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Midway through disaster of changing table names.

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This commit is contained in:
Landon Wark
2024-01-19 15:17:07 -06:00
parent d66d861262
commit 319f72cab2
31 changed files with 1040 additions and 1457 deletions
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11
src/submissions/backend/validators/__init__.py
View File

@@ -113,12 +113,15 @@ class RSLNamer(object):
@classmethod
def construct_new_plate_name(cls, data:dict) -> str:
if "submitted_date" in data.keys():
if data['submitted_date']['value'] != None:
today = data['submitted_date']['value']
if isinstance(data['submitted_date'], dict):
if data['submitted_date']['value'] != None:
today = data['submitted_date']['value']
else:
today = datetime.now()
else:
today = datetime.now()
today = data['submitted_date']
else:
today = re.search(r"\d{4}(_|-)?\d{2}(_|-)?\d{2}", instr)
today = re.search(r"\d{4}(_|-)?\d{2}(_|-)?\d{2}", data['rsl_plate_num'])
try:
today = parse(today.group())
except AttributeError:

135
src/submissions/backend/validators/pydant.py
View File

@@ -106,7 +106,7 @@ class PydReagent(BaseModel):
if self.model_extra != None:
self.__dict__.update(self.model_extra)
logger.debug(f"Reagent SQL constructor is looking up type: {self.type}, lot: {self.lot}")
reagent = Reagent.query(lot_number=self.lot)
reagent = Reagent.query(lot_number=self.lot, name=self.name)
logger.debug(f"Result: {reagent}")
if reagent == None:
reagent = Reagent()
@@ -209,6 +209,56 @@ class PydSample(BaseModel, extra='allow'):
instance.metadata.session.rollback()
return instance, out_associations, report
class PydEquipment(BaseModel, extra='ignore'):
asset_number: str
name: str
nickname: str|None
processes: List[str]|None
role: str|None
@field_validator('processes', mode='before')
@classmethod
def make_empty_list(cls, value):
# logger.debug(f"Pydantic value: {value}")
if value == None:
value = ['']
if len(value)==0:
value=['']
return value
# def toForm(self, parent):
# from frontend.widgets.equipment_usage import EquipmentCheckBox
# return EquipmentCheckBox(parent=parent, equipment=self)
def toSQL(self, submission:BasicSubmission|str=None):
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_number=submission)
equipment = Equipment.query(asset_number=self.asset_number)
if equipment == None:
return
if submission != None:
assoc = SubmissionEquipmentAssociation(submission=submission, equipment=equipment)
process = Process.query(name=self.processes[0])
if process == None:
from frontend.widgets.pop_ups import QuestionAsker
dlg = QuestionAsker(title="Add Process?", message=f"Unable to find {self.processes[0]} in the database.\nWould you like to add it?")
if dlg.exec():
kit = submission.extraction_kit
submission_type = submission.submission_type
process = Process(name=self.processes[0])
process.kit_types.append(kit)
process.submission_types.append(submission_type)
process.equipment.append(equipment)
process.save()
assoc.process = process
assoc.role = self.role
# equipment.equipment_submission_associations.append(assoc)
equipment.equipment_submission_associations.append(assoc)
else:
assoc = None
return equipment, assoc
class PydSubmission(BaseModel, extra='allow'):
filepath: Path
submission_type: dict|None
@@ -453,8 +503,10 @@ class PydSubmission(BaseModel, extra='allow'):
for equip in self.equipment:
equip, association = equip.toSQL(submission=instance)
if association != None:
association.save()
logger.debug(f"Equipment association SQL object to be added to submission: {association.__dict__}")
instance.submission_equipment_associations.append(association)
case _:
try:
instance.set_attribute(key=key, value=value)
@@ -570,9 +622,7 @@ class PydSubmission(BaseModel, extra='allow'):
logger.debug(f"New reagents: {new_reagents}")
logger.debug(f"New info: {new_info}")
# get list of sheet names
sheets = workbook.sheetnames
# logger.debug(workbook.sheetnames)
for sheet in sheets:
for sheet in workbook.sheetnames:
# open sheet
worksheet=workbook[sheet]
# Get relevant reagents for that sheet
@@ -613,11 +663,14 @@ class PydSubmission(BaseModel, extra='allow'):
logger.debug(f"Workbook sheets: {workbook.sheetnames}")
worksheet = workbook[sample_info["lookup_table"]['sheet']]
samples = sorted(self.samples, key=attrgetter('column', 'row'))
custom_sampler = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type).adjust_autofill_samples
samples = custom_sampler(samples=samples)
logger.debug(f"Samples: {pformat(samples)}")
# Fail safe against multiple instances of the same sample
for iii, sample in enumerate(samples, start=1):
row = sample_info['lookup_table']['start_row'] + iii
fields = [field for field in list(sample.model_fields.keys()) + list(sample.model_extra.keys()) if field in sample_info['sample_columns'].keys()]
for field in fields:
column = sample_info['sample_columns'][field]
value = getattr(sample, field)
@@ -630,6 +683,42 @@ class PydSubmission(BaseModel, extra='allow'):
value = row_map[value]
worksheet.cell(row=row, column=column, value=value)
return workbook
def autofill_equipment(self, workbook:Workbook) -> Workbook:
equipment_map = SubmissionType.query(name=self.submission_type['value']).construct_equipment_map()
logger.debug(f"Equipment map: {equipment_map}")
# See if all equipment has a location map
# If not, create a new sheet to store them in.
if not all([len(item.keys()) > 1 for item in equipment_map]):
logger.warning("Creating 'Equipment' sheet to hold unmapped equipment")
workbook.create_sheet("Equipment")
equipment = []
for ii, equip in enumerate(self.equipment, start=1):
loc = [item for item in equipment_map if item['role'] == equip.role][0]
try:
loc['name']['value'] = equip.name
loc['process']['value'] = equip.processes[0]
except KeyError:
loc['name'] = dict(row=ii, column=2)
loc['process'] = dict(row=ii, column=3)
loc['name']['value'] = equip.name
loc['process']['value'] = equip.processes[0]
loc['sheet'] = "Equipment"
equipment.append(loc)
logger.debug(f"Using equipment: {equipment}")
for sheet in workbook.sheetnames:
logger.debug(f"Looking at: {sheet}")
worksheet = workbook[sheet]
relevant = [item for item in equipment if item['sheet'] == sheet]
for rel in relevant:
match sheet:
case "Equipment":
worksheet.cell(row=rel['name']['row'], column=1, value=rel['role'])
case _:
pass
worksheet.cell(row=rel['name']['row'], column=rel['name']['column'], value=rel['name']['value'])
worksheet.cell(row=rel['process']['row'], column=rel['process']['column'], value=rel['process']['value'])
return workbook
def construct_filename(self) -> str:
"""
@@ -774,42 +863,6 @@ class PydKit(BaseModel):
[item.toSQL(instance) for item in self.reagent_types]
return instance, report
class PydEquipment(BaseModel, extra='ignore'):
asset_number: str
name: str
nickname: str|None
process: str|None
role: str|None
# @field_validator('process')
# @classmethod
# def remove_dupes(cls, value):
# if isinstance(value, list):
# return list(set(value))
# else:
# return value
# def toForm(self, parent):
# from frontend.widgets.equipment_usage import EquipmentCheckBox
# return EquipmentCheckBox(parent=parent, equipment=self)
def toSQL(self, submission:BasicSubmission|str=None):
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_number=submission)
equipment = Equipment.query(asset_number=self.asset_number)
if equipment == None:
return
if submission != None:
assoc = SubmissionEquipmentAssociation(submission=submission, equipment=equipment)
assoc.process = self.process
assoc.role = self.role
# equipment.equipment_submission_associations.append(assoc)
equipment.equipment_submission_associations.append(assoc)
else:
assoc = None
return equipment, assoc
class PydEquipmentRole(BaseModel):
name: str
@@ -819,4 +872,4 @@ class PydEquipmentRole(BaseModel):
def toForm(self, parent, submission_type, used):
from frontend.widgets.equipment_usage import RoleComboBox
return RoleComboBox(parent=parent, role=self, submission_type=submission_type, used=used)