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Post code-cleanup, moments before disaster.

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This commit is contained in:
lwark
2025-03-26 14:19:13 -05:00
parent 3ec79fdcfe
commit d844211e1b
21 changed files with 183 additions and 285 deletions
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36
src/submissions/backend/validators/__init__.py
View File

@@ -28,7 +28,8 @@ class RSLNamer(object):
logger.info(f"got submission type: {self.submission_type}")
if self.submission_type:
self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(submission_type=submission_type))
self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(
submission_type=submission_type))
if not data:
data = dict(submission_type=self.submission_type)
if "submission_type" not in data.keys():
@@ -50,24 +51,36 @@ class RSLNamer(object):
Returns:
str: parsed submission type
"""
def st_from_path(filename:Path) -> str:
if filename.exists():
wb = load_workbook(filename)
def st_from_path(filepath: Path) -> str:
"""
Sub def to get submissiontype from a file path
Args:
filepath ():
Returns:
"""
if filepath.exists():
wb = load_workbook(filepath)
try:
# NOTE: Gets first category in the metadata.
categories = wb.properties.category.split(";")
submission_type = next(item.strip().title() for item in categories)
except (StopIteration, AttributeError):
sts = {item.name: item.template_file_sheets for item in SubmissionType.query() if item.template_file}
sts = {item.name: item.template_file_sheets for item in SubmissionType.query() if
item.template_file}
try:
submission_type = next(k.title() for k,v in sts.items() if wb.sheetnames==v)
submission_type = next(k.title() for k, v in sts.items() if wb.sheetnames == v)
except StopIteration:
# NOTE: On failure recurse using filename as string for string method
submission_type = cls.retrieve_submission_type(filename=filename.stem.__str__())
# NOTE: On failure recurse using filepath as string for string method
submission_type = cls.retrieve_submission_type(filename=filepath.stem.__str__())
else:
submission_type = cls.retrieve_submission_type(filename=filename.stem.__str__())
submission_type = cls.retrieve_submission_type(filename=filepath.stem.__str__())
return submission_type
def st_from_str(filename:str) -> str:
def st_from_str(filename: str) -> str:
if filename.startswith("tmp"):
return "Bacterial Culture"
regex = BasicSubmission.regex
@@ -78,9 +91,10 @@ class RSLNamer(object):
submission_type = None
logger.critical(f"No submission type found or submission type found!: {e}")
return submission_type
match filename:
case Path():
submission_type = st_from_path(filename=filename)
submission_type = st_from_path(filepath=filename)
case str():
submission_type = st_from_str(filename=filename)
case _:

21
src/submissions/backend/validators/omni_gui_objects.py
View File

@@ -1,5 +1,5 @@
from __future__ import annotations
import logging, sys
import logging
from pydantic import BaseModel, field_validator, Field
from typing import List, ClassVar
from backend.db.models import *
@@ -16,7 +16,7 @@ class BaseOmni(BaseModel):
try:
return f"<{self.__class__.__name__}({self.name})>"
except AttributeError:
return f"<{self.__class__.__name__}(NO NAME)>"
return f"<{self.__class__.__name__}({self.__repr_name__})>"
@classproperty
def aliases(cls):
@@ -478,7 +478,6 @@ class OmniProcess(BaseOmni):
# NOTE: How am I going to figure out relatioinships without getting into recursion issues?
name: str = Field(default="", description="property") #: Process name
# version: str = Field(default="", description="property") #: Version (string to account for "in_use" or whatever)
submission_types: List[OmniSubmissionType] | List[str] = Field(default=[], description="relationship",
title="SubmissionType")
equipment_roles: List[OmniEquipmentRole] | List[str] = Field(default=[], description="relationship",
@@ -507,13 +506,6 @@ class OmniProcess(BaseOmni):
return ""
return value
# @field_validator("version", mode="before")
# @classmethod
# def rescue_name_none(cls, value):
# if not value:
# return "1"
# return value
def to_sql(self):
instance, new = self.class_object.query_or_create(name=self.name)
for st in self.submission_types:
@@ -539,12 +531,8 @@ class OmniKitType(BaseOmni):
class_object: ClassVar[Any] = KitType
name: str = Field(default="", description="property")
kit_submissiontype_associations: List[OmniSubmissionTypeKitTypeAssociation] | List[str] = Field(default=[],
description="relationship",
title="SubmissionTypeKitTypeAssociation")
kit_reagentrole_associations: List[OmniKitTypeReagentRoleAssociation] | List[str] = Field(default=[],
description="relationship",
title="KitTypeReagentRoleAssociation")
kit_submissiontype_associations: List[OmniSubmissionTypeKitTypeAssociation] | List[str] = Field(default=[], description="relationship", title="SubmissionTypeKitTypeAssociation")
kit_reagentrole_associations: List[OmniKitTypeReagentRoleAssociation] | List[str] = Field(default=[], description="relationship", title="KitTypeReagentRoleAssociation")
processes: List[OmniProcess] | List[str] = Field(default=[], description="relationship", title="Process")
@field_validator("name", mode="before")
@@ -577,7 +565,6 @@ class OmniKitType(BaseOmni):
new_rr.append(new_assoc)
logger.debug(f"Setting kit_reagentrole_associations to {pformat([item.__dict__ for item in new_rr])}")
kit.kit_reagentrole_associations = new_rr
# sys.exit()
new_st = []
for st_assoc in self.kit_submissiontype_associations:
new_assoc = st_assoc.to_sql()

