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Mid-progress adding controls to pydantic creation.

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This commit is contained in:
lwark
2024-11-21 08:46:41 -06:00
parent 506aac80c1
commit 7d1e6dc606
16 changed files with 224 additions and 187 deletions
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4
CHANGELOG.md
View File

@@ -1,3 +1,7 @@
## 202411.04
- Add reagent from scrape now limits roles to those found in kit to prevent confusion.
## 202411.01
- Code clean up.

2
TODO.md
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@@ -1,4 +1,4 @@
- [ ] Find a way to merge omni_search and sample_search
- [x] Find a way to merge omni_search and sample_search
- [x] Allow parsing of custom fields to a json 'custom' field in _basicsubmissions
- [x] Upgrade to generators when returning lists.
- [x] Revamp frontend.widgets.controls_chart to include visualizations?

40
src/submissions/backend/db/__init__.py
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@@ -1,8 +1,10 @@
"""
All database related operations.
"""
from sqlalchemy import event
import sqlalchemy.orm
from sqlalchemy import event, inspect
from sqlalchemy.engine import Engine
from tools import ctx
@@ -34,3 +36,39 @@ def set_sqlite_pragma(dbapi_connection, connection_record):
from .models import *
def update_log(mapper, connection, target):
logger.debug("\n\nBefore update\n\n")
state = inspect(target)
logger.debug(state)
update = dict(user=getuser(), time=datetime.now(), object=str(state.object), changes=[])
logger.debug(update)
for attr in state.attrs:
hist = attr.load_history()
if not hist.has_changes():
continue
added = [str(item) for item in hist.added]
deleted = [str(item) for item in hist.deleted]
change = dict(field=attr.key, added=added, deleted=deleted)
logger.debug(f"Adding: {pformat(change)}")
try:
update['changes'].append(change)
except Exception as e:
logger.error(f"Something went horribly wrong adding attr: {attr.key}: {e}")
continue
logger.debug(f"Adding to audit logs: {pformat(update)}")
if update['changes']:
# 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
table = AuditLog.__table__
logger.debug(f"Adding to {table}")
connection.execute(table.insert().values(**update))
# logger.debug("Here is where I would insert values, if I was able.")
else:
logger.info(f"No changes detected, not updating logs.")
# event.listen(LogMixin, 'after_update', update_log, propagate=True)
# event.listen(LogMixin, 'after_insert', update_log, propagate=True)

22
src/submissions/backend/db/models/__init__.py
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@@ -5,7 +5,7 @@ from __future__ import annotations
import sys, logging
import pandas as pd
from sqlalchemy import Column, INTEGER, String, JSON
from sqlalchemy import Column, INTEGER, String, JSON, event, inspect
from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session
from sqlalchemy.ext.declarative import declared_attr
from sqlalchemy.exc import ArgumentError
@@ -22,6 +22,12 @@ Base: DeclarativeMeta = declarative_base()
logger = logging.getLogger(f"submissions.{__name__}")
class LogMixin(Base):
__abstract__ = True
class BaseClass(Base):
"""
Abstract class to pass ctx values to all SQLAlchemy objects.
@@ -99,6 +105,15 @@ class BaseClass(Base):
singles = list(set(cls.singles + BaseClass.singles))
return dict(singles=singles)
@classmethod
def find_regular_subclass(cls, name: str | None = None):
if not name:
return cls
if " " in name:
search = name.title().replace(" ", "")
logger.debug(f"Searching for subclass: {search}")
return next((item for item in cls.__subclasses__() if item.__name__ == search), cls)
@classmethod
def fuzzy_search(cls, **kwargs):
query: Query = cls.__database_session__.query(cls)
@@ -175,9 +190,11 @@ class BaseClass(Base):
"""
# logger.debug(f"Saving object: {pformat(self.__dict__)}")
report = Report()
state = inspect(self)
try:
self.__database_session__.add(self)
self.__database_session__.commit()
return state
except Exception as e:
logger.critical(f"Problem saving object: {e}")
logger.error(f"Error message: {type(e)}")
@@ -186,6 +203,8 @@ class BaseClass(Base):
return report
class ConfigItem(BaseClass):
"""
Key:JSON objects to store config settings in database.
@@ -222,6 +241,7 @@ from .controls import *
from .organizations import *
from .kits import *
from .submissions import *
from .audit import AuditLog
# NOTE: Add a creator to the submission for reagent association. Assigned here due to circular import constraints.
# https://docs.sqlalchemy.org/en/20/orm/extensions/associationproxy.html#sqlalchemy.ext.associationproxy.association_proxy.params.creator

