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Split Concentration controls on the chart so they are individually selectable.

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This commit is contained in:
lwark
2025-04-11 12:54:27 -05:00
parent 96f178c09f
commit ae6717bc77
19 changed files with 380 additions and 457 deletions
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17
src/submissions/backend/validators/__init__.py
View File

@@ -80,26 +80,25 @@ class RSLNamer(object):
submission_type = cls.retrieve_submission_type(filename=filepath.stem.__str__())
return submission_type
def st_from_str(filename: str) -> str:
if filename.startswith("tmp"):
def st_from_str(file_name: str) -> str:
if file_name.startswith("tmp"):
return "Bacterial Culture"
regex = BasicSubmission.regex
m = regex.search(filename)
m = regex.search(file_name)
try:
submission_type = m.lastgroup
sub_type = m.lastgroup
except AttributeError as e:
submission_type = None
sub_type = None
logger.critical(f"No submission type found or submission type found!: {e}")
return submission_type
return sub_type
match filename:
case Path():
submission_type = st_from_path(filepath=filename)
case str():
submission_type = st_from_str(filename=filename)
submission_type = st_from_str(file_name=filename)
case _:
raise TypeError(f"Unsupported filename type: {type(filename)}.")
submission_type = None
try:
check = submission_type is None
except UnboundLocalError:
@@ -137,7 +136,7 @@ class RSLNamer(object):
if m is not None:
try:
parsed_name = m.group().upper().strip(".")
except:
except AttributeError:
parsed_name = None
else:
parsed_name = None

79
src/submissions/backend/validators/omni_gui_objects.py
View File

@@ -1,3 +1,7 @@
"""
Collection of pydantic objects to be used in the Gui system.
"""
from __future__ import annotations
import logging
from pydantic import BaseModel, field_validator, Field
@@ -10,6 +14,7 @@ logger = logging.getLogger(f"submissions.{__name__}")
class BaseOmni(BaseModel):
instance_object: Any | None = Field(default=None)
def __repr__(self):
@@ -23,23 +28,23 @@ class BaseOmni(BaseModel):
return cls.class_object.aliases
def check_all_attributes(self, attributes: dict) -> bool:
logger.debug(f"Incoming attributes: {attributes}")
# logger.debug(f"Incoming attributes: {attributes}")
attributes = {k : v for k, v in attributes.items() if k in self.list_searchables.keys()}
for key, value in attributes.items():
try:
logger.debug(f"Check if {value.__class__} is subclass of {BaseOmni}")
# logger.debug(f"Check if {value.__class__} is subclass of {BaseOmni}")
check = issubclass(value.__class__, BaseOmni)
except TypeError as e:
logger.error(f"Couldn't check if {value.__class__} is subclass of {BaseOmni} due to {e}")
check = False
if check:
logger.debug(f"Checking for subclass name.")
# logger.debug(f"Checking for subclass name.")
value = value.name
self_value = self.list_searchables[key]
if value != self_value:
logger.debug(f"Value {key} is False, these are not the same object.")
# logger.debug(f"Value {key} is False, these are not the same object.")
return False
logger.debug("Everything checks out, these are the same object.")
# logger.debug("Everything checks out, these are the same object.")
return True
def __setattr__(self, key, value):
@@ -51,24 +56,24 @@ class BaseOmni(BaseModel):
new_key = class_value.impl.key
except AttributeError:
new_key = None
logger.debug(f"Class value before new key: {class_value.property}")
# logger.debug(f"Class value before new key: {class_value.property}")
if new_key and new_key != key:
class_value = getattr(self.class_object, new_key)
logger.debug(f"Class value after new key: {class_value.property}")
# logger.debug(f"Class value after new key: {class_value.property}")
if isinstance(class_value, InstrumentedAttribute):
logger.debug(f"{key} is an InstrumentedAttribute with class_value.property: {class_value.property}.")
