landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Updating AddEdit to hopefully include ReagentAdd

Browse Source
This commit is contained in:
lwark
2025-01-06 09:15:43 -06:00
parent b55258f677
commit 8662bbdc2f
9 changed files with 67 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
src/submissions/backend/db/models/kits.py
View File

@@ -608,7 +608,7 @@ class Reagent(BaseClass, LogMixin):
if isinstance(value, str):
field_value = datetime.strptime(value, "%Y-%m-%d")
elif isinstance(value, date):
field_value = datetime.combine(value, datetime.min.time())
field_value = datetime.combine(value, datetime.max.time())
else:
field_value = value
field_value.replace(tzinfo=timezone)

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

@@ -1502,6 +1502,25 @@ class Wastewater(BasicSubmission):
logger.error(f"Error handling couldn't get csv due to: {e}")
return input_dict
@classmethod
def parse_samples(cls, input_dict: dict) -> dict:
"""
Update sample dictionary with type specific information. Extends parent
Args:
input_dict (dict): Input sample dictionary
Returns:
dict: Updated sample dictionary
"""
input_dict = super().parse_samples(input_dict=input_dict)
# NOTE: Had to put in this section due to ENs not having rsl_number and therefore not getting PCR results.
check = check_key_or_attr("rsl_number", input_dict)
if not check:
input_dict['rsl_number'] = input_dict['submitter_id']
# logger.debug(pformat(input_dict, indent=4))
return input_dict
@classmethod
def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> Generator[dict, None, None]:
"""
@@ -1633,6 +1652,7 @@ class Wastewater(BasicSubmission):
self.save(original=False)
for sample in self.samples:
try:
# NOTE: Fix for ENs which have no rsl_number...
sample_dict = next(item for item in pcr_samples if item['sample'] == sample.rsl_number)
except StopIteration:
continue
@@ -2539,7 +2559,7 @@ class WastewaterSample(BasicSample):
Custom sample parser. Extends parent
Args:
input_dict (dict): Basic parser results.
input_dict (dict): Basic parser results for this sample.
Returns:
dict: Updated parser results.
@@ -2554,6 +2574,8 @@ class WastewaterSample(BasicSample):
output_dict['rsl_number'] = "RSL-WW-" + output_dict['ww_processing_num']
if output_dict['ww_full_sample_id'] is not None and output_dict["submitter_id"] in disallowed:
output_dict["submitter_id"] = output_dict['ww_full_sample_id']
check = check_key_or_attr("rsl_number", output_dict, check_none=True)
# logger.debug(pformat(output_dict, indent=4))
return output_dict
@classmethod

8
src/submissions/backend/validators/pydant.py
View File

@@ -144,7 +144,9 @@ class PydReagent(BaseModel):
case "expiry":
if isinstance(value, str):
value = date(year=1970, month=1, day=1)
value = datetime.combine(value, datetime.min.time())
# NOTE: if min time is used, any reagent set to expire today (Bac postive control, eg) will have expired at midnight and therefore be flagged.
# NOTE: Make expiry at date given, plus now time + 1 hour
value = datetime.combine(value, datetime.max.time())
reagent.expiry = value.replace(tzinfo=timezone)
case _:
try:
@@ -826,7 +828,7 @@ class PydSubmission(BaseModel, extra='allow'):
case item if item in instance.timestamps():
logger.warning(f"Incoming timestamp key: {item}, with value: {value}")
if isinstance(value, date):
value = datetime.combine(value, datetime.min.time())
value = datetime.combine(value, datetime.max.time())
value = value.replace(tzinfo=timezone)
elif isinstance(value, str):
value: datetime = datetime.strptime(value, "%Y-%m-%d")
@@ -961,7 +963,7 @@ class PydSubmission(BaseModel, extra='allow'):
if reagent not in exempt:
role_expiry = ReagentRole.query(name=reagent.role).eol_ext
try:
dt = datetime.combine(reagent.expiry, datetime.min.time())
dt = datetime.combine(reagent.expiry, datetime.max.time())
except TypeError:
continue
if datetime.now() > dt + role_expiry:

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

@@ -117,7 +117,7 @@ class App(QMainWindow):
connect menu and tool bar item to functions
"""
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.new_add_reagent)
self.joinExtractionAction.triggered.connect(self.table_widget.sub_wid.link_extractions)
self.joinPCRAction.triggered.connect(self.table_widget.sub_wid.link_pcr)
self.helpAction.triggered.connect(self.showAbout)

19
src/submissions/frontend/widgets/omni_add_edit.py
View File

@@ -1,3 +1,4 @@
from datetime import date
from typing import Any
from PyQt6.QtWidgets import (
@@ -12,7 +13,7 @@ logger = logging.getLogger(f"submissions.{__name__}")
class AddEdit(QDialog):
def __init__(self, parent, instance: Any):
def __init__(self, parent, instance: Any|None=None):
super().__init__(parent)
self.instance = instance
self.object_type = instance.__class__
@@ -22,13 +23,16 @@ class AddEdit(QDialog):
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
fields = {k: v for k, v in self.object_type.__dict__.items() if
isinstance(v, InstrumentedAttribute) and k != "id"}
# fields = {k: v for k, v in self.object_type.__dict__.items() if
# isinstance(v, InstrumentedAttribute) and k != "id"}
fields = {k: v for k, v in self.object_type.__dict__.items() if k != "id"}
for key, field in fields.items():
logger.debug(f"")
try:
widget = EditProperty(self, key=key, column_type=field.property.expression.type,
value=getattr(self.instance, key))
except AttributeError:
except AttributeError as e:
logger.error(f"Problem setting widget {key}: {e}")
continue
self.layout.addWidget(widget, self.layout.rowCount(), 0)
self.layout.addWidget(self.buttonBox)
@@ -62,14 +66,19 @@ class EditProperty(QWidget):
self.setObjectName(key)
match column_type:
case String():
if not value:
value = ""
self.widget = QLineEdit(self)
self.widget.setText(value)
case TIMESTAMP():
self.widget = QDateEdit(self)
self.widget = QDateEdit(self, calendarPopup=True)
if not value:
value = date.today()
self.widget.setDate(value)
case _:
logger.error(f"{column_type} not a supported type.")
self.widget = None
return
self.layout.addWidget(self.widget, 0, 1, 1, 3)
self.setLayout(self.layout)

10
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -19,6 +19,7 @@ from backend.db import (
from pprint import pformat
from .pop_ups import QuestionAsker, AlertPop
from .misc import AddReagentForm
from .omni_add_edit import AddEdit
from typing import List, Tuple
from datetime import date
@@ -139,6 +140,15 @@ class SubmissionFormContainer(QWidget):
self.layout().addWidget(self.form)
return report
def new_add_reagent(self):
instance = Reagent()
dlg = AddEdit(parent=self, instance=instance)
if dlg.exec():
obj = dlg.parse_form()
print(obj)
@report_result
def add_reagent(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
name: str | None = None, kit: str | KitType | None = None) -> Tuple[PydReagent, Report]:

5
src/submissions/tools/__init__.py
View File

@@ -449,7 +449,10 @@ class Settings(BaseSettings, extra="allow"):
def set_from_db(self):
if 'pytest' in sys.modules:
output = dict(power_users=['lwark', 'styson', 'ruwang'])
output = dict(power_users=['lwark', 'styson', 'ruwang'],
startup_scripts=dict(hello=None),
teardown_scripts=dict(goodbye=None)
)
else:
# print(f"Hello from database settings getter.")
# print(self.__dict__)