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

@@ -16,6 +16,7 @@ from typing import List, Literal, Tuple, Generator
from dateutil.parser import parse
from re import Pattern
logger = logging.getLogger(f"submissions.{__name__}")
@@ -429,6 +430,10 @@ class PCRControl(Control):
fig = PCRFigure(df=df, modes=[])
return report, fig
def to_pydantic(self):
from backend.validators import PydPCRControl
return PydPCRControl(**self.to_sub_dict())
class IridaControl(Control):
@@ -878,3 +883,7 @@ class IridaControl(Control):
exclude = [re.sub(rerun_regex, "", sample) for sample in sample_names if rerun_regex.search(sample)]
df = df[df.name not in exclude]
return df
def to_pydantic(self):
from backend.validators import PydIridaControl
return PydIridaControl(**self.__dict__)

5
src/submissions/backend/db/models/kits.py
View File

@@ -567,7 +567,7 @@ class Reagent(BaseClass):
return cls.execute_query(query=query, limit=limit)
@check_authorization
def edit_from_search(self, **kwargs):
def edit_from_search(self, obj, **kwargs):
from frontend.widgets.misc import AddReagentForm
role = ReagentRole.query(kwargs['role'])
if role:
@@ -1279,7 +1279,10 @@ class SubmissionReagentAssociation(BaseClass):
Returns:
str: Representation of this SubmissionReagentAssociation
"""
try:
return f"<{self.submission.rsl_plate_num} & {self.reagent.lot}>"
except AttributeError:
return f"<Unknown Submission & {self.reagent.lot}"
def __init__(self, reagent=None, submission=None):
if isinstance(reagent, list):

23
src/submissions/backend/db/models/submissions.py
View File

@@ -12,8 +12,8 @@ from zipfile import ZipFile
from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
from pprint import pformat
from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, LogMixin
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, event, inspect
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.orm.attributes import flag_modified
from sqlalchemy.ext.associationproxy import association_proxy
@@ -36,7 +36,7 @@ from PIL import Image
logger = logging.getLogger(f"submissions.{__name__}")
class BasicSubmission(BaseClass):
class BasicSubmission(BaseClass, LogMixin):
"""
Concrete of basic submission which polymorphs into BacterialCulture and Wastewater
"""
@@ -544,7 +544,7 @@ class BasicSubmission(BaseClass):
field_value = len(self.samples)
else:
field_value = value
case "ctx" | "csv" | "filepath" | "equipment":
case "ctx" | "csv" | "filepath" | "equipment" | "controls":
return
case item if item in self.jsons():
match key:
@@ -577,6 +577,9 @@ class BasicSubmission(BaseClass):
except AttributeError:
field_value = value
# NOTE: insert into field
current = self.__getattribute__(key)
if field_value and current != field_value:
logger.debug(f"Updated value: {key}: {current} to {field_value}")
try:
self.__setattr__(key, field_value)
except AttributeError as e:
@@ -1339,7 +1342,7 @@ class BasicSubmission(BaseClass):
# Below are the custom submission types
class BacterialCulture(BasicSubmission):
class BacterialCulture(BasicSubmission, LogMixin):
"""
derivative submission type from BasicSubmission
"""
@@ -1426,7 +1429,7 @@ class BacterialCulture(BasicSubmission):
return input_dict
class Wastewater(BasicSubmission):
class Wastewater(BasicSubmission, LogMixin):
"""
derivative submission type from BasicSubmission
"""
@@ -2189,6 +2192,8 @@ class BasicSample(BaseClass):
Base of basic sample which polymorphs into BCSample and WWSample
"""
searchables = ['submitter_id']
id = Column(INTEGER, primary_key=True) #: primary key
submitter_id = Column(String(64), nullable=False, unique=True) #: identification from submitter
sample_type = Column(String(32)) #: mode_sub_type of sample
@@ -2509,6 +2514,9 @@ class BasicSample(BaseClass):
if dlg.exec():
pass
def edit_from_search(self, obj, **kwargs):
self.show_details(obj)
# Below are the custom sample types
@@ -2516,6 +2524,9 @@ class WastewaterSample(BasicSample):
"""
Derivative wastewater sample
"""
searchables = BasicSample.searchables + ['ww_processing_num', 'ww_full_sample_id', 'rsl_number']
id = Column(INTEGER, ForeignKey('_basicsample.id'), primary_key=True)
ww_processing_num = Column(String(64)) #: wastewater processing number
ww_full_sample_id = Column(String(64)) #: full id given by entrics

