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mid refactor for improved rebustness and readability

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This commit is contained in:
Landon Wark
2023-03-15 15:38:02 -05:00
parent fc334155ff
commit c645d3a9cf
15 changed files with 337 additions and 468 deletions
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176
src/submissions/backend/db/__init__.py
View File

@@ -21,19 +21,13 @@ from pathlib import Path
logger = logging.getLogger(f"submissions.{__name__}")
# The below should allow automatic creation of foreign keys in the database
# The below _should_ allow automatic creation of foreign keys in the database
@event.listens_for(Engine, "connect")
def set_sqlite_pragma(dbapi_connection, connection_record):
cursor = dbapi_connection.cursor()
cursor.execute("PRAGMA foreign_keys=ON")
cursor.close()
def get_kits_by_use( ctx:dict, kittype_str:str|None) -> list:
pass
# ctx dict should contain the database session
def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None|dict:
"""
Upserts submissions into database
@@ -73,21 +67,22 @@ def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None|d
def store_reagent(ctx:dict, reagent:models.Reagent) -> None|dict:
"""
_summary_
Inserts a reagent into the database.
Args:
ctx (dict): settings passed down from gui
reagent (models.Reagent): Reagent object to be added to db
Returns:
None|dict: obejct indicating issue to be reported in the gui
None|dict: object indicating issue to be reported in the gui
"""
logger.debug(reagent.__dict__)
logger.debug(f"Reagent dictionary: {reagent.__dict__}")
ctx['database_session'].add(reagent)
try:
ctx['database_session'].commit()
except (sqlite3.OperationalError, sqlalchemy.exc.OperationalError):
return {"message":"The database is locked for editing."}
return None
def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmission:
@@ -103,12 +98,12 @@ 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
# Ensure an rsl plate number exists for the plate
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."}
# check database for existing object
instance = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num==info_dict['rsl_plate_num']).first()
# get model based on submission type converted above
logger.debug(f"Looking at models for submission type: {query}")
@@ -142,7 +137,8 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
field_value = lookup_org_by_name(ctx=ctx, name=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...
# Because of unique constraint, there will be problems with
# multiple submissions named 'None', so...
logger.debug(f"Submitter plate id: {info_dict[item]}")
if info_dict[item] == None or info_dict[item] == "None":
logger.debug(f"Got None as a submitter plate number, inserting random string to preserve database unique constraint.")
@@ -156,7 +152,8 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
except AttributeError:
logger.debug(f"Could not set attribute: {item} to {info_dict[item]}")
continue
# calculate cost of the run: immutable cost + mutable times number of columns
# calculate cost of the run: immutable cost + mutable times number of columns
# This is now attached to submission upon creation to preserve at-run costs incase of cost increase in the future.
try:
instance.run_cost = instance.extraction_kit.immutable_cost + (instance.extraction_kit.mutable_cost * ((instance.sample_count / 8)/12))
except (TypeError, AttributeError):
@@ -167,7 +164,7 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
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)
logger.debug(f"Constructed submissions message: {msg}")
return instance, {'code':code, 'message':msg}
@@ -194,7 +191,7 @@ def construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
case "type":
reagent.type = lookup_reagenttype_by_name(ctx=ctx, rt_name=info_dict[item].replace(" ", "_").lower())
# add end-of-life extension from reagent type to expiry date
# Edit: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
# NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
# try:
# reagent.expiry = reagent.expiry + reagent.type.eol_ext
# except TypeError as e:
@@ -204,7 +201,6 @@ def construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
return reagent
def lookup_reagent(ctx:dict, reagent_lot:str) -> models.Reagent:
"""
Query db for reagent based on lot number
@@ -219,6 +215,7 @@ def lookup_reagent(ctx:dict, reagent_lot:str) -> models.Reagent:
lookedup = ctx['database_session'].query(models.Reagent).filter(models.Reagent.lot==reagent_lot).first()
return lookedup
def get_all_reagenttype_names(ctx:dict) -> list[str]:
"""
Lookup all reagent types and get names
@@ -232,6 +229,7 @@ def get_all_reagenttype_names(ctx:dict) -> list[str]:
lookedup = [item.__str__() for item in ctx['database_session'].query(models.ReagentType).all()]
return lookedup
def lookup_reagenttype_by_name(ctx:dict, rt_name:str) -> models.ReagentType:
"""
Lookup a single reagent type by name
@@ -251,7 +249,7 @@ def lookup_reagenttype_by_name(ctx:dict, rt_name:str) -> models.ReagentType:
def lookup_kittype_by_use(ctx:dict, used_by:str) -> list[models.KitType]:
"""
Lookup a kit by an sample type its used for
Lookup kits by a sample type its used for
Args:
ctx (dict): settings passed from gui
@@ -262,6 +260,7 @@ 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)).all()
def lookup_kittype_by_name(ctx:dict, name:str) -> models.KitType:
"""
Lookup a kit type by name
@@ -288,7 +287,6 @@ def lookup_regent_by_type_name(ctx:dict, type_name:str) -> list[models.Reagent]:
Returns:
list[models.Reagent]: list of retrieved reagents
"""
# return [item for item in ctx['database_session'].query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name==type_name).all()]
return ctx['database_session'].query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name==type_name).all()
@@ -308,8 +306,7 @@ 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)
# add filter for kit name...
try:
check = not np.isnan(kit_name)
except TypeError:
@@ -317,12 +314,10 @@ def lookup_regent_by_type_name_and_kit_name(ctx:dict, type_name:str, kit_name:st
if check:
kit_type = lookup_kittype_by_name(ctx=ctx, name=kit_name)
logger.debug(f"reagenttypes: {[item.name for item in rt_types.all()]}, kit: {kit_type.name}")
# add in lookup for related kit_id
rt_types = rt_types.join(reagenttypes_kittypes).filter(reagenttypes_kittypes.c.kits_id==kit_type.id).first()
# for item in by_type:
# logger.debug([thing.name for thing in item.type.kits])
# output = [item for item in by_type if kit_name in [thing.name for thing in item.type.kits]]
# else:
else:
rt_types = rt_types.first()
output = rt_types.instances
return output
@@ -336,7 +331,7 @@ def lookup_all_submissions_by_type(ctx:dict, sub_type:str|None=None) -> list[mod
type (str | None, optional): submission type (should be string in D3 of excel sheet). Defaults to None.
Returns:
_type_: list of retrieved submissions
list[models.BasicSubmission]: list of retrieved submissions
"""
if sub_type == None:
subs = ctx['database_session'].query(models.BasicSubmission).all()
@@ -358,7 +353,7 @@ def lookup_all_orgs(ctx:dict) -> list[models.Organization]:
def lookup_org_by_name(ctx:dict, name:str|None) -> models.Organization:
"""
Lookup organization (lab) by name.
Lookup organization (lab) by (startswith) name.
Args:
ctx (dict): settings passed from gui
@@ -368,7 +363,6 @@ 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.startswith(name)).first()
def submissions_to_df(ctx:dict, sub_type:str|None=None) -> pd.DataFrame:
@@ -383,10 +377,11 @@ def submissions_to_df(ctx:dict, sub_type:str|None=None) -> pd.DataFrame:
pd.DataFrame: dataframe constructed from retrieved submissions
"""
logger.debug(f"Type: {sub_type}")
# pass to lookup function
# use lookup function to create list of dicts
subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, sub_type=sub_type)]
# make df from dicts (records) in list
df = pd.DataFrame.from_records(subs)
# logger.debug(f"Pre: {df['Technician']}")
# Exclude sub information
try:
df = df.drop("controls", axis=1)
except:
@@ -395,7 +390,6 @@ def submissions_to_df(ctx:dict, sub_type:str|None=None) -> pd.DataFrame:
df = df.drop("ext_info", axis=1)
except:
logger.warning(f"Couldn't drop 'controls' column from submissionsheet df.")
# logger.debug(f"Post: {df['Technician']}")
return df
@@ -413,13 +407,9 @@ def lookup_submission_by_id(ctx:dict, id:int) -> models.BasicSubmission:
return ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.id==id).first()
def create_submission_details(ctx:dict, sub_id:int) -> dict:
pass
def lookup_submissions_by_date_range(ctx:dict, start_date:datetime.date, end_date:datetime.date) -> list[models.BasicSubmission]:
"""
Lookup submissions by range of submitted dates
Lookup submissions greater than start_date and less than end_date
Args:
ctx (dict): settings passed from gui
@@ -429,18 +419,21 @@ def lookup_submissions_by_date_range(ctx:dict, start_date:datetime.date, end_dat
Returns:
list[models.BasicSubmission]: list of retrieved submissions
"""
return ctx['database_session'].query(models.BasicSubmission).filter(and_(models.BasicSubmission.submitted_date > start_date, models.BasicSubmission.submitted_date < end_date)).all()
# return ctx['database_session'].query(models.BasicSubmission).filter(and_(models.BasicSubmission.submitted_date > start_date, models.BasicSubmission.submitted_date < end_date)).all()
start_date = start_date.strftime("%Y-%m-%d")
end_date = end_date.strftime("%Y-%m-%d")
return ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.submitted_date.between(start_date, end_date)).all()
def get_all_Control_Types_names(ctx:dict) -> list[models.ControlType]:
def get_all_Control_Types_names(ctx:dict) -> list[str]:
"""
Grabs all control type names from db.
Args:
settings (dict): settings passed down from click. Defaults to {}.
settings (dict): settings passed down from gui.
Returns:
list: names list
list: list of controltype names
"""
conTypes = ctx['database_session'].query(models.ControlType).all()
conTypes = [conType.name for conType in conTypes]
@@ -451,6 +444,7 @@ def get_all_Control_Types_names(ctx:dict) -> list[models.ControlType]:
def create_kit_from_yaml(ctx:dict, exp:dict) -> dict:
"""
Create and store a new kit in the database based on a .yml file
TODO: split into create and store functions
Args:
ctx (dict): Context dictionary passed down from frontend
@@ -459,18 +453,20 @@ 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:
# Don't want just anyone adding kits
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.", "status":"warning"}
# iterate through keys in dict
for type in exp:
if type == "password":
continue
# A submission type may use multiple kits.
for kt in exp[type]['kits']:
kit = models.KitType(name=kt, used_for=[type.replace("_", " ").title()], cost_per_run=exp[type]["kits"][kt]["cost"])
kit = models.KitType(name=kt, used_for=[type.replace("_", " ").title()], constant_cost=exp[type]["kits"][kt]["constant_cost"], mutable_cost=exp[type]["kits"][kt]["mutable_cost"])
# A kit contains multiple reagent types.
for r in exp[type]['kits'][kt]['reagenttypes']:
# check if reagent type already exists.
look_up = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name==r).first()
if look_up == None:
rt = models.ReagentType(name=r.replace(" ", "_").lower(), eol_ext=timedelta(30*exp[type]['kits'][kt]['reagenttypes'][r]['eol_ext']), kits=[kit])
@@ -478,15 +474,15 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> dict:
rt = look_up
rt.kits.append(kit)
# add this because I think it's necessary to get proper back population
# rt.kit_id.append(kit.id)
kit.reagent_types_id.append(rt.id)
ctx['database_session'].add(rt)
logger.debug(rt.__dict__)
logger.debug(kit.__dict__)
logger.debug(f"Kit construction reagent type: {rt.__dict__}")
logger.debug(f"Kit construction kit: {kit.__dict__}")
ctx['database_session'].add(kit)
ctx['database_session'].commit()
return {'code':0, 'message':'Kit has been added', 'status': 'information'}
def create_org_from_yaml(ctx:dict, org:dict) -> dict:
"""
Create and store a new organization based on a .yml file
@@ -498,30 +494,26 @@ 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:
# Don't want just anyone adding in clients
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."}
# the yml can contain multiple clients
for client in org:
cli_org = models.Organization(name=client.replace(" ", "_").lower(), cost_centre=org[client]['cost centre'])
# a client can contain multiple contacts
for contact in org[client]['contacts']:
cont_name = list(contact.keys())[0]
# check if contact already exists
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__)
logger.debug(f"Client creation contact: {cli_cont.__dict__}")
logger.debug(f"Client creation client: {cli_org.__dict__}")
ctx['database_session'].add(cli_org)
ctx["database_session"].commit()
return {"code":0, "message":"Organization has been added."}
@@ -538,11 +530,11 @@ def lookup_all_sample_types(ctx:dict) -> list[str]:
list[str]: list of sample type names
"""
uses = [item.used_for for item in ctx['database_session'].query(models.KitType).all()]
# flattened list of lists
uses = list(set([item for sublist in uses for item in sublist]))
return uses
def get_all_available_modes(ctx:dict) -> list[str]:
"""
Get types of analysis for controls
@@ -553,6 +545,7 @@ def get_all_available_modes(ctx:dict) -> list[str]:
Returns:
list[str]: list of analysis types
"""
# Only one control is necessary since they all share the same control types.
rel = ctx['database_session'].query(models.Control).first()
try:
cols = [item.name for item in list(rel.__table__.columns) if isinstance(item.type, JSON)]
@@ -562,54 +555,49 @@ def get_all_available_modes(ctx:dict) -> list[str]:
return cols
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.
Between dates if supplied.
Args:
con_type (str): Name of the control type.
ctx (dict): Settings passed down from gui.
ctx (dict): Settings passed down from gui
con_type (str): Name of control type.
start_date (date | None, optional): Start date of query. Defaults to None.
end_date (date | None, optional): End date of query. Defaults to None.
Returns:
list: Control instances.
"""
list[models.Control]: list of control samples.
"""
logger.debug(f"Using dates: {start_date} to {end_date}")
if start_date != None and end_date != None:
output = ctx['database_session'].query(models.Control).join(models.ControlType).filter_by(name=con_type).filter(models.Control.submitted_date.between(start_date.strftime("%Y-%m-%d"), end_date.strftime("%Y-%m-%d"))).all()
start_date = start_date.strftime("%Y-%m-%d")
end_date = end_date.strftime("%Y-%m-%d")
output = ctx['database_session'].query(models.Control).join(models.ControlType).filter_by(name=con_type).filter(models.Control.submitted_date.between(start_date, end_date)).all()
else:
output = ctx['database_session'].query(models.Control).join(models.ControlType).filter_by(name=con_type).all()
logger.debug(f"Returned controls between dates: {output}")
return output
# query = ctx['database_session'].query(models.ControlType).filter_by(name=con_type)
# try:
# output = query.first().instances
# except AttributeError:
# output = 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]
# # logger.debug(f"Type {con_type}: {query.first()}")
# return output
def get_control_subtypes(ctx:dict, type:str, mode:str) -> list[str]:
"""
Get subtypes for a control analysis type
Get subtypes for a control analysis mode
Args:
ctx (dict): settings passed from gui
type (str): control type name
mode (str): analysis type name
mode (str): analysis mode name
Returns:
list[str]: list of subtype names
"""
# Only the first control of type is necessary since they all share subtypes
try:
outs = get_all_controls_by_type(ctx=ctx, con_type=type)[0]
except TypeError:
return []
# Get analysis mode data as dict
jsoner = json.loads(getattr(outs, mode))
logger.debug(f"JSON out: {jsoner}")
try:
@@ -620,11 +608,30 @@ def get_control_subtypes(ctx:dict, type:str, mode:str) -> list[str]:
return subtypes
def get_all_controls(ctx:dict):
def get_all_controls(ctx:dict) -> list[models.Control]:
"""
Retrieve a list of all controls from the database
Args:
ctx (dict): settings passed down from the gui.
Returns:
list[models.Control]: list of all control objects
"""
return ctx['database_session'].query(models.Control).all()
def lookup_submission_by_rsl_num(ctx:dict, rsl_num:str):
def lookup_submission_by_rsl_num(ctx:dict, rsl_num:str) -> models.BasicSubmission:
"""
Retrieve a submission from the database based on rsl plate number
Args:
ctx (dict): settings passed down from gui
rsl_num (str): rsl plate number
Returns:
models.BasicSubmission: Submissions object retrieved from database
"""
return ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num.startswith(rsl_num)).first()
@@ -641,10 +648,15 @@ def delete_submission_by_id(ctx:dict, id:int) -> None:
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.
# Retrieve submission
sub = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.id==id).first()
# Convert to dict for storing backup as a yml
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)
try:
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)
except KeyError:
pass
sub.reagents = []
for sample in sub.samples:
ctx['database_session'].delete(sample)

6
src/submissions/backend/db/models/kits.py
View File

@@ -21,7 +21,7 @@ class KitType(Base):
name = Column(String(64), unique=True) #: name of kit
submissions = relationship("BasicSubmission", back_populates="extraction_kit") #: submissions this kit was used for
used_for = Column(JSON) #: list of names of sample types this kit can process
cost_per_run = Column(FLOAT(2)) #: dollar amount for each full run of this kit
cost_per_run = Column(FLOAT(2)) #: dollar amount for each full run of this kit NOTE: depreciated, use the constant and mutable costs instead
mutable_cost = Column(FLOAT(2)) #: dollar amount that can change with number of columns (reagents, tips, etc)
constant_cost = Column(FLOAT(2)) #: dollar amount that will remain constant (plates, man hours, etc)
reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes) #: reagent types this kit contains
@@ -81,9 +81,7 @@ class Reagent(Base):
Returns:
str: string representing this object's type and lot number
"""
lot = str(self.lot)
r_type = str(self.type)
return f"{r_type} - {lot}"
return str(self.lot)
def to_sub_dict(self) -> dict:
"""

5
src/submissions/backend/db/models/samples.py
View File

@@ -16,6 +16,9 @@ class WWSample(Base):
rsl_plate = relationship("Wastewater", back_populates="samples") #: relationship to parent plate
rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWS_submission_id"))
collection_date = Column(TIMESTAMP) #: Date submission received
well_number = Column(String(8)) #: location on plate
# The following are fields from the sample tracking excel sheet Ruth put together.
# I have no idea when they will be implemented or how.
testing_type = Column(String(64))
site_status = Column(String(64))
notes = Column(String(2000))
@@ -24,7 +27,7 @@ class WWSample(Base):
seq_submitted = Column(BOOLEAN())
ww_seq_run_id = Column(String(64))
sample_type = Column(String(8))
well_number = Column(String(8)) #: location on plate
def to_string(self) -> str:
"""

13
src/submissions/backend/db/models/submissions.py
View File

@@ -35,6 +35,7 @@ class BasicSubmission(Base):
run_cost = Column(FLOAT(2)) #: total cost of running the plate. Set from kit costs at time of creation.
uploaded_by = Column(String(32)) #: user name of person who submitted the submission to the database.
# Allows for subclassing into ex. BacterialCulture, Wastewater, etc.
__mapper_args__ = {
"polymorphic_identity": "basic_submission",
"polymorphic_on": submission_type,
@@ -148,23 +149,25 @@ class BasicSubmission(Base):
}
return output
# Below are the custom submission
# Below are the custom submission types
class BacterialCulture(BasicSubmission):
"""
derivative submission type from BasicSubmission
"""
# control_id = Column(INTEGER, ForeignKey("_control_samples.id", ondelete="SET NULL", name="fk_BC_control_id"))
controls = relationship("Control", back_populates="submission", uselist=True) #: A control sample added to submission
samples = relationship("BCSample", back_populates="rsl_plate", uselist=True)
# bc_sample_id = Column(INTEGER, ForeignKey("_bc_samples.id", ondelete="SET NULL", name="fk_BC_sample_id"))
__mapper_args__ = {"polymorphic_identity": "bacterial_culture", "polymorphic_load": "inline"}
def to_dict(self) -> dict:
"""
Extends parent class method to add controls to dict
Returns:
dict: dictionary used in submissions summary
"""
output = super().to_dict()
output['controls'] = [item.to_sub_dict() for item in self.controls]
# logger.debug(f"{self.rsl_plate_num} technician: {output}")
return output

3
src/submissions/backend/excel/__init__.py
View File

@@ -2,7 +2,6 @@ from pandas import DataFrame
import re
def get_unique_values_in_df_column(df: DataFrame, column_name: str) -> list:
"""
get all unique values in a dataframe column by name
@@ -40,3 +39,5 @@ def drop_reruns_from_df(ctx:dict, df: DataFrame) -> DataFrame:
# logger.debug(f"First run: {first_run}")
df = df.drop(df[df.name == first_run].index)
return df
else:
return None

65
src/submissions/backend/excel/parser.py
View File

@@ -74,16 +74,15 @@ class SheetParser(object):
Returns:
pd.DataFrame: relevant dataframe from excel sheet
"""
"""
# self.xl is a pd.ExcelFile so we need to parse it into a df
submission_info = self.xl.parse(sheet_name=sheet_name, dtype=object)
self.sub['submitter_plate_num'] = submission_info.iloc[0][1]
self.sub['rsl_plate_num'] = submission_info.iloc[10][1]
self.sub['submitted_date'] = submission_info.iloc[1][1]
self.sub['submitting_lab'] = submission_info.iloc[0][3]
self.sub['sample_count'] = submission_info.iloc[2][3]
self.sub['extraction_kit'] = submission_info.iloc[3][3]
return submission_info
@@ -104,10 +103,6 @@ class SheetParser(object):
if ii == 11:
continue
logger.debug(f"Running reagent parse for {row[1]} with type {type(row[1])} and value: {row[2]} with type {type(row[2])}")
# try:
# check = not np.isnan(row[1])
# except TypeError:
# check = True
if not isinstance(row[2], float) and check_not_nan(row[1]):
# must be prefixed with 'lot_' to be recognized by gui
try:
@@ -122,13 +117,7 @@ class SheetParser(object):
logger.debug(f"Couldn't upperize {row[2]}, must be a number")
output_var = row[2]
logger.debug(f"Output variable is {output_var}")
# self.sub[f"lot_{reagent_type}"] = output_var
# update 2023-02-10 to above allowing generation of expiry date in adding reagent to db.
logger.debug(f"Expiry date for imported reagent: {row[3]}")
# try:
# check = not np.isnan(row[3])
# except TypeError:
# check = True
if check_not_nan(row[3]):
expiry = row[3].date()
else:
@@ -146,19 +135,8 @@ class SheetParser(object):
# reagents
# must be prefixed with 'lot_' to be recognized by gui
# Todo: find a more adaptable way to read reagents.
reagent_range = submission_info.iloc[1:13, 4:8]
_parse_reagents(reagent_range)
# self.sub['lot_wash_1'] = submission_info.iloc[1][6] #if pd.isnull(submission_info.iloc[1][6]) else string_formatter(submission_info.iloc[1][6])
# self.sub['lot_wash_2'] = submission_info.iloc[2][6] #if pd.isnull(submission_info.iloc[2][6]) else string_formatter(submission_info.iloc[2][6])
# self.sub['lot_binding_buffer'] = submission_info.iloc[3][6] #if pd.isnull(submission_info.iloc[3][6]) else string_formatter(submission_info.iloc[3][6])
# self.sub['lot_magnetic_beads'] = submission_info.iloc[4][6] #if pd.isnull(submission_info.iloc[4][6]) else string_formatter(submission_info.iloc[4][6])
# self.sub['lot_lysis_buffer'] = submission_info.iloc[5][6] #if np.nan(submission_info.iloc[5][6]) else string_formatter(submission_info.iloc[5][6])
# self.sub['lot_elution_buffer'] = submission_info.iloc[6][6] #if pd.isnull(submission_info.iloc[6][6]) else string_formatter(submission_info.iloc[6][6])
# self.sub['lot_isopropanol'] = submission_info.iloc[9][6] #if pd.isnull(submission_info.iloc[9][6]) else string_formatter(submission_info.iloc[9][6])
# self.sub['lot_ethanol'] = submission_info.iloc[10][6] #if pd.isnull(submission_info.iloc[10][6]) else string_formatter(submission_info.iloc[10][6])
# self.sub['lot_positive_control'] = submission_info.iloc[103][1] #if pd.isnull(submission_info.iloc[103][1]) else string_formatter(submission_info.iloc[103][1])
# self.sub['lot_plate'] = submission_info.iloc[12][6] #if pd.isnull(submission_info.iloc[12][6]) else string_formatter(submission_info.iloc[12][6])
# get individual sample info
sample_parser = SampleParser(submission_info.iloc[15:111])
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
@@ -178,12 +156,8 @@ class SheetParser(object):
Args:
df (pd.DataFrame): input sub dataframe
"""
# logger.debug(df)
# iterate through sub-df rows
for ii, row in df.iterrows():
# try:
# check = not np.isnan(row[5])
# except TypeError:
# check = True
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.
@@ -202,34 +176,26 @@ class SheetParser(object):
else:
expiry = date.today()
self.sub[f"lot_{output_key}"] = {'lot':output_var, 'exp':expiry}
# parse submission sheet
submission_info = self._parse_generic("WW Submissions (ENTER HERE)")
# parse enrichment sheet
enrichment_info = self.xl.parse("Enrichment Worksheet", dtype=object)
# set enrichment reagent range
enr_reagent_range = enrichment_info.iloc[0:4, 9:20]
# parse extraction sheet
extraction_info = self.xl.parse("Extraction Worksheet", dtype=object)
# set extraction reagent range
ext_reagent_range = extraction_info.iloc[0:5, 9:20]
# parse qpcr sheet
qprc_info = self.xl.parse("qPCR Worksheet", dtype=object)
# set qpcr reagent range
pcr_reagent_range = qprc_info.iloc[0:5, 9:20]
# compile technician info
self.sub['technician'] = f"Enr: {enrichment_info.columns[2]}, Ext: {extraction_info.columns[2]}, PCR: {qprc_info.columns[2]}"
_parse_reagents(enr_reagent_range)
_parse_reagents(ext_reagent_range)
_parse_reagents(pcr_reagent_range)
# reagents
# logger.debug(qprc_info)
# self.sub['lot_lysis_buffer'] = enrichment_info.iloc[0][14] #if pd.isnull(enrichment_info.iloc[0][14]) else string_formatter(enrichment_info.iloc[0][14])
# self.sub['lot_proteinase_K'] = enrichment_info.iloc[1][14] #if pd.isnull(enrichment_info.iloc[1][14]) else string_formatter(enrichment_info.iloc[1][14])
# self.sub['lot_magnetic_virus_particles'] = enrichment_info.iloc[2][14] #if pd.isnull(enrichment_info.iloc[2][14]) else string_formatter(enrichment_info.iloc[2][14])
# self.sub['lot_enrichment_reagent_1'] = enrichment_info.iloc[3][14] #if pd.isnull(enrichment_info.iloc[3][14]) else string_formatter(enrichment_info.iloc[3][14])
# self.sub['lot_binding_buffer'] = extraction_info.iloc[0][14] #if pd.isnull(extraction_info.iloc[0][14]) else string_formatter(extraction_info.iloc[0][14])
# self.sub['lot_magnetic_beads'] = extraction_info.iloc[1][14] #if pd.isnull(extraction_info.iloc[1][14]) else string_formatter(extraction_info.iloc[1][14])
# self.sub['lot_wash'] = extraction_info.iloc[2][14] #if pd.isnull(extraction_info.iloc[2][14]) else string_formatter(extraction_info.iloc[2][14])
# self.sub['lot_ethanol'] = extraction_info.iloc[3][14] #if pd.isnull(extraction_info.iloc[3][14]) else string_formatter(extraction_info.iloc[3][14])
# self.sub['lot_elution_buffer'] = extraction_info.iloc[4][14] #if pd.isnull(extraction_info.iloc[4][14]) else string_formatter(extraction_info.iloc[4][14])
# self.sub['lot_master_mix'] = qprc_info.iloc[0][14] #if pd.isnull(qprc_info.iloc[0][14]) else string_formatter(qprc_info.iloc[0][14])
# self.sub['lot_pre_mix_1'] = qprc_info.iloc[1][14] #if pd.isnull(qprc_info.iloc[1][14]) else string_formatter(qprc_info.iloc[1][14])
# self.sub['lot_pre_mix_2'] = qprc_info.iloc[2][14] #if pd.isnull(qprc_info.iloc[2][14]) else string_formatter(qprc_info.iloc[2][14])
# self.sub['lot_positive_control'] = qprc_info.iloc[3][14] #if pd.isnull(qprc_info.iloc[3][14]) else string_formatter(qprc_info.iloc[3][14])
# self.sub['lot_ddh2o'] = qprc_info.iloc[4][14] #if pd.isnull(qprc_info.iloc[4][14]) else string_formatter(qprc_info.iloc[4][14])
# get individual sample info
# parse samples
sample_parser = SampleParser(submission_info.iloc[16:40])
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
self.sub['samples'] = sample_parse()
@@ -241,6 +207,12 @@ class SampleParser(object):
"""
def __init__(self, df:pd.DataFrame) -> None:
"""
convert sample sub-dataframe to dictionary of records
Args:
df (pd.DataFrame): input sample dataframe
"""
self.samples = df.to_dict("records")
@@ -287,6 +259,7 @@ class SampleParser(object):
not_a_nan = not np.isnan(sample['Unnamed: 3'])
except TypeError:
not_a_nan = True
# if we don't have a sample full id, make one up
if not_a_nan:
new.ww_sample_full_id = sample['Unnamed: 3']
else:

93
src/submissions/backend/excel/reports.py
View File

@@ -1,8 +1,6 @@
from pandas import DataFrame, concat
from operator import itemgetter
from pandas import DataFrame
# from backend.db import models
import json
import logging
from jinja2 import Environment, FileSystemLoader
from datetime import date, timedelta
@@ -38,13 +36,8 @@ def make_report_xlsx(records:list[dict]) -> DataFrame:
df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Extraction Kit':'count', 'Cost': 'sum', 'Sample Count':'sum'})
df2 = df2.rename(columns={"Extraction Kit": 'Kit Count'})
logger.debug(f"Output daftaframe for xlsx: {df2.columns}")
# apply formating to cost column
# 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:
@@ -63,23 +56,20 @@ 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 {ii}: {row}")
lab = row[0][0]
logger.debug(type(row))
logger.debug(f"Old lab: {old_lab}, Current lab: {lab}")
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 this is the same lab as before add together
if lab == old_lab:
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']
# if not the same lab, make a new one
else:
adder = dict(lab=lab, kits=[kit], total_cost=kit['cost'], total_samples=kit['sample_count'], total_plates=kit['plate_count'])
output.append(adder)
@@ -91,83 +81,6 @@ def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
return html
# def split_controls_dictionary(ctx:dict, input_dict) -> list[dict]:
# # this will be the date in string form
# dict_name = list(input_dict.keys())[0]
# # the data associated with the date key
# sub_dict = input_dict[dict_name]
# # How many "count", "Percent", etc are in the dictionary
# data_size = get_dict_size(sub_dict)
# output = []
# for ii in range(data_size):
# new_dict = {}
# for genus in sub_dict:
# logger.debug(genus)
# sub_name = list(sub_dict[genus].keys())[ii]
# new_dict[genus] = sub_dict[genus][sub_name]
# output.append({"date":dict_name, "name": sub_name, "data": new_dict})
# return output
# def get_dict_size(input:dict):
# return max(len(input[item]) for item in input)
# def convert_all_controls(ctx:dict, data:list) -> dict:
# dfs = {}
# dict_list = [split_controls_dictionary(ctx, datum) for datum in data]
# dict_list = [item for sublist in dict_list for item in sublist]
# names = list(set([datum['name'] for datum in dict_list]))
# for name in names:
# # df = DataFrame()
# # entries = [{item['date']:item['data']} for item in dict_list if item['name']==name]
# # series_list = []
# # df = pd.json_normalize(entries)
# # for entry in entries:
# # col_name = list(entry.keys())[0]
# # col_dict = entry[col_name]
# # series = pd.Series(data=col_dict.values(), index=col_dict.keys(), name=col_name)
# # # df[col_name] = series.values
# # # logger.debug(df.index)
# # series_list.append(series)
# # df = DataFrame(series_list).T.fillna(0)
# # logger.debug(df)
# dfs['name'] = df
# return dfs
# def convert_control_by_mode(ctx:dict, control:models.Control, mode:str) -> list[dict]:
# """
# split control object into analysis types... can I move this into the class itself?
# turns out I can
# Args:
# ctx (dict): settings passed from gui
# control (models.Control): control to be parsed into list
# mode (str): analysis type
# Returns:
# list[dict]: list of records
# """
# output = []
# data = json.loads(getattr(control, mode))
# for genus in data:
# _dict = {}
# _dict['name'] = control.name
# _dict['submitted_date'] = control.submitted_date
# _dict['genus'] = genus
# _dict['target'] = 'Target' if genus.strip("*") in control.controltype.targets else "Off-target"
# for key in data[genus]:
# _dict[key] = data[genus][key]
# output.append(_dict)
# # logger.debug(output)
# return output
def convert_data_list_to_df(ctx:dict, input:list[dict], subtype:str|None=None) -> DataFrame:
"""
Convert list of control records to dataframe

34
src/submissions/configure/__init__.py
View File

@@ -3,7 +3,6 @@ import sys, os, stat, platform, getpass
import logging
from logging import handlers
from pathlib import Path
# from getpass import getuser
from sqlalchemy.orm import Session
from sqlalchemy import create_engine
@@ -26,9 +25,6 @@ main_aux_dir = Path.home().joinpath(f"{os_config_dir}/submissions")
CONFIGDIR = main_aux_dir.joinpath("config")
LOGDIR = main_aux_dir.joinpath("logs")
class GroupWriteRotatingFileHandler(handlers.RotatingFileHandler):
def doRollover(self):
@@ -43,7 +39,6 @@ class GroupWriteRotatingFileHandler(handlers.RotatingFileHandler):
def _open(self):
prevumask=os.umask(0o002)
#os.fdopen(os.open('/path/to/file', os.O_WRONLY, 0600))
rtv=handlers.RotatingFileHandler._open(self)
os.umask(prevumask)
return rtv
@@ -74,12 +69,12 @@ def get_config(settings_path: str|None=None) -> dict:
Returns:
setting: dictionary of settings.
"""
# custom pyyaml constructor to join fields
def join(loader, node):
seq = loader.construct_sequence(node)
return ''.join([str(i) for i in seq])
## register the tag handler
# register the tag handler
yaml.add_constructor('!join', join)
logger.debug(f"Making directory: {CONFIGDIR.__str__()}")
# make directories
try:
@@ -97,7 +92,7 @@ def get_config(settings_path: str|None=None) -> dict:
# Check user .config/submissions directory
if CONFIGDIR.joinpath("config.yml").exists():
settings_path = CONFIGDIR.joinpath("config.yml")
# Check user .ozma directory
# Check user .submissions directory
elif Path.home().joinpath(".submissions", "config.yml").exists():
settings_path = Path.home().joinpath(".submissions", "config.yml")
# finally look in the local config
@@ -108,10 +103,11 @@ def get_config(settings_path: str|None=None) -> dict:
settings_path = package_dir.joinpath('config.yml')
# Tell program we need to copy the config.yml to the user directory
copy_settings_trigger = True
# shutil.copyfile(settings_path.__str__(), CONFIGDIR.joinpath("config.yml").__str__())
else:
# check if user defined path is directory
if Path(settings_path).is_dir():
settings_path = settings_path.joinpath("config.yml")
# check if user defined path is file
elif Path(settings_path).is_file():
settings_path = settings_path
else:
@@ -132,7 +128,7 @@ def get_config(settings_path: str|None=None) -> dict:
def create_database_session(database_path: Path|str|None=None) -> Session:
"""
Get database settings from path or default if blank.
Get database settings from path or default database if database_path is blank.
Args:
database_path (Path | str | None, optional): path to sqlite database. Defaults to None.
@@ -140,17 +136,22 @@ def create_database_session(database_path: Path|str|None=None) -> Session:
Returns:
Session: database session
"""
# convert string to path object
if isinstance(database_path, str):
database_path = Path(database_path)
# check if database path defined by user
if database_path == None:
# check in user's .submissions directory for submissions.db
if Path.home().joinpath(".submissions", "submissions.db").exists():
database_path = Path.home().joinpath(".submissions", "submissions.db")
# finally, look in the local dir
else:
database_path = package_dir.joinpath("submissions.db")
else:
# check if user defined path is directory
if database_path.is_dir():
database_path = database_path.joinpath("submissions.db")
# check if user defined path is a file
elif database_path.is_file():
database_path = database_path
else:
@@ -177,17 +178,16 @@ def setup_logger(verbosity:int=3):
# create file handler which logs even debug messages
try:
Path(LOGDIR).mkdir(parents=True)
# fh = GroupWriteRotatingFileHandler(LOGDIR.joinpath('submissions.log'), mode='a', maxBytes=100000, backupCount=3, encoding=None, delay=False)
# except FileNotFoundError as e:
except FileExistsError:
pass
fh = GroupWriteRotatingFileHandler(LOGDIR.joinpath('submissions.log'), mode='a', maxBytes=100000, backupCount=3, encoding=None, delay=False)
# file logging will always be debug
fh.setLevel(logging.DEBUG)
fh.name = "File"
# create console handler with a higher log level
ch = logging.StreamHandler(stream=sys.stdout)
# create custom logger with STERR -> log
# ch = StreamToLogger(logger=logger, log_level=verbosity)
ch = logging.StreamHandler(stream=sys.stdout)
# set looging level based on verbosity
match verbosity:
case 3:
ch.setLevel(logging.DEBUG)
@@ -203,14 +203,12 @@ def setup_logger(verbosity:int=3):
# add the handlers to the logger
logger.addHandler(fh)
logger.addHandler(ch)
# Output exception and traceback to logger
def handle_exception(exc_type, exc_value, exc_traceback):
if issubclass(exc_type, KeyboardInterrupt):
sys.__excepthook__(exc_type, exc_value, exc_traceback)
return
logger.critical("Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback))
# sys.exit(f"Uncaught error: {exc_type}, {exc_traceback}, check logs.")
sys.excepthook = handle_exception
return logger
@@ -233,5 +231,3 @@ def copy_settings(settings_path:Path, settings:dict) -> dict:
with open(settings_path, 'w') as f:
yaml.dump(settings, f)
return settings

74
src/submissions/frontend/__init__.py
View File

@@ -1,12 +1,11 @@
import json
import re
from typing import Tuple
from PyQt6.QtWidgets import (
QMainWindow, QLabel, QToolBar,
QTabWidget, QWidget, QVBoxLayout,
QPushButton, QFileDialog,
QLineEdit, QMessageBox, QComboBox, QDateEdit, QHBoxLayout,
QSpinBox, QScrollArea
QScrollArea
)
from PyQt6.QtGui import QAction
from PyQt6.QtCore import QSignalBlocker
@@ -27,15 +26,13 @@ from backend.db import (construct_submission_info, lookup_reagent,
lookup_regent_by_type_name, lookup_all_orgs, lookup_submissions_by_date_range,
get_all_Control_Types_names, create_kit_from_yaml, get_all_available_modes, get_all_controls_by_type,
get_control_subtypes, lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num,
create_org_from_yaml
create_org_from_yaml, store_reagent
)
from backend.db import lookup_kittype_by_name
from .functions import check_kit_integrity
from tools import check_not_nan
from tools import check_not_nan, extract_form_info
from backend.excel.reports import make_report_xlsx, make_report_html
import numpy
from frontend.custom_widgets.sub_details import SubmissionsSheet
from frontend.custom_widgets.pop_ups import AlertPop, QuestionAsker
from frontend.custom_widgets import AddReagentForm, ReportDatePicker, KitAdder, ControlsDatePicker, ImportReagent
@@ -233,12 +230,18 @@ class App(QMainWindow):
# hold samples in 'self' until form submitted
logger.debug(f"{item}: {prsr.sub[item]}")
self.samples = prsr.sub[item]
add_widget = None
case _:
# anything else gets added in as a line edit
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
add_widget = QLineEdit()
add_widget.setText(str(prsr.sub[item]).replace("_", " "))
self.table_widget.formlayout.addWidget(add_widget)
try:
add_widget.setObjectName(item)
logger.debug(f"Widget name set to: {add_widget.objectName()}")
self.table_widget.formlayout.addWidget(add_widget)
except AttributeError as e:
logger.error(e)
# compare self.reagents with expected reagents in kit
if hasattr(self, 'ext_kit'):
kit = lookup_kittype_by_name(ctx=self.ctx, name=self.ext_kit)
@@ -261,9 +264,10 @@ class App(QMainWindow):
Attempt to add sample to database when 'submit' button clicked
"""
# get info from form
labels, values = self.extract_form_info(self.table_widget.tab1)
info = {item[0]:item[1] for item in zip(labels, values) if not item[0].startswith("lot_")}
reagents = {item[0]:item[1] for item in zip(labels, values) if item[0].startswith("lot_")}
info = extract_form_info(self.table_widget.tab1)
reagents = {k:v for k,v in info.items() if k.startswith("lot_")}
info = {k:v for k,v in info.items() if not k.startswith("lot_")}
logger.debug(f"Info: {info}")
logger.debug(f"Reagents: {reagents}")
parsed_reagents = []
# compare reagents in form to reagent database
@@ -308,7 +312,6 @@ class App(QMainWindow):
# add reagents to submission object
for reagent in parsed_reagents:
base_submission.reagents.append(reagent)
# base_submission.reagents_id = reagent.id
logger.debug("Checking kit integrity...")
kit_integrity = check_kit_integrity(base_submission)
if kit_integrity != None:
@@ -317,7 +320,7 @@ class App(QMainWindow):
return
logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
result = store_submission(ctx=self.ctx, base_submission=base_submission)
# # check result of storing for issues
# check result of storing for issues
if result != None:
msg = AlertPop(result['message'])
msg.exec()
@@ -345,48 +348,17 @@ class App(QMainWindow):
dlg = AddReagentForm(ctx=self.ctx, reagent_lot=reagent_lot, reagent_type=reagent_type, expiry=expiry)
if dlg.exec():
# extract form info
labels, values = self.extract_form_info(dlg)
info = {item[0]:item[1] for item in zip(labels, values)}
info = extract_form_info(dlg)
logger.debug(f"dictionary from form: {info}")
# return None
logger.debug(f"Reagent info: {info}")
# create reagent object
reagent = construct_reagent(ctx=self.ctx, info_dict=info)
# send reagent to db
# store_reagent(ctx=self.ctx, reagent=reagent)
store_reagent(ctx=self.ctx, reagent=reagent)
return reagent
def extract_form_info(self, object) -> Tuple[list, list]:
"""
retrieves arbitrary number of labels, values from form
Args:
object (_type_): the form widget
Returns:
_type_: _description_
"""
labels = []
values = []
# grab all widgets in form
prev_item = None
for item in object.layout.parentWidget().findChildren(QWidget):
match item:
case QLabel():
labels.append(item.text().replace(" ", "_").lower())
case QLineEdit():
# ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox):
logger.debug(f"Previous: {prev_item}")
logger.debug(f"Item: {item}")
values.append(item.text())
case QComboBox():
values.append(item.currentText())
case QDateEdit():
values.append(item.date().toPyDate())
# value for ad hoc check above
prev_item = item
return labels, values
def generateReport(self):
"""
Action to create a summary of sheet data per client
@@ -394,8 +366,10 @@ class App(QMainWindow):
# Custom two date picker for start & end dates
dlg = ReportDatePicker()
if dlg.exec():
labels, values = self.extract_form_info(dlg)
info = {item[0]:item[1] for item in zip(labels, values)}
# labels, values = extract_form_info(dlg)
# info = {item[0]:item[1] for item in zip(labels, values)}
info = extract_form_info(dlg)
logger.debug(f"Report info: {info}")
# find submissions based on date range
subs = lookup_submissions_by_date_range(ctx=self.ctx, start_date=info['start_date'], end_date=info['end_date'])
# convert each object to dict
@@ -404,7 +378,7 @@ class App(QMainWindow):
html = make_report_html(df=df, start_date=info['start_date'], end_date=info['end_date'])
# make dataframe from record dictionaries
# df = make_report_xlsx(records=records)
# # setup filedialog to handle save location of report
# setup filedialog to handle save location of report
home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf").resolve().__str__()
# fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".xlsx")[0])
fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])

160
src/submissions/frontend/custom_widgets/__init__.py
View File

@@ -5,12 +5,11 @@ from PyQt6.QtWidgets import (
QDialogButtonBox, QDateEdit, QSizePolicy, QWidget,
QGridLayout, QPushButton, QSpinBox,
QScrollBar, QHBoxLayout,
QMessageBox
)
from PyQt6.QtCore import Qt, QDate, QSize
# from PyQt6.QtGui import QFontMetrics, QAction
from tools import check_not_nan
from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, lookup_regent_by_type_name
# from submissions.backend.db import lookup_regent_by_type_name_and_kit_name
from tools import check_not_nan, extract_form_info
from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml, lookup_regent_by_type_name, lookup_regent_by_type_name_and_kit_name
from backend.excel.parser import SheetParser
from jinja2 import Environment, FileSystemLoader
import sys
@@ -46,18 +45,19 @@ class AddReagentForm(QDialog):
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
# get lot info
# widget to get lot info
lot_input = QLineEdit()
lot_input.setObjectName("lot")
lot_input.setText(reagent_lot)
# get expiry info
# widget to get expiry info
exp_input = QDateEdit(calendarPopup=True)
exp_input.setObjectName('expiry')
# if expiry is not passed in from gui, use today
if expiry == None:
exp_input.setDate(QDate.currentDate())
else:
exp_input.setDate(expiry)
# get reagent type info
# widget to get reagent type info
type_input = QComboBox()
type_input.setObjectName('type')
type_input.addItems([item.replace("_", " ").title() for item in get_all_reagenttype_names(ctx=ctx)])
@@ -97,8 +97,10 @@ class ReportDatePicker(QDialog):
self.buttonBox.rejected.connect(self.reject)
# widgets to ask for dates
start_date = QDateEdit(calendarPopup=True)
start_date.setObjectName("start_date")
start_date.setDate(QDate.currentDate())
end_date = QDateEdit(calendarPopup=True)
end_date.setObjectName("end_date")
end_date.setDate(QDate.currentDate())
self.layout = QVBoxLayout()
self.layout.addWidget(QLabel("Start Date"))
@@ -121,28 +123,34 @@ class KitAdder(QWidget):
# insert submit button at top
self.submit_btn = QPushButton("Submit")
self.grid.addWidget(self.submit_btn,0,0,1,1)
# need to exclude ordinary users to mitigate garbage database entries
# self.grid.addWidget(QLabel("Password:"),1,0)
# self.grid.addWidget(QLineEdit(),1,1)
self.grid.addWidget(QLabel("Kit Name:"),2,0)
self.grid.addWidget(QLineEdit(),2,1)
# widget to get kit name
kit_name = QLineEdit()
kit_name.setObjectName("kit_name")
self.grid.addWidget(kit_name,2,1)
self.grid.addWidget(QLabel("Used For Sample Type:"),3,0)
# widget to get uses of kit
used_for = QComboBox()
used_for.setObjectName("used_for")
# Insert all existing sample types
used_for.addItems(lookup_all_sample_types(ctx=parent_ctx))
used_for.setEditable(True)
self.grid.addWidget(used_for,3,1)
# set cost per run
self.grid.addWidget(QLabel("Constant cost per full plate (plates, work hours, etc.):"),4,0)
cost = QSpinBox()
cost.setMinimum(0)
cost.setMaximum(9999)
self.grid.addWidget(cost,4,1)
# widget to get constant cost
const_cost = QSpinBox()
const_cost.setObjectName("const_cost")
const_cost.setMinimum(0)
const_cost.setMaximum(9999)
self.grid.addWidget(const_cost,4,1)
self.grid.addWidget(QLabel("Mutable cost per full plate (tips, reagents, etc.):"),5,0)
cost = QSpinBox()
cost.setMinimum(0)
cost.setMaximum(9999)
self.grid.addWidget(cost,5,1)
# widget to get mutable costs
mut_cost = QSpinBox()
mut_cost.setObjectName("mut_cost")
mut_cost.setMinimum(0)
mut_cost.setMaximum(9999)
self.grid.addWidget(mut_cost,5,1)
# button to add additional reagent types
self.add_RT_btn = QPushButton("Add Reagent Type")
self.grid.addWidget(self.add_RT_btn)
@@ -153,8 +161,11 @@ class KitAdder(QWidget):
"""
insert new reagent type row
"""
# get bottommost row
maxrow = self.grid.rowCount()
self.grid.addWidget(ReagentTypeForm(parent_ctx=self.ctx), maxrow + 1,0,1,2)
reg_form = ReagentTypeForm(parent_ctx=self.ctx)
reg_form.setObjectName(f"ReagentForm_{maxrow}")
self.grid.addWidget(reg_form, maxrow + 1,0,1,2)
def submit(self) -> None:
@@ -162,80 +173,65 @@ class KitAdder(QWidget):
send kit to database
"""
# get form info
labels, values, reagents = self.extract_form_info(self)
info = {item[0]:item[1] for item in zip(labels, values)}
logger.debug(info)
info, reagents = extract_form_info(self)
logger.debug(f"kit info: {info}")
yml_type = {}
try:
yml_type['password'] = info['password']
except KeyError:
pass
used = info['used_for_sample_type'].replace(" ", "_").lower()
used = info['used_for'].replace(" ", "_").lower()
yml_type[used] = {}
yml_type[used]['kits'] = {}
yml_type[used]['kits'][info['kit_name']] = {}
yml_type[used]['kits'][info['kit_name']]['constant_cost'] = info["Constant cost per full plate (plates, work hours, etc.)"]
yml_type[used]['kits'][info['kit_name']]['mutable_cost'] = info["Mutable cost per full plate (tips, reagents, etc.)"]
yml_type[used]['kits'][info['kit_name']]['constant_cost'] = info["const_cost"]
yml_type[used]['kits'][info['kit_name']]['mutable_cost'] = info["mut_cost"]
yml_type[used]['kits'][info['kit_name']]['reagenttypes'] = reagents
logger.debug(yml_type)
# send to kit constructor
result = create_kit_from_yaml(ctx=self.ctx, exp=yml_type)
# result = create_kit_from_yaml(ctx=self.ctx, exp=exp)
msg = AlertPop(message=result['message'], status=result['status'])
# match result['code']:
# case 0:
# msg = AlertPop(message=result['message'], status="information")
# # msg.setText()
# # msg.setInformativeText(result['message'])
# # msg.setWindowTitle("Kit added")
# case 1:
# msg = AlertPop(m)
# msg.setText("Permission Error")
# msg.setInformativeText(result['message'])
# msg.setWindowTitle("Permission Error")
msg.exec()
def extract_form_info(self, object):
"""
retrieves arbitrary number of labels, values from form
Args:
object (_type_): the object to extract info from
Returns:
_type_: _description_
"""
labels = []
values = []
reagents = {}
for item in object.findChildren(QWidget):
logger.debug(item.parentWidget())
# if not isinstance(item.parentWidget(), ReagentTypeForm):
match item:
case QLabel():
labels.append(item.text().replace(" ", "_").strip(":").lower())
case QLineEdit():
# ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox) and not isinstance(prev_item, QScrollBar):
logger.debug(f"Previous: {prev_item}")
logger.debug(f"Item: {item}, {item.text()}")
values.append(item.text().strip())
case QComboBox():
values.append(item.currentText().strip())
case QDateEdit():
values.append(item.date().toPyDate())
case QSpinBox():
values.append(item.value())
case ReagentTypeForm():
re_labels, re_values, _ = self.extract_form_info(item)
reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
logger.debug(reagent)
# reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
reagents[reagent["name_(*exactly*_as_it_appears_in_the_excel_submission_form)"].strip()] = {'eol_ext':int(reagent['extension_of_life_(months)'])}
prev_item = item
return labels, values, reagents
# def extract_form_info(self, object):
# """
# retrieves arbitrary number of labels, values from form
# Args:
# object (_type_): the object to extract info from
# Returns:
# _type_: _description_
# """
# labels = []
# values = []
# reagents = {}
# for item in object.findChildren(QWidget):
# logger.debug(item.parentWidget())
# # if not isinstance(item.parentWidget(), ReagentTypeForm):
# match item:
# case QLabel():
# labels.append(item.text().replace(" ", "_").strip(":").lower())
# case QLineEdit():
# # ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
# if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox) and not isinstance(prev_item, QScrollBar):
# logger.debug(f"Previous: {prev_item}")
# logger.debug(f"Item: {item}, {item.text()}")
# values.append(item.text().strip())
# case QComboBox():
# values.append(item.currentText().strip())
# case QDateEdit():
# values.append(item.date().toPyDate())
# case QSpinBox():
# values.append(item.value())
# case ReagentTypeForm():
# re_labels, re_values, _ = self.extract_form_info(item)
# reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
# logger.debug(reagent)
# # reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
# reagents[reagent["name_(*exactly*_as_it_appears_in_the_excel_submission_form)"].strip()] = {'eol_ext':int(reagent['extension_of_life_(months)'])}
# prev_item = item
# return labels, values, reagents
class ReagentTypeForm(QWidget):
"""
@@ -246,14 +242,17 @@ class ReagentTypeForm(QWidget):
grid = QGridLayout()
self.setLayout(grid)
grid.addWidget(QLabel("Name (*Exactly* as it appears in the excel submission form):"),0,0)
# Widget to get reagent info
reagent_getter = QComboBox()
reagent_getter.setObjectName("name")
# lookup all reagent type names from db
reagent_getter.addItems(get_all_reagenttype_names(ctx=parent_ctx))
reagent_getter.setEditable(True)
grid.addWidget(reagent_getter,0,1)
grid.addWidget(QLabel("Extension of Life (months):"),0,2)
# get extension of life
# widget toget extension of life
eol = QSpinBox()
eol.setObjectName('eol')
eol.setMinimum(0)
grid.addWidget(eol, 0,3)
@@ -277,7 +276,6 @@ class ControlsDatePicker(QWidget):
self.layout.addWidget(self.start_date)
self.layout.addWidget(QLabel("End Date"))
self.layout.addWidget(self.end_date)
self.setLayout(self.layout)
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
@@ -304,15 +302,17 @@ class ImportReagent(QComboBox):
logger.debug(f"Attempting lookup of reagents by type: {query_var}")
# below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name(ctx=ctx, type_name=query_var)]#, kit_name=prsr.sub['extraction_kit'])]
# relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name_and_kit_name(ctx=ctx, type_name=query_var, kit_name=prsr.sub['extraction_kit'])]
output_reg = []
for reagent in relevant_reagents:
# extract strings from any sets.
if isinstance(reagent, set):
for thing in reagent:
output_reg.append(thing)
elif isinstance(reagent, str):
output_reg.append(reagent)
relevant_reagents = output_reg
# if reagent in sheet is not found insert it into items
# if reagent in sheet is not found insert it into the front of relevant reagents so it shows
if prsr != None:
logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':

58
src/submissions/frontend/custom_widgets/pop_ups.py
View File

@@ -1,12 +1,7 @@
# from datetime import date
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QDialog,
QDialogButtonBox, QMessageBox
)
# from PyQt6.QtCore import Qt, QDate, QSize
# from PyQt6.QtGui import QFontMetrics, QAction
# from backend.db import get_all_reagenttype_names, lookup_all_sample_types, create_kit_from_yaml
from jinja2 import Environment, FileSystemLoader
import sys
from pathlib import Path
@@ -14,6 +9,7 @@ import logging
logger = logging.getLogger(f"submissions.{__name__}")
# determine if pyinstaller launcher is being used
if getattr(sys, 'frozen', False):
loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
else:
@@ -22,50 +18,6 @@ loader = FileSystemLoader(loader_path)
env = Environment(loader=loader)
# class AddReagentQuestion(QDialog):
# """
# dialog to ask about adding a new reagne to db
# """
# def __init__(self, reagent_type:str, reagent_lot:str) -> QDialog:
# super().__init__()
# self.setWindowTitle(f"Add {reagent_lot}?")
# QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
# self.buttonBox = QDialogButtonBox(QBtn)
# self.buttonBox.accepted.connect(self.accept)
# self.buttonBox.rejected.connect(self.reject)
# self.layout = QVBoxLayout()
# message = QLabel(f"Couldn't find reagent type {reagent_type.replace('_', ' ').title().strip('Lot')}: {reagent_lot} in the database.\n\nWould you like to add it?")
# self.layout.addWidget(message)
# self.layout.addWidget(self.buttonBox)
# self.setLayout(self.layout)
# class OverwriteSubQuestion(QDialog):
# """
# dialog to ask about overwriting existing submission
# """
# def __init__(self, message:str, rsl_plate_num:str) -> QDialog:
# super().__init__()
# self.setWindowTitle(f"Overwrite {rsl_plate_num}?")
# QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
# self.buttonBox = QDialogButtonBox(QBtn)
# self.buttonBox.accepted.connect(self.accept)
# self.buttonBox.rejected.connect(self.reject)
# self.layout = QVBoxLayout()
# message = QLabel(message)
# self.layout.addWidget(message)
# self.layout.addWidget(self.buttonBox)
# self.setLayout(self.layout)
class QuestionAsker(QDialog):
"""
dialog to ask yes/no questions
@@ -73,23 +25,27 @@ class QuestionAsker(QDialog):
def __init__(self, title:str, message:str) -> QDialog:
super().__init__()
self.setWindowTitle(title)
# set yes/no buttons
QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
self.layout = QVBoxLayout()
# Text for the yes/no question
message = QLabel(message)
self.layout.addWidget(message)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
class AlertPop(QMessageBox):
"""
Dialog to show an alert.
"""
def __init__(self, message:str, status:str) -> QMessageBox:
super().__init__()
# select icon by string
icon = getattr(QMessageBox.Icon, status.title())
self.setIcon(icon)
# msg.setText("Error")
self.setInformativeText(message)
self.setWindowTitle(status.title())

45
src/submissions/frontend/custom_widgets/sub_details.py
View File

@@ -1,20 +1,17 @@
from datetime import date
from PyQt6.QtWidgets import (
QVBoxLayout, QDialog, QTableView,
QTextEdit, QPushButton, QScrollArea,
QMessageBox, QFileDialog, QMenu
)
from PyQt6.QtCore import Qt, QAbstractTableModel
from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
from PyQt6.QtGui import QFontMetrics, QAction, QCursor
from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id
from jinja2 import Environment, FileSystemLoader
from xhtml2pdf import pisa
import sys
from pathlib import Path
import logging
from .pop_ups import AlertPop, QuestionAsker
from tools import check_is_power_user
from .pop_ups import QuestionAsker
logger = logging.getLogger(f"submissions.{__name__}")
@@ -45,7 +42,7 @@ class pandasModel(QAbstractTableModel):
"""
return self._data.shape[0]
def columnCount(self, parnet=None) -> int:
def columnCount(self, parent=None) -> int:
"""
does what it says
@@ -85,7 +82,7 @@ class SubmissionsSheet(QTableView):
self.setData()
self.resizeColumnsToContents()
self.resizeRowsToContents()
# self.clicked.connect(self.test)
self.setSortingEnabled(True)
self.doubleClicked.connect(self.show_details)
def setData(self) -> None:
@@ -93,6 +90,8 @@ class SubmissionsSheet(QTableView):
sets data in model
"""
self.data = submissions_to_df(ctx=self.ctx)
self.data['id'] = self.data['id'].apply(str)
self.data['id'] = self.data['id'].str.zfill(3)
try:
del self.data['samples']
except KeyError:
@@ -101,8 +100,11 @@ class SubmissionsSheet(QTableView):
del self.data['reagents']
except KeyError:
pass
self.model = pandasModel(self.data)
self.setModel(self.model)
proxyModel = QSortFilterProxyModel()
proxyModel.setSourceModel(pandasModel(self.data))
# self.model = pandasModel(self.data)
# self.setModel(self.model)
self.setModel(proxyModel)
# self.resize(800,600)
def show_details(self) -> None:
@@ -110,22 +112,22 @@ class SubmissionsSheet(QTableView):
creates detailed data to show in seperate window
"""
index = (self.selectionModel().currentIndex())
# logger.debug(index)
value = index.sibling(index.row(),0).data()
dlg = SubmissionDetails(ctx=self.ctx, id=value)
# dlg.show()
if dlg.exec():
pass
def contextMenuEvent(self, event):
"""
Creates actions for right click menu events.
Args:
event (_type_): the item of interest
"""
self.menu = QMenu(self)
renameAction = QAction('Delete', self)
detailsAction = QAction('Details', self)
# Originally I intended to limit deletions to power users.
# renameAction.setEnabled(False)
# if check_is_power_user(ctx=self.ctx):
# renameAction.setEnabled(True)
renameAction.triggered.connect(lambda: self.delete_item(event))
detailsAction.triggered.connect(lambda: self.show_details())
self.menu.addAction(detailsAction)
@@ -164,12 +166,8 @@ class SubmissionDetails(QDialog):
# get submision from db
data = lookup_submission_by_id(ctx=ctx, id=id)
self.base_dict = data.to_dict()
# logger.debug(f"Base dict: {self.base_dict}")
# don't want id
del self.base_dict['id']
# convert sub objects to dicts
# self.base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
# self.base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
# retrieve jinja template
template = env.get_template("submission_details.txt")
# render using object dict
@@ -192,24 +190,18 @@ class SubmissionDetails(QDialog):
interior.setWidget(txt_editor)
self.layout = QVBoxLayout()
self.setFixedSize(w, 900)
# button to export a pdf version
btn = QPushButton("Export PDF")
btn.setParent(self)
btn.setFixedWidth(w)
btn.clicked.connect(self.export)
# def _create_actions(self):
# self.exportAction = QAction("Export", self)
def export(self):
template = env.get_template("submission_details.html")
html = template.render(sub=self.base_dict)
# logger.debug(f"Submission details: {self.base_dict}")
home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
# logger.debug(f"report output name: {fname}")
# df.to_excel(fname, engine='openpyxl')
if fname.__str__() == ".":
logger.debug("Saving pdf was cancelled.")
return
@@ -223,4 +215,3 @@ class SubmissionDetails(QDialog):
msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
msg.setWindowTitle("Permission Error")
msg.exec()

11
src/submissions/frontend/functions.py
View File

@@ -2,7 +2,6 @@
from backend.db.models import *
import logging
logger = logging.getLogger(f"submissions.{__name__}")
def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None) -> dict|None:
@@ -21,6 +20,7 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
match sub:
case BasicSubmission():
ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types]
# Overwrite function parameter reagenttypes
reagenttypes = [reagent.type.name for reagent in sub.reagents]
case KitType():
ext_kit_rtypes = [reagenttype.name for reagenttype in sub.reagent_types]
@@ -30,13 +30,14 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
check = set(ext_kit_rtypes) == set(reagenttypes)
logger.debug(f"Checking if reagents match kit contents: {check}")
# what reagent types are in both lists?
common = list(set(ext_kit_rtypes).intersection(reagenttypes))
logger.debug(f"common reagents types: {common}")
# common = list(set(ext_kit_rtypes).intersection(reagenttypes))
missing = list(set(ext_kit_rtypes).difference(reagenttypes))
logger.debug(f"Missing reagents types: {missing}")
# if lists are equal return no problem
if check:
if len(missing)==0:
result = None
else:
missing = [x for x in ext_kit_rtypes if x not in common]
# missing = [x for x in ext_kit_rtypes if x not in common]
result = {'message' : f"Couldn't verify reagents match listed kit components.\n\nIt looks like you are missing: {[item.upper() for item in missing]}\n\nAlternatively, you may have set the wrong extraction kit.", 'missing': missing}
return result

10
src/submissions/frontend/visualizations/charts.py
View File

@@ -25,7 +25,6 @@ def create_charts(ctx:dict, df:pd.DataFrame, ytitle:str|None=None) -> Figure:
genera = []
if df.empty:
return None
for item in df['genus'].to_list():
try:
if item[-1] == "*":
@@ -95,7 +94,6 @@ def generic_figure_markers(fig:Figure, modes:list=[], ytitle:str|None=None) -> F
])
)
)
# logger.debug(f"Returning figure {fig}")
assert type(fig) == Figure
return fig
@@ -148,8 +146,7 @@ def output_figures(settings:dict, figs:list, group_name:str):
except AttributeError:
logger.error(f"The following figure was a string: {fig}")
# Below are the individual construction functions. They must be named "construct_{mode}_chart" and
# take only json_in and mode to hook into the main processor.
def construct_chart(ctx:dict, df:pd.DataFrame, modes:list, ytitle:str|None=None) -> Figure:
fig = Figure()
@@ -186,14 +183,15 @@ def construct_chart(ctx:dict, df:pd.DataFrame, modes:list, ytitle:str|None=None)
# sys.exit(f"number of traces={len(fig.data)}")
return generic_figure_markers(fig=fig, modes=modes, ytitle=ytitle)
# Below are the individual construction functions. They must be named "construct_{mode}_chart" and
# take only json_in and mode to hook into the main processor.
def construct_refseq_chart(settings:dict, df:pd.DataFrame, group_name:str, mode:str) -> Figure:
"""
Constructs intial refseq chart for both contains and matches (depreciated).
Args:
settings (dict): settings passed down from click.
settings (dict): settings passed down from gui.
df (pd.DataFrame): dataframe containing all sample data for the group.
group_name (str): name of the group being processed.
mode (str): contains or matches, overwritten by hardcoding, so don't think about it too hard.

52
src/submissions/tools/__init__.py
View File

@@ -1,6 +1,14 @@
import numpy as np
import logging
import getpass
from PyQt6.QtWidgets import (
QMainWindow, QLabel, QToolBar,
QTabWidget, QWidget, QVBoxLayout,
QPushButton, QFileDialog,
QLineEdit, QMessageBox, QComboBox, QDateEdit, QHBoxLayout,
QSpinBox, QScrollArea
)
logger = logging.getLogger(f"submissions.{__name__}")
@@ -26,4 +34,46 @@ def check_is_power_user(ctx:dict) -> bool:
def create_reagent_list(in_dict:dict) -> list[str]:
return [item.strip("lot_") for item in in_dict.keys()]
return [item.strip("lot_") for item in in_dict.keys()]
def extract_form_info(object) -> dict:
"""
retrieves object names and values from form
Args:
object (_type_): the form widget
Returns:
dict: dictionary of objectName:text items
"""
from frontend.custom_widgets import ReagentTypeForm
dicto = {}
reagents = {}
logger.debug(f"Object type: {type(object)}")
# grab all widgets in form
try:
all_children = object.layout.parentWidget().findChildren(QWidget)
except AttributeError:
all_children = object.layout().parentWidget().findChildren(QWidget)
for item in all_children:
logger.debug(f"Looking at: {item.objectName()}")
match item:
case QLineEdit():
dicto[item.objectName()] = item.text()
case QComboBox():
dicto[item.objectName()] = item.currentText()
case QDateEdit():
dicto[item.objectName()] = item.date().toPyDate()
case QSpinBox():
dicto[item.objectName()] = item.value()
case ReagentTypeForm():
reagent = extract_form_info(item)
# reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
logger.debug(reagent)
# reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
reagents[reagent["name"].strip()] = {'eol_ext':int(reagent['eol'])}
# value for ad hoc check above
if reagents != {}:
return dicto, reagents
return dicto