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Post code-cleanup, moments before disaster.

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This commit is contained in:
lwark
2025-03-26 14:19:13 -05:00
parent 3ec79fdcfe
commit d844211e1b
21 changed files with 183 additions and 285 deletions
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9
src/submissions/backend/db/models/__init__.py
View File

@@ -56,6 +56,12 @@ class BaseClass(Base):
omni_inheritable = []
searchables = []
def __repr__(self) -> str:
try:
return f"<{self.__class__.__name__}({self.name})>"
except AttributeError:
return f"<{self.__class__.__name__}({self.__name__})>"
# @classproperty
# def skip_on_edit(cls):
# if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
@@ -444,6 +450,9 @@ class BaseClass(Base):
else:
return super().__setattr__(key, value)
def delete(self):
logger.error(f"Delete has not been implemented for {self.__class__.__name__}")
class ConfigItem(BaseClass):
"""

52
src/submissions/backend/db/models/controls.py
View File

@@ -2,6 +2,8 @@
All control related models.
"""
from __future__ import annotations
import itertools
from pprint import pformat
from PyQt6.QtWidgets import QWidget, QCheckBox, QLabel
from pandas import DataFrame
@@ -16,7 +18,6 @@ from typing import List, Literal, Tuple, Generator
from dateutil.parser import parse
from re import Pattern
logger = logging.getLogger(f"submissions.{__name__}")
@@ -29,8 +30,8 @@ class ControlType(BaseClass):
targets = Column(JSON) #: organisms checked for
instances = relationship("Control", back_populates="controltype") #: control samples created of this type.
def __repr__(self) -> str:
return f"<ControlType({self.name})>"
# def __repr__(self) -> str:
# return f"<ControlType({self.name})>"
@classmethod
@setup_lookup
@@ -88,7 +89,7 @@ class ControlType(BaseClass):
Returns:
Control: Associated Control class
"""
"""
return Control.find_polymorphic_subclass(polymorphic_identity=self.name)
@classmethod
@@ -103,7 +104,7 @@ class ControlType(BaseClass):
return (k for k, v in ct.items() if v)
@classmethod
def build_positive_regex(cls, control_type:str) -> Pattern:
def build_positive_regex(cls, control_type: str) -> Pattern:
"""
Creates a re.Pattern that will look for positive control types
@@ -305,10 +306,10 @@ class PCRControl(Control):
id = Column(INTEGER, ForeignKey('_control.id'), primary_key=True)
subtype = Column(String(16)) #: PC or NC
target = Column(String(16)) #: N1, N2, etc.
ct = Column(FLOAT) #: PCR result
ct = Column(FLOAT) #: PCR result
reagent_lot = Column(String(64), ForeignKey("_reagent.lot", ondelete="SET NULL",
name="fk_reagent_lot"))
reagent = relationship("Reagent", foreign_keys=reagent_lot) #: reagent used for this control
reagent = relationship("Reagent", foreign_keys=reagent_lot) #: reagent used for this control
__mapper_args__ = dict(polymorphic_identity="PCR Control",
polymorphic_load="inline",
@@ -320,7 +321,7 @@ class PCRControl(Control):
Returns:
dict: Output dict of name, ct, subtype, target, reagent_lot and submitted_date
"""
"""
return dict(
name=self.name,
ct=self.ct,
@@ -343,7 +344,7 @@ class PCRControl(Control):
Returns:
Tuple[Report, "PCRFigure"]: Report of status and resulting figure.
"""
"""
from frontend.visualizations.pcr_charts import PCRFigure
parent.mode_typer.clear()
parent.mode_typer.setEnabled(False)
@@ -352,6 +353,7 @@ class PCRControl(Control):
end_date=chart_settings['end_date'])
data = [control.to_sub_dict() for control in controls]
df = DataFrame.from_records(data)
# NOTE: Get all PCR controls with ct over 0
try:
df = df[df.ct > 0.0]
except AttributeError:
@@ -361,11 +363,11 @@ class PCRControl(Control):
def to_pydantic(self):
from backend.validators import PydPCRControl
return PydPCRControl(**self.to_sub_dict(), controltype_name=self.controltype_name, submission_id=self.submission_id)
return PydPCRControl(**self.to_sub_dict(), controltype_name=self.controltype_name,
submission_id=self.submission_id)
class IridaControl(Control):
subtyping_allowed = ['kraken']
id = Column(INTEGER, ForeignKey('_control.id'), primary_key=True)
@@ -379,11 +381,19 @@ class IridaControl(Control):
sample = relationship("BacterialCultureSample", back_populates="control") #: This control's submission sample
sample_id = Column(INTEGER,
ForeignKey("_basicsample.id", ondelete="SET NULL", name="cont_BCS_id")) #: sample id key
__mapper_args__ = dict(polymorphic_identity="Irida Control",
polymorphic_load="inline",
inherit_condition=(id == Control.id))
@property
def targets(self):
if self.controltype.targets:
return list(itertools.chain.from_iterable([value for key, value in self.controltype.targets.items()
if key == self.subtype]))
else:
return ["None"]
@validates("subtype")
def enforce_subtype_literals(self, key: str, value: str) -> str:
"""
@@ -398,7 +408,7 @@ class IridaControl(Control):
Returns:
str: Validated string.
"""
"""
acceptables = ['ATCC49226', 'ATCC49619', 'EN-NOS', "EN-SSTI", "MCS-NOS", "MCS-SSTI", "SN-NOS", "SN-SSTI"]
if value.upper() not in acceptables:
raise KeyError(f"Sub-type must be in {acceptables}")
@@ -416,19 +426,15 @@ class IridaControl(Control):
except TypeError:
kraken = {}
kraken_cnt_total = sum([item['kraken_count'] for item in kraken.values()])
new_kraken = [dict(name=item, kraken_count=kraken[item]['kraken_count'],
kraken_percent=f"{kraken[item]['kraken_count'] / kraken_cnt_total:0.2%}",
target=item in self.controltype.targets)
for item in kraken]
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)
if self.controltype.targets:
targets = self.controltype.targets
else:
targets = ["None"]
output = dict(
name=self.name,
type=self.controltype.name,
targets=", ".join(targets),
targets=", ".join(self.targets),
kraken=new_kraken[0:10]
)
return output
@@ -521,7 +527,7 @@ class IridaControl(Control):
Returns:
Tuple[Report, "IridaFigure"]: Report of status and resulting figure.
"""
"""
from frontend.visualizations import IridaFigure
try:
checker = parent.findChild(QCheckBox, name="irida_check")

144
src/submissions/backend/db/models/kits.py
View File

@@ -16,7 +16,6 @@ from pandas import ExcelFile
from pathlib import Path
from . import Base, BaseClass, Organization, LogMixin
from io import BytesIO
from inspect import getouterframes, currentframe
logger = logging.getLogger(f'submissions.{__name__}')
@@ -98,7 +97,6 @@ class KitType(BaseClass):
Base of kits used in submission processing
"""
# query_alias = "kit_type"
omni_sort = BaseClass.omni_sort + ["kit_submissiontype_associations", "kit_reagentrole_associations", "processes"]
id = Column(INTEGER, primary_key=True) #: primary key
@@ -128,13 +126,6 @@ class KitType(BaseClass):
creator=lambda ST: SubmissionTypeKitTypeAssociation(
submission_type=ST)) #: Association proxy to SubmissionTypeKitTypeAssociation
def __repr__(self) -> str:
"""
Returns:
str: A representation of the object.
"""
return f"<KitType({self.name})>"
@classproperty
def aliases(cls):
return super().aliases + [cls.query_alias, "kit_types", "kit_type"]
@@ -187,9 +178,7 @@ class KitType(BaseClass):
# NOTE: Account for submission_type variable type.
match submission_type:
case str():
# assocs = [item for item in self.kit_reagentrole_associations if
# item.submission_type.name == submission_type]
logger.debug(f"Query for {submission_type}")
# logger.debug(f"Query for {submission_type}")
submission_type = SubmissionType.query(name=submission_type)
case SubmissionType():
pass
@@ -213,18 +202,12 @@ class KitType(BaseClass):
)
if dlg.exec():
dlg_result = dlg.parse_form()
logger.debug(f"Dialog result: {dlg_result}")
# logger.debug(f"Dialog result: {dlg_result}")
new_kit = self.__class__.query(name=dlg_result)
logger.debug(f"Query result: {new_kit}")
# return new_kit.construct_xl_map_for_use(submission_type=submission_type)
# logger.debug(f"Query result: {new_kit}")
else:
return None, new_kit
assocs = [item for item in new_kit.kit_reagentrole_associations if item.submission_type == submission_type]
# for assoc in assocs:
# try:
# yield assoc.reagent_role.name, assoc.uses
# except TypeError:
# continue
output = {assoc.reagent_role.name: assoc.uses for assoc in assocs}
# logger.debug(f"Output: {output}")
return output, new_kit
@@ -232,7 +215,6 @@ class KitType(BaseClass):
@classmethod
def query_or_create(cls, **kwargs) -> Tuple[KitType, bool]:
from backend.validators.pydant import PydKitType
from backend.validators.omni_gui_objects import BaseOmni
new = False
disallowed = ['expiry']
sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
@@ -248,7 +230,7 @@ class KitType(BaseClass):
@setup_lookup
def query(cls,
name: str = None,
used_for: str | SubmissionType | None = None,
submissiontype: str | SubmissionType | None = None,
id: int | None = None,
limit: int = 0,
**kwargs
@@ -266,11 +248,11 @@ class KitType(BaseClass):
KitType|List[KitType]: KitType(s) of interest.
"""
query: Query = cls.__database_session__.query(cls)
match used_for:
match submissiontype:
case str():
query = query.filter(cls.used_for.any(name=used_for))
query = query.filter(cls.submissiontype.any(name=submissiontype))
case SubmissionType():
query = query.filter(cls.used_for.contains(used_for))
query = query.filter(cls.submissiontype.contains(submissiontype))
case _:
pass
match name:
@@ -399,9 +381,6 @@ class KitType(BaseClass):
def to_omni(self, expand: bool = False) -> "OmniKitType":
from backend.validators.omni_gui_objects import OmniKitType
# logger.debug(f"self.name: {self.name}")
# level = len(getouterframes(currentframe()))
# logger.warning(f"Function level is {level}")
if expand:
processes = [item.to_omni() for item in self.processes]
kit_reagentrole_associations = [item.to_omni() for item in self.kit_reagentrole_associations]
@@ -425,6 +404,8 @@ class ReagentRole(BaseClass):
Base of reagent type abstract
"""
skip_on_edit = False
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64)) #: name of role reagent plays
instances = relationship("Reagent", back_populates="role",
@@ -442,13 +423,6 @@ class ReagentRole(BaseClass):
creator=lambda kit: KitTypeReagentRoleAssociation(
kit_type=kit)) #: Association proxy to KitTypeReagentRoleAssociation
def __repr__(self) -> str:
"""
Returns:
str: Representation of object
"""
return f"<ReagentRole({self.name})>"
@classmethod
def query_or_create(cls, **kwargs) -> Tuple[ReagentRole, bool]:
new = False
@@ -603,7 +577,6 @@ class Reagent(BaseClass, LogMixin):
Returns:
dict: representation of the reagent's attributes
"""
if extraction_kit is not None:
# NOTE: Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType
reagent_role = next((item for item in set(self.role).intersection(extraction_kit.reagent_roles)),
@@ -713,8 +686,6 @@ class Reagent(BaseClass, LogMixin):
limit = 1
case _:
pass
# if not role and "reagentrole" in kwargs.keys():
# role = kwargs['reagentrole']
match role:
case str():
query = query.join(cls.role).filter(ReagentRole.name == role)
@@ -772,6 +743,7 @@ class Reagent(BaseClass, LogMixin):
@check_authorization
def edit_from_search(self, obj, **kwargs):
from frontend.widgets.omni_add_edit import AddEdit
# logger.debug(f"Calling edit_from_search for {self.name}")
dlg = AddEdit(parent=None, instance=self)
if dlg.exec():
pyd = dlg.parse_form()
@@ -1377,20 +1349,6 @@ class SubmissionType(BaseClass):
def to_omni(self, expand: bool = False):
from backend.validators.omni_gui_objects import OmniSubmissionType
# level = len(getouterframes(currentframe()))
# logger.warning(f"Function level is {level}")
# try:
# info_map = self.submission_type.info_map
# except AttributeError:
# info_map = {}
# try:
# defaults = self.submission_type.defaults
# except AttributeError:
# defaults = {}
# try:
# sample_map = self.submission_type.sample_map
# except AttributeError:
# sample_map = {}
try:
template_file = self.template_file
except AttributeError:
@@ -1555,8 +1513,6 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
def to_omni(self, expand: bool = False):
from backend.validators.omni_gui_objects import OmniSubmissionTypeKitTypeAssociation
# level = len(getouterframes(currentframe()))
# logger.warning(f"Function level is {level}")
if expand:
try:
submissiontype = self.submission_type.to_omni()
@@ -1569,10 +1525,6 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
else:
submissiontype = self.submission_type.name
kittype = self.kit_type.name
# try:
# processes = [item.to_omni() for item in self.submission_type.processes]
# except AttributeError:
# processes = []
return OmniSubmissionTypeKitTypeAssociation(
instance_object=self,
submissiontype=submissiontype,
@@ -1580,7 +1532,6 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
mutable_cost_column=self.mutable_cost_column,
mutable_cost_sample=self.mutable_cost_sample,
constant_cost=self.constant_cost
# processes=processes,
)
@@ -1719,7 +1670,6 @@ class KitTypeReagentRoleAssociation(BaseClass):
pass
setattr(instance, k, v)
logger.info(f"Instance from query or create: {instance.__dict__}\nis new: {new}")
# sys.exit()
return instance, new
@classmethod
@@ -1854,6 +1804,8 @@ class SubmissionReagentAssociation(BaseClass):
DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
"""
skip_on_edit = True
reagent_id = Column(INTEGER, ForeignKey("_reagent.id"), primary_key=True) #: id of associated reagent
submission_id = Column(INTEGER, ForeignKey("_basicsubmission.id"), primary_key=True) #: id of associated submission
comments = Column(String(1024)) #: Comments about reagents
@@ -1869,10 +1821,10 @@ class SubmissionReagentAssociation(BaseClass):
str: Representation of this SubmissionReagentAssociation
"""
try:
return f"<{self.submission.rsl_plate_num} & {self.reagent.lot}>"
return f"<SubmissionReagentAssociation({self.submission.rsl_plate_num} & {self.reagent.lot})>"
except AttributeError:
logger.error(f"Reagent {self.reagent.lot} submission association {self.reagent_id} has no submissions!")
return f"<Unknown Submission & {self.reagent.lot}>"
return f"<SubmissionReagentAssociation(Unknown Submission & {self.reagent.lot})>"
def __init__(self, reagent=None, submission=None):
if isinstance(reagent, list):
