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

Troubleshooting reports

Browse Source
This commit is contained in:
Landon Wark
2023-02-16 15:30:38 -06:00
parent 85dad791ec
commit 1c89c31d25
11 changed files with 146 additions and 40 deletions
Download Patch File Download Diff File Expand all files Collapse all files

55
src/submissions/backend/db/__init__.py
View File

@@ -15,7 +15,9 @@ import json
# from dateutil.relativedelta import relativedelta
from getpass import getuser
import numpy as np
from tools import check_not_nan
from tools import check_not_nan, check_is_power_user
import yaml
from pathlib import Path
logger = logging.getLogger(f"submissions.{__name__}")
@@ -367,7 +369,8 @@ def lookup_org_by_name(ctx:dict, name:str|None) -> models.Organization:
models.Organization: retrieved organization
"""
logger.debug(f"Querying organization: {name}")
return ctx['database_session'].query(models.Organization).filter(models.Organization.name==name).first()
# return ctx['database_session'].query(models.Organization).filter(models.Organization.name==name).first()
return ctx['database_session'].query(models.Organization).filter(models.Organization.name.startswith(name)).first()
def submissions_to_df(ctx:dict, sub_type:str|None=None) -> pd.DataFrame:
"""
@@ -457,13 +460,10 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> dict:
Returns:
dict: a dictionary containing results of db addition
"""
try:
power_users = ctx['power_users']
except KeyError:
logger.debug("This user does not have permission to add kits.")
return {'code':1,'message':"This user does not have permission to add kits."}
logger.debug(f"Adding kit for user: {getuser()}")
if getuser() not in power_users:
# try:
# power_users = ctx['power_users']
# except KeyError:
if not check_is_power_user(ctx=ctx):
logger.debug(f"{getuser()} does not have permission to add kits.")
return {'code':1, 'message':"This user does not have permission to add kits."}
for type in exp:
@@ -499,13 +499,14 @@ def create_org_from_yaml(ctx:dict, org:dict) -> dict:
Returns:
dict: dictionary containing results of db addition
"""
try:
power_users = ctx['power_users']
except KeyError:
logger.debug("This user does not have permission to add kits.")
return {'code':1,'message':"This user does not have permission to add organizations."}
logger.debug(f"Adding organization for user: {getuser()}")
if getuser() not in power_users:
# try:
# power_users = ctx['power_users']
# except KeyError:
# logger.debug("This user does not have permission to add kits.")
# return {'code':1,'message':"This user does not have permission to add organizations."}
# logger.debug(f"Adding organization for user: {getuser()}")
# if getuser() not in power_users:
if not check_is_power_user(ctx=ctx):
logger.debug(f"{getuser()} does not have permission to add kits.")
return {'code':1, 'message':"This user does not have permission to add organizations."}
for client in org:
@@ -623,4 +624,24 @@ def lookup_submission_by_rsl_num(ctx:dict, rsl_num:str):
def lookup_submissions_using_reagent(ctx:dict, reagent:models.Reagent) -> list[models.BasicSubmission]:
return ctx['database_session'].query(models.BasicSubmission).join(reagents_submissions).filter(reagents_submissions.c.reagent_id==reagent.id).all()
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.
Args:
ctx (dict): settings passed down from gui
id (int): id of submission to be deleted.
"""
# In order to properly do this Im' going to have to delete all of the secondary table stuff as well.
sub = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.id==id).first()
backup = sub.to_dict()
with open(Path(ctx['backup_path']).joinpath(f"{sub.rsl_plate_num}-backup({date.today().strftime('%Y%m%d')}).yml"), "w") as f:
yaml.dump(backup, f)
sub.reagents = []
for sample in sub.samples:
ctx['database_session'].delete(sample)
ctx["database_session"].delete(sub)
ctx["database_session"].commit()

