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

Refactored to increase ui robustness.

Browse Source
This commit is contained in:
Landon Wark
2023-04-04 09:31:37 -05:00
parent 3c9f095937
commit 4398517a3e
15 changed files with 1580 additions and 672 deletions
Download Patch File Download Diff File Expand all files Collapse all files

83
src/submissions/backend/db/functions.py
View File

@@ -5,7 +5,7 @@ Convenience functions for interacting with the database.
from . import models
from .models.kits import reagenttypes_kittypes
from .models.submissions import reagents_submissions
from .models.samples import WWSample
# from .models.samples import WWSample
import pandas as pd
import sqlalchemy.exc
import sqlite3
@@ -18,7 +18,6 @@ from sqlalchemy.engine import Engine
import json
from getpass import getuser
import numpy as np
import yaml
from pathlib import Path
@@ -42,8 +41,10 @@ def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None|d
Returns:
None|dict : object that indicates issue raised for reporting in gui
"""
from tools import format_rsl_number
logger.debug(f"Hello from store_submission")
# Add all samples to sample table
base_submission.rsl_plate_num = format_rsl_number(base_submission.rsl_plate_num)
for sample in base_submission.samples:
sample.rsl_plate = base_submission
logger.debug(f"Attempting to add sample: {sample.to_string()}")
@@ -60,14 +61,13 @@ def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None|d
except (sqlite3.IntegrityError, sqlalchemy.exc.IntegrityError) as e:
logger.debug(f"Hit an integrity error : {e}")
ctx['database_session'].rollback()
return {"message":"This plate number already exists, so we can't add it."}
return {"message":"This plate number already exists, so we can't add it.", "status":"Critical"}
except (sqlite3.OperationalError, sqlalchemy.exc.IntegrityError) as e:
logger.debug(f"Hit an operational error: {e}")
ctx['database_session'].rollback()
return {"message":"The database is locked for editing."}
return {"message":"The database is locked for editing.", "status":"Critical"}
return None
def store_reagent(ctx:dict, reagent:models.Reagent) -> None|dict:
"""
Inserts a reagent into the database.
@@ -87,7 +87,6 @@ def store_reagent(ctx:dict, reagent:models.Reagent) -> None|dict:
return {"message":"The database is locked for editing."}
return None
def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmission:
"""
Construct submission object from dictionary
@@ -99,14 +98,17 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
Returns:
models.BasicSubmission: Constructed submission object
"""
from tools import check_not_nan
from tools import check_regex_match, RSLNamer
# convert submission type into model name
query = info_dict['submission_type'].replace(" ", "")
# Ensure an rsl plate number exists for the plate
if info_dict["rsl_plate_num"] == 'nan' or info_dict["rsl_plate_num"] == None or not check_not_nan(info_dict["rsl_plate_num"]):
# if info_dict["rsl_plate_num"] == 'nan' or info_dict["rsl_plate_num"] == None or not check_not_nan(info_dict["rsl_plate_num"]):
if not check_regex_match("^RSL", info_dict["rsl_plate_num"]):
instance = None
msg = "A proper RSL plate number is required."
return instance, {'code': 2, 'message': "A proper RSL plate number is required."}
else:
info_dict['rsl_plate_num'] = RSLNamer(info_dict["rsl_plate_num"]).parsed_name
# check database for existing object
instance = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num==info_dict['rsl_plate_num']).first()
# get model based on submission type converted above
@@ -171,7 +173,6 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
logger.debug(f"Constructed submissions message: {msg}")
return instance, {'code':code, 'message':msg}
def construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
"""
Construct reagent object from dictionary
@@ -204,7 +205,6 @@ def construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
# pass
return reagent
def lookup_reagent(ctx:dict, reagent_lot:str) -> models.Reagent:
"""
Query db for reagent based on lot number
@@ -219,7 +219,6 @@ def lookup_reagent(ctx:dict, reagent_lot:str) -> models.Reagent:
lookedup = ctx['database_session'].query(models.Reagent).filter(models.Reagent.lot==reagent_lot).first()
return lookedup
def get_all_reagenttype_names(ctx:dict) -> list[str]:
"""
Lookup all reagent types and get names
@@ -233,7 +232,6 @@ def get_all_reagenttype_names(ctx:dict) -> list[str]:
lookedup = [item.__str__() for item in ctx['database_session'].query(models.ReagentType).all()]
return lookedup
def lookup_reagenttype_by_name(ctx:dict, rt_name:str) -> models.ReagentType:
"""
Lookup a single reagent type by name
@@ -250,7 +248,6 @@ def lookup_reagenttype_by_name(ctx:dict, rt_name:str) -> models.ReagentType:
logger.debug(f"Found ReagentType: {lookedup}")
return lookedup
def lookup_kittype_by_use(ctx:dict, used_by:str) -> list[models.KitType]:
"""
Lookup kits by a sample type its used for
@@ -264,7 +261,6 @@ def lookup_kittype_by_use(ctx:dict, used_by:str) -> list[models.KitType]:
"""
return ctx['database_session'].query(models.KitType).filter(models.KitType.used_for.contains(used_by)).all()
def lookup_kittype_by_name(ctx:dict, name:str) -> models.KitType:
"""
Lookup a kit type by name
@@ -279,7 +275,6 @@ def lookup_kittype_by_name(ctx:dict, name:str) -> models.KitType:
logger.debug(f"Querying kittype: {name}")
return ctx['database_session'].query(models.KitType).filter(models.KitType.name==name).first()
def lookup_regent_by_type_name(ctx:dict, type_name:str) -> list[models.Reagent]:
"""
Lookup reagents by their type name
@@ -293,7 +288,6 @@ def lookup_regent_by_type_name(ctx:dict, type_name:str) -> list[models.Reagent]:
"""
return ctx['database_session'].query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name==type_name).all()
def lookup_regent_by_type_name_and_kit_name(ctx:dict, type_name:str, kit_name:str) -> list[models.Reagent]:
"""
Lookup reagents by their type name and kits they belong to (Broken... maybe cursed, I'm not sure.)
@@ -325,7 +319,6 @@ def lookup_regent_by_type_name_and_kit_name(ctx:dict, type_name:str, kit_name:st
output = rt_types.instances
return output
def lookup_all_submissions_by_type(ctx:dict, sub_type:str|None=None) -> list[models.BasicSubmission]:
"""
Get all submissions, filtering by type if given
@@ -399,7 +392,6 @@ def submissions_to_df(ctx:dict, sub_type:str|None=None) -> pd.DataFrame:
except:
logger.warning(f"Couldn't drop 'pcr_info' column from submissionsheet df.")
return df
def lookup_submission_by_id(ctx:dict, id:int) -> models.BasicSubmission:
"""
@@ -414,7 +406,6 @@ def lookup_submission_by_id(ctx:dict, id:int) -> models.BasicSubmission:
"""
return ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.id==id).first()
def lookup_submissions_by_date_range(ctx:dict, start_date:datetime.date, end_date:datetime.date) -> list[models.BasicSubmission]:
"""
Lookup submissions greater than start_date and less than end_date
@@ -432,7 +423,6 @@ def lookup_submissions_by_date_range(ctx:dict, start_date:datetime.date, end_dat
end_date = end_date.strftime("%Y-%m-%d")
return ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.submitted_date.between(start_date, end_date)).all()
def get_all_Control_Types_names(ctx:dict) -> list[str]:
"""
Grabs all control type names from db.
@@ -448,7 +438,6 @@ def get_all_Control_Types_names(ctx:dict) -> list[str]:
logger.debug(f"Control Types: {conTypes}")
return conTypes
def create_kit_from_yaml(ctx:dict, exp:dict) -> dict:
"""
Create and store a new kit in the database based on a .yml file
@@ -491,7 +480,6 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> dict:
ctx['database_session'].commit()
return {'code':0, 'message':'Kit has been added', 'status': 'information'}
def create_org_from_yaml(ctx:dict, org:dict) -> dict:
"""
Create and store a new organization based on a .yml file
@@ -528,7 +516,6 @@ def create_org_from_yaml(ctx:dict, org:dict) -> dict:
ctx["database_session"].commit()
return {"code":0, "message":"Organization has been added."}
def lookup_all_sample_types(ctx:dict) -> list[str]:
"""
Lookup all sample types and get names
@@ -544,7 +531,6 @@ def lookup_all_sample_types(ctx:dict) -> list[str]:
uses = list(set([item for sublist in uses for item in sublist]))
return uses
def get_all_available_modes(ctx:dict) -> list[str]:
"""
Get types of analysis for controls
@@ -564,7 +550,6 @@ def get_all_available_modes(ctx:dict) -> list[str]:
cols = []
return cols
def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None, end_date:date|None=None) -> list[models.Control]:
"""
Returns a list of control objects that are instances of the input controltype.
@@ -589,7 +574,6 @@ def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None,
logger.debug(f"Returned controls between dates: {output}")
return output
def get_control_subtypes(ctx:dict, type:str, mode:str) -> list[str]:
"""
Get subtypes for a control analysis mode
@@ -617,7 +601,6 @@ def get_control_subtypes(ctx:dict, type:str, mode:str) -> list[str]:
subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item]
return subtypes
def get_all_controls(ctx:dict) -> list[models.Control]:
"""
Retrieve a list of all controls from the database
@@ -630,7 +613,6 @@ def get_all_controls(ctx:dict) -> list[models.Control]:
"""
return ctx['database_session'].query(models.Control).all()
def lookup_submission_by_rsl_num(ctx:dict, rsl_num:str) -> models.BasicSubmission:
"""
Retrieve a submission from the database based on rsl plate number
