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logging and scrollable form

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This commit is contained in:
Landon Wark
2023-01-24 15:22:15 -06:00
parent 7a53cfd9a1
commit f53d420d56
9 changed files with 129 additions and 121 deletions
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48
src/submissions/backend/db/__init__.py
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@@ -11,7 +11,7 @@ from sqlalchemy import JSON
import json
from dateutil.relativedelta import relativedelta
logger = logging.getLogger(__name__)
logger = logging.getLogger(f"submissions.{__name__}")
def get_kits_by_use( ctx:dict, kittype_str:str|None) -> list:
pass
@@ -35,7 +35,7 @@ def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None:
def store_reagent(ctx:dict, reagent:models.Reagent) -> None:
print(reagent.__dict__)
logger.debug(reagent.__dict__)
ctx['database_session'].add(reagent)
ctx['database_session'].commit()
@@ -46,18 +46,18 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
info_dict['submission_type'] = info_dict['submission_type'].replace(" ", "_").lower()
instance = model()
for item in info_dict:
print(f"Setting {item} to {info_dict[item]}")
logger.debug(f"Setting {item} to {info_dict[item]}")
match item:
case "extraction_kit":
q_str = info_dict[item]
print(f"Looking up kit {q_str}")
logger.debug(f"Looking up kit {q_str}")
field_value = lookup_kittype_by_name(ctx=ctx, name=q_str)
print(f"Got {field_value} for kit {q_str}")
logger.debug(f"Got {field_value} for kit {q_str}")
case "submitting_lab":
q_str = info_dict[item].replace(" ", "_").lower()
print(f"looking up organization: {q_str}")
logger.debug(f"looking up organization: {q_str}")
field_value = lookup_org_by_name(ctx=ctx, name=q_str)
print(f"Got {field_value} for organization {q_str}")
logger.debug(f"Got {field_value} for organization {q_str}")
case "submitter_plate_num":
# Because of unique constraint, the submitter plate number cannot be None, so...
if info_dict[item] == None:
@@ -72,16 +72,16 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
try:
setattr(instance, item, field_value)
except AttributeError:
print(f"Could not set attribute: {item} to {info_dict[item]}")
logger.debug(f"Could not set attribute: {item} to {info_dict[item]}")
continue
# print(instance.__dict__)
# logger.debug(instance.__dict__)
return instance
# looked_up = []
# for reagent in reagents:
# my_reagent = lookup_reagent(reagent)
# print(my_reagent)
# logger.debug(my_reagent)
# looked_up.append(my_reagent)
# print(looked_up)
# logger.debug(looked_up)
# instance.reagents = looked_up
# ctx['database_session'].add(instance)
# ctx['database_session'].commit()
@@ -89,7 +89,7 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
def construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
reagent = models.Reagent()
for item in info_dict:
print(f"Reagent info item: {item}")
logger.debug(f"Reagent info item: {item}")
match item:
case "lot":
reagent.lot = info_dict[item].upper()
@@ -100,7 +100,7 @@ def construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
try:
reagent.expiry = reagent.expiry + reagent.type.eol_ext
except TypeError as e:
print(f"WE got a type error: {e}.")
logger.debug(f"WE got a type error: {e}.")
except AttributeError:
pass
return reagent
@@ -116,9 +116,9 @@ def get_all_reagenttype_names(ctx:dict) -> list[str]:
return lookedup
def lookup_reagenttype_by_name(ctx:dict, rt_name:str) -> models.ReagentType:
print(f"Looking up ReagentType by name: {rt_name}")
logger.debug(f"Looking up ReagentType by name: {rt_name}")
lookedup = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name==rt_name).first()
print(f"Found ReagentType: {lookedup}")
logger.debug(f"Found ReagentType: {lookedup}")
return lookedup
@@ -127,7 +127,7 @@ def lookup_kittype_by_use(ctx:dict, used_by:str) -> list[models.KitType]:
return ctx['database_session'].query(models.KitType).filter(models.KitType.used_for.contains(used_by))
def lookup_kittype_by_name(ctx:dict, name:str) -> models.KitType:
print(f"Querying kittype: {name}")
logger.debug(f"Querying kittype: {name}")
return ctx['database_session'].query(models.KitType).filter(models.KitType.name==name).first()
@@ -154,11 +154,11 @@ def lookup_all_orgs(ctx:dict) -> list[models.Organization]:
return ctx['database_session'].query(models.Organization).all()
def lookup_org_by_name(ctx:dict, name:str|None) -> models.Organization:
print(f"Querying organization: {name}")
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):
print(f"Type: {type}")
logger.debug(f"Type: {type}")
subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, type=type)]
df = pd.DataFrame.from_records(subs)
return df
@@ -205,7 +205,7 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
except (UnicodeDecodeError, AttributeError):
exp['password'] = exp['password'].encode()
if base64.b64encode(exp['password']) != b'cnNsX3N1Ym1pNTVpb25z':
print(f"Not the correct password.")
logger.debug(f"Not the correct password.")
return
for type in exp:
if type == "password":
@@ -220,8 +220,8 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
rt = look_up
rt.kits.append(kit)
ctx['database_session'].add(rt)
print(rt.__dict__)
print(kit.__dict__)
logger.debug(rt.__dict__)
logger.debug(kit.__dict__)
ctx['database_session'].add(kit)
ctx['database_session'].commit()
@@ -252,7 +252,7 @@ def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None,
list: Control instances.
"""
# print(f"Using dates: {start_date} to {end_date}")
# logger.debug(f"Using dates: {start_date} to {end_date}")
query = ctx['database_session'].query(models.ControlType).filter_by(name=con_type)
try:
output = query.first().instances
@@ -261,7 +261,7 @@ def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None,
# Hacky solution to my not being able to get the sql query to work.
if start_date != None and end_date != None:
output = [item for item in output if item.submitted_date.date() > start_date and item.submitted_date.date() < end_date]
# print(f"Type {con_type}: {query.first()}")
# logger.debug(f"Type {con_type}: {query.first()}")
return output
@@ -271,7 +271,7 @@ def get_control_subtypes(ctx:dict, type:str, mode:str):
except TypeError:
return []
jsoner = json.loads(getattr(outs, mode))
print(f"JSON out: {jsoner}")
logger.debug(f"JSON out: {jsoner}")
try:
genera = list(jsoner.keys())[0]
except IndexError: