documentation and converted to username based exclusion of adding new kits
This commit is contained in:
Landon Wark
@@ -12,6 +12,7 @@ import base64
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from sqlalchemy import JSON
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import json
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from dateutil.relativedelta import relativedelta
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from getpass import getuser
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logger = logging.getLogger(f"submissions.{__name__}")
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@@ -20,8 +21,19 @@ def get_kits_by_use( ctx:dict, kittype_str:str|None) -> list:
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# ctx dict should contain the database session
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def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None:
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def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None|dict:
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"""
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Upserts submissions into database
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Args:
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ctx (dict): settings passed down from gui
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base_submission (models.BasicSubmission): submission to be add to db
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Returns:
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None|dict : object that indicates issue raised for reporting in gui
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"""
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logger.debug(f"Hello from store_submission")
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# Add all samples to sample table
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for sample in base_submission.samples:
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sample.rsl_plate = base_submission
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logger.debug(f"Attempting to add sample: {sample.to_string()}")
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@@ -30,6 +42,7 @@ def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None:
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except (sqlite3.IntegrityError, sqlalchemy.exc.IntegrityError) as e:
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logger.debug(f"Hit an integrity error : {e}")
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continue
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# Add submission to submission table
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ctx['database_session'].add(base_submission)
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logger.debug(f"Attempting to add submission: {base_submission.rsl_plate_num}")
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try:
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@@ -45,26 +58,51 @@ def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None:
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return None
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def store_reagent(ctx:dict, reagent:models.Reagent) -> None:
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def store_reagent(ctx:dict, reagent:models.Reagent) -> None|dict:
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"""
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_summary_
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Args:
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ctx (dict): settings passed down from gui
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reagent (models.Reagent): Reagent object to be added to db
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Returns:
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None|dict: obejct indicating issue to be reported in the gui
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"""
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logger.debug(reagent.__dict__)
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ctx['database_session'].add(reagent)
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try:
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ctx['database_session'].commit()
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except OperationalError:
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except (sqlite3.OperationalError, sqlalchemy.exc.OperationalError):
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return {"message":"The database is locked for editing."}
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def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmission:
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"""
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Construct submission obejct from dictionary
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Args:
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ctx (dict): settings passed down from gui
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info_dict (dict): dictionary to be transformed
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Returns:
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models.BasicSubmission: Constructed submission object
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"""
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# convert submission type into model name
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query = info_dict['submission_type'].replace(" ", "")
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# check database for existing object
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instance = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num==info_dict['rsl_plate_num']).first()
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msg = "This submission already exists.\nWould you like to overwrite?"
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# get model based on submission type converted above
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model = getattr(models, query)
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info_dict['submission_type'] = info_dict['submission_type'].replace(" ", "_").lower()
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# if query return nothing, ie doesn't already exist in db
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if instance == None:
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instance = model()
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msg = None
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for item in info_dict:
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logger.debug(f"Setting {item} to {info_dict[item]}")
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# set fields based on keys in dictionary
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match item:
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case "extraction_kit":
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q_str = info_dict[item]
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@@ -86,35 +124,34 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
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logger.debug(f"Got None as a submitter plate number, inserting random string to preserve database unique constraint.")
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info_dict[item] = uuid.uuid4().hex.upper()
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field_value = info_dict[item]
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# case "samples":
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# for sample in info_dict[item]:
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# instance.samples.append(sample)
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# continue
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case _:
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field_value = info_dict[item]
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# insert into field
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try:
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setattr(instance, item, field_value)
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except AttributeError:
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logger.debug(f"Could not set attribute: {item} to {info_dict[item]}")
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continue
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# logger.debug(instance.__dict__)
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logger.debug(f"Constructed instance: {instance.to_string()}")
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logger.debug(msg)
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return instance, {'message':msg}
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# looked_up = []
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# for reagent in reagents:
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# my_reagent = lookup_reagent(reagent)
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# logger.debug(my_reagent)
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# looked_up.append(my_reagent)
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# logger.debug(looked_up)
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# instance.reagents = looked_up
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# ctx['database_session'].add(instance)
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# ctx['database_session'].commit()
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def construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
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"""
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Construct reagent object from dictionary
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Args:
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ctx (dict): settings passed down from gui
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info_dict (dict): dictionary to be converted
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Returns:
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models.Reagent: Constructed reagent object
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"""
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reagent = models.Reagent()
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for item in info_dict:
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logger.debug(f"Reagent info item: {item}")
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# set fields based on keys in dictionary
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match item:
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case "lot":
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reagent.lot = info_dict[item].upper()
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@@ -122,25 +159,55 @@ def construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
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reagent.expiry = info_dict[item]
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case "type":
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reagent.type = lookup_reagenttype_by_name(ctx=ctx, rt_name=info_dict[item].replace(" ", "_").lower())
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# add end-of-life extension from reagent type to expiry date
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try:
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reagent.expiry = reagent.expiry + reagent.type.eol_ext
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except TypeError as e:
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logger.debug(f"WE got a type error: {e}.")
