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Converted client manager to new Omni pydantic version.

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This commit is contained in:
lwark
2025-04-04 13:09:54 -05:00
parent 3a318fff38
commit ac85be6414
12 changed files with 255 additions and 954 deletions
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55
src/submissions/backend/db/models/__init__.py
View File

@@ -60,28 +60,26 @@ class BaseClass(Base):
try:
return f"<{self.__class__.__name__}({self.name})>"
except AttributeError:
return f"<{self.__class__.__name__}(Unknown)>"
# @classproperty
# def skip_on_edit(cls):
# if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
# return True
# else:
# return False
return f"<{self.__class__.__name__}(Name Unavailable)>"
@classproperty
def aliases(cls):
def aliases(cls) -> List[str]:
"""
List of other names this class might be known by.
Returns:
List[str]: List of names
"""
return [cls.query_alias]
# @classproperty
# def level(cls):
# if "association" in cls.__name__.lower() or cls.__name__.lower() == "discount":
# return 2
# else:
# return 1
@classproperty
def query_alias(cls):
def query_alias(cls) -> str:
"""
What to query this class as.
Returns:
str: query name
"""
return cls.__name__.lower()
@classmethod
@@ -153,21 +151,23 @@ class BaseClass(Base):
return dict(singles=singles)
@classmethod
def find_regular_subclass(cls, name: str = "") -> Any:
def find_regular_subclass(cls, name: str|None = None) -> Any:
"""
Args:
name (str): name of subclass of interest.
Returns:
Any: Subclass of this object
Any: Subclass of this object.
"""
if " " in name:
search = name.title().replace(" ", "")
if name:
if " " in name:
search = name.title().replace(" ", "")
else:
search = name
return next((item for item in cls.__subclasses__() if item.__name__ == search), cls)
else:
search = name
return next((item for item in cls.__subclasses__() if item.__name__ == search), cls)
return cls.__subclasses__()
@classmethod
def fuzzy_search(cls, **kwargs) -> List[Any]:
@@ -193,7 +193,7 @@ class BaseClass(Base):
return query.limit(50).all()
@classmethod
def results_to_df(cls, objects: list|None=None, **kwargs) -> DataFrame:
def results_to_df(cls, objects: list | None = None, **kwargs) -> DataFrame:
"""
Converts class sub_dicts into a Dataframe for all instances of the class.
@@ -395,7 +395,8 @@ class BaseClass(Base):
if check:
logger.debug(f"Checking for subclass name.")
self_value = self_value.name
logger.debug(f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
logger.debug(
f"Checking self_value {self_value} of type {type(self_value)} against attribute {value} of type {type(value)}")
if self_value != value:
output = False
logger.debug(f"Value {key} is False, returning.")

14
src/submissions/backend/db/models/controls.py
View File

@@ -425,17 +425,23 @@ class IridaControl(Control):
kraken = self.kraken
except TypeError:
kraken = {}
kraken_cnt_total = sum([item['kraken_count'] for item in kraken.values()])
new_kraken = [dict(name=key, kraken_count=value['kraken_count'],
try:
kraken_cnt_total = sum([item['kraken_count'] for item in kraken.values()])
except AttributeError:
kraken_cnt_total = 0
try:
new_kraken = [dict(name=key, kraken_count=value['kraken_count'],
kraken_percent=f"{value['kraken_count'] / kraken_cnt_total:0.2%}",
target=key in self.controltype.targets)
for key, value in kraken.items()]
new_kraken = sorted(new_kraken, key=itemgetter('kraken_count'), reverse=True)
new_kraken = sorted(new_kraken, key=itemgetter('kraken_count'), reverse=True)[0:10]
except (AttributeError, ZeroDivisionError):
new_kraken = []
output = dict(
name=self.name,
type=self.controltype.name,
targets=", ".join(self.targets),
kraken=new_kraken[0:10]
kraken=new_kraken
)
return output

