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

update to First Strand constructor

Browse Source
This commit is contained in:
Landon Wark
2023-10-12 13:09:12 -05:00
parent 1b6d415788
commit 957edb814a
13 changed files with 236 additions and 56 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
src/submissions/backend/db/functions/lookups.py
View File

@@ -417,7 +417,8 @@ def lookup_reagenttype_kittype_association(ctx:Settings,
def lookup_submission_sample_association(ctx:Settings,
submission:models.BasicSubmission|str|None=None,
sample:models.BasicSample|str|None=None,
limit:int=0
limit:int=0,
chronologic:bool=False
) -> models.SubmissionSampleAssociation|List[models.SubmissionSampleAssociation]:
query = setup_lookup(ctx=ctx, locals=locals()).query(models.SubmissionSampleAssociation)
match submission:
@@ -435,6 +436,8 @@ def lookup_submission_sample_association(ctx:Settings,
case _:
pass
logger.debug(f"Query count: {query.count()}")
if chronologic:
query.join(models.BasicSubmission).order_by(models.BasicSubmission.submitted_date)
if query.count() == 1:
limit = 1
return query_return(query=query, limit=limit)

2
src/submissions/backend/db/functions/misc.py
View File

@@ -247,6 +247,8 @@ def get_polymorphic_subclass(base:object, polymorphic_identity:str|None=None):
Returns:
_type_: Subclass, or parent class on
"""
if isinstance(polymorphic_identity, dict):
polymorphic_identity = polymorphic_identity['value']
if polymorphic_identity == None:
return base
else:

90
src/submissions/backend/db/models/submissions.py
View File

@@ -1,6 +1,7 @@
'''
Models for the main submission types.
'''
from getpass import getuser
import math
from . import Base
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT, case
@@ -15,7 +16,8 @@ from pandas import Timestamp
from dateutil.parser import parse
import re
import pandas as pd
from tools import row_map
from openpyxl import Workbook
from tools import check_not_nan, row_map
logger = logging.getLogger(f"submissions.{__name__}")
@@ -238,6 +240,20 @@ class BasicSubmission(Base):
continue
return output_list
@classmethod
def custom_platemap(cls, xl:pd.ExcelFile, plate_map:pd.DataFrame) -> pd.DataFrame:
"""
Stupid stopgap solution to there being an issue with the Bacterial Culture plate map
Args:
xl (pd.ExcelFile): original xl workbook
plate_map (pd.DataFrame): original plate map
Returns:
pd.DataFrame: updated plate map.
"""
return plate_map
@classmethod
def parse_info(cls, input_dict:dict, xl:pd.ExcelFile|None=None) -> dict:
"""
@@ -265,6 +281,19 @@ class BasicSubmission(Base):
"""
logger.debug(f"Called {cls.__name__} sample parser")
return input_dict
@classmethod
def custom_autofill(cls, input_excel:Workbook) -> Workbook:
"""
Adds custom autofill methods for submission
Args:
input_excel (Workbook): input workbook
Returns:
Workbook: updated workbook
"""
return input_excel
# Below are the custom submission types
@@ -286,6 +315,49 @@ class BacterialCulture(BasicSubmission):
if full_data:
output['controls'] = [item.to_sub_dict() for item in self.controls]
return output
@classmethod
def custom_platemap(cls, xl: pd.ExcelFile, plate_map: pd.DataFrame) -> pd.DataFrame:
"""
Stupid stopgap solution to there being an issue with the Bacterial Culture plate map. Extends parent.
Args:
xl (pd.ExcelFile): original xl workbook
plate_map (pd.DataFrame): original plate map
Returns:
pd.DataFrame: updated plate map.
"""
plate_map = super().custom_platemap(xl, plate_map)
num1 = xl.parse("Sample List").iloc[40,1]
num2 = xl.parse("Sample List").iloc[41,1]
logger.debug(f"Broken: {plate_map.iloc[5,0]}, {plate_map.iloc[6,0]}")
logger.debug(f"Replace: {num1}, {num2}")
if not check_not_nan(plate_map.iloc[5,0]):
plate_map.iloc[5,0] = num1
if not check_not_nan(plate_map.iloc[6,0]):
plate_map.iloc[6,0] = num2
return plate_map
@classmethod
def custom_autofill(cls, input_excel: Workbook) -> Workbook:
"""
Stupid stopgap solution to there being an issue with the Bacterial Culture plate map. Extends parent.
Args:
input_excel (Workbook): Input openpyxl workbook
Returns:
Workbook: Updated openpyxl workbook
"""
input_excel = super().custom_autofill(input_excel)
sheet = input_excel['Plate Map']
if sheet.cell(12,2).value == None:
sheet.cell(row=12, column=2, value="=IF(ISBLANK('Sample List'!$B42),\"\",'Sample List'!$B42)")
if sheet.cell(13,2).value == None:
sheet.cell(row=13, column=2, value="=IF(ISBLANK('Sample List'!$B43),\"\",'Sample List'!$B43)")
input_excel["Sample List"].cell(row=15, column=2, value=getuser()[0:2].upper())
return input_excel
class Wastewater(BasicSubmission):
"""
@@ -326,8 +398,7 @@ class Wastewater(BasicSubmission):
if xl != None:
input_dict['csv'] = xl.parse("Copy to import file")
return input_dict
class WastewaterArtic(BasicSubmission):
"""
derivative submission type for artic wastewater
@@ -371,7 +442,6 @@ class WastewaterArtic(BasicSubmission):
input_dict['submitter_id'] = re.sub(r"\s\(.+\)$", "", str(input_dict['submitter_id'])).strip()
return input_dict
class BasicSample(Base):
"""
Base of basic sample which polymorphs into BCSample and WWSample
@@ -457,7 +527,7 @@ class BasicSample(Base):
Sample name: {self.submitter_id}<br>
Well: {row_map[assoc.row]}{assoc.column}
"""
return dict(name=self.submitter_id, positive=False, tooltip=tooltip_text)
return dict(name=self.submitter_id[:10], positive=False, tooltip=tooltip_text)
class WastewaterSample(BasicSample):
"""
@@ -538,6 +608,16 @@ class WastewaterSample(BasicSample):
except (TypeError, AttributeError) as e:
logger.error(f"Couldn't set tooltip for {self.rsl_number}. Looks like there isn't PCR data.")
return sample
def get_recent_ww_submission(self):
results = [sub for sub in self.submissions if isinstance(sub, Wastewater)]
if len(results) > 1:
results = results.sort(key=lambda sub: sub.submitted_date)
try:
return results[0]
except IndexError:
return None
class BacterialCultureSample(BasicSample):
"""