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Improved form regeneration for artic.

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This commit is contained in:
Landon Wark
2024-01-04 13:29:18 -06:00
parent c688aa160c
commit 19448cc8f3
18 changed files with 519 additions and 123 deletions
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83
src/submissions/backend/validators/pydant.py
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@@ -1,6 +1,7 @@
'''
Contains pydantic models and accompanying validators
'''
from __future__ import annotations
from operator import attrgetter
import uuid, re, logging
from pydantic import BaseModel, field_validator, Field
@@ -189,6 +190,7 @@ class PydSample(BaseModel, extra='allow'):
continue
case _:
instance.set_attribute(name=key, value=value)
out_associations = []
if submission != None:
assoc_type = self.sample_type.replace("Sample", "").strip()
for row, column in zip(self.row, self.column):
@@ -198,12 +200,14 @@ class PydSample(BaseModel, extra='allow'):
submission=submission,
sample=instance,
row=row, column=column)
logger.debug(f"Using submission_sample_association: {association}")
try:
instance.sample_submission_associations.append(association)
out_associations.append(association)
except IntegrityError as e:
logger.error(f"Could not attach submission sample association due to: {e}")
instance.metadata.session.rollback()
return instance, report
return instance, out_associations, report
class PydSubmission(BaseModel, extra='allow'):
filepath: Path
@@ -220,7 +224,16 @@ class PydSubmission(BaseModel, extra='allow'):
submission_category: dict|None = Field(default=dict(value=None, missing=True), validate_default=True)
comment: dict|None = Field(default=dict(value="", missing=True), validate_default=True)
reagents: List[dict]|List[PydReagent] = []
samples: List[Any]
samples: List[PydSample]
equipment: List[PydEquipment]|None
@field_validator('equipment', mode='before')
@classmethod
def convert_equipment_dict(cls, value):
logger.debug(f"Equipment: {value}")
if isinstance(value, dict):
return value['value']
return value
@field_validator('comment', mode='before')
@classmethod
@@ -425,7 +438,17 @@ class PydSubmission(BaseModel, extra='allow'):
match key:
case "samples":
for sample in self.samples:
sample, _ = sample.toSQL(submission=instance)
sample, associations, _ = sample.toSQL(submission=instance)
logger.debug(f"Sample SQL object to be added to submission: {sample.__dict__}")
for assoc in associations:
instance.submission_sample_associations.append(assoc)
case "equipment":
logger.debug(f"Equipment: {pformat(self.equipment)}")
for equip in self.equipment:
equip, association = equip.toSQL(submission=instance)
if association != None:
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)
@@ -559,6 +582,7 @@ class PydSubmission(BaseModel, extra='allow'):
except Exception as e:
logger.error(f"Could not write name {reagent['name']['value']} due to {e}")
# Get relevant info for that sheet
new_info = [item for item in new_info if isinstance(item['location'], dict)]
sheet_info = [item for item in new_info if sheet in item['location']['sheets']]
for item in sheet_info:
logger.debug(f"Attempting: {item['type']} in row {item['location']['row']}, column {item['location']['column']}")
@@ -579,9 +603,11 @@ class PydSubmission(BaseModel, extra='allow'):
Workbook: Updated excel workbook
"""
sample_info = SubmissionType.query(name=self.submission_type['value']).info_map['samples']
logger.debug(f"Sample info: {pformat(sample_info)}")
logger.debug(f"Workbook sheets: {workbook.sheetnames}")
worksheet = workbook[sample_info["lookup_table"]['sheet']]
samples = sorted(self.samples, key=attrgetter('column', 'row'))
logger.debug(f"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
@@ -744,33 +770,46 @@ class PydKit(BaseModel):
class PydEquipment(BaseModel, extra='ignore'):
asset_number: str
name: str
nickname: str|None
asset_number: str
pool_name: str|None
static: bool|int
process: List[str]|None
role: str|None
@field_validator("static")
@field_validator('process')
@classmethod
def to_boolean(cls, value):
match value:
case int():
if value == 0:
return False
else:
return True
case _:
return value
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[0]
assoc.role = self.role
# equipment.equipment_submission_associations.append(assoc)
equipment.equipment_submission_associations.append(assoc)
else:
assoc = None
return equipment, assoc
class PydEquipmentPool(BaseModel):
class PydEquipmentRole(BaseModel):
name: str
equipment: List[PydEquipment]
def toForm(self, parent):
from frontend.widgets.equipment_usage import PoolComboBox
return PoolComboBox(parent=parent, pool=self)
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)