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Everything working pretty well.

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This commit is contained in:
Landon Wark
2024-02-20 14:36:58 -06:00
parent a7e915995e
commit 1e711149f1
14 changed files with 62 additions and 37 deletions
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29
src/submissions/backend/db/models/kits.py
View File

@@ -4,10 +4,10 @@ All kit and reagent related models
from __future__ import annotations
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.ext.associationproxy import association_proxy, AssociationProxy
from sqlalchemy.ext.associationproxy import association_proxy
from datetime import date
import logging, re
from tools import check_authorization, setup_lookup, Report, Result, Settings
from tools import check_authorization, setup_lookup, Report, Result
from typing import List
from pandas import ExcelFile
from pathlib import Path
@@ -921,23 +921,32 @@ class SubmissionReagentAssociation(BaseClass):
from . import BasicSubmission
query: Query = cls.__database_session__.query(cls)
match reagent:
case Reagent():
case Reagent() | str():
# logger.debug(f"Lookup SubmissionReagentAssociation by reagent Reagent {reagent}")
if isinstance(reagent, str):
reagent = Reagent.query(lot_number=reagent)
query = query.filter(cls.reagent==reagent)
case str():
# logger.debug(f"Lookup SubmissionReagentAssociation by reagent str {reagent}")
query = query.join(Reagent).filter(Reagent.lot==reagent)
# case str():
# logger.debug(f"Lookup SubmissionReagentAssociation by reagent str {reagent}")
# query = query.filter(cls.reagent==reagent)
# logger.debug(f"Result: {query.all()}")
case _:
pass
match submission:
case BasicSubmission():
case BasicSubmission() | str():
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_number=submission)
# logger.debug(f"Lookup SubmissionReagentAssociation by submission BasicSubmission {submission}")
query = query.filter(cls.submission==submission)
case str():
# logger.debug(f"Lookup SubmissionReagentAssociation by submission str {submission}")
query = query.join(BasicSubmission).filter(BasicSubmission.rsl_plate_num==submission)
# case str():
# logger.debug(f"Lookup SubmissionReagentAssociation by submission str {submission}")
# submission = BasicSubmission.query(rsl_number=submission)
# query = query.filter(cls.submission==submission)
# logger.debug(f"Result: {query.all()}")
case int():
# logger.debug(f"Lookup SubmissionReagentAssociation by submission id {submission}")
submission = BasicSubmission.query(id=submission)
query = query.join(BasicSubmission).filter(BasicSubmission.id==submission)
case _:
pass

22
src/submissions/backend/db/models/submissions.py
View File

@@ -338,7 +338,7 @@ class BasicSubmission(BaseClass):
logger.debug(f"Got {len(subs)} submissions.")
df = pd.DataFrame.from_records(subs)
# Exclude sub information
for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents', 'equipment']:
for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents', 'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number']:
try:
df = df.drop(item, axis=1)
except:
@@ -1068,7 +1068,21 @@ class BacterialCulture(BasicSubmission):
outstr = re.sub(r"BC(\d{6})", r"BC-\1", outstr, flags=re.IGNORECASE)
except (AttributeError, TypeError) as e:
outstr = RSLNamer.construct_new_plate_name(data=data)
return outstr
try:
plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
# logger.debug(f"Plate number is: {plate_number}")
except AttributeError as e:
plate_number = "1"
outstr = re.sub(r"(\d{8})(-|_)?\d?(R\d?)?", rf"\1-{plate_number}\3", outstr)
# logger.debug(f"After addition of plate number the plate name is: {outstr}")
try:
repeat = re.search(r"-\dR(?P<repeat>\d)?", outstr).groupdict()['repeat']
if repeat == None:
repeat = "1"
except AttributeError as e:
repeat = ""
return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
# return outstr
@classmethod
def get_regex(cls) -> str:
@@ -1078,7 +1092,7 @@ class BacterialCulture(BasicSubmission):
Returns:
str: string for regex construction
"""
return "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\s]|$)?R?\d?)?)"
return "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
@classmethod
def filename_template(cls):
@@ -1244,7 +1258,7 @@ class Wastewater(BasicSubmission):
Returns:
str: String for regex construction
"""
return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\s]|$)?R?\d?)?)"
return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
@classmethod
def adjust_autofill_samples(cls, samples: List[Any]) -> List[Any]: