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moved frontend function check_not_nan to tools

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Landon Wark
2023-02-15 09:29:03 -06:00
parent a9ce9514fc
commit 85dad791ec
15 changed files with 275 additions and 156 deletions
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88
src/submissions/backend/excel/parser.py
View File

@@ -1,13 +1,13 @@
import pandas as pd
from pathlib import Path
from backend.db.models.samples import WWSample, BCSample
from backend.db.models import WWSample, BCSample
import logging
from collections import OrderedDict
import re
import numpy as np
from datetime import date
import uuid
from frontend.functions import check_not_nan
from tools import check_not_nan
logger = logging.getLogger(f"submissions.{__name__}")
@@ -15,7 +15,7 @@ class SheetParser(object):
"""
object to pull and contain data from excel file
"""
def __init__(self, filepath:Path|None = None, **kwargs) -> None:
def __init__(self, filepath:Path|None = None, **kwargs):
"""
Args:
filepath (Path | None, optional): file path to excel sheet. Defaults to None.
@@ -77,12 +77,12 @@ class SheetParser(object):
"""
submission_info = self.xl.parse(sheet_name=sheet_name, dtype=object)
self.sub['submitter_plate_num'] = submission_info.iloc[0][1] #if pd.isnull(submission_info.iloc[0][1]) else string_formatter(submission_info.iloc[0][1])
self.sub['rsl_plate_num'] = submission_info.iloc[10][1] #if pd.isnull(submission_info.iloc[10][1]) else string_formatter(submission_info.iloc[10][1])
self.sub['submitted_date'] = submission_info.iloc[1][1] #if pd.isnull(submission_info.iloc[1][1]) else submission_info.iloc[1][1].date()#.strftime("%Y-%m-%d")
self.sub['submitting_lab'] = submission_info.iloc[0][3] #if pd.isnull(submission_info.iloc[0][3]) else string_formatter(submission_info.iloc[0][3])
self.sub['sample_count'] = submission_info.iloc[2][3] #if pd.isnull(submission_info.iloc[2][3]) else string_formatter(submission_info.iloc[2][3])
self.sub['extraction_kit'] = submission_info.iloc[3][3] #if #pd.isnull(submission_info.iloc[3][3]) else string_formatter(submission_info.iloc[3][3])
self.sub['submitter_plate_num'] = submission_info.iloc[0][1]
self.sub['rsl_plate_num'] = submission_info.iloc[10][1]
self.sub['submitted_date'] = submission_info.iloc[1][1]
self.sub['submitting_lab'] = submission_info.iloc[0][3]
self.sub['sample_count'] = submission_info.iloc[2][3]
self.sub['extraction_kit'] = submission_info.iloc[3][3]
return submission_info
@@ -93,6 +93,12 @@ class SheetParser(object):
"""
def _parse_reagents(df:pd.DataFrame) -> None:
"""
Pulls reagents from the bacterial sub-dataframe
Args:
df (pd.DataFrame): input sub dataframe
"""
for ii, row in df.iterrows():
# skip positive control
if ii == 11:
@@ -119,16 +125,15 @@ class SheetParser(object):
# self.sub[f"lot_{reagent_type}"] = output_var
# update 2023-02-10 to above allowing generation of expiry date in adding reagent to db.
logger.debug(f"Expiry date for imported reagent: {row[3]}")
try:
check = not np.isnan(row[3])
except TypeError:
check = True
if check:
# try:
# check = not np.isnan(row[3])
# except TypeError:
# check = True
if check_not_nan(row[3]):
expiry = row[3].date()
else:
expiry = date.today()
self.sub[f"lot_{reagent_type}"] = {'lot':output_var, 'exp':expiry}
submission_info = self._parse_generic("Sample List")
# iloc is [row][column] and the first row is set as header row so -2
tech = str(submission_info.iloc[11][1])
@@ -160,9 +165,6 @@ class SheetParser(object):
logger.debug(f"Parser result: {self.sub}")
self.sub['samples'] = sample_parse()
def _parse_wastewater(self) -> None:
"""
@@ -170,23 +172,32 @@ class SheetParser(object):
"""
def _parse_reagents(df:pd.DataFrame) -> None:
logger.debug(df)
"""
Pulls reagents from the bacterial sub-dataframe
Args:
df (pd.DataFrame): input sub dataframe
"""
# logger.debug(df)
for ii, row in df.iterrows():
try:
check = not np.isnan(row[5])
except TypeError:
check = True
if not isinstance(row[5], float) and check:
# try:
# check = not np.isnan(row[5])
# except TypeError:
# check = True
if not isinstance(row[5], float) and check_not_nan(row[5]):
# must be prefixed with 'lot_' to be recognized by gui
# regex below will remove 80% from 80% ethanol in the Wastewater kit.
output_key = re.sub(r"\d{1,3}%", "", row[0].lower().strip().replace(' ', '_'))
try:
output_var = row[5].upper()
except AttributeError:
logger.debug(f"Couldn't upperize {row[2]}, must be a number")
logger.debug(f"Couldn't upperize {row[5]}, must be a number")
output_var = row[5]
self.sub[f"lot_{output_key}"] = output_var
# submission_info = self.xl.parse("WW Submissions (ENTER HERE)")
if check_not_nan(row[7]):
expiry = row[7].date()
else:
expiry = date.today()
self.sub[f"lot_{output_key}"] = {'lot':output_var, 'exp':expiry}
submission_info = self._parse_generic("WW Submissions (ENTER HERE)")
enrichment_info = self.xl.parse("Enrichment Worksheet", dtype=object)
enr_reagent_range = enrichment_info.iloc[0:4, 9:20]
@@ -214,17 +225,11 @@ class SheetParser(object):
# self.sub['lot_pre_mix_2'] = qprc_info.iloc[2][14] #if pd.isnull(qprc_info.iloc[2][14]) else string_formatter(qprc_info.iloc[2][14])
# self.sub['lot_positive_control'] = qprc_info.iloc[3][14] #if pd.isnull(qprc_info.iloc[3][14]) else string_formatter(qprc_info.iloc[3][14])
# self.sub['lot_ddh2o'] = qprc_info.iloc[4][14] #if pd.isnull(qprc_info.iloc[4][14]) else string_formatter(qprc_info.iloc[4][14])
# gt individual sample info
# get individual sample info
sample_parser = SampleParser(submission_info.iloc[16:40])
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
self.sub['samples'] = sample_parse()
class SampleParser(object):
"""
@@ -241,7 +246,8 @@ class SampleParser(object):
Returns:
list[BCSample]: list of sample objects
"""
"""
# logger.debug(f"Samples: {self.samples}")
new_list = []
for sample in self.samples:
new = BCSample()
@@ -297,13 +303,3 @@ class SampleParser(object):
new.well_number = sample['Unnamed: 1']
new_list.append(new)
return new_list
# def string_formatter(input):
# logger.debug(f"{input} : {type(input)}")
# match input:
# case int() | float() | np.float64:
# return "{:0.0f}".format(input)
# case _:
# return input

1
src/submissions/backend/excel/reports.py
View File

@@ -10,6 +10,7 @@ from pathlib import Path
logger = logging.getLogger(f"submissions.{__name__}")
# set path of templates depending on pyinstaller/raw python
if getattr(sys, 'frozen', False):
loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
else: