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Code cleanup, dependency update, various bug fixes

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lwark
2024-05-24 13:02:46 -05:00
parent 2814be8980
commit e047d1a9ee
24 changed files with 403 additions and 561 deletions
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3
CHANGELOG.md
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@@ -1,7 +1,6 @@
## 202405.04 ## 202405.04
## 202405.04 - Improved Webview of submission details.
- Fixed Reagents not being updated on edit. - Fixed Reagents not being updated on edit.
- Fixed data resorting after submitting new run. - Fixed data resorting after submitting new run.

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requirements.txt
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4
src/submissions/backend/db/models/__init__.py
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@@ -102,7 +102,7 @@ class BaseClass(Base):
@classmethod @classmethod
def query(cls, **kwargs) -> Any | List[Any]: def query(cls, **kwargs) -> Any | List[Any]:
""" """
Default query function for models Default query function for models. Overridden in most models.
Returns: Returns:
Any | List[Any]: Result of query execution. Any | List[Any]: Result of query execution.
@@ -128,7 +128,7 @@ class BaseClass(Base):
query: Query = cls.__database_session__.query(model) query: Query = cls.__database_session__.query(model)
# logger.debug(f"Grabbing singles using {model.get_default_info}") # logger.debug(f"Grabbing singles using {model.get_default_info}")
singles = model.get_default_info('singles') singles = model.get_default_info('singles')
logger.debug(f"Querying: {model}, with kwargs: {kwargs}") logger.info(f"Querying: {model}, with kwargs: {kwargs}")
for k, v in kwargs.items(): for k, v in kwargs.items():
# logger.debug(f"Using key: {k} with value: {v}") # logger.debug(f"Using key: {k} with value: {v}")
try: try:

15
src/submissions/backend/db/models/controls.py
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@@ -63,16 +63,16 @@ class ControlType(BaseClass):
Returns: Returns:
List[str]: list of subtypes available List[str]: list of subtypes available
""" """
# Get first instance since all should have same subtypes # NOTE: Get first instance since all should have same subtypes
# Get mode of instance # NOTE: Get mode of instance
jsoner = getattr(self.instances[0], mode) jsoner = getattr(self.instances[0], mode)
# logger.debug(f"JSON out: {jsoner.keys()}") # logger.debug(f"JSON out: {jsoner.keys()}")
try: try:
# Pick genera (all should have same subtypes) # NOTE: Pick genera (all should have same subtypes)
genera = list(jsoner.keys())[0] genera = list(jsoner.keys())[0]
except IndexError: except IndexError:
return [] return []
# remove items that don't have relevant data # NOTE: remove items that don't have relevant data
subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item] subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item]
return subtypes return subtypes
@@ -135,7 +135,6 @@ class Control(BaseClass):
""" """
# logger.debug("loading json string into dict") # logger.debug("loading json string into dict")
try: try:
# kraken = json.loads(self.kraken)
kraken = self.kraken kraken = self.kraken
except TypeError: except TypeError:
kraken = {} kraken = {}
@@ -178,7 +177,7 @@ class Control(BaseClass):
data = self.__getattribute__(mode) data = self.__getattribute__(mode)
except TypeError: except TypeError:
data = {} data = {}
logger.debug(f"Length of data: {len(data)}") # logger.debug(f"Length of data: {len(data)}")
# logger.debug("dict keys are genera of bacteria, e.g. 'Streptococcus'") # logger.debug("dict keys are genera of bacteria, e.g. 'Streptococcus'")
for genus in data: for genus in data:
_dict = dict( _dict = dict(
@@ -236,7 +235,7 @@ class Control(BaseClass):
models.Control|List[models.Control]: Control object of interest. models.Control|List[models.Control]: Control object of interest.
""" """
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
# by control type # NOTE: by control type
match control_type: match control_type:
case ControlType(): case ControlType():
# logger.debug(f"Looking up control by control type: {control_type}") # logger.debug(f"Looking up control by control type: {control_type}")
@@ -246,7 +245,7 @@ class Control(BaseClass):
query = query.join(ControlType).filter(ControlType.name == control_type) query = query.join(ControlType).filter(ControlType.name == control_type)
case _: case _:
pass pass
# by date range # NOTE: by date range
if start_date is not None and end_date is None: if start_date is not None and end_date is None:
logger.warning(f"Start date with no end date, using today.") logger.warning(f"Start date with no end date, using today.")
end_date = date.today() end_date = date.today()

62
src/submissions/backend/db/models/kits.py
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@@ -120,8 +120,8 @@ class KitType(BaseClass):
submission_type (str | Submissiontype | None, optional): Submission type to narrow results. Defaults to None. submission_type (str | Submissiontype | None, optional): Submission type to narrow results. Defaults to None.
Returns: Returns:
list: List of reagent types List[ReagentType]: List of reagents linked to this kit.
""" """
match submission_type: match submission_type:
case SubmissionType(): case SubmissionType():
# logger.debug(f"Getting reagents by SubmissionType {submission_type}") # logger.debug(f"Getting reagents by SubmissionType {submission_type}")
@@ -152,17 +152,15 @@ class KitType(BaseClass):
dict: Dictionary containing information locations. dict: Dictionary containing information locations.
""" """
info_map = {} info_map = {}
# Account for submission_type variable type. # NOTE: Account for submission_type variable type.
match submission_type: match submission_type:
case str(): case str():
# logger.debug(f"Constructing xl map with str {submission_type}") # logger.debug(f"Constructing xl map with str {submission_type}")
assocs = [item for item in self.kit_reagenttype_associations if assocs = [item for item in self.kit_reagenttype_associations if
item.submission_type.name == submission_type] item.submission_type.name == submission_type]
# st_assoc = [item for item in self.used_for if submission_type == item.name][0]
case SubmissionType(): case SubmissionType():
# logger.debug(f"Constructing xl map with SubmissionType {submission_type}") # logger.debug(f"Constructing xl map with SubmissionType {submission_type}")
assocs = [item for item in self.kit_reagenttype_associations if item.submission_type == submission_type] assocs = [item for item in self.kit_reagenttype_associations if item.submission_type == submission_type]
# st_assoc = submission_type
case _: case _:
raise ValueError(f"Wrong variable type: {type(submission_type)} used!") raise ValueError(f"Wrong variable type: {type(submission_type)} used!")
# logger.debug("Get all KitTypeReagentTypeAssociation for SubmissionType") # logger.debug("Get all KitTypeReagentTypeAssociation for SubmissionType")
@@ -371,10 +369,10 @@ class Reagent(BaseClass):
dict: representation of the reagent's attributes dict: representation of the reagent's attributes
""" """
if extraction_kit is not None: if extraction_kit is not None:
# Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType # NOTE: Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType
try: try:
reagent_role = list(set(self.type).intersection(extraction_kit.reagent_types))[0] reagent_role = list(set(self.type).intersection(extraction_kit.reagent_types))[0]
# Most will be able to fall back to first ReagentType in itself because most will only have 1. # NOTE: Most will be able to fall back to first ReagentType in itself because most will only have 1.
except: except:
reagent_role = self.type[0] reagent_role = self.type[0]
else: else:
@@ -383,7 +381,7 @@ class Reagent(BaseClass):
rtype = reagent_role.name.replace("_", " ") rtype = reagent_role.name.replace("_", " ")
except AttributeError: except AttributeError:
rtype = "Unknown" rtype = "Unknown"
# Calculate expiry with EOL from ReagentType # NOTE: Calculate expiry with EOL from ReagentType
try: try:
place_holder = self.expiry + reagent_role.eol_ext place_holder = self.expiry + reagent_role.eol_ext
except (TypeError, AttributeError) as e: except (TypeError, AttributeError) as e:
@@ -467,7 +465,7 @@ class Reagent(BaseClass):
match name: match name:
case str(): case str():
# logger.debug(f"Looking up reagent by name str: {name}") # logger.debug(f"Looking up reagent by name str: {name}")
# Not limited due to multiple reagents having same name. # NOTE: Not limited due to multiple reagents having same name.
query = query.filter(cls.name == name) query = query.filter(cls.name == name)
case _: case _:
pass pass
@@ -475,7 +473,7 @@ class Reagent(BaseClass):
case str(): case str():
# logger.debug(f"Looking up reagent by lot number str: {lot_number}") # logger.debug(f"Looking up reagent by lot number str: {lot_number}")
query = query.filter(cls.lot == lot_number) query = query.filter(cls.lot == lot_number)
# In this case limit number returned. # NOTE: In this case limit number returned.
limit = 1 limit = 1
case _: case _:
pass pass
@@ -516,10 +514,6 @@ class Discount(BaseClass):
organization (models.Organization | str | int): Organization receiving discount. organization (models.Organization | str | int): Organization receiving discount.
kit_type (models.KitType | str | int): Kit discount received on. kit_type (models.KitType | str | int): Kit discount received on.
Raises:
ValueError: Invalid Organization
ValueError: Invalid kit.
Returns: Returns:
models.Discount|List[models.Discount]: Discount(s) of interest. models.Discount|List[models.Discount]: Discount(s) of interest.
""" """
@@ -535,7 +529,6 @@ class Discount(BaseClass):
# logger.debug(f"Looking up discount with organization id: {organization}") # logger.debug(f"Looking up discount with organization id: {organization}")
query = query.join(Organization).filter(Organization.id == organization) query = query.join(Organization).filter(Organization.id == organization)
case _: case _:
# raise ValueError(f"Invalid value for organization: {organization}")
pass pass
match kit_type: match kit_type:
case KitType(): case KitType():
@@ -548,7 +541,6 @@ class Discount(BaseClass):
# logger.debug(f"Looking up discount with kit type id: {kit_type}") # logger.debug(f"Looking up discount with kit type id: {kit_type}")
query = query.join(KitType).filter(KitType.id == kit_type) query = query.join(KitType).filter(KitType.id == kit_type)
case _: case _:
# raise ValueError(f"Invalid value for kit type: {kit_type}")
pass pass
return cls.execute_query(query=query) return cls.execute_query(query=query)
@@ -634,11 +626,18 @@ class SubmissionType(BaseClass):
self.save() self.save()
def construct_info_map(self, mode: Literal['read', 'write']) -> dict: def construct_info_map(self, mode: Literal['read', 'write']) -> dict:
"""
Make of map of where all fields are located in excel sheet
Args:
mode (Literal["read", "write"]): Which mode to get locations for
Returns:
dict: Map of locations
"""
info = self.info_map info = self.info_map
# logger.debug(f"Info map: {info}") # logger.debug(f"Info map: {info}")
output = {} output = {}
# for k,v in info.items():
# info[k]['write'] += info[k]['read']
match mode: match mode:
case "read": case "read":
output = {k: v[mode] for k, v in info.items() if v[mode]} output = {k: v[mode] for k, v in info.items() if v[mode]}
@@ -647,7 +646,13 @@ class SubmissionType(BaseClass):
output = {k: v for k, v in output.items() if all([isinstance(item, dict) for item in v])} output = {k: v for k, v in output.items() if all([isinstance(item, dict) for item in v])}
return output return output
def construct_sample_map(self): def construct_sample_map(self) -> dict:
"""
Returns sample map
Returns:
dict: sample location map
"""
return self.sample_map return self.sample_map
def construct_equipment_map(self) -> dict: def construct_equipment_map(self) -> dict:
@@ -655,7 +660,7 @@ class SubmissionType(BaseClass):
Constructs map of equipment to excel cells. Constructs map of equipment to excel cells.
Returns: Returns:
List[dict]: List of equipment locations in excel sheet dict: Map equipment locations in excel sheet
""" """
output = {} output = {}
# logger.debug("Iterating through equipment roles") # logger.debug("Iterating through equipment roles")
@@ -671,7 +676,7 @@ class SubmissionType(BaseClass):
Returns PydEquipmentRole of all equipment associated with this SubmissionType Returns PydEquipmentRole of all equipment associated with this SubmissionType
Returns: Returns:
List['PydEquipmentRole']: List of equipment roles List[PydEquipmentRole]: List of equipment roles
""" """
return [item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment] return [item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment]
@@ -702,7 +707,13 @@ class SubmissionType(BaseClass):
raise TypeError(f"Type {type(equipment_role)} is not allowed") raise TypeError(f"Type {type(equipment_role)} is not allowed")
return list(set([item for items in relevant for item in items if item != None])) return list(set([item for items in relevant for item in items if item != None]))
def get_submission_class(self): def get_submission_class(self) -> "BasicSubmission":
"""
Gets submission class associated with this submission type.
Returns:
BasicSubmission: Submission class
"""
from .submissions import BasicSubmission from .submissions import BasicSubmission
return BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.name) return BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.name)
@@ -1063,7 +1074,7 @@ class Equipment(BaseClass):
processes (bool, optional): Whether to include processes. Defaults to False. processes (bool, optional): Whether to include processes. Defaults to False.
Returns: Returns:
dict: _description_ dict: Dictionary representation of this equipment
""" """
if not processes: if not processes:
return {k: v for k, v in self.__dict__.items() if k != 'processes'} return {k: v for k, v in self.__dict__.items() if k != 'processes'}
@@ -1152,7 +1163,7 @@ class Equipment(BaseClass):
extraction_kit (str | KitType | None, optional): Relevant KitType. Defaults to None. extraction_kit (str | KitType | None, optional): Relevant KitType. Defaults to None.
Returns: Returns:
PydEquipment: _description_ PydEquipment: pydantic equipment object
""" """
from backend.validators.pydant import PydEquipment from backend.validators.pydant import PydEquipment
return PydEquipment( return PydEquipment(
@@ -1179,7 +1190,6 @@ class Equipment(BaseClass):
class EquipmentRole(BaseClass): class EquipmentRole(BaseClass):
""" """
Abstract roles for equipment Abstract roles for equipment
""" """
id = Column(INTEGER, primary_key=True) #: Role id, primary key id = Column(INTEGER, primary_key=True) #: Role id, primary key
@@ -1331,7 +1341,7 @@ class SubmissionEquipmentAssociation(BaseClass):
equipment = relationship(Equipment, back_populates="equipment_submission_associations") #: associated equipment equipment = relationship(Equipment, back_populates="equipment_submission_associations") #: associated equipment
def __repr__(self): def __repr__(self):
return f"<SubmissionEquipmentAssociation({self.submission.rsl_plate_num}&{self.equipment.name})>" return f"<SubmissionEquipmentAssociation({self.submission.rsl_plate_num} & {self.equipment.name})>"
def __init__(self, submission, equipment, role: str = "None"): def __init__(self, submission, equipment, role: str = "None"):
self.submission = submission self.submission = submission

83
src/submissions/backend/db/models/submissions.py
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@@ -107,6 +107,12 @@ class BasicSubmission(BaseClass):
@classmethod @classmethod
def jsons(cls) -> List[str]: def jsons(cls) -> List[str]:
"""
Get list of JSON db columns
Returns:
List[str]: List of column names
"""
output = [item.name for item in cls.__table__.columns if isinstance(item.type, JSON)] output = [item.name for item in cls.__table__.columns if isinstance(item.type, JSON)]
if issubclass(cls, BasicSubmission) and not cls.__name__ == "BasicSubmission": if issubclass(cls, BasicSubmission) and not cls.__name__ == "BasicSubmission":
output += BasicSubmission.jsons() output += BasicSubmission.jsons()
@@ -114,6 +120,12 @@ class BasicSubmission(BaseClass):
@classmethod @classmethod
def timestamps(cls) -> List[str]: def timestamps(cls) -> List[str]:
"""
Get list of TIMESTAMP columns
Returns:
List[str]: List of column names
"""
output = [item.name for item in cls.__table__.columns if isinstance(item.type, TIMESTAMP)] output = [item.name for item in cls.__table__.columns if isinstance(item.type, TIMESTAMP)]
if issubclass(cls, BasicSubmission) and not cls.__name__ == "BasicSubmission": if issubclass(cls, BasicSubmission) and not cls.__name__ == "BasicSubmission":
output += BasicSubmission.timestamps() output += BasicSubmission.timestamps()
@@ -122,7 +134,7 @@ class BasicSubmission(BaseClass):
# TODO: Beef up this to include info_map from DB # TODO: Beef up this to include info_map from DB
@classmethod @classmethod
def get_default_info(cls, *args): def get_default_info(cls, *args):
# Create defaults for all submission_types # NOTE: Create defaults for all submission_types
parent_defs = super().get_default_info() parent_defs = super().get_default_info()
recover = ['filepath', 'samples', 'csv', 'comment', 'equipment'] recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
dicto = dict( dicto = dict(
@@ -132,9 +144,7 @@ class BasicSubmission(BaseClass):
# NOTE: Fields not placed in ui form # NOTE: Fields not placed in ui form
form_ignore=['reagents', 'ctx', 'id', 'cost', 'extraction_info', 'signed_by', 'comment'] + recover, form_ignore=['reagents', 'ctx', 'id', 'cost', 'extraction_info', 'signed_by', 'comment'] + recover,
# NOTE: Fields not placed in ui form to be moved to pydantic # NOTE: Fields not placed in ui form to be moved to pydantic
form_recover=recover, form_recover=recover
# parser_ignore=['samples', 'signed_by'] + [item for item in cls.jsons() if item != "comment"],
# excel_ignore=[],
) )
# logger.debug(dicto['singles']) # logger.debug(dicto['singles'])
# NOTE: Singles tells the query which fields to set limit to 1 # NOTE: Singles tells the query which fields to set limit to 1
@@ -151,7 +161,6 @@ class BasicSubmission(BaseClass):
st = cls.get_submission_type() st = cls.get_submission_type()
if st is None: if st is None:
logger.error("No default info for BasicSubmission.") logger.error("No default info for BasicSubmission.")
# return output
else: else:
output['submission_type'] = st.name output['submission_type'] = st.name
for k, v in st.defaults.items(): for k, v in st.defaults.items():
@@ -169,16 +178,37 @@ class BasicSubmission(BaseClass):
return output return output
@classmethod @classmethod
def get_submission_type(cls): def get_submission_type(cls) -> SubmissionType:
"""
Gets the SubmissionType associated with this class
Returns:
SubmissionType: SubmissionType with name equal to this polymorphic identity
"""
name = cls.__mapper_args__['polymorphic_identity'] name = cls.__mapper_args__['polymorphic_identity']
return SubmissionType.query(name=name) return SubmissionType.query(name=name)
@classmethod @classmethod
def construct_info_map(cls, mode:Literal['read', 'write']): def construct_info_map(cls, mode:Literal["read", "write"]) -> dict:
"""
Method to call submission type's construct info map.
Args:
mode (Literal["read", "write"]): Which map to construct.
Returns:
dict: Map of info locations.
"""
return cls.get_submission_type().construct_info_map(mode=mode) return cls.get_submission_type().construct_info_map(mode=mode)
@classmethod @classmethod
def construct_sample_map(cls): def construct_sample_map(cls) -> dict:
"""
Method to call submission type's construct_sample_map
Returns:
dict: sample location map
"""
return cls.get_submission_type().construct_sample_map() return cls.get_submission_type().construct_sample_map()
def to_dict(self, full_data: bool = False, backup: bool = False, report: bool = False) -> dict: def to_dict(self, full_data: bool = False, backup: bool = False, report: bool = False) -> dict:
@@ -192,7 +222,7 @@ class BasicSubmission(BaseClass):
Returns: Returns:
dict: dictionary used in submissions summary and details dict: dictionary used in submissions summary and details
""" """
# get lab from nested organization object # NOTE: get lab from nested organization object
# logger.debug(f"Converting {self.rsl_plate_num} to dict...") # logger.debug(f"Converting {self.rsl_plate_num} to dict...")
try: try:
sub_lab = self.submitting_lab.name sub_lab = self.submitting_lab.name
@@ -202,12 +232,12 @@ class BasicSubmission(BaseClass):
sub_lab = sub_lab.replace("_", " ").title() sub_lab = sub_lab.replace("_", " ").title()
except AttributeError: except AttributeError:
pass pass
# get extraction kit name from nested kit object # NOTE: get extraction kit name from nested kit object
try: try:
ext_kit = self.extraction_kit.name ext_kit = self.extraction_kit.name
except AttributeError: except AttributeError:
ext_kit = None ext_kit = None
# load scraped extraction info # NOTE: load scraped extraction info
try: try:
ext_info = self.extraction_info ext_info = self.extraction_info
except TypeError: except TypeError:
@@ -324,7 +354,7 @@ class BasicSubmission(BaseClass):
def make_plate_map(self, plate_rows: int = 8, plate_columns=12) -> str: def make_plate_map(self, plate_rows: int = 8, plate_columns=12) -> str:
""" """
Constructs an html based plate map. Constructs an html based plate map for submission details.
Args: Args:
sample_list (list): List of submission samples sample_list (list): List of submission samples
@@ -386,7 +416,7 @@ class BasicSubmission(BaseClass):
subs = [item.to_dict() for item in cls.query(submission_type=submission_type, limit=limit, chronologic=chronologic)] subs = [item.to_dict() for item in cls.query(submission_type=submission_type, limit=limit, chronologic=chronologic)]
# logger.debug(f"Got {len(subs)} submissions.") # logger.debug(f"Got {len(subs)} submissions.")
df = pd.DataFrame.from_records(subs) df = pd.DataFrame.from_records(subs)
# Exclude sub information # NOTE: Exclude sub information
for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents', for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls']: 'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls']:
try: try:
@@ -414,9 +444,6 @@ class BasicSubmission(BaseClass):
# logger.debug(f"Looking up organization: {value}") # logger.debug(f"Looking up organization: {value}")
field_value = Organization.query(name=value) field_value = Organization.query(name=value)
# logger.debug(f"Got {field_value} for organization {value}") # logger.debug(f"Got {field_value} for organization {value}")
# case "submitter_plate_num":
# # logger.debug(f"Submitter plate id: {value}")
# field_value = value
case "samples": case "samples":
for sample in value: for sample in value:
# logger.debug(f"Parsing {sample} to sql.") # logger.debug(f"Parsing {sample} to sql.")
@@ -436,17 +463,6 @@ class BasicSubmission(BaseClass):
field_value = value field_value = value
case "ctx" | "csv" | "filepath" | "equipment": case "ctx" | "csv" | "filepath" | "equipment":
return return
# case "comment":
# if value == "" or value == None or value == 'null':
# field_value = None
# else:
# field_value = dict(name=getuser(), text=value, time=datetime.now())
# # if self.comment is None:
# # self.comment = [field_value]
# # else:
# # self.comment.append(field_value)
# self.update_json(field=key, value=field_value)
# return
case item if item in self.jsons(): case item if item in self.jsons():
logger.debug(f"Setting JSON attribute.") logger.debug(f"Setting JSON attribute.")
existing = self.__getattribute__(key) existing = self.__getattribute__(key)
@@ -1852,13 +1868,6 @@ class WastewaterArtic(BasicSubmission):
set_plate = None set_plate = None
for assoc in self.submission_sample_associations: for assoc in self.submission_sample_associations:
dicto = assoc.to_sub_dict() dicto = assoc.to_sub_dict()
# old_sub = assoc.sample.get_previous_ww_submission(current_artic_submission=self)
# try:
# dicto['plate_name'] = old_sub.rsl_plate_num
# except AttributeError:
# dicto['plate_name'] = ""
# old_assoc = WastewaterAssociation.query(submission=old_sub, sample=assoc.sample, limit=1)
# dicto['well'] = f"{row_map[old_assoc.row]}{old_assoc.column}"
for item in self.source_plates: for item in self.source_plates:
old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1) old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
if old_plate is not None: if old_plate is not None:
@@ -1879,6 +1888,12 @@ class WastewaterArtic(BasicSubmission):
events['Gel Box'] = self.gel_box events['Gel Box'] = self.gel_box
return events return events
def set_attribute(self, key: str, value):
super().set_attribute(key=key, value=value)
if key == 'gel_info':
if len(self.gel_info) > 3:
self.gel_info = self.gel_info[-3:]
def gel_box(self, obj): def gel_box(self, obj):
""" """
Creates widget to perform gel viewing operations Creates widget to perform gel viewing operations

77
src/submissions/backend/excel/parser.py
View File

@@ -543,7 +543,6 @@ class EquipmentParser(object):
def __init__(self, xl: Workbook, submission_type: str|SubmissionType) -> None: def __init__(self, xl: Workbook, submission_type: str|SubmissionType) -> None:
if isinstance(submission_type, str): if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type) submission_type = SubmissionType.query(name=submission_type)
self.submission_type = submission_type self.submission_type = submission_type
self.xl = xl self.xl = xl
self.map = self.fetch_equipment_map() self.map = self.fetch_equipment_map()
@@ -555,7 +554,6 @@ class EquipmentParser(object):
Returns: Returns:
List[dict]: List of locations List[dict]: List of locations
""" """
# submission_type = SubmissionType.query(name=self.submission_type)
return self.submission_type.construct_equipment_map() return self.submission_type.construct_equipment_map()
def get_asset_number(self, input: str) -> str: def get_asset_number(self, input: str) -> str:
@@ -569,7 +567,7 @@ class EquipmentParser(object):
str: asset number str: asset number
""" """
regex = Equipment.get_regex() regex = Equipment.get_regex()
logger.debug(f"Using equipment regex: {regex} on {input}") # logger.debug(f"Using equipment regex: {regex} on {input}")
try: try:
return regex.search(input).group().strip("-") return regex.search(input).group().strip("-")
except AttributeError: except AttributeError:
@@ -582,11 +580,10 @@ class EquipmentParser(object):
Returns: Returns:
List[PydEquipment]: list of equipment List[PydEquipment]: list of equipment
""" """
logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}") # logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}")
output = [] output = []
# logger.debug(f"Sheets: {sheets}") # logger.debug(f"Sheets: {sheets}")
for sheet in self.xl.sheetnames: for sheet in self.xl.sheetnames:
# df = self.xl.parse(sheet, header=None, dtype=object)
ws = self.xl[sheet] ws = self.xl[sheet]
try: try:
relevant = [item for item in self.map if item['sheet'] == sheet] relevant = [item for item in self.map if item['sheet'] == sheet]
@@ -595,7 +592,6 @@ class EquipmentParser(object):
# logger.debug(f"Relevant equipment: {pformat(relevant)}") # logger.debug(f"Relevant equipment: {pformat(relevant)}")
previous_asset = "" previous_asset = ""
for equipment in relevant: for equipment in relevant:
# asset = df.iat[equipment['name']['row']-1, equipment['name']['column']-1]
asset = ws.cell(equipment['name']['row'], equipment['name']['column']) asset = ws.cell(equipment['name']['row'], equipment['name']['column'])
if not check_not_nan(asset): if not check_not_nan(asset):
asset = previous_asset asset = previous_asset
@@ -603,7 +599,6 @@ class EquipmentParser(object):
previous_asset = asset previous_asset = asset
asset = self.get_asset_number(input=asset) asset = self.get_asset_number(input=asset)
eq = Equipment.query(asset_number=asset) eq = Equipment.query(asset_number=asset)
# process = df.iat[equipment['process']['row']-1, equipment['process']['column']-1]
process = ws.cell(row=equipment['process']['row'], column=equipment['process']['column']) process = ws.cell(row=equipment['process']['row'], column=equipment['process']['column'])
try: try:
output.append( output.append(
@@ -614,72 +609,6 @@ class EquipmentParser(object):
# logger.debug(f"Here is the output so far: {pformat(output)}") # logger.debug(f"Here is the output so far: {pformat(output)}")
return output return output
# class PCRParser(object):
# """
# Object to pull data from Design and Analysis PCR export file.
# """
#
# def __init__(self, filepath: Path | None = None) -> None:
# """
# Initializes object.
#
# Args:
# filepath (Path | None, optional): file to parse. Defaults to None.
# """
# logger.debug(f"Parsing {filepath.__str__()}")
# if filepath == None:
# logger.error(f"No filepath given.")
# self.xl = None
# else:
# try:
# self.xl = pd.ExcelFile(filepath.__str__())
# except ValueError as e:
# logger.error(f"Incorrect value: {e}")
# self.xl = None
# except PermissionError:
# logger.error(f"Couldn't get permissions for {filepath.__str__()}. Operation might have been cancelled.")
# return
# self.parse_general(sheet_name="Results")
# namer = RSLNamer(filename=filepath.__str__())
# self.plate_num = namer.parsed_name
# self.submission_type = namer.submission_type
# logger.debug(f"Set plate number to {self.plate_num} and type to {self.submission_type}")
# parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
# self.samples = parser.parse_pcr(xl=self.xl, rsl_number=self.plate_num)
#
# def parse_general(self, sheet_name: str):
# """
# Parse general info rows for all types of PCR results
#
# Args:
# sheet_name (str): Name of sheet in excel workbook that holds info.
# """
# self.pcr = {}
# df = self.xl.parse(sheet_name=sheet_name, dtype=object).fillna("")
# self.pcr['comment'] = df.iloc[0][1]
# self.pcr['operator'] = df.iloc[1][1]
# self.pcr['barcode'] = df.iloc[2][1]
# self.pcr['instrument'] = df.iloc[3][1]
# self.pcr['block_type'] = df.iloc[4][1]
# self.pcr['instrument_name'] = df.iloc[5][1]
# self.pcr['instrument_serial'] = df.iloc[6][1]
# self.pcr['heated_cover_serial'] = df.iloc[7][1]
# self.pcr['block_serial'] = df.iloc[8][1]
# self.pcr['run-start'] = df.iloc[9][1]
# self.pcr['run_end'] = df.iloc[10][1]
# self.pcr['run_duration'] = df.iloc[11][1]
# self.pcr['sample_volume'] = df.iloc[12][1]
# self.pcr['cover_temp'] = df.iloc[13][1]
# self.pcr['passive_ref'] = df.iloc[14][1]
# self.pcr['pcr_step'] = df.iloc[15][1]
# self.pcr['quant_cycle_method'] = df.iloc[16][1]
# self.pcr['analysis_time'] = df.iloc[17][1]
# self.pcr['software'] = df.iloc[18][1]
# self.pcr['plugin'] = df.iloc[19][1]
# self.pcr['exported_on'] = df.iloc[20][1]
# self.pcr['imported_by'] = getuser()
class PCRParser(object): class PCRParser(object):
"""Object to pull data from Design and Analysis PCR export file.""" """Object to pull data from Design and Analysis PCR export file."""
@@ -690,7 +619,7 @@ class PCRParser(object):
Args: Args:
filepath (Path | None, optional): file to parse. Defaults to None. filepath (Path | None, optional): file to parse. Defaults to None.
""" """
logger.debug(f'Parsing {filepath.__str__()}') # logger.debug(f'Parsing {filepath.__str__()}')
if filepath is None: if filepath is None:
logger.error('No filepath given.') logger.error('No filepath given.')
self.xl = None self.xl = None

34
src/submissions/backend/excel/reports.py
View File

@@ -27,7 +27,7 @@ def make_report_xlsx(records:list[dict]) -> Tuple[DataFrame, DataFrame]:
# aggregate cost and sample count columns # aggregate cost and sample count columns
df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Extraction Kit':'count', 'Cost': 'sum', 'Sample Count':'sum'}) df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Extraction Kit':'count', 'Cost': 'sum', 'Sample Count':'sum'})
df2 = df2.rename(columns={"Extraction Kit": 'Run Count'}) df2 = df2.rename(columns={"Extraction Kit": 'Run Count'})
logger.debug(f"Output daftaframe for xlsx: {df2.columns}") # logger.debug(f"Output daftaframe for xlsx: {df2.columns}")
df = df.drop('id', axis=1) df = df.drop('id', axis=1)
df = df.sort_values(['Submitting Lab', "Submitted Date"]) df = df.sort_values(['Submitting Lab', "Submitted Date"])
return df, df2 return df, df2
@@ -47,13 +47,13 @@ def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
""" """
old_lab = "" old_lab = ""
output = [] output = []
logger.debug(f"Report DataFrame: {df}") # logger.debug(f"Report DataFrame: {df}")
for ii, row in enumerate(df.iterrows()): for ii, row in enumerate(df.iterrows()):
logger.debug(f"Row {ii}: {row}") # logger.debug(f"Row {ii}: {row}")
lab = row[0][0] lab = row[0][0]
logger.debug(type(row)) # logger.debug(type(row))
logger.debug(f"Old lab: {old_lab}, Current lab: {lab}") # logger.debug(f"Old lab: {old_lab}, Current lab: {lab}")
logger.debug(f"Name: {row[0][1]}") # logger.debug(f"Name: {row[0][1]}")
data = [item for item in row[1]] data = [item for item in row[1]]
kit = dict(name=row[0][1], cost=data[1], run_count=int(data[0]), sample_count=int(data[2])) kit = dict(name=row[0][1], cost=data[1], run_count=int(data[0]), sample_count=int(data[2]))
# if this is the same lab as before add together # if this is the same lab as before add together
@@ -67,7 +67,7 @@ def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
adder = dict(lab=lab, kits=[kit], total_cost=kit['cost'], total_samples=kit['sample_count'], total_runs=kit['run_count']) adder = dict(lab=lab, kits=[kit], total_cost=kit['cost'], total_samples=kit['sample_count'], total_runs=kit['run_count'])
output.append(adder) output.append(adder)
old_lab = lab old_lab = lab
logger.debug(output) # logger.debug(output)
dicto = {'start_date':start_date, 'end_date':end_date, 'labs':output}#, "table":table} dicto = {'start_date':start_date, 'end_date':end_date, 'labs':output}#, "table":table}
temp = env.get_template('summary_report.html') temp = env.get_template('summary_report.html')
html = temp.render(input=dicto) html = temp.render(input=dicto)
@@ -91,14 +91,14 @@ def convert_data_list_to_df(input:list[dict], subtype:str|None=None) -> DataFram
for column in df.columns: for column in df.columns:
if "percent" in column: if "percent" in column:
count_col = [item for item in df.columns if "count" in item][0] count_col = [item for item in df.columns if "count" in item][0]
# The actual percentage from kraken was off due to exclusion of NaN, recalculating. # NOTE: The actual percentage from kraken was off due to exclusion of NaN, recalculating.
df[column] = 100 * df[count_col] / df.groupby('name')[count_col].transform('sum') df[column] = 100 * df[count_col] / df.groupby('name')[count_col].transform('sum')
if column not in safe: if column not in safe:
if subtype != None and column != subtype: if subtype != None and column != subtype:
del df[column] del df[column]
# move date of sample submitted on same date as previous ahead one. # NOTE: move date of sample submitted on same date as previous ahead one.
df = displace_date(df) df = displace_date(df)
# ad hoc method to make data labels more accurate. # NOTE: ad hoc method to make data labels more accurate.
df = df_column_renamer(df=df) df = df_column_renamer(df=df)
return df return df
@@ -131,8 +131,8 @@ def displace_date(df:DataFrame) -> DataFrame:
Returns: Returns:
DataFrame: output dataframe with dates incremented. DataFrame: output dataframe with dates incremented.
""" """
logger.debug(f"Unique items: {df['name'].unique()}") # logger.debug(f"Unique items: {df['name'].unique()}")
# get submitted dates for each control # NOTE: get submitted dates for each control
dict_list = [dict(name=item, date=df[df.name == item].iloc[0]['submitted_date']) for item in sorted(df['name'].unique())] dict_list = [dict(name=item, date=df[df.name == item].iloc[0]['submitted_date']) for item in sorted(df['name'].unique())]
previous_dates = [] previous_dates = []
for _, item in enumerate(dict_list): for _, item in enumerate(dict_list):
@@ -157,10 +157,10 @@ def check_date(df:DataFrame, item:dict, previous_dates:list) -> Tuple[DataFrame,
check = False check = False
previous_dates.append(item['date']) previous_dates.append(item['date'])
if check: if check:
logger.debug(f"We found one! Increment date!\n\t{item['date']} to {item['date'] + timedelta(days=1)}") # logger.debug(f"We found one! Increment date!\n\t{item['date']} to {item['date'] + timedelta(days=1)}")
# get df locations where name == item name # NOTE: get df locations where name == item name
mask = df['name'] == item['name'] mask = df['name'] == item['name']
# increment date in dataframe # NOTE: increment date in dataframe
df.loc[mask, 'submitted_date'] = df.loc[mask, 'submitted_date'].apply(lambda x: x + timedelta(days=1)) df.loc[mask, 'submitted_date'] = df.loc[mask, 'submitted_date'].apply(lambda x: x + timedelta(days=1))
item['date'] += timedelta(days=1) item['date'] += timedelta(days=1)
passed = False passed = False
@@ -170,9 +170,9 @@ def check_date(df:DataFrame, item:dict, previous_dates:list) -> Tuple[DataFrame,
# logger.debug(f"DF: {type(df)}, previous_dates: {type(previous_dates)}") # logger.debug(f"DF: {type(df)}, previous_dates: {type(previous_dates)}")
# if run didn't lead to changed date, return values # if run didn't lead to changed date, return values
if passed: if passed:
logger.debug(f"Date check passed, returning.") # logger.debug(f"Date check passed, returning.")
return df, previous_dates return df, previous_dates
# if date was changed, rerun with new date # NOTE: if date was changed, rerun with new date
else: else:
logger.warning(f"Date check failed, running recursion") logger.warning(f"Date check failed, running recursion")
df, previous_dates = check_date(df, item, previous_dates) df, previous_dates = check_date(df, item, previous_dates)

