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post documentation and code clean-up.

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This commit is contained in:
lwark
2024-07-05 14:00:25 -05:00
parent c460e5eeca
commit e589420815
8 changed files with 106 additions and 46 deletions
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8
src/submissions/backend/db/__init__.py
View File

@@ -1,9 +1,10 @@
'''
"""
All database related operations.
'''
"""
from sqlalchemy import event
from sqlalchemy.engine import Engine
@event.listens_for(Engine, "connect")
def set_sqlite_pragma(dbapi_connection, connection_record):
"""
@@ -19,4 +20,5 @@ def set_sqlite_pragma(dbapi_connection, connection_record):
cursor.execute("PRAGMA foreign_keys=ON")
cursor.close()
from .models import *
from .models import *

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

@@ -1,6 +1,6 @@
'''
"""
Contains all models for sqlalchemy
'''
"""
from __future__ import annotations
import sys, logging
from sqlalchemy import Column, INTEGER, String, JSON
@@ -27,6 +27,7 @@ class BaseClass(Base):
__table_args__ = {'extend_existing': True} #: Will only add new columns
@classmethod
@declared_attr
def __tablename__(cls) -> str:
"""
@@ -37,6 +38,7 @@ class BaseClass(Base):
"""
return f"_{cls.__name__.lower()}"
@classmethod
@declared_attr
def __database_session__(cls) -> Session:
"""
@@ -51,6 +53,7 @@ class BaseClass(Base):
from test_settings import ctx
return ctx.database_session
@classmethod
@declared_attr
def __directory_path__(cls) -> Path:
"""
@@ -65,6 +68,7 @@ class BaseClass(Base):
from test_settings import ctx
return ctx.directory_path
@classmethod
@declared_attr
def __backup_path__(cls) -> Path:
"""
@@ -192,3 +196,4 @@ from .controls import *
from .organizations import *
from .kits import *
from .submissions import *
BasicSubmission.reagents.creator = lambda reg: SubmissionReagentAssociation(reagent=reg)

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

@@ -8,7 +8,7 @@ from sqlalchemy.ext.associationproxy import association_proxy
from datetime import date
import logging, re
from tools import check_authorization, setup_lookup, Report, Result
from typing import List, Literal, Any
from typing import List, Literal
from pandas import ExcelFile
from pathlib import Path
from . import Base, BaseClass, Organization
@@ -126,8 +126,9 @@ class KitType(BaseClass):
cascade="all, delete-orphan",
) #: Relation to SubmissionType
used_for = association_proxy("kit_submissiontype_associations",
"submission_type") #: Association proxy to SubmissionTypeKitTypeAssociation
used_for = association_proxy("kit_submissiontype_associations", "submission_type",
creator=lambda ST: SubmissionTypeKitTypeAssociation(
submission_type=ST)) #: Association proxy to SubmissionTypeKitTypeAssociation
def __repr__(self) -> str:
"""
@@ -375,8 +376,9 @@ class Reagent(BaseClass):
cascade="all, delete-orphan",
) #: Relation to SubmissionSampleAssociation
submissions = association_proxy("reagent_submission_associations",
"submission") #: Association proxy to SubmissionSampleAssociation.samples
submissions = association_proxy("reagent_submission_associations", "submission",
creator=lambda sub: SubmissionReagentAssociation(
submission=sub)) #: Association proxy to SubmissionSampleAssociation.samples
def __repr__(self):
if self.name is not None:
@@ -597,7 +599,9 @@ class SubmissionType(BaseClass):
cascade="all, delete-orphan",
) #: Association of kittypes
kit_types = association_proxy("submissiontype_kit_associations", "kit_type") #: Proxy of kittype association
kit_types = association_proxy("submissiontype_kit_associations", "kit_type",
creator=lambda kit: SubmissionTypeKitTypeAssociation(
kit_type=kit)) #: Proxy of kittype association
submissiontype_equipmentrole_associations = relationship(
"SubmissionTypeEquipmentRoleAssociation",
@@ -605,8 +609,8 @@ class SubmissionType(BaseClass):
cascade="all, delete-orphan"
) #: Association of equipmentroles
equipment = association_proxy("submissiontype_equipmentrole_associations",
"equipment_role") #: Proxy of equipmentrole associations
equipment = association_proxy("submissiontype_equipmentrole_associations", "equipment_role",
creator=lambda eq: SubmissionTypeEquipmentRoleAssociation(equipment_role=eq)) #: Proxy of equipmentrole associations
submissiontype_kit_rt_associations = relationship(
"KitTypeReagentRoleAssociation",
@@ -710,7 +714,7 @@ class SubmissionType(BaseClass):
Returns:
dict: Tip locations in the excel sheet.
"""
"""
output = {}
for item in self.submissiontype_tiprole_associations:
tmap = item.uses
@@ -827,12 +831,13 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
submission_type = relationship(SubmissionType,
back_populates="submissiontype_kit_associations") #: joined submission type
def __init__(self, kit_type=None, submission_type=None):
def __init__(self, kit_type=None, submission_type=None,
mutable_cost_column: int = 0.00, mutable_cost_sample: int = 0.00, constant_cost: int = 0.00):
self.kit_type = kit_type
self.submission_type = submission_type
self.mutable_cost_column = 0.00
self.mutable_cost_sample = 0.00
self.constant_cost = 0.00
self.mutable_cost_column = mutable_cost_column
self.mutable_cost_sample = mutable_cost_sample
self.constant_cost = constant_cost
def __repr__(self) -> str:
"""
@@ -1539,15 +1544,15 @@ class Process(BaseClass):
pass
return cls.execute_query(query=query, limit=limit)
@check_authorization
def save(self):
super().save()
class TipRole(BaseClass):
"""
An abstract role that a tip fills during a process
"""
"""
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64)) #: name of reagent type
instances = relationship("Tips", back_populates="role",
@@ -1564,7 +1569,7 @@ class TipRole(BaseClass):
def __repr__(self):
return f"<TipRole({self.name})>"
@check_authorization
def save(self):
super().save()
@@ -1573,7 +1578,7 @@ class TipRole(BaseClass):
class Tips(BaseClass):
"""
A concrete instance of tips.
"""
"""
id = Column(INTEGER, primary_key=True) #: primary key
role = relationship("TipRole", back_populates="instances",
secondary=tiproles_tips) #: joined parent reagent type
@@ -1606,7 +1611,7 @@ class Tips(BaseClass):
Returns:
Tips | List[Tips]: Tips matching criteria
"""
"""
query = cls.__database_session__.query(cls)
match name:
case str():
@@ -1622,7 +1627,7 @@ class Tips(BaseClass):
case _:
pass
return cls.execute_query(query=query, limit=limit)
@check_authorization
def save(self):
super().save()
@@ -1642,7 +1647,7 @@ class SubmissionTypeTipRoleAssociation(BaseClass):
back_populates="submissiontype_tiprole_associations") #: associated submission
tip_role = relationship(TipRole,
back_populates="tiprole_submissiontype_associations") #: associated equipment
@check_authorization
def save(self):
super().save()
@@ -1651,7 +1656,7 @@ class SubmissionTypeTipRoleAssociation(BaseClass):
class SubmissionTipsAssociation(BaseClass):
"""
Association between a concrete submission instance and concrete tips
"""
"""
tip_id = Column(INTEGER, ForeignKey("_tips.id"), primary_key=True) #: id of associated equipment
submission_id = Column(INTEGER, ForeignKey("_basicsubmission.id"), primary_key=True) #: id of associated submission
submission = relationship("BasicSubmission",
@@ -1668,5 +1673,5 @@ class SubmissionTipsAssociation(BaseClass):
Returns:
dict: Values of this object
"""
"""
return dict(role=self.role_name, name=self.tips.name, lot=self.tips.lot)

