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Added ability to not import reagents on first import.

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This commit is contained in:
lwark
2024-12-11 15:04:26 -06:00
parent 51c419e470
commit b174eb1221
15 changed files with 209 additions and 27 deletions
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37
src/submissions/__main__.py
View File

@@ -1,17 +1,50 @@
import sys, os
from tools import ctx, setup_logger, check_if_app
from backend import scripts
# environment variable must be set to enable qtwebengine in network path
if check_if_app():
os.environ['QTWEBENGINE_DISABLE_SANDBOX'] = "1"
# setup custom logger
logger = setup_logger(verbosity=3)
# create settings object
from PyQt6.QtWidgets import QApplication
from frontend.widgets.app import App
def run_startup():
try:
startup_scripts = ctx.startup_scripts
except AttributeError as e:
logger.error(f"Couldn't get startup scripts due to {e}")
return
for script in startup_scripts:
try:
func = getattr(scripts, script)
except AttributeError as e:
logger.error(f"Couldn't run startup script {script} due to {e}")
continue
func(ctx)
def run_teardown():
try:
teardown_scripts = ctx.teardown_scripts
except AttributeError as e:
logger.error(f"Couldn't get teardown scripts due to {e}")
return
for script in teardown_scripts:
try:
func = getattr(scripts, script)
except AttributeError as e:
logger.error(f"Couldn't run teardown script {script} due to {e}")
continue
func(ctx)
if __name__ == '__main__':
run_startup()
app = QApplication(['', '--no-sandbox'])
ex = App(ctx=ctx)
sys.exit(app.exec())
app.exec()
sys.exit(run_teardown())

11
src/submissions/backend/db/__init__.py
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@@ -37,10 +37,11 @@ from .models import *
def update_log(mapper, connection, target):
logger.debug("\n\nBefore update\n\n")
# 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=[])
object_name = state.object.truncated_name()
update = dict(user=getuser(), time=datetime.now(), object=object_name, changes=[])
# logger.debug(update)
for attr in state.attrs:
hist = attr.load_history()
@@ -49,8 +50,10 @@ def update_log(mapper, connection, target):
if attr.key == "custom":
continue
added = [str(item) for item in hist.added]
if attr.key in ['submission_sample_associations', 'submission_reagent_associations']:
added = ['Numbers truncated for space purposes.']
if attr.key in ['artic_technician', 'submission_sample_associations', 'submission_reagent_associations',
'submission_equipment_associations', 'submission_tips_associations', 'contact_id', 'gel_info',
'gel_controls', 'source_plates']:
continue
deleted = [str(item) for item in hist.deleted]
change = dict(field=attr.key, added=added, deleted=deleted)
# logger.debug(f"Adding: {pformat(change)}")

10
src/submissions/backend/db/models/__init__.py
View File

@@ -25,6 +25,16 @@ logger = logging.getLogger(f"submissions.{__name__}")
class LogMixin(Base):
__abstract__ = True
def truncated_name(self):
name = str(self)
if len(name) > 64:
name = name.replace("<", "").replace(">", "")
if len(name) > 64:
name = name.replace("agent", "")
if len(name) > 64:
name = f"...{name[-61:]}"
return name
class BaseClass(Base):
"""

2
src/submissions/backend/db/models/controls.py
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@@ -539,7 +539,7 @@ class IridaControl(Control):
except AttributeError:
consolidate = False
report = Report()
logger.debug(f"settings: {pformat(chart_settings)}")
# logger.debug(f"settings: {pformat(chart_settings)}")
controls = cls.query(subtype=chart_settings['sub_type'], start_date=chart_settings['start_date'],
end_date=chart_settings['end_date'])
# logger.debug(f"Controls found: {controls}")

