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

moved frontend function check_not_nan to tools

Browse Source
This commit is contained in:
Landon Wark
2023-02-15 09:29:03 -06:00
parent a9ce9514fc
commit 85dad791ec
15 changed files with 275 additions and 156 deletions
Download Patch File Download Diff File Expand all files Collapse all files

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

@@ -15,6 +15,7 @@ import json
# from dateutil.relativedelta import relativedelta
from getpass import getuser
import numpy as np
from tools import check_not_nan
logger = logging.getLogger(f"submissions.{__name__}")
@@ -101,8 +102,13 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
# convert submission type into model name
query = info_dict['submission_type'].replace(" ", "")
# check database for existing object
if info_dict["rsl_plate_num"] == 'nan' or info_dict["rsl_plate_num"] == None or not check_not_nan(info_dict["rsl_plate_num"]):
code = 2
instance = None
msg = "A proper RSL plate number is required."
return instance, {'code': 2, 'message': "A proper RSL plate number is required."}
instance = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num==info_dict['rsl_plate_num']).first()
msg = "This submission already exists.\nWould you like to overwrite?"
# get model based on submission type converted above
logger.debug(f"Looking at models for submission type: {query}")
model = getattr(models, query)
@@ -113,6 +119,10 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
instance = model()
logger.debug(f"Submission doesn't exist yet, creating new instance: {instance}")
msg = None
code =0
else:
code = 1
msg = "This submission already exists.\nWould you like to overwrite?"
for item in info_dict:
logger.debug(f"Setting {item} to {info_dict[item]}")
# set fields based on keys in dictionary
@@ -151,9 +161,14 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
except (TypeError, AttributeError):
logger.debug(f"Looks like that kit doesn't have cost breakdown yet, using full plate cost.")
instance.run_cost = instance.extraction_kit.cost_per_run
logger.debug(f"Constructed instance: {instance.to_string()}")
# We need to make sure there's a proper rsl plate number
try:
logger.debug(f"Constructed instance: {instance.to_string()}")
except AttributeError as e:
logger.debug(f"Something went wrong constructing instance {info_dict['rsl_plate_num']}: {e}")
logger.debug(msg)
return instance, {'message':msg}
return instance, {'code':code, 'message':msg}
def construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
@@ -244,7 +259,7 @@ def lookup_kittype_by_use(ctx:dict, used_by:str) -> list[models.KitType]:
Returns:
list[models.KitType]: list of kittypes that have that sample type in their uses
"""
return ctx['database_session'].query(models.KitType).filter(models.KitType.used_for.contains(used_by))
return ctx['database_session'].query(models.KitType).filter(models.KitType.used_for.contains(used_by)).all()
def lookup_kittype_by_name(ctx:dict, name:str) -> models.KitType:
"""
@@ -278,7 +293,7 @@ def lookup_regent_by_type_name(ctx:dict, type_name:str) -> list[models.Reagent]:
def lookup_regent_by_type_name_and_kit_name(ctx:dict, type_name:str, kit_name:str) -> list[models.Reagent]:
"""
Lookup reagents by their type name and kits they belong to (Broken)
Lookup reagents by their type name and kits they belong to (Broken... maybe cursed, I'm not sure.)
Args:
ctx (dict): settings pass by gui
@@ -292,10 +307,6 @@ def lookup_regent_by_type_name_and_kit_name(ctx:dict, type_name:str, kit_name:st
# Hang on, this is going to be a long one.
# by_type = ctx['database_session'].query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name.endswith(type_name)).all()
rt_types = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name.endswith(type_name))
# add filter for kit name... which I can not get to work.
# add_in = by_type.join(models.ReagentType.kits).filter(models.KitType.name==kit_name)
try:
@@ -315,7 +326,7 @@ def lookup_regent_by_type_name_and_kit_name(ctx:dict, type_name:str, kit_name:st
return output
def lookup_all_submissions_by_type(ctx:dict, type:str|None=None) -> list[models.BasicSubmission]:
def lookup_all_submissions_by_type(ctx:dict, sub_type:str|None=None) -> list[models.BasicSubmission]:
"""
Get all submissions, filtering by type if given
@@ -326,10 +337,10 @@ def lookup_all_submissions_by_type(ctx:dict, type:str|None=None) -> list[models.
Returns:
_type_: list of retrieved submissions
"""
if type == None:
if sub_type == None:
subs = ctx['database_session'].query(models.BasicSubmission).all()
else:
subs = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.submission_type==type.lower().replace(" ", "_")).all()
subs = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.submission_type==sub_type.lower().replace(" ", "_")).all()
return subs
def lookup_all_orgs(ctx:dict) -> list[models.Organization]:
@@ -358,7 +369,7 @@ def lookup_org_by_name(ctx:dict, name:str|None) -> models.Organization:
logger.debug(f"Querying organization: {name}")
return ctx['database_session'].query(models.Organization).filter(models.Organization.name==name).first()
def submissions_to_df(ctx:dict, type:str|None=None) -> pd.DataFrame:
def submissions_to_df(ctx:dict, sub_type:str|None=None) -> pd.DataFrame:
"""
Convert submissions looked up by type to dataframe
@@ -369,9 +380,9 @@ def submissions_to_df(ctx:dict, type:str|None=None) -> pd.DataFrame:
Returns:
pd.DataFrame: dataframe constructed from retrieved submissions
"""
logger.debug(f"Type: {type}")
logger.debug(f"Type: {sub_type}")
# pass to lookup function
subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, type=type)]
subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, sub_type=sub_type)]
df = pd.DataFrame.from_records(subs)
# logger.debug(f"Pre: {df['Technician']}")
try:
@@ -435,14 +446,17 @@ def get_all_Control_Types_names(ctx:dict) -> list[models.ControlType]:
return conTypes
def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
def create_kit_from_yaml(ctx:dict, exp:dict) -> dict:
"""
Create and store a new kit in the database based on a .yml file
Args:
ctx (dict): Context dictionary passed down from frontend
exp (dict): Experiment dictionary created from yaml file
"""
Returns:
dict: a dictionary containing results of db addition
"""
try:
power_users = ctx['power_users']
except KeyError:
@@ -474,6 +488,44 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
ctx['database_session'].commit()
return {'code':0, 'message':'Kit has been added'}
def create_org_from_yaml(ctx:dict, org:dict) -> dict:
"""
Create and store a new organization based on a .yml file
Args:
ctx (dict): Context dictionary passed down from frontend
org (dict): Dictionary containing organization info.
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:
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:
cli_org = models.Organization(name=client.replace(" ", "_").lower(), cost_centre=org[client]['cost centre'])
for contact in org[client]['contacts']:
cont_name = list(contact.keys())[0]
look_up = ctx['database_session'].query(models.Contact).filter(models.Contact.name==cont_name).first()
if look_up == None:
cli_cont = models.Contact(name=cont_name, phone=contact[cont_name]['phone'], email=contact[cont_name]['email'], organization=[cli_org])
else:
cli_cont = look_up
cli_cont.organization.append(cli_org)
# cli_org.contacts.append(cli_cont)
# cli_org.contact_ids.append_foreign_key(cli_cont.id)
ctx['database_session'].add(cli_cont)
logger.debug(cli_cont.__dict__)
ctx['database_session'].add(cli_org)
ctx["database_session"].commit()
return {"code":0, "message":"Organization has been added."}
def lookup_all_sample_types(ctx:dict) -> list[str]:
"""
@@ -511,7 +563,7 @@ def get_all_available_modes(ctx:dict) -> list[str]:
def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None, end_date:date|None=None) -> list:
def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None, end_date:date|None=None) -> list[models.Control]:
"""
Returns a list of control objects that are instances of the input controltype.
@@ -571,4 +623,4 @@ 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)
return ctx['database_session'].query(models.BasicSubmission).join(reagents_submissions).filter(reagents_submissions.c.reagent_id==reagent.id).all()