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Addition of new reagent lots updated.

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This commit is contained in:
lwark
2025-10-03 10:19:17 -05:00
parent 1445d2b93b
commit ccee4b3afe
8 changed files with 112 additions and 114 deletions
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1
src/submissions/backend/db/models/__init__.py
View File

@@ -520,6 +520,7 @@ class BaseClass(Base):
if isinstance(field_type, InstrumentedAttribute):
match field_type.property:
case ColumnProperty():
return super().__setattr__(key, value)
case _RelationshipDeclared():
if field_type.property.uselist:

2
src/submissions/backend/db/models/procedures.py
View File

@@ -346,6 +346,7 @@ class Reagent(BaseClass, LogMixin):
return [dict(name=self.name, lot=lot.lot, expiry=lot.expiry + self.eol_ext) for lot in self.reagentlot]
class ReagentLot(BaseClass):
pyd_model_name = "Reagent"
@@ -445,6 +446,7 @@ class ReagentLot(BaseClass):
output['reagent'] = output['reagent'].name
return output
class Discount(BaseClass):
"""
Relationship table for client labs for certain kits.

6
src/submissions/backend/db/models/submissions.py
View File

@@ -43,7 +43,7 @@ class ClientSubmission(BaseClass, LogMixin):
submission_category = Column(String(64)) #: i.e. Surveillance
sample_count = Column(INTEGER) #: Number of sample in the procedure
full_batch_size = Column(INTEGER) #: Number of wells in provided plate. 0 if no plate.
comment = Column(JSON) #: comment objects from users.
comments = Column(JSON) #: comment objects from users.
run = relationship("Run", back_populates="clientsubmission") #: many-to-one relationship
contact = relationship("Contact", back_populates="clientsubmission") #: contact representing submitting lab.
contact_id = Column(INTEGER, ForeignKey("_contact.id", ondelete="SET NULL",
@@ -240,9 +240,9 @@ class ClientSubmission(BaseClass, LogMixin):
custom = None
runs = None
try:
comments = self.comment
comments = self.comments
except Exception as e:
logger.error(f"Error setting comment: {self.comment}, {e}")
logger.error(f"Error setting comment: {self.comments}, {e}")
comments = None
try:
contact = self.contact.name

5
src/submissions/backend/excel/parsers/clientsubmission_parser.py
View File

@@ -3,6 +3,8 @@ Module for clientsubmission parsing
"""
from __future__ import annotations
import logging
import sys
from datetime import datetime
from pathlib import Path
from string import ascii_lowercase
from typing import Generator, TYPE_CHECKING
@@ -135,6 +137,9 @@ class ClientSubmissionInfoParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
output['submissiontype']['value'] = self.submissiontype.name.title()
except KeyError:
pass
if isinstance(output['submitted_date']['value'], datetime):
output['submitted_date']['value'] = output['submitted_date']['value'].date()
return output

184
src/submissions/backend/validators/pydant.py
View File

@@ -37,17 +37,21 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
def prevalidate(cls, data):
sql_fields = [k for k, v in cls._sql_object.__dict__.items() if isinstance(v, InstrumentedAttribute)]
output = {}
try:
items = data.items()
except AttributeError as e:
logger.error(f"Could not prevalidate {cls.__name__} due to {e} for {pformat(data)}")
return data
for key, value in items:
new_key = key.replace("_", "")
if new_key in sql_fields:
output[new_key] = value
else:
output[key] = value
match data:
case dict():
try:
items = data.items()
except AttributeError as e:
logger.error(f"Could not prevalidate {cls.__name__} due to {e} for {pformat(data)}")
return data
for key, value in items:
new_key = key.replace("_", "")
if new_key in sql_fields:
output[new_key] = value
else:
output[key] = value
case _:
output = data
return output
@model_validator(mode='after')
@@ -135,6 +139,7 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
continue
return list(set(output))
class PydResults(PydBaseClass, arbitrary_types_allowed=True):
result: dict = Field(default={})
result_type: str = Field(default="NA")
@@ -186,9 +191,9 @@ class PydReagentLot(PydBaseClass):
class PydReagent(PydBaseClass):
lot: str | None
# lot: str | None
reagentrole: str | None
expiry: date | datetime | Literal['NA'] | None = Field(default=None, validate_default=True)
# expiry: date | datetime | Literal['NA'] | None = Field(default=None, validate_default=True)
name: str | None = Field(default=None, validate_default=True)
missing: bool = Field(default=True)
comment: str | None = Field(default="", validate_default=True)
@@ -219,47 +224,47 @@ class PydReagent(PydBaseClass):
return value
return value
@field_validator("lot", mode='before')
@classmethod
def rescue_lot_string(cls, value):
if value is not None:
return convert_nans_to_nones(str(value).strip())
return value
@field_validator("lot")
@classmethod
def enforce_lot_string(cls, value):
if value is not None:
return value.upper().strip()
return value
@field_validator("expiry", mode="before")
@classmethod
def enforce_date(cls, value):
if value is not None:
match value:
case int():
return datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value - 2)
case 'NA':
return value
case str():
return parse(value)
case date():
return datetime.combine(value, datetime.max.time())
case datetime():
return value
case _:
return convert_nans_to_nones(str(value))
if value is None:
value = datetime.combine(date.today(), datetime.max.time())
return value
@field_validator("expiry")
@classmethod
def date_na(cls, value):
if isinstance(value, date) and value.year == 1970:
value = "NA"
return value
# @field_validator("lot", mode='before')
# @classmethod
# def rescue_lot_string(cls, value):
# if value is not None:
# return convert_nans_to_nones(str(value).strip())
# return value
#
# @field_validator("lot")
# @classmethod
# def enforce_lot_string(cls, value):
# if value is not None:
# return value.upper().strip()
# return value
#
# @field_validator("expiry", mode="before")
# @classmethod
# def enforce_date(cls, value):
# if value is not None:
# match value:
# case int():
# return datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value - 2)
# case 'NA':
# return value
# case str():
# return parse(value)
# case date():
# return datetime.combine(value, datetime.max.time())
# case datetime():
# return value
# case _:
# return convert_nans_to_nones(str(value))
# if value is None:
# value = datetime.combine(date.today(), datetime.max.time())
# return value
#
# @field_validator("expiry")
# @classmethod
# def date_na(cls, value):
# if isinstance(value, date) and value.year == 1970:
# value = "NA"
# return value
@field_validator("name", mode="before")
@classmethod
@@ -269,7 +274,6 @@ class PydReagent(PydBaseClass):
else:
return values.data['reagentrole'].strip()
def improved_dict(self) -> dict:
"""
Constructs a dictionary consisting of model.fields and model.extras
@@ -292,14 +296,17 @@ class PydReagent(PydBaseClass):
Returns:
Tuple[Reagent, Report]: Reagent instance and result of function
"""
from backend.db.models import ReagentLot, Reagent
report = Report()
if self.model_extra is not None:
self.__dict__.update(self.model_extra)
reagentlot, new = ReagentLot.query_or_create(lot=self.lot, name=self.name)
if new:
reagent = Reagent.query(name=self.name)
reagent = Reagent.query(name=self.name, limit=1)
reagentlot.reagent = reagent
reagentlot.expiry = self.expiry
if isinstance(reagentlot.expiry, str):
reagentlot.expiry = datetime.combine(datetime.strptime(reagentlot.expiry, "%Y-%m-%d"), datetime.max.time())
return reagentlot, report
@@ -371,6 +378,7 @@ class PydTips(PydBaseClass):
Returns:
SubmissionTipsAssociation: Association between queried tips and procedure
"""
from backend.db.models import TipsLot