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

@@ -427,9 +427,10 @@ class Reagent(BaseClass, LogMixin):
def __repr__(self):
if self.name:
return f"<Reagent({self.name}-{self.lot})>"
name = f"<Reagent({self.name}-{self.lot})>"
else:
return f"<Reagent({self.role.name}-{self.lot})>"
name = f"<Reagent({self.role.name}-{self.lot})>"
return name
def to_sub_dict(self, extraction_kit: KitType = None, full_data: bool = False, **kwargs) -> dict:
"""
@@ -1347,7 +1348,7 @@ class SubmissionReagentAssociation(BaseClass):
return PydReagent(**self.to_sub_dict(extraction_kit=extraction_kit))
class Equipment(BaseClass):
class Equipment(BaseClass, LogMixin):
"""
A concrete instance of equipment
"""
@@ -1851,7 +1852,7 @@ class TipRole(BaseClass):
super().save()
class Tips(BaseClass):
class Tips(BaseClass, LogMixin):
"""
A concrete instance of tips.
"""

3
src/submissions/backend/db/models/submissions.py
View File

@@ -174,7 +174,8 @@ class BasicSubmission(BaseClass, LogMixin):
'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', 'cost_centre'] + recover,
'submission_object', "tips", 'contact_phone', 'custom', 'cost_centre', 'completed_date',
'controls'] + recover,
# NOTE: Fields not placed in ui form to be moved to pydantic
form_recover=recover
))

16
src/submissions/backend/excel/writer.py
View File

@@ -3,6 +3,7 @@ contains writer objects for pushing values to submission sheet templates.
"""
import logging
from copy import copy
from datetime import date
from operator import itemgetter
from pprint import pformat
from typing import List, Generator, Tuple
@@ -214,6 +215,10 @@ class ReagentWriter(object):
Returns:
List[dict]: merged dictionary
"""
filled_roles = [item['role'] for item in reagent_list]
for map_obj in reagent_map.keys():
if map_obj not in filled_roles:
reagent_list.append(dict(name="Not Applicable", role=map_obj, lot="Not Applicable", expiry="Not Applicable"))
for reagent in reagent_list:
try:
mp_info = reagent_map[reagent['role']]
@@ -268,6 +273,7 @@ class SampleWriter(object):
# NOTE: exclude any samples without a submission rank.
samples = [item for item in self.reconcile_map(sample_list) if item['submission_rank'] > 0]
self.samples = sorted(samples, key=itemgetter('submission_rank'))
self.blank_lookup_table()
def reconcile_map(self, sample_list: list) -> Generator[dict, None, None]:
"""
@@ -291,6 +297,16 @@ class SampleWriter(object):
new[k] = v
yield new
def blank_lookup_table(self):
"""
Blanks out columns in the lookup table to ensure help values are removed before writing.
"""
sheet = self.xl[self.sample_map['sheet']]
for row in range(self.sample_map['start_row'], self.sample_map['end_row'] + 1):
for column in self.sample_map['sample_columns'].values():
if sheet.cell(row, column).data_type != 'f':
sheet.cell(row=row, column=column, value="")
def write_samples(self) -> Workbook:
"""
Performs writing operations.

7
src/submissions/backend/scripts/__init__.py Normal file
View File

@@ -0,0 +1,7 @@
from .irida import import_irida
def hello(ctx):
print("\n\nHello!\n\n")
def goodbye(ctx):
print("\n\nGoodbye\n\n")