17
src/submissions/backend/excel/writer.py
View File

@@ -31,7 +31,6 @@ class SheetWriter(object):
case 'filepath': case 'filepath':
self.__setattr__(k, v) self.__setattr__(k, v)
case 'submission_type': case 'submission_type':
# self.__setattr__('submission_type', submission.submission_type['value'])
self.sub[k] = v['value'] self.sub[k] = v['value']
self.submission_type = SubmissionType.query(name=v['value']) self.submission_type = SubmissionType.query(name=v['value'])
self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type) self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
@@ -40,7 +39,7 @@ class SheetWriter(object):
self.sub[k] = v['value'] self.sub[k] = v['value']
else: else:
self.sub[k] = v self.sub[k] = v
logger.debug(f"\n\nWriting to {submission.filepath.__str__()}\n\n") # logger.debug(f"\n\nWriting to {submission.filepath.__str__()}\n\n")
if self.filepath.stem.startswith("tmp"): if self.filepath.stem.startswith("tmp"):
template = self.submission_type.template_file template = self.submission_type.template_file
@@ -95,7 +94,7 @@ class InfoWriter(object):
self.xl = xl self.xl = xl
map = submission_type.construct_info_map(mode='write') map = submission_type.construct_info_map(mode='write')
self.info = self.reconcile_map(info_dict, map) self.info = self.reconcile_map(info_dict, map)
logger.debug(pformat(self.info)) # logger.debug(pformat(self.info))
def reconcile_map(self, info_dict: dict, map: dict) -> dict: def reconcile_map(self, info_dict: dict, map: dict) -> dict:
output = {} output = {}
@@ -121,8 +120,7 @@ class InfoWriter(object):
logger.error(f"No locations for {k}, skipping") logger.error(f"No locations for {k}, skipping")
continue continue
for loc in locations: for loc in locations:
# logger.debug(f"Writing {k} to {loc['sheet']}, row: {loc['row']}, column: {loc['column']}")
logger.debug(f"Writing {k} to {loc['sheet']}, row: {loc['row']}, column: {loc['column']}")
sheet = self.xl[loc['sheet']] sheet = self.xl[loc['sheet']]
sheet.cell(row=loc['row'], column=loc['column'], value=v['value']) sheet.cell(row=loc['row'], column=loc['column'], value=v['value'])
return self.sub_object.custom_info_writer(self.xl, info=self.info) return self.sub_object.custom_info_writer(self.xl, info=self.info)
@@ -152,7 +150,7 @@ class ReagentWriter(object):
try: try:
dicto = dict(value=v, row=mp_info[k]['row'], column=mp_info[k]['column']) dicto = dict(value=v, row=mp_info[k]['row'], column=mp_info[k]['column'])
except KeyError as e: except KeyError as e:
# logger.error(f"Keyerror: {e}") logger.error(f"KeyError: {e}")
dicto = v dicto = v
placeholder[k] = dicto placeholder[k] = dicto
placeholder['sheet'] = mp_info['sheet'] placeholder['sheet'] = mp_info['sheet']
@@ -197,7 +195,6 @@ class SampleWriter(object):
def write_samples(self): def write_samples(self):
sheet = self.xl[self.map['sheet']] sheet = self.xl[self.map['sheet']]
columns = self.map['sample_columns'] columns = self.map['sample_columns']
# rows = range(self.map['start_row'], self.map['end_row']+1)
for ii, sample in enumerate(self.samples): for ii, sample in enumerate(self.samples):
row = self.map['start_row'] + (sample['submission_rank'] - 1) row = self.map['start_row'] + (sample['submission_rank'] - 1)
for k, v in sample.items(): for k, v in sample.items():
@@ -229,8 +226,6 @@ class EquipmentWriter(object):
for jj, (k, v) in enumerate(equipment.items(), start=1): for jj, (k, v) in enumerate(equipment.items(), start=1):
dicto = dict(value=v, row=ii, column=jj) dicto = dict(value=v, row=ii, column=jj)
placeholder[k] = dicto placeholder[k] = dicto
# output.append(placeholder)
else: else:
for jj, (k, v) in enumerate(equipment.items(), start=1): for jj, (k, v) in enumerate(equipment.items(), start=1):
try: try:
@@ -258,8 +253,8 @@ class EquipmentWriter(object):
for k, v in equipment.items(): for k, v in equipment.items():
if not isinstance(v, dict): if not isinstance(v, dict):
continue continue
logger.debug( # logger.debug(
f"Writing {k}: {v['value']} to {equipment['sheet']}, row: {v['row']}, column: {v['column']}") # f"Writing {k}: {v['value']} to {equipment['sheet']}, row: {v['row']}, column: {v['column']}")
if isinstance(v['value'], list): if isinstance(v['value'], list):
v['value'] = v['value'][0] v['value'] = v['value'][0]
try: try:

18
src/submissions/backend/validators/__init__.py
View File

@@ -23,7 +23,7 @@ class RSLNamer(object):
if self.submission_type is None: if self.submission_type is None:
# logger.debug("Creating submission type because none exists") # logger.debug("Creating submission type because none exists")
self.submission_type = self.retrieve_submission_type(filename=filename) self.submission_type = self.retrieve_submission_type(filename=filename)
logger.debug(f"got submission type: {self.submission_type}") # logger.debug(f"got submission type: {self.submission_type}")
if self.submission_type is not None: if self.submission_type is not None:
# logger.debug("Retrieving BasicSubmission subclass") # logger.debug("Retrieving BasicSubmission subclass")
self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type) self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
@@ -47,7 +47,7 @@ class RSLNamer(object):
""" """
match filename: match filename:
case Path(): case Path():
logger.debug(f"Using path method for {filename}.") # logger.debug(f"Using path method for {filename}.")
if filename.exists(): if filename.exists():
wb = load_workbook(filename) wb = load_workbook(filename)
try: try:
@@ -67,7 +67,7 @@ class RSLNamer(object):
submission_type = cls.retrieve_submission_type(filename=filename.stem.__str__()) submission_type = cls.retrieve_submission_type(filename=filename.stem.__str__())
case str(): case str():
regex = BasicSubmission.construct_regex() regex = BasicSubmission.construct_regex()
logger.debug(f"Using string method for {filename}.") # logger.debug(f"Using string method for {filename}.")
m = regex.search(filename) m = regex.search(filename)
try: try:
submission_type = m.lastgroup submission_type = m.lastgroup
@@ -100,17 +100,17 @@ class RSLNamer(object):
regex (str): string to construct pattern regex (str): string to construct pattern
filename (str): string to be parsed filename (str): string to be parsed
""" """
logger.debug(f"Input string to be parsed: {filename}") # logger.debug(f"Input string to be parsed: {filename}")
if regex is None: if regex is None:
regex = BasicSubmission.construct_regex() regex = BasicSubmission.construct_regex()
else: else:
regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE) regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
logger.debug(f"Using regex: {regex}") # logger.debug(f"Using regex: {regex}")
match filename: match filename:
case Path(): case Path():
m = regex.search(filename.stem) m = regex.search(filename.stem)
case str(): case str():
logger.debug(f"Using string method.") # logger.debug(f"Using string method.")
m = regex.search(filename) m = regex.search(filename)
case _: case _:
m = None m = None
@@ -121,7 +121,7 @@ class RSLNamer(object):
parsed_name = None parsed_name = None
else: else:
parsed_name = None parsed_name = None
logger.debug(f"Got parsed submission name: {parsed_name}") # logger.debug(f"Got parsed submission name: {parsed_name}")
return parsed_name return parsed_name
@classmethod @classmethod
@@ -167,8 +167,8 @@ class RSLNamer(object):
Returns: Returns:
str: output file name. str: output file name.
""" """
logger.debug(f"Kwargs: {kwargs}") # logger.debug(f"Kwargs: {kwargs}")
logger.debug(f"Template: {template}") # logger.debug(f"Template: {template}")
environment = jinja_template_loading() environment = jinja_template_loading()
template = environment.from_string(template) template = environment.from_string(template)
return template.render(**kwargs) return template.render(**kwargs)