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logger.debug(f"We got a type error: {e}.")
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except AttributeError:
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pass
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return reagent
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def lookup_reagent(ctx:dict, reagent_lot:str):
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def lookup_reagent(ctx:dict, reagent_lot:str) -> models.Reagent:
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"""
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Query db for reagent based on lot number
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Args:
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ctx (dict): settings passed down from gui
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reagent_lot (str): lot number to query
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Returns:
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models.Reagent: looked up reagent
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"""
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lookedup = ctx['database_session'].query(models.Reagent).filter(models.Reagent.lot==reagent_lot).first()
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return lookedup
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def get_all_reagenttype_names(ctx:dict) -> list[str]:
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"""
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Lookup all reagent types and get names
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Args:
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ctx (dict): settings passed from gui
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Returns:
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list[str]: reagent type names
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"""
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lookedup = [item.__str__() for item in ctx['database_session'].query(models.ReagentType).all()]
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return lookedup
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def lookup_reagenttype_by_name(ctx:dict, rt_name:str) -> models.ReagentType:
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"""
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Lookup a single reagent type by name
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Args:
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ctx (dict): settings passed from gui
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rt_name (str): reagent type name to look up
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Returns:
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models.ReagentType: looked up reagent type
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"""
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logger.debug(f"Looking up ReagentType by name: {rt_name}")
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lookedup = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name==rt_name).first()
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logger.debug(f"Found ReagentType: {lookedup}")
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@@ -148,27 +215,78 @@ def lookup_reagenttype_by_name(ctx:dict, rt_name:str) -> models.ReagentType:
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def lookup_kittype_by_use(ctx:dict, used_by:str) -> list[models.KitType]:
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# return [item for item in
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"""
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Lookup a kit by an sample type its used for
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Args:
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ctx (dict): settings passed from gui
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used_by (str): sample type (should be string in D3 of excel sheet)
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Returns:
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list[models.KitType]: list of kittypes that have that sample type in their uses
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"""
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return ctx['database_session'].query(models.KitType).filter(models.KitType.used_for.contains(used_by))
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def lookup_kittype_by_name(ctx:dict, name:str) -> models.KitType:
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"""
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Lookup a kit type by name
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Args:
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ctx (dict): settings passed from bui
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name (str): name of kit to query
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Returns:
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models.KitType: retrieved kittype
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"""
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logger.debug(f"Querying kittype: {name}")
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return ctx['database_session'].query(models.KitType).filter(models.KitType.name==name).first()
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def lookup_regent_by_type_name(ctx:dict, type_name:str) -> list[models.ReagentType]:
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def lookup_regent_by_type_name(ctx:dict, type_name:str) -> list[models.Reagent]:
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"""
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Lookup reagents by their type name
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Args:
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ctx (dict): settings passed from gui
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type_name (str): reagent type name
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Returns:
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list[models.Reagent]: list of retrieved reagents
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"""
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# return [item for item in ctx['database_session'].query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name==type_name).all()]
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return ctx['database_session'].query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name==type_name).all()
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def lookup_regent_by_type_name_and_kit_name(ctx:dict, type_name:str, kit_name:str) -> list[models.Reagent]:
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"""
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Lookup reagents by their type name and kits they belong to
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Args:
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ctx (dict): settings pass by gui
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type_name (str): reagent type name
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kit_name (str): kit name
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Returns:
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list[models.Reagent]: list of retrieved reagents
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"""
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# Hang on, this is going to be a long one.
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by_type = ctx['database_session'].query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name.endswith(type_name))
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# add filter for kit name
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add_in = by_type.join(models.ReagentType.kits).filter(models.KitType.name==kit_name)
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return add_in
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def lookup_all_submissions_by_type(ctx:dict, type:str|None=None):
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def lookup_all_submissions_by_type(ctx:dict, type:str|None=None) -> list[models.BasicSubmission]:
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"""
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Get all submissions, filtering by type if given
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Args:
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ctx (dict): settings pass from gui
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type (str | None, optional): submission type (should be string in D3 of excel sheet). Defaults to None.
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Returns:
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_type_: list of retrieved submissions
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"""
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if type == None:
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subs = ctx['database_session'].query(models.BasicSubmission).all()
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else:
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@@ -176,20 +294,60 @@ def lookup_all_submissions_by_type(ctx:dict, type:str|None=None):
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return subs
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def lookup_all_orgs(ctx:dict) -> list[models.Organization]:
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"""
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Lookup all organizations (labs)
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Args:
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ctx (dict): settings passed from gui
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Returns:
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list[models.Organization]: list of retrieved organizations
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"""
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return ctx['database_session'].query(models.Organization).all()
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def lookup_org_by_name(ctx:dict, name:str|None) -> models.Organization:
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"""
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Lookup organization (lab) by name.
