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Working new version.

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This commit is contained in:
Landon Wark
2023-09-11 13:45:10 -05:00
parent e0b80f6c7a
commit 5a978c9bff
15 changed files with 417 additions and 743 deletions
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83
src/submissions/backend/db/models/kits.py
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@@ -12,16 +12,6 @@ import logging
logger = logging.getLogger(f'submissions.{__name__}')
# # Table containing reagenttype-kittype relationships
# reagenttypes_kittypes = Table("_reagentstypes_kittypes", Base.metadata,
# Column("reagent_types_id", INTEGER, ForeignKey("_reagent_types.id")),
# Column("kits_id", INTEGER, ForeignKey("_kits.id")),
# # The entry will look like ["Bacteria Culture":{"row":1, "column":4}]
# Column("uses", JSON),
# # is the reagent required for that kit?
# Column("required", INTEGER)
# )
reagenttypes_reagents = Table("_reagenttypes_reagents", Base.metadata, Column("reagent_id", INTEGER, ForeignKey("_reagents.id")), Column("reagenttype_id", INTEGER, ForeignKey("_reagent_types.id")))
@@ -34,13 +24,7 @@ class KitType(Base):
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64), unique=True) #: name of kit
submissions = relationship("BasicSubmission", back_populates="extraction_kit") #: submissions this kit was used for
# used_for = Column(JSON) #: list of names of sample types this kit can process
# used_for = relationship("SubmissionType", back_populates="extraction_kits", uselist=True, secondary=submissiontype_kittypes)
# cost_per_run = Column(FLOAT(2)) #: dollar amount for each full run of this kit NOTE: depreciated, use the constant and mutable costs instead
# reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes) #: reagent types this kit contains
# reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id")) #: joined reagent type id
# kit_reagenttype_association =
kit_reagenttype_associations = relationship(
"KitTypeReagentTypeAssociation",
back_populates="kit_type",
@@ -51,7 +35,6 @@ class KitType(Base):
# to "keyword" attribute
reagent_types = association_proxy("kit_reagenttype_associations", "reagent_type")
kit_submissiontype_associations = relationship(
"SubmissionTypeKitTypeAssociation",
back_populates="kit_type",
@@ -60,7 +43,6 @@ class KitType(Base):
used_for = association_proxy("kit_submissiontype_associations", "submission_type")
def __repr__(self) -> str:
return f"<KitType({self.name})>"
@@ -74,6 +56,15 @@ class KitType(Base):
return self.name
def get_reagents(self, required:bool=False) -> list:
"""
Return ReagentTypes linked to kit through KitTypeReagentTypeAssociation.
Args:
required (bool, optional): If true only return required types. Defaults to False.
Returns:
list: List of ReagentTypes
"""
if required:
return [item.reagent_type for item in self.kit_reagenttype_associations if item.required == 1]
else:
@@ -81,14 +72,24 @@ class KitType(Base):
def construct_xl_map_for_use(self, use:str) -> dict:
# map = self.used_for[use]
"""
Creates map of locations in excel workbook for a SubmissionType
Args:
use (str): Submissiontype.name
Returns:
dict: Dictionary containing information locations.
"""
map = {}
# Get all KitTypeReagentTypeAssociation for SubmissionType
assocs = [item for item in self.kit_reagenttype_associations if use in item.uses]
for assoc in assocs:
try:
map[assoc.reagent_type.name] = assoc.uses[use]
except TypeError:
continue
# Get SubmissionType info map
try:
st_assoc = [item for item in self.used_for if use == item.name][0]
map['info'] = st_assoc.info_map
@@ -106,7 +107,6 @@ class KitTypeReagentTypeAssociation(Base):
kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True)
uses = Column(JSON)
required = Column(INTEGER)
# reagent_type_name = Column(INTEGER, ForeignKey("_reagent_types.name"))
kit_type = relationship(KitType, back_populates="kit_reagenttype_associations")
@@ -139,11 +139,8 @@ class ReagentType(Base):
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64)) #: name of reagent type
# kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", use_alter=True, name="fk_RT_kits_id")) #: id of joined kit type
# kits = relationship("KitType", back_populates="reagent_types", uselist=True, foreign_keys=[kit_id]) #: kits this reagent is used in
instances = relationship("Reagent", back_populates="type", secondary=reagenttypes_reagents) #: concrete instances of this reagent type
eol_ext = Column(Interval()) #: extension of life interval
# required = Column(INTEGER, server_default="1") #: sqlite boolean to determine if reagent type is essential for the kit
last_used = Column(String(32)) #: last used lot number of this type of reagent
@validates('required')
@@ -202,8 +199,10 @@ class Reagent(Base):
dict: gui friendly dictionary
"""
if extraction_kit != None:
# Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType
try:
reagent_role = list(set(self.type).intersection(extraction_kit.reagent_types))[0]
# Most will be able to fall back to first ReagentType in itself because most will only have 1.
except:
reagent_role = self.type[0]
else:
@@ -212,9 +211,9 @@ class Reagent(Base):
rtype = reagent_role.name.replace("_", " ").title()
except AttributeError:
rtype = "Unknown"
# Calculate expiry with EOL from ReagentType
try:
place_holder = self.expiry + reagent_role.eol_ext
# logger.debug(f"EOL_ext for {self.lot} -- {self.expiry} + {self.type.eol_ext} = {place_holder}")
except TypeError as e:
place_holder = date.today()
logger.debug(f"We got a type error setting {self.lot} expiry: {e}. setting to today for testing")
@@ -227,9 +226,28 @@ class Reagent(Base):
"expiry": place_holder.strftime("%Y-%m-%d")
}
def to_reagent_dict(self) -> dict:
def to_reagent_dict(self, extraction_kit:KitType=None) -> dict:
"""
Returns basic reagent dictionary.
Returns:
dict: Basic reagent dictionary of 'type', 'lot', 'expiry'
"""
if extraction_kit != None:
# Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType
try:
reagent_role = list(set(self.type).intersection(extraction_kit.reagent_types))[0]
# Most will be able to fall back to first ReagentType in itself because most will only have 1.
except:
reagent_role = self.type[0]
else:
reagent_role = self.type[0]
try:
rtype = reagent_role.name
except AttributeError:
rtype = "Unknown"
return {
"type": type,
"type": rtype,
"lot": self.lot,
"expiry": self.expiry.strftime("%Y-%m-%d")
}
@@ -249,12 +267,14 @@ class Discount(Base):
amount = Column(FLOAT(2))
class SubmissionType(Base):
"""
Abstract of types of submissions.
"""
__tablename__ = "_submission_types"
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(128), unique=True) #: name of submission type
info_map = Column(JSON)
info_map = Column(JSON) #: Where basic information is found in the excel workbook corresponding to this type.
instances = relationship("BasicSubmission", backref="submission_type")
submissiontype_kit_associations = relationship(
@@ -269,14 +289,15 @@ class SubmissionType(Base):
return f"<SubmissionType({self.name})>"
class SubmissionTypeKitTypeAssociation(Base):
"""
Abstract of relationship between kits and their submission type.
"""
__tablename__ = "_submissiontypes_kittypes"
submission_types_id = Column(INTEGER, ForeignKey("_submission_types.id"), primary_key=True)
kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True)
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)
# reagent_type_name = Column(INTEGER, ForeignKey("_reagent_types.name"))
kit_type = relationship(KitType, back_populates="kit_submissiontype_associations")