49
src/submissions/backend/db/models/organizations.py
View File

@@ -10,7 +10,7 @@ from sqlalchemy.ext.hybrid import hybrid_property
from sqlalchemy.orm import relationship, Query
from . import Base, BaseClass
from tools import check_authorization, setup_lookup, yaml_regex_creator
from typing import List
from typing import List, Tuple
logger = logging.getLogger(f"submissions.{__name__}")
@@ -123,6 +123,20 @@ class Organization(BaseClass):
organ.contacts.append(cont)
organ.save()
def to_omni(self, expand: bool = False):
from backend.validators.omni_gui_objects import OmniOrganization
if self.cost_centre:
cost_centre = self.cost_centre
else:
cost_centre = "NA"
if self.name:
name = self.name
else:
name = "NA"
return OmniOrganization(instance_object=self,
name=name, cost_centre=cost_centre,
contact=[item.to_omni() for item in self.contacts])
class Contact(BaseClass):
"""
@@ -144,6 +158,20 @@ class Contact(BaseClass):
def searchables(cls):
return []
@classmethod
def query_or_create(cls, **kwargs) -> Tuple[Contact, bool]:
new = False
disallowed = []
sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
instance = cls.query(**sanitized_kwargs)
if not instance or isinstance(instance, list):
instance = cls()
new = True
for k, v in sanitized_kwargs.items():
setattr(instance, k, v)
logger.info(f"Instance from contact query or create: {instance}")
return instance, new
@classmethod
@setup_lookup
def query(cls,
@@ -195,3 +223,22 @@ class Contact(BaseClass):
def to_pydantic(self) -> "PydContact":
from backend.validators import PydContact
return PydContact(name=self.name, email=self.email, phone=self.phone)
def to_omni(self, expand: bool = False):
from backend.validators.omni_gui_objects import OmniContact
if self.email:
email = self.email
else:
email = "NA"
if self.name:
name = self.name
else:
name = "NA"
if self.phone:
phone = self.phone
else:
phone = "NA"
return OmniContact(instance_object=self,
name=name, email=email,
phone=phone)

150
src/submissions/backend/db/models/submissions.py
View File

@@ -3,6 +3,7 @@ Models for the main submission and sample types.
"""
from __future__ import annotations
import itertools
import pickle
from copy import deepcopy
from getpass import getuser
@@ -12,6 +13,8 @@ from zipfile import ZipFile, BadZipfile
from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
from pprint import pformat
from pandas import DataFrame
from sqlalchemy.ext.hybrid import hybrid_property
from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, LogMixin, SubmissionReagentAssociation
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func
@@ -287,6 +290,7 @@ class BasicSubmission(BaseClass, LogMixin):
Constructs dictionary used in submissions summary
Args:
expand (bool, optional): indicates if generators to be expanded. Defaults to False.
report (bool, optional): indicates if to be used for a report. Defaults to False.
full_data (bool, optional): indicates if sample dicts to be constructed. Defaults to False.
backup (bool, optional): passed to adjust_to_dict_samples. Defaults to False.
@@ -393,6 +397,33 @@ class BasicSubmission(BaseClass, LogMixin):
output["completed_date"] = self.completed_date
return output
@classmethod
def archive_submissions(cls, start_date: date | datetime | str | int | None = None,
end_date: date | datetime | str | int | None = None,
submissiontype: List[str] | None = None):
if submissiontype:
if isinstance(submissiontype, str):
submissiontype = [submissiontype]
query_out = []
for sub_type in submissiontype:
subs = cls.query(page_size=0, start_date=start_date, end_date=end_date, submissiontype=sub_type)
# logger.debug(f"Sub results: {subs}")
query_out.append(subs)
query_out = list(itertools.chain.from_iterable(query_out))
else:
query_out = cls.query(page_size=0, start_date=start_date, end_date=end_date)
records = []
for sub in query_out:
output = sub.to_dict(full_data=True)
for k, v in output.items():
if isinstance(v, types.GeneratorType):
output[k] = [item for item in v]
records.append(output)
df = DataFrame.from_records(records)
df.sort_values(by="id", inplace=True)
df.set_index("id", inplace=True)
return df
@property
def column_count(self) -> int:
"""
@@ -590,61 +621,18 @@ class BasicSubmission(BaseClass, LogMixin):
except AttributeError as e:
logger.error(f"Could not set {self} attribute {key} to {value} due to \n{e}")
# def update_subsampassoc(self, sample: BasicSample, input_dict: dict) -> SubmissionSampleAssociation:
# """
# Update a joined submission sample association.
#
# Args:
# sample (BasicSample): Associated sample.
# input_dict (dict): values to be updated
#
# Returns:
# SubmissionSampleAssociation: Updated association
# """
# try:
# logger.debug(f"Searching for sample {sample} at column {input_dict['column']} and row {input_dict['row']}")
# assoc = next((item for item in self.submission_sample_associations
# if item.sample == sample and
# item.row == input_dict['row'] and
# item.column == input_dict['column']))
# logger.debug(f"Found assoc {pformat(assoc.__dict__)}")
# except StopIteration:
# report = Report()
# report.add_result(
# Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
# return report
# for k, v in input_dict.items():
# try:
# # logger.debug(f"Setting assoc {assoc} with key {k} to value {v}")
# setattr(assoc, k, v)
# # NOTE: for some reason I don't think assoc.__setattr__(k, v) works here.
# except AttributeError:
# logger.error(f"Can't set {k} to {v}")
# return assoc
def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
"""
Update a joined submission sample association.
Args:
sample (BasicSample): Associated sample.
input_dict (dict): values to be updated
assoc (SubmissionSampleAssociation): Sample association to be updated.
input_dict (dict): updated values to insert.
Returns:
SubmissionSampleAssociation: Updated association
"""
# try:
# logger.debug(f"Searching for sample {sample} at column {input_dict['column']} and row {input_dict['row']}")
# assoc = next((item for item in self.submission_sample_associations
# if item.sample == sample and
# item.row == input_dict['row'] and
# item.column == input_dict['column']))
# logger.debug(f"Found assoc {pformat(assoc.__dict__)}")
# except StopIteration:
# report = Report()
# report.add_result(
# Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
# return report
# NOTE: No longer searches for association here, done in caller function
for k, v in input_dict.items():
try:
# logger.debug(f"Setting assoc {assoc} with key {k} to value {v}")
@@ -771,8 +759,8 @@ class BasicSubmission(BaseClass, LogMixin):
return regex
@classmethod
def find_polymorphic_subclass(cls, polymorphic_identity: str | SubmissionType | None = None,
attrs: dict | None = None) -> BasicSubmission:
def find_polymorphic_subclass(cls, polymorphic_identity: str | SubmissionType | list | None = None,
attrs: dict | None = None) -> BasicSubmission | List[BasicSubmission]:
"""
Find subclass based on polymorphic identity or relevant attributes.
@@ -795,6 +783,13 @@ class BasicSubmission(BaseClass, LogMixin):
except Exception as e:
logger.error(
f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, falling back to BasicSubmission")
case list():
output = []
for identity in polymorphic_identity:
if isinstance(identity, SubmissionType):
identity = polymorphic_identity.name
output.append(cls.__mapper__.polymorphic_map[identity].class_)
return output
case _:
pass
if attrs and any([not hasattr(cls, attr) for attr in attrs.keys()]):
@@ -1855,18 +1850,6 @@ class Wastewater(BasicSubmission):
result = assoc.save()
if result:
report.add_result(result)
# for sample in self.samples:
# logger.debug(f"Checking pcr_samples for {sample.rsl_number}, {sample.ww_full_sample_id}")
# try:
# # NOTE: Fix for ENs which have no rsl_number...
# sample_dict = next(item for item in pcr_samples if item['sample'] == sample.rsl_number)
# logger.debug(f"Found sample {sample_dict} at index {pcr_samples.index(sample_dict)}: {pcr_samples[pcr_samples.index(sample_dict)]}")
# except StopIteration:
# logger.error(f"Couldn't find {sample} in the Parser samples")
# continue
# assoc = self.update_subsampassoc(sample=sample, input_dict=sample_dict)
# result = assoc.save()
# report.add_result(result)
controltype = ControlType.query(name="PCR Control")
submitted_date = datetime.strptime(" ".join(parser.pcr_info['run_start_date/time'].split(" ")[:-1]),
"%Y-%m-%d %I:%M:%S %p")
@@ -1880,35 +1863,6 @@ class Wastewater(BasicSubmission):
new_control.save()
return report
# def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
# """
# Updates a joined submission sample association by assigning ct values to n1 or n2 based on alphabetical sorting.
#
# Args:
# sample (BasicSample): Associated sample.
# input_dict (dict): values to be updated
#
# Returns:
# SubmissionSampleAssociation: Updated association
# """
# # logger.debug(f"Input dict: {pformat(input_dict)}")
# #
# assoc = super().update_subsampassoc(assoc=assoc, input_dict=input_dict)
# # targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
# # assert 0 < len(targets) <= 2
# # for k, v in targets.items():
# # # logger.debug(f"Setting sample {sample} with key {k} to value {v}")
# # # update_key = f"ct_n{i}"
# # current_value = getattr(assoc, k)
# # logger.debug(f"Current value came back as: {current_value}")
# # if current_value is None:
# # setattr(assoc, k, v)
# # else:
# # logger.debug(f"Have a value already, {current_value}... skipping.")
# if assoc.column == 3:
# logger.debug(f"Final association for association {assoc}:\n{pformat(assoc.__dict__)}")
# return assoc
class WastewaterArtic(BasicSubmission):
"""
@@ -2196,14 +2150,14 @@ class WastewaterArtic(BasicSubmission):
# logger.debug(processed)
# NOTE: Remove brackets at end
processed = re.sub(r"\(.*\)$", "", processed).strip()
logger.debug(processed)
# logger.debug(processed)
processed = re.sub(r"-RPT", "", processed, flags=re.IGNORECASE)
# NOTE: Remove any non-R letters at end.
processed = re.sub(r"[A-QS-Z]+\d*", "", processed)
logger.debug(processed)
# logger.debug(processed)
# NOTE: Remove trailing '-' if any
processed = processed.strip("-")
logger.debug(processed)
# logger.debug(processed)
try:
plate_num = re.search(r"\-\d{1}R?\d?$", processed).group()
processed = rreplace(processed, plate_num, "")
@@ -2221,20 +2175,20 @@ class WastewaterArtic(BasicSubmission):
plate_num = re.sub(r"R", rf"R{repeat_num}", plate_num)
except AttributeError:
logger.error(f"Problem re-evaluating plate number for {processed}")
logger.debug(processed)
# logger.debug(processed)
# NOTE: Remove any redundant -digits
processed = re.sub(r"-\d$", "", processed)
logger.debug(processed)
# logger.debug(processed)
day = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, day, "")
logger.debug(processed)
# logger.debug(processed)
month = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, month, "")
processed = processed.replace("--", "")
logger.debug(processed)
# logger.debug(processed)
year = re.search(r'^(?:\d{2})?\d{2}', processed).group()
year = f"20{year}"
logger.debug(processed)
# logger.debug(processed)
final_en_name = f"PBS{year}{month}{day}-{plate_num}"
return final_en_name
@@ -2881,7 +2835,7 @@ class BacterialCultureSample(BasicSample):
sample['organism'] = self.organism
try:
sample['concentration'] = f"{float(self.concentration):.2f}"
except TypeError:
except (TypeError, ValueError):
sample['concentration'] = 0.0
if self.control is not None:
sample['colour'] = [0, 128, 0]

54
src/submissions/backend/validators/omni_gui_objects.py
View File

@@ -593,3 +593,57 @@ class OmniKitType(BaseOmni):
for item in kit.kit_reagentrole_associations:
logger.debug(f"KTRRassoc: {item.__dict__}")
return kit
class OmniOrganization(BaseOmni):
class_object: ClassVar[Any] = Organization
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}")
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
return dict(
name=self.name,
cost_centre=self.cost_centre,
contacts=self.contact
)
class OmniContact(BaseOmni):
class_object: ClassVar[Any] = Contact
name: str = Field(default="", description="property")
email: str = Field(default="", description="property")
phone: str = Field(default="", description="property")
@property
def list_searchables(self):
return dict(name=self.name, email=self.email)
def __init__(self, instance_object: Any, **data):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
return dict(
name=self.name,
email=self.email,
phone=self.phone
)
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}")
return contact