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Converted client manager to new Omni pydantic version.

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This commit is contained in:
lwark
2025-04-04 13:09:54 -05:00
parent 3a318fff38
commit ac85be6414
12 changed files with 255 additions and 954 deletions
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1
CHANGELOG.md
View File

@@ -1,5 +1,6 @@
# 202504.01
- Added in method to backup submissions to xlsx (partly).
- Added in checkbox to use all samples in Concentrations tab (very slow).
# 202503.05

2
TODO.md
View File

@@ -1,4 +1,4 @@
- [ ] Change "Manage Organizations" to the Pydantic version.
- [x] Change "Manage Organizations" to the Pydantic version.
- [x] Can my "to_dict", "to_sub_dict", "to_pydantic" methods be rewritten as properties?
- [ ] Stop displacing date on Irida controls and just do what Turnaround time does.
- [x] Get Manager window working for KitType, maybe SubmissionType

45
src/submissions/backend/db/models/__init__.py
View File

@@ -60,28 +60,26 @@ class BaseClass(Base):
try:
return f"<{self.__class__.__name__}({self.name})>"
except AttributeError:
return f"<{self.__class__.__name__}(Unknown)>"
# @classproperty
# def skip_on_edit(cls):
# if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
# return True
# else:
# return False
return f"<{self.__class__.__name__}(Name Unavailable)>"
@classproperty
def aliases(cls):
def aliases(cls) -> List[str]:
"""
List of other names this class might be known by.
Returns:
List[str]: List of names
"""
return [cls.query_alias]
# @classproperty
# def level(cls):
# if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
# return 2
# else:
# return 1
@classproperty
def query_alias(cls):
def query_alias(cls) -> str:
"""
What to query this class as.
Returns:
str: query name
"""
return cls.__name__.lower()
@classmethod
@@ -153,21 +151,23 @@ class BaseClass(Base):
return dict(singles=singles)
@classmethod
def find_regular_subclass(cls, name: str = "") -> Any:
def find_regular_subclass(cls, name: str|None = None) -> Any:
"""
Args:
name (str): name of subclass of interest.
Returns:
Any: Subclass of this object
Any: Subclass of this object.
"""
if name:
if " " in name:
search = name.title().replace(" ", "")
else:
search = name
return next((item for item in cls.__subclasses__() if item.__name__ == search), cls)
else:
return cls.__subclasses__()
@classmethod
def fuzzy_search(cls, **kwargs) -> List[Any]:
@@ -395,7 +395,8 @@ class BaseClass(Base):
if check:
logger.debug(f"Checking for subclass name.")
self_value = self_value.name
logger.debug(f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
logger.debug(
f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
if self_value != value:
output = False
logger.debug(f"Value {key} is False, returning.")

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

@@ -425,17 +425,23 @@ class IridaControl(Control):
kraken = self.kraken
except TypeError:
kraken = {}
try:
kraken_cnt_total = sum([item['kraken_count'] for item in kraken.values()])
except AttributeError:
kraken_cnt_total = 0
try:
new_kraken = [dict(name=key, kraken_count=value['kraken_count'],
kraken_percent=f"{value['kraken_count'] / kraken_cnt_total:0.2%}",
target=key in self.controltype.targets)
for key, value in kraken.items()]
new_kraken = sorted(new_kraken, key=itemgetter('kraken_count'), reverse=True)
new_kraken = sorted(new_kraken, key=itemgetter('kraken_count'), reverse=True)[0:10]
except (AttributeError, ZeroDivisionError):
new_kraken = []
output = dict(
name=self.name,
type=self.controltype.name,
targets=", ".join(self.targets),
kraken=new_kraken[0:10]
kraken=new_kraken
)
return output

49
src/submissions/backend/db/models/organizations.py
View File

@@ -10,7 +10,7 @@ from sqlalchemy.ext.hybrid import hybrid_property
from sqlalchemy.orm import relationship, Query
from . import Base, BaseClass
from tools import check_authorization, setup_lookup, yaml_regex_creator
from typing import List
from typing import List, Tuple
logger = logging.getLogger(f"submissions.{__name__}")
@@ -123,6 +123,20 @@ class Organization(BaseClass):
organ.contacts.append(cont)
organ.save()
def to_omni(self, expand: bool = False):
from backend.validators.omni_gui_objects import OmniOrganization
if self.cost_centre:
cost_centre = self.cost_centre
else:
cost_centre = "NA"
if self.name:
name = self.name
else:
name = "NA"
return OmniOrganization(instance_object=self,
name=name, cost_centre=cost_centre,
contact=[item.to_omni() for item in self.contacts])
class Contact(BaseClass):
"""
@@ -144,6 +158,20 @@ class Contact(BaseClass):
def searchables(cls):
return []
@classmethod
def query_or_create(cls, **kwargs) -> Tuple[Contact, bool]:
new = False
disallowed = []
sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
instance = cls.query(**sanitized_kwargs)
if not instance or isinstance(instance, list):
instance = cls()
new = True
for k, v in sanitized_kwargs.items():
setattr(instance, k, v)
logger.info(f"Instance from contact query or create: {instance}")
return instance, new
@classmethod
@setup_lookup
def query(cls,
@@ -195,3 +223,22 @@ class Contact(BaseClass):
def to_pydantic(self) -> "PydContact":
from backend.validators import PydContact
return PydContact(name=self.name, email=self.email, phone=self.phone)
def to_omni(self, expand: bool = False):
from backend.validators.omni_gui_objects import OmniContact
if self.email:
email = self.email
else:
email = "NA"
if self.name:
name = self.name
else:
name = "NA"
if self.phone:
phone = self.phone
else:
phone = "NA"
return OmniContact(instance_object=self,
name=name, email=email,
phone=phone)

150
src/submissions/backend/db/models/submissions.py
View File

@@ -3,6 +3,7 @@ Models for the main submission and sample types.
"""
from __future__ import annotations
import itertools
import pickle
from copy import deepcopy
from getpass import getuser
@@ -12,6 +13,8 @@ from zipfile import ZipFile, BadZipfile
from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
from pprint import pformat
from pandas import DataFrame
from sqlalchemy.ext.hybrid import hybrid_property
from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, LogMixin, SubmissionReagentAssociation
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func
@@ -287,6 +290,7 @@ class BasicSubmission(BaseClass, LogMixin):
Constructs dictionary used in submissions summary
Args:
expand (bool, optional): indicates if generators to be expanded. Defaults to False.
report (bool, optional): indicates if to be used for a report. Defaults to False.
full_data (bool, optional): indicates if sample dicts to be constructed. Defaults to False.
backup (bool, optional): passed to adjust_to_dict_samples. Defaults to False.
@@ -393,6 +397,33 @@ class BasicSubmission(BaseClass, LogMixin):
output["completed_date"] = self.completed_date
return output
@classmethod
def archive_submissions(cls, start_date: date | datetime | str | int | None = None,
end_date: date | datetime | str | int | None = None,
submissiontype: List[str] | None = None):
if submissiontype:
if isinstance(submissiontype, str):
submissiontype = [submissiontype]
query_out = []
for sub_type in submissiontype:
subs = cls.query(page_size=0, start_date=start_date, end_date=end_date, submissiontype=sub_type)
# logger.debug(f"Sub results: {subs}")
query_out.append(subs)
query_out = list(itertools.chain.from_iterable(query_out))
else:
query_out = cls.query(page_size=0, start_date=start_date, end_date=end_date)
records = []
for sub in query_out:
output = sub.to_dict(full_data=True)
for k, v in output.items():
if isinstance(v, types.GeneratorType):
output[k] = [item for item in v]
records.append(output)
df = DataFrame.from_records(records)
df.sort_values(by="id", inplace=True)
df.set_index("id", inplace=True)
return df
@property
def column_count(self) -> int:
"""
@@ -590,61 +621,18 @@ class BasicSubmission(BaseClass, LogMixin):
except AttributeError as e:
logger.error(f"Could not set {self} attribute {key} to {value} due to \n{e}")
# def update_subsampassoc(self, sample: BasicSample, input_dict: dict) -> SubmissionSampleAssociation:
# """
# Update a joined submission sample association.
#
# Args:
# sample (BasicSample): Associated sample.
# input_dict (dict): values to be updated
#
# Returns:
# SubmissionSampleAssociation: Updated association
# """
# try:
# logger.debug(f"Searching for sample {sample} at column {input_dict['column']} and row {input_dict['row']}")
# assoc = next((item for item in self.submission_sample_associations
# if item.sample == sample and
# item.row == input_dict['row'] and
# item.column == input_dict['column']))
# logger.debug(f"Found assoc {pformat(assoc.__dict__)}")
# except StopIteration:
# report = Report()
# report.add_result(
# Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
# return report
# for k, v in input_dict.items():
# try:
# # logger.debug(f"Setting assoc {assoc} with key {k} to value {v}")
# setattr(assoc, k, v)
# # NOTE: for some reason I don't think assoc.__setattr__(k, v) works here.
# except AttributeError:
# logger.error(f"Can't set {k} to {v}")
# return assoc
def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
"""
Update a joined submission sample association.
Args:
sample (BasicSample): Associated sample.
input_dict (dict): values to be updated
assoc (SubmissionSampleAssociation): Sample association to be updated.
input_dict (dict): updated values to insert.
Returns:
SubmissionSampleAssociation: Updated association
"""
# try:
# logger.debug(f"Searching for sample {sample} at column {input_dict['column']} and row {input_dict['row']}")
# assoc = next((item for item in self.submission_sample_associations
# if item.sample == sample and
# item.row == input_dict['row'] and
# item.column == input_dict['column']))
# logger.debug(f"Found assoc {pformat(assoc.__dict__)}")
# except StopIteration:
# report = Report()
# report.add_result(
# Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
# return report
# NOTE: No longer searches for association here, done in caller function
for k, v in input_dict.items():
try:
# logger.debug(f"Setting assoc {assoc} with key {k} to value {v}")
@@ -771,8 +759,8 @@ class BasicSubmission(BaseClass, LogMixin):
return regex
@classmethod
def find_polymorphic_subclass(cls, polymorphic_identity: str | SubmissionType | None = None,
attrs: dict | None = None) -> BasicSubmission:
def find_polymorphic_subclass(cls, polymorphic_identity: str | SubmissionType | list | None = None,
attrs: dict | None = None) -> BasicSubmission | List[BasicSubmission]:
"""
Find subclass based on polymorphic identity or relevant attributes.
@@ -795,6 +783,13 @@ class BasicSubmission(BaseClass, LogMixin):
except Exception as e:
logger.error(
f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, falling back to BasicSubmission")
case list():
output = []
for identity in polymorphic_identity:
if isinstance(identity, SubmissionType):
identity = polymorphic_identity.name
output.append(cls.__mapper__.polymorphic_map[identity].class_)
return output
case _:
pass
if attrs and any([not hasattr(cls, attr) for attr in attrs.keys()]):
@@ -1855,18 +1850,6 @@ class Wastewater(BasicSubmission):
result = assoc.save()
if result:
report.add_result(result)
# for sample in self.samples:
# logger.debug(f"Checking pcr_samples for {sample.rsl_number}, {sample.ww_full_sample_id}")
# 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)
# logger.debug(f"Found sample {sample_dict} at index {pcr_samples.index(sample_dict)}: {pcr_samples[pcr_samples.index(sample_dict)]}")
# except StopIteration:
# logger.error(f"Couldn't find {sample} in the Parser samples")
# continue
# assoc = self.update_subsampassoc(sample=sample, input_dict=sample_dict)
# result = assoc.save()
# report.add_result(result)
controltype = ControlType.query(name="PCR Control")
submitted_date = datetime.strptime(" ".join(parser.pcr_info['run_start_date/time'].split(" ")[:-1]),
"%Y-%m-%d %I:%M:%S %p")
@@ -1880,35 +1863,6 @@ class Wastewater(BasicSubmission):
new_control.save()
return report
# def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
# """
# Updates a joined submission sample association by assigning ct values to n1 or n2 based on alphabetical sorting.
#
# Args:
# sample (BasicSample): Associated sample.
# input_dict (dict): values to be updated
#
# Returns:
# SubmissionSampleAssociation: Updated association
# """
# # logger.debug(f"Input dict: {pformat(input_dict)}")
# #
# assoc = super().update_subsampassoc(assoc=assoc, input_dict=input_dict)
# # targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
# # assert 0 < len(targets) <= 2
# # for k, v in targets.items():
# # # logger.debug(f"Setting sample {sample} with key {k} to value {v}")
# # # update_key = f"ct_n{i}"
# # current_value = getattr(assoc, k)
# # logger.debug(f"Current value came back as: {current_value}")
# # if current_value is None:
# # setattr(assoc, k, v)
# # else:
# # logger.debug(f"Have a value already, {current_value}... skipping.")
# if assoc.column == 3:
# logger.debug(f"Final association for association {assoc}:\n{pformat(assoc.__dict__)}")
# return assoc
class WastewaterArtic(BasicSubmission):
"""
@@ -2196,14 +2150,14 @@ class WastewaterArtic(BasicSubmission):
# logger.debug(processed)
# NOTE: Remove brackets at end
processed = re.sub(r"\(.*\)$", "", processed).strip()
logger.debug(processed)
# logger.debug(processed)
processed = re.sub(r"-RPT", "", processed, flags=re.IGNORECASE)
# NOTE: Remove any non-R letters at end.
processed = re.sub(r"[A-QS-Z]+\d*", "", processed)
logger.debug(processed)
# logger.debug(processed)
# NOTE: Remove trailing '-' if any
processed = processed.strip("-")
logger.debug(processed)
# logger.debug(processed)
try:
plate_num = re.search(r"\-\d{1}R?\d?$", processed).group()
processed = rreplace(processed, plate_num, "")
@@ -2221,20 +2175,20 @@ class WastewaterArtic(BasicSubmission):
plate_num = re.sub(r"R", rf"R{repeat_num}", plate_num)
except AttributeError:
logger.error(f"Problem re-evaluating plate number for {processed}")
logger.debug(processed)
# logger.debug(processed)
# NOTE: Remove any redundant -digits
processed = re.sub(r"-\d$", "", processed)
logger.debug(processed)
# logger.debug(processed)
day = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, day, "")
logger.debug(processed)
# logger.debug(processed)
month = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, month, "")
processed = processed.replace("--", "")
logger.debug(processed)
# logger.debug(processed)
year = re.search(r'^(?:\d{2})?\d{2}', processed).group()
year = f"20{year}"
logger.debug(processed)
# logger.debug(processed)
final_en_name = f"PBS{year}{month}{day}-{plate_num}"
return final_en_name
@@ -2881,7 +2835,7 @@ class BacterialCultureSample(BasicSample):
sample['organism'] = self.organism
try:
sample['concentration'] = f"{float(self.concentration):.2f}"
except TypeError:
except (TypeError, ValueError):
sample['concentration'] = 0.0
if self.control is not None:
sample['colour'] = [0, 128, 0]

