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Pending large code cleanup

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This commit is contained in:
Landon Wark
2024-01-31 15:21:07 -06:00
parent 319f72cab2
commit eda62fba5a
19 changed files with 741 additions and 103 deletions
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45
src/submissions/backend/db/models/kits.py
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@@ -18,8 +18,8 @@ logger = logging.getLogger(f'submissions.{__name__}')
reagenttypes_reagents = Table(
"_reagenttypes_reagents",
Base.metadata,
Column("reagent_id", INTEGER, ForeignKey("_reagents.id")),
Column("reagenttype_id", INTEGER, ForeignKey("_reagent_types.id")),
Column("reagent_id", INTEGER, ForeignKey("_reagent.id")),
Column("reagenttype_id", INTEGER, ForeignKey("_reagenttype.id")),
extend_existing = True
)
@@ -27,7 +27,7 @@ equipmentroles_equipment = Table(
"_equipmentroles_equipment",
Base.metadata,
Column("equipment_id", INTEGER, ForeignKey("_equipment.id")),
Column("equipmentroles_id", INTEGER, ForeignKey("_equipment_roles.id")),
Column("equipmentroles_id", INTEGER, ForeignKey("_equipmentrole.id")),
extend_existing=True
)
@@ -43,7 +43,7 @@ equipmentroles_processes = Table(
"_equipmentroles_processes",
Base.metadata,
Column("process_id", INTEGER, ForeignKey("_process.id")),
Column("equipmentrole_id", INTEGER, ForeignKey("_equipment_roles.id")),
Column("equipmentrole_id", INTEGER, ForeignKey("_equipmentrole.id")),
extend_existing=True
)
@@ -51,7 +51,7 @@ submissiontypes_processes = Table(
"_submissiontypes_processes",
Base.metadata,
Column("process_id", INTEGER, ForeignKey("_process.id")),
Column("equipmentroles_id", INTEGER, ForeignKey("_submission_types.id")),
Column("equipmentroles_id", INTEGER, ForeignKey("_submissiontype.id")),
extend_existing=True
)
@@ -59,7 +59,7 @@ kittypes_processes = Table(
"_kittypes_processes",
Base.metadata,
Column("process_id", INTEGER, ForeignKey("_process.id")),
Column("kit_id", INTEGER, ForeignKey("_kits.id")),
Column("kit_id", INTEGER, ForeignKey("_kittype.id")),
extend_existing=True
)
@@ -304,7 +304,7 @@ class Reagent(BaseClass):
id = Column(INTEGER, primary_key=True) #: primary key
type = relationship("ReagentType", back_populates="instances", secondary=reagenttypes_reagents) #: joined parent reagent type
type_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', name="fk_reagent_type_id")) #: id of parent reagent type
type_id = Column(INTEGER, ForeignKey("_reagenttype.id", ondelete='SET NULL', name="fk_reagent_type_id")) #: id of parent reagent type
name = Column(String(64)) #: reagent name
lot = Column(String(64)) #: lot number of reagent
expiry = Column(TIMESTAMP) #: expiry date - extended by eol_ext of parent programmatically
@@ -442,9 +442,9 @@ class Discount(BaseClass):
id = Column(INTEGER, primary_key=True) #: primary key
kit = relationship("KitType") #: joined parent reagent type
kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete='SET NULL', name="fk_kit_type_id")) #: id of joined kit
kit_id = Column(INTEGER, ForeignKey("_kittype.id", ondelete='SET NULL', name="fk_kit_type_id")) #: id of joined kit
client = relationship("Organization") #: joined client lab
client_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete='SET NULL', name="fk_org_id")) #: id of joined client
client_id = Column(INTEGER, ForeignKey("_organization.id", ondelete='SET NULL', name="fk_org_id")) #: id of joined client
name = Column(String(128)) #: Short description
amount = Column(FLOAT(2)) #: Dollar amount of discount
@@ -625,8 +625,9 @@ class SubmissionType(BaseClass):
"""
Adds this instances to the database and commits.
"""
self.__database_session__.add(self)
self.__database_session__.commit()
# self.__database_session__.add(self)
# self.__database_session__.commit()
super().save()
class SubmissionTypeKitTypeAssociation(BaseClass):
"""
@@ -634,8 +635,8 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
"""
# __tablename__ = "_submissiontypes_kittypes"
submission_types_id = Column(INTEGER, ForeignKey("_submission_types.id"), primary_key=True) #: id of joined submission type
kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True) #: id of joined kit
submission_types_id = Column(INTEGER, ForeignKey("_submissiontype.id"), primary_key=True) #: id of joined submission type
kits_id = Column(INTEGER, ForeignKey("_kittype.id"), primary_key=True) #: id of joined kit
mutable_cost_column = Column(FLOAT(2)) #: dollar amount per 96 well plate that can change with number of columns (reagents, tips, etc)
mutable_cost_sample = Column(FLOAT(2)) #: dollar amount that can change with number of samples (reagents, tips, etc)
constant_cost = Column(FLOAT(2)) #: dollar amount per plate that will remain constant (plates, man hours, etc)
@@ -707,9 +708,9 @@ class KitTypeReagentTypeAssociation(BaseClass):
"""
# __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)
reagent_types_id = Column(INTEGER, ForeignKey("_reagenttype.id"), primary_key=True) #: id of associated reagent type
kits_id = Column(INTEGER, ForeignKey("_kittype.id"), primary_key=True) #: id of associated reagent type
submission_type_id = Column(INTEGER, ForeignKey("_submissiontype.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
@@ -810,8 +811,8 @@ class SubmissionReagentAssociation(BaseClass):
# __tablename__ = "_reagents_submissions"
reagent_id = Column(INTEGER, ForeignKey("_reagents.id"), primary_key=True) #: id of associated sample
submission_id = Column(INTEGER, ForeignKey("_submissions.id"), primary_key=True)
reagent_id = Column(INTEGER, ForeignKey("_reagent.id"), primary_key=True) #: id of associated sample
submission_id = Column(INTEGER, ForeignKey("_basicsubmission.id"), primary_key=True)
comments = Column(String(1024))
submission = relationship("BasicSubmission", back_populates="submission_reagent_associations") #: associated submission
@@ -1060,7 +1061,7 @@ class SubmissionEquipmentAssociation(BaseClass):
# __tablename__ = "_equipment_submissions"
equipment_id = Column(INTEGER, ForeignKey("_equipment.id"), primary_key=True) #: id of associated equipment
submission_id = Column(INTEGER, ForeignKey("_submissions.id"), primary_key=True) #: id of associated submission
submission_id = Column(INTEGER, ForeignKey("_basicsubmission.id"), primary_key=True) #: id of associated submission
role = Column(String(64), primary_key=True) #: name of the role the equipment fills
# process = Column(String(64)) #: name of the process run on this equipment
process_id = Column(INTEGER, ForeignKey("_process.id",ondelete="SET NULL", name="SEA_Process_id"))
@@ -1090,8 +1091,8 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
# __tablename__ = "_submissiontype_equipmentrole"
equipmentrole_id = Column(INTEGER, ForeignKey("_equipment_roles.id"), primary_key=True) #: id of associated equipment
submissiontype_id = Column(INTEGER, ForeignKey("_submission_types.id"), primary_key=True) #: id of associated submission
equipmentrole_id = Column(INTEGER, ForeignKey("_equipmentrole.id"), primary_key=True) #: id of associated equipment
submissiontype_id = Column(INTEGER, ForeignKey("_submissiontype.id"), primary_key=True) #: id of associated submission
uses = Column(JSON) #: locations of equipment on the submission type excel sheet.
static = Column(INTEGER, default=1) #: if 1 this piece of equipment will always be used, otherwise it will need to be selected from list?
@@ -1156,7 +1157,7 @@ class Process(BaseClass):
@classmethod
@setup_lookup
def query(cls, name:str|None, limit:int=0):
def query(cls, name:str|None=None, limit:int=0):
query = cls.__database_session__.query(cls)
match name:
case str():