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Added SubmissionType to KitRTAssoc

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This commit is contained in:
Landon Wark
2024-01-08 13:19:27 -06:00
parent 8c688df75f
commit d66d861262
3 changed files with 275 additions and 103 deletions
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34
alembic/versions/4606a7be32e8_adding_submissiontype_to_.py Normal file
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@@ -0,0 +1,34 @@
"""Adding SubmissionType to KitReagentTypeAssociations
Revision ID: 4606a7be32e8
Revises: 67fa77849024
Create Date: 2024-01-08 09:04:46.917615
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '4606a7be32e8'
down_revision = '67fa77849024'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_reagenttypes_kittypes', schema=None) as batch_op:
batch_op.add_column(sa.Column('submission_type_id', sa.INTEGER(), nullable=False))
batch_op.create_foreign_key("st_kt_rt_assoc", '_submission_types', ['submission_type_id'], ['id'])
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_reagenttypes_kittypes', schema=None) as batch_op:
batch_op.drop_constraint(None, type_='foreignkey')
batch_op.drop_column('submission_type_id')
# ### end Alembic commands ###

341
src/submissions/backend/db/models/kits.py
View File

@@ -94,9 +94,9 @@ class KitType(BaseClass):
""" """
match submission_type: match submission_type:
case SubmissionType(): case SubmissionType():
relevant_associations = [item for item in self.kit_reagenttype_associations if submission_type.name in item.uses.keys()] relevant_associations = [item for item in self.kit_reagenttype_associations if item.submission_type==submission_type]
case str(): case str():
relevant_associations = [item for item in self.kit_reagenttype_associations if submission_type in item.uses.keys()] relevant_associations = [item for item in self.kit_reagenttype_associations if item.submission_type.name==submission_type]
case _: case _:
relevant_associations = [item for item in self.kit_reagenttype_associations] relevant_associations = [item for item in self.kit_reagenttype_associations]
if required: if required:
@@ -104,7 +104,7 @@ class KitType(BaseClass):
else: else:
return [item.reagent_type for item in relevant_associations] return [item.reagent_type for item in relevant_associations]
def construct_xl_map_for_use(self, use:str) -> dict: def construct_xl_map_for_use(self, submission_type:str|SubmissionType) -> dict:
""" """
Creates map of locations in excel workbook for a SubmissionType Creates map of locations in excel workbook for a SubmissionType
@@ -115,16 +115,25 @@ class KitType(BaseClass):
dict: Dictionary containing information locations. dict: Dictionary containing information locations.
""" """
map = {} map = {}
match submission_type:
case str():
assocs = [item for item in self.kit_reagenttype_associations if item.submission_type.name==submission_type]
st_assoc = [item for item in self.used_for if submission_type == item.name][0]
case SubmissionType():
assocs = [item for item in self.kit_reagenttype_associations if item.submission_type==submission_type]
st_assoc = submission_type
case _:
raise ValueError(f"Wrong variable type: {type(submission_type)} used!")
# Get all KitTypeReagentTypeAssociation for SubmissionType # Get all KitTypeReagentTypeAssociation for SubmissionType
assocs = [item for item in self.kit_reagenttype_associations if use in item.uses] # assocs = [item for item in self.kit_reagenttype_associations if item.submission_type==submission_type]
for assoc in assocs: for assoc in assocs:
try: try:
map[assoc.reagent_type.name] = assoc.uses[use] map[assoc.reagent_type.name] = assoc.uses
except TypeError: except TypeError:
continue continue
# Get SubmissionType info map # Get SubmissionType info map
try: try:
st_assoc = [item for item in self.used_for if use == item.name][0] # st_assoc = [item for item in self.used_for if use == item.name][0]
map['info'] = st_assoc.info_map map['info'] = st_assoc.info_map
except IndexError as e: except IndexError as e:
map['info'] = {} map['info'] = {}
@@ -273,120 +282,123 @@ class ReagentType(BaseClass):
from backend.validators.pydant import PydReagent from backend.validators.pydant import PydReagent
return PydReagent(lot=None, type=self.name, name=self.name, expiry=date.today()) return PydReagent(lot=None, type=self.name, name=self.name, expiry=date.today())
class KitTypeReagentTypeAssociation(BaseClass): # class KitTypeReagentTypeAssociation(BaseClass):
""" # """
table containing reagenttype/kittype associations # table containing reagenttype/kittype associations
DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html # DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
""" # """
__tablename__ = "_reagenttypes_kittypes" # __tablename__ = "_reagenttypes_kittypes"
reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id"), primary_key=True) #: id of associated reagent type # reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id"), primary_key=True) #: id of associated reagent type
kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True) #: id of associated reagent type # kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True) #: id of associated reagent type
uses = Column(JSON) #: map to location on excel sheets of different submission types # submission_type_id = (Column(INTEGER), ForeignKey("_submission_types.id"), primary_key=True)
required = Column(INTEGER) #: whether the reagent type is required for the kit (Boolean 1 or 0) # uses = Column(JSON) #: map to location on excel sheets of different submission types
last_used = Column(String(32)) #: last used lot number of this type of reagent # required = Column(INTEGER) #: whether the reagent type is required for the kit (Boolean 1 or 0)
# last_used = Column(String(32)) #: last used lot number of this type of reagent
kit_type = relationship(KitType, back_populates="kit_reagenttype_associations") #: relationship to associated kit # kit_type = relationship(KitType, back_populates="kit_reagenttype_associations") #: relationship to associated kit
# reference to the "ReagentType" object # # reference to the "ReagentType" object
reagent_type = relationship(ReagentType, back_populates="reagenttype_kit_associations") #: relationship to associated reagent type # reagent_type = relationship(ReagentType, back_populates="reagenttype_kit_associations") #: relationship to associated reagent type
def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1): # submission_type = relationship(SubmissionType, back_populates="submissiontype_kit_rt_associations")
# logger.debug(f"Parameters: Kit={kit_type}, RT={reagent_type}, Uses={uses}, Required={required}")
self.kit_type = kit_type
self.reagent_type = reagent_type
self.uses = uses
self.required = required
def __repr__(self) -> str: # def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1):
return f"<KitTypeReagentTypeAssociation({self.kit_type} & {self.reagent_type})>" # # logger.debug(f"Parameters: Kit={kit_type}, RT={reagent_type}, Uses={uses}, Required={required}")
# self.kit_type = kit_type
# self.reagent_type = reagent_type
# self.uses = uses
# self.required = required
@validates('required') # def __repr__(self) -> str:
def validate_age(self, key, value): # return f"<KitTypeReagentTypeAssociation({self.kit_type} & {self.reagent_type})>"
"""
Ensures only 1 & 0 used in 'required'
Args: # @validates('required')
key (str): name of attribute # def validate_age(self, key, value):
value (_type_): value of attribute # """
# Ensures only 1 & 0 used in 'required'
Raises: # Args:
ValueError: Raised if bad value given # key (str): name of attribute
# value (_type_): value of attribute
Returns: # Raises:
_type_: value # ValueError: Raised if bad value given
"""
if not 0 <= value < 2: # Returns:
raise ValueError(f'Invalid required value {value}. Must be 0 or 1.') # _type_: value
return value # """
# if not 0 <= value < 2:
# raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
# return value
@validates('reagenttype') # @validates('reagenttype')
def validate_reagenttype(self, key, value): # def validate_reagenttype(self, key, value):
""" # """
Ensures reagenttype is an actual ReagentType # Ensures reagenttype is an actual ReagentType
Args: # Args:
key (str)): name of attribute # key (str)): name of attribute
value (_type_): value of attribute # value (_type_): value of attribute
Raises: # Raises:
ValueError: raised if reagenttype is not a ReagentType # ValueError: raised if reagenttype is not a ReagentType
Returns: # Returns:
_type_: ReagentType # _type_: ReagentType
""" # """
if not isinstance(value, ReagentType): # if not isinstance(value, ReagentType):
raise ValueError(f'{value} is not a reagenttype') # raise ValueError(f'{value} is not a reagenttype')
return value # return value
@classmethod # @classmethod
@setup_lookup # @setup_lookup
def query(cls, # def query(cls,
kit_type:KitType|str|None=None, # kit_type:KitType|str|None=None,
reagent_type:ReagentType|str|None=None, # reagent_type:ReagentType|str|None=None,
limit:int=0 # limit:int=0
) -> KitTypeReagentTypeAssociation|List[KitTypeReagentTypeAssociation]: # ) -> KitTypeReagentTypeAssociation|List[KitTypeReagentTypeAssociation]:
""" # """
Lookup junction of ReagentType and KitType # Lookup junction of ReagentType and KitType
Args: # Args:
kit_type (models.KitType | str | None): KitType of interest. # kit_type (models.KitType | str | None): KitType of interest.