54
src/submissions/backend/validators/omni_gui_objects.py
View File

@@ -593,3 +593,57 @@ class OmniKitType(BaseOmni):
for item in kit.kit_reagentrole_associations:
logger.debug(f"KTRRassoc: {item.__dict__}")
return kit
class OmniOrganization(BaseOmni):
class_object: ClassVar[Any] = Organization
name: str = Field(default="", description="property")
cost_centre: str = Field(default="", description="property")
# TODO: add in List[OmniContacts]
contact: List[str] | List[OmniContact] = Field(default=[], description="relationship", title="Contact")
def __init__(self, instance_object: Any, **data):
logger.debug(f"Incoming data: {data}")
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
return dict(
name=self.name,
cost_centre=self.cost_centre,
contacts=self.contact
)
class OmniContact(BaseOmni):
class_object: ClassVar[Any] = Contact
name: str = Field(default="", description="property")
email: str = Field(default="", description="property")
phone: str = Field(default="", description="property")
@property
def list_searchables(self):
return dict(name=self.name, email=self.email)
def __init__(self, instance_object: Any, **data):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
return dict(
name=self.name,
email=self.email,
phone=self.phone
)
def to_sql(self):
contact, is_new = Contact.query_or_create(name=self.name, email=self.email, phone=self.phone)
if is_new:
logger.debug(f"New contact made: {contact}")
else:
logger.debug(f"Contact retrieved: {contact}")
return contact

77
src/submissions/frontend/widgets/app.py
View File

@@ -9,17 +9,19 @@ from PyQt6.QtWidgets import (
QHBoxLayout, QScrollArea, QMainWindow,
QToolBar
)
# import pickle
from PyQt6.QtGui import QAction
from pathlib import Path
from markdown import markdown
from pandas import ExcelWriter
from __init__ import project_path
from backend import SubmissionType, Reagent, BasicSample, Organization, KitType
from backend import SubmissionType, Reagent, BasicSample, Organization, KitType, BasicSubmission
from tools import (
check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user, under_development
check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user,
under_development
)
from .functions import select_save_file, select_open_file
from .pop_ups import HTMLPop, AlertPop
from .date_type_picker import DateTypePicker
from .functions import select_save_file
from .pop_ups import HTMLPop
from .misc import Pagifier
from .submission_table import SubmissionsSheet
from .submission_widget import SubmissionFormContainer
@@ -80,7 +82,7 @@ class App(QMainWindow):
helpMenu.addAction(self.docsAction)
helpMenu.addAction(self.githubAction)
fileMenu.addAction(self.importAction)
# fileMenu.addAction(self.yamlExportAction)
fileMenu.addAction(self.archiveSubmissionsAction)
# fileMenu.addAction(self.yamlImportAction)
methodsMenu.addAction(self.searchSample)
maintenanceMenu.addAction(self.joinExtractionAction)
@@ -112,8 +114,7 @@ class App(QMainWindow):
self.docsAction = QAction("&Docs", self)
self.searchSample = QAction("Search Sample", self)
self.githubAction = QAction("Github", self)
# self.yamlExportAction = QAction("Export Type Example", self)
# self.yamlImportAction = QAction("Import Type Template", self)
self.archiveSubmissionsAction = QAction("Submissions to Excel", self)
self.editReagentAction = QAction("Edit Reagent", self)
self.manageOrgsAction = QAction("Manage Clients", self)
self.manageKitsAction = QAction("Manage Kits", self)
@@ -130,8 +131,7 @@ class App(QMainWindow):
self.docsAction.triggered.connect(self.openDocs)
self.searchSample.triggered.connect(self.runSampleSearch)
self.githubAction.triggered.connect(self.openGithub)
# self.yamlExportAction.triggered.connect(self.export_ST_yaml)
# self.yamlImportAction.triggered.connect(self.import_ST_yaml)
self.archiveSubmissionsAction.triggered.connect(self.submissions_to_excel)
self.table_widget.pager.current_page.textChanged.connect(self.update_data)
self.editReagentAction.triggered.connect(self.edit_reagent)
self.manageOrgsAction.triggered.connect(self.manage_orgs)
@@ -186,60 +186,18 @@ class App(QMainWindow):
dlg = SearchBox(parent=self, object_type=Reagent, extras=[dict(name='Role', field="role")])
dlg.exec()
# def export_ST_yaml(self):
# """
# Copies submission type yaml to file system for editing and remport
#
# Returns:
# None
# """
# if check_if_app():
# yaml_path = Path(sys._MEIPASS).joinpath("files", "resources", "viral_culture.yml")
# else:
# yaml_path = project_path.joinpath("src", "submissions", "resources", "viral_culture.yml")
# fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml")
# shutil.copyfile(yaml_path, fname)
# @check_authorization
# def import_ST_yaml(self, *args, **kwargs):
# """
# Imports a yml form into a submission type.
#
# Args:
# *args ():
# **kwargs ():
#
# Returns:
#
# """
# fname = select_open_file(obj=self, file_extension="yml")
# if not fname:
# logger.info(f"Import cancelled.")
# return
# ap = AlertPop(message="This function will proceed in the debug window.", status="Warning", owner=self)
# ap.exec()
# st = SubmissionType.import_from_json(filepath=fname)
# if st:
# # NOTE: Do not delete the print statement below.
# choice = input("Save the above submission type? [y/N]: ")
# if choice.lower() == "y":
# pass
# else:
# logger.warning("Save of submission type cancelled.")
def update_data(self):
self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size)
# TODO: Change this to the Pydantic version.
def manage_orgs(self):
from frontend.widgets.omni_manager_pydant import ManagerWindow as ManagerWindowPyd
dlg = ManagerWindow(parent=self, object_type=Organization, extras=[], add_edit='edit', managers=set())
# dlg = ManagerWindow(parent=self, object_type=Organization, extras=[], add_edit='edit', managers=set())
dlg = ManagerWindowPyd(parent=self, object_type=Organization, extras=[], add_edit='edit', managers=set())
if dlg.exec():
new_org = dlg.parse_form()
new_org.save()
# logger.debug(new_org.__dict__)
@under_development
def manage_kits(self, *args, **kwargs):
from frontend.widgets.omni_manager_pydant import ManagerWindow as ManagerWindowPyd
dlg = ManagerWindowPyd(parent=self, object_type=KitType, extras=[], add_edit='edit', managers=set())
@@ -252,6 +210,17 @@ class App(QMainWindow):
assert isinstance(sql, KitType)
sql.save()
@under_development
def submissions_to_excel(self, *args, **kwargs):
dlg = DateTypePicker(self)
if dlg.exec():
output = dlg.parse_form()
df = BasicSubmission.archive_submissions(**output)
filepath = select_save_file(self, f"Submissions {output['start_date']}-{output['end_date']}", "xlsx")
writer = ExcelWriter(filepath, "openpyxl")
df.to_excel(writer)
writer.close()
class AddSubForm(QWidget):

36
src/submissions/frontend/widgets/date_type_picker.py Normal file
View File

@@ -0,0 +1,36 @@
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QDialog,
QDialogButtonBox, QMessageBox, QComboBox
)
from .misc import CheckableComboBox, StartEndDatePicker
from backend.db import SubmissionType
class DateTypePicker(QDialog):
def __init__(self, parent):
super().__init__(parent)
self.layout = QVBoxLayout()
self.setFixedWidth(500)
self.typepicker = CheckableComboBox(parent=self)
self.typepicker.setEditable(False)
self.typepicker.addItem("Select", header=True)
for org in [org.name for org in SubmissionType.query()]:
self.typepicker.addItem(org)
self.datepicker = StartEndDatePicker(-180)
self.layout.addWidget(self.typepicker)
self.layout.addWidget(self.datepicker)
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
def parse_form(self):
sub_types = [self.typepicker.itemText(i) for i in range(self.typepicker.count()) if self.typepicker.itemChecked(i)]
start_date = self.datepicker.start_date.date().toPyDate()
end_date = self.datepicker.end_date.date().toPyDate()
return dict(submissiontype=sub_types, start_date=start_date, end_date=end_date)

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

@@ -269,6 +269,7 @@ class EditRelationship(QWidget):
from backend.db import models
super().__init__(parent)
self.class_object = getattr(models, class_object)
logger.debug(f"Attempt value: {value}")
# logger.debug(f"Class object: {self.class_object}")
self.setParent(parent)
# logger.debug(f"Edit relationship class_object: {self.class_object}")
@@ -388,7 +389,7 @@ class EditRelationship(QWidget):
"""
sets data in model
"""
# logger.debug(f"Self.data: {self.data}")
logger.debug(f"Self.data: {self.data}")
try:
records = [item.to_dataframe_dict() for item in self.data]
except AttributeError:

429
src/submissions/resources/viral_culture.json
View File

@@ -1,429 +0,0 @@
{
"name": "Viral Culture",
"defaults": {
"abbreviation": "VE",
"details_ignore": [
],
"form_ignore": [
"cost_centre"
],
"regex": "(?P<Viral_Culture>RSL(?:-|_)?VE(?:-|_)?20\\d{2}-?\\d{2}-?\\d{2}(?:(_|-)?\\d?([^_0123456789\\sA-QS-Z]|$)?R?\\d?)?)",
"sample_type": "Basic Sample"
},
"info": {
"comment": {
"read": [
{
"column": 2,
"row": 34,
"sheet": "Sample List"
}
],
"write": []
},
"contact": {
"read": [
{
"column": 2,
"row": 4,
"sheet": "Sample List"
}
],
"write": []
},
"contact_phone": {
"read": [],
"write": [
{
"column": 2,
"row": 5,
"sheet": "Sample List"
}
]
},
"cost_centre": {
"read": [
{
"column": 2,
"row": 6,
"sheet": "Sample List"
}
],
"write": []
},
"custom": {},
"extraction_kit": {
"read": [
{
"column": 4,
"row": 5,
"sheet": "Sample List"
}
],
"write": []
},
"rsl_plate_num": {
"read": [
{
"column": 2,
"row": 13,
"sheet": "Sample List"
}
],
"write": []
},
"sample_count": {
"read": [
{
"column": 4,
"row": 4,
"sheet": "Sample List"
}
],
"write": []
},
"signed_by": {
"read": [],
"write": [
{
"column": 2,
"row": 15,
"sheet": "Sample List"
}
]
},
"submission_category": {
"read": [
{
"column": 4,
"row": 6,
"sheet": "Sample List"
}
],
"write": []
},
"submission_type": {
"read": [
{
"column": 4,
"row": 3,
"sheet": "Sample List"
}
],
"write": []
},
"submitted_date": {
"read": [
{
"column": 2,
"row": 3,
"sheet": "Sample List"
}
],
"write": []
},
"submitter_plate_num": {
"read": [
{
"column": 2,
"row": 2,
"sheet": "Sample List"
}
],
"write": []
},
"submitting_lab": {
"read": [
{
"column": 4,
"row": 2,
"sheet": "Sample List"
}
],
"write": []
},
"technician": {
"read": [
{
"column": 2,
"row": 14,
"sheet": "Sample List"
}
],
"write": []
}
},
"samples": {
"lookup_table": {
"end_row": 132,
"merge_on_id": "submitter_id",
"sample_columns": {
"column": 6,
"concentration": 4,
"organism": 3,
"row": 5,
"submitter_id": 2
},
"sheet": "Sample List",
"start_row": 37
},
"plate_map": {
"end_column": 13,
"end_row": 14,
"sheet": "Plate Map",
"start_column": 2,
"start_row": 7
}
},
"kits": [
{
"constant_cost": 0.00,
"mutable_cost_column": 0.00,
"mutable_cost_sample": 0.00,
"kit_type": {
"name": "MagMAX-96 Viral RNA Isolation Kit",
"reagent roles": [
{
"expiry": {
"column": 4,
"row": 19
},
"lot": {
"column": 3,
"row": 19
},
"name": {
"column": 2,
"row": 19
},
"sheet": "Sample List",
"required": 1,
"role": "Wash Solution 1 (MagMAX-96 Viral)",
"extension_of_life": 0
},
{
"expiry": {
"column": 4,
"row": 20
},
"lot": {
"column": 3,
"row": 20
},
"name": {
"column": 2,
"row": 20
},
"sheet": "Sample List",
"required": 1,
"role": "Wash Solution 2 (MagMAX-96 Viral)",
"extension_of_life": 0
},
{
"expiry": {
"column": 4,
"row": 21
},
"lot": {
"column": 3,
"row": 21
},
"name": {
"column": 2,
"row": 21
},
"sheet": "Sample List",
"required": 1,
"role": "Lysis/Binding Solution (MagMAX-96 Viral)",
"extension_of_life": 0
},
{
"expiry": {
"column": 4,
"row": 22
},
"lot": {
"column": 3,
"row": 22
},
"name": {
"column": 2,
"row": 22
},
"sheet": "Sample List",
"required": 1,
"role": "RNA Binding Beads (MagMAX-96 Viral)",
"extension_of_life": 0
},
{
"expiry": {
"column": 4,
"row": 23
},
"lot": {
"column": 3,
"row": 23
},
"name": {
"column": 2,
"row": 23
},
"sheet": "Sample List",
"required": 1,
"role": "Lysis/Binding Enhancer (MagMAX-96 Viral)",
"extension_of_life": 0
},
{
"expiry": {
"column": 4,
"row": 24
},
"lot": {
"column": 3,
"row": 24
},
"name": {
"column": 2,
"row": 24
},
"sheet": "Sample List",
"required": 0,
"role": "Bacterial-Lysis Buffer",
"extension_of_life": 0
},
{
"expiry": {
"column": 4,
"row": 25
},
"lot": {
"column": 3,
"row": 25
},
"name": {
"column": 2,
"row": 25
},
"sheet": "Sample List",
"required": 1,
"role": "Elution Buffer (MagMAX-96 Viral)",
"extension_of_life": 0
},
{
"expiry": {
"column": 4,
"row": 30
},
"lot": {
"column": 3,
"row": 30
},
"name": {
"column": 2,
"row": 30
},
"sheet": "Sample List",
"required": 0,
"role": "Bacterial-Positive Control",
"extension_of_life": 0
},
{
"expiry": {
"column": 4,
"row": 31
},
"lot": {
"column": 3,
"row": 31
},
"name": {
"column": 2,
"row": 31
},
"sheet": "Sample List",
"required": 1,
"role": "Bead Plate",
"extension_of_life": 0
},
{
"expiry": {
"column": 4,
"row": 28
},
"lot": {
"column": 3,
"row": 28
},
"name": {
"column": 2,
"row": 28
},
"sheet": "Sample List",
"required": 1,
"role": "Isopropanol",
"extension_of_life": 0
},
{
"expiry": {
"column": 4,
"row": 29
},
"lot": {
"column": 3,
"row": 29
},
"name": {
"column": 2,
"row": 29
},
"sheet": "Sample List",
"required": 1,
"role": "Ethanol",
"extension_of_life": 0
},
{
"expiry": {
"column": 4,
"row": 32
},
"lot": {
"column": 3,
"row": 32
},
"name": {
"column": 2,
"row": 32
},
"sheet": "Sample List",
"required": 1,
"role": "Carrier RNA",
"extension_of_life": 0
}
],
"equipment roles": [
{
"static": 0,
"role": "Extractor",
"processes": [
"OBT_M4029_KFF_v1.0"
]
},
{
"static": 1,
"role": "Momentum - Extraction",
"processes": [
"Omega_MagBind_Universal_VarCol"
]
},
{
"static": 1,
"role": "Liquid Handler",
"processes": [
"Bacterial_Core_Submission"
]
}
]
}
}
]
}

