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documentation and converted to username based exclusion of adding new kits

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This commit is contained in:
Landon Wark
2023-01-30 12:07:38 -06:00
parent bbb65d3fe6
commit 1f832dccf2
16 changed files with 876 additions and 296 deletions
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2
src/submissions/__init__.py
View File

@@ -1,4 +1,4 @@
# __init__.py
# Version of the realpython-reader package
__version__ = "1.0.0"
__version__ = "1.1.2"

8
src/submissions/__main__.py
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@@ -1,19 +1,27 @@
import sys
from pathlib import Path
import os
# must be set to enable qtwebengine in network path
if getattr(sys, 'frozen', False):
os.environ['QTWEBENGINE_DISABLE_SANDBOX'] = "1"
else :
pass
from configure import get_config, create_database_session, setup_logger
# setup custom logger
logger = setup_logger(verbosity=3)
# import config
ctx = get_config(None)
from PyQt6.QtWidgets import QApplication
from frontend import App
import __init__ as package
# create database session for use with gui session
ctx["database_session"] = create_database_session(Path(ctx['database']))
# set package information fro __init__
ctx['package'] = package
if __name__ == '__main__':
#
app = QApplication(['', '--no-sandbox'])
ex = App(ctx=ctx)
sys.exit(app.exec())

260
src/submissions/backend/db/__init__.py
View File

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

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

@@ -1,5 +1,5 @@
from . import Base
from sqlalchemy import Column, String, TIMESTAMP, text, JSON, INTEGER, ForeignKey, UniqueConstraint
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey
from sqlalchemy.orm import relationship
class ControlType(Base):
@@ -32,6 +32,6 @@ class Control(Base):
matches = Column(JSON) #: unstructured hashes in matches.tsv for each organism
kraken = Column(JSON) #: unstructured output from kraken_report
# UniqueConstraint('name', name='uq_control_name')
submission_id = Column(INTEGER, ForeignKey("_submissions.id"))
submission = relationship("BacterialCulture", back_populates="controls", foreign_keys=[submission_id])
submission_id = Column(INTEGER, ForeignKey("_submissions.id")) #: parent submission id
submission = relationship("BacterialCulture", back_populates="controls", foreign_keys=[submission_id]) #: parent submission

84
src/submissions/backend/db/models/kits.py
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@@ -3,57 +3,88 @@ from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Int
from sqlalchemy.orm import relationship
# Table containing reagenttype-kittype relationships
reagenttypes_kittypes = Table("_reagentstypes_kittypes", Base.metadata, Column("reagent_types_id", INTEGER, ForeignKey("_reagent_types.id")), Column("kits_id", INTEGER, ForeignKey("_kits.id")))
class KitType(Base):
"""
Base of kits used in submission processing
"""
__tablename__ = "_kits"
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64), unique=True)
submissions = relationship("BasicSubmission", back_populates="extraction_kit")
used_for = Column(JSON)
cost_per_run = Column(FLOAT(2))
reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes)
reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id"))
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
reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes) #: reagent types this kit contains
reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id")) #: joined reagent type id
def __str__(self):
def __str__(self) -> str:
"""
a string representing this object
Returns:
str: a string representing this object's name
"""
return self.name
class ReagentType(Base):
"""
Base of reagent type abstract
"""
__tablename__ = "_reagent_types"
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64))
kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", use_alter=True, name="fk_RT_kits_id"))
kits = relationship("KitType", back_populates="reagent_types", uselist=True, foreign_keys=[kit_id])
instances = relationship("Reagent", back_populates="type")
name = Column(String(64)) #: name of reagent type
kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", use_alter=True, name="fk_RT_kits_id")) #: id of joined kit type
kits = relationship("KitType", back_populates="reagent_types", uselist=True, foreign_keys=[kit_id]) #: kits this reagent is used in
instances = relationship("Reagent", back_populates="type") #: concrete instances of this reagent type
# instances_id = Column(INTEGER, ForeignKey("_reagents.id", ondelete='SET NULL'))
eol_ext = Column(Interval())
eol_ext = Column(Interval()) #: extension of life interval
def __str__(self):
def __str__(self) -> str:
"""
string representing this object
Returns:
str: string representing this object's name
"""
return self.name
class Reagent(Base):
"""
Concrete reagent instance
"""
__tablename__ = "_reagents"
id = Column(INTEGER, primary_key=True) #: primary key
type = relationship("ReagentType", back_populates="instances")
type_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', name="fk_reagent_type_id"))
name = Column(String(64))
lot = Column(String(64))
expiry = Column(TIMESTAMP)
submissions = relationship("BasicSubmission", back_populates="reagents", uselist=True)
type = relationship("ReagentType", back_populates="instances") #: joined parent reagent type
type_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', name="fk_reagent_type_id")) #: id of parent reagent type
name = Column(String(64)) #: reagent name
lot = Column(String(64)) #: lot number of reagent
expiry = Column(TIMESTAMP) #: expiry date - extended by eol_ext of parent programmatically
submissions = relationship("BasicSubmission", back_populates="reagents", uselist=True) #: submissions this reagent is used in
def __str__(self):
def __str__(self) -> str:
"""
string representing this object
Returns:
str: string representing this object's lot number
"""
return self.lot
def to_sub_dict(self):
def to_sub_dict(self) -> dict:
"""
dictionary containing values necessary for gui
Returns:
dict: gui friendly dictionary
"""
try:
type = self.type.name.replace("_", " ").title()
except AttributeError:
@@ -62,7 +93,4 @@ class Reagent(Base):
"type": type,
"lot": self.lot,
"expiry": self.expiry.strftime("%Y-%m-%d")
}
}

37
src/submissions/backend/db/models/organizations.py
View File

@@ -3,32 +3,43 @@ from sqlalchemy import Column, String, TIMESTAMP, JSON, Float, INTEGER, ForeignK
from sqlalchemy.orm import relationship, validates
# table containing organization/contact relationship
orgs_contacts = Table("_orgs_contacts", Base.metadata, Column("org_id", INTEGER, ForeignKey("_organizations.id")), Column("contact_id", INTEGER, ForeignKey("_contacts.id")))
class Organization(Base):
"""
Base of organization
"""
__tablename__ = "_organizations"
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64))
submissions = relationship("BasicSubmission", back_populates="submitting_lab")
cost_centre = Column(String())
contacts = relationship("Contact", back_populates="organization", secondary=orgs_contacts)
contact_ids = Column(INTEGER, ForeignKey("_contacts.id", ondelete="SET NULL", name="fk_org_contact_id"))
name = Column(String(64)) #: organization name
submissions = relationship("BasicSubmission", back_populates="submitting_lab") #: submissions this organization has submitted
cost_centre = Column(String()) #: cost centre used by org for payment
contacts = relationship("Contact", back_populates="organization", secondary=orgs_contacts) #: contacts involved with this org
contact_ids = Column(INTEGER, ForeignKey("_contacts.id", ondelete="SET NULL", name="fk_org_contact_id")) #: contact ids of this organization
def __str__(self):
def __str__(self) -> str:
"""
String representing organization
Returns:
str: string representing organization name
"""
return self.name.replace("_", " ").title()
class Contact(Base):
"""
Base of Contace
"""
__tablename__ = "_contacts"
id = id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64))
email = Column(String(64))
phone = Column(String(32))
organization = relationship("Organization", back_populates="contacts", uselist=True)
# organization_id = Column(INTEGER, ForeignKey("_organizations.id"))
name = Column(String(64)) #: contact name
email = Column(String(64)) #: contact email
phone = Column(String(32)) #: contact phone number
organization = relationship("Organization", back_populates="contacts", uselist=True, secondary=orgs_contacts) #: relationship to joined organization
organization_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete="SET NULL", name="fk_contact_org_id")) #: joined organization ids

62
src/submissions/backend/db/models/samples.py
View File

@@ -1,18 +1,20 @@
from . import Base
from sqlalchemy import Column, String, TIMESTAMP, text, JSON, INTEGER, ForeignKey, FLOAT, BOOLEAN
from sqlalchemy.orm import relationship, relationships
from sqlalchemy.orm import relationship
class WWSample(Base):
"""
Base wastewater sample
"""
__tablename__ = "_ww_samples"
id = Column(INTEGER, primary_key=True) #: primary key
ww_processing_num = Column(String(64))
ww_sample_full_id = Column(String(64), nullable=False)
rsl_number = Column(String(64))
rsl_plate = relationship("Wastewater", back_populates="samples")
rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWS_sample_id"))
rsl_number = Column(String(64)) #: rsl plate identification number
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
testing_type = Column(String(64))
site_status = Column(String(64))
@@ -22,12 +24,24 @@ class WWSample(Base):
seq_submitted = Column(BOOLEAN())
ww_seq_run_id = Column(String(64))
sample_type = Column(String(8))
well_number = Column(String(8))
well_number = Column(String(8)) #: location on plate
def to_string(self):
def to_string(self) -> str:
"""
string representing sample object
Returns:
str: string representing location and sample id
"""
return f"{self.well_number}: {self.ww_sample_full_id}"
def to_sub_dict(self):
def to_sub_dict(self) -> dict:
"""
gui friendly dictionary
Returns:
dict: well location and id
"""
return {
"well": self.well_number,
"name": self.ww_sample_full_id,
@@ -35,21 +49,35 @@ class WWSample(Base):
class BCSample(Base):
"""
base of bacterial culture sample
"""
__tablename__ = "_bc_samples"
id = Column(INTEGER, primary_key=True) #: primary key
well_number = Column(String(8))
sample_id = Column(String(64), nullable=False)
organism = Column(String(64))
concentration = Column(String(16))
rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_BCS_sample_id"))
rsl_plate = relationship("BacterialCulture", back_populates="samples")
well_number = Column(String(8)) #: location on parent plate
sample_id = Column(String(64), nullable=False) #: identification from submitter
organism = Column(String(64)) #: bacterial specimen
concentration = Column(String(16)) #:
rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_BCS_sample_id")) #: id of parent plate
rsl_plate = relationship("BacterialCulture", back_populates="samples") #: relationship to parent plate
def to_string(self):
def to_string(self) -> str:
"""
string representing object
Returns:
str: string representing well location, sample id and organism
"""
return f"{self.well_number}: {self.sample_id} - {self.organism}"
def to_sub_dict(self):
def to_sub_dict(self) -> dict:
"""
gui friendly dictionary
Returns:
dict: well location and name (sample id, organism)
"""
return {
"well": self.well_number,
"name": f"{self.sample_id} - ({self.organism})",

50
src/submissions/backend/db/models/submissions.py
View File

@@ -3,26 +3,29 @@ from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table
from sqlalchemy.orm import relationship
from datetime import datetime as dt
# table containing reagents/submission relationships
reagents_submissions = Table("_reagents_submissions", Base.metadata, Column("reagent_id", INTEGER, ForeignKey("_reagents.id")), Column("submission_id", INTEGER, ForeignKey("_submissions.id")))
class BasicSubmission(Base):
"""
Base of basic submission which polymorphs into BacterialCulture and Wastewater
"""
__tablename__ = "_submissions"
id = Column(INTEGER, primary_key=True) #: primary key
rsl_plate_num = Column(String(32), unique=True) #: RSL name (e.g. RSL-22-0012)
submitter_plate_num = Column(String(127), unique=True) #: The number given to the submission by the submitting lab
submitted_date = Column(TIMESTAMP) #: Date submission received
submitting_lab = relationship("Organization", back_populates="submissions") #: client
submitting_lab = relationship("Organization", back_populates="submissions") #: client org
submitting_lab_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete="SET NULL", name="fk_BS_sublab_id"))
sample_count = Column(INTEGER) #: Number of samples in the submission
extraction_kit = relationship("KitType", back_populates="submissions") #: The extraction kit used
extraction_kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", name="fk_BS_extkit_id"))
submission_type = Column(String(32))
technician = Column(String(64))
submission_type = Column(String(32)) #: submission type (should be string in D3 of excel sheet)
technician = Column(String(64)) #: initials of processing tech
# Move this into custom types?
reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions)
reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id"))
reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions) #: relationship to reagents
reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id")) #: id of used reagents
__mapper_args__ = {
"polymorphic_identity": "basic_submission",
@@ -30,10 +33,23 @@ class BasicSubmission(Base):
"with_polymorphic": "*",
}
def to_string(self):
def to_string(self) -> str:
"""
string presenting basic submission
Returns:
str: string representing rsl plate number and submitter plate number
"""
return f"{self.rsl_plate_num} - {self.submitter_plate_num}"
def to_dict(self):
def to_dict(self) -> dict:
"""
dictionary used in submissions summary
Returns:
dict: dictionary used in submissions summary
"""
# get lab from nested organization object
try:
sub_lab = self.submitting_lab.name
except AttributeError:
@@ -42,6 +58,7 @@ class BasicSubmission(Base):
sub_lab = sub_lab.replace("_", " ").title()
except AttributeError:
pass
# get extraction kit name from nested kit object
try:
ext_kit = self.extraction_kit.name
except AttributeError:
@@ -60,7 +77,14 @@ class BasicSubmission(Base):
return output
def report_dict(self):
def report_dict(self) -> dict:
"""
dictionary used in creating reports
Returns:
dict: dictionary used in creating reports
"""
# get lab name from nested organization object
try:
sub_lab = self.submitting_lab.name
except AttributeError:
@@ -69,10 +93,12 @@ class BasicSubmission(Base):
sub_lab = sub_lab.replace("_", " ").title()
except AttributeError:
pass
# get extraction kit name from nested kittype object
try:
ext_kit = self.extraction_kit.name
except AttributeError:
ext_kit = None
# get extraction kit cost from nested kittype object
try:
cost = self.extraction_kit.cost_per_run
except AttributeError:
@@ -93,6 +119,9 @@ class BasicSubmission(Base):
# Below are the custom submission
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)
@@ -101,6 +130,9 @@ class BacterialCulture(BasicSubmission):
class Wastewater(BasicSubmission):
"""
derivative submission type from BasicSubmission
"""
samples = relationship("WWSample", back_populates="rsl_plate", uselist=True)
# ww_sample_id = Column(String, ForeignKey("_ww_samples.id", ondelete="SET NULL", name="fk_WW_sample_id"))
__mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}

11
src/submissions/backend/excel/__init__.py
View File

@@ -1,4 +1,3 @@
from pandas import DataFrame
import re
@@ -6,14 +5,14 @@ import re
def get_unique_values_in_df_column(df: DataFrame, column_name: str) -> list:
"""
_summary_
get all unique values in a dataframe column by name
Args:
df (DataFrame): _description_
column_name (str): _description_
df (DataFrame): input dataframe
column_name (str): name of column of interest
Returns:
list: _description_
list: sorted list of unique values
"""
return sorted(df[column_name].unique())
@@ -23,7 +22,7 @@ def drop_reruns_from_df(ctx:dict, df: DataFrame) -> DataFrame:
Removes semi-duplicates from dataframe after finding sequencing repeats.
Args:
settings (dict): settings passed down from click
settings (dict): settings passed from gui
df (DataFrame): initial dataframe
Returns:

95
src/submissions/backend/excel/parser.py
View File

@@ -11,40 +11,68 @@ import uuid
logger = logging.getLogger(f"submissions.{__name__}")
class SheetParser(object):
def __init__(self, filepath:Path|None = None, **kwargs):
"""
object to pull and contain data from excel file
"""
def __init__(self, filepath:Path|None = None, **kwargs) -> None:
"""
Args:
filepath (Path | None, optional): file path to excel sheet. Defaults to None.
"""
logger.debug(f"Parsing {filepath.__str__()}")
# set attributes based on kwargs from gui ctx
for kwarg in kwargs:
setattr(self, f"_{kwarg}", kwargs[kwarg])
if filepath == None:
logger.debug(f"No filepath.")
logger.error(f"No filepath given.")
self.xl = None
else:
try:
self.xl = pd.ExcelFile(filepath.__str__())
except ValueError:
except ValueError as e:
logger.error(f"Incorrect value: {e}")
self.xl = None
self.sub = OrderedDict()
self.sub['submission_type'] = self._type_decider()
# make decision about type of sample we have
self.sub['submission_type'] = self._type_decider()
# select proper parser based on sample type
parse_sub = getattr(self, f"_parse_{self.sub['submission_type'].lower()}")
parse_sub()
def _type_decider(self):
def _type_decider(self) -> str:
"""
makes decisions about submission type based on structure of excel file
Returns:
str: submission type name
"""
try:
for type in self._submission_types:
if self.xl.sheet_names == self._submission_types[type]['excel_map']:
return type.title()
return "Unknown"
except:
except Exception as e:
logger.warning(f"We were unable to parse the submission type due to: {e}")
return "Unknown"
def _parse_unknown(self):
def _parse_unknown(self) -> None:
"""
Dummy function to handle unknown excel structures
"""
self.sub = None
def _parse_generic(self, sheet_name:str):
def _parse_generic(self, sheet_name:str) -> pd.DataFrame:
"""
Pulls information common to all submission types and passes on dataframe
Args:
sheet_name (str): name of excel worksheet to pull from
Returns:
pd.DataFrame: relevant dataframe from excel sheet
"""
submission_info = self.xl.parse(sheet_name=sheet_name, dtype=object)
self.sub['submitter_plate_num'] = submission_info.iloc[0][1] #if pd.isnull(submission_info.iloc[0][1]) else string_formatter(submission_info.iloc[0][1])
@@ -57,7 +85,10 @@ class SheetParser(object):
return submission_info
def _parse_bacterial_culture(self):
def _parse_bacterial_culture(self) -> None:
"""
pulls info specific to bacterial culture sample type
"""
submission_info = self._parse_generic("Sample List")
# iloc is [row][column] and the first row is set as header row so -2
tech = str(submission_info.iloc[11][1])
@@ -68,7 +99,7 @@ class SheetParser(object):
tech = ", ".join(tech_reg.findall(tech))
self.sub['technician'] = tech
# reagents
# must be prefixed with 'lot_' to be recognized by gui
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])
@@ -79,13 +110,17 @@ class SheetParser(object):
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")
logger.debug(f"Parser result: {self.sub}")
self.sub['samples'] = sample_parse()
def _parse_wastewater(self):
def _parse_wastewater(self) -> None:
"""
pulls info specific to wastewater sample type
"""
# submission_info = self.xl.parse("WW Submissions (ENTER HERE)")
submission_info = self._parse_generic("WW Submissions (ENTER HERE)")
enrichment_info = self.xl.parse("Enrichment Worksheet", dtype=object)
@@ -108,19 +143,28 @@ class SheetParser(object):
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])
# gt individual sample info
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()
class SampleParser(object):
"""
object to pull data for samples in excel sheet and construct individual sample objects
"""
def __init__(self, df:pd.DataFrame) -> None:
self.samples = df.to_dict("records")
def parse_bacterial_culture_samples(self) -> list[BCSample]:
"""
construct bacterial culture specific sample objects
Returns:
list[BCSample]: list of sample objects
"""
new_list = []
for sample in self.samples:
new = BCSample()
@@ -130,6 +174,7 @@ class SampleParser(object):
new.concentration = sample['Unnamed: 3']
# logger.debug(f"Sample object: {new.sample_id} = {type(new.sample_id)}")
logger.debug(f"Got sample_id: {new.sample_id}")
# need to exclude empties and blanks
try:
not_a_nan = not np.isnan(new.sample_id) and str(new.sample_id).lower() != 'blank'
except TypeError:
@@ -140,10 +185,17 @@ class SampleParser(object):
def parse_wastewater_samples(self) -> list[WWSample]:
"""
construct wastewater specific sample objects
Returns:
list[WWSample]: list of sample objects
"""
new_list = []
for sample in self.samples:
new = WWSample()
new.ww_processing_num = sample['Unnamed: 2']
# need to ensure we have a sample id for database integrity
try:
not_a_nan = not np.isnan(sample['Unnamed: 3'])
except TypeError:
@@ -153,6 +205,7 @@ class SampleParser(object):
else:
new.ww_sample_full_id = uuid.uuid4().hex.upper()
new.rsl_number = sample['Unnamed: 9']
# need to ensure we get a collection date
try:
not_a_nan = not np.isnan(sample['Unnamed: 5'])
except TypeError:
@@ -169,11 +222,11 @@ class SampleParser(object):
return new_list
def string_formatter(input):
logger.debug(f"{input} : {type(input)}")
match input:
case int() | float() | np.float64:
return "{:0.0f}".format(input)
case _:
return input
# def string_formatter(input):
# logger.debug(f"{input} : {type(input)}")
# match input:
# case int() | float() | np.float64:
# return "{:0.0f}".format(input)
# case _:
# return input

39
src/submissions/backend/excel/reports.py
View File

@@ -8,13 +8,22 @@ import logging
logger = logging.getLogger(f"submissions.{__name__}")
def make_report_xlsx(records:list[dict]) -> DataFrame:
"""
create the dataframe for a report
Args:
records (list[dict]): list of dictionaries created from submissions
Returns:
DataFrame: output dataframe
"""
df = DataFrame.from_records(records)
# put submissions with the same lab together
df = df.sort_values("Submitting Lab")
# table = df.pivot_table(values="Cost", index=["Submitting Lab", "Extraction Kit"], columns=["Cost", "Sample Count"], aggfunc={'Cost':np.sum,'Sample Count':np.sum})
# aggregate cost and sample count columns
df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Cost': ['sum', 'count'], 'Sample Count':['sum']})
# df2['Cost'] = df2['Cost'].map('${:,.2f}'.format)
logger.debug(df2.columns)
# df2['Cost']['sum'] = df2['Cost']['sum'].apply('${:,.2f}'.format)
# 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
@@ -65,7 +74,18 @@ def make_report_xlsx(records:list[dict]) -> DataFrame:
# dfs['name'] = df
# return dfs
def convert_control_by_mode(ctx:dict, control:models.Control, mode:str):
def convert_control_by_mode(ctx:dict, control:models.Control, mode:str) -> list[dict]:
"""
split control object into analysis types
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:
@@ -82,6 +102,17 @@ def convert_control_by_mode(ctx:dict, control:models.Control, mode:str):
def convert_data_list_to_df(ctx:dict, input:list[dict], subtype:str|None=None) -> DataFrame:
"""
Convert list of control records to dataframe
Args:
ctx (dict): settings passed from gui
input (list[dict]): list of dictionaries containing records
subtype (str | None, optional): _description_. Defaults to None.
Returns:
DataFrame: _description_
"""
df = DataFrame.from_records(input)
safe = ['name', 'submitted_date', 'genus', 'target']
logger.debug(df)

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

@@ -1,9 +1,9 @@
import yaml
import sys, os, stat, platform, shutil
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
@@ -64,8 +64,9 @@ class StreamToLogger(object):
self.logger.log(self.log_level, line.rstrip())
def get_config(settings_path: str|None) -> dict:
"""Get configuration settings from path or default if blank.
def get_config(settings_path: str|None=None) -> dict:
"""
Get configuration settings from path or default if blank.
Args:
settings_path (str, optional): _description_. Defaults to "".
@@ -91,6 +92,7 @@ def get_config(settings_path: str|None) -> dict:
except FileExistsError:
pass
# if user hasn't defined config path in cli args
copy_settings_trigger = False
if settings_path == None:
# Check user .config/submissions directory
if CONFIGDIR.joinpath("config.yml").exists():
@@ -104,7 +106,9 @@ def get_config(settings_path: str|None) -> dict:
settings_path = Path(sys._MEIPASS).joinpath("files", "config.yml")
else:
settings_path = package_dir.joinpath('config.yml')
shutil.copyfile(settings_path.__str__(), CONFIGDIR.joinpath("config.yml").__str__())
# 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:
if Path(settings_path).is_dir():
settings_path = settings_path.joinpath("config.yml")
@@ -120,11 +124,15 @@ def get_config(settings_path: str|None) -> dict:
except yaml.YAMLError as exc:
logger.error(f'Error reading yaml file {settings_path}: {exc}')
return {}
# copy settings to config directory
if copy_settings_trigger:
settings = copy_settings(settings_path=CONFIGDIR.joinpath("config.yml"), settings=settings)
return settings
def create_database_session(database_path: Path|None) -> Session:
"""Get database settings from path or default if blank.
"""
Get database settings from path or default if blank.
Args:
database_path (str, optional): _description_. Defaults to "".
@@ -153,7 +161,8 @@ def create_database_session(database_path: Path|None) -> Session:
def setup_logger(verbosity:int=3):
"""Set logger levels using settings.
"""
Set logger levels using settings.
Args:
verbose (bool, optional): _description_. Defaults to False.
@@ -203,15 +212,22 @@ def setup_logger(verbosity:int=3):
sys.excepthook = handle_exception
return logger
# def set_logger_verbosity(verbosity):
# """Does what it says.
# """
# handler = [item for item in logger.parent.handlers if item.name == "Stream"][0]
# match verbosity:
# case 3:
# handler.setLevel(logging.DEBUG)
# case 2:
# handler.setLevel(logging.INFO)
# case 1:
# handler.setLevel(logging.WARNING)
def copy_settings(settings_path:Path, settings:dict) -> dict:
"""
copies relevant settings dictionary from the default config.yml to a new directory
Args:
settings_path (Path): path to write the file to
settings (dict): settings dictionary obtained from default config.yml
Returns:
dict: output dictionary for use in first run
"""
# if the current user is not a superuser remove the superusers entry
if not getpass.getuser() in settings['super_users']:
del settings['super_users']
with open(settings_path, 'w') as f:
yaml.dump(settings, f)
return settings

270
src/submissions/frontend/__init__.py
View File

@@ -1,20 +1,20 @@
import re
from PyQt6.QtWidgets import (
QMainWindow, QLabel, QToolBar, QStatusBar,
QMainWindow, QLabel, QToolBar,
QTabWidget, QWidget, QVBoxLayout,
QPushButton, QMenuBar, QFileDialog,
QPushButton, QFileDialog,
QLineEdit, QMessageBox, QComboBox, QDateEdit, QHBoxLayout,
QSpinBox, QScrollArea, QScrollBar, QSizePolicy
QSpinBox, QScrollArea
)
from PyQt6.QtGui import QAction, QIcon
from PyQt6.QtCore import pyqtSlot, QDateTime, QDate, QSignalBlocker, Qt
from PyQt6.QtGui import QAction
from PyQt6.QtCore import QSignalBlocker
from PyQt6.QtWebEngineWidgets import QWebEngineView
import pandas as pd
# import pandas as pd
from pathlib import Path
import plotly
import plotly.express as px
# import plotly.express as px
import yaml
from backend.excel.parser import SheetParser
@@ -30,41 +30,45 @@ import numpy
from frontend.custom_widgets import AddReagentQuestion, AddReagentForm, SubmissionsSheet, ReportDatePicker, KitAdder, ControlsDatePicker, OverwriteSubQuestion
import logging
import difflib
from datetime import date
from frontend.visualizations.charts import create_charts
logger = logging.getLogger(__name__)
logger.info("Hello, I am a logger")
class App(QMainWindow):
# class App(QScrollArea):
def __init__(self, ctx: dict = {}):
super().__init__()
self.ctx = ctx
self.title = 'Submissions App - PyQT6'
try:
self.title = f"Submissions App (v{ctx['package'].__version__})"
except AttributeError:
self.title = f"Submissions App"
# set initial app position and size
self.left = 0
self.top = 0
self.width = 1300
self.height = 1000
self.setWindowTitle(self.title)
self.setGeometry(self.left, self.top, self.width, self.height)
# insert tabs into main app
self.table_widget = AddSubForm(self)
self.setCentralWidget(self.table_widget)
# run initial setups
self._createActions()
self._createMenuBar()
self._createToolBar()
self._connectActions()
# self.renderPage()
self.controls_getter()
self.show()
def _createMenuBar(self):
"""
adds items to menu bar
"""
menuBar = self.menuBar()
fileMenu = menuBar.addMenu("&File")
# menuBar.addMenu(fileMenu)
# Creating menus using a title
editMenu = menuBar.addMenu("&Edit")
reportMenu = menuBar.addMenu("&Reports")
@@ -73,12 +77,18 @@ class App(QMainWindow):
reportMenu.addAction(self.generateReportAction)
def _createToolBar(self):
"""
adds items to toolbar
"""
toolbar = QToolBar("My main toolbar")
self.addToolBar(toolbar)
toolbar.addAction(self.addReagentAction)
toolbar.addAction(self.addKitAction)
def _createActions(self):
"""
creates actions
"""
self.importAction = QAction("&Import", self)
self.addReagentAction = QAction("Add Reagent", self)
self.generateReportAction = QAction("Make Report", self)
@@ -86,6 +96,9 @@ class App(QMainWindow):
def _connectActions(self):
"""
connect menu and tool bar item to functions
"""
self.importAction.triggered.connect(self.importSubmission)
self.addReagentAction.triggered.connect(self.add_reagent)
self.generateReportAction.triggered.connect(self.generateReport)
@@ -97,21 +110,27 @@ class App(QMainWindow):
def importSubmission(self):
"""
import submission from excel sheet into form
"""
logger.debug(self.ctx)
# initialize samples
self.samples = []
# set file dialog
home_dir = str(Path(self.ctx["directory_path"]))
fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir)[0])
logger.debug(f"Attempting to parse file: {fname}")
assert fname.exists()
# create sheetparser using excel sheet and context from gui
try:
prsr = SheetParser(fname, **self.ctx)
except PermissionError:
return
logger.debug(f"prsr.sub = {prsr.sub}")
# replace formlayout with tab1.layout
# self.form = self.table_widget.formlayout
# destroy any widgets from previous imports
for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
item.setParent(None)
# regex to parser out different variable types for decision making
variable_parser = re.compile(r"""
# (?x)
(?P<extraction_kit>^extraction_kit$) |
@@ -119,11 +138,10 @@ class App(QMainWindow):
(?P<submitting_lab>)^submitting_lab$ |
(?P<samples>)^samples$ |
(?P<reagent>^lot_.*$)
""", re.VERBOSE)
for item in prsr.sub:
logger.debug(f"Item: {item}")
# attempt to match variable name to regex group
try:
mo = variable_parser.fullmatch(item).lastgroup
except AttributeError:
@@ -131,17 +149,23 @@ class App(QMainWindow):
logger.debug(f"Mo: {mo}")
match mo:
case 'submitting_lab':
# create label
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
logger.debug(f"{item}: {prsr.sub[item]}")
# create combobox to hold looked up submitting labs
add_widget = QComboBox()
labs = [item.__str__() for item in lookup_all_orgs(ctx=self.ctx)]
# try to set closest match to top of list
try:
labs = difflib.get_close_matches(prsr.sub[item], labs, len(labs), 0)
except (TypeError, ValueError):
pass
# set combobox values to lookedup values
add_widget.addItems(labs)
case 'extraction_kit':
# create label
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
# if extraction kit not available, all other values fail
if prsr.sub[item] == 'nan':
msg = QMessageBox()
# msg.setIcon(QMessageBox.critical)
@@ -150,18 +174,27 @@ class App(QMainWindow):
msg.setWindowTitle("Error")
msg.exec()
break
# create combobox to hold looked up kits
add_widget = QComboBox()
# lookup existing kits by 'submission_type' decided on by sheetparser
uses = [item.__str__() for item in lookup_kittype_by_use(ctx=self.ctx, used_by=prsr.sub['submission_type'])]
if len(uses) > 0:
add_widget.addItems(uses)
else:
add_widget.addItems(['bacterial_culture'])
case 'submitted_date':
# create label
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
# uses base calendar
add_widget = QDateEdit(calendarPopup=True)
# add_widget.setDateTime(QDateTime.date(prsr.sub[item]))
add_widget.setDate(prsr.sub[item])
# sets submitted date based on date found in excel sheet
try:
add_widget.setDate(prsr.sub[item])
# if not found, use today
except:
add_widget.setDate(date.today())
case 'reagent':
# create label
self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
add_widget = QComboBox()
add_widget.setEditable(True)
@@ -174,8 +207,10 @@ class App(QMainWindow):
prsr.sub[item] = int(prsr.sub[item])
except ValueError:
pass
# query for reagents using type name from sheet and kit from sheet
relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name_and_kit_name(ctx=self.ctx, type_name=query_var, kit_name=prsr.sub['extraction_kit'])]
logger.debug(f"Relevant reagents: {relevant_reagents}")
# if reagent in sheet is not found insert it into items
if prsr.sub[item] not in relevant_reagents and prsr.sub[item] != 'nan':
try:
check = not numpy.isnan(prsr.sub[item])
@@ -187,49 +222,35 @@ class App(QMainWindow):
add_widget.addItems(relevant_reagents)
# TODO: make samples not appear in frame.
case 'samples':
# hold samples in 'self' until form submitted
logger.debug(f"{item}: {prsr.sub[item]}")
self.samples = prsr.sub[item]
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)
# create submission button
submit_btn = QPushButton("Submit")
self.table_widget.formlayout.addWidget(submit_btn)
submit_btn.clicked.connect(self.submit_new_sample)
# self.table_widget.interior.setSizePolicy(QSizePolicy.Policy.Preferred, QSizePolicy.Policy.MinimumExpanding)
print(self.table_widget.formwidget.size())
# def renderPage(self):
# """
# Test function for plotly chart rendering
# """
# df = pd.read_excel("C:\\Users\\lwark\\Desktop\\test_df.xlsx", engine="openpyxl")
# fig = px.bar(df, x="submitted_date", y="kraken_percent", color="genus", title="Long-Form Input")
# fig.update_layout(
# xaxis_title="Submitted Date (* - Date parsed from fastq file creation date)",
# yaxis_title="Kraken Percent",
# showlegend=True,
# barmode='stack'
# )
# html = '<html><body>'
# html += plotly.offline.plot(fig, output_type='div', include_plotlyjs='cdn', auto_open=True, image = 'png', image_filename='plot_image')
# html += '</body></html>'
# self.table_widget.webengineview.setHtml(html)
# self.table_widget.webengineview.update()
def submit_new_sample(self):
"""
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_")}
logger.debug(f"Reagents: {reagents}")
parsed_reagents = []
# compare reagents in form to reagent database
for reagent in reagents:
wanted_reagent = lookup_reagent(ctx=self.ctx, reagent_lot=reagents[reagent])
logger.debug(wanted_reagent)
logger.debug(f"Looked up reagent: {wanted_reagent}")
# if reagent not found offer to add to database
if wanted_reagent == None:
dlg = AddReagentQuestion(reagent_type=reagent, reagent_lot=reagents[reagent])
if dlg.exec():
@@ -239,49 +260,78 @@ class App(QMainWindow):
if wanted_reagent != None:
parsed_reagents.append(wanted_reagent)
logger.debug(info)
# move samples into preliminary submission dict
info['samples'] = self.samples
# construct submission object
base_submission, output = construct_submission_info(ctx=self.ctx, info_dict=info)
# check output message for issues
if output['message'] != None:
dlg = OverwriteSubQuestion(output['message'], base_submission.rsl_plate_num)
if dlg.exec():
base_submission.reagents = []
else:
return
# add reagents to submission object
for reagent in parsed_reagents:
base_submission.reagents.append(reagent)
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
if result != None:
msg = QMessageBox()
# msg.setIcon(QMessageBox.critical)
msg.setText("Error")
msg.setInformativeText(result['message'])
msg.setWindowTitle("Error")
msg.show()
msg.exec()
# update summary sheet
self.table_widget.sub_wid.setData()
# reset form
for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
item.setParent(None)
def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None):
"""
Action to create new reagent in DB.
Args:
reagent_lot (str | None, optional): Parsed reagent from import form. Defaults to None.
reagent_type (str | None, optional): Parsed reagent type from import form. Defaults to None.
Returns:
models.Reagent: the constructed reagent object to add to submission
"""
if isinstance(reagent_lot, bool):
reagent_lot = ""
# create form
dlg = AddReagentForm(ctx=self.ctx, reagent_lot=reagent_lot, reagent_type=reagent_type)
if dlg.exec():
# extract form info
labels, values = self.extract_form_info(dlg)
info = {item[0]:item[1] for item in zip(labels, values)}
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)
return reagent
def extract_form_info(self, object):
"""
retrieves arbitrary number of labels, values from form
Args:
object (_type_): _description_
Returns:
_type_: _description_
"""
labels = []
values = []
# grab all widgets in form
for item in object.layout.parentWidget().findChildren(QWidget):
match item:
case QLabel():
labels.append(item.text().replace(" ", "_").lower())
@@ -295,19 +345,29 @@ class App(QMainWindow):
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
"""
# 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)}
# 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
records = [item.report_dict() for item in subs]
# make dataframe from record dictionaries
df = make_report_xlsx(records=records)
home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submissions_{info['start_date']}-{info['end_date']}.xlsx").resolve().__str__()
# 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']}.xlsx").resolve().__str__()
fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".xlsx")[0])
# save file
try:
df.to_excel(fname, engine="openpyxl")
except PermissionError:
@@ -315,9 +375,14 @@ class App(QMainWindow):
def add_kit(self):
"""
Constructs new kit from yaml and adds to DB.
"""
# setup file dialog to find yaml flie
home_dir = str(Path(self.ctx["directory_path"]))
fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir, filter = "yml(*.yml)")[0])
assert fname.exists()
# read yaml file
try:
with open(fname.__str__(), "r") as stream:
try:
@@ -327,64 +392,96 @@ class App(QMainWindow):
return {}
except PermissionError:
return
create_kit_from_yaml(ctx=self.ctx, exp=exp)
# send to kit creator function
result = create_kit_from_yaml(ctx=self.ctx, exp=exp)
msg = QMessageBox()
# msg.setIcon(QMessageBox.critical)
match result['code']:
case 0:
msg.setText("Kit added")
msg.setInformativeText(result['message'])
msg.setWindowTitle("Kit added")
case 1:
msg.setText("Permission Error")
msg.setInformativeText(result['message'])
msg.setWindowTitle("Permission Error")
msg.exec()
def controls_getter(self):
# self.table_widget.webengineview.setHtml("")
"""
Lookup controls from database and send to chartmaker
"""
# subtype defaults to disabled
try:
self.table_widget.sub_typer.disconnect()
except TypeError:
pass
# correct start date being more recent than end date and rerun
if self.table_widget.datepicker.start_date.date() > self.table_widget.datepicker.end_date.date():
logger.warning("Start date after end date is not allowed!")
# self.table_widget.datepicker.start_date.setDate(e_date)
threemonthsago = self.table_widget.datepicker.end_date.date().addDays(-90)
# block signal that will rerun controls getter and set start date
with QSignalBlocker(self.table_widget.datepicker.start_date) as blocker:
self.table_widget.datepicker.start_date.setDate(threemonthsago)
self.controls_getter()
return
# convert to python useable date object
self.start_date = self.table_widget.datepicker.start_date.date().toPyDate()
self.end_date = self.table_widget.datepicker.end_date.date().toPyDate()
self.con_type = self.table_widget.control_typer.currentText()
self.mode = self.table_widget.mode_typer.currentText()
self.table_widget.sub_typer.clear()
# lookup subtypes
sub_types = get_control_subtypes(ctx=self.ctx, type=self.con_type, mode=self.mode)
if sub_types != []:
# block signal that will rerun controls getter and update sub_typer
with QSignalBlocker(self.table_widget.sub_typer) as blocker:
self.table_widget.sub_typer.addItems(sub_types)
self.table_widget.sub_typer.setEnabled(True)
self.table_widget.sub_typer.currentTextChanged.connect(self.chart_maker)
else:
self.table_widget.sub_typer.clear()
self.table_widget.sub_typer.setEnabled(False)
self.chart_maker()
def chart_maker(self):
"""
Creates plotly charts for webview
"""
logger.debug(f"Control getter context: \n\tControl type: {self.con_type}\n\tMode: {self.mode}\n\tStart Date: {self.start_date}\n\tEnd Date: {self.end_date}")
if self.table_widget.sub_typer.currentText() == "":
self.subtype = None
else:
self.subtype = self.table_widget.sub_typer.currentText()
logger.debug(f"Subtype: {self.subtype}")
# query all controls using the type/start and end dates from the gui
controls = get_all_controls_by_type(ctx=self.ctx, con_type=self.con_type, start_date=self.start_date, end_date=self.end_date)
# if no data found from query set fig to none for reporting in webview
if controls == None:
return
data = []
for control in controls:
dicts = convert_control_by_mode(ctx=self.ctx, control=control, mode=self.mode)
data.append(dicts)
data = [item for sublist in data for item in sublist]
# logger.debug(data)
df = convert_data_list_to_df(ctx=self.ctx, input=data, subtype=self.subtype)
if self.subtype == None:
title = self.mode
# return
fig = None
else:
title = f"{self.mode} - {self.subtype}"
fig = create_charts(ctx=self.ctx, df=df, ytitle=title)
data = []
for control in controls:
# change each control to list of dicts
dicts = convert_control_by_mode(ctx=self.ctx, control=control, mode=self.mode)
data.append(dicts)
# flatten data to one dimensional list
data = [item for sublist in data for item in sublist]
# logger.debug(data)
# send to dataframe creator
df = convert_data_list_to_df(ctx=self.ctx, input=data, subtype=self.subtype)
if self.subtype == None:
title = self.mode
else:
title = f"{self.mode} - {self.subtype}"
# send dataframe to chart maker
fig = create_charts(ctx=self.ctx, df=df, ytitle=title)
logger.debug(f"Updating figure...")
# construct html for webview
html = '<html><body>'
if fig != None:
html += plotly.offline.plot(fig, output_type='div', include_plotlyjs='cdn')#, image = 'png', auto_open=True, image_filename='plot_image')
@@ -393,24 +490,12 @@ class App(QMainWindow):
html += '</body></html>'
# with open("C:\\Users\\lwark\\Desktop\\test.html", "w") as f:
# f.write(html)
# add html to webview and update.
self.table_widget.webengineview.setHtml(html)
self.table_widget.webengineview.update()
logger.debug("Figure updated... I hope.")
# def datechange(self):
# s_date = self.table_widget.datepicker.start_date.date()
# e_date = self.table_widget.datepicker.end_date.date()
# if s_date > e_date:
# logger.debug("that is not allowed!")
# # self.table_widget.datepicker.start_date.setDate(e_date)
# threemonthsago = e_date.addDays(-90)
# self.table_widget.datepicker.start_date.setDate(threemonthsago)
# self.chart_maker()
class AddSubForm(QWidget):
def __init__(self, parent):
@@ -428,64 +513,57 @@ class AddSubForm(QWidget):
self.tabs.addTab(self.tab1,"Submissions")
self.tabs.addTab(self.tab2,"Controls")
self.tabs.addTab(self.tab3, "Add Kit")
# Create first tab
# self.scroller = QWidget()
# self.scroller.layout = QVBoxLayout(self)
# self.scroller.setLayout(self.scroller.layout)
# self.tab1.setMaximumHeight(1000)
# Create submission adder form
self.formwidget = QWidget(self)
self.formlayout = QVBoxLayout(self)
self.formwidget.setLayout(self.formlayout)
self.formwidget.setFixedWidth(300)
# Make scrollable interior for form
self.interior = QScrollArea(self.tab1)
# self.interior.verticalScrollBar()
# self.interior.setVerticalScrollBarPolicy(Qt.ScrollBarPolicy.ScrollBarAlwaysOn)
self.interior.setWidgetResizable(True)
self.interior.setFixedWidth(325)
# self.interior.setParent(self.tab1)
self.interior.setWidget(self.formwidget)
# Create sheet to hold existing submissions
self.sheetwidget = QWidget(self)
self.sheetlayout = QVBoxLayout(self)
self.sheetwidget.setLayout(self.sheetlayout)
self.sub_wid = SubmissionsSheet(parent.ctx)
self.sheetlayout.addWidget(self.sub_wid)
# Create layout of first tab to hold form and sheet
self.tab1.layout = QHBoxLayout(self)
self.tab1.setLayout(self.tab1.layout)
# self.tab1.layout.addLayout(self.formlayout)
self.tab1.layout.addWidget(self.interior)
# self.tab1.layout.addWidget(self.formwidget)
self.tab1.layout.addWidget(self.sheetwidget)
# self.tab1.layout.addLayout(self.sheetlayout)
# create widgets for tab 2
self.datepicker = ControlsDatePicker()
self.webengineview = QWebEngineView()
# set tab2 layout
self.tab2.layout = QVBoxLayout(self)
self.control_typer = QComboBox()
# fetch types of controls
con_types = get_all_Control_Types_names(ctx=parent.ctx)
self.control_typer.addItems(con_types)
# create custom widget to get types of analysis
self.mode_typer = QComboBox()
mode_types = get_all_available_modes(ctx=parent.ctx)
self.mode_typer.addItems(mode_types)
# create custom widget to get subtypes of analysis
self.sub_typer = QComboBox()
self.sub_typer.setEnabled(False)
# add widgets to tab2 layout
self.tab2.layout.addWidget(self.datepicker)
self.tab2.layout.addWidget(self.control_typer)
self.tab2.layout.addWidget(self.mode_typer)
self.tab2.layout.addWidget(self.sub_typer)
self.tab2.layout.addWidget(self.webengineview)
self.tab2.setLayout(self.tab2.layout)
# Add tabs to widget
# create custom widget to add new tabs
adder = KitAdder(parent_ctx=parent.ctx)
self.tab3.layout = QVBoxLayout(self)
self.tab3.layout.addWidget(adder)
self.tab3.setLayout(self.tab3.layout)
# add tabs to main widget
self.layout.addWidget(self.tabs)
self.setLayout(self.layout)
print(self.tab1.layout.parentWidget().findChildren(QScrollArea))

181
src/submissions/frontend/custom_widgets/__init__.py
View File

@@ -4,7 +4,8 @@ from PyQt6.QtWidgets import (
QDialogButtonBox, QDateEdit, QTableView,
QTextEdit, QSizePolicy, QWidget,
QGridLayout, QPushButton, QSpinBox,
QScrollBar, QScrollArea, QHBoxLayout
QScrollBar, QScrollArea, QHBoxLayout,
QMessageBox
)
from PyQt6.QtCore import Qt, QDate, QAbstractTableModel, QSize
from PyQt6.QtGui import QFontMetrics
@@ -26,7 +27,10 @@ loader = FileSystemLoader(loader_path)
env = Environment(loader=loader)
class AddReagentQuestion(QDialog):
def __init__(self, reagent_type:str, reagent_lot:str):
"""
dialog to ask about adding a new reagne to db
"""
def __init__(self, reagent_type:str, reagent_lot:str) -> None:
super().__init__()
self.setWindowTitle(f"Add {reagent_lot}?")
@@ -45,7 +49,10 @@ class AddReagentQuestion(QDialog):
class OverwriteSubQuestion(QDialog):
def __init__(self, message:str, rsl_plate_num:str):
"""
dialog to ask about overwriting existing submission
"""
def __init__(self, message:str, rsl_plate_num:str) -> None:
super().__init__()
self.setWindowTitle(f"Overwrite {rsl_plate_num}?")
@@ -64,7 +71,10 @@ class OverwriteSubQuestion(QDialog):
class AddReagentForm(QDialog):
def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None):
"""
dialog to add gather info about new reagent
"""
def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None) -> None:
super().__init__()
if reagent_lot == None:
@@ -77,20 +87,23 @@ class AddReagentForm(QDialog):
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
# get lot info
lot_input = QLineEdit()
lot_input.setText(reagent_lot)
# get expiry info
exp_input = QDateEdit(calendarPopup=True)
exp_input.setDate(QDate.currentDate())
# get reagent type info
type_input = QComboBox()
type_input.addItems([item.replace("_", " ").title() for item in get_all_reagenttype_names(ctx=ctx)])
logger.debug(f"Trying to find index of {reagent_type}")
# convert input to user friendly string?
try:
reagent_type = reagent_type.replace("_", " ").title()
except AttributeError:
reagent_type = None
# set parsed reagent type to top of list
index = type_input.findText(reagent_type, Qt.MatchFlag.MatchEndsWith)
if index >= 0:
type_input.setCurrentIndex(index)
self.layout = QVBoxLayout()
@@ -106,18 +119,38 @@ class AddReagentForm(QDialog):
class pandasModel(QAbstractTableModel):
def __init__(self, data):
"""
pandas model for inserting summary sheet into gui
"""
def __init__(self, data) -> None:
QAbstractTableModel.__init__(self)
self._data = data
def rowCount(self, parent=None):
def rowCount(self, parent=None) -> int:
"""
does what it says
Args:
parent (_type_, optional): _description_. Defaults to None.
Returns:
int: number of rows in data
"""
return self._data.shape[0]
def columnCount(self, parnet=None):
def columnCount(self, parnet=None) -> int:
"""
does what it says
Args:
parnet (_type_, optional): _description_. Defaults to None.
Returns:
int: number of columns in data
"""
return self._data.shape[1]
def data(self, index, role=Qt.ItemDataRole.DisplayRole):
def data(self, index, role=Qt.ItemDataRole.DisplayRole) -> str|None:
if index.isValid():
if role == Qt.ItemDataRole.DisplayRole:
return str(self._data.iloc[index.row(), index.column()])
@@ -130,7 +163,16 @@ class pandasModel(QAbstractTableModel):
class SubmissionsSheet(QTableView):
def __init__(self, ctx:dict):
"""
presents submission summary to user in tab1
"""
def __init__(self, ctx:dict) -> None:
"""
initialize
Args:
ctx (dict): settings passed from gui
"""
super().__init__()
self.ctx = ctx
self.setData()
@@ -139,20 +181,19 @@ class SubmissionsSheet(QTableView):
# self.clicked.connect(self.test)
self.doubleClicked.connect(self.show_details)
def setData(self):
# horHeaders = []
# for n, key in enumerate(sorted(self.data.keys())):
# horHeaders.append(key)
# for m, item in enumerate(self.data[key]):
# newitem = QTableWidgetItem(item)
# self.setItem(m, n, newitem)
# self.setHorizontalHeaderLabels(horHeaders)
def setData(self) -> None:
"""
sets data in model
"""
self.data = submissions_to_df(ctx=self.ctx)
self.model = pandasModel(self.data)
self.setModel(self.model)
# self.resize(800,600)
def show_details(self, item):
def show_details(self) -> None:
"""
creates detailed data to show in seperate window
"""
index=(self.selectionModel().currentIndex())
# logger.debug(index)
value=index.sibling(index.row(),0).data()
@@ -165,60 +206,65 @@ class SubmissionsSheet(QTableView):
class SubmissionDetails(QDialog):
"""
a window showing text details of submission
"""
def __init__(self, ctx:dict, id:int) -> None:
super().__init__()
self.setWindowTitle("Submission Details")
# create scrollable interior
interior = QScrollArea()
interior.setParent(self)
# get submision from db
data = lookup_submission_by_id(ctx=ctx, id=id)
base_dict = data.to_dict()
# don't want id
del base_dict['id']
# convert sub objects to dicts
base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
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
text = template.render(sub=base_dict)
# create text field
txt_editor = QTextEdit(self)
txt_editor.setReadOnly(True)
txt_editor.document().setPlainText(text)
# resize
font = txt_editor.document().defaultFont()
fontMetrics = QFontMetrics(font)
textSize = fontMetrics.size(0, txt_editor.toPlainText())
w = textSize.width() + 10
h = textSize.height() + 10
txt_editor.setMinimumSize(w, h)
txt_editor.setMaximumSize(w, h)
txt_editor.resize(w, h)
interior.resize(w,900)
# txt_field.setSizePolicy(QSizePolicy.Policy.Preferred, QSizePolicy.Policy.MinimumExpanding)
# QBtn = QDialogButtonBox.StandardButton.Ok
# self.buttonBox = QDialogButtonBox(QBtn)
# self.buttonBox.accepted.connect(self.accept)
txt_editor.setText(text)
# txt_editor.verticalScrollBar()
interior.setWidget(txt_editor)
self.layout = QVBoxLayout()
self.setFixedSize(w, 900)
# self.layout.addWidget(txt_editor)
# self.layout.addStretch()
self.layout.addWidget(interior)
class ReportDatePicker(QDialog):
"""
custom dialog to ask for report start/stop dates
"""
def __init__(self) -> None:
super().__init__()
self.setWindowTitle("Select Report Date Range")
# make confirm/reject buttons
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
# widgets to ask for dates
start_date = QDateEdit(calendarPopup=True)
start_date.setDate(QDate.currentDate())
end_date = QDateEdit(calendarPopup=True)
@@ -233,46 +279,61 @@ class ReportDatePicker(QDialog):
class KitAdder(QWidget):
def __init__(self, parent_ctx:dict):
"""
dialog to get information to add kit
"""
def __init__(self, parent_ctx:dict) -> None:
super().__init__()
self.ctx = parent_ctx
self.grid = QGridLayout()
self.setLayout(self.grid)
# insert submit button at top
self.submit_btn = QPushButton("Submit")
self.grid.addWidget(self.submit_btn,0,0,1,1)
self.grid.addWidget(QLabel("Password:"),1,0)
self.grid.addWidget(QLineEdit(),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)
self.grid.addWidget(QLabel("Used For Sample Type:"),3,0)
used_for = QComboBox()
# 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("Cost per run:"),4,0)
cost = QSpinBox()
cost.setMinimum(0)
cost.setMaximum(9999)
self.grid.addWidget(cost,4,1)
# button to add additional reagent types
self.add_RT_btn = QPushButton("Add Reagent Type")
self.grid.addWidget(self.add_RT_btn)
self.add_RT_btn.clicked.connect(self.add_RT)
self.submit_btn.clicked.connect(self.submit)
def add_RT(self):
def add_RT(self) -> None:
"""
insert new reagent type row
"""
maxrow = self.grid.rowCount()
self.grid.addWidget(ReagentTypeForm(parent_ctx=self.ctx), maxrow + 1,0,1,2)
def submit(self):
def submit(self) -> None:
"""
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['reagenttypes'] = reagents
# del info['name']
# del info['extension_of_life_(months)']
yml_type = {}
yml_type['password'] = info['password']
try:
yml_type['password'] = info['password']
except KeyError:
pass
used = info['used_for_sample_type'].replace(" ", "_").lower()
yml_type[used] = {}
yml_type[used]['kits'] = {}
@@ -280,9 +341,32 @@ class KitAdder(QWidget):
yml_type[used]['kits'][info['kit_name']]['cost'] = info['cost_per_run']
yml_type[used]['kits'][info['kit_name']]['reagenttypes'] = reagents
logger.debug(yml_type)
create_kit_from_yaml(ctx=self.ctx, exp=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 = QMessageBox()
# msg.setIcon(QMessageBox.critical)
match result['code']:
case 0:
msg.setText("Kit added")
msg.setInformativeText(result['message'])
msg.setWindowTitle("Kit added")
case 1:
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 = {}
@@ -317,26 +401,35 @@ class KitAdder(QWidget):
class ReagentTypeForm(QWidget):
"""
custom widget to add information about a new reagenttype
"""
def __init__(self, parent_ctx:dict) -> None:
super().__init__()
grid = QGridLayout()
self.setLayout(grid)
grid.addWidget(QLabel("Name:"),0,0)
reagent_getter = QComboBox()
# 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
eol = QSpinBox()
eol.setMinimum(0)
grid.addWidget(eol, 0,3)
class ControlsDatePicker(QWidget):
"""
custom widget to pick start and end dates for controls graphs
"""
def __init__(self) -> None:
super().__init__()
self.start_date = QDateEdit(calendarPopup=True)
# start date is three month prior to end date by default
threemonthsago = QDate.currentDate().addDays(-90)
self.start_date.setDate(threemonthsago)
self.end_date = QDateEdit(calendarPopup=True)
@@ -350,5 +443,5 @@ class ControlsDatePicker(QWidget):
self.setLayout(self.layout)
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
def sizeHint(self):
def sizeHint(self) -> QSize:
return QSize(80,20)