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Args:
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ctx (dict): settings passed from gui
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name (str | None): name of organization
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Returns:
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models.Organization: retrieved organization
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"""
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logger.debug(f"Querying organization: {name}")
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return ctx['database_session'].query(models.Organization).filter(models.Organization.name==name).first()
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def submissions_to_df(ctx:dict, type:str|None=None):
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def submissions_to_df(ctx:dict, type:str|None=None) -> pd.DataFrame:
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"""
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Convert submissions looked up by type to dataframe
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Args:
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ctx (dict): settings passed by gui
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type (str | None, optional): submission type (should be string in D3 of excel sheet) Defaults to None.
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Returns:
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pd.DataFrame: dataframe constructed from retrieved submissions
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"""
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logger.debug(f"Type: {type}")
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# pass to lookup function
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subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, type=type)]
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df = pd.DataFrame.from_records(subs)
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return df
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def lookup_submission_by_id(ctx:dict, id:int) -> models.BasicSubmission:
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"""
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Lookup submission by id number
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Args:
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ctx (dict): settings passed from gui
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id (int): submission id number
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Returns:
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models.BasicSubmission: retrieved submission
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"""
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return ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.id==id).first()
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@@ -198,6 +356,17 @@ def create_submission_details(ctx:dict, sub_id:int) -> dict:
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def lookup_submissions_by_date_range(ctx:dict, start_date:datetime.date, end_date:datetime.date) -> list[models.BasicSubmission]:
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"""
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Lookup submissions by range of submitted dates
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Args:
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ctx (dict): settings passed from gui
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start_date (datetime.date): date to start looking
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end_date (datetime.date): date to end looking
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Returns:
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list[models.BasicSubmission]: list of retrieved submissions
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"""
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return ctx['database_session'].query(models.BasicSubmission).filter(and_(models.BasicSubmission.submitted_date > start_date, models.BasicSubmission.submitted_date < end_date)).all()
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@@ -226,12 +395,13 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
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exp (dict): Experiment dictionary created from yaml file
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"""
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try:
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exp['password'].decode()
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except (UnicodeDecodeError, AttributeError):
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exp['password'] = exp['password'].encode()
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if base64.b64encode(exp['password']) != b'cnNsX3N1Ym1pNTVpb25z':
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logger.debug(f"Not the correct password.")
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return
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super_users = ctx['super_users']
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except KeyError:
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logger.debug("This user does not have permission to add kits.")
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return {'code':1,'message':"This user does not have permission to add kits."}
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if getuser not in super_users:
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logger.debug("This user does not have permission to add kits.")
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return {'code':1, 'message':"This user does not have permission to add kits."}
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for type in exp:
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if type == "password":
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continue
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@@ -249,9 +419,19 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
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logger.debug(kit.__dict__)
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ctx['database_session'].add(kit)
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ctx['database_session'].commit()
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return {'code':0, 'message':'Kit has been added'}
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def lookup_all_sample_types(ctx:dict) -> list[str]:
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"""
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Lookup all sample types and get names
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Args:
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ctx (dict): settings pass from gui
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Returns:
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list[str]: list of sample type names
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"""
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uses = [item.used_for for item in ctx['database_session'].query(models.KitType).all()]
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uses = list(set([item for sublist in uses for item in sublist]))
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return uses
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@@ -259,6 +439,15 @@ def lookup_all_sample_types(ctx:dict) -> list[str]:
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def get_all_available_modes(ctx:dict) -> list[str]:
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"""
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Get types of analysis for controls
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Args:
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ctx (dict): settings passed from gui
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Returns:
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list[str]: list of analysis types
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"""
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rel = ctx['database_session'].query(models.Control).first()
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try:
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cols = [item.name for item in list(rel.__table__.columns) if isinstance(item.type, JSON)]
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@@ -294,7 +483,18 @@ def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None,
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return output
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def get_control_subtypes(ctx:dict, type:str, mode:str):
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def get_control_subtypes(ctx:dict, type:str, mode:str) -> list[str]:
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"""
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Get subtypes for a control analysis type
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Args:
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ctx (dict): settings passed from gui
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type (str): control type name
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mode (str): analysis type name
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Returns:
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list[str]: list of subtype names
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"""
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try:
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outs = get_all_controls_by_type(ctx=ctx, con_type=type)[0]
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except TypeError:
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Reference in New Issue
Block a user