@@ -644,7 +626,6 @@ def lookup_submission_by_rsl_num(ctx:dict, rsl_num:str) -> models.BasicSubmissio
"""
return ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num.startswith(rsl_num)).first()
def lookup_submissions_using_reagent(ctx:dict, reagent:models.Reagent) -> list[models.BasicSubmission]:
"""
Retrieves each submission using a specified reagent.
@@ -658,7 +639,6 @@ def lookup_submissions_using_reagent(ctx:dict, reagent:models.Reagent) -> list[m
"""
return ctx['database_session'].query(models.BasicSubmission).join(reagents_submissions).filter(reagents_submissions.c.reagent_id==reagent.id).all()
def delete_submission_by_id(ctx:dict, id:int) -> None:
"""
Deletes a submission and its associated samples from the database.
@@ -683,13 +663,12 @@ def delete_submission_by_id(ctx:dict, id:int) -> None:
ctx["database_session"].delete(sub)
ctx["database_session"].commit()
def lookup_ww_sample_by_rsl_sample_number(ctx:dict, rsl_number:str) -> models.WWSample:
"""
Retrieves wastewater sampel from database by rsl sample number
Retrieves wastewater sample from database by rsl sample number
Args:
ctx (dict): settings passed dwon from gui
ctx (dict): settings passed down from gui
rsl_number (str): sample number assigned by robotics lab
Returns:
@@ -697,6 +676,39 @@ def lookup_ww_sample_by_rsl_sample_number(ctx:dict, rsl_number:str) -> models.WW
"""
return ctx['database_session'].query(models.WWSample).filter(models.WWSample.rsl_number==rsl_number).first()
def lookup_ww_sample_by_sub_sample_rsl(ctx:dict, sample_rsl:str, plate_rsl:str) -> models.WWSample:
"""
Retrieves a wastewater sample from the database by its rsl sample number and parent rsl plate number.
This will likely replace simply looking up by the sample rsl above cine I need to control for repeats.
Args:
ctx (dict): settings passed down from the gui
sample_rsl (str): rsl number of the relevant sample
plate_rsl (str): rsl number of the parent plate
Returns:
models.WWSample: Relevant wastewater object
"""
return ctx['database_session'].query(models.WWSample).join(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num==plate_rsl).filter(models.WWSample.rsl_number==sample_rsl).first()
def lookup_ww_sample_by_sub_sample_well(ctx:dict, sample_rsl:str, well_num:str, plate_rsl:str) -> models.WWSample:
"""
Retrieves a wastewater sample from the database by its rsl sample number and parent rsl plate number.
This will likely replace simply looking up by the sample rsl above cine I need to control for repeats.
Args:
ctx (dict): settings passed down from the gui
sample_rsl (str): rsl number of the relevant sample
well_num (str): well number of the relevant sample
plate_rsl (str): rsl number of the parent plate
Returns:
models.WWSample: Relevant wastewater object
"""
return ctx['database_session'].query(models.WWSample).join(models.BasicSubmission) \
.filter(models.BasicSubmission.rsl_plate_num==plate_rsl) \
.filter(models.WWSample.rsl_number==sample_rsl) \
.filter(models.WWSample.well_number==well_num).first()
def update_ww_sample(ctx:dict, sample_obj:dict):
"""
@@ -706,7 +718,10 @@ def update_ww_sample(ctx:dict, sample_obj:dict):
ctx (dict): settings passed down from gui
sample_obj (dict): dictionary representing new values for database object
"""
ww_samp = lookup_ww_sample_by_rsl_sample_number(ctx=ctx, rsl_number=sample_obj['sample'])
# ww_samp = lookup_ww_sample_by_rsl_sample_number(ctx=ctx, rsl_number=sample_obj['sample'])
logger.debug(f"Looking up {sample_obj['sample']} in plate {sample_obj['plate_rsl']}")
ww_samp = lookup_ww_sample_by_sub_sample_rsl(ctx=ctx, sample_rsl=sample_obj['sample'], plate_rsl=sample_obj['plate_rsl'])
# ww_samp = lookup_ww_sample_by_sub_sample_well(ctx=ctx, sample_rsl=sample_obj['sample'], well_num=sample_obj['well_num'], plate_rsl=sample_obj['plate_rsl'])
if ww_samp != None:
for key, value in sample_obj.items():
logger.debug(f"Setting {key} to {value}")

4
src/submissions/backend/db/models/samples.py
View File

@@ -27,6 +27,8 @@ class WWSample(Base):
notes = Column(String(2000))
ct_n1 = Column(FLOAT(2)) #: AKA ct for N1
ct_n2 = Column(FLOAT(2)) #: AKA ct for N2
n1_status = Column(String(32))
n2_status = Column(String(32))
seq_submitted = Column(BOOLEAN())
ww_seq_run_id = Column(String(64))
sample_type = Column(String(8))
@@ -50,7 +52,7 @@ class WWSample(Base):
dict: well location and id NOTE: keys must sync with BCSample to_sub_dict below
"""
if self.ct_n1 != None and self.ct_n2 != None:
name = f"{self.ww_sample_full_id}\n\t- ct N1: {'{:.2f}'.format(self.ct_n1)}, ct N2: {'{:.2f}'.format(self.ct_n1)}"
name = f"{self.ww_sample_full_id}\n\t- ct N1: {'{:.2f}'.format(self.ct_n1)} ({self.n1_status})\n\t- ct N2: {'{:.2f}'.format(self.ct_n2)} ({self.n2_status})"
else:
name = self.ww_sample_full_id
return {