLabel(key=key, value=value)
self.input: QWidget = self.set_widget(parent=self, key=key, value=value, submission_type=submission_type)
self.input: QWidget = self.set_widget(parent=self, key=key, value=value, submission_type=submission_type, sub_obj=sub_obj)
self.setObjectName(key)
try:
self.missing: bool = value['missing']
@@ -436,7 +439,7 @@ class SubmissionFormWidget(QWidget):
return None, None
return self.input.objectName(), dict(value=value, missing=self.missing)
def set_widget(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None) -> QWidget:
def set_widget(self, parent: QWidget, key: str, value: dict, submission_type: str | None = None, sub_obj:BasicSubmission|None=None) -> QWidget:
"""
Creates form widget
@@ -449,6 +452,8 @@ class SubmissionFormWidget(QWidget):
Returns:
QWidget: Form object
"""
if sub_obj is None:
sub_obj = SubmissionType.query(name=submission_type).get_submission_class()
try:
value = value['value']
except (TypeError, KeyError):
@@ -488,15 +493,15 @@ class SubmissionFormWidget(QWidget):
logger.error(f"Couldn't find {obj.prsr.sub['extraction_kit']}")
obj.ext_kit = uses[0]
add_widget.addItems(uses)
case 'submitted_date':
# NOTE: uses base calendar
add_widget = QDateEdit(calendarPopup=True)
# NOTE: sets submitted date based on date found in excel sheet
try:
add_widget.setDate(value)
# NOTE: if not found, use today
except:
add_widget.setDate(date.today())
# case 'submitted_date':
# # NOTE: uses base calendar
# add_widget = QDateEdit(calendarPopup=True)
# # NOTE: sets submitted date based on date found in excel sheet
# try:
# add_widget.setDate(value)
# # NOTE: if not found, use today
# except:
# add_widget.setDate(date.today())
case 'submission_category':
add_widget = QComboBox()
cats = ['Diagnostic', "Surveillance", "Research"]
@@ -507,13 +512,23 @@ class SubmissionFormWidget(QWidget):
cats.insert(0, cats.pop(cats.index(submission_type)))
add_widget.addItems(cats)
case _:
# NOTE: anything else gets added in as a line edit
add_widget = QLineEdit()
# logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
add_widget.setText(str(value).replace("_", " "))
if key in sub_obj.timestamps():
add_widget = QDateEdit(calendarPopup=True)
# NOTE: sets submitted date based on date found in excel sheet
try:
add_widget.setDate(value)
# NOTE: if not found, use today
except:
add_widget.setDate(date.today())
else:
# NOTE: anything else gets added in as a line edit
add_widget = QLineEdit()
# logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
add_widget.setText(str(value).replace("_", " "))
if add_widget is not None:
add_widget.setObjectName(key)
add_widget.setParent(parent)
# add_widget.setStyleSheet(main_form_style)
return add_widget
def update_missing(self):
@@ -569,6 +584,7 @@ class SubmissionFormWidget(QWidget):
self.label = self.ReagentParsedLabel(reagent=reagent)
layout.addWidget(self.label)
self.lot = self.ReagentLot(reagent=reagent, extraction_kit=extraction_kit)
# self.lot.setStyleSheet(main_form_style)
layout.addWidget(self.lot)
# NOTE: Remove spacing between reagents
layout.setContentsMargins(0, 0, 0, 0)
@@ -615,7 +631,7 @@ class SubmissionFormWidget(QWidget):
Set widget status to updated
"""
self.missing = True
self.label.updated(self.reagent.type)
self.label.updated(self.reagent.role)
class ReagentParsedLabel(QLabel):
@@ -692,4 +708,4 @@ class SubmissionFormWidget(QWidget):
# logger.debug(f"New relevant reagents: {relevant_reagents}")
self.setObjectName(f"lot_{reagent.role}")
self.addItems(relevant_reagents)
self.setStyleSheet("{ background-color: white }")
# self.setStyleSheet(main_form_style)