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Beginning prelim code cleanup.

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This commit is contained in:
lwark
2025-03-19 13:50:37 -05:00
parent 942c46e8b2
commit ea24a8ffd4
10 changed files with 529 additions and 110 deletions
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8
src/submissions/backend/db/models/__init__.py
View File

@@ -46,7 +46,7 @@ class BaseClass(Base):
"""
Abstract class to pass ctx values to all SQLAlchemy objects.
"""
__abstract__ = True #: NOTE: Will not be added to DB
__abstract__ = True #: NOTE: Will not be added to DB as a table
__table_args__ = {'extend_existing': True} #: Will only add new columns
@@ -54,6 +54,7 @@ class BaseClass(Base):
omni_removes = ["id", 'submissions', "omnigui_class_dict", "omnigui_instance_dict"]
omni_sort = ["name"]
omni_inheritable = []
searchables = []
@classproperty
def skip_on_edit(cls):
@@ -416,7 +417,10 @@ class BaseClass(Base):
else:
value = existing + [value]
else:
value = [value]
if isinstance(value, list):
value = value
else:
value = [value]
value = list(set(value))
logger.debug(f"Final value for {key}: {value}")
return super().__setattr__(key, value)

206
src/submissions/backend/db/models/kits.py
View File

@@ -858,7 +858,7 @@ class SubmissionType(BaseClass):
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(128), unique=True) #: name of submission type
info_map = Column(JSON) #: Where basic information is found in the excel workbook corresponding to this type.
info_map = Column(JSON) #: Where parsable information is found in the excel workbook corresponding to this type.
defaults = Column(JSON) #: Basic information about this submission type
instances = relationship("BasicSubmission", backref="submission_type") #: Concrete instances of this type.
template_file = Column(BLOB) #: Blank form for this type stored as binary.
@@ -866,6 +866,200 @@ class SubmissionType(BaseClass):
secondary=submissiontypes_processes) #: Relation to equipment processes used for this type.
sample_map = Column(JSON) #: Where sample information is found in the excel sheet corresponding to this type.
"""
Example info_map (Bacterial Culture)
NOTE: read locations will be appended to write locations.
{
"comment": {
"read": [
{
"column": 2,
"row": 34,
"sheet": "Sample List"
}
],
"write": []
},
"contact": {
"read": [
{
"column": 2,
"row": 4,
"sheet": "Sample List"
}
],
"write": []
},
"contact_phone": {
"read": [],
"write": [
{
"column": 2,
"row": 5,
"sheet": "Sample List"
}
]
},
"cost_centre": {
"read": [
{
"column": 2,
"row": 6,
"sheet": "Sample List"
}
],
"write": []
},
"custom": {},
"extraction_kit": {
"read": [
{
"column": 4,
"row": 5,
"sheet": "Sample List"
}
],
"write": []
},
"rsl_plate_num": {
"read": [
{
"column": 2,
"row": 13,
"sheet": "Sample List"
}
],
"write": []
},
"sample_count": {
"read": [
{
"column": 4,
"row": 4,
"sheet": "Sample List"
}
],
"write": []
},
"signed_by": {
"read": [],
"write": [
{
"column": 2,
"row": 15,
"sheet": "Sample List"
}
]
},
"submission_category": {
"read": [
{
"column": 4,
"row": 6,
"sheet": "Sample List"
}
],
"write": []
},
"submission_type": {
"read": [
{
"column": 4,
"row": 3,
"sheet": "Sample List"
}
],
"write": []
},
"submitted_date": {
"read": [
{
"column": 2,
"row": 3,
"sheet": "Sample List"
}
],
"write": []
},
"submitter_plate_num": {
"read": [
{
"column": 2,
"row": 2,
"sheet": "Sample List"
}
],
"write": []
},
"submitting_lab": {
"read": [
{
"column": 4,
"row": 2,
"sheet": "Sample List"
}
],
"write": []
},
"technician": {
"read": [
{
"column": 2,
"row": 14,
"sheet": "Sample List"
}
],
"write": []
}
}
"""
"""
Example defaults (for Bacterial Culture)
{
"abbreviation": "BC",
"details_ignore": [
"controls"
],
"form_ignore": [
"controls",
"cost_centre"
],
"regex": "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\\d{2}-?\\d{2}-?\\d{2}(?:(_|-)?\\d?([^_0123456789\\sA-QS-Z]|$)?R?\\d?)?)",
"sample_type": "Bacterial Culture Sample",
"turnaround_time": 3
}
"""
"""
Example sample_map (Bacterial Culture)
{
"lookup_table": {
"end_row": 132,
"merge_on_id": "submitter_id",
"sample_columns": {
"column": 6,
"concentration": 4,
"organism": 3,
"row": 5,
"submitter_id": 2
},
"sheet": "Sample List",
"start_row": 37
},
"plate_map": {
"end_column": 13,
"end_row": 14,
"sheet": "Plate Map",
"start_column": 2,
"start_row": 7
}
}
"""
submissiontype_kit_associations = relationship(
"SubmissionTypeKitTypeAssociation",
back_populates="submission_type",
@@ -1218,6 +1412,11 @@ class SubmissionType(BaseClass):
sample_map=self.sample_map
)
@classproperty
def info_map_json_edit_fields(cls):
dicto = dict()
return dicto
class SubmissionTypeKitTypeAssociation(BaseClass):
"""
@@ -1519,7 +1718,7 @@ class KitTypeReagentRoleAssociation(BaseClass):
case _:
pass
setattr(instance, k, v)
logger.info(f"Instance from query or create: {instance.__dict__}")
logger.info(f"Instance from query or create: {instance.__dict__}\nis new: {new}")
# sys.exit()
return instance, new
@@ -2196,6 +2395,7 @@ class Process(BaseClass):
id = Column(INTEGER, primary_key=True) #: Process id, primary key
name = Column(String(64), unique=True) #: Process name
# version = Column(String(32))
submission_types = relationship("SubmissionType", back_populates='processes',
secondary=submissiontypes_processes) #: relation to SubmissionType
equipment = relationship("Equipment", back_populates='processes',
@@ -2209,6 +2409,7 @@ class Process(BaseClass):
tip_roles = relationship("TipRole", back_populates='processes',
secondary=process_tiprole) #: relation to KitType
def __repr__(self) -> str:
"""
Returns:
@@ -2308,6 +2509,7 @@ class Process(BaseClass):
return OmniProcess(
instance_object=self,
name=self.name,
# version=self.version,
submission_types=[item.to_omni() for item in self.submission_types],
equipment_roles=[item.to_omni() for item in self.equipment_roles],
tip_roles=[item.to_omni() for item in self.tip_roles]

57
src/submissions/backend/db/models/submissions.py
View File

@@ -32,7 +32,6 @@ from jinja2 import Template
from PIL import Image
logger = logging.getLogger(f"submissions.{__name__}")
@@ -460,7 +459,7 @@ class BasicSubmission(BaseClass, LogMixin):
"""
rows = range(1, plate_rows + 1)
columns = range(1, plate_columns + 1)
logger.debug(f"sample list for plate map: {pformat(sample_list)}")
# logger.debug(f"sample list for plate map: {pformat(sample_list)}")
# NOTE: An overly complicated list comprehension create a list of sample locations
# NOTE: next will return a blank cell if no value found for row/column
output_samples = [next((item for item in sample_list if item['row'] == row and item['column'] == column),
@@ -1340,8 +1339,7 @@ class BasicSubmission(BaseClass, LogMixin):
for equip in equipment:
logger.debug(f"Parsed equipment: {equip}")
_, assoc = equip.to_sql(submission=self)
logger.debug(f"Got equipment association: {assoc.__dict__}")
logger.debug(f"Got equipment association: {assoc} for {equip}")
try:
assoc.save()
except AttributeError as e:
@@ -1488,6 +1486,55 @@ class BacterialCulture(BasicSubmission):
input_dict = super().custom_info_parser(input_dict=input_dict, xl=xl, custom_fields=custom_fields)
return input_dict
def custom_context_events(self) -> dict:
"""
Sets context events for main widget
Returns:
dict: Context menu items for this instance.
"""
events = super().custom_context_events()
events['Import Concentration'] = self.import_concentration
return events
@report_result
def import_concentration(self, obj) -> Report:
from frontend.widgets import select_open_file
from backend.excel.parser import ConcentrationParser
report = Report()
fname = select_open_file(obj=obj, file_extension="xlsx")
if not fname:
report.add_result(Result(msg="No file selected, cancelling.", status="Warning"))
return report
parser = ConcentrationParser(filepath=fname, submission=self)
conc_samples = [sample for sample in parser.samples]
for sample in self.samples:
logger.debug(f"Sample {sample.submitter_id}")
try:
# NOTE: Fix for ENs which have no rsl_number...
sample_dict = next(item for item in conc_samples if item['submitter_id'] == sample.submitter_id)
except StopIteration:
continue
logger.debug(f"Sample {sample.submitter_id} conc. = {sample_dict['concentration']}")
if sample_dict['concentration']:
sample.concentration = sample_dict['concentration']
else:
continue
sample.save()
# logger.debug(conc_samples)
return report
@classmethod
def parse_concentration(cls, xl: Workbook, rsl_plate_num: str) -> Generator[dict, None, None]:
lookup_table = cls.get_submission_type().sample_map['lookup_table']
logger.debug(lookup_table)
main_sheet = xl[lookup_table['sheet']]
for row in main_sheet.iter_rows(min_row=lookup_table['start_row'], max_row=lookup_table['end_row']):
idx = row[0].row
sample = dict(submitter_id=main_sheet.cell(row=idx, column=lookup_table['sample_columns']['submitter_id']).value)
sample['concentration'] = main_sheet.cell(row=idx, column=lookup_table['sample_columns']['concentration']).value
yield sample
class Wastewater(BasicSubmission):
"""
@@ -2598,7 +2645,7 @@ class BasicSample(BaseClass, LogMixin):
self.show_details(obj)
# Below are the custom sample types
# NOTE: Below are the custom sample types
class WastewaterSample(BasicSample):
"""

