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Bug fixes.

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This commit is contained in:
lwark
2024-08-02 14:58:01 -05:00
parent 88f3e92069
commit 1a55b52f31
2 changed files with 75 additions and 4 deletions
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77
src/submissions/backend/db/models/kits.py
View File

@@ -2,6 +2,9 @@
All kit and reagent related models
"""
from __future__ import annotations
from pprint import pprint
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.ext.associationproxy import association_proxy
@@ -253,6 +256,32 @@ class KitType(BaseClass):
super().save()
def to_export_dict(self, submission_type: SubmissionType):
base_dict = {}
base_dict['reagent roles'] = []
base_dict['equipment roles'] = []
for k, v in self.construct_xl_map_for_use(submission_type=submission_type):
logger.debug(f"Value: {v}")
try:
assoc = [item for item in self.kit_reagentrole_associations if item.reagent_role.name == k][0]
except IndexError as e:
continue
for kk, vv in assoc.to_export_dict().items():
v[kk] = vv
base_dict['reagent roles'].append(v)
for k, v in submission_type.construct_equipment_map():
try:
assoc = [item for item in submission_type.submissiontype_equipmentrole_associations if item.equipment_role.name == k][0]
except IndexError:
continue
for kk, vv in assoc.to_export_dict(kit_type=self).items():
logger.debug(f"{kk}:{vv}")
v[kk] = vv
base_dict['equipment roles'].append(v)
logger.debug(f"KT returning {base_dict}")
return base_dict
class ReagentRole(BaseClass):
"""
Base of reagent type abstract
@@ -351,6 +380,9 @@ class ReagentRole(BaseClass):
from backend.validators.pydant import PydReagent
return PydReagent(lot=None, role=self.name, name=self.name, expiry=date.today())
def to_export_dict(self):
return dict(role=self.name, extension_of_life=self.eol_ext.days)
@check_authorization
def save(self):
super().save()
@@ -665,7 +697,7 @@ class SubmissionType(BaseClass):
self.template_file = data
self.save()
def construct_info_map(self, mode: Literal['read', 'write']) -> dict:
def construct_info_map(self, mode: Literal['read', 'write', 'export']) -> dict:
"""
Make of map of where all fields are located in Excel sheet
@@ -683,6 +715,8 @@ class SubmissionType(BaseClass):
case "write":
output = {k: v[mode] + v['read'] for k, v in info.items() if v[mode] or v['read']}
output = {k: v for k, v in output.items() if all([isinstance(item, dict) for item in v])}
case "export":
return self.info_map
case _:
output = {}
output['custom'] = self.info_map['custom']
@@ -810,6 +844,17 @@ class SubmissionType(BaseClass):
pass
return cls.execute_query(query=query, limit=limit)
def to_dict(self):
base_dict = {}
base_dict['info'] = self.construct_info_map(mode='export')
# base_dict['excel location maps']['kits'] = [{k: v for k, v in item.kit_type.construct_xl_map_for_use(submission_type=self)} for item in
# self.submissiontype_kit_associations]
base_dict['samples'] = self.construct_sample_map()
# base_dict['excel location maps']['equipment_roles'] = {k: v for k, v in self.construct_equipment_map()}
base_dict['kits'] = [item.to_export_dict() for item in self.submissiontype_kit_associations]
return base_dict
@check_authorization
def save(self):
"""
@@ -895,6 +940,13 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
limit = query.count()
return cls.execute_query(query=query, limit=limit)
def to_export_dict(self):
exclude = ['_sa_instance_state', 'submission_types_id', 'kits_id', 'submission_type', 'kit_type']
base_dict = {k:v for k,v in self.__dict__.items() if k not in exclude}
base_dict['kit_type'] = self.kit_type.to_export_dict(submission_type=self.submission_type)
logger.debug(f"STKTA returning: {base_dict}")
return base_dict
class KitTypeReagentRoleAssociation(BaseClass):
"""
@@ -1008,6 +1060,13 @@ class KitTypeReagentRoleAssociation(BaseClass):
limit = 1
return cls.execute_query(query=query, limit=limit)
def to_export_dict(self):
base_dict={}
base_dict['required'] = self.required
for k, v in self.reagent_role.to_export_dict().items():
base_dict[k] = v
return base_dict
class SubmissionReagentAssociation(BaseClass):
"""
@@ -1372,10 +1431,10 @@ class EquipmentRole(BaseClass):
match extraction_kit:
case str():
# logger.debug(f"Filtering processes by extraction_kit str {extraction_kit}")
processes = [item for item in processes if extraction_kit in [kit.name for kit in item.kit_type]]
processes = [item for item in processes if extraction_kit in [kit.name for kit in item.kit_types]]
case KitType():
# logger.debug(f"Filtering processes by extraction_kit KitType {extraction_kit}")
processes = [item for item in processes if extraction_kit in [kit for kit in item.kit_type]]
processes = [item for item in processes if extraction_kit in [kit for kit in item.kit_types]]
case _:
pass
output = [item.name for item in processes]
@@ -1384,6 +1443,12 @@ class EquipmentRole(BaseClass):
else:
return output
def to_export_dict(self, submission_type: SubmissionType, kit_type: KitType):
base_dict = {}
base_dict['role'] = self.name
base_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=kit_type)
return base_dict
class SubmissionEquipmentAssociation(BaseClass):
"""
@@ -1492,6 +1557,12 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
def save(self):
super().save()
def to_export_dict(self, kit_type: KitType):
base_dict = dict(static=self.static)
for k, v in self.equipment_role.to_export_dict(submission_type=self.submission_type, kit_type=kit_type).items():
base_dict[k] = v
return base_dict
class Process(BaseClass):
"""

2
src/submissions/backend/validators/pydant.py
View File

@@ -851,7 +851,7 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Template rendered as: {render}")
return render
@report_result
# @report_result
def check_kit_integrity(self, extraction_kit: str | dict | None = None) -> Tuple[List[PydReagent], Report]:
"""
Ensures all reagents expected in kit are listed in Submission