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Tips parser complete.

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This commit is contained in:
lwark
2024-06-13 09:11:53 -05:00
parent 78c92cd31f
commit e0e3080af0
7 changed files with 311 additions and 66 deletions
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2
src/submissions/backend/validators/__init__.py
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@@ -179,4 +179,4 @@ class RSLNamer(object):
from .pydant import PydSubmission, PydKit, PydContact, PydOrganization, PydSample, PydReagent, PydReagentRole, \
PydEquipment, PydEquipmentRole
PydEquipment, PydEquipmentRole, PydTips

35
src/submissions/backend/validators/pydant.py
View File

@@ -245,7 +245,10 @@ class PydSample(BaseModel, extra='allow'):
instance.__setattr__(key, value)
out_associations = []
if submission is not None:
assoc_type = self.sample_type.replace("Sample", "").strip()
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_plate_num=submission)
assoc_type = submission.submission_type_name
# 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):
# logger.debug(f"Looking up association with identity: ({submission.submission_type_name} Association)")
# logger.debug(f"Looking up association with identity: ({assoc_type} Association)")
@@ -254,7 +257,7 @@ class PydSample(BaseModel, extra='allow'):
sample=instance,
row=row, column=column, id=aid,
submission_rank=submission_rank)
# logger.debug(f"Using submission_sample_association: {association}")
logger.debug(f"Using submission_sample_association: {association}")
try:
# instance.sample_submission_associations.append(association)
out_associations.append(association)
@@ -272,12 +275,24 @@ class PydSample(BaseModel, extra='allow'):
return {k: getattr(self, k) for k in fields}
class PydTips(BaseModel):
name: str
lot: str|None = Field(default=None)
role: str
def to_sql(self, submission:BasicSubmission):
tips = Tips.query(name=self.name, lot=self.lot, limit=1)
assoc = SubmissionTipsAssociation(submission=submission, tips=tips, role_name=self.role)
return assoc
class PydEquipment(BaseModel, extra='ignore'):
asset_number: str
name: str
nickname: str | None
processes: List[str] | None
role: str | None
tips: List[PydTips]|None = Field(default=None)
@field_validator('processes', mode='before')
@classmethod
@@ -703,18 +718,23 @@ class PydSubmission(BaseModel, extra='allow'):
instance.submission_sample_associations.append(assoc)
case "equipment":
# logger.debug(f"Equipment: {pformat(self.equipment)}")
try:
for equip in self.equipment:
if equip is None:
continue
except UnboundLocalError:
continue
for equip in self.equipment:
equip, association = equip.toSQL(submission=instance)
if association is not None:
association.save()
# association.save()
# logger.debug(
# f"Equipment association SQL object to be added to submission: {association.__dict__}")
instance.submission_equipment_associations.append(association)
case "tips":
for tips in self.tips:
if tips is None:
continue
association = tips.to_sql()
if association is not None:
# association.save()
instance.submission_tips_associations.append(association)
case item if item in instance.jsons():
# logger.debug(f"{item} is a json.")
try:
@@ -949,3 +969,4 @@ class PydEquipmentRole(BaseModel):
"""
from frontend.widgets.equipment_usage import RoleComboBox
return RoleComboBox(parent=parent, role=self, used=used)