report = Report()
tips = TipsLot.query(lot=self.lot, limit=1)
return tips, report
@@ -388,6 +396,7 @@ class PydEquipment(PydBaseClass):
@field_validator('equipmentrole', mode='before')
@classmethod
def get_role_name(cls, value):
from backend.db.models import EquipmentRole
match value:
case list():
value = value[0]
@@ -402,6 +411,7 @@ class PydEquipment(PydBaseClass):
@field_validator('processes', mode='before')
@classmethod
def process_to_pydantic(cls, value, values):
from backend.db.models import ProcessVersion, Process
if isinstance(value, GeneratorType):
value = [item for item in value]
value = convert_nans_to_nones(value)
@@ -431,6 +441,7 @@ class PydEquipment(PydBaseClass):
@field_validator('tips', mode='before')
@classmethod
def tips_to_pydantic(cls, value, values):
from backend.db.models import TipsLot
if isinstance(value, GeneratorType):
value = [item for item in value]
value = convert_nans_to_nones(value)
@@ -467,6 +478,7 @@ class PydEquipment(PydBaseClass):
Returns:
Tuple[Equipment, RunEquipmentAssociation]: SQL objects
"""
from backend.db.models import Equipment, ProcedureEquipmentAssociation, Process
report = Report()
if isinstance(procedure, str):
procedure = Procedure.query(name=procedure)
@@ -680,6 +692,7 @@ class PydProcess(PydBaseClass, extra="allow"):
@report_result
def to_sql(self):
from backend.db.models import ProcessVersion
report = Report()
name = self.name.split("-")[0]
# NOTE: can't use query_or_create due to name not being part of ProcessVersion
@@ -725,12 +738,12 @@ class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
# NOTE: Generified objects below:
class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
proceduretype: ProcedureType | None = Field(default=None)
run: Run | str | None = Field(default=None)
proceduretype: Any | None = Field(default=None)
run: Any | str | None = Field(default=None)
name: dict = Field(default=dict(value="NA", missing=True), validate_default=True)
technician: dict = Field(default=dict(value="NA", missing=True))
repeat: bool = Field(default=False)
repeat_of: Procedure | None = Field(default=None)
repeat_of: Any | None = Field(default=None)
plate_map: str | None = Field(default=None)
reagent: list | None = Field(default=[])
reagentrole: dict | None = Field(default={}, validate_default=True)
@@ -919,7 +932,10 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
reg.save()
def to_sql(self, new: bool = False):
from backend.db.models import RunSampleAssociation, ProcedureSampleAssociation
from backend.db.models import (
RunSampleAssociation, ProcedureSampleAssociation, Procedure, ProcedureReagentLotAssociation,
ProcedureEquipmentAssociation
)
logger.debug(f"incoming pyd: {pformat([item.__dict__ for item in self.equipment])}")
if new:
sql = Procedure()
@@ -1042,9 +1058,11 @@ class PydClientSubmission(PydBaseClass):
def enforce_submitted_date(cls, value):
match value:
case str():
value = dict(value=datetime.strptime(value, "%Y-%m-%d %H:%M:%S"), missing=False)
case date() | datetime():
value = dict(value=datetime.strptime(value, "%Y-%m-%d %H:%M:%S").date(), missing=False)
case date():
value = dict(value=value, missing=False)
case datetime():
value = dict(value=value.date(), missing=False)
case _:
pass
return value
@@ -1162,6 +1180,7 @@ class PydClientSubmission(PydBaseClass):
def to_sql(self):
sql = super().to_sql()
from backend.db.models import SubmissionType
assert not any([isinstance(item, PydSample) for item in sql.sample])
sql.sample = []
if not sql.submissiontype:
@@ -1662,44 +1681,3 @@ class PydRun(PydBaseClass): #, extra='allow'):
samples.append(sample)
samples = sorted(samples, key=itemgetter("submission_rank"))
return samples
# class PydResults(PydBaseClass, arbitrary_types_allowed=True):
# result: dict = Field(default={})
# result_type: str = Field(default="NA")
# img: None | bytes = Field(default=None)
# parent: Procedure | ProcedureSampleAssociation | None = Field(default=None)
# date_analyzed: datetime | None = Field(default=None)
#
# @field_validator("date_analyzed")
# @classmethod
# def set_today(cls, value):
# match value:
# case str():
# value = datetime.strptime(value, "%Y-%m-%d %H:%M:%S")
# case datetime():
# pass
# case date():
# value = datetime.combine(value, datetime.max.time())
# case _:
# value = datetime.now()
# return value
#
# def to_sql(self):
# sql, _ = Results.query_or_create(result_type=self.result_type, result=self.results)
# try:
# check = sql.image
# except FileNotFoundError:
# check = False
# if not check:
# sql.image = self.img
# if not sql.date_analyzed:
# sql.date_analyzed = self.date_analyzed
# match self.parent:
# case ProcedureSampleAssociation():
# sql.sampleprocedureassociation = self.parent
# case Procedure():
# sql.procedure = self.parent
# case _:
# logger.error("Improper association found.")
# return sql