82
src/submissions/backend/validators/pydant.py
View File

@@ -134,15 +134,15 @@ class PydReagent(BaseModel):
# logger.debug("Adding extra fields.") # logger.debug("Adding extra fields.")
if self.model_extra != None: if self.model_extra != None:
self.__dict__.update(self.model_extra) self.__dict__.update(self.model_extra)
logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}") # logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}")
reagent = Reagent.query(lot_number=self.lot, name=self.name) reagent = Reagent.query(lot_number=self.lot, name=self.name)
logger.debug(f"Result: {reagent}") # logger.debug(f"Result: {reagent}")
if reagent is None: if reagent is None:
reagent = Reagent() reagent = Reagent()
for key, value in self.__dict__.items(): for key, value in self.__dict__.items():
if isinstance(value, dict): if isinstance(value, dict):
value = value['value'] value = value['value']
logger.debug(f"Reagent info item for {key}: {value}") # logger.debug(f"Reagent info item for {key}: {value}")
# set fields based on keys in dictionary # set fields based on keys in dictionary
match key: match key:
case "lot": case "lot":
@@ -191,7 +191,7 @@ class PydSample(BaseModel, extra='allow'):
@model_validator(mode='after') @model_validator(mode='after')
@classmethod @classmethod
def validate_model(cls, data): def validate_model(cls, data):
logger.debug(f"Data for pydsample: {data}") # logger.debug(f"Data for pydsample: {data}")
model = BasicSample.find_polymorphic_subclass(polymorphic_identity=data.sample_type) model = BasicSample.find_polymorphic_subclass(polymorphic_identity=data.sample_type)
for k, v in data.model_extra.items(): for k, v in data.model_extra.items():
print(k, v) print(k, v)
@@ -200,7 +200,7 @@ class PydSample(BaseModel, extra='allow'):
v = datetime.strptime(v, "%Y-%m-%d") v = datetime.strptime(v, "%Y-%m-%d")
data.__setattr__(k, v) data.__setattr__(k, v)
# print(dir(data)) # print(dir(data))
logger.debug(f"Data coming out of validation: {pformat(data)}") # logger.debug(f"Data coming out of validation: {pformat(data)}")
return data return data
@field_validator("row", "column", "assoc_id", "submission_rank") @field_validator("row", "column", "assoc_id", "submission_rank")
@@ -233,7 +233,7 @@ class PydSample(BaseModel, extra='allow'):
""" """
report = None report = None
self.__dict__.update(self.model_extra) self.__dict__.update(self.model_extra)
logger.debug(f"Here is the incoming sample dict: \n{self.__dict__}") # logger.debug(f"Here is the incoming sample dict: \n{self.__dict__}")
instance = BasicSample.query_or_create(sample_type=self.sample_type, submitter_id=self.submitter_id) instance = BasicSample.query_or_create(sample_type=self.sample_type, submitter_id=self.submitter_id)
for key, value in self.__dict__.items(): for key, value in self.__dict__.items():
match key: match key:
@@ -246,8 +246,8 @@ class PydSample(BaseModel, extra='allow'):
if submission is not None: if submission is not None:
assoc_type = self.sample_type.replace("Sample", "").strip() assoc_type = self.sample_type.replace("Sample", "").strip()
for row, column, aid, submission_rank in zip(self.row, self.column, self.assoc_id, self.submission_rank): for row, column, aid, submission_rank in zip(self.row, self.column, self.assoc_id, self.submission_rank):
logger.debug(f"Looking up association with identity: ({submission.submission_type_name} Association)") # logger.debug(f"Looking up association with identity: ({submission.submission_type_name} Association)")
logger.debug(f"Looking up association with identity: ({assoc_type} Association)") # logger.debug(f"Looking up association with identity: ({assoc_type} Association)")
association = SubmissionSampleAssociation.query_or_create(association_type=f"{assoc_type} Association", association = SubmissionSampleAssociation.query_or_create(association_type=f"{assoc_type} Association",
submission=submission, submission=submission,
sample=instance, sample=instance,
@@ -357,7 +357,7 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator('equipment', mode='before') @field_validator('equipment', mode='before')
@classmethod @classmethod
def convert_equipment_dict(cls, value): def convert_equipment_dict(cls, value):
logger.debug(f"Equipment: {value}") # logger.debug(f"Equipment: {value}")
if isinstance(value, dict): if isinstance(value, dict):
return value['value'] return value['value']
return value return value
@@ -381,7 +381,7 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("submitted_date", mode="before") @field_validator("submitted_date", mode="before")
@classmethod @classmethod
def rescue_date(cls, value): def rescue_date(cls, value):
logger.debug(f"\n\nDate coming into pydantic: {value}\n\n") # logger.debug(f"\n\nDate coming into pydantic: {value}\n\n")
try: try:
check = value['value'] == None check = value['value'] == None
except TypeError: except TypeError:
@@ -426,7 +426,7 @@ class PydSubmission(BaseModel, extra='allow'):
@classmethod @classmethod
def lookup_submitting_lab(cls, value): def lookup_submitting_lab(cls, value):
if isinstance(value['value'], str): if isinstance(value['value'], str):
logger.debug(f"Looking up organization {value['value']}") # logger.debug(f"Looking up organization {value['value']}")
try: try:
value['value'] = Organization.query(name=value['value']).name value['value'] = Organization.query(name=value['value']).name
except AttributeError: except AttributeError:
@@ -457,12 +457,12 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("rsl_plate_num") @field_validator("rsl_plate_num")
@classmethod @classmethod
def rsl_from_file(cls, value, values): def rsl_from_file(cls, value, values):
logger.debug(f"RSL-plate initial value: {value['value']} and other values: {values.data}") # logger.debug(f"RSL-plate initial value: {value['value']} and other values: {values.data}")
sub_type = values.data['submission_type']['value'] sub_type = values.data['submission_type']['value']
if check_not_nan(value['value']): if check_not_nan(value['value']):
return value return value
else: else:
logger.debug("Constructing plate name.") # logger.debug("Constructing plate name.")
output = RSLNamer(filename=values.data['filepath'].__str__(), sub_type=sub_type, output = RSLNamer(filename=values.data['filepath'].__str__(), sub_type=sub_type,
data=values.data).parsed_name data=values.data).parsed_name
return dict(value=output, missing=True) return dict(value=output, missing=True)
@@ -649,32 +649,32 @@ class PydSubmission(BaseModel, extra='allow'):
rsl_plate_num=self.rsl_plate_num['value']) rsl_plate_num=self.rsl_plate_num['value'])
result = Result(msg=msg, code=code) result = Result(msg=msg, code=code)
self.handle_duplicate_samples() self.handle_duplicate_samples()
logger.debug(f"Here's our list of duplicate removed samples: {self.samples}") # logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
# for key, value in self.__dict__.items(): # for key, value in self.__dict__.items():
for key, value in dicto.items(): for key, value in dicto.items():
if isinstance(value, dict): if isinstance(value, dict):
value = value['value'] value = value['value']
logger.debug(f"Setting {key} to {value}") # logger.debug(f"Setting {key} to {value}")
match key: match key:
case "reagents": case "reagents":
if code == 1: if code == 1:
instance.submission_reagent_associations = [] instance.submission_reagent_associations = []
logger.debug(f"Looking through {self.reagents}") # logger.debug(f"Looking through {self.reagents}")
for reagent in self.reagents: for reagent in self.reagents:
reagent, assoc = reagent.toSQL(submission=instance) reagent, assoc = reagent.toSQL(submission=instance)
logger.debug(f"Association: {assoc}") # logger.debug(f"Association: {assoc}")
if assoc is not None:# and assoc not in instance.submission_reagent_associations: if assoc is not None:# and assoc not in instance.submission_reagent_associations:
instance.submission_reagent_associations.append(assoc) instance.submission_reagent_associations.append(assoc)
# instance.reagents.append(reagent) # instance.reagents.append(reagent)
case "samples": case "samples":
for sample in self.samples: for sample in self.samples:
sample, associations, _ = sample.toSQL(submission=instance) sample, associations, _ = sample.toSQL(submission=instance)
logger.debug(f"Sample SQL object to be added to submission: {sample.__dict__}") # logger.debug(f"Sample SQL object to be added to submission: {sample.__dict__}")
for assoc in associations: for assoc in associations:
if assoc is not None and assoc not in instance.submission_sample_associations: if assoc is not None and assoc not in instance.submission_sample_associations:
instance.submission_sample_associations.append(assoc) instance.submission_sample_associations.append(assoc)
case "equipment": case "equipment":
logger.debug(f"Equipment: {pformat(self.equipment)}") # logger.debug(f"Equipment: {pformat(self.equipment)}")
try: try:
if equip is None: if equip is None:
continue continue
@@ -684,11 +684,11 @@ class PydSubmission(BaseModel, extra='allow'):
equip, association = equip.toSQL(submission=instance) equip, association = equip.toSQL(submission=instance)
if association is not None: if association is not None:
association.save() association.save()
logger.debug( # logger.debug(
f"Equipment association SQL object to be added to submission: {association.__dict__}") # f"Equipment association SQL object to be added to submission: {association.__dict__}")
instance.submission_equipment_associations.append(association) instance.submission_equipment_associations.append(association)
case item if item in instance.jsons(): case item if item in instance.jsons():
logger.debug(f"{item} is a json.") # logger.debug(f"{item} is a json.")
try: try:
ii = value.items() ii = value.items()
except AttributeError: except AttributeError:
@@ -701,38 +701,38 @@ class PydSubmission(BaseModel, extra='allow'):
try: try:
instance.set_attribute(key=key, value=value) instance.set_attribute(key=key, value=value)
except AttributeError as e: except AttributeError as e:
logger.debug(f"Could not set attribute: {key} to {value} due to: \n\n {e}") logger.error(f"Could not set attribute: {key} to {value} due to: \n\n {e}")
continue continue
except KeyError: except KeyError:
continue continue
try: try:
logger.debug(f"Calculating costs for procedure...") # logger.debug(f"Calculating costs for procedure...")
instance.calculate_base_cost() instance.calculate_base_cost()
except (TypeError, AttributeError) as e: except (TypeError, AttributeError) as e:
logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using full plate cost.") # logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using full plate cost.")
try: try:
instance.run_cost = instance.extraction_kit.cost_per_run instance.run_cost = instance.extraction_kit.cost_per_run
except AttributeError: except AttributeError:
instance.run_cost = 0 instance.run_cost = 0
logger.debug(f"Calculated base run cost of: {instance.run_cost}") # logger.debug(f"Calculated base run cost of: {instance.run_cost}")
# Apply any discounts that are applicable for client and kit. # Apply any discounts that are applicable for client and kit.
try: try:
logger.debug("Checking and applying discounts...") # logger.debug("Checking and applying discounts...")
discounts = [item.amount for item in discounts = [item.amount for item in
Discount.query(kit_type=instance.extraction_kit, organization=instance.submitting_lab)] Discount.query(kit_type=instance.extraction_kit, organization=instance.submitting_lab)]
logger.debug(f"We got discounts: {discounts}") # logger.debug(f"We got discounts: {discounts}")
if len(discounts) > 0: if len(discounts) > 0:
discounts = sum(discounts) discounts = sum(discounts)
instance.run_cost = instance.run_cost - discounts instance.run_cost = instance.run_cost - discounts
except Exception as e: except Exception as e:
logger.error(f"An unknown exception occurred when calculating discounts: {e}") logger.error(f"An unknown exception occurred when calculating discounts: {e}")
# We need to make sure there's a proper rsl plate number # We need to make sure there's a proper rsl plate number
logger.debug(f"We've got a total cost of {instance.run_cost}") # logger.debug(f"We've got a total cost of {instance.run_cost}")
try: # try:
logger.debug(f"Constructed instance: {instance}") # logger.debug(f"Constructed instance: {instance}")
except AttributeError as e: # except AttributeError as e:
logger.debug(f"Something went wrong constructing instance {self.rsl_plate_num}: {e}") # logger.debug(f"Something went wrong constructing instance {self.rsl_plate_num}: {e}")
logger.debug(f"Constructed submissions message: {msg}") # logger.debug(f"Constructed submissions message: {msg}")
return instance, result return instance, result
def to_form(self, parent: QWidget): def to_form(self, parent: QWidget):
@@ -777,26 +777,26 @@ class PydSubmission(BaseModel, extra='allow'):
Report: Result object containing a message and any missing components. Report: Result object containing a message and any missing components.
""" """
report = Report() report = Report()
logger.debug(f"Extraction kit: {extraction_kit}. Is it a string? {isinstance(extraction_kit, str)}") # logger.debug(f"Extraction kit: {extraction_kit}. Is it a string? {isinstance(extraction_kit, str)}")
if isinstance(extraction_kit, str): if isinstance(extraction_kit, str):
extraction_kit = dict(value=extraction_kit) extraction_kit = dict(value=extraction_kit)
if extraction_kit is not None and extraction_kit != self.extraction_kit['value']: if extraction_kit is not None and extraction_kit != self.extraction_kit['value']:
self.extraction_kit['value'] = extraction_kit['value'] self.extraction_kit['value'] = extraction_kit['value']
logger.debug(f"Looking up {self.extraction_kit['value']}") # logger.debug(f"Looking up {self.extraction_kit['value']}")
ext_kit = KitType.query(name=self.extraction_kit['value']) ext_kit = KitType.query(name=self.extraction_kit['value'])
ext_kit_rtypes = [item.to_pydantic() for item in ext_kit_rtypes = [item.to_pydantic() for item in
ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])] ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])]
logger.debug(f"Kit reagents: {ext_kit_rtypes}") # logger.debug(f"Kit reagents: {ext_kit_rtypes}")
logger.debug(f"Submission reagents: {self.reagents}") # logger.debug(f"Submission reagents: {self.reagents}")
# Exclude any reagenttype found in this pyd not expected in kit. # Exclude any reagenttype found in this pyd not expected in kit.
expected_check = [item.type for item in ext_kit_rtypes] expected_check = [item.type for item in ext_kit_rtypes]
output_reagents = [rt for rt in self.reagents if rt.type in expected_check] output_reagents = [rt for rt in self.reagents if rt.type in expected_check]
logger.debug(f"Already have these reagent types: {output_reagents}") # logger.debug(f"Already have these reagent types: {output_reagents}")
missing_check = [item.type for item in output_reagents] missing_check = [item.type for item in output_reagents]
missing_reagents = [rt for rt in ext_kit_rtypes if rt.type not in missing_check] missing_reagents = [rt for rt in ext_kit_rtypes if rt.type not in missing_check]
missing_reagents += [rt for rt in output_reagents if rt.missing] missing_reagents += [rt for rt in output_reagents if rt.missing]
output_reagents += [rt for rt in missing_reagents if rt not in output_reagents] output_reagents += [rt for rt in missing_reagents if rt not in output_reagents]
logger.debug(f"Missing reagents types: {missing_reagents}") # logger.debug(f"Missing reagents types: {missing_reagents}")
# if lists are equal return no problem # if lists are equal return no problem
if len(missing_reagents) == 0: if len(missing_reagents) == 0:
result = None result = None
@@ -873,7 +873,7 @@ class PydReagentType(BaseModel):
instance: ReagentType = ReagentType.query(name=self.name) instance: ReagentType = ReagentType.query(name=self.name)
if instance == None: if instance == None:
instance = ReagentType(name=self.name, eol_ext=self.eol_ext) instance = ReagentType(name=self.name, eol_ext=self.eol_ext)
logger.debug(f"This is the reagent type instance: {instance.__dict__}") # logger.debug(f"This is the reagent type instance: {instance.__dict__}")
try: try:
assoc = KitTypeReagentTypeAssociation.query(reagent_type=instance, kit_type=kit) assoc = KitTypeReagentTypeAssociation.query(reagent_type=instance, kit_type=kit)
except StatementError: except StatementError:

2
src/submissions/frontend/visualizations/control_charts.py
View File

@@ -48,7 +48,7 @@ def create_charts(ctx:Settings, df:pd.DataFrame, ytitle:str|None=None) -> Figure
# Set descending for any columns that have "{mode}" in the header. # Set descending for any columns that have "{mode}" in the header.
ascending = [False if item == "target" else True for item in sorts] ascending = [False if item == "target" else True for item in sorts]
df = df.sort_values(by=sorts, ascending=ascending) df = df.sort_values(by=sorts, ascending=ascending)
logger.debug(df[df.isna().any(axis=1)]) # logger.debug(df[df.isna().any(axis=1)])
# actual chart construction is done by # actual chart construction is done by
fig = construct_chart(df=df, modes=modes, ytitle=ytitle) fig = construct_chart(df=df, modes=modes, ytitle=ytitle)
return fig return fig

26
src/submissions/frontend/widgets/app.py
View File

@@ -25,7 +25,7 @@ logger.info("Hello, I am a logger")
class App(QMainWindow): class App(QMainWindow):
def __init__(self, ctx: Settings = None): def __init__(self, ctx: Settings = None):
logger.debug(f"Initializing main window...") # logger.debug(f"Initializing main window...")
super().__init__() super().__init__()
self.ctx = ctx self.ctx = ctx
self.last_dir = ctx.directory_path self.last_dir = ctx.directory_path
@@ -58,7 +58,7 @@ class App(QMainWindow):
""" """
adds items to menu bar adds items to menu bar
""" """
logger.debug(f"Creating menu bar...") # logger.debug(f"Creating menu bar...")
menuBar = self.menuBar() menuBar = self.menuBar()
fileMenu = menuBar.addMenu("&File") fileMenu = menuBar.addMenu("&File")
# Creating menus using a title # Creating menus using a title
@@ -79,7 +79,7 @@ class App(QMainWindow):
""" """
adds items to toolbar adds items to toolbar
""" """
logger.debug(f"Creating toolbar...") # logger.debug(f"Creating toolbar...")
toolbar = QToolBar("My main toolbar") toolbar = QToolBar("My main toolbar")
self.addToolBar(toolbar) self.addToolBar(toolbar)
toolbar.addAction(self.addReagentAction) toolbar.addAction(self.addReagentAction)
@@ -90,7 +90,7 @@ class App(QMainWindow):
""" """
creates actions creates actions
""" """
logger.debug(f"Creating actions...") # logger.debug(f"Creating actions...")
self.importAction = QAction("&Import Submission", self) self.importAction = QAction("&Import Submission", self)
# self.importPCRAction = QAction("&Import PCR Results", self) # self.importPCRAction = QAction("&Import PCR Results", self)
self.addReagentAction = QAction("Add Reagent", self) self.addReagentAction = QAction("Add Reagent", self)
@@ -107,7 +107,7 @@ class App(QMainWindow):
""" """
connect menu and tool bar item to functions connect menu and tool bar item to functions
""" """
logger.debug(f"Connecting actions...") # logger.debug(f"Connecting actions...")
self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission) self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission)
# self.importPCRAction.triggered.connect(self.table_widget.formwidget.import_pcr_results) # self.importPCRAction.triggered.connect(self.table_widget.formwidget.import_pcr_results)
self.addReagentAction.triggered.connect(self.table_widget.formwidget.add_reagent) self.addReagentAction.triggered.connect(self.table_widget.formwidget.add_reagent)
@@ -134,7 +134,7 @@ class App(QMainWindow):
url = Path(sys._MEIPASS).joinpath("files", "docs", "index.html") url = Path(sys._MEIPASS).joinpath("files", "docs", "index.html")
else: else:
url = Path("docs\\build\\index.html").absolute() url = Path("docs\\build\\index.html").absolute()
logger.debug(f"Attempting to open {url}") # logger.debug(f"Attempting to open {url}")
webbrowser.get('windows-default').open(f"file://{url.__str__()}") webbrowser.get('windows-default').open(f"file://{url.__str__()}")
def result_reporter(self): def result_reporter(self):
@@ -144,11 +144,11 @@ class App(QMainWindow):
Args: Args:
result (dict | None, optional): The result from a function. Defaults to None. result (dict | None, optional): The result from a function. Defaults to None.
""" """
logger.debug(f"Running results reporter for: {self.report.results}") # logger.debug(f"Running results reporter for: {self.report.results}")
if len(self.report.results) > 0: if len(self.report.results) > 0:
logger.debug(f"We've got some results!") # logger.debug(f"We've got some results!")
for result in self.report.results: for result in self.report.results:
logger.debug(f"Showing result: {result}") # logger.debug(f"Showing result: {result}")
if result != None: if result != None:
alert = result.report() alert = result.report()
if alert.exec(): if alert.exec():
@@ -164,17 +164,17 @@ class App(QMainWindow):
def backup_database(self): def backup_database(self):
month = date.today().strftime("%Y-%m") month = date.today().strftime("%Y-%m")
# day = date.today().strftime("%Y-%m-%d") # day = date.today().strftime("%Y-%m-%d")
logger.debug(f"Here is the db directory: {self.ctx.database_path}") # logger.debug(f"Here is the db directory: {self.ctx.database_path}")
logger.debug(f"Here is the backup directory: {self.ctx.backup_path}") # logger.debug(f"Here is the backup directory: {self.ctx.backup_path}")
current_month_bak = Path(self.ctx.backup_path).joinpath(f"submissions_backup-{month}").resolve().with_suffix(".db") current_month_bak = Path(self.ctx.backup_path).joinpath(f"submissions_backup-{month}").resolve().with_suffix(".db")
if not current_month_bak.exists() and "demo" not in self.ctx.database_path.__str__(): if not current_month_bak.exists() and "demo" not in self.ctx.database_path.__str__():
logger.debug("No backup found for this month, backing up database.") logger.info("No backup found for this month, backing up database.")
shutil.copyfile(self.ctx.database_path, current_month_bak) shutil.copyfile(self.ctx.database_path, current_month_bak)
class AddSubForm(QWidget): class AddSubForm(QWidget):
def __init__(self, parent:QWidget): def __init__(self, parent:QWidget):
logger.debug(f"Initializating subform...") # logger.debug(f"Initializating subform...")
super(QWidget, self).__init__(parent) super(QWidget, self).__init__(parent)
self.layout = QVBoxLayout(self) self.layout = QVBoxLayout(self)
# Initialize tab screen # Initialize tab screen

12
src/submissions/frontend/widgets/controls_chart.py
View File

@@ -112,13 +112,13 @@ class ControlsViewer(QWidget):
Tuple[QMainWindow, dict]: Collection of new main app window and result dict Tuple[QMainWindow, dict]: Collection of new main app window and result dict
""" """
report = Report() report = Report()
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}") # 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}")
# set the subtype for kraken # set the subtype for kraken
if self.sub_typer.currentText() == "": if self.sub_typer.currentText() == "":
self.subtype = None self.subtype = None
else: else:
self.subtype = self.sub_typer.currentText() self.subtype = self.sub_typer.currentText()
logger.debug(f"Subtype: {self.subtype}") # logger.debug(f"Subtype: {self.subtype}")
# query all controls using the type/start and end dates from the gui # query all controls using the type/start and end dates from the gui
controls = Control.query(control_type=self.con_type, start_date=self.start_date, end_date=self.end_date) controls = Control.query(control_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 no data found from query set fig to none for reporting in webview
@@ -129,7 +129,7 @@ class ControlsViewer(QWidget):
data = [control.convert_by_mode(mode=self.mode) for control in controls] data = [control.convert_by_mode(mode=self.mode) for control in controls]
# flatten data to one dimensional list # flatten data to one dimensional list
data = [item for sublist in data for item in sublist] data = [item for sublist in data for item in sublist]
logger.debug(f"Control objects going into df conversion: {type(data)}") # logger.debug(f"Control objects going into df conversion: {type(data)}")
if data == []: if data == []:
self.report.add_result(Result(status="Critical", msg="No data found for controls in given date range.")) self.report.add_result(Result(status="Critical", msg="No data found for controls in given date range."))
return return
@@ -141,13 +141,13 @@ class ControlsViewer(QWidget):
title = f"{self.mode} - {self.subtype}" title = f"{self.mode} - {self.subtype}"
# send dataframe to chart maker # send dataframe to chart maker
fig = create_charts(ctx=self.app.ctx, df=df, ytitle=title) fig = create_charts(ctx=self.app.ctx, df=df, ytitle=title)
logger.debug(f"Updating figure...") # logger.debug(f"Updating figure...")
# construct html for webview # construct html for webview
html = construct_html(figure=fig) html = construct_html(figure=fig)
logger.debug(f"The length of html code is: {len(html)}") # logger.debug(f"The length of html code is: {len(html)}")
self.webengineview.setHtml(html) self.webengineview.setHtml(html)
self.webengineview.update() self.webengineview.update()
logger.debug("Figure updated... I hope.") # logger.debug("Figure updated... I hope.")
self.report.add_result(report) self.report.add_result(report)
class ControlsDatePicker(QWidget): class ControlsDatePicker(QWidget):

