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Context menu for runs working.

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This commit is contained in:
lwark
2025-05-22 10:00:25 -05:00
parent 75c665ea05
commit d850166e08
40 changed files with 2852 additions and 3329 deletions
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116
src/submissions/backend/db/models/__init__.py
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@@ -3,6 +3,8 @@ Contains all models for sqlalchemy
"""
from __future__ import annotations
import sys, logging
from dateutil.parser import parse
from pandas import DataFrame
from pydantic import BaseModel
from sqlalchemy import Column, INTEGER, String, JSON
@@ -21,7 +23,7 @@ if 'pytest' in sys.modules:
# NOTE: For inheriting in LogMixin
Base: DeclarativeMeta = declarative_base()
logger = logging.getLogger(f"submissions.{__name__}")
logger = logging.getLogger(f"procedure.{__name__}")
class BaseClass(Base):
@@ -33,12 +35,12 @@ class BaseClass(Base):
__table_args__ = {'extend_existing': True} #: NOTE Will only add new columns
singles = ['id']
omni_removes = ["id", 'runs', "omnigui_class_dict", "omnigui_instance_dict"]
omni_removes = ["id", 'run', "omnigui_class_dict", "omnigui_instance_dict"]
omni_sort = ["name"]
omni_inheritable = []
searchables = []
misc_info = Column(JSON)
_misc_info = Column(JSON)
def __repr__(self) -> str:
try:
@@ -122,6 +124,10 @@ class BaseClass(Base):
from test_settings import ctx
return ctx.backup_path
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._misc_info = dict()
@classproperty
def jsons(cls) -> List[str]:
"""
@@ -130,7 +136,10 @@ class BaseClass(Base):
Returns:
List[str]: List of column names
"""
return [item.name for item in cls.__table__.columns if isinstance(item.type, JSON)]
try:
return [item.name for item in cls.__table__.columns if isinstance(item.type, JSON)]
except AttributeError:
return []
@classproperty
def timestamps(cls) -> List[str]:
@@ -140,7 +149,10 @@ class BaseClass(Base):
Returns:
List[str]: List of column names
"""
return [item.name for item in cls.__table__.columns if isinstance(item.type, TIMESTAMP)]
try:
return [item.name for item in cls.__table__.columns if isinstance(item.type, TIMESTAMP)]
except AttributeError:
return []
@classmethod
def get_default_info(cls, *args) -> dict | list | str:
@@ -155,7 +167,7 @@ class BaseClass(Base):
return dict(singles=singles)
@classmethod
def find_regular_subclass(cls, name: str|None = None) -> Any:
def find_regular_subclass(cls, name: str | None = None) -> Any:
"""
Args:
name (str): name of subclass of interest.
@@ -198,11 +210,11 @@ class BaseClass(Base):
@classmethod
def results_to_df(cls, objects: list | None = None, **kwargs) -> DataFrame:
"""
Converts class sub_dicts into a Dataframe for all controls of the class.
Converts class sub_dicts into a Dataframe for all control of the class.
Args:
objects (list): Objects to be converted to dataframe.
**kwargs (): Arguments necessary for the to_sub_dict method. eg extraction_kit=X
**kwargs (): Arguments necessary for the to_sub_dict method. eg kittype=X
Returns:
Dataframe
@@ -219,6 +231,24 @@ class BaseClass(Base):
records = [{k: v['instance_attr'] for k, v in obj.omnigui_instance_dict.items()} for obj in objects]
return DataFrame.from_records(records)
@classmethod
def query_or_create(cls, **kwargs) -> Tuple[Any, bool]:
new = False
allowed = [k for k, v in cls.__dict__.items() if isinstance(v, InstrumentedAttribute)
and not isinstance(v.property, _RelationshipDeclared)]
sanitized_kwargs = {k: v for k, v in kwargs.items() if k in allowed}
logger.debug(f"Sanitized kwargs: {sanitized_kwargs}")
instance = cls.query(**sanitized_kwargs)
if not instance or isinstance(instance, list):
instance = cls()
new = True
for k, v in sanitized_kwargs.items():
logger.debug(f"QorC Setting {k} to {v}")
setattr(instance, k, v)
logger.info(f"Instance from query or create: {instance}, new: {new}")
return instance, new
@classmethod
def query(cls, **kwargs) -> Any | List[Any]:
"""
@@ -227,6 +257,8 @@ class BaseClass(Base):
Returns:
Any | List[Any]: Result of query execution.
