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Can now calculate turnaround time including holidays.

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This commit is contained in:
lwark
2024-11-25 13:34:02 -06:00
parent 7d1e6dc606
commit 7f0b7feb5d
13 changed files with 533 additions and 300 deletions
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65
src/submissions/backend/validators/pydant.py
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@@ -807,22 +807,28 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Setting {key} to {value}")
match key:
case "reagents":
if report.results[0].code == 1:
instance.submission_reagent_associations = []
# if report.results[0].code == 1:
# instance.submission_reagent_associations = []
# logger.debug(f"Looking through {self.reagents}")
for reagent in self.reagents:
reagent, assoc, _ = reagent.toSQL(submission=instance)
# logger.debug(f"Association: {assoc}")
if assoc is not None: # and assoc not in instance.submission_reagent_associations:
instance.submission_reagent_associations.append(assoc)
if assoc not in instance.submission_reagent_associations:
instance.submission_reagent_associations.append(assoc)
else:
logger.warning(f"Reagent association {assoc} is already present in {instance}")
case "samples":
for sample in self.samples:
sample, associations, _ = sample.toSQL(submission=instance)
# logger.debug(f"Sample SQL object to be added to submission: {sample.__dict__}")
logger.debug(associations)
# logger.debug(associations)
for assoc in associations:
if assoc is not None and assoc not in instance.submission_sample_associations:
instance.submission_sample_associations.append(assoc)
if assoc is not None:
if assoc not in instance.submission_sample_associations:
instance.submission_sample_associations.append(assoc)
else:
logger.warning(f"Sample association {assoc} is already present in {instance}")
case "equipment":
# logger.debug(f"Equipment: {pformat(self.equipment)}")
for equip in self.equipment:
@@ -841,8 +847,11 @@ class PydSubmission(BaseModel, extra='allow'):
association = tips.to_sql(submission=instance)
except AttributeError:
continue
if association is not None and association not in instance.submission_tips_associations:
instance.submission_tips_associations.append(association)
if association is not None:
if association not in instance.submission_tips_associations:
instance.submission_tips_associations.append(association)
else:
logger.warning(f"Tips association {association} is already present in {instance}")
case item if item in instance.timestamps():
logger.warning(f"Incoming timestamp key: {item}, with value: {value}")
# value = value.replace(tzinfo=timezone)
@@ -871,14 +880,20 @@ class PydSubmission(BaseModel, extra='allow'):
instance.set_attribute(key=key, value=value)
case _:
try:
instance.set_attribute(key=key, value=value)
# instance.update({key:value})
except AttributeError as e:
logger.error(f"Could not set attribute: {key} to {value} due to: \n\n {e}")
check = instance.__getattribute__(key) != value
except AttributeError:
continue
except KeyError:
continue
print(f"\n\n{instance}\n\n")
if check:
try:
instance.set_attribute(key=key, value=value)
# instance.update({key:value})
except AttributeError as e:
logger.error(f"Could not set attribute: {key} to {value} due to: \n\n {e}")
continue
except KeyError:
continue
else:
logger.warning(f"{key} already == {value} so no updating.")
try:
# logger.debug(f"Calculating costs for procedure...")
instance.calculate_base_cost()
@@ -1119,6 +1134,16 @@ class PydPCRControl(BaseModel):
submission_id: int
controltype_name: str
def to_sql(self):
instance = PCRControl.query(name=self.name)
if not instance:
instance = PCRControl()
for key in self.model_fields:
field_value = self.__getattribute__(key)
if instance.__getattribute__(key) != field_value:
instance.__setattr__(key, field_value)
return instance
class PydIridaControl(BaseModel, extra='ignore'):
name: str
@@ -1133,3 +1158,13 @@ class PydIridaControl(BaseModel, extra='ignore'):
submitted_date: datetime #: Date submitted to Robotics
submission_id: int
controltype_name: str
def to_sql(self):
instance = IridaControl.query(name=self.name)
if not instance:
instance = IridaControl()
for key in self.model_fields:
field_value = self.__getattribute__(key)
if instance.__getattribute__(key) != field_value:
instance.__setattr__(key, field_value)
return instance