8
src/submissions/frontend/widgets/equipment_usage.py
View File

@@ -17,9 +17,9 @@ class EquipmentUsage(QDialog):
self.setWindowTitle("Equipment Checklist") self.setWindowTitle("Equipment Checklist")
self.used_equipment = self.submission.get_used_equipment() self.used_equipment = self.submission.get_used_equipment()
self.kit = self.submission.extraction_kit self.kit = self.submission.extraction_kit
logger.debug(f"Existing equipment: {self.used_equipment}") # logger.debug(f"Existing equipment: {self.used_equipment}")
self.opt_equipment = submission.submission_type.get_equipment() self.opt_equipment = submission.submission_type.get_equipment()
logger.debug(f"EquipmentRoles: {self.opt_equipment}") # logger.debug(f"EquipmentRoles: {self.opt_equipment}")
self.layout = QVBoxLayout() self.layout = QVBoxLayout()
self.setLayout(self.layout) self.setLayout(self.layout)
self.populate_form() self.populate_form()
@@ -115,9 +115,9 @@ class RoleComboBox(QWidget):
Changes processes when equipment is changed Changes processes when equipment is changed
""" """
equip = self.box.currentText() equip = self.box.currentText()
logger.debug(f"Updating equipment: {equip}") # logger.debug(f"Updating equipment: {equip}")
equip2 = [item for item in self.role.equipment if item.name==equip][0] equip2 = [item for item in self.role.equipment if item.name==equip][0]
logger.debug(f"Using: {equip2}") # logger.debug(f"Using: {equip2}")
self.process.clear() self.process.clear()
self.process.addItems([item for item in equip2.processes if item in self.role.processes]) self.process.addItems([item for item in equip2.processes if item in self.role.processes])

2
src/submissions/frontend/widgets/gel_checker.py
View File

@@ -145,5 +145,5 @@ class ControlsForm(QWidget):
dicto['values'].append(dict(name=label[1], value=le.text())) dicto['values'].append(dict(name=label[1], value=le.text()))
if label[0] not in [item['name'] for item in output]: if label[0] not in [item['name'] for item in output]:
output.append(dicto) output.append(dicto)
logger.debug(pformat(output)) # logger.debug(pformat(output))
return output, self.comment_field.toPlainText() return output, self.comment_field.toPlainText()

18
src/submissions/frontend/widgets/kit_creator.py
View File

@@ -93,10 +93,10 @@ class KitAdder(QWidget):
# get form info # get form info
info, reagents = self.parse_form() info, reagents = self.parse_form()
info = {k:v for k,v in info.items() if k in [column.name for column in self.columns] + ['kit_name', 'used_for']} info = {k:v for k,v in info.items() if k in [column.name for column in self.columns] + ['kit_name', 'used_for']}
logger.debug(f"kit info: {pformat(info)}") # logger.debug(f"kit info: {pformat(info)}")
logger.debug(f"kit reagents: {pformat(reagents)}") # logger.debug(f"kit reagents: {pformat(reagents)}")
info['reagent_types'] = reagents info['reagent_types'] = reagents
logger.debug(pformat(info)) # logger.debug(pformat(info))
# send to kit constructor # send to kit constructor
kit = PydKit(name=info['kit_name']) kit = PydKit(name=info['kit_name'])
for reagent in info['reagent_types']: for reagent in info['reagent_types']:
@@ -108,7 +108,7 @@ class KitAdder(QWidget):
'expiry':reagent['expiry'] 'expiry':reagent['expiry']
}} }}
kit.reagent_types.append(PydReagentType(name=reagent['rtname'], eol_ext=reagent['eol'], uses=uses)) kit.reagent_types.append(PydReagentType(name=reagent['rtname'], eol_ext=reagent['eol'], uses=uses))
logger.debug(f"Output pyd object: {kit.__dict__}") # logger.debug(f"Output pyd object: {kit.__dict__}")
sqlobj, result = kit.toSQL(self.ctx) sqlobj, result = kit.toSQL(self.ctx)
report.add_result(result=result) report.add_result(result=result)
sqlobj.save() sqlobj.save()
@@ -122,7 +122,7 @@ class KitAdder(QWidget):
Returns: Returns:
Tuple[dict, list]: dict=info, list=reagents Tuple[dict, list]: dict=info, list=reagents
""" """
logger.debug(f"Hello from {self.__class__} parser!") # logger.debug(f"Hello from {self.__class__} parser!")
info = {} info = {}
reagents = [] reagents = []
widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore and not isinstance(widget.parent(), ReagentTypeForm)] widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore and not isinstance(widget.parent(), ReagentTypeForm)]
@@ -153,7 +153,7 @@ class ReagentTypeForm(QWidget):
self.reagent_getter.setObjectName("rtname") self.reagent_getter.setObjectName("rtname")
# lookup all reagent type names from db # lookup all reagent type names from db
lookup = ReagentType.query() lookup = ReagentType.query()
logger.debug(f"Looked up ReagentType names: {lookup}") # logger.debug(f"Looked up ReagentType names: {lookup}")
self.reagent_getter.addItems([item.name for item in lookup]) self.reagent_getter.addItems([item.name for item in lookup])
self.reagent_getter.setEditable(True) self.reagent_getter.setEditable(True)
grid.addWidget(self.reagent_getter,0,1) grid.addWidget(self.reagent_getter,0,1)
@@ -205,14 +205,14 @@ class ReagentTypeForm(QWidget):
Returns: Returns:
dict: _description_ dict: _description_
""" """
logger.debug(f"Hello from {self.__class__} parser!") # logger.debug(f"Hello from {self.__class__} parser!")
info = {} info = {}
info['eol'] = self.eol.value() info['eol'] = self.eol.value()
info['sheet'] = self.location_sheet_name.text() info['sheet'] = self.location_sheet_name.text()
info['rtname'] = self.reagent_getter.currentText() info['rtname'] = self.reagent_getter.currentText()
widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore] widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore]
for widget in widgets: for widget in widgets:
logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)} with parent {widget.parent()}") # logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)} with parent {widget.parent()}")
match widget: match widget:
case QLineEdit(): case QLineEdit():
info[widget.objectName()] = widget.text() info[widget.objectName()] = widget.text()
@@ -225,7 +225,7 @@ class ReagentTypeForm(QWidget):
key, sub_key = widget.objectName().split("_") key, sub_key = widget.objectName().split("_")
if key not in info.keys(): if key not in info.keys():
info[key] = {} info[key] = {}
logger.debug(f"Adding key {key}, {sub_key} and value {widget.value()} to {info}") # logger.debug(f"Adding key {key}, {sub_key} and value {widget.value()} to {info}")
info[key][sub_key] = widget.value() info[key][sub_key] = widget.value()
return info return info

6
src/submissions/frontend/widgets/misc.py
View File

@@ -58,7 +58,7 @@ class AddReagentForm(QDialog):
self.type_input = QComboBox() self.type_input = QComboBox()
self.type_input.setObjectName('type') self.type_input.setObjectName('type')
self.type_input.addItems([item.name for item in ReagentType.query()]) self.type_input.addItems([item.name for item in ReagentType.query()])
logger.debug(f"Trying to find index of {reagent_type}") # logger.debug(f"Trying to find index of {reagent_type}")
# convert input to user friendly string? # convert input to user friendly string?
try: try:
reagent_type = reagent_type.replace("_", " ").title() reagent_type = reagent_type.replace("_", " ").title()
@@ -97,7 +97,7 @@ class AddReagentForm(QDialog):
""" """
Updates reagent names form field with examples from reagent type Updates reagent names form field with examples from reagent type
""" """
logger.debug(self.type_input.currentText()) # logger.debug(self.type_input.currentText())
self.name_input.clear() self.name_input.clear()
lookup = Reagent.query(reagent_type=self.type_input.currentText()) lookup = Reagent.query(reagent_type=self.type_input.currentText())
self.name_input.addItems(list(set([item.name for item in lookup]))) self.name_input.addItems(list(set([item.name for item in lookup])))
@@ -210,7 +210,7 @@ class LogParser(QDialog):
""" """
count: int = 0 count: int = 0
total: int = 0 total: int = 0
logger.debug(f"Current search term: {self.phrase_looker.currentText()}") # logger.debug(f"Current search term: {self.phrase_looker.currentText()}")
try: try:
with open(self.fname, "r") as f: with open(self.fname, "r") as f:
for chunk in readInChunks(fileObj=f): for chunk in readInChunks(fileObj=f):

38
src/submissions/frontend/widgets/submission_details.py
View File

@@ -1,4 +1,4 @@
from PyQt6.QtWidgets import (QDialog, QScrollArea, QPushButton, QVBoxLayout, QMessageBox, from PyQt6.QtWidgets import (QDialog, QPushButton, QVBoxLayout, QMessageBox,
QDialogButtonBox, QTextEdit) QDialogButtonBox, QTextEdit)
from PyQt6.QtWebEngineWidgets import QWebEngineView from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtWebChannel import QWebChannel from PyQt6.QtWebChannel import QWebChannel
@@ -10,7 +10,6 @@ from .functions import select_save_file
from io import BytesIO from io import BytesIO
from tempfile import TemporaryFile, TemporaryDirectory from tempfile import TemporaryFile, TemporaryDirectory
from pathlib import Path from pathlib import Path
# from xhtml2pdf import pisa
import logging, base64 import logging, base64
from getpass import getuser from getpass import getuser
from datetime import datetime from datetime import datetime
@@ -33,24 +32,19 @@ class SubmissionDetails(QDialog):
self.app = parent.parent().parent().parent().parent().parent().parent() self.app = parent.parent().parent().parent().parent().parent().parent()
except AttributeError: except AttributeError:
self.app = None self.app = None
# self.setWindowTitle(f"Submission Details - {sub.rsl_plate_num}")
# create scrollable interior
interior = QScrollArea()
interior.setParent(self)
self.webview = QWebEngineView(parent=self) self.webview = QWebEngineView(parent=self)
self.webview.setMinimumSize(900, 500) self.webview.setMinimumSize(900, 500)
self.webview.setMaximumSize(900, 500) self.webview.setMaximumSize(900, 500)
# self.webview.setHtml(self.html)
self.layout = QVBoxLayout() self.layout = QVBoxLayout()
interior.resize(900, 500)
interior.setWidget(self.webview)
self.setFixedSize(900, 500) self.setFixedSize(900, 500)
# button to export a pdf version # NOTE: button to export a pdf version
btn = QPushButton("Export PDF") btn = QPushButton("Export PDF")
btn.setParent(self) btn.setFixedWidth(875)
btn.setFixedWidth(900)
btn.clicked.connect(self.export) btn.clicked.connect(self.export)
# setup channel self.layout.addWidget(btn)
self.layout.addWidget(self.webview)
self.setLayout(self.layout)
# NOTE: setup channel
self.channel = QWebChannel() self.channel = QWebChannel()
self.channel.registerObject('backend', self) self.channel.registerObject('backend', self)
self.submission_details(submission=sub) self.submission_details(submission=sub)
@@ -80,31 +74,25 @@ class SubmissionDetails(QDialog):
Args: Args:
submission (str | BasicSubmission): Submission of interest. submission (str | BasicSubmission): Submission of interest.
""" """
logger.debug(f"Details for: {submission}") # logger.debug(f"Details for: {submission}")
if isinstance(submission, str): if isinstance(submission, str):
# submission = BasicSubmission.query(rsl_number=submission)
submission = BasicSubmission.query(rsl_plate_num=submission) submission = BasicSubmission.query(rsl_plate_num=submission)
self.base_dict = submission.to_dict(full_data=True) self.base_dict = submission.to_dict(full_data=True)
logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}") # logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}")
# don't want id # NOTE: don't want id
del self.base_dict['id'] del self.base_dict['id']
# logger.debug(f"Creating barcode.") # logger.debug(f"Creating barcode.")
# if not check_if_app(): # logger.debug(f"Making platemap...")
# self.base_dict['barcode'] = base64.b64encode(submission.make_plate_barcode(width=120, height=30)).decode('utf-8')
logger.debug(f"Making platemap...")
self.base_dict['platemap'] = submission.make_plate_map() self.base_dict['platemap'] = submission.make_plate_map()
self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict) self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user()) self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user())
self.webview.setHtml(self.html) self.webview.setHtml(self.html)
self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}") self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
# with open("details.html", "w") as f:
# f.write(self.html)
@pyqtSlot(str) @pyqtSlot(str)
def sign_off(self, submission:str|BasicSubmission): def sign_off(self, submission:str|BasicSubmission):
logger.debug(f"Signing off on {submission} - ({getuser()})") # logger.debug(f"Signing off on {submission} - ({getuser()})")
if isinstance(submission, str): if isinstance(submission, str):
# submission = BasicSubmission.query(rsl_number=submission)
submission = BasicSubmission.query(rsl_plate_num=submission) submission = BasicSubmission.query(rsl_plate_num=submission)
submission.signed_by = getuser() submission.signed_by = getuser()
submission.save() submission.save()
@@ -177,6 +165,6 @@ class SubmissionComment(QDialog):
comment = self.txt_editor.toPlainText() comment = self.txt_editor.toPlainText()
dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S") dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
full_comment = {"name":commenter, "time": dt, "text": comment} full_comment = {"name":commenter, "time": dt, "text": comment}
logger.debug(f"Full comment: {full_comment}") # logger.debug(f"Full comment: {full_comment}")
return full_comment return full_comment