13
src/submissions/frontend/visualizations/charts.py
View File

@@ -13,14 +13,15 @@ def create_charts(ctx:dict, df:pd.DataFrame, ytitle:str|None=None) -> Figure:
Constructs figures based on parsed pandas dataframe.
Args:
settings (dict): settings passed down from click
settings (dict): settings passed down from gui
df (pd.DataFrame): input dataframe
group_name (str): controltype
Returns:
Figure: _description_
Figure: plotly figure
"""
from backend.excel import drop_reruns_from_df
# converts starred genera to normal and splits off list of starred
genera = []
if df.empty:
return None
@@ -35,15 +36,17 @@ def create_charts(ctx:dict, df:pd.DataFrame, ytitle:str|None=None) -> Figure:
df['genus'] = df['genus'].replace({'\*':''}, regex=True)
df['genera'] = genera
df = df.dropna()
# remove original runs, using reruns if applicable
df = drop_reruns_from_df(ctx=ctx, df=df)
# sort by and exclude from
sorts = ['submitted_date', "target", "genus"]
exclude = ['name', 'genera']
modes = [item for item in df.columns if item not in sorts and item not in exclude and "_hashes" not in item]
# Set descending for any columns that have "{mode}" in the header.
ascending = [False if item == "target" else True for item in sorts]
df = df.sort_values(by=sorts, ascending=ascending)
# actual chart construction is done by
fig = construct_chart(ctx=ctx, df=df, modes=modes, ytitle=ytitle)
return fig
@@ -186,7 +189,7 @@ def construct_chart(ctx:dict, df:pd.DataFrame, modes:list, ytitle:str|None=None)
def construct_refseq_chart(settings:dict, df:pd.DataFrame, group_name:str, mode:str) -> Figure:
"""
Constructs intial refseq chart for both contains and matches.
Constructs intial refseq chart for both contains and matches (depreciated).
Args:
settings (dict): settings passed down from click.
@@ -218,7 +221,7 @@ def construct_refseq_chart(settings:dict, df:pd.DataFrame, group_name:str, mode:
def construct_kraken_chart(settings:dict, df:pd.DataFrame, group_name:str, mode:str) -> Figure:
"""
Constructs intial refseq chart for each mode in the kraken config settings.
Constructs intial refseq chart for each mode in the kraken config settings. (depreciated)
Args:
settings (dict): settings passed down from click.

2
src/submissions/templates/submission_details.txt
View File

@@ -1,4 +1,4 @@
{# template for constructing submission details #}
{% for key, value in sub.items() if key != 'reagents' and key != 'samples' %}
{{ key }}: {{ value }}