reagent_type (models.ReagentType | str | None): ReagentType of interest. # reagent_type (models.ReagentType | str | None): ReagentType of interest.
limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0. # limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
Returns: # Returns:
models.KitTypeReagentTypeAssociation|List[models.KitTypeReagentTypeAssociation]: Junction of interest. # models.KitTypeReagentTypeAssociation|List[models.KitTypeReagentTypeAssociation]: Junction of interest.
""" # """
query: Query = cls.__database_session__.query(cls) # query: Query = cls.__database_session__.query(cls)
match kit_type: # match kit_type:
case KitType(): # case KitType():
query = query.filter(cls.kit_type==kit_type) # query = query.filter(cls.kit_type==kit_type)
case str(): # case str():
query = query.join(KitType).filter(KitType.name==kit_type) # query = query.join(KitType).filter(KitType.name==kit_type)
case _: # case _:
pass # pass
match reagent_type: # match reagent_type:
case ReagentType(): # case ReagentType():
query = query.filter(cls.reagent_type==reagent_type) # query = query.filter(cls.reagent_type==reagent_type)
case str(): # case str():
query = query.join(ReagentType).filter(ReagentType.name==reagent_type) # query = query.join(ReagentType).filter(ReagentType.name==reagent_type)
case _: # case _:
pass # pass
if kit_type != None and reagent_type != None: # if kit_type != None and reagent_type != None:
limit = 1 # limit = 1
return query_return(query=query, limit=limit) # return query_return(query=query, limit=limit)
def save(self) -> Report: # def save(self) -> Report:
""" # """
Adds this instance to the database and commits. # Adds this instance to the database and commits.
Returns: # Returns:
Report: Result of save action # Report: Result of save action
""" # """
report = Report() # report = Report()
self.__database_session__.add(self) # self.__database_session__.add(self)
self.__database_session__.commit() # self.__database_session__.commit()
return report # return report
class Reagent(BaseClass): class Reagent(BaseClass):
""" """
@@ -622,6 +634,12 @@ class SubmissionType(BaseClass):
equipment = association_proxy("submissiontype_equipmentrole_associations", "equipment_role") equipment = association_proxy("submissiontype_equipmentrole_associations", "equipment_role")
submissiontype_kit_rt_associations = relationship(
"KitTypeReagentTypeAssociation",
back_populates="submission_type",
cascade="all, delete-orphan"
)
def __repr__(self) -> str: def __repr__(self) -> str:
return f"<SubmissionType({self.name})>" return f"<SubmissionType({self.name})>"
@@ -778,6 +796,125 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
limit = query.count() limit = query.count()
return query_return(query=query, limit=limit) return query_return(query=query, limit=limit)
class KitTypeReagentTypeAssociation(BaseClass):
"""
table containing reagenttype/kittype associations
DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
"""
__tablename__ = "_reagenttypes_kittypes"
reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id"), primary_key=True) #: id of associated reagent type
kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True) #: id of associated reagent type
submission_type_id = Column(INTEGER, ForeignKey("_submission_types.id"), primary_key=True)
uses = Column(JSON) #: map to location on excel sheets of different submission types
required = Column(INTEGER) #: whether the reagent type is required for the kit (Boolean 1 or 0)
last_used = Column(String(32)) #: last used lot number of this type of reagent
kit_type = relationship(KitType, back_populates="kit_reagenttype_associations") #: relationship to associated kit
# reference to the "ReagentType" object
reagent_type = relationship(ReagentType, back_populates="reagenttype_kit_associations") #: relationship to associated reagent type
submission_type = relationship(SubmissionType, back_populates="submissiontype_kit_rt_associations")
def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1):