2
src/submissions/backend/validators/__init__.py
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@@ -203,4 +203,4 @@ class RSLNamer(object):
from .pydant import PydSubmission, PydKit, PydContact, PydOrganization, PydSample, PydReagent, PydReagentRole, \
PydEquipment, PydEquipmentRole, PydTips
PydEquipment, PydEquipmentRole, PydTips, PydPCRControl, PydIridaControl

35
src/submissions/backend/validators/pydant.py
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@@ -786,9 +786,10 @@ class PydSubmission(BaseModel, extra='allow'):
"""
report = Report()
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'],
rsl_plate_num=self.rsl_plate_num['value'])
logger.debug(f"Result of query or create: {type(result)}")
logger.debug(f"Result of query or create: {instance}")
report.add_result(result)
self.handle_duplicate_samples()
# logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
@@ -830,7 +831,7 @@ class PydSubmission(BaseModel, extra='allow'):
equip, association = equip.toSQL(submission=instance)
if association is not None:
instance.submission_equipment_associations.append(association)
logger.debug(f"Equipment associations:\n\n{pformat(instance.submission_equipment_associations)}")
logger.debug(f"Equipment associations: {instance.submission_equipment_associations}")
case "tips":
for tips in self.tips:
if tips is None:
@@ -871,16 +872,18 @@ class PydSubmission(BaseModel, extra='allow'):
case _:
try:
instance.set_attribute(key=key, value=value)
# instance.update({key:value})
except AttributeError as e:
logger.error(f"Could not set attribute: {key} to {value} due to: \n\n {e}")
continue
except KeyError:
continue
print(f"\n\n{instance}\n\n")
try:
# logger.debug(f"Calculating costs for procedure...")
instance.calculate_base_cost()
except (TypeError, AttributeError) as e:
# logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using full plate cost.")
logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using 0.")
try:
instance.run_cost = instance.extraction_kit.cost_per_run
except AttributeError:
@@ -1104,3 +1107,29 @@ class PydEquipmentRole(BaseModel):
"""
from frontend.widgets.equipment_usage import RoleComboBox
return RoleComboBox(parent=parent, role=self, used=used)
class PydPCRControl(BaseModel):
name: str
subtype: str
target: str
ct: float
reagent_lot: str
submitted_date: datetime #: Date submitted to Robotics
submission_id: int
controltype_name: str
class PydIridaControl(BaseModel, extra='ignore'):
name: str
contains: list | dict #: unstructured hashes in contains.tsv for each organism
matches: list | dict #: unstructured hashes in matches.tsv for each organism
kraken: list | dict #: unstructured output from kraken_report
subtype: str #: EN-NOS, MCS-NOS, etc
refseq_version: str #: version of refseq used in fastq parsing
kraken2_version: str
kraken2_db_version: str
sample_id: int
submitted_date: datetime #: Date submitted to Robotics
submission_id: int
controltype_name: str

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

@@ -13,7 +13,7 @@ from PyQt6.QtGui import QAction
from pathlib import Path
from markdown import markdown
from __init__ import project_path
from backend import SubmissionType, Reagent
from backend import SubmissionType, Reagent, BasicSample
from tools import check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size
from .functions import select_save_file, select_open_file
from datetime import date
@@ -23,7 +23,7 @@ import logging, webbrowser, sys, shutil
from .submission_table import SubmissionsSheet
from .submission_widget import SubmissionFormContainer
from .controls_chart import ControlsViewer
from .sample_search import SampleSearchBox
# from .sample_search import SampleSearchBox
from .summary import Summary
from .omni_search import SearchBox
@@ -138,6 +138,7 @@ class App(QMainWindow):
self.yamlImportAction.triggered.connect(self.import_ST_yaml)
self.table_widget.pager.current_page.textChanged.connect(self.update_data)
self.editReagentAction.triggered.connect(self.edit_reagent)
self.destroyed.connect(self.final_commit)
def showAbout(self):
"""
@@ -186,7 +187,8 @@ class App(QMainWindow):
"""
Create a search for samples.
"""
dlg = SampleSearchBox(self)
# dlg = SampleSearchBox(self)
dlg = SearchBox(self, object_type=BasicSample, extras=[])
dlg.exec()
def backup_database(self):
@@ -251,6 +253,9 @@ class App(QMainWindow):
def update_data(self):
self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size)
def final_commit(self):
logger.debug("Running final commit")
self.ctx.database_session.commit()
class AddSubForm(QWidget):

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

@@ -28,7 +28,7 @@ class AddReagentForm(QDialog):
"""
def __init__(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
reagent_name: str | None = None) -> None:
reagent_name: str | None = None, kit: str | KitType | None = None) -> None:
super().__init__()
if reagent_name is None:
reagent_name = reagent_role
@@ -58,7 +58,15 @@ class AddReagentForm(QDialog):
self.exp_input.setDate(QDate(1970, 1, 1))
# NOTE: widget to get reagent type info
self.type_input = QComboBox()
self.type_input.setObjectName('type')
self.type_input.setObjectName('role')
if kit:
match kit:
case str():
kit = KitType.query(name=kit)
case _:
pass
self.type_input.addItems([item.name for item in ReagentRole.query() if kit in item.kit_types])
else:
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?