8
src/submissions/backend/db/models/submissions.py
View File

@@ -79,7 +79,7 @@ class BasicSubmission(BaseClass):
) #: Relation to SubmissionSampleAssociation
samples = association_proxy("submission_sample_associations",
"sample") #: Association proxy to SubmissionSampleAssociation.samples
"sample", creator=lambda sample: SubmissionSampleAssociation(sample=sample)) #: Association proxy to SubmissionSampleAssociation.samples
submission_reagent_associations = relationship(
"SubmissionReagentAssociation",
@@ -853,14 +853,14 @@ class BasicSubmission(BaseClass):
@classmethod
def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
"""
_summary_
Updates row information
Args:
sample (_type_): _description_
worksheet (Workbook): _description_
Returns:
int: _description_
int: New row number
"""
return None
@@ -1307,7 +1307,6 @@ class BacterialCulture(BasicSubmission):
row = idx.index.to_list()[0]
return row + 1
class Wastewater(BasicSubmission):
"""
derivative submission type from BasicSubmission
@@ -2053,7 +2052,6 @@ class BasicSample(BaseClass):
dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
"""
# logger.debug(f"Converting {self} to dict.")
# start = time()
sample = {}
sample['submitter_id'] = self.submitter_id
sample['sample_type'] = self.sample_type

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

@@ -69,6 +69,7 @@ class App(QMainWindow):
helpMenu = menuBar.addMenu("&Help")
helpMenu.addAction(self.helpAction)
helpMenu.addAction(self.docsAction)
helpMenu.addAction(self.githubAction)
fileMenu.addAction(self.importAction)
methodsMenu.addAction(self.searchLog)
methodsMenu.addAction(self.searchSample)
@@ -103,6 +104,7 @@ class App(QMainWindow):
self.docsAction = QAction("&Docs", self)
self.searchLog = QAction("Search Log", self)
self.searchSample = QAction("Search Sample", self)
self.githubAction = QAction("Github", self)
def _connectActions(self):
"""
@@ -118,6 +120,7 @@ class App(QMainWindow):
self.docsAction.triggered.connect(self.openDocs)
self.searchLog.triggered.connect(self.runSearch)
self.searchSample.triggered.connect(self.runSampleSearch)
self.githubAction.triggered.connect(self.openGithub)
def showAbout(self):
"""
@@ -138,6 +141,14 @@ class App(QMainWindow):
# logger.debug(f"Attempting to open {url}")
webbrowser.get('windows-default').open(f"file://{url.__str__()}")
def openGithub(self):
"""
Opens the instructions html page
"""
url = "https://github.com/landowark/submissions"
webbrowser.get('windows-default').open(url)
def result_reporter(self):
"""
Report any anomolous results - if any - to the user

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

@@ -18,7 +18,7 @@ class EquipmentUsage(QDialog):
def __init__(self, parent, submission: BasicSubmission) -> QDialog:
super().__init__(parent)
self.submission = submission
self.setWindowTitle("Equipment Checklist")
self.setWindowTitle(f"Equipment Checklist - {submission.rsl_plate_num}")
self.used_equipment = self.submission.get_used_equipment()
self.kit = self.submission.extraction_kit
# logger.debug(f"Existing equipment: {self.used_equipment}")