36
src/submissions/backend/validators/pydant.py
View File

@@ -288,8 +288,6 @@ class PydTips(BaseModel):
tips = Tips.query(name=self.name, limit=1)
# logger.debug(f"Tips query has yielded: {tips}")
assoc = SubmissionTipsAssociation.query_or_create(tips=tips, submission=submission, role=self.role, limit=1)
# if assoc is None:
# assoc = SubmissionTipsAssociation(submission=submission, tips=tips, role_name=self.role)
return assoc, report
@@ -355,14 +353,13 @@ class PydEquipment(BaseModel, extra='ignore'):
# TODO: This seems precarious. What if there is more than one process?
# NOTE: It looks like the way fetching the processes is done in the SQL model, this shouldn't be a problem, but I'll include a failsafe.
# NOTE: I need to find a way to filter this by the kit involved.
if len(self.processes) > 1:
process = Process.query(submissiontype=submission.get_submission_type(), kittype=extraction_kit, equipmentrole=self.role)
else:
process = Process.query(name=self.processes[0])
if process is None:
logger.error(f"Found unknown process: {process}.")
logger.debug(f"Using process: {process}")
# logger.debug(f"Using process: {process}")
assoc.process = process
assoc.role = self.role
else:
@@ -746,7 +743,16 @@ class PydSubmission(BaseModel, extra='allow'):
output = {k: self.filter_field(k) for k in fields}
return output
def filter_field(self, key: str):
def filter_field(self, key: str) -> Any:
"""
Attempts to get value from field dictionary
Args:
key (str): name of the field of interest
Returns:
Any (): Value found.
"""
item = getattr(self, key)
match item:
case dict():
@@ -780,9 +786,8 @@ class PydSubmission(BaseModel, extra='allow'):
"""
report = Report()
dicto = self.improved_dict()
logger.debug(f"Pydantic submission type: {self.submission_type['value']}")
logger.debug(f"Pydantic improved_dict: {pformat(dicto)}")
# At this point, pcr_info is not duplicated
# logger.debug(f"Pydantic submission type: {self.submission_type['value']}")
# logger.debug(f"Pydantic improved_dict: {pformat(dicto)}")
instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
rsl_plate_num=self.rsl_plate_num['value'])
# logger.debug(f"Created or queried instance: {instance}")
@@ -792,8 +797,7 @@ class PydSubmission(BaseModel, extra='allow'):
report.add_result(result)
self.handle_duplicate_samples()
for key, value in dicto.items():
logger.debug(f"Checking key {key}, value {value}")
# At this point, pcr_info is not duplicated.
# logger.debug(f"Checking key {key}, value {value}")
if isinstance(value, dict):
try:
value = value['value']
@@ -849,8 +853,7 @@ class PydSubmission(BaseModel, extra='allow'):
value = value
instance.set_attribute(key=key, value=value)
case item if item in instance.jsons:
# At this point pcr_info is not duplicated
logger.debug(f"Validating json value: {item} to value:{pformat(value)}")
# logger.debug(f"Validating json value: {item} to value:{pformat(value)}")
try:
ii = value.items()
except AttributeError:
@@ -860,8 +863,7 @@ class PydSubmission(BaseModel, extra='allow'):
value[k] = v.strftime("%Y-%m-%d %H:%M:%S")
else:
pass
logger.debug(f"Setting json value: {item} to value:{pformat(value)}")
# At this point, pcr_info is not duplicated.
# logger.debug(f"Setting json value: {item} to value:{pformat(value)}")
instance.set_attribute(key=key, value=value)
case _:
try:
@@ -878,7 +880,6 @@ class PydSubmission(BaseModel, extra='allow'):
continue
else:
logger.warning(f"{key} already == {value} so no updating.")
logger.debug(f"Entering cost calculation for {instance}")
try:
instance.calculate_base_cost()
except (TypeError, AttributeError) as e:
@@ -937,7 +938,6 @@ class PydSubmission(BaseModel, extra='allow'):
"/", "")
return render
# @report_result
def check_kit_integrity(self, extraction_kit: str | dict | None = None, exempt: List[PydReagent] = []) -> Tuple[
List[PydReagent], Report, List[PydReagent]]:
"""
@@ -1212,7 +1212,6 @@ class PydIridaControl(BaseModel, extra='ignore'):
contains: list | dict #: unstructured hashes in contains.tsv for each organism
matches: list | dict #: unstructured hashes in matches.tsv for each organism
kraken: list | dict #: unstructured output from kraken_report
# subtype: str #: EN-NOS, MCS-NOS, etc
subtype: Literal["ATCC49226", "ATCC49619", "EN-NOS", "EN-SSTI", "MCS-NOS", "MCS-SSTI", "SN-NOS", "SN-SSTI"]
refseq_version: str #: version of refseq used in fastq parsing
kraken2_version: str
@@ -1264,7 +1263,6 @@ class PydProcess(BaseModel, extra="allow"):
instance = Process.query(name=self.name)
if not instance:
instance = Process()
# dicto = instance.omnigui_instance_dict
fields = [item for item in self.model_fields]
for field in fields:
logger.debug(f"Field: {field}")
@@ -1315,5 +1313,3 @@ class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
field_value = getattr(self, field)
self.instance.__setattr__(field, field_value)
return self.instance