60
src/submissions/frontend/widgets/omni_search.py
View File

@@ -19,17 +19,24 @@ class SearchBox(QDialog):
def __init__(self, parent, object_type: Any, extras: List[str], **kwargs):
super().__init__(parent)
self.object_type = object_type
# options = ["Any"] + [cls.__name__ for cls in self.object_type.__subclasses__()]
# self.sub_class = QComboBox(self)
# self.sub_class.setObjectName("sub_class")
# self.sub_class.currentTextChanged.connect(self.update_widgets)
# self.sub_class.addItems(options)
# self.sub_class.setEditable(False)
self.object_type = self.original_type = object_type
self.extras = extras
self.context = kwargs
self.layout = QGridLayout(self)
self.setMinimumSize(600, 600)
# self.sub_class.setMinimumWidth(self.minimumWidth())
# self.layout.addWidget(self.sub_class, 0, 0)
self.results = SearchResults(parent=self, object_type=self.object_type, extras=extras, **kwargs)
options = ["Any"] + [cls.__name__ for cls in self.object_type.__subclasses__()]
if len(options) > 1:
self.sub_class = QComboBox(self)
self.sub_class.setObjectName("sub_class")
self.sub_class.addItems(options)
self.sub_class.currentTextChanged.connect(self.update_widgets)
self.sub_class.setEditable(False)
self.sub_class.setMinimumWidth(self.minimumWidth())
self.layout.addWidget(self.sub_class, 0, 0)
else:
self.sub_class = None
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.setLayout(self.layout)
self.setWindowTitle(f"Search {self.object_type.__name__}")
@@ -40,10 +47,23 @@ class SearchBox(QDialog):
"""
Changes form inputs based on sample type
"""
deletes = [item for item in self.findChildren(FieldSearch)]
# logger.debug(deletes)
for item in deletes:
item.setParent(None)
if not self.sub_class:
self.update_data()
else:
if self.sub_class.currentText() == "Any":
self.object_type = self.original_type
else:
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):
self.widget = FieldSearch(parent=self, label=searchable, field_name=searchable)
self.layout.addWidget(self.widget, 1, 0)
self.widget.search_widget.textChanged.connect(self.update_data)
widget = FieldSearch(parent=self, label=searchable, field_name=searchable)
widget.setObjectName(searchable)
self.layout.addWidget(widget, 1+iii, 0)
widget.search_widget.textChanged.connect(self.update_data)
self.update_data()
def parse_form(self) -> dict:
@@ -60,11 +80,11 @@ class SearchBox(QDialog):
"""
Shows dataframe of relevant samples.
"""
# logger.debug(f"Running update_data with sample type: {self.type}")
fields = self.parse_form()
# logger.debug(f"Got fields: {fields}")
sample_list_creator = self.object_type.fuzzy_search(**fields)
data = self.object_type.results_to_df(objects=sample_list_creator)
# Setting results moved to here from __init__ 202411118
self.results.setData(df=data)
@@ -108,7 +128,6 @@ class SearchResults(QTableView):
sets data in model
"""
self.data = df
print(self.data)
try:
self.columns_of_interest = [dict(name=item, column=self.data.columns.get_loc(item)) for item in self.extras]
except KeyError:
@@ -125,14 +144,15 @@ class SearchResults(QTableView):
def parse_row(self, x):
context = {item['name']: x.sibling(x.row(), item['column']).data() for item in self.columns_of_interest}
logger.debug(f"Context: {context}")
try:
object = self.object_type.query(**{self.object_type.search: context[self.object_type.search]})
# object = self.object_type.query(**{self.object_type.searchables: context[self.object_type.searchables]})
object = self.object_type.query(**context)
except KeyError:
object = None
try:
object.edit_from_search(**context)
except AttributeError:
pass
object.edit_from_search(obj=self.parent, **context)
except AttributeError as e:
logger.error(f"Error getting object function: {e}")
self.doubleClicked.disconnect()
self.parent.update_data()