2
src/submissions/backend/db/models/controls.py
View File

@@ -56,7 +56,7 @@ class Control(Base):
output = {
"name" : self.name,
"type" : self.controltype.name,
"targets" : " ,".join(targets),
"targets" : ", ".join(targets),
"kraken" : new_kraken[0:5]
}
return output

10
src/submissions/backend/db/models/submissions.py
View File

@@ -74,6 +74,14 @@ class BasicSubmission(Base):
ext_info = json.loads(self.extraction_info)
except TypeError:
ext_info = None
try:
reagents = [item.to_sub_dict() for item in self.reagents]
except:
reagents = None
try:
samples = [item.to_sub_dict() for item in self.samples]
except:
samples = None
output = {
"id": self.id,
"Plate Number": self.rsl_plate_num,
@@ -85,6 +93,8 @@ class BasicSubmission(Base):
"Extraction Kit": ext_kit,
"Technician": self.technician,
"Cost": self.run_cost,
"reagents": reagents,
"samples": samples,
"ext_info": ext_info
}
# logger.debug(f"{self.rsl_plate_num} extraction: {output['Extraction Status']}")

8
src/submissions/backend/excel/parser.py
View File

@@ -187,14 +187,18 @@ class SheetParser(object):
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(' ', '_'))
output_key = re.sub(r"^\d{1,3}%\s?", "", row[0].lower().strip().replace(' ', '_'))
output_key = output_key.strip("_")
try:
output_var = row[5].upper()
except AttributeError:
logger.debug(f"Couldn't upperize {row[5]}, must be a number")
output_var = row[5]
if check_not_nan(row[7]):
expiry = row[7].date()
try:
expiry = row[7].date()
except AttributeError:
expiry = date.today()
else:
expiry = date.today()
self.sub[f"lot_{output_key}"] = {'lot':output_var, 'exp':expiry}

25
src/submissions/backend/excel/reports.py
View File

@@ -41,6 +41,9 @@ def make_report_xlsx(records:list[dict]) -> DataFrame:
# df2.iloc[:, (df2.columns.get_level_values(1)=='sum') & (df2.columns.get_level_values(0)=='Cost')] = df2.iloc[:, (df2.columns.get_level_values(1)=='sum') & (df2.columns.get_level_values(0)=='Cost')].applymap('${:,.2f}'.format)
return df2
# def split_row_item(item:str) -> float:
# return item.split(" ")[-1]
def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
@@ -59,17 +62,23 @@ def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
output = []
logger.debug(f"Report DataFrame: {df}")
for ii, row in enumerate(df.iterrows()):
row = [item for item in row]
logger.debug(f"Row: {row}")
# row = [item for item in row]
logger.debug(f"Row {ii}: {row}")
lab = row[0][0]
logger.debug(type(row))
logger.debug(f"Old lab: {old_lab}, Current lab: {lab}")
kit = dict(name=row[0][1], cost=row[1]['Cost'], plate_count=int(row[1]['Kit Count']), sample_count=int(row[1]['Sample Count']))
logger.debug(f"Name: {row[0][1]}")
data = [item for item in row[1]]
# logger.debug(data)
# logger.debug(f"Cost: {split_row_item(data[1])}")
# logger.debug(f"Kit count: {split_row_item(data[0])}")
# logger.debug(f"Sample Count: {split_row_item(data[2])}")
kit = dict(name=row[0][1], cost=data[1], plate_count=int(data[0]), sample_count=int(data[2]))
if lab == old_lab:
output[ii-1]['kits'].append(kit)
output[ii-1]['total_cost'] += kit['cost']
output[ii-1]['total_samples'] += kit['sample_count']
output[ii-1]['total_plates'] += kit['plate_count']
output[-1]['kits'].append(kit)
output[-1]['total_cost'] += kit['cost']
output[-1]['total_samples'] += kit['sample_count']
output[-1]['total_plates'] += kit['plate_count']
else:
adder = dict(lab=lab, kits=[kit], total_cost=kit['cost'], total_samples=kit['sample_count'], total_plates=kit['plate_count'])
output.append(adder)