14
src/submissions/frontend/widgets/procedure_creation.py
View File

@@ -80,7 +80,6 @@ class ProcedureCreation(QDialog):
proceduretype_dict['equipment'] = [sanitize_object_for_json(object) for object in proceduretype_dict['equipment']]
regex = re.compile(r".*R\d$")
proceduretype_dict['previous'] = [""] + [item.name for item in self.run.procedure if item.proceduretype == self.proceduretype and not bool(regex.match(item.name))]
# sys.exit(f"ProcedureDict:\n{pformat(proceduretype_dict)}")
html = render_details_template(
template_name="procedure_creation",
js_in=["procedure_form", "grid_drag", "context_menu"],
@@ -90,12 +89,13 @@ class ProcedureCreation(QDialog):
plate_map=self.plate_map,
edit=self.edit
)
# with open("procedure_creation.html", "w") as f:
# f.write(html)
self.webview.setHtml(html)
@pyqtSlot(str, str, str, str)
def update_equipment(self, equipmentrole: str, equipment: str, processversion: str, tips: str):
from backend.db.models import Equipment, ProcessVersion, TipsLot
logger.debug(f"\n\nEquipmentRole: {equipmentrole}, Equipment: {equipment}, Process: {processversion}, Tips: {tips}\n\n")
try:
equipment_of_interest = next(
(item for item in self.procedure.equipment if item.equipmentrole == equipmentrole))
@@ -156,10 +156,10 @@ class ProcedureCreation(QDialog):
@pyqtSlot(str, str, str, str)
def add_new_reagent(self, reagentrole: str, name: str, lot: str, expiry: str):
from backend.validators.pydant import PydReagent
from backend.validators.pydant import PydReagentLot
expiry = datetime.datetime.strptime(expiry, "%Y-%m-%d")
logger.debug(f"{reagentrole}, {name}, {lot}, {expiry}")
pyd = PydReagent(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
pyd = PydReagentLot(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
self.procedure.reagentrole[reagentrole].insert(0, pyd)
self.set_html()
@@ -171,6 +171,12 @@ class ProcedureCreation(QDialog):
return
self.procedure.update_reagents(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
@pyqtSlot(str, result=list)
def get_reagent_names(self, reagentrole_name: str):
from backend.db.models import ReagentRole
reagentrole = ReagentRole.query(name=reagentrole_name)
return [item.name for item in reagentrole.get_reagents(proceduretype=self.procedure.proceduretype)]
def return_sql(self, new: bool = False):
output = self.procedure.to_sql(new=new)
return output

2
src/submissions/templates/js/context_menu.js
View File

@@ -194,7 +194,7 @@ function contextListener() {
function clickListener() {
document.addEventListener( "click", function(e) {
var clickeElIsLink = clickInsideElement( e, contextMenuLinkClassName );
backend.log(e.target.id)
if ( clickeElIsLink ) {
e.preventDefault();
menuItemListener( clickeElIsLink );

12
src/submissions/templates/js/procedure_form.js
View File

@@ -42,7 +42,7 @@ var changed_it = new Event('change');
var reagentRoles = document.getElementsByClassName("reagentrole");
for(let i = 0; i < reagentRoles.length; i++) {
reagentRoles[i].addEventListener("change", function() {
reagentRoles[i].addEventListener("change", async function() {
if (reagentRoles[i].value.includes("--New--")) {
// alert("Create new reagent.")
var br = document.createElement("br");
@@ -50,9 +50,15 @@ for(let i = 0; i < reagentRoles.length; i++) {
var new_form = document.createElement("form");
new_form.setAttribute("class", "new_reagent_form")
new_form.setAttribute("id", reagentRoles[i].id + "_addition")
var rr_name = document.createElement("input");
rr_name.setAttribute("type", "text");
var rr_name = document.createElement("select");
rr_name.setAttribute("id", "new_" + reagentRoles[i].id + "_name");
var rr_options = await backend.get_reagent_names(reagentRoles[i].id).then(
function(result) {
result.forEach( function(item) {
rr_name.options.add( new Option(item));
});
}
);
var rr_name_label = document.createElement("label");
rr_name_label.setAttribute("for", "new_" + reagentRoles[i].id + "_name");
rr_name_label.innerHTML = "Name:";