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Importing submission type from json.

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This commit is contained in:
lwark
2024-09-04 09:45:17 -05:00
parent 482bfa5728
commit 452d1b4a77
2 changed files with 80 additions and 13 deletions
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87
src/submissions/backend/db/models/kits.py
View File

@@ -3,6 +3,8 @@ All kit and reagent related models
"""
from __future__ import annotations
import datetime
import json
from pprint import pprint
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
@@ -255,9 +257,8 @@ class KitType(BaseClass):
def save(self):
super().save()
def to_export_dict(self, submission_type: SubmissionType):
base_dict = {}
base_dict = dict(name=self.name)
base_dict['reagent roles'] = []
base_dict['equipment roles'] = []
for k, v in self.construct_xl_map_for_use(submission_type=submission_type):
@@ -271,7 +272,8 @@ class KitType(BaseClass):
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]
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():
@@ -845,8 +847,9 @@ class SubmissionType(BaseClass):
return cls.execute_query(query=query, limit=limit)
def to_dict(self):
base_dict = {}
base_dict = dict(name=self.name)
base_dict['info'] = self.construct_info_map(mode='export')
base_dict['defaults'] = self.defaults
# 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()
@@ -854,7 +857,6 @@ class SubmissionType(BaseClass):
base_dict['kits'] = [item.to_export_dict() for item in self.submissiontype_kit_associations]
return base_dict
@check_authorization
def save(self):
"""
@@ -862,6 +864,63 @@ class SubmissionType(BaseClass):
"""
super().save()
@classmethod
@check_authorization
def import_from_json(cls, filepath:Path|str):
if isinstance(filepath, str):
filepath = Path(filepath)
if not filepath.exists():
logging.critical(f"Given file could not be found.")
return None
with open(filepath, "r") as f:
import_dict = json.load(fp=f)
submission_type = cls.query(name=import_dict['name'])
if submission_type:
return submission_type
submission_type = cls()
submission_type.name = import_dict['name']
submission_type.info_map = import_dict['info']
submission_type.sample_map = import_dict['samples']
submission_type.defaults = import_dict['defaults']
for kit in import_dict['kits']:
new_kit = KitType.query(name=kit['kit_type']['name'])
if not new_kit:
new_kit = KitType(name=kit['kit_type']['name'])
for role in kit['kit_type']['reagent roles']:
new_role = ReagentRole.query(name=role['role'])
eol = datetime.timedelta(role['extension_of_life'])
if not new_role:
new_role = ReagentRole(name=role['role'], eol_ext=eol)
uses = dict(expiry=role['expiry'], lot=role['lot'], name=role['name'], sheet=role['sheet'])
ktrr_assoc = KitTypeReagentRoleAssociation(kit_type=new_kit, reagent_role=new_role, uses=uses)
ktrr_assoc.submission_type = submission_type
ktrr_assoc.required = role['required']
ktst_assoc = SubmissionTypeKitTypeAssociation(
kit_type=new_kit,
submission_type=submission_type,
mutable_cost_sample=kit['mutable_cost_sample'],
mutable_cost_column=kit['mutable_cost_column'],
constant_cost=kit['constant_cost']
)
for role in kit['kit_type']['equipment roles']:
new_role = EquipmentRole.query(name=role['role'])
if not new_role:
new_role = EquipmentRole(name=role['role'])
ster_assoc = SubmissionTypeEquipmentRoleAssociation(submission_type=submission_type, equipment_role=new_role)
try:
uses = dict(name=role['name'], process=role['process'], sheet=role['sheet'], static=role['static'])
except KeyError:
uses = None
ster_assoc.uses = uses
for process in role['processes']:
new_process = Process.query(name=process)
if not new_process:
new_process = Process(name=process)
new_process.submission_types.append(submission_type)
new_process.kit_types.append(new_kit)
new_process.equipment_roles.append(new_role)
return submission_type
class SubmissionTypeKitTypeAssociation(BaseClass):
"""
@@ -942,7 +1001,7 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
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 = {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
@@ -1061,7 +1120,7 @@ class KitTypeReagentRoleAssociation(BaseClass):
return cls.execute_query(query=query, limit=limit)
def to_export_dict(self):
base_dict={}
base_dict = {}
base_dict['required'] = self.required
for k, v in self.reagent_role.to_export_dict().items():
base_dict[k] = v
@@ -1494,16 +1553,17 @@ class SubmissionEquipmentAssociation(BaseClass):
@classmethod
@setup_lookup
def query(cls, equipment_id:int, submission_id:int, role:str|None=None, limit:int=0, **kwargs) -> Any | List[Any]:
def query(cls, equipment_id: int, submission_id: int, role: str | None = None, limit: int = 0, **kwargs) -> Any | \
List[
Any]:
query: Query = cls.__database_session__.query(cls)
query = query.filter(cls.equipment_id==equipment_id)
query = query.filter(cls.submission_id==submission_id)
query = query.filter(cls.equipment_id == equipment_id)
query = query.filter(cls.submission_id == submission_id)
if role is not None:
query = query.filter(cls.role==role)
query = query.filter(cls.role == role)
return cls.execute_query(query=query, limit=limit, **kwargs)
class SubmissionTypeEquipmentRoleAssociation(BaseClass):
"""
Abstract association between SubmissionType and EquipmentRole
@@ -1767,7 +1827,8 @@ class SubmissionTipsAssociation(BaseClass):
@classmethod
@setup_lookup
def query(cls, tip_id: int, role: str, submission_id: int|None=None, limit: int = 0, **kwargs) -> Any | List[Any]:
def query(cls, tip_id: int, role: str, submission_id: int | None = None, limit: int = 0, **kwargs) -> Any | List[
Any]:
query: Query = cls.__database_session__.query(cls)
query = query.filter(cls.tip_id == tip_id)
if submission_id is not None:

6
src/submissions/backend/db/models/submissions.py
View File

@@ -1322,6 +1322,12 @@ class BacterialCulture(BasicSubmission):
row = idx.index.to_list()[0]
return row + 1
@classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict:
input_dict = super().custom_info_parser(input_dict=input_dict, xl=xl, custom_fields=custom_fields)
logger.debug(f"\n\nInfo dictionary:\n\n{pformat(input_dict)}\n\n")
return input_dict
class Wastewater(BasicSubmission):
"""