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