@@ -1963,12 +1915,12 @@ class Equipment(BaseClass, LogMixin):
submissions = association_proxy("equipment_submission_associations",
"submission") #: proxy to equipment_submission_associations.submission
def __repr__(self) -> str:
"""
Returns:
str: representation of this Equipment
"""
return f"<Equipment({self.name})>"
# def __repr__(self) -> str:
# """
# Returns:
# str: representation of this Equipment
# """
# return f"<Equipment({self.name})>"
def to_dict(self, processes: bool = False) -> dict:
"""
@@ -1987,7 +1939,7 @@ class Equipment(BaseClass, LogMixin):
def get_processes(self, submission_type: str | SubmissionType | None = None,
extraction_kit: str | KitType | None = None,
equipment_role: str | EquipmentRole | None = None) -> List[str]:
equipment_role: str | EquipmentRole | None = None) -> Generator[Process, None, None]:
"""
Get all processes associated with this Equipment for a given SubmissionType
@@ -2133,12 +2085,12 @@ class EquipmentRole(BaseClass):
submission_types = association_proxy("equipmentrole_submissiontype_associations",
"submission_type") #: proxy to equipmentrole_submissiontype_associations.submission_type
def __repr__(self) -> str:
"""
Returns:
str: Representation of this EquipmentRole
"""
return f"<EquipmentRole({self.name})>"
# def __repr__(self) -> str:
# """
# Returns:
# str: Representation of this EquipmentRole
# """
# return f"<EquipmentRole({self.name})>"
def to_dict(self) -> dict:
"""
@@ -2395,7 +2347,6 @@ class Process(BaseClass):
id = Column(INTEGER, primary_key=True) #: Process id, primary key
name = Column(String(64), unique=True) #: Process name
# version = Column(String(32))
submission_types = relationship("SubmissionType", back_populates='processes',
secondary=submissiontypes_processes) #: relation to SubmissionType
equipment = relationship("Equipment", back_populates='processes',
@@ -2410,12 +2361,12 @@ class Process(BaseClass):
secondary=process_tiprole) #: relation to KitType
def __repr__(self) -> str:
"""
Returns:
str: Representation of this Process
"""
return f"<Process({self.name})>"
# def __repr__(self) -> str:
# """
# Returns:
# str: Representation of this Process
# """
# return f"<Process({self.name})>"
def set_attribute(self, key, value):
match key:
@@ -2506,13 +2457,20 @@ class Process(BaseClass):
def to_omni(self, expand: bool = False):
from backend.validators.omni_gui_objects import OmniProcess
if expand:
submission_types = [item.to_omni() for item in self.submission_types]
equipment_roles = [item.to_omni() for item in self.equipment_roles]
tip_roles = [item.to_omni() for item in self.tip_roles]
else:
submission_types = [item.name for item in self.submission_types]
equipment_roles = [item.name for item in self.equipment_roles]
tip_roles = [item.name for item in self.tip_roles]
return OmniProcess(
instance_object=self,
name=self.name,
# version=self.version,
submission_types=[item.to_omni() for item in self.submission_types],
equipment_roles=[item.to_omni() for item in self.equipment_roles],
tip_roles=[item.to_omni() for item in self.tip_roles]
submission_types=submission_types,
equipment_roles=equipment_roles,
tip_roles=tip_roles
)
@@ -2538,8 +2496,8 @@ class TipRole(BaseClass):
def tips(self):
return self.instances
def __repr__(self):
return f"<TipRole({self.name})>"
# def __repr__(self):
# return f"<TipRole({self.name})>"
@classmethod
def query_or_create(cls, **kwargs) -> Tuple[TipRole, bool]:
@@ -2573,10 +2531,14 @@ class TipRole(BaseClass):
def to_omni(self, expand: bool = False):
from backend.validators.omni_gui_objects import OmniTipRole
if expand:
tips = [item.to_omni() for item in self.tips]
else:
tips = [item.name for item in self.tips]
return OmniTipRole(
instance_object=self,
name=self.name,
tips=[item.to_omni() for item in self.tips]
tips=tips
)
@@ -2605,8 +2567,8 @@ class Tips(BaseClass, LogMixin):
def tiprole(self):
return self.role
def __repr__(self):
return f"<Tips({self.name})>"
# def __repr__(self):
# return f"<Tips({self.name})>"
@classmethod
def query_or_create(cls, **kwargs) -> Tuple[Tips, bool]:

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

@@ -29,8 +29,6 @@ class Organization(BaseClass):
Base of organization
"""
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64)) #: organization name
submissions = relationship("BasicSubmission",
@@ -43,8 +41,8 @@ class Organization(BaseClass):
def contact(self):
return self.contacts
def __repr__(self) -> str:
return f"<Organization({self.name})>"
# def __repr__(self) -> str:
# return f"<Organization({self.name})>"
@classmethod
@setup_lookup
@@ -139,8 +137,8 @@ class Contact(BaseClass):
secondary=orgs_contacts) #: relationship to joined organization
submissions = relationship("BasicSubmission", back_populates="contact") #: submissions this contact has submitted
def __repr__(self) -> str:
return f"<Contact({self.name})>"
# def __repr__(self) -> str:
# return f"<Contact({self.name})>"
@classproperty
def searchables(cls):

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

@@ -402,7 +402,6 @@ class BasicSubmission(BaseClass, LogMixin):
columns = set([assoc.column for assoc in self.submission_sample_associations])
return len(columns)
def calculate_base_cost(self) -> None:
"""
Calculates cost of the plate
@@ -733,7 +732,7 @@ class BasicSubmission(BaseClass, LogMixin):
@classmethod
def find_polymorphic_subclass(cls, polymorphic_identity: str | SubmissionType | None = None,
attrs: dict | None = None):
attrs: dict | None = None) -> BasicSubmission:
"""
Find subclass based on polymorphic identity or relevant attributes.