landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Minor bug fixes.

Browse Source
This commit is contained in:
Landon Wark
2023-12-07 12:50:03 -06:00
parent cbf36a5b0b
commit 0dd51827a0
22 changed files with 308 additions and 370 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
src/submissions/backend/validators/__init__.py
View File

@@ -3,7 +3,6 @@ from pathlib import Path
from openpyxl import load_workbook
from backend.db.models import BasicSubmission, SubmissionType
logger = logging.getLogger(f"submissions.{__name__}")
class RSLNamer(object):

74
src/submissions/backend/validators/pydant.py
View File

@@ -2,7 +2,7 @@
Contains pydantic models and accompanying validators
'''
from operator import attrgetter
import uuid
import uuid, re, logging
from pydantic import BaseModel, field_validator, Field
from datetime import date, datetime, timedelta
from dateutil.parser import parse
@@ -10,8 +10,6 @@ from dateutil.parser._parser import ParserError
from typing import List, Any, Tuple
from . import RSLNamer
from pathlib import Path
import re
import logging
from tools import check_not_nan, convert_nans_to_nones, jinja_template_loading, Report, Result, row_map
from backend.db.models import *
from sqlalchemy.exc import StatementError, IntegrityError
@@ -28,6 +26,14 @@ class PydReagent(BaseModel):
expiry: date|None
name: str|None
missing: bool = Field(default=True)
comment: str|None = Field(default="", validate_default=True)
@field_validator('comment', mode='before')
@classmethod
def create_comment(cls, value):
if value == None:
return ""
return value
@field_validator("type", mode='before')
@classmethod
@@ -88,7 +94,7 @@ class PydReagent(BaseModel):
else:
return values.data['type']
def toSQL(self) -> Tuple[Reagent, Report]:
def toSQL(self, submission:BasicSubmission|str=None) -> Tuple[Reagent, Report]:
"""
Converts this instance into a backend.db.models.kit.Reagent instance
@@ -96,6 +102,8 @@ class PydReagent(BaseModel):
Tuple[Reagent, Report]: Reagent instance and result of function
"""
report = Report()
if self.model_extra != None:
self.__dict__.update(self.model_extra)
logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}")
reagent = Reagent.query(lot_number=self.lot)
logger.debug(f"Result: {reagent}")
@@ -117,6 +125,11 @@ class PydReagent(BaseModel):
reagent.type.append(reagent_type)
case "name":
reagent.name = value
case "comment":
continue
assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
assoc.comments = self.comment
reagent.reagent_submission_associations.append(assoc)
# add end-of-life extension from reagent type to expiry date
# NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
return reagent, report
@@ -203,9 +216,17 @@ class PydSubmission(BaseModel, extra='allow'):
extraction_kit: dict|None
technician: dict|None
submission_category: dict|None = Field(default=dict(value=None, missing=True), validate_default=True)
comment: dict|None = Field(default=dict(value="", missing=True), validate_default=True)
reagents: List[dict]|List[PydReagent] = []
samples: List[Any]
@field_validator('comment', mode='before')
@classmethod
def create_comment(cls, value):
if value == None:
return ""
return value
@field_validator("submitter_plate_num")
@classmethod
def enforce_with_uuid(cls, value):
@@ -218,13 +239,19 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("submitted_date", mode="before")
@classmethod
def rescue_date(cls, value):
if value == None:
logger.debug(f"\n\nDate coming into pydantic: {value}\n\n")
try:
check = value['value'] == None
except TypeError:
check = True
if check:
return dict(value=date.today(), missing=True)
return value
@field_validator("submitted_date")
@classmethod
def strip_datetime_string(cls, value):
if isinstance(value['value'], datetime):
return value
if isinstance(value['value'], date):
@@ -307,7 +334,6 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("submission_type", mode='before')
@classmethod
def make_submission_type(cls, value, values):
logger.debug(f"Submission type coming into pydantic: {value}")
if not isinstance(value, dict):
value = {"value": value}
if check_not_nan(value['value']):
@@ -331,8 +357,8 @@ class PydSubmission(BaseModel, extra='allow'):
def handle_duplicate_samples(self):
"""
Collapses multiple samples with same submitter id into one with lists for rows, columns
TODO: Find out if this is really necessary
Collapses multiple samples with same submitter id into one with lists for rows, columns.
Necessary to prevent trying to create duplicate samples in SQL creation.
"""
submitter_ids = list(set([sample.submitter_id for sample in self.samples]))
output = []
@@ -581,9 +607,37 @@ class PydSubmission(BaseModel, extra='allow'):
logger.debug(f"Template rendered as: {render}")
return render
class PydContact(BaseModel):
def check_kit_integrity(self, reagenttypes:list=[]) -> Report:
"""
Ensures all reagents expected in kit are listed in Submission
Args:
reagenttypes (list | None, optional): List to check against complete list. Defaults to None.
Returns:
Report: Result object containing a message and any missing components.
"""
report = Report()
ext_kit = KitType.query(name=self.extraction_kit['value'])
ext_kit_rtypes = [item.name for item in ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])]
reagenttypes = [item.type for item in self.reagents]
logger.debug(f"Kit reagents: {ext_kit_rtypes}")
logger.debug(f"Submission reagents: {reagenttypes}")
# check if lists are equal
check = set(ext_kit_rtypes) == set(reagenttypes)
logger.debug(f"Checking if reagents match kit contents: {check}")
# what reagent types are in both lists?
missing = list(set(ext_kit_rtypes).difference(reagenttypes))
logger.debug(f"Missing reagents types: {missing}")
# if lists are equal return no problem
if len(missing)==0:
result = None
else:
result = Result(msg=f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.upper() for item in missing]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!", status="Warning")
report.add_result(result)
return report
class PydContact(BaseModel):
name: str
phone: str|None
email: str|None