29
src/submissions/backend/excel/parser.py
View File

@@ -677,10 +677,7 @@ class PCRParser(object):
def pcr_info(self) -> dict:
"""
Parse general info rows for all types of PCR results
Args:
sheet_name (str): Name of sheet in excel workbook that holds info.
"""
"""
info_map = self.submission_obj.get_submission_type().sample_map['pcr_general_info']
sheet = self.xl[info_map['sheet']]
iter_rows = sheet.iter_rows(min_row=info_map['start_row'], max_row=info_map['end_row'])
@@ -695,3 +692,27 @@ class PCRParser(object):
pcr[key] = value
pcr['imported_by'] = getuser()
return pcr
class ConcentrationParser(object):
def __init__(self, filepath: Path | None = None, submission: BasicSubmission | None = None) -> None:
if filepath is None:
logger.error('No filepath given.')
self.xl = None
else:
try:
self.xl = load_workbook(filepath)
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 None
if submission is None:
self.submission_obj = BacterialCulture
rsl_plate_num = None
else:
self.submission_obj = submission
rsl_plate_num = self.submission_obj.rsl_plate_num
self.samples = self.submission_obj.parse_concentration(xl=self.xl, rsl_plate_num=rsl_plate_num)

222
src/submissions/backend/validators/omni_gui_objects.py
View File

@@ -10,7 +10,6 @@ logger = logging.getLogger(f"submissions.{__name__}")
class BaseOmni(BaseModel):
instance_object: Any | None = Field(default=None)
def __repr__(self):
@@ -23,67 +22,107 @@ class BaseOmni(BaseModel):
def aliases(cls):
return cls.class_object.aliases
# NOTE: Okay, this will not work for editing, since by definition not all attributes will line up.
# def check_all_attributes(self, attributes: dict) -> bool:
# """
# Checks this instance against a dictionary of attributes to determine if they are a match.
#
# Args:
# attributes (dict): A dictionary of attributes to be check for equivalence
#
# Returns:
# bool: If a single unequivocal value is found will be false, else true.
# """
# logger.debug(f"Incoming attributes: {attributes}")
# for key, value in attributes.items():
# logger.debug(f"Comparing value class: {value.__class__} to omni class")
# if isinstance(value, str):
# try:
# check = value.lower() == "none"
# except AttributeError:
# continue
# if check:
# value = None
# logger.debug(f"Attempting to grab attribute: {key}")
# try:
# self_value = getattr(self, key)
# class_attr = getattr(self.class_object, key)
# except AttributeError:
# continue
# try:
# logger.debug(f"Check if {self_value.__class__} is subclass of {BaseOmni}")
# check = issubclass(self_value.__class__, BaseOmni)
# except TypeError as e:
# logger.error(f"Couldn't check if {self_value.__class__} is subclass of {BaseOmni} due to {e}")
# check = False
# if check:
# logger.debug(f"Checking for subclass name.")
# self_value = self_value.name
# try:
# logger.debug(f"Check if {value.__class__} is subclass of {BaseOmni}")
# check = issubclass(value.__class__, BaseOmni)
# except TypeError as e:
# logger.error(f"Couldn't check if {value.__class__} is subclass of {BaseOmni} due to {e}")
# check = False
# if check:
# logger.debug(f"Checking for subclass name.")
# value = value.name
# logger.debug(f"Self value: {self_value}, class attr: {class_attr} of type: {type(class_attr)}")
# if isinstance(class_attr, property):
# filter = "property"
# else:
# filter = class_attr.property
# match filter:
# case ColumnProperty():
# match class_attr.type:
# case INTEGER():
# if value.lower() == "true":
# value = 1
# elif value.lower() == "false":
# value = 0
# else:
# value = int(value)
# case FLOAT():
# value = float(value)
# case "property":
# pass
# case _RelationshipDeclared():
# logger.debug(f"Checking relationship value: {self_value}")
# try:
# self_value = self_value.name
# except AttributeError:
# pass
# if class_attr.property.uselist:
# self_value = self_value.__str__()
# logger.debug(
# f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
# if self_value != value:
# output = False
# logger.debug(f"Value {key} is False, returning.")
# return output
# return True
def check_all_attributes(self, attributes: dict) -> bool:
"""
Checks this instance against a dictionary of attributes to determine if they are a match.
Args:
attributes (dict): A dictionary of attributes to be check for equivalence
Returns:
bool: If a single unequivocal value is found will be false, else true.
"""
logger.debug(f"Incoming attributes: {attributes}")
attributes = {k : v for k, v in attributes.items() if k in self.list_searchables.keys()}
for key, value in attributes.items():
if value.lower() == "none":
value = None
logger.debug(f"Attempting to grab attribute: {key}")
self_value = getattr(self, key)
class_attr = getattr(self.class_object, key)
# logger.debug(f"Self value: {self_value}, class attr: {class_attr} of type: {type(class_attr)}")
if isinstance(class_attr, property):
filter = "property"
else:
filter = class_attr.property
match filter:
case ColumnProperty():
match class_attr.type:
case INTEGER():
if value.lower() == "true":
value = 1
elif value.lower() == "false":
value = 0
else:
value = int(value)
case FLOAT():
value = float(value)
case "property":
pass
case _RelationshipDeclared():
logger.debug(f"Checking {self_value}")
try:
self_value = self_value.name
except AttributeError:
pass
if class_attr.property.uselist:
self_value = self_value.__str__()
try:
logger.debug(f"Check if {self_value.__class__} is subclass of {self.__class__}")
check = issubclass(self_value.__class__, self.__class__)
logger.debug(f"Check if {value.__class__} is subclass of {BaseOmni}")
check = issubclass(value.__class__, BaseOmni)
except TypeError as e:
logger.error(f"Couldn't check if {self_value.__class__} is subclass of {self.__class__} due to {e}")
logger.error(f"Couldn't check if {value.__class__} is subclass of {BaseOmni} due to {e}")
check = False
if check:
logger.debug(f"Checking for subclass name.")
self_value = self_value.name
logger.debug(
f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
if self_value != value:
output = False
logger.debug(f"Value {key} is False, returning.")
return output
value = value.name
self_value = self.list_searchables[key]
if value != self_value:
logger.debug(f"Value {key} is False, these are not the same object.")
return False
logger.debug("Everything checks out, these are the same object.")
return True
def __setattr__(self, key, value):
try:
class_value = getattr(self.class_object, key)
@@ -176,6 +215,13 @@ class OmniSubmissionType(BaseOmni):
return {}
return value
@field_validator("template_file", mode="before")
@classmethod
def provide_blank_template_file(cls, value):
if value is None:
value = bytes()
return value
def __init__(self, instance_object: Any, **data):
super().__init__(**data)
self.instance_object = instance_object
@@ -296,7 +342,6 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
constant_cost=self.constant_cost
)
def to_sql(self):
logger.debug(f"Self kittype: {self.submissiontype}")
if issubclass(self.submissiontype.__class__, BaseOmni):
@@ -315,6 +360,18 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
instance.constant_cost = self.constant_cost
return instance
@property
def list_searchables(self):
if isinstance(self.kittype, OmniKitType):
kit = self.kittype.name
else:
kit = self.kittype
if isinstance(self.submissiontype, OmniSubmissionType):
subtype = self.submissiontype.name
else:
subtype = self.submissiontype
return dict(kittype=kit, submissiontype=subtype)
class OmniKitTypeReagentRoleAssociation(BaseOmni):
class_object: ClassVar[Any] = KitTypeReagentRoleAssociation
@@ -325,6 +382,11 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
submission_type: str | OmniSubmissionType = Field(default="", description="relationship", title="SubmissionType")
kit_type: str | OmniKitType = Field(default="", description="relationship", title="KitType")
def __repr__(self):
try:
return f"<OmniKitTypeReagentRoleAssociation({self.kit_type.name}&{self.reagent_role.name})>"
except AttributeError:
return f"<OmniKitTypeReagentRoleAssociation(NO NAME)>"
@field_validator("uses", mode="before")
@classmethod
@@ -362,19 +424,46 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
reagent_role = self.reagent_role.name
else:
reagent_role = self.reagent_role
if issubclass(self.submission_type.__class__, BaseOmni):
submissiontype = self.submission_type.name
else:
submissiontype = self.submission_type
if issubclass(self.kit_type.__class__, BaseOmni):
kittype = self.kit_type.name
else:
kittype = self.kit_type
instance, new = self.class_object.query_or_create(
reagentrole=reagent_role,
kittype=self.kit_type,
submissiontype=self.submission_type
kittype=kittype,
submissiontype=submissiontype
)
logger.debug(f"KitTypeReagentRoleAssociation coming out of query_or_create: {instance.__dict__}\nnew: {new}")
if new:
logger.warning(f"This is a new instance: {instance.__dict__}")
reagent_role = self.reagent_role.to_sql()
instance.reagent_role = reagent_role
logger.debug(f"KTRRAssoc uses: {self.uses}")
instance.uses = self.uses
instance.required = int(self.required)
logger.debug(f"KitTypeReagentRoleAssociation: {pformat(instance.__dict__)}")
return instance
@property
def list_searchables(self):
if isinstance(self.kit_type, OmniKitType):
kit = self.kit_type.name
else:
kit = self.kit_type
if isinstance(self.submission_type, OmniSubmissionType):
subtype = self.submission_type.name
else:
subtype = self.submission_type
if isinstance(self.reagent_role, OmniReagentRole):
reagentrole = self.reagent_role.name
else:
reagentrole = self.reagent_role
return dict(kit_type=kit, submission_type=subtype, reagent_role=reagentrole)
class OmniEquipmentRole(BaseOmni):
class_object: ClassVar[Any] = EquipmentRole
@@ -463,6 +552,7 @@ class OmniProcess(BaseOmni):
# NOTE: How am I going to figure out relatioinships without getting into recursion issues?
name: str = Field(default="", description="property") #: Process name
# version: str = Field(default="", description="property") #: Version (string to account for "in_use" or whatever)
submission_types: List[OmniSubmissionType] | List[str] = Field(default=[], description="relationship",
title="SubmissionType")
equipment_roles: List[OmniEquipmentRole] | List[str] = Field(default=[], description="relationship",
@@ -491,6 +581,13 @@ class OmniProcess(BaseOmni):
return ""
return value
# @field_validator("version", mode="before")
# @classmethod
# def rescue_name_none(cls, value):
# if not value:
# return "1"
# return value
def to_sql(self):
instance, new = self.class_object.query_or_create(name=self.name)
for st in self.submission_types:
@@ -507,17 +604,21 @@ class OmniProcess(BaseOmni):
instance.tip_roles.append(new_assoc)
return instance
@property
def list_searchables(self):
return dict(name=self.name)
class OmniKitType(BaseOmni):
class_object: ClassVar[Any] = KitType
name: str = Field(default="", description="property")
kit_submissiontype_associations: List[OmniSubmissionTypeKitTypeAssociation] | List[str] = Field(default=[],
description="relationship",
title="SubmissionTypeKitTypeAssociation")
description="relationship",
title="SubmissionTypeKitTypeAssociation")
kit_reagentrole_associations: List[OmniKitTypeReagentRoleAssociation] | List[str] = Field(default=[],
description="relationship",
title="KitTypeReagentRoleAssociation")
description="relationship",
title="KitTypeReagentRoleAssociation")
processes: List[OmniProcess] | List[str] = Field(default=[], description="relationship", title="Process")
@field_validator("name", mode="before")
@@ -548,8 +649,9 @@ class OmniKitType(BaseOmni):
if new_assoc not in new_rr:
logger.debug(f"Adding {new_assoc} to kit_reagentrole_associations")
new_rr.append(new_assoc)
logger.debug(f"Setting kit_reagentrole_associations to {new_rr}")
logger.debug(f"Setting kit_reagentrole_associations to {pformat([item.__dict__ for item in new_rr])}")
kit.kit_reagentrole_associations = new_rr
# sys.exit()
new_st = []
for st_assoc in self.kit_submissiontype_associations:
new_assoc = st_assoc.to_sql()

1
src/submissions/backend/validators/pydant.py
View File

@@ -1244,6 +1244,7 @@ class PydIridaControl(BaseModel, extra='ignore'):
class PydProcess(BaseModel, extra="allow"):
name: str
version: str = Field(default="1")
submission_types: List[str]
equipment: List[str]
equipment_roles: List[str]