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Updates to details interface.

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This commit is contained in:
lwark
2025-07-16 14:12:03 -05:00
parent 02c88256f2
commit 53c6668ce1
12 changed files with 276 additions and 71 deletions
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44
src/submissions/backend/validators/pydant.py
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@@ -1500,7 +1500,7 @@ class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
proceduretype: ProcedureType | None = Field(default=None)
run: Run | None = Field(default=None)
run: Run | str | None = Field(default=None)
name: dict = Field(default=dict(value="NA", missing=True), validate_default=True)
technician: dict = Field(default=dict(value="NA", missing=True))
repeat: bool = Field(default=False)
@@ -1590,6 +1590,13 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
value = {item.name: item.reagent for item in kittype.reagentrole}
return value
@field_validator("run")
@classmethod
def lookup_run(cls, value):
if isinstance(value, str):
value = Run.query(name=value)
return value
def update_kittype_reagentroles(self, kittype: str | KitType):
if kittype == self.__class__.model_fields['kittype'].default['value']:
return
@@ -1701,13 +1708,24 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
# NOTE: reset reagent associations.
sql.procedurereagentassociation = []
for reagent in self.reagent:
logger.debug(reagent)
if isinstance(reagent, dict):
reagent = PydReagent(**reagent)
logger.debug(reagent)
reagentrole = reagent.reagentrole
reagent = reagent.to_sql()
logger.debug(reagentrole)
if reagent not in sql.reagent:
# NOTE: Remove any previous association for this role.
removable = ProcedureReagentAssociation.query(procedure=sql, reagentrole=reagentrole)
logger.debug(f"Removable: {removable}")
if removable:
if isinstance(removable, list):
for r in removable:
r.delete()
else:
removable.delete()
logger.debug(f"Adding {reagent} to {sql}")
reagent_assoc = ProcedureReagentAssociation(reagent=reagent, procedure=sql)
reagent_assoc = ProcedureReagentAssociation(reagent=reagent, procedure=sql, reagentrole=reagentrole)
try:
start_index = max([item.id for item in ProcedureSampleAssociation.query()]) + 1
except ValueError:
@@ -1733,7 +1751,11 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
kittype = KitType.query(name=self.kittype['value'], limit=1)
if kittype:
sql.kittype = kittype
logger.debug(self.reagent)
# logger.debug(self.reagent)
# for reagent in self.reagent:
# reagent = reagent.to_sql()
# if reagent not in sql.reagent:
# reagent_assoc = ProcedureReagentAssociation(reagent=reagent, procedure=sql)
for equipment in self.equipment:
equip = Equipment.query(name=equipment.name)
if equip not in sql.equipment:
@@ -1742,6 +1764,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
process = equipment.process.to_sql()
equip_assoc.process = process
# logger.debug(f"Output sql: {[pformat(item.__dict__) for item in sql.procedureequipmentassociation]}")
logger.debug(pformat(sql.__dict__))
return sql, None
@@ -1854,20 +1877,29 @@ class PydClientSubmission(PydBaseClass):
"""
from frontend.widgets.submission_widget import ClientSubmissionFormWidget
if not samples:
samples = self.samples
samples = self.sample
return ClientSubmissionFormWidget(parent=parent, clientsubmission=self, samples=samples, disable=disable)
def to_sql(self):
sql = super().to_sql()
assert not any([isinstance(item, PydSample) for item in sql.sample])
sql.sample = []
if "info_placement" not in sql._misc_info:
sql._misc_info['info_placement'] = []
info_placement = []
for k in list(self.model_fields.keys()) + list(self.model_extra.keys()):
logger.debug(f"Running {k}")
attribute = getattr(self, k)
match k:
case "filepath":
sql._misc_info[k] = attribute.__str__()
continue
# case "sample":
# sample = [item.to_sql() for item in self.sample]
# logger.debug(sample)
# for s in sample:
# logger.debug(f"adding {s}")
# sql.add_sample(sample=s)
case _:
pass
logger.debug(f"Setting {k} to {attribute}")
@@ -1876,7 +1908,7 @@ class PydClientSubmission(PydBaseClass):
info_placement.append(dict(name=k, location=attribute['location']))
else:
info_placement.append(dict(name=k, location=None))
max_row = max([value['location']['row'] for value in info_placement if value])
# max_row = max([value['location']['row'] for value in info_placement if value])
sql._misc_info['info_placement'] = info_placement
return sql