339
src/submissions/resources/viral_culture.yml
View File

@@ -1,339 +0,0 @@
name: &NAME Viral Culture
# The defaults section helps us with some parsing and writing functions
defaults:
# The abbreviation gets put in the RSL-{abbreviation}-20XXXXXX-1 plate name
abbreviation: &ABBREV VE
# Details ignore tells us what to leave out of the details view.
# For basic submissions this is typically and empty list or '[]'
# To add entries, remove [] and add list entries preceded by dashes (see 'form_ignore' as an example)
details_ignore: []
# Form ignore tells us what to leave out of the form created when importing the submission.
# It is in list format. Each entry is preceded by a dash.
form_ignore:
- cost_centre
sample_type: Basic Sample
# The regex is used to identify a submission type by its file name, example: RSL-WW-20240924-1R1
# By default the regex will be programmatically constructed using the submission type name and abbreviation
# https://stackoverflow.com/a/23212501
regex: !regex [*NAME, *ABBREV]
# The info section holds a map of where submission info can be located in the submission form.
# For example, below the 'comment' field is found on the 'Sample List' tab in column 2 of tow 34.
# 'read' is a list of where the info can be parsed from, write is a list of where it will be written to.
# By default, items in the 'read' list will be appended to the 'write' list.
# These fields are common to all submissions. Without programming changes, at present no new fields can be added.
info:
comment:
read:
- column: 2
row: 34
sheet: Sample List
write: []
contact:
read:
- column: 2
row: 4
sheet: Sample List
write: []
contact_phone:
read: []
write:
- column: 2
row: 5
sheet: Sample List
cost_centre:
read:
- column: 2
row: 6
sheet: Sample List
write: []
# The 'custom' field is currently under development and will allow parsing, storage and writing of new fields in
# generic submission types.
# Examples of the types of fields are given below.
custom: {
# The 'cell' type will read a single cell from the excel sheet and write it to the same cell as well as
# any specified in the write list.
# "test cell": {
# "read": {
# "column": 3,
# "row": 1,
# "sheet": "Plate Map"
# },
# "type": "cell",
# "write": [{
# "column": 8,
# "row": 8,
# "sheet": "Sample List"
# }]
# },
# The 'range' type will read a group of cells, store them as a list of values, row and column integers
# and write to that range.
# "test range": {
# "sheet": "First Strand",
# "start_row": 1,
# "end_row":9,
# "start_column": 1,
# "end_column": 5
# }
}
extraction_kit:
read:
- column: 4
row: 5
sheet: Sample List
write: []
rsl_plate_num:
read:
- column: 2
row: 13
sheet: Sample List
write: []
sample_count:
read:
- column: 4
row: 4
sheet: Sample List
write: []
signed_by:
read: []
write:
- column: 2
row: 15
sheet: Sample List
submission_category:
read:
- column: 4
row: 6
sheet: Sample List
write: []
submission_type:
read:
- column: 4
row: 3
sheet: Sample List
write: []
submitted_date:
read:
- column: 2
row: 3
sheet: Sample List
write: []
submitter_plate_num:
read:
- column: 2
row: 2
sheet: Sample List
write: []
submitting_lab:
read:
- column: 4
row: 2
sheet: Sample List
write: []
technician:
read:
- column: 2
row: 14
sheet: Sample List
write: []
# The 'kits' field holds reagents, equipment and tips information. It's a list of kit_type objects.
kits:
- kit_type:
name: MagMAX-96 Viral RNA Isolation Kit
equipment roles:
- role: Extractor
processes:
- OBT_M4029_KFF_v1.0
static: 0
- processes:
- Omega_MagBind_Universal_VarCol
role: Momentum - Extraction
static: 1
- processes:
- Bacterial_Core_Submission
role: Liquid Handler
static: 1
reagent roles:
- expiry:
column: 4
row: 19
extension_of_life: 0
lot:
column: 3
row: 19
name:
column: 2
row: 19
required: 1
role: Wash Solution 1 (MagMAX-96 Viral)
sheet: Sample List
- expiry:
column: 4
row: 20
extension_of_life: 0
lot:
column: 3
row: 20
name:
column: 2
row: 20
required: 1
role: Wash Solution 2 (MagMAX-96 Viral)
sheet: Sample List
- expiry:
column: 4
row: 21
extension_of_life: 0
lot:
column: 3
row: 21
name:
column: 2
row: 21
required: 1
role: Lysis/Binding Solution (MagMAX-96 Viral)
sheet: Sample List
- expiry:
column: 4
row: 22
extension_of_life: 0
lot:
column: 3
row: 22
name:
column: 2
row: 22
required: 1
role: RNA Binding Beads (MagMAX-96 Viral)
sheet: Sample List
- expiry:
column: 4
row: 23
extension_of_life: 0
lot:
column: 3
row: 23
name:
column: 2
row: 23
required: 1
role: Lysis/Binding Enhancer (MagMAX-96 Viral)
sheet: Sample List
- expiry:
column: 4
row: 24
extension_of_life: 0
lot:
column: 3
row: 24
name:
column: 2
row: 24
required: 0
role: Bacterial-Lysis Buffer
sheet: Sample List
- expiry:
column: 4
row: 25
extension_of_life: 0
lot:
column: 3
row: 25
name:
column: 2
row: 25
required: 1
role: Elution Buffer (MagMAX-96 Viral)
sheet: Sample List
- expiry:
column: 4
row: 30
extension_of_life: 0
lot:
column: 3
row: 30
name:
column: 2
row: 30
required: 0
role: Bacterial-Positive Control
sheet: Sample List
- expiry:
column: 4
row: 31
extension_of_life: 0
lot:
column: 3
row: 31
name:
column: 2
row: 31
required: 0
role: Bead Plate
sheet: Sample List
- expiry:
column: 4
row: 28
extension_of_life: 0
lot:
column: 3
row: 28
name:
column: 2
row: 28
required: 1
role: Isopropanol
sheet: Sample List
- expiry:
column: 4
row: 29
extension_of_life: 0
lot:
column: 3
row: 29
name:
column: 2
row: 29
required: 1
role: Ethanol
sheet: Sample List
- expiry:
column: 4
row: 32
extension_of_life: 0
lot:
column: 3
row: 32
name:
column: 2
row: 32
required: 1
role: Carrier RNA
sheet: Sample List
constant_cost: 0.0
mutable_cost_column: 0.0
mutable_cost_sample: 0.0
samples:
lookup_table:
end_row: 132
merge_on_id: submitter_id
sample_columns:
column: 6
concentration: 4
organism: 3
row: 5
submitter_id: 2
sheet: Sample List
start_row: 37
plate_map:
end_column: 13
end_row: 14
sheet: Plate Map
start_column: 2
start_row: 7
orgs:
- name: IRVC-Genomics
cost_centre: xxx
contacts:
- name: Ruimin Gao
phone: (204) 789-5078
email: Ruimin.Gao@phac-aspc.gc.ca