"""
if "name" in kwargs.keys():
kwargs['limit'] = 1
return cls.execute_query(**kwargs)
@classmethod
@@ -243,16 +275,17 @@ class BaseClass(Base):
Any | List[Any]: Single result if limit = 1 or List if other.
"""
# logger.debug(f"Kwargs: {kwargs}")
if model is None:
model = cls
# if model is None:
# model = cls
# logger.debug(f"Model: {model}")
if query is None:
query: Query = cls.__database_session__.query(model)
singles = model.get_default_info('singles')
query: Query = cls.__database_session__.query(cls)
singles = cls.get_default_info('singles')
for k, v in kwargs.items():
logger.info(f"Using key: {k} with value: {v}")
try:
attr = getattr(model, k)
attr = getattr(cls, k)
# NOTE: account for attrs that use list.
if attr.property.uselist:
query = query.filter(attr.contains(v))
@@ -341,6 +374,26 @@ class BaseClass(Base):
"""
return dict()
@classproperty
def details_template(cls) -> Template:
"""
Get the details jinja template for the correct class
Args:
base_dict (dict): incoming dictionary of Submission fields
Returns:
Tuple(dict, Template): (Updated dictionary, Template to be rendered)
"""
env = jinja_template_loading()
temp_name = f"{cls.__name__.lower()}_details.html"
try:
template = env.get_template(temp_name)
except TemplateNotFound as e:
# logger.error(f"Couldn't find template {e}")
template = env.get_template("details.html")
return template
def check_all_attributes(self, attributes: dict) -> bool:
"""
Checks this instance against a dictionary of attributes to determine if they are a match.
@@ -405,15 +458,29 @@ class BaseClass(Base):
"""
Custom dunder method to handle potential list relationship issues.
"""
# logger.debug(f"Attempting to set: {key} to {value}")
if key.startswith("_"):
return super().__setattr__(key, value)
try:
check = not hasattr(self, key)
except:
return
if check:
try:
json.dumps(value)
except TypeError:
value = str(value)
self._misc_info.update({key: value})
return
try:
field_type = getattr(self.__class__, key)
except AttributeError:
return super().__setattr__(key, value)
if isinstance(field_type, InstrumentedAttribute):
logger.debug(f"{key} is an InstrumentedAttribute.")
# logger.debug(f"{key} is an InstrumentedAttribute.")
match field_type.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}")
@@ -446,10 +513,13 @@ class BaseClass(Base):
try:
return super().__setattr__(key, value)
except AttributeError:
logger.debug(f"Possible attempt to set relationship to simple var type.")
logger.debug(f"Possible attempt to set relationship {key} to simple var type. {value}")
relationship_class = field_type.property.entity.entity
value = relationship_class.query(name=value)
return super().__setattr__(key, value)
try:
return super().__setattr__(key, value)
except AttributeError:
return super().__setattr__(key, None)
case _:
return super().__setattr__(key, value)
else:
@@ -458,7 +528,7 @@ class BaseClass(Base):
def delete(self):
logger.error(f"Delete has not been implemented for {self.__class__.__name__}")
def rectify_query_date(input_date, eod: bool = False) -> str:
def rectify_query_date(input_date: datetime, eod: bool = False) -> str:
"""
Converts input into a datetime string for querying purposes
@@ -486,8 +556,7 @@ class BaseClass(Base):
class LogMixin(Base):
tracking_exclusion: ClassVar = ['artic_technician', 'submission_sample_associations',
tracking_exclusion: ClassVar = ['artic_technician', 'clientsubmissionsampleassociation',
'submission_reagent_associations', 'submission_equipment_associations',
'submission_tips_associations', 'contact_id', 'gel_info', 'gel_controls',
'source_plates']
@@ -540,13 +609,12 @@ class ConfigItem(BaseClass):
from .controls import *
# NOTE: import order must go: orgs, kit, runs due to circular import issues
# NOTE: import order must go: orgs, kittype, run due to circular import issues
from .organizations import *
from .runs import *
from .kits import *
from .submissions import *
from .audit import AuditLog
# NOTE: Add a creator to the run for reagent association. Assigned here due to circular import constraints.
# NOTE: Add a creator to the procedure for reagent association. Assigned here due to circular import constraints.
# https://docs.sqlalchemy.org/en/20/orm/extensions/associationproxy.html#sqlalchemy.ext.associationproxy.association_proxy.params.creator
Procedure.reagents.creator = lambda reg: ProcedureReagentAssociation(reagent=reg)
# Procedure.reagents.creator = lambda reg: ProcedureReagentAssociation(reagent=reg)