# logger.debug(f"Parameters: Kit={kit_type}, RT={reagent_type}, Uses={uses}, Required={required}")
self.kit_type = kit_type
self.reagent_type = reagent_type
self.uses = uses
self.required = required
def __repr__(self) -> str:
return f"<KitTypeReagentTypeAssociation({self.kit_type} & {self.reagent_type})>"
@validates('required')
def validate_age(self, key, value):
"""
Ensures only 1 & 0 used in 'required'
Args:
key (str): name of attribute
value (_type_): value of attribute
Raises:
ValueError: Raised if bad value given
Returns:
_type_: value
"""
if not 0 <= value < 2:
raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
return value
@validates('reagenttype')
def validate_reagenttype(self, key, value):
"""
Ensures reagenttype is an actual ReagentType
Args:
key (str)): name of attribute
value (_type_): value of attribute
Raises:
ValueError: raised if reagenttype is not a ReagentType
Returns:
_type_: ReagentType
"""
if not isinstance(value, ReagentType):
raise ValueError(f'{value} is not a reagenttype')
return value
@classmethod
@setup_lookup
def query(cls,
kit_type:KitType|str|None=None,
reagent_type:ReagentType|str|None=None,
limit:int=0
) -> KitTypeReagentTypeAssociation|List[KitTypeReagentTypeAssociation]:
"""
Lookup junction of ReagentType and KitType
Args:
kit_type (models.KitType | str | None): KitType of interest.
reagent_type (models.ReagentType | str | None): ReagentType of interest.
limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
Returns:
models.KitTypeReagentTypeAssociation|List[models.KitTypeReagentTypeAssociation]: Junction of interest.
"""
query: Query = cls.__database_session__.query(cls)
match kit_type:
case KitType():
query = query.filter(cls.kit_type==kit_type)
case str():
query = query.join(KitType).filter(KitType.name==kit_type)
case _:
pass
match reagent_type:
case ReagentType():
query = query.filter(cls.reagent_type==reagent_type)
case str():
query = query.join(ReagentType).filter(ReagentType.name==reagent_type)
case _:
pass
if kit_type != None and reagent_type != None:
limit = 1
return query_return(query=query, limit=limit)
def save(self) -> Report:
"""
Adds this instance to the database and commits.
Returns:
Report: Result of save action
"""
report = Report()
self.__database_session__.add(self)
self.__database_session__.commit()
return report
class SubmissionReagentAssociation(BaseClass): class SubmissionReagentAssociation(BaseClass):
__tablename__ = "_reagents_submissions" __tablename__ = "_reagents_submissions"

3
src/submissions/backend/excel/parser.py
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@@ -211,6 +211,7 @@ class ReagentParser(object):
logger.debug("\n\nHello from ReagentParser!\n\n") logger.debug("\n\nHello from ReagentParser!\n\n")
# self.ctx = ctx # self.ctx = ctx
self.map = self.fetch_kit_info_map(extraction_kit=extraction_kit, submission_type=submission_type) self.map = self.fetch_kit_info_map(extraction_kit=extraction_kit, submission_type=submission_type)
logger.debug(f"Reagent Parser map: {self.map}")
self.xl = xl self.xl = xl
def fetch_kit_info_map(self, extraction_kit:dict, submission_type:str) -> dict: def fetch_kit_info_map(self, extraction_kit:dict, submission_type:str) -> dict:
@@ -523,7 +524,7 @@ class EquipmentParser(object):
asset = self.get_asset_number(input=asset) asset = self.get_asset_number(input=asset)
eq = Equipment.query(asset_number=asset) eq = Equipment.query(asset_number=asset)
process = df.iat[equipment['process']['row']-1, equipment['process']['column']-1] process = df.iat[equipment['process']['row']-1, equipment['process']['column']-1]
output.append(PydEquipment(name=eq.name, process=[process], role=equipment['role'], asset_number=asset, nickname=eq.nickname)) output.append(PydEquipment(name=eq.name, process=process, role=equipment['role'], asset_number=asset, nickname=eq.nickname))
# logger.debug(f"Here is the output so far: {pformat(output)}") # logger.debug(f"Here is the output so far: {pformat(output)}")
return output return output