# logger.debug(f"{key} is an InstrumentedAttribute with class_value.property: {class_value.property}.")
match class_value.property:
case ColumnProperty():
logger.debug(f"Setting ColumnProperty to {value}")
# logger.debug(f"Setting ColumnProperty to {value}")
return super().__setattr__(key, value)
case _RelationshipDeclared():
logger.debug(f" {self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
# logger.debug(f" {self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
if class_value.property.uselist:
logger.debug(f"Setting {key} with uselist")
# logger.debug(f"Setting {key} with uselist")
existing = self.__getattribute__(key)
if existing is not None:
# NOTE: Getting some really weird duplicates for OmniSubmissionTypeKitTypeAssociation here.
logger.debug(f"Existing: {existing}, incoming: {value}")
# logger.debug(f"Existing: {existing}, incoming: {value}")
if isinstance(value, list):
if value != existing:
value = existing + value
@@ -82,7 +87,7 @@ class BaseOmni(BaseModel):
if issubclass(value.__class__, self.__class__):
value = value.to_sql()
value = [value]
logger.debug(f"Final value for {key}: {value}")
# logger.debug(f"Final value for {key}: {value}")
return super().__setattr__(key, value)
else:
if isinstance(value, list):
@@ -98,6 +103,7 @@ class BaseOmni(BaseModel):
class OmniSubmissionType(BaseOmni):
class_object: ClassVar[Any] = SubmissionType
name: str = Field(default="", description="property")
@@ -161,6 +167,7 @@ class OmniSubmissionType(BaseOmni):
class OmniReagentRole(BaseOmni):
class_object: ClassVar[Any] = ReagentRole
name: str = Field(default="", description="property")
@@ -197,6 +204,7 @@ class OmniReagentRole(BaseOmni):
class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
class_object: ClassVar[Any] = SubmissionTypeKitTypeAssociation
submissiontype: str | OmniSubmissionType = Field(default="", description="relationship", title="SubmissionType")
@@ -262,7 +270,7 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
)
def to_sql(self):
logger.debug(f"Self kittype: {self.submissiontype}")
# logger.debug(f"Self kittype: {self.submissiontype}")
if issubclass(self.submissiontype.__class__, BaseOmni):
submissiontype = SubmissionType.query(name=self.submissiontype.name)
else:
@@ -272,7 +280,7 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
else:
kittype = KitType.query(name=self.kittype)
# logger.debug(f"Self kittype: {self.kittype}")
logger.debug(f"Query or create with {kittype}, {submissiontype}")
# logger.debug(f"Query or create with {kittype}, {submissiontype}")
instance, is_new = self.class_object.query_or_create(kittype=kittype, submissiontype=submissiontype)
instance.mutable_cost_column = self.mutable_cost_column
instance.mutable_cost_sample = self.mutable_cost_sample
@@ -293,6 +301,7 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
class OmniKitTypeReagentRoleAssociation(BaseOmni):
class_object: ClassVar[Any] = KitTypeReagentRoleAssociation
reagent_role: str | OmniReagentRole = Field(default="", description="relationship", title="ReagentRole")
@@ -363,7 +372,7 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
kittype=kittype,
submissiontype=submissiontype
)
logger.debug(f"KitTypeReagentRoleAssociation coming out of query_or_create: {instance.__dict__}\nnew: {new}")
# logger.debug(f"KitTypeReagentRoleAssociation coming out of query_or_create: {instance.__dict__}\nnew: {new}")
if new:
logger.warning(f"This is a new instance: {instance.__dict__}")
try:
@@ -371,10 +380,10 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
except AttributeError:
reagent_role = ReagentRole.query(name=self.reagent_role)
instance.reagent_role = reagent_role
logger.debug(f"KTRRAssoc uses: {self.uses}")
# logger.debug(f"KTRRAssoc uses: {self.uses}")
instance.uses = self.uses
instance.required = int(self.required)
logger.debug(f"KitTypeReagentRoleAssociation: {pformat(instance.__dict__)}")
# logger.debug(f"KitTypeReagentRoleAssociation: {pformat(instance.__dict__)}")
return instance
@property
@@ -395,6 +404,7 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
class OmniEquipmentRole(BaseOmni):
class_object: ClassVar[Any] = EquipmentRole
name: str = Field(default="", description="property")
@@ -421,6 +431,7 @@ class OmniEquipmentRole(BaseOmni):
class OmniTips(BaseOmni):
class_object: ClassVar[Any] = Tips
name: str = Field(default="", description="property")
@@ -447,6 +458,7 @@ class OmniTips(BaseOmni):
class OmniTipRole(BaseOmni):
class_object: ClassVar[Any] = TipRole
name: str = Field(default="", description="property")
@@ -477,6 +489,7 @@ class OmniTipRole(BaseOmni):
class OmniProcess(BaseOmni):
class_object: ClassVar[Any] = Process
# NOTE: How am I going to figure out relatioinships without getting into recursion issues?
@@ -540,6 +553,7 @@ class OmniProcess(BaseOmni):
class OmniKitType(BaseOmni):
class_object: ClassVar[Any] = KitType
name: str = Field(default="", description="property")
@@ -565,17 +579,17 @@ class OmniKitType(BaseOmni):
def to_sql(self) -> KitType:
kit, is_new = KitType.query_or_create(name=self.name)
if is_new:
logger.debug(f"New kit made: {kit}")
else:
logger.debug(f"Kit retrieved: {kit}")
# if is_new:
# logger.debug(f"New kit made: {kit}")
# else:
# logger.debug(f"Kit retrieved: {kit}")
new_rr = []
for rr_assoc in self.kit_reagentrole_associations:
new_assoc = rr_assoc.to_sql()
if new_assoc not in new_rr:
logger.debug(f"Adding {new_assoc} to kit_reagentrole_associations")
# logger.debug(f"Adding {new_assoc} to kit_reagentrole_associations")
new_rr.append(new_assoc)
logger.debug(f"Setting kit_reagentrole_associations to {pformat([item.__dict__ for item in new_rr])}")
# logger.debug(f"Setting kit_reagentrole_associations to {pformat([item.__dict__ for item in new_rr])}")
kit.kit_reagentrole_associations = new_rr
new_st = []
for st_assoc in self.kit_submissiontype_associations:
@@ -589,9 +603,9 @@ class OmniKitType(BaseOmni):
if new_process not in new_processes:
new_processes.append(new_process)
kit.processes = new_processes
logger.debug(f"Kit: {pformat(kit.__dict__)}")
for item in kit.kit_reagentrole_associations:
logger.debug(f"KTRRassoc: {item.__dict__}")
# logger.debug(f"Kit: {pformat(kit.__dict__)}")
# for item in kit.kit_reagentrole_associations:
# logger.debug(f"KTRRassoc: {item.__dict__}")
return kit
@@ -601,11 +615,10 @@ class OmniOrganization(BaseOmni):
name: str = Field(default="", description="property")
cost_centre: str = Field(default="", description="property")
# TODO: add in List[OmniContacts]
contact: List[str] | List[OmniContact] = Field(default=[], description="relationship", title="Contact")
def __init__(self, instance_object: Any, **data):
logger.debug(f"Incoming data: {data}")
# logger.debug(f"Incoming data: {data}")
super().__init__(**data)
self.instance_object = instance_object
@@ -642,8 +655,8 @@ class OmniContact(BaseOmni):
def to_sql(self):
contact, is_new = Contact.query_or_create(name=self.name, email=self.email, phone=self.phone)
if is_new:
logger.debug(f"New contact made: {contact}")
else:
logger.debug(f"Contact retrieved: {contact}")
# if is_new:
# logger.debug(f"New contact made: {contact}")
# else:
# logger.debug(f"Contact retrieved: {contact}")
return contact

25
src/submissions/backend/validators/pydant.py
View File

@@ -22,6 +22,7 @@ logger = logging.getLogger(f"submissions.{__name__}")
class PydReagent(BaseModel):
lot: str | None
role: str | None
expiry: date | datetime | Literal['NA'] | None = Field(default=None, validate_default=True)
@@ -131,7 +132,7 @@ class PydReagent(BaseModel):
if self.model_extra is not None:
self.__dict__.update(self.model_extra)
reagent = Reagent.query(lot=self.lot, name=self.name)
logger.debug(f"Reagent: {reagent}")
# logger.debug(f"Reagent: {reagent}")
if reagent is None:
reagent = Reagent()
for key, value in self.__dict__.items():
@@ -151,6 +152,7 @@ class PydReagent(BaseModel):
class PydSample(BaseModel, extra='allow'):
submitter_id: str
sample_type: str
row: int | List[int] | None
@@ -252,6 +254,7 @@ class PydSample(BaseModel, extra='allow'):
class PydTips(BaseModel):
name: str
lot: str | None = Field(default=None)
role: str
@@ -282,6 +285,7 @@ class PydTips(BaseModel):
class PydEquipment(BaseModel, extra='ignore'):
asset_number: str
name: str
nickname: str | None
@@ -376,6 +380,7 @@ class PydEquipment(BaseModel, extra='ignore'):
class PydSubmission(BaseModel, extra='allow'):
filepath: Path
submission_type: dict | None
submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
@@ -948,7 +953,7 @@ class PydSubmission(BaseModel, extra='allow'):
self.extraction_kit['value'] = extraction_kit['value']
ext_kit = KitType.query(name=self.extraction_kit['value'])
ext_kit_rtypes = [item.to_pydantic() for item in
ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])]
ext_kit.get_reagents(required_only=True, submission_type=self.submission_type['value'])]
# NOTE: Exclude any reagenttype found in this pyd not expected in kit.
expected_check = [item.role for item in ext_kit_rtypes]
output_reagents = [rt for rt in self.reagents if rt.role in expected_check]
@@ -1014,6 +1019,7 @@ class PydSubmission(BaseModel, extra='allow'):
class PydContact(BaseModel):
name: str
phone: str | None
email: str | None
@@ -1061,6 +1067,7 @@ class PydContact(BaseModel):
class PydOrganization(BaseModel):
name: str
cost_centre: str
contacts: List[PydContact] | None
@@ -1101,6 +1108,7 @@ class PydOrganization(BaseModel):
class PydReagentRole(BaseModel):
name: str
eol_ext: timedelta | int | None
uses: dict | None
@@ -1139,6 +1147,7 @@ class PydReagentRole(BaseModel):
class PydKitType(BaseModel):
name: str
reagent_roles: List[PydReagent] = []
@@ -1160,6 +1169,7 @@ class PydKitType(BaseModel):
class PydEquipmentRole(BaseModel):
name: str
equipment: List[PydEquipment]
processes: List[str] | None
@@ -1187,6 +1197,7 @@ class PydEquipmentRole(BaseModel):
class PydPCRControl(BaseModel):
name: str
subtype: str
target: str
@@ -1210,6 +1221,7 @@ class PydPCRControl(BaseModel):
class PydIridaControl(BaseModel, extra='ignore'):
name: str
contains: list | dict #: unstructured hashes in contains.tsv for each organism
matches: list | dict #: unstructured hashes in matches.tsv for each organism
@@ -1244,6 +1256,7 @@ class PydIridaControl(BaseModel, extra='ignore'):
class PydProcess(BaseModel, extra="allow"):
name: str
version: str = Field(default="1")
submission_types: List[str]
@@ -1297,7 +1310,7 @@ class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
@report_result
def to_sql(self):
print(self.instance)
# print(self.instance)
fields = [item for item in self.model_extra]
for field in fields:
try:
@@ -1307,11 +1320,11 @@ class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
continue
match field_type:
case _RelationshipDeclared():
logger.debug(f"{field} is a relationship with {field_type.entity.class_}")
# logger.debug(f"{field} is a relationship with {field_type.entity.class_}")
field_value = field_type.entity.class_.argument.query(name=getattr(self, field))
logger.debug(f"{field} query result: {field_value}")
# logger.debug(f"{field} query result: {field_value}")
case ColumnProperty():
logger.debug(f"{field} is a property.")
# logger.debug(f"{field} is a property.")
field_value = getattr(self, field)
self.instance.__setattr__(field, field_value)
return self.instance