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Update to autofill.

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This commit is contained in:
Landon Wark
2023-09-20 09:19:59 -05:00
parent 0c843d1561
commit 82ab06efad
13 changed files with 378 additions and 149 deletions
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86
src/submissions/backend/db/models/kits.py
View File

@@ -97,39 +97,7 @@ class KitType(Base):
map['info'] = {}
return map
class KitTypeReagentTypeAssociation(Base):
"""
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)
kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True)
uses = Column(JSON)
required = Column(INTEGER)
kit_type = relationship(KitType, back_populates="kit_reagenttype_associations")
# reference to the "ReagentType" object
reagent_type = relationship("ReagentType")
def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1):
self.kit_type = kit_type
self.reagent_type = reagent_type
self.uses = uses
self.required = required
@validates('required')
def validate_age(self, key, 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):
if not isinstance(value, ReagentType):
raise ValueError(f'{value} is not a reagenttype')
return value
class ReagentType(Base):
"""
@@ -141,7 +109,16 @@ class ReagentType(Base):
name = Column(String(64)) #: name of reagent type
instances = relationship("Reagent", back_populates="type", secondary=reagenttypes_reagents) #: concrete instances of this reagent type
eol_ext = Column(Interval()) #: extension of life interval
last_used = Column(String(32)) #: last used lot number of this type of reagent
reagenttype_kit_associations = relationship(
"KitTypeReagentTypeAssociation",
back_populates="reagent_type",
cascade="all, delete-orphan",
)
# association proxy of "user_keyword_associations" collection
# to "keyword" attribute
kit_types = association_proxy("kit_reagenttype_associations", "kit_type")
@validates('required')
def validate_age(self, key, value):
@@ -160,6 +137,44 @@ class ReagentType(Base):
def __repr__(self):
return f"ReagentType({self.name})"
class KitTypeReagentTypeAssociation(Base):
"""
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)
kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True)
uses = Column(JSON)
required = Column(INTEGER)
last_used = Column(String(32)) #: last used lot number of this type of reagent
kit_type = relationship(KitType, back_populates="kit_reagenttype_associations")
# reference to the "ReagentType" object
reagent_type = relationship(ReagentType, back_populates="reagenttype_kit_associations")
def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1):
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):
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):
if not isinstance(value, ReagentType):
raise ValueError(f'{value} is not a reagenttype')
return value
class Reagent(Base):
"""
@@ -247,10 +262,12 @@ class Reagent(Base):
except AttributeError:
rtype = "Unknown"
return {
"name":self.name,
"type": rtype,
"lot": self.lot,
"expiry": self.expiry.strftime("%Y-%m-%d")
}
class Discount(Base):
"""
@@ -266,6 +283,9 @@ class Discount(Base):
name = Column(String(128))
amount = Column(FLOAT(2))
def __repr__(self) -> str:
return f"<Discount({self.name})>"
class SubmissionType(Base):
"""
Abstract of types of submissions.

3
src/submissions/backend/db/models/organizations.py
View File

@@ -47,3 +47,6 @@ class Contact(Base):
phone = Column(String(32)) #: contact phone number
organization = relationship("Organization", back_populates="contacts", uselist=True, secondary=orgs_contacts) #: relationship to joined organization
def __repr__(self) -> str:
return f"<Contact({self.name})>"

36
src/submissions/backend/db/models/submissions.py
View File

@@ -13,8 +13,6 @@ from sqlalchemy.ext.associationproxy import association_proxy
import uuid
from pandas import Timestamp
from dateutil.parser import parse
import pprint
from tools import check_not_nan
logger = logging.getLogger(f"submissions.{__name__}")
@@ -348,7 +346,7 @@ class BasicSample(Base):
return value
def __repr__(self) -> str:
return f"<{self.sample_type.replace('_', ' ').title(). replace(' ', '')}({self.submitter_id})>"
return f"<{self.sample_type.replace('_', ' ').title().replace(' ', '')}({self.submitter_id})>"
def set_attribute(self, name, value):
# logger.debug(f"Setting {name} to {value}")
@@ -417,56 +415,36 @@ class WastewaterSample(BasicSample):
logger.debug(f"Validating {key}: {value}")
return value or self.submitter_id
# def __init__(self, **kwargs):
# # Had a problem getting collection date from excel as text only.
# if 'collection_date' in kwargs.keys():
# logger.debug(f"Got collection_date: {kwargs['collection_date']}. Attempting parse.")
# if isinstance(kwargs['collection_date'], str):
# logger.debug(f"collection_date is a string...")
# kwargs['collection_date'] = parse(kwargs['collection_date'])
# logger.debug(f"output is {kwargs['collection_date']}")
# # Due to the plate map being populated with RSL numbers, we have to do some shuffling.
# try:
# kwargs['rsl_number'] = kwargs['submitter_id']
# except KeyError as e:
# logger.error(f"Error using {kwargs} for submitter_id")
# try:
# check = check_not_nan(kwargs['ww_full_sample_id'])
# except KeyError:
# logger.error(f"Error using {kwargs} for ww_full_sample_id")
# check = False
# if check:
# kwargs['submitter_id'] = kwargs["ww_full_sample_id"]
# super().__init__(**kwargs)
def set_attribute(self, name:str, value):
"""
Set an attribute of this object. Extends parent.
Args:
name (str): _description_
value (_type_): _description_
name (str): name of the attribute
value (_type_): value to be set
"""
# Due to the plate map being populated with RSL numbers, we have to do some shuffling.
# logger.debug(f"Input - {name}:{value}")
match name:
case "submitter_id":
# If submitter_id already has a value, stop
if self.submitter_id != None:
return
# otherwise also set rsl_number to the same value
else:
super().set_attribute("rsl_number", value)
case "ww_full_sample_id":
# If value present, set ww_full_sample_id and make this the submitter_id
if value != None:
super().set_attribute(name, value)
name = "submitter_id"
case 'collection_date':
# If this is a string use dateutils to parse into date()
if isinstance(value, str):
logger.debug(f"collection_date {value} is a string. Attempting parse...")
value = parse(value)
case "rsl_number":
if value == None:
value = self.submitter_id
# logger.debug(f"Output - {name}:{value}")
super().set_attribute(name, value)