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Conversion of some functions to generators.

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This commit is contained in:
lwark
2024-07-31 13:08:56 -05:00
parent eb6cdc63e2
commit 8266275354
15 changed files with 374 additions and 369 deletions
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61
src/submissions/backend/db/models/kits.py
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@@ -8,7 +8,7 @@ from sqlalchemy.ext.associationproxy import association_proxy
from datetime import date
import logging, re
from tools import check_authorization, setup_lookup, Report, Result
from typing import List, Literal
from typing import List, Literal, Generator
from pandas import ExcelFile
from pathlib import Path
from . import Base, BaseClass, Organization
@@ -168,9 +168,9 @@ class KitType(BaseClass):
return [item.reagent_role for item in relevant_associations]
# TODO: Move to BasicSubmission?
def construct_xl_map_for_use(self, submission_type: str | SubmissionType) -> dict:
def construct_xl_map_for_use(self, submission_type: str | SubmissionType) -> Generator[str, str]:
"""
Creates map of locations in excel workbook for a SubmissionType
Creates map of locations in Excel workbook for a SubmissionType
Args:
submission_type (str | SubmissionType): Submissiontype.name
@@ -178,7 +178,7 @@ class KitType(BaseClass):
Returns:
dict: Dictionary containing information locations.
"""
info_map = {}
# info_map = {}
# NOTE: Account for submission_type variable type.
match submission_type:
case str():
@@ -193,10 +193,10 @@ class KitType(BaseClass):
# logger.debug("Get all KitTypeReagentTypeAssociation for SubmissionType")
for assoc in assocs:
try:
info_map[assoc.reagent_role.name] = assoc.uses
yield assoc.reagent_role.name, assoc.uses
except TypeError:
continue
return info_map
# return info_map
@classmethod
@setup_lookup
@@ -409,6 +409,7 @@ class Reagent(BaseClass):
rtype = reagent_role.name.replace("_", " ")
except AttributeError:
rtype = "Unknown"
# logger.debug(f"Role for {self.name}: {rtype}")
# NOTE: Calculate expiry with EOL from ReagentType
try:
place_holder = self.expiry + reagent_role.eol_ext
@@ -611,7 +612,8 @@ class SubmissionType(BaseClass):
) #: Association of equipmentroles
equipment = association_proxy("submissiontype_equipmentrole_associations", "equipment_role",
creator=lambda eq: SubmissionTypeEquipmentRoleAssociation(equipment_role=eq)) #: Proxy of equipmentrole associations
creator=lambda eq: SubmissionTypeEquipmentRoleAssociation(
equipment_role=eq)) #: Proxy of equipmentrole associations
submissiontype_kit_rt_associations = relationship(
"KitTypeReagentRoleAssociation",
@@ -665,7 +667,7 @@ class SubmissionType(BaseClass):
def construct_info_map(self, mode: Literal['read', 'write']) -> dict:
"""
Make of map of where all fields are located in excel sheet
Make of map of where all fields are located in Excel sheet
Args:
mode (Literal["read", "write"]): Which mode to get locations for
@@ -673,15 +675,16 @@ class SubmissionType(BaseClass):
Returns:
dict: Map of locations
"""
info = {k:v for k,v in self.info_map.items() if k != "custom"}
info = {k: v for k, v in self.info_map.items() if k != "custom"}
logger.debug(f"Info map: {info}")
output = {}
match mode:
case "read":
output = {k: v[mode] for k, v in info.items() if v[mode]}
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 _:
output = {}
output['custom'] = self.info_map['custom']
return output
@@ -694,36 +697,38 @@ class SubmissionType(BaseClass):
"""
return self.sample_map
def construct_equipment_map(self) -> dict:
def construct_equipment_map(self) -> Generator[str, dict]:
"""
Constructs map of equipment to excel cells.
Returns:
dict: Map equipment locations in excel sheet
"""
output = {}
# output = {}
# logger.debug("Iterating through equipment roles")
for item in self.submissiontype_equipmentrole_associations:
emap = item.uses
if emap is None:
emap = {}
output[item.equipment_role.name] = emap
return output
# output[item.equipment_role.name] = emap
yield item.equipment_role.name, emap
# return output
def construct_tips_map(self) -> dict:
def construct_tips_map(self) -> Generator[str, dict]:
"""
Constructs map of tips to excel cells.
Returns:
dict: Tip locations in the excel sheet.
"""
output = {}
# output = {}
for item in self.submissiontype_tiprole_associations:
tmap = item.uses
if tmap is None:
tmap = {}
output[item.tip_role.name] = tmap
return output
# output[item.tip_role.name] = tmap
yield item.tip_role.name, tmap
# return output
def get_equipment(self, extraction_kit: str | KitType | None = None) -> List['PydEquipmentRole']:
"""
@@ -1280,15 +1285,16 @@ class EquipmentRole(BaseClass):
Returns:
dict: This EquipmentRole dict
"""
output = {}
for key, value in self.__dict__.items():
match key:
case "processes":
pass
case _:
value = value
output[key] = value
return output
# output = {}
return {key: value for key, value in self.__dict__.items() if key != "processes"}
# match key:
# case "processes":
# pass
# case _:
# value = value
# yield key, value
# # output[key] = value
# return output
def to_pydantic(self, submission_type: SubmissionType,
extraction_kit: str | KitType | None = None) -> "PydEquipmentRole":
@@ -1668,7 +1674,6 @@ class SubmissionTipsAssociation(BaseClass):
back_populates="tips_submission_associations") #: associated equipment
role_name = Column(String(32), primary_key=True) #, ForeignKey("_tiprole.name"))
def to_sub_dict(self) -> dict:
"""
This item as a dictionary