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Mid-progress adding controls to pydantic creation.

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This commit is contained in:
lwark
2024-11-21 08:46:41 -06:00
parent 506aac80c1
commit 7d1e6dc606
16 changed files with 224 additions and 187 deletions
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35
src/submissions/backend/validators/pydant.py
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@@ -786,9 +786,10 @@ class PydSubmission(BaseModel, extra='allow'):
"""
report = Report()
dicto = self.improved_dict()
logger.warning(f"\n\nQuery or create: {self.submission_type['value']}, {self.rsl_plate_num['value']}")
instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
rsl_plate_num=self.rsl_plate_num['value'])
logger.debug(f"Result of query or create: {type(result)}")
logger.debug(f"Result of query or create: {instance}")
report.add_result(result)
self.handle_duplicate_samples()
# logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
@@ -830,7 +831,7 @@ class PydSubmission(BaseModel, extra='allow'):
equip, association = equip.toSQL(submission=instance)
if association is not None:
instance.submission_equipment_associations.append(association)
logger.debug(f"Equipment associations:\n\n{pformat(instance.submission_equipment_associations)}")
logger.debug(f"Equipment associations: {instance.submission_equipment_associations}")
case "tips":
for tips in self.tips:
if tips is None:
@@ -871,16 +872,18 @@ class PydSubmission(BaseModel, extra='allow'):
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}")
continue
except KeyError:
continue
print(f"\n\n{instance}\n\n")
try:
# logger.debug(f"Calculating costs for procedure...")
instance.calculate_base_cost()
except (TypeError, AttributeError) as e:
# logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using full plate cost.")
logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using 0.")
try:
instance.run_cost = instance.extraction_kit.cost_per_run
except AttributeError:
@@ -1104,3 +1107,29 @@ class PydEquipmentRole(BaseModel):
"""
from frontend.widgets.equipment_usage import RoleComboBox
return RoleComboBox(parent=parent, role=self, used=used)
class PydPCRControl(BaseModel):
name: str
subtype: str
target: str
ct: float
reagent_lot: str
submitted_date: datetime #: Date submitted to Robotics
submission_id: int
controltype_name: str
class PydIridaControl(BaseModel, extra='ignore'):
name: str
contains: list | dict #: unstructured hashes in contains.tsv for each organism
matches: list | dict #: unstructured hashes in matches.tsv for each organism
kraken: list | dict #: unstructured output from kraken_report
subtype: str #: EN-NOS, MCS-NOS, etc
refseq_version: str #: version of refseq used in fastq parsing
kraken2_version: str
kraken2_db_version: str
sample_id: int
submitted_date: datetime #: Date submitted to Robotics
submission_id: int
controltype_name: str