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

Expanded testing capabilities.

Browse Source
This commit is contained in:
Landon Wark
2023-04-11 14:06:10 -05:00
parent 4398517a3e
commit d926ca7c9c
4 changed files with 20 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files

7
src/submissions/backend/db/models/kits.py
View File

@@ -4,6 +4,7 @@ All kit and reagent related models
from . import Base
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT
from sqlalchemy.orm import relationship
from datetime import date
import logging
logger = logging.getLogger(f'submissions.{__name__}')
@@ -100,9 +101,11 @@ class Reagent(Base):
place_holder = self.expiry + self.type.eol_ext
# logger.debug(f"EOL_ext for {self.lot} -- {self.expiry} + {self.type.eol_ext} = {place_holder}")
except TypeError as e:
logger.debug(f"We got a type error setting {self.lot} expiry: {e}.")
place_holder = date.today()
logger.debug(f"We got a type error setting {self.lot} expiry: {e}. setting to today for testing")
except AttributeError as e:
logger.debug(f"We got an attribute error setting {self.lot} expiry: {e}.")
place_holder = date.today()
logger.debug(f"We got an attribute error setting {self.lot} expiry: {e}. Setting to today for testing")
return {
"type": type,
"lot": self.lot,

19
src/submissions/backend/excel/reports.py
View File

@@ -99,7 +99,7 @@ def convert_data_list_to_df(ctx:dict, input:list[dict], subtype:str|None=None) -
"""
df = DataFrame.from_records(input)
df.to_excel("test.xlsx", engine="openpyxl")
# df.to_excel("test.xlsx", engine="openpyxl")
safe = ['name', 'submitted_date', 'genus', 'target']
for column in df.columns:
if "percent" in column:
@@ -139,6 +139,7 @@ def df_column_renamer(df:DataFrame) -> DataFrame:
def displace_date(df:DataFrame) -> DataFrame:
"""
This function serves to split samples that were submitted on the same date by incrementing dates.
It will shift the date forward by one day if it is the same day as an existing date in a list.
Args:
df (DataFrame): input dataframe composed of control records
@@ -149,17 +150,23 @@ def displace_date(df:DataFrame) -> DataFrame:
logger.debug(f"Unique items: {df['name'].unique()}")
# get submitted dates for each control
dict_list = [dict(name=item, date=df[df.name == item].iloc[0]['submitted_date']) for item in sorted(df['name'].unique())]
previous_dates = []
for ii, item in enumerate(dict_list):
try:
check = item['date'] == dict_list[ii-1]['date']
# check = item['date'] == dict_list[ii-1]['date']
check = item['date'] in previous_dates
except IndexError:
check = False
if check:
# occurences = previous_dates.count(item['date'])
logger.debug(f"We found one! Increment date!\n\t{item['date'] - timedelta(days=1)}")
# get df locations where name == item name
mask = df['name'] == item['name']
# increment date in dataframe
df.loc[mask, 'submitted_date'] = df.loc[mask, 'submitted_date'].apply(lambda x: x + timedelta(days=1))
previous_dates.append(item['date'] + timedelta(days=1))
else:
previous_dates.append(item['date'])
return df
@@ -188,8 +195,8 @@ def drop_reruns_from_df(ctx:dict, df: DataFrame) -> DataFrame:
Returns:
DataFrame: dataframe with originals removed in favour of repeats.
"""
sample_names = get_unique_values_in_df_column(df, column_name="name")
if 'rerun_regex' in ctx:
sample_names = get_unique_values_in_df_column(df, column_name="name")
# logger.debug(f"Compiling regex from: {settings['rerun_regex']}")
rerun_regex = re.compile(fr"{ctx['rerun_regex']}")
for sample in sample_names:
@@ -199,6 +206,6 @@ def drop_reruns_from_df(ctx:dict, df: DataFrame) -> DataFrame:
first_run = re.sub(rerun_regex, "", sample)
# logger.debug(f"First run: {first_run}")
df = df.drop(df[df.name == first_run].index)
return df
else:
return None
return df
# else:
# return df