111
src/submissions/frontend/widgets/submission_table.py
View File

@@ -110,7 +110,7 @@ class SubmissionsSheet(QTableView):
self.menu = QMenu(self) self.menu = QMenu(self)
self.con_actions = submission.custom_context_events() self.con_actions = submission.custom_context_events()
for k in self.con_actions.keys(): for k in self.con_actions.keys():
logger.debug(f"Adding {k}") # logger.debug(f"Adding {k}")
action = QAction(k, self) action = QAction(k, self)
action.triggered.connect(lambda _, action_name=k: self.triggered_action(action_name=action_name)) action.triggered.connect(lambda _, action_name=k: self.triggered_action(action_name=action_name))
self.menu.addAction(action) self.menu.addAction(action)
@@ -124,8 +124,8 @@ class SubmissionsSheet(QTableView):
Args: Args:
action_name (str): name of the action from the menu action_name (str): name of the action from the menu
""" """
logger.debug(f"Action: {action_name}") # logger.debug(f"Action: {action_name}")
logger.debug(f"Responding with {self.con_actions[action_name]}") # logger.debug(f"Responding with {self.con_actions[action_name]}")
func = self.con_actions[action_name] func = self.con_actions[action_name]
func(obj=self) func(obj=self)
@@ -162,50 +162,20 @@ class SubmissionsSheet(QTableView):
experiment_name=run[4].strip(), experiment_name=run[4].strip(),
end_time=run[5].strip() end_time=run[5].strip()
) )
# elution columns are item 6 in the comma split list to the end # NOTE: elution columns are item 6 in the comma split list to the end
for ii in range(6, len(run)): for ii in range(6, len(run)):
new_run[f"column{str(ii-5)}_vol"] = run[ii] new_run[f"column{str(ii-5)}_vol"] = run[ii]
# Lookup imported submissions # NOTE: Lookup imported submissions
# sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num'])
sub = BasicSubmission.query(rsl_plate_num=new_run['rsl_plate_num']) sub = BasicSubmission.query(rsl_plate_num=new_run['rsl_plate_num'])
# If no such submission exists, move onto the next run # NOTE: If no such submission exists, move onto the next run
if sub == None: if sub == None:
continue continue
try: try:
logger.debug(f"Found submission: {sub.rsl_plate_num}") # logger.debug(f"Found submission: {sub.rsl_plate_num}")
count += 1 count += 1
except AttributeError: except AttributeError:
continue continue
sub.set_attribute('extraction_info', new_run) sub.set_attribute('extraction_info', new_run)
# if sub.extraction_info != None:
# # existing = json.loads(sub.extraction_info)
# existing = sub.extraction_info
# else:
# existing = None
# # Check if the new info already exists in the imported submission
# try:
# # if json.dumps(new_run) in sub.extraction_info:
# if new_run in sub.extraction_info:
# logger.debug(f"Looks like we already have that info.")
# continue
# except TypeError:
# pass
# # Update or create the extraction info
# if existing != None:
# try:
# logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
# existing.append(new_run)
# logger.debug(f"Setting: {existing}")
# # sub.extraction_info = json.dumps(existing)
# sub.extraction_info = existing
# except TypeError:
# logger.error(f"Error updating!")
# # sub.extraction_info = json.dumps([new_run])
# sub.extraction_info = [new_run]
# logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.extraction_info}")
# else:
# # sub.extraction_info = json.dumps([new_run])
# sub.extraction_info = [new_run]
sub.save() sub.save()
self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information')) self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
@@ -230,7 +200,7 @@ class SubmissionsSheet(QTableView):
""" """
fname = select_open_file(self, file_extension="csv") fname = select_open_file(self, file_extension="csv")
with open(fname.__str__(), 'r') as f: with open(fname.__str__(), 'r') as f:
# split csv rows on comma # NOTE: split csv rows on comma
runs = [col.strip().split(",") for col in f.readlines()] runs = [col.strip().split(",") for col in f.readlines()]
count = 0 count = 0
for run in runs: for run in runs:
@@ -242,49 +212,17 @@ class SubmissionsSheet(QTableView):
experiment_name=run[4].strip(), experiment_name=run[4].strip(),
end_time=run[5].strip() end_time=run[5].strip()
) )
# lookup imported submission # NOTE: lookup imported submission
# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
# sub = lookup_submissions(ctx=obj.ctx, rsl_number=new_run['rsl_plate_num'])
sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num']) sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num'])
# if imported submission doesn't exist move on to next run # NOTE: if imported submission doesn't exist move on to next run
if sub == None: if sub == None:
continue continue
try:
logger.debug(f"Found submission: {sub.rsl_plate_num}")
except AttributeError:
continue
sub.set_attribute('pcr_info', new_run)
# # check if pcr_info already exists
# if hasattr(sub, 'pcr_info') and sub.pcr_info != None:
# # existing = json.loads(sub.pcr_info)
# existing = sub.pcr_info
# else:
# existing = None
# # check if this entry already exists in imported submission
# try: # try:
# # if json.dumps(new_run) in sub.pcr_info: # logger.debug(f"Found submission: {sub.rsl_plate_num}")
# if new_run in sub.pcr_info: # except AttributeError:
# logger.debug(f"Looks like we already have that info.") # continue
# continue sub.set_attribute('pcr_info', new_run)
# else: # NOTE: check if pcr_info already exists
# count += 1
# except TypeError:
# logger.error(f"No json to dump")
# if existing is not None:
# try:
# logger.debug(f"Updating {type(existing)}: {existing} with {type(new_run)}: {new_run}")
# existing.append(new_run)
# logger.debug(f"Setting: {existing}")
# # sub.pcr_info = json.dumps(existing)
# sub.pcr_info = existing
# except TypeError:
# logger.error(f"Error updating!")
# # sub.pcr_info = json.dumps([new_run])
# sub.pcr_info = [new_run]
# logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.pcr_info}")
# else:
# # sub.pcr_info = json.dumps([new_run])
# sub.pcr_info = [new_run]
sub.save() sub.save()
self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information')) self.report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
@@ -308,23 +246,21 @@ class SubmissionsSheet(QTableView):
Tuple[QMainWindow, dict]: Collection of new main app window and result dict Tuple[QMainWindow, dict]: Collection of new main app window and result dict
""" """
report = Report() report = Report()
# ask for date ranges # NOTE: ask for date ranges
dlg = ReportDatePicker() dlg = ReportDatePicker()
if dlg.exec(): if dlg.exec():
info = dlg.parse_form() info = dlg.parse_form()
logger.debug(f"Report info: {info}") # logger.debug(f"Report info: {info}")
# find submissions based on date range # NOTE: find submissions based on date range
subs = BasicSubmission.query(start_date=info['start_date'], end_date=info['end_date']) subs = BasicSubmission.query(start_date=info['start_date'], end_date=info['end_date'])
# convert each object to dict # NOTE: convert each object to dict
records = [item.to_dict(report=True) for item in subs] records = [item.to_dict(report=True) for item in subs]
logger.debug(f"Records: {pformat(records)}") logger.debug(f"Records: {pformat(records)}")
# make dataframe from record dictionaries # NOTE: make dataframe from record dictionaries
detailed_df, summary_df = make_report_xlsx(records=records) detailed_df, summary_df = make_report_xlsx(records=records)
html = make_report_html(df=summary_df, start_date=info['start_date'], end_date=info['end_date']) html = make_report_html(df=summary_df, start_date=info['start_date'], end_date=info['end_date'])
# get save location of report # NOTE: get save location of report
fname = select_save_file(obj=self, default_name=f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf", extension="pdf") fname = select_save_file(obj=self, default_name=f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf", extension="pdf")
# with open(fname, "w+b") as f:
# pisa.CreatePDF(html, dest=f)
html_to_pdf(html=html, output_file=fname) html_to_pdf(html=html, output_file=fname)
writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl') writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl')
summary_df.to_excel(writer, sheet_name="Report") summary_df.to_excel(writer, sheet_name="Report")
@@ -337,14 +273,13 @@ class SubmissionsSheet(QTableView):
len(str(series.name)) # len of column name/header len(str(series.name)) # len of column name/header
)) + 20 # adding a little extra space )) + 20 # adding a little extra space
try: try:
# worksheet.column_dimensions[get_column_letter(idx=idx)].width = max_len # NOTE: Convert idx to letter
# Convert idx to letter
col_letter = chr(ord('@') + idx) col_letter = chr(ord('@') + idx)
worksheet.column_dimensions[col_letter].width = max_len worksheet.column_dimensions[col_letter].width = max_len
except ValueError: except ValueError:
pass pass
blank_row = get_first_blank_df_row(summary_df) + 1 blank_row = get_first_blank_df_row(summary_df) + 1
logger.debug(f"Blank row index = {blank_row}") # logger.debug(f"Blank row index = {blank_row}")
for col in range(3,6): for col in range(3,6):
col_letter = row_map[col] col_letter = row_map[col]
worksheet.cell(row=blank_row, column=col, value=f"=SUM({col_letter}2:{col_letter}{str(blank_row-1)})") worksheet.cell(row=blank_row, column=col, value=f"=SUM({col_letter}2:{col_letter}{str(blank_row-1)})")

6
src/submissions/frontend/widgets/submission_type_creator.py
View File

@@ -26,11 +26,11 @@ class SubmissionTypeAdder(QWidget):
scrollContent = QWidget(scroll) scrollContent = QWidget(scroll)
self.grid = QGridLayout() self.grid = QGridLayout()
scrollContent.setLayout(self.grid) scrollContent.setLayout(self.grid)
# insert submit button at top # NOTE: insert submit button at top
self.submit_btn = QPushButton("Submit") self.submit_btn = QPushButton("Submit")
self.grid.addWidget(self.submit_btn,0,0,1,1) self.grid.addWidget(self.submit_btn,0,0,1,1)
self.grid.addWidget(QLabel("Submission Type Name:"),2,0) self.grid.addWidget(QLabel("Submission Type Name:"),2,0)
# widget to get kit name # NOTE: widget to get kit name
self.st_name = QLineEdit() self.st_name = QLineEdit()
self.st_name.setObjectName("submission_type_name") self.st_name.setObjectName("submission_type_name")
self.grid.addWidget(self.st_name,2,1,1,2) self.grid.addWidget(self.st_name,2,1,1,2)
@@ -39,7 +39,7 @@ class SubmissionTypeAdder(QWidget):
self.grid.addWidget(template_selector,3,1) self.grid.addWidget(template_selector,3,1)
self.template_label = QLabel("None") self.template_label = QLabel("None")
self.grid.addWidget(self.template_label,3,2) self.grid.addWidget(self.template_label,3,2)
# widget to get uses of kit # NOTE: widget to get uses of kit
exclude = ['id', 'submitting_lab_id', 'extraction_kit_id', 'reagents_id', 'extraction_info', 'pcr_info', 'run_cost'] exclude = ['id', 'submitting_lab_id', 'extraction_kit_id', 'reagents_id', 'extraction_info', 'pcr_info', 'run_cost']
self.columns = {key:value for key, value in BasicSubmission.__dict__.items() if isinstance(value, InstrumentedAttribute)} self.columns = {key:value for key, value in BasicSubmission.__dict__.items() if isinstance(value, InstrumentedAttribute)}
self.columns = {key:value for key, value in self.columns.items() if hasattr(value, "type") and key not in exclude} self.columns = {key:value for key, value in self.columns.items() if hasattr(value, "type") and key not in exclude}

136
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -30,7 +30,7 @@ class SubmissionFormContainer(QWidget):
import_drag = pyqtSignal(Path) import_drag = pyqtSignal(Path)
def __init__(self, parent: QWidget) -> None: def __init__(self, parent: QWidget) -> None:
logger.debug(f"Setting form widget...") # logger.debug(f"Setting form widget...")
super().__init__(parent) super().__init__(parent)
self.app = self.parent().parent() self.app = self.parent().parent()
self.report = Report() self.report = Report()
@@ -52,7 +52,7 @@ class SubmissionFormContainer(QWidget):
Sets filename when file dropped Sets filename when file dropped
""" """
fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0]) fname = Path([u.toLocalFile() for u in event.mimeData().urls()][0])
logger.debug(f"App: {self.app}") # logger.debug(f"App: {self.app}")
self.app.last_dir = fname.parent self.app.last_dir = fname.parent
self.import_drag.emit(fname) self.import_drag.emit(fname)
@@ -63,7 +63,7 @@ class SubmissionFormContainer(QWidget):
self.app.raise_() self.app.raise_()
self.app.activateWindow() self.app.activateWindow()
self.import_submission_function(fname) self.import_submission_function(fname)
logger.debug(f"Result from result reporter: {self.report.results}") # logger.debug(f"Result from result reporter: {self.report.results}")
self.app.report.add_result(self.report) self.app.report.add_result(self.report)
self.report = Report() self.report = Report()
self.app.result_reporter() self.app.result_reporter()
@@ -78,7 +78,7 @@ class SubmissionFormContainer(QWidget):
Returns: Returns:
Tuple[QMainWindow, dict|None]: Collection of new main app window and result dict Tuple[QMainWindow, dict|None]: Collection of new main app window and result dict
""" """
logger.debug(f"\n\nStarting Import...\n\n") logger.info(f"\n\nStarting Import...\n\n")
report = Report() report = Report()
try: try:
self.form.setParent(None) self.form.setParent(None)
@@ -90,7 +90,7 @@ class SubmissionFormContainer(QWidget):
# set file dialog # set file dialog
if isinstance(fname, bool) or fname == None: if isinstance(fname, bool) or fname == None:
fname = select_open_file(self, file_extension="xlsx") fname = select_open_file(self, file_extension="xlsx")
logger.debug(f"Attempting to parse file: {fname}") # logger.debug(f"Attempting to parse file: {fname}")
if not fname.exists(): if not fname.exists():
report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical")) report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
self.report.add_result(report) self.report.add_result(report)
@@ -103,16 +103,16 @@ class SubmissionFormContainer(QWidget):
return return
except AttributeError: except AttributeError:
self.prsr = SheetParser(filepath=fname) self.prsr = SheetParser(filepath=fname)
logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}") # logger.debug(f"Submission dictionary:\n{pformat(self.prsr.sub)}")
self.pyd = self.prsr.to_pydantic() self.pyd = self.prsr.to_pydantic()
logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n") # logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
self.form = self.pyd.to_form(parent=self) self.form = self.pyd.to_form(parent=self)
self.layout().addWidget(self.form) self.layout().addWidget(self.form)
# if self.prsr.sample_result != None: # if self.prsr.sample_result != None:
# report.add_result(msg=self.prsr.sample_result, status="Warning") # report.add_result(msg=self.prsr.sample_result, status="Warning")
self.report.add_result(report) self.report.add_result(report)
logger.debug(f"Outgoing report: {self.report.results}") # logger.debug(f"Outgoing report: {self.report.results}")
logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}") # logger.debug(f"All attributes of submission container:\n{pformat(self.__dict__)}")
def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, name:str|None=None): def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None, expiry:date|None=None, name:str|None=None):
""" """
@@ -135,7 +135,7 @@ class SubmissionFormContainer(QWidget):
if dlg.exec(): if dlg.exec():
# extract form info # extract form info
info = dlg.parse_form() info = dlg.parse_form()
logger.debug(f"Reagent info: {info}") # logger.debug(f"Reagent info: {info}")
# create reagent object # create reagent object
reagent = PydReagent(ctx=self.app.ctx, **info, missing=False) reagent = PydReagent(ctx=self.app.ctx, **info, missing=False)
# send reagent to db # send reagent to db
@@ -216,10 +216,10 @@ class SubmissionFormWidget(QWidget):
caller = inspect.stack()[1].function.__repr__().replace("'", "") caller = inspect.stack()[1].function.__repr__().replace("'", "")
# self.reagents = [] # self.reagents = []
# logger.debug(f"Self.reagents: {self.reagents}") # logger.debug(f"Self.reagents: {self.reagents}")
logger.debug(f"\n\n{pformat(caller)}\n\n") # logger.debug(f"\n\n{pformat(caller)}\n\n")
# logger.debug(f"SubmissionType: {self.submission_type}") # logger.debug(f"SubmissionType: {self.submission_type}")
report = Report() report = Report()
logger.debug(f"Extraction kit: {extraction_kit}") # logger.debug(f"Extraction kit: {extraction_kit}")
# Remove previous reagent widgets # Remove previous reagent widgets
try: try:
old_reagents = self.find_widgets() old_reagents = self.find_widgets()
@@ -249,7 +249,7 @@ class SubmissionFormWidget(QWidget):
add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.pyd.extraction_kit) add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.pyd.extraction_kit)
self.layout.addWidget(add_widget) self.layout.addWidget(add_widget)
report.add_result(integrity_report) report.add_result(integrity_report)
logger.debug(f"Outgoing report: {report.results}") # logger.debug(f"Outgoing report: {report.results}")
if hasattr(self.pyd, "csv"): if hasattr(self.pyd, "csv"):
export_csv_btn = QPushButton("Export CSV") export_csv_btn = QPushButton("Export CSV")
export_csv_btn.setObjectName("export_csv_btn") export_csv_btn.setObjectName("export_csv_btn")
@@ -263,46 +263,6 @@ class SubmissionFormWidget(QWidget):
self.app.report.add_result(report) self.app.report.add_result(report)
self.app.result_reporter() self.app.result_reporter()
# def kit_integrity_completion_function(self, extraction_kit:str|None=None):
# """
# Compare kit contents to parsed contents and creates widgets.
#
# Args:
# obj (QMainWindow): The original app window
#
# Returns:
# Tuple[QMainWindow, dict]: Collection of new main app window and result dict
# """
# report = Report()
# missing_reagents = []
# # logger.debug(inspect.currentframe().f_back.f_code.co_name)
# # find the widget that contains kit info
# if extraction_kit is None:
# kit_widget = self.find_widgets(object_name="extraction_kit")[0].input
# logger.debug(f"Kit selector: {kit_widget}")
# # get current kit being used
# self.ext_kit = kit_widget.currentText()
# else:
# self.ext_kit = extraction_kit
# for reagent in self.reagents:
# logger.debug(f"Creating widget for {reagent}")
# add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.ext_kit)
# # self.form.layout().addWidget(add_widget)
# self.layout.addWidget(add_widget)
# if reagent.missing:
# missing_reagents.append(reagent)
# logger.debug(f"Checking integrity of {self.ext_kit}")
# # TODO: put check_kit_integrity here instead of what's here?
# # see if there are any missing reagents
# if len(missing_reagents) > 0:
# result = Result(msg=f"""The submission you are importing is missing some reagents expected by the kit.\n\n
# It looks like you are missing: {[item.type.upper() for item in missing_reagents]}\n\n
# Alternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.
# \n\nPlease make sure you check the lots carefully!""".replace(" ", ""), status="Warning")
# report.add_result(result)
# self.report.add_result(report)
# logger.debug(f"Outgoing report: {self.report.results}")
def clear_form(self): def clear_form(self):
""" """
Removes all form widgets Removes all form widgets
@@ -335,24 +295,23 @@ class SubmissionFormWidget(QWidget):
Returns: Returns:
Tuple[QMainWindow, dict]: Collection of new main app window and result dict Tuple[QMainWindow, dict]: Collection of new main app window and result dict
""" """
logger.debug(f"\n\nBeginning Submission\n\n") logger.info(f"\n\nBeginning Submission\n\n")
report = Report() report = Report()
# self.pyd: PydSubmission = self.parse_form()
result = self.parse_form() result = self.parse_form()
report.add_result(result) report.add_result(result)
logger.debug(f"Submission: {pformat(self.pyd)}") # logger.debug(f"Submission: {pformat(self.pyd)}")
logger.debug("Checking kit integrity...") # logger.debug("Checking kit integrity...")
_, result = self.pyd.check_kit_integrity() _, result = self.pyd.check_kit_integrity()
report.add_result(result) report.add_result(result)
if len(result.results) > 0: if len(result.results) > 0:
self.app.report.add_result(report) self.app.report.add_result(report)
self.app.result_reporter() self.app.result_reporter()
return return
logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n") # logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n")
base_submission, result = self.pyd.to_sql() base_submission, result = self.pyd.to_sql()
logger.debug(f"SQL object: {pformat(base_submission.__dict__)}") # logger.debug(f"SQL object: {pformat(base_submission.__dict__)}")
# logger.debug(f"Base submission: {base_submission.to_dict()}") # logger.debug(f"Base submission: {base_submission.to_dict()}")
# check output message for issues # NOTE: check output message for issues
match result.code: match result.code:
# code 0: everything is fine. # code 0: everything is fine.
case 0: case 0:
@@ -379,11 +338,10 @@ class SubmissionFormWidget(QWidget):
# logger.debug(f"Updating: {reagent} with {reagent.lot}") # logger.debug(f"Updating: {reagent} with {reagent.lot}")
reagent.update_last_used(kit=base_submission.extraction_kit) reagent.update_last_used(kit=base_submission.extraction_kit)
# logger.debug(f"Final reagents: {pformat(base_submission.reagents)}") # logger.debug(f"Final reagents: {pformat(base_submission.reagents)}")
# sys.exit("Programmed stop submission_widget.py, line 381")
base_submission.save() base_submission.save()
# update summary sheet # NOTE: update summary sheet
self.app.table_widget.sub_wid.setData() self.app.table_widget.sub_wid.setData()
# reset form # NOTE: reset form
self.setParent(None) self.setParent(None)
# logger.debug(f"All attributes of obj: {pformat(self.__dict__)}") # logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
self.app.report.add_result(report) self.app.report.add_result(report)
@@ -396,16 +354,14 @@ class SubmissionFormWidget(QWidget):
Args: Args:
fname (Path | None, optional): Input filename. Defaults to None. fname (Path | None, optional): Input filename. Defaults to None.
""" """
# self.parse_form()
if isinstance(fname, bool) or fname == None: if isinstance(fname, bool) or fname == None:
fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv") fname = select_save_file(obj=self, default_name=self.pyd.construct_filename(), extension="csv")
try: try:
# logger.debug(f'')
# self.pyd.csv.to_csv(fname.__str__(), index=False) # self.pyd.csv.to_csv(fname.__str__(), index=False)
workbook_2_csv(worksheet=self.pyd.csv, filename=fname) workbook_2_csv(worksheet=self.pyd.csv, filename=fname)
except PermissionError: except PermissionError:
logger.debug(f"Could not get permissions to {fname}. Possibly the request was cancelled.") logger.warning(f"Could not get permissions to {fname}. Possibly the request was cancelled.")
except AttributeError: except AttributeError:
logger.error(f"No csv file found in the submission at this point.") logger.error(f"No csv file found in the submission at this point.")
@@ -417,7 +373,7 @@ class SubmissionFormWidget(QWidget):
Report: Report on status of parse. Report: Report on status of parse.
""" """
report = Report() report = Report()
logger.debug(f"Hello from form parser!") logger.info(f"Hello from form parser!")
info = {} info = {}
reagents = [] reagents = []
for widget in self.findChildren(QWidget): for widget in self.findChildren(QWidget):
@@ -431,21 +387,19 @@ class SubmissionFormWidget(QWidget):
field, value = widget.parse_form() field, value = widget.parse_form()
if field is not None: if field is not None:
info[field] = value info[field] = value
logger.debug(f"Info: {pformat(info)}") # logger.debug(f"Info: {pformat(info)}")
logger.debug(f"Reagents going into pyd: {pformat(reagents)}") # logger.debug(f"Reagents going into pyd: {pformat(reagents)}")
self.pyd.reagents = reagents self.pyd.reagents = reagents
# logger.debug(f"Attrs not in info: {[k for k, v in self.__dict__.items() if k not in info.keys()]}") # logger.debug(f"Attrs not in info: {[k for k, v in self.__dict__.items() if k not in info.keys()]}")
for item in self.recover: for item in self.recover:
logger.debug(f"Attempting to recover: {item}") # logger.debug(f"Attempting to recover: {item}")
if hasattr(self, item): if hasattr(self, item):
value = getattr(self, item) value = getattr(self, item)
logger.debug(f"Setting {item}") # logger.debug(f"Setting {item}")
info[item] = value info[item] = value
# submission = PydSubmission(reagents=reagents, **info)
for k,v in info.items(): for k,v in info.items():
self.pyd.set_attribute(key=k, value=v) self.pyd.set_attribute(key=k, value=v)
# return submission # NOTE: return submission
report.add_result(report) report.add_result(report)
return report return report
@@ -510,7 +464,7 @@ class SubmissionFormWidget(QWidget):
except (TypeError, KeyError): except (TypeError, KeyError):
pass pass
obj = parent.parent().parent() obj = parent.parent().parent()
logger.debug(f"Creating widget for: {key}") # logger.debug(f"Creating widget for: {key}")
match key: match key:
case 'submitting_lab': case 'submitting_lab':
add_widget = QComboBox() add_widget = QComboBox()
@@ -531,12 +485,12 @@ class SubmissionFormWidget(QWidget):
# create combobox to hold looked up kits # create combobox to hold looked up kits
add_widget = QComboBox() add_widget = QComboBox()
# lookup existing kits by 'submission_type' decided on by sheetparser # lookup existing kits by 'submission_type' decided on by sheetparser
logger.debug(f"Looking up kits used for {submission_type}") # logger.debug(f"Looking up kits used for {submission_type}")
uses = [item.name for item in KitType.query(used_for=submission_type)] uses = [item.name for item in KitType.query(used_for=submission_type)]
obj.uses = uses obj.uses = uses
logger.debug(f"Kits received for {submission_type}: {uses}") # logger.debug(f"Kits received for {submission_type}: {uses}")
if check_not_nan(value): if check_not_nan(value):
logger.debug(f"The extraction kit in parser was: {value}") # logger.debug(f"The extraction kit in parser was: {value}")
uses.insert(0, uses.pop(uses.index(value))) uses.insert(0, uses.pop(uses.index(value)))
obj.ext_kit = value obj.ext_kit = value
else: else:
@@ -565,7 +519,7 @@ class SubmissionFormWidget(QWidget):
case _: case _:
# anything else gets added in as a line edit # anything else gets added in as a line edit
add_widget = QLineEdit() add_widget = QLineEdit()
logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}") # logger.debug(f"Setting widget text to {str(value).replace('_', ' ')}")
add_widget.setText(str(value).replace("_", " ")) add_widget.setText(str(value).replace("_", " "))
if add_widget != None: if add_widget != None:
add_widget.setObjectName(key) add_widget.setObjectName(key)
@@ -639,14 +593,6 @@ class SubmissionFormWidget(QWidget):
# If changed set self.missing to True and update self.label # If changed set self.missing to True and update self.label
self.lot.currentTextChanged.connect(self.updated) self.lot.currentTextChanged.connect(self.updated)
# def check_uncheck(self):
# if self.check_box.isChecked():
# self.lot.setCurrentIndex(0)
# self.lot.setEnabled(True)
# else:
# self.lot.setCurrentText("Not Applicable")
# self.lot.setEnabled(False)
def parse_form(self) -> Tuple[PydReagent, dict]: def parse_form(self) -> Tuple[PydReagent, dict]:
""" """
Pulls form info into PydReagent Pulls form info into PydReagent
@@ -657,17 +603,17 @@ class SubmissionFormWidget(QWidget):
# if not self.check_box.isChecked(): # if not self.check_box.isChecked():
# return None, None # return None, None
lot = self.lot.currentText() lot = self.lot.currentText()
logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}") # logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type) wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type)
# if reagent doesn't exist in database, offer to add it (uses App.add_reagent) # NOTE: if reagent doesn't exist in database, offer to add it (uses App.add_reagent)
if wanted_reagent == None: if wanted_reagent == None:
dlg = QuestionAsker(title=f"Add {lot}?", message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?") dlg = QuestionAsker(title=f"Add {lot}?", message=f"Couldn't find reagent type {self.reagent.type}: {lot} in the database.\n\nWould you like to add it?")
if dlg.exec(): if dlg.exec():
wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name) wanted_reagent = self.parent().parent().add_reagent(reagent_lot=lot, reagent_type=self.reagent.type, expiry=self.reagent.expiry, name=self.reagent.name)
return wanted_reagent, None return wanted_reagent, None
else: else:
# In this case we will have an empty reagent and the submission will fail kit integrity check # NOTE: In this case we will have an empty reagent and the submission will fail kit integrity check
logger.debug("Will not add reagent.") # logger.debug("Will not add reagent.")
return None, Result(msg="Failed integrity check", status="Critical") return None, Result(msg="Failed integrity check", status="Critical")
else: else:
# Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name # Since this now gets passed in directly from the parser -> pyd -> form and the parser gets the name
@@ -712,8 +658,8 @@ class SubmissionFormWidget(QWidget):
def __init__(self, reagent, extraction_kit:str) -> None: def __init__(self, reagent, extraction_kit:str) -> None:
super().__init__() super().__init__()
self.setEditable(True) self.setEditable(True)
logger.debug(f"Attempting lookup of reagents by type: {reagent.type}") # logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
# below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work. # NOTE: below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
lookup = Reagent.query(reagent_type=reagent.type) lookup = Reagent.query(reagent_type=reagent.type)
relevant_reagents = [str(item.lot) for item in lookup] relevant_reagents = [str(item.lot) for item in lookup]
output_reg = [] output_reg = []
@@ -725,8 +671,8 @@ class SubmissionFormWidget(QWidget):
elif isinstance(rel_reagent, str): elif isinstance(rel_reagent, str):
output_reg.append(rel_reagent) output_reg.append(rel_reagent)
relevant_reagents = output_reg relevant_reagents = output_reg
# if reagent in sheet is not found insert it into the front of relevant reagents so it shows # NOTE: if reagent in sheet is not found insert it into the front of relevant reagents so it shows
logger.debug(f"Relevant reagents for {reagent.lot}: {relevant_reagents}") # logger.debug(f"Relevant reagents for {reagent.lot}: {relevant_reagents}")
if str(reagent.lot) not in relevant_reagents: if str(reagent.lot) not in relevant_reagents:
if check_not_nan(reagent.lot): if check_not_nan(reagent.lot):
relevant_reagents.insert(0, str(reagent.lot)) relevant_reagents.insert(0, str(reagent.lot))