56
src/submissions/backend/scripts/irida.py Normal file
View File

@@ -0,0 +1,56 @@
import logging, sqlite3, json
from pprint import pformat, pprint
from datetime import datetime
from tools import Settings
from backend import BasicSample
from backend.db import IridaControl, ControlType
logger = logging.getLogger(f"submissions.{__name__}")
def import_irida(ctx:Settings):
"""
Grabs Irida controls from secondary database.
Args:
ctx (Settings): Settings inherited from app.
"""
ct = ControlType.query(name="Irida Control")
existing_controls = [item.name for item in IridaControl.query()]
prm_list = ", ".join([f"'{thing}'" for thing in existing_controls])
ctrl_db_path = ctx.directory_path.joinpath("submissions_parser_output", "submissions.db")
# print(f"Incoming settings: {pformat(ctx)}")
try:
conn = sqlite3.connect(ctrl_db_path)
except AttributeError as e:
print(f"Error, could not import from irida due to {e}")
return
sql = f"SELECT name, submitted_date, submission_id, contains, matches, kraken, subtype, refseq_version, " \
f"kraken2_version, kraken2_db_version, sample_id FROM _iridacontrol INNER JOIN _control on _control.id " \
f"= _iridacontrol.id WHERE _control.name NOT IN ({prm_list})"
cursor = conn.execute(sql)
records = [dict(name=row[0], submitted_date=row[1], submission_id=row[2], contains=row[3], matches=row[4], kraken=row[5],
subtype=row[6], refseq_version=row[7], kraken2_version=row[8], kraken2_db_version=row[9],
sample_id=row[10]) for row in cursor]
# incoming_controls = set(item['name'] for item in records)
# relevant = list(incoming_controls - existing_controls)
for record in records:
instance = IridaControl.query(name=record['name'])
if instance:
logger.warning(f"Irida Control {instance.name} already exists, skipping.")
continue
record['contains'] = json.loads(record['contains'])
assert isinstance(record['contains'], dict)
record['matches'] = json.loads(record['matches'])
assert isinstance(record['matches'], dict)
record['kraken'] = json.loads(record['kraken'])
assert isinstance(record['kraken'], dict)
record['submitted_date'] = datetime.strptime(record['submitted_date'], "%Y-%m-%d %H:%M:%S.%f")
assert isinstance(record['submitted_date'], datetime)
instance = IridaControl(controltype=ct, **record)
sample = BasicSample.query(submitter_id=instance.name)
if sample:
instance.sample = sample
instance.submission = sample.submissions[0]
# pprint(instance.__dict__)
instance.save()

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

@@ -27,7 +27,7 @@ from .turnaround import TurnaroundTime
from .omni_search import SearchBox
logger = logging.getLogger(f'submissions.{__name__}')
logger.info("Hello, I am a logger")
# logger.info("Hello, I am a logger")
class App(QMainWindow):

3
src/submissions/frontend/widgets/submission_details.py
View File

@@ -64,9 +64,6 @@ class SubmissionDetails(QDialog):
self.reagent_details(reagent=sub)
self.webview.page().setWebChannel(self.channel)
# def back_function(self):
# self.webview.back()
def activate_export(self):
title = self.webview.title()
self.setWindowTitle(title)

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

@@ -3,9 +3,9 @@ Contains all submission related frontend functions
'''
from PyQt6.QtWidgets import (
QWidget, QPushButton, QVBoxLayout,
QComboBox, QDateEdit, QLineEdit, QLabel
QComboBox, QDateEdit, QLineEdit, QLabel, QCheckBox, QBoxLayout, QHBoxLayout, QGridLayout
)
from PyQt6.QtCore import pyqtSignal, Qt
from PyQt6.QtCore import pyqtSignal, Qt, QSignalBlocker
from . import select_open_file, select_save_file
import logging
from pathlib import Path
@@ -228,9 +228,26 @@ class SubmissionFormWidget(QWidget):
# if k == "extraction_kit":
if k in self.__class__.update_reagent_fields:
add_widget.input.currentTextChanged.connect(self.scrape_reagents)
self.disabler = self.DisableReagents(self)
self.disabler.checkbox.setChecked(True)
self.layout.addWidget(self.disabler)
self.disabler.checkbox.checkStateChanged.connect(self.disable_reagents)
self.setStyleSheet(main_form_style)
self.scrape_reagents(self.extraction_kit)
def disable_reagents(self):
for reagent in self.findChildren(self.ReagentFormWidget):
# if self.disabler.checkbox.isChecked():
# # reagent.setVisible(True)
# # with QSignalBlocker(self.disabler.checkbox) as b:
# reagent.flip_check()
# else:
# # reagent.setVisible(False)
# # with QSignalBlocker(self.disabler.checkbox) as b:
# reagent.check.setChecked(False)
reagent.flip_check(self.disabler.checkbox.isChecked())
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":
@@ -350,8 +367,9 @@ class SubmissionFormWidget(QWidget):
report.add_result(result)
# logger.debug(f"Submission: {pformat(self.pyd)}")
# logger.debug("Checking kit integrity...")
_, result = self.pyd.check_kit_integrity()
report.add_result(result)
if self.disabler.checkbox.isChecked():
_, result = self.pyd.check_kit_integrity()
report.add_result(result)
if len(result.results) > 0:
return
# logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n")
@@ -665,11 +683,15 @@ class SubmissionFormWidget(QWidget):
self.app = self.parent().parent().parent().parent().parent().parent().parent().parent()
self.reagent = reagent
self.extraction_kit = extraction_kit
layout = QVBoxLayout()
layout = QGridLayout()
self.check = QCheckBox()
self.check.setChecked(True)
self.check.checkStateChanged.connect(self.disable)
layout.addWidget(self.check, 0, 0, 1, 1)
self.label = self.ReagentParsedLabel(reagent=reagent)
layout.addWidget(self.label)
layout.addWidget(self.label, 0, 1, 1, 9)
self.lot = self.ReagentLot(scrollWidget=parent, reagent=reagent, extraction_kit=extraction_kit)
layout.addWidget(self.lot)
layout.addWidget(self.lot, 1, 0, 1, 10)
# NOTE: Remove spacing between reagents
layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(layout)
@@ -678,6 +700,20 @@ class SubmissionFormWidget(QWidget):
# NOTE: If changed set self.missing to True and update self.label
self.lot.currentTextChanged.connect(self.updated)
def flip_check(self, checked:bool):
with QSignalBlocker(self.check) as b:
self.check.setChecked(checked)
self.lot.setEnabled(checked)
self.label.setEnabled(checked)
def disable(self):
self.lot.setEnabled(self.check.isChecked())
self.label.setEnabled(self.check.isChecked())
if not any([item.lot.isEnabled() for item in self.parent().findChildren(self.__class__)]):
self.parent().disabler.checkbox.setChecked(False)
else:
self.parent().disabler.checkbox.setChecked(True)
def parse_form(self) -> Tuple[PydReagent | None, Report]:
"""
Pulls form info into PydReagent
@@ -686,6 +722,8 @@ class SubmissionFormWidget(QWidget):
Tuple[PydReagent, dict]: PydReagent and Report(?)
"""
report = Report()
if not self.lot.isEnabled():
return None, report
lot = self.lot.currentText()
# logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
wanted_reagent = Reagent.query(lot=lot, role=self.reagent.role)
@@ -786,3 +824,15 @@ 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}")
class DisableReagents(QWidget):
def __init__(self, parent: QWidget):
super().__init__(parent)
self.app = self.parent().parent().parent().parent().parent().parent().parent().parent()
layout = QHBoxLayout()
self.label = QLabel("Import Reagents")
self.checkbox = QCheckBox()
layout.addWidget(self.label)
layout.addWidget(self.checkbox)
self.setLayout(layout)

4
src/submissions/templates/basicsubmission_details.html
View File

@@ -17,12 +17,12 @@
{% if sub['custom'] %}{% for key, value in sub['custom'].items() %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{{ value }}<br>
{% endfor %}{% endif %}</p>
{% if sub['reagents'] %}
<h3><u>Reagents:</u></h3>
<p>{% for item in sub['reagents'] %}
&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['role'] }}</b>: <a class="data-link reagent" id="{{ item['lot'] }}">{{ item['lot'] }} (EXP: {{ item['expiry'] }})</a><br>
{% endfor %}</p>
{% endif %}
{% if sub['equipment'] %}
<h3><u>Equipment:</u></h3>
<p>{% for item in sub['equipment'] %}

4
src/submissions/tools/__init__.py
View File

@@ -418,13 +418,13 @@ class Settings(BaseSettings, extra="allow"):
super().__init__(*args, **kwargs)
self.set_from_db()
pprint(f"User settings:\n{self.__dict__}")
# pprint(f"User settings:\n{self.__dict__}")
def set_from_db(self):
if 'pytest' in sys.modules:
output = dict(power_users=['lwark', 'styson', 'ruwang'])
else:
print(f"Hello from database settings getter.")
# print(f"Hello from database settings getter.")
# print(self.__dict__)
session = self.database_session
metadata = MetaData()