128
src/submissions/frontend/widgets/sample_search.py
View File

@@ -1,128 +0,0 @@
'''
Search box that performs fuzzy search for samples
'''
from pprint import pformat
from typing import Tuple
from pandas import DataFrame
from PyQt6.QtCore import QSortFilterProxyModel
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QDialog,
QComboBox, QTableView, QWidget, QLineEdit, QGridLayout
)
from backend.db.models import BasicSample
from .submission_table import pandasModel
import logging
logger = logging.getLogger(f"submissions.{__name__}")
class SampleSearchBox(QDialog):
def __init__(self, parent):
super().__init__(parent)
self.layout = QGridLayout(self)
self.sample_type = QComboBox(self)
self.sample_type.setObjectName("sample_type")
self.sample_type.currentTextChanged.connect(self.update_widgets)
options = ["Any"] + [cls.__mapper_args__['polymorphic_identity'] for cls in BasicSample.__subclasses__()]
self.sample_type.addItems(options)
self.sample_type.setEditable(False)
self.setMinimumSize(600, 600)
self.sample_type.setMinimumWidth(self.minimumWidth())
self.layout.addWidget(self.sample_type, 0, 0)
self.results = SearchResults()
self.layout.addWidget(self.results, 5, 0)
self.setLayout(self.layout)
self.update_widgets()
self.update_data()
def update_widgets(self):
"""
Changes form inputs based on sample type
"""
deletes = [item for item in self.findChildren(FieldSearch)]
# logger.debug(deletes)
for item in deletes:
item.setParent(None)
if self.sample_type.currentText() == "Any":
self.type = BasicSample
else:
self.type = BasicSample.find_polymorphic_subclass(self.sample_type.currentText())
# logger.debug(f"Sample type: {self.type}")
searchables = self.type.get_searchables()
start_row = 1
for iii, item in enumerate(searchables):
widget = FieldSearch(parent=self, label=item['label'], field_name=item['field'])
self.layout.addWidget(widget, start_row+iii, 0)
widget.search_widget.textChanged.connect(self.update_data)
self.update_data()
def parse_form(self) -> dict:
"""
Converts form into dictionary.
Returns:
dict: Fields dictionary
"""
fields = [item.parse_form() for item in self.findChildren(FieldSearch)]
return {item[0]:item[1] for item in fields if item[1] is not None}
def update_data(self):
"""
Shows dataframe of relevant samples.
"""
# logger.debug(f"Running update_data with sample type: {self.type}")
fields = self.parse_form()
# logger.debug(f"Got fields: {fields}")
sample_list_creator = self.type.fuzzy_search(**fields)
data = self.type.samples_to_df(sample_list=sample_list_creator)
# logger.debug(f"Data: {data}")
self.results.setData(df=data)
class FieldSearch(QWidget):
def __init__(self, parent, label, field_name):
super().__init__(parent)
self.layout = QVBoxLayout(self)
label_widget = QLabel(label)
self.layout.addWidget(label_widget)
self.search_widget = QLineEdit()
self.search_widget.setObjectName(field_name)
self.layout.addWidget(self.search_widget)
self.setLayout(self.layout)
self.search_widget.returnPressed.connect(self.enter_pressed)
def enter_pressed(self):
"""
Triggered when enter is pressed on this input field.
"""
self.parent().update_data()
def parse_form(self) -> Tuple:
field_value = self.search_widget.text()
if field_value == "":
field_value = None
return self.search_widget.objectName(), field_value
class SearchResults(QTableView):
def __init__(self):
super().__init__()
self.doubleClicked.connect(lambda x: BasicSample.query(submitter_id=x.sibling(x.row(), 0).data()).show_details(self))
def setData(self, df:DataFrame) -> None:
"""
sets data in model
"""
self.data = df
try:
self.data['id'] = self.data['id'].apply(str)
self.data['id'] = self.data['id'].str.zfill(3)
except (TypeError, KeyError):
logger.error("Couldn't format id string.")
proxy_model = QSortFilterProxyModel()
proxy_model.setSourceModel(pandasModel(self.data))
self.setModel(proxy_model)

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

@@ -45,7 +45,8 @@ class SubmissionDetails(QDialog):
self.btn.clicked.connect(self.export)
self.back = QPushButton("Back")
self.back.setFixedWidth(100)
self.back.clicked.connect(self.back_function)
# self.back.clicked.connect(self.back_function)
self.back.clicked.connect(self.webview.back)
self.layout.addWidget(self.back, 0, 0, 1, 1)
self.layout.addWidget(self.btn, 0, 1, 1, 9)
self.layout.addWidget(self.webview, 1, 0, 10, 10)
@@ -63,8 +64,8 @@ class SubmissionDetails(QDialog):
self.reagent_details(reagent=sub)
self.webview.page().setWebChannel(self.channel)
def back_function(self):
self.webview.back()
# def back_function(self):
# self.webview.back()
def activate_export(self):
title = self.webview.title()
@@ -75,7 +76,11 @@ class SubmissionDetails(QDialog):
# logger.debug(f"Updating export plate to: {self.export_plate}")
else:
self.btn.setEnabled(False)
if title == self.webview.history().items()[0].title():
try:
check = self.webview.history().items()[0].title()
except IndexError as e:
check = title
if title == check:
# logger.debug("Disabling back button")
self.back.setEnabled(False)
else:
@@ -96,7 +101,7 @@ class SubmissionDetails(QDialog):
exclude = ['submissions', 'excluded', 'colour', 'tooltip']
base_dict['excluded'] = exclude
template = sample.get_details_template()
template_path = Path(self.template.environment.loader.__getattribute__("searchpath")[0])
template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
with open(template_path.joinpath("css", "styles.css"), "r") as f:
css = f.read()
html = template.render(sample=base_dict, css=css)

17
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -31,6 +31,7 @@ class MyQComboBox(QComboBox):
"""
Custom combobox that disables wheel events until focussed on.
"""
def __init__(self, scrollWidget=None, *args, **kwargs):
super(MyQComboBox, self).__init__(*args, **kwargs)
self.scrollWidget = scrollWidget
@@ -48,6 +49,7 @@ class MyQDateEdit(QDateEdit):
"""
Custom date editor that disables wheel events until focussed on.
"""
def __init__(self, scrollWidget=None, *args, **kwargs):
super(MyQDateEdit, self).__init__(*args, **kwargs)
self.scrollWidget = scrollWidget
@@ -150,7 +152,7 @@ class SubmissionFormContainer(QWidget):
@report_result
def add_reagent(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
name: str | None = None) -> Tuple[PydReagent, Report]:
name: str | None = None, kit: str | KitType | None = None) -> Tuple[PydReagent, Report]:
"""
Action to create new reagent in DB.
@@ -167,7 +169,8 @@ class SubmissionFormContainer(QWidget):
if isinstance(reagent_lot, bool):
reagent_lot = ""
# NOTE: create form
dlg = AddReagentForm(reagent_lot=reagent_lot, reagent_role=reagent_role, expiry=expiry, reagent_name=name)
dlg = AddReagentForm(reagent_lot=reagent_lot, reagent_role=reagent_role, expiry=expiry, reagent_name=name,
kit=kit)
if dlg.exec():
# NOTE: extract form info
info = dlg.parse_form()
@@ -228,7 +231,7 @@ class SubmissionFormWidget(QWidget):
# self.scrape_reagents(self.pyd.extraction_kit)
self.scrape_reagents(self.extraction_kit)
def create_widget(self, key: str, value: dict | PydReagent, submission_type: str | SubmissionType| None = None,
def create_widget(self, key: str, value: dict | PydReagent, submission_type: str | SubmissionType | None = None,
extraction_kit: str | None = None, sub_obj: BasicSubmission | None = None,
disable: bool = False) -> "self.InfoItem":
"""
@@ -506,7 +509,8 @@ 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 | SubmissionType | None = None,
def set_widget(self, parent: QWidget, key: str, value: dict,
submission_type: str | SubmissionType | None = None,
sub_obj: BasicSubmission | None = None) -> QWidget:
"""
Creates form widget
@@ -684,7 +688,9 @@ class SubmissionFormWidget(QWidget):
wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot,
reagent_role=self.reagent.role,
expiry=self.reagent.expiry,
name=self.reagent.name)
name=self.reagent.name,
kit=self.extraction_kit
)
return wanted_reagent, report
else:
# NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check
@@ -772,4 +778,3 @@ class SubmissionFormWidget(QWidget):
self.setObjectName(f"lot_{reagent.role}")
self.addItems(relevant_reagents)
self.setToolTip(f"Enter lot number for the reagent used for {reagent.role}")

8
src/submissions/tools/__init__.py
View File

@@ -13,6 +13,7 @@ from jinja2 import Environment, FileSystemLoader
from logging import handlers
from pathlib import Path
from sqlalchemy.orm import Session
from sqlalchemy.orm.state import InstanceState
from sqlalchemy import create_engine, text, MetaData
from pydantic import field_validator, BaseModel, Field
from pydantic_settings import BaseSettings, SettingsConfigDict
@@ -952,6 +953,10 @@ def report_result(func):
match output:
case Report():
report = output
# case InstanceState():
# for attr in output.attrs:
# print(f"{attr}: {attr.load_history()}")
# return
case tuple():
try:
report = [item for item in output if isinstance(item, Report)][0]
@@ -959,6 +964,7 @@ def report_result(func):
report = None
case _:
report = None
return report
logger.debug(f"Got report: {report}")
try:
results = report.results
@@ -982,3 +988,5 @@ def report_result(func):
# logger.debug(f"Returning true output: {true_output}")
return true_output
return wrapper