2
src/submissions/templates/basicsubmission_details.html
View File

@@ -27,12 +27,12 @@
left: 50%; left: 50%;
margin-left: -60px; margin-left: -60px;
} }
/* Show the tooltip text when you mouse over the tooltip container */ /* Show the tooltip text when you mouse over the tooltip container */
.tooltip:hover .tooltiptext { .tooltip:hover .tooltiptext {
visibility: visible; visibility: visible;
font-size: large; font-size: large;
} }
</style> </style>
<title>Submission Details for {{ sub['Plate Number'] }}</title> <title>Submission Details for {{ sub['Plate Number'] }}</title>
<script src="qrc:///qtwebchannel/qwebchannel.js"></script> <script src="qrc:///qtwebchannel/qwebchannel.js"></script>

202
src/submissions/tools.py
View File

@@ -40,8 +40,9 @@ main_aux_dir = Path.home().joinpath(f"{os_config_dir}/submissions")
CONFIGDIR = main_aux_dir.joinpath("config") CONFIGDIR = main_aux_dir.joinpath("config")
LOGDIR = main_aux_dir.joinpath("logs") LOGDIR = main_aux_dir.joinpath("logs")
row_map = {1:"A", 2:"B", 3:"C", 4:"D", 5:"E", 6:"F", 7:"G", 8:"H"} row_map = {1: "A", 2: "B", 3: "C", 4: "D", 5: "E", 6: "F", 7: "G", 8: "H"}
row_keys = {v:k for k,v in row_map.items()} row_keys = {v: k for k, v in row_map.items()}
def check_not_nan(cell_contents) -> bool: def check_not_nan(cell_contents) -> bool:
""" """
@@ -52,7 +53,7 @@ def check_not_nan(cell_contents) -> bool:
Returns: Returns:
bool: True if cell has value, else, false. bool: True if cell has value, else, false.
""" """
# check for nan as a string first # check for nan as a string first
exclude = ['unnamed:', 'blank', 'void'] exclude = ['unnamed:', 'blank', 'void']
try: try:
@@ -88,7 +89,8 @@ def check_not_nan(cell_contents) -> bool:
logger.debug(f"Check encountered unknown error: {type(e).__name__} - {e}") logger.debug(f"Check encountered unknown error: {type(e).__name__} - {e}")
return False return False
def convert_nans_to_nones(input_str) -> str|None:
def convert_nans_to_nones(input_str) -> str | None:
""" """
Get rid of various "nan", "NAN", "NaN", etc/ Get rid of various "nan", "NAN", "NaN", etc/
@@ -97,19 +99,21 @@ def convert_nans_to_nones(input_str) -> str|None:
Returns: Returns:
str: _description_ str: _description_
""" """
# logger.debug(f"Input value of: {input_str}") # logger.debug(f"Input value of: {input_str}")
if check_not_nan(input_str): if check_not_nan(input_str):
return input_str return input_str
return None return None
def is_missing(value:Any) -> Tuple[Any, bool]:
def is_missing(value: Any) -> Tuple[Any, bool]:
if check_not_nan(value): if check_not_nan(value):
return value, False return value, False
else: else:
return convert_nans_to_nones(value), True return convert_nans_to_nones(value), True
def check_regex_match(pattern:str, check:str) -> bool:
def check_regex_match(pattern: str, check: str) -> bool:
""" """
Determines if a pattern matches a str Determines if a pattern matches a str
@@ -119,13 +123,14 @@ def check_regex_match(pattern:str, check:str) -> bool:
Returns: Returns:
bool: match found? bool: match found?
""" """
try: try:
return bool(re.match(fr"{pattern}", check)) return bool(re.match(fr"{pattern}", check))
except TypeError: except TypeError:
return False return False
def get_first_blank_df_row(df:pd.DataFrame) -> int:
def get_first_blank_df_row(df: pd.DataFrame) -> int:
""" """
For some reason I need a whole function for this. For some reason I need a whole function for this.
@@ -134,9 +139,10 @@ def get_first_blank_df_row(df:pd.DataFrame) -> int:
Returns: Returns:
int: Index of the row after the last used row. int: Index of the row after the last used row.
""" """
return df.shape[0] + 1 return df.shape[0] + 1
# Settings # Settings
class Settings(BaseSettings, extra="allow"): class Settings(BaseSettings, extra="allow"):
@@ -146,16 +152,16 @@ class Settings(BaseSettings, extra="allow"):
Raises: Raises:
FileNotFoundError: Error if database not found. FileNotFoundError: Error if database not found.
""" """
directory_path: Path directory_path: Path
database_path: Path|str|None = None database_path: Path | str | None = None
backup_path: Path|str|None = None backup_path: Path | str | None = None
# super_users: list|None = None # super_users: list|None = None
# power_users: list|None = None # power_users: list|None = None
# rerun_regex: str # rerun_regex: str
submission_types: dict|None = None submission_types: dict | None = None
database_session: Session|None = None database_session: Session | None = None
package: Any|None = None package: Any | None = None
model_config = SettingsConfigDict(env_file_encoding='utf-8') model_config = SettingsConfigDict(env_file_encoding='utf-8')
@@ -178,10 +184,10 @@ class Settings(BaseSettings, extra="allow"):
if isinstance(value, str): if isinstance(value, str):
value = Path(value) value = Path(value)
if not value.exists(): if not value.exists():
value = Path().home() value = Path().home()
# metadata.directory_path = value # metadata.directory_path = value
return value return value
@field_validator('database_path', mode="before") @field_validator('database_path', mode="before")
@classmethod @classmethod
def ensure_database_exists(cls, value, values): def ensure_database_exists(cls, value, values):
@@ -196,7 +202,7 @@ class Settings(BaseSettings, extra="allow"):
return value return value
else: else:
raise FileNotFoundError(f"Couldn't find database at {value}") raise FileNotFoundError(f"Couldn't find database at {value}")
@field_validator('database_session', mode="before") @field_validator('database_session', mode="before")
@classmethod @classmethod
def create_database_session(cls, value, values): def create_database_session(cls, value, values):
@@ -223,7 +229,7 @@ class Settings(BaseSettings, extra="allow"):
else: else:
raise FileNotFoundError("No database file found. Exiting program.") raise FileNotFoundError("No database file found. Exiting program.")
logger.debug(f"Using {database_path} for database file.") logger.debug(f"Using {database_path} for database file.")
engine = create_engine(f"sqlite:///{database_path}")#, echo=True, future=True) engine = create_engine(f"sqlite:///{database_path}") #, echo=True, future=True)
session = Session(engine) session = Session(engine)
# metadata.session = session # metadata.session = session
return session return session
@@ -240,19 +246,20 @@ class Settings(BaseSettings, extra="allow"):
super().__init__(*args, **kwargs) super().__init__(*args, **kwargs)
self.set_from_db(db_path=kwargs['database_path']) self.set_from_db(db_path=kwargs['database_path'])
def set_from_db(self, db_path:Path): def set_from_db(self, db_path: Path):
if 'pytest' in sys.modules: if 'pytest' in sys.modules:
config_items = dict(power_users=['lwark', 'styson', 'ruwang']) config_items = dict(power_users=['lwark', 'styson', 'ruwang'])
else: else:
session = Session(create_engine(f"sqlite:///{db_path}")) session = Session(create_engine(f"sqlite:///{db_path}"))
config_items = session.execute(text("SELECT * FROM _configitem")).all() config_items = session.execute(text("SELECT * FROM _configitem")).all()
session.close() session.close()
config_items = {item[1]:json.loads(item[2]) for item in config_items} config_items = {item[1]: json.loads(item[2]) for item in config_items}
for k, v in config_items.items(): for k, v in config_items.items():
if not hasattr(self, k): if not hasattr(self, k):
self.__setattr__(k, v) self.__setattr__(k, v)
def get_config(settings_path: Path|str|None=None) -> Settings:
def get_config(settings_path: Path | str | None = None) -> Settings:
""" """
Get configuration settings from path or default if blank. Get configuration settings from path or default if blank.
@@ -262,36 +269,38 @@ def get_config(settings_path: Path|str|None=None) -> Settings:
Returns: Returns:
Settings: Pydantic settings object Settings: Pydantic settings object
""" """
logger.debug(f"Creating settings...") # logger.debug(f"Creating settings...")
if isinstance(settings_path, str): if isinstance(settings_path, str):
settings_path = Path(settings_path) settings_path = Path(settings_path)
# custom pyyaml constructor to join fields # custom pyyaml constructor to join fields
def join(loader, node): def join(loader, node):
seq = loader.construct_sequence(node) seq = loader.construct_sequence(node)
return ''.join([str(i) for i in seq]) return ''.join([str(i) for i in seq])
# register the tag handler # register the tag handler
yaml.add_constructor('!join', join) yaml.add_constructor('!join', join)
logger.debug(f"Making directory: {CONFIGDIR.__str__()}")
# make directories # make directories
try: try:
CONFIGDIR.mkdir(parents=True) CONFIGDIR.mkdir(parents=True)
except FileExistsError: except FileExistsError:
pass logger.warning(f"Config directory {CONFIGDIR} already exists.")
logger.debug(f"Making directory: {LOGDIR.__str__()}")
try: try:
LOGDIR.mkdir(parents=True) LOGDIR.mkdir(parents=True)
except FileExistsError: except FileExistsError:
pass logger.warning(f"Logging directory {LOGDIR} already exists.")
# if user hasn't defined config path in cli args # NOTE: if user hasn't defined config path in cli args
if settings_path == None: if settings_path == None:
# Check user .config/submissions directory # NOTE: Check user .config/submissions directory
if CONFIGDIR.joinpath("config.yml").exists(): if CONFIGDIR.joinpath("config.yml").exists():
settings_path = CONFIGDIR.joinpath("config.yml") settings_path = CONFIGDIR.joinpath("config.yml")
# Check user .submissions directory # NOTE: Check user .submissions directory
elif Path.home().joinpath(".submissions", "config.yml").exists(): elif Path.home().joinpath(".submissions", "config.yml").exists():
settings_path = Path.home().joinpath(".submissions", "config.yml") settings_path = Path.home().joinpath(".submissions", "config.yml")
# finally look in the local config # NOTE: finally look in the local config
else: else:
if check_if_app(): if check_if_app():
settings_path = Path(sys._MEIPASS).joinpath("files", "config.yml") settings_path = Path(sys._MEIPASS).joinpath("files", "config.yml")
@@ -299,14 +308,14 @@ def get_config(settings_path: Path|str|None=None) -> Settings:
settings_path = package_dir.joinpath('config.yml') settings_path = package_dir.joinpath('config.yml')
with open(settings_path, "r") as dset: with open(settings_path, "r") as dset:
default_settings = yaml.load(dset, Loader=yaml.Loader) default_settings = yaml.load(dset, Loader=yaml.Loader)
# Tell program we need to copy the config.yml to the user directory # NOTE: Tell program we need to copy the config.yml to the user directory
# copy settings to config directory # NOTE: copy settings to config directory
return Settings(**copy_settings(settings_path=CONFIGDIR.joinpath("config.yml"), settings=default_settings)) return Settings(**copy_settings(settings_path=CONFIGDIR.joinpath("config.yml"), settings=default_settings))
else: else:
# check if user defined path is directory # NOTE: check if user defined path is directory
if settings_path.is_dir(): if settings_path.is_dir():
settings_path = settings_path.joinpath("config.yml") settings_path = settings_path.joinpath("config.yml")
# check if user defined path is file # NOTE: check if user defined path is file
elif settings_path.is_file(): elif settings_path.is_file():
settings_path = settings_path settings_path = settings_path
else: else:
@@ -314,11 +323,12 @@ def get_config(settings_path: Path|str|None=None) -> Settings:
with open(settings_path, "r") as dset: with open(settings_path, "r") as dset:
default_settings = yaml.load(dset, Loader=yaml.Loader) default_settings = yaml.load(dset, Loader=yaml.Loader)
return Settings(**copy_settings(settings_path=settings_path, settings=default_settings)) return Settings(**copy_settings(settings_path=settings_path, settings=default_settings))
logger.debug(f"Using {settings_path} for config file.") # logger.debug(f"Using {settings_path} for config file.")
with open(settings_path, "r") as stream: with open(settings_path, "r") as stream:
settings = yaml.load(stream, Loader=yaml.Loader) settings = yaml.load(stream, Loader=yaml.Loader)
return Settings(**settings) return Settings(**settings)
# Logging formatters # Logging formatters
class GroupWriteRotatingFileHandler(handlers.RotatingFileHandler): class GroupWriteRotatingFileHandler(handlers.RotatingFileHandler):
@@ -334,13 +344,13 @@ class GroupWriteRotatingFileHandler(handlers.RotatingFileHandler):
os.chmod(self.baseFilename, currMode | stat.S_IWGRP) os.chmod(self.baseFilename, currMode | stat.S_IWGRP)
def _open(self): def _open(self):
prevumask=os.umask(0o002) prevumask = os.umask(0o002)
rtv=handlers.RotatingFileHandler._open(self) rtv = handlers.RotatingFileHandler._open(self)
os.umask(prevumask) os.umask(prevumask)
return rtv return rtv
class CustomFormatter(logging.Formatter):
class CustomFormatter(logging.Formatter):
class bcolors: class bcolors:
HEADER = '\033[95m' HEADER = '\033[95m'
OKBLUE = '\033[94m' OKBLUE = '\033[94m'
@@ -367,6 +377,7 @@ class CustomFormatter(logging.Formatter):
formatter = logging.Formatter(log_fmt) formatter = logging.Formatter(log_fmt)
return formatter.format(record) return formatter.format(record)
class StreamToLogger(object): class StreamToLogger(object):
""" """
Fake file-like stream object that redirects writes to a logger instance. Fake file-like stream object that redirects writes to a logger instance.
@@ -381,31 +392,33 @@ class StreamToLogger(object):
for line in buf.rstrip().splitlines(): for line in buf.rstrip().splitlines():
self.logger.log(self.log_level, line.rstrip()) self.logger.log(self.log_level, line.rstrip())
def setup_logger(verbosity:int=3):
def setup_logger(verbosity: int = 3):
""" """
Set logger levels using settings. Set logger levels using settings.
Args: Args:
verbosit (int, optional): Level of verbosity desired 3 is highest. Defaults to 3. verbosity (int, optional): Level of verbosity desired 3 is highest. Defaults to 3.
Returns: Returns:
logger: logger object logger: logger object
""" """
logger = logging.getLogger("submissions") logger = logging.getLogger("submissions")
logger.setLevel(logging.DEBUG) logger.setLevel(logging.DEBUG)
# create file handler which logs even debug messages # NOTE: create file handler which logs even debug messages
try: try:
Path(LOGDIR).mkdir(parents=True) Path(LOGDIR).mkdir(parents=True)
except FileExistsError: except FileExistsError:
pass logger.warning(f"Logging directory {LOGDIR} already exists.")
# NOTE: logging to file turned off due to repeated permission errors
# fh = GroupWriteRotatingFileHandler(LOGDIR.joinpath('submissions.log'), mode='a', maxBytes=100000, backupCount=3, encoding=None, delay=False) # fh = GroupWriteRotatingFileHandler(LOGDIR.joinpath('submissions.log'), mode='a', maxBytes=100000, backupCount=3, encoding=None, delay=False)
# file logging will always be debug # file logging will always be debug
# fh.setLevel(logging.DEBUG) # fh.setLevel(logging.DEBUG)
# fh.name = "File" # fh.name = "File"
# create console handler with a higher log level # NOTE: create console handler with a higher log level
# create custom logger with STERR -> log # NOTE: create custom logger with STERR -> log
ch = logging.StreamHandler(stream=sys.stdout) ch = logging.StreamHandler(stream=sys.stdout)
# set looging level based on verbosity # NOTE: set looging level based on verbosity
match verbosity: match verbosity:
case 3: case 3:
ch.setLevel(logging.DEBUG) ch.setLevel(logging.DEBUG)
@@ -414,24 +427,26 @@ def setup_logger(verbosity:int=3):
case 1: case 1:
ch.setLevel(logging.WARNING) ch.setLevel(logging.WARNING)
ch.name = "Stream" ch.name = "Stream"
# create formatter and add it to the handlers # NOTE: create formatter and add it to the handlers
# formatter = logging.Formatter('%(asctime)s - %(levelname)s - {%(pathname)s:%(lineno)d} - %(message)s')
formatter = CustomFormatter() formatter = CustomFormatter()
# fh.setFormatter(formatter) # fh.setFormatter(formatter)
ch.setFormatter(formatter) ch.setFormatter(formatter)
# add the handlers to the logger # NOTE: add the handlers to the logger
# logger.addHandler(fh) # logger.addHandler(fh)
logger.addHandler(ch) logger.addHandler(ch)
# Output exception and traceback to logger
# NOTE: Output exception and traceback to logger
def handle_exception(exc_type, exc_value, exc_traceback): def handle_exception(exc_type, exc_value, exc_traceback):
if issubclass(exc_type, KeyboardInterrupt): if issubclass(exc_type, KeyboardInterrupt):
sys.__excepthook__(exc_type, exc_value, exc_traceback) sys.__excepthook__(exc_type, exc_value, exc_traceback)
return return
logger.critical("Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback)) logger.critical("Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback))
sys.excepthook = handle_exception sys.excepthook = handle_exception
return logger return logger
def copy_settings(settings_path:Path, settings:dict) -> dict:
def copy_settings(settings_path: Path, settings: dict) -> dict:
""" """
copies relevant settings dictionary from the default config.yml to a new directory copies relevant settings dictionary from the default config.yml to a new directory
@@ -441,8 +456,8 @@ def copy_settings(settings_path:Path, settings:dict) -> dict:
Returns: Returns:
dict: output dictionary for use in first run dict: output dictionary for use in first run
""" """
# if the current user is not a superuser remove the superusers entry # NOTE: if the current user is not a superuser remove the superusers entry
if not getpass.getuser() in settings['super_users']: if not getpass.getuser() in settings['super_users']:
del settings['super_users'] del settings['super_users']
if not getpass.getuser() in settings['power_users']: if not getpass.getuser() in settings['power_users']:
@@ -452,40 +467,40 @@ def copy_settings(settings_path:Path, settings:dict) -> dict:
yaml.dump(settings, f) yaml.dump(settings, f)
return settings return settings
def jinja_template_loading() -> Environment: def jinja_template_loading() -> Environment:
""" """
Returns jinja2 template environment. Returns jinja2 template environment.
Returns: Returns:
_type_: _description_ _type_: _description_
""" """
# determine if pyinstaller launcher is being used # NOTE: determine if pyinstaller launcher is being used
if check_if_app(): if check_if_app():
loader_path = Path(sys._MEIPASS).joinpath("files", "templates") loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
else: else:
loader_path = Path(__file__).parent.joinpath('templates').absolute()#.__str__() loader_path = Path(__file__).parent.joinpath('templates').absolute() #.__str__()
# jinja template loading # NOTE: jinja template loading
loader = FileSystemLoader(loader_path) loader = FileSystemLoader(loader_path)
env = Environment(loader=loader) env = Environment(loader=loader)
env.globals['STATIC_PREFIX'] = loader_path.joinpath("static", "css") env.globals['STATIC_PREFIX'] = loader_path.joinpath("static", "css")
return env return env
def check_if_app() -> bool: def check_if_app() -> bool:
""" """
Checks if the program is running from pyinstaller compiled Checks if the program is running from pyinstaller compiled
Args:
ctx (dict, optional): Settings passed down from gui. Defaults to None.
Returns: Returns:
bool: True if running from pyinstaller. Else False. bool: True if running from pyinstaller. Else False.
""" """
if getattr(sys, 'frozen', False): if getattr(sys, 'frozen', False):
return True return True
else: else:
return False return False
def convert_well_to_row_column(input_str:str) -> Tuple[int, int]:
def convert_well_to_row_column(input_str: str) -> Tuple[int, int]:
""" """
Converts typical alphanumeric (i.e. "A2") to row, column Converts typical alphanumeric (i.e. "A2") to row, column
@@ -494,22 +509,24 @@ def convert_well_to_row_column(input_str:str) -> Tuple[int, int]:
Returns: Returns:
Tuple[int, int]: row, column Tuple[int, int]: row, column
""" """
row_keys = {v:k for k,v in row_map.items()} row_keys = {v: k for k, v in row_map.items()}
try: try:
row = int(row_keys[input_str[0].upper()]) row = int(row_keys[input_str[0].upper()])
column = int(input_str[1:]) column = int(input_str[1:])
except IndexError: except IndexError:
return None, None return None, None
return row, column return row, column
def setup_lookup(func): def setup_lookup(func):
""" """
Checks to make sure all args are allowed Checks to make sure all args are allowed
Args: Args:
func (_type_): _description_ func (_type_): wrapped function
""" """
def wrapper(*args, **kwargs): def wrapper(*args, **kwargs):
sanitized_kwargs = {} sanitized_kwargs = {}
for k, v in locals()['kwargs'].items(): for k, v in locals()['kwargs'].items():
@@ -521,20 +538,23 @@ def setup_lookup(func):
elif v is not None: elif v is not None:
sanitized_kwargs[k] = v sanitized_kwargs[k] = v
return func(*args, **sanitized_kwargs) return func(*args, **sanitized_kwargs)
return wrapper return wrapper
class Result(BaseModel):
class Result(BaseModel):
owner: str = Field(default="", validate_default=True) owner: str = Field(default="", validate_default=True)
code: int = Field(default=0) code: int = Field(default=0)
msg: str msg: str
status: Literal["NoIcon", "Question", "Information", "Warning", "Critical"] = Field(default="NoIcon") status: Literal["NoIcon", "Question", "Information", "Warning", "Critical"] = Field(default="NoIcon")
@field_validator('status', mode='before') @field_validator('status', mode='before')
@classmethod @classmethod
def to_title(cls, value:str): def to_title(cls, value: str):
return value.title() if value.lower().replace(" ", "") == "noicon":
return "NoIcon"
else:
return value.title()
def __repr__(self) -> str: def __repr__(self) -> str:
return f"Result({self.owner})" return f"Result({self.owner})"
@@ -546,15 +566,15 @@ class Result(BaseModel):
def report(self): def report(self):
from frontend.widgets.misc import AlertPop from frontend.widgets.misc import AlertPop
return AlertPop(message=self.msg, status=self.status, owner=self.owner) return AlertPop(message=self.msg, status=self.status, owner=self.owner)
class Report(BaseModel):
class Report(BaseModel):
results: List[Result] = Field(default=[]) results: List[Result] = Field(default=[])
def __repr__(self): def __repr__(self):
return f"Report(result_count:{len(self.results)})" return f"Report(result_count:{len(self.results)})"
def add_result(self, result:Result|Report|None): def add_result(self, result: Result | Report | None):
match result: match result:
case Result(): case Result():
logger.debug(f"Adding {result} to results.") logger.debug(f"Adding {result} to results.")
@@ -568,36 +588,41 @@ class Report(BaseModel):
logger.debug(f"Adding {res} from to results.") logger.debug(f"Adding {res} from to results.")
self.results.append(res) self.results.append(res)
case _: case _:
pass logger.error(f"Unknown variable type: {type(result)}")
def rreplace(s, old, new):
return (s[::-1].replace(old[::-1],new[::-1], 1))[::-1]
def html_to_pdf(html, output_file:Path|str):
def rreplace(s, old, new):
return (s[::-1].replace(old[::-1], new[::-1], 1))[::-1]
def html_to_pdf(html, output_file: Path | str):
if isinstance(output_file, str): if isinstance(output_file, str):
output_file = Path(output_file) output_file = Path(output_file)
# document = QTextDocument()
document = QWebEngineView() document = QWebEngineView()
document.setHtml(html) document.setHtml(html)
printer = QPrinter(QPrinter.PrinterMode.HighResolution) printer = QPrinter(QPrinter.PrinterMode.HighResolution)
printer.setOutputFormat(QPrinter.OutputFormat.PdfFormat) printer.setOutputFormat(QPrinter.OutputFormat.PdfFormat)
printer.setOutputFileName(output_file.absolute().__str__()) printer.setOutputFileName(output_file.absolute().__str__())
printer.setPageSize(QPageSize(QPageSize.PageSizeId.A4)) printer.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
document.print(printer) document.print(printer)
def remove_key_from_list_of_dicts(input:list, key:str):
def remove_key_from_list_of_dicts(input: list, key: str):
for item in input: for item in input:
del item[key] del item[key]
return input return input
def workbook_2_csv(worksheet: Worksheet, filename:Path):
def workbook_2_csv(worksheet: Worksheet, filename: Path):
with open(filename, 'w', newline="") as f: with open(filename, 'w', newline="") as f:
c = csv.writer(f) c = csv.writer(f)
for r in worksheet.rows: for r in worksheet.rows:
c.writerow([cell.value for cell in r]) c.writerow([cell.value for cell in r])
ctx = get_config(None) ctx = get_config(None)
def is_power_user() -> bool: def is_power_user() -> bool:
try: try:
check = getpass.getuser() in ctx.power_users check = getpass.getuser() in ctx.power_users
@@ -605,13 +630,14 @@ def is_power_user() -> bool:
check = False check = False
return check return check
def check_authorization(func): def check_authorization(func):
""" """
Decorator to check if user is authorized to access function Decorator to check if user is authorized to access function
Args: Args:
func (_type_): Function to be used. func (_type_): Function to be used.
""" """
def wrapper(*args, **kwargs): def wrapper(*args, **kwargs):
logger.debug(f"Checking authorization") logger.debug(f"Checking authorization")
if is_power_user(): if is_power_user():