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lwark
2024-05-16 14:07:18 -05:00
parent 84fac23890
commit bbcbd35127
6 changed files with 466 additions and 365 deletions
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6
CHANGELOG.md
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@@ -1,3 +1,9 @@
## 202405.03
- Settings can now pull values from the db.
- Improved generic and WW specific PCR parsers.
- Various bug fixes.
## 202405.01
- New Excel writers

6
alembic.ini
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@@ -55,10 +55,10 @@ version_path_separator = os # Use os.pathsep. Default configuration used for ne
# are written from script.py.mako
# output_encoding = utf-8
sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
;sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\Submissions_app_backups\DB_backups\submissions-demo.db
; sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\Submissions_app_backups\DB_backups\submissions-demo.db
;sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\Submissions_app_backups\DB_backups\submissions-prototypes.db
;sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\mytests\test_assets\submissions-test.db
sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\mytests\test_assets\submissions-test.db
[post_write_hooks]

28
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 sqlalchemy import Column, INTEGER, String, JSON
from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session
from sqlalchemy.ext.declarative import declared_attr
from sqlalchemy.exc import ArgumentError
@@ -11,8 +13,6 @@ from pathlib import Path
# Load testing environment
if 'pytest' in sys.modules:
from pathlib import Path
sys.path.append(Path(__file__).parents[4].absolute().joinpath("tests").__str__())
Base: DeclarativeMeta = declarative_base()
@@ -46,7 +46,7 @@ class BaseClass(Base):
Returns:
Session: DB session from ctx settings.
"""
if not 'pytest' in sys.modules:
if 'pytest' not in sys.modules:
from tools import ctx
else:
from test_settings import ctx
@@ -60,7 +60,7 @@ class BaseClass(Base):
Returns:
Path: Location of the Submissions directory in Settings object
"""
if not 'pytest' in sys.modules:
if 'pytest' not in sys.modules:
from tools import ctx
else:
from test_settings import ctx
@@ -74,7 +74,7 @@ class BaseClass(Base):
Returns:
Path: Location of the Submissions backup directory in Settings object
"""
if not 'pytest' in sys.modules:
if 'pytest' not in sys.modules:
from tools import ctx
else:
from test_settings import ctx
@@ -104,8 +104,9 @@ class BaseClass(Base):
Execute sqlalchemy query.
Args:
query (Query): input query object
limit (int): Maximum number of results. (0 = all)
model (Any, optional): model to be queried. Defaults to None
query (Query, optional): input query object. Defaults to None
limit (int): Maximum number of results. (0 = all). Defaults to 0
Returns:
Any | List[Any]: Single result if limit = 1 or List if other.
@@ -153,6 +154,19 @@ class BaseClass(Base):
self.__database_session__.rollback()
class ConfigItem(BaseClass):
id = Column(INTEGER, primary_key=True)
key = Column(String(32))
value = Column(JSON)
def __repr__(self):
return f"ConfigItem({self.key} : {self.value})"
@classmethod
def get_config_items(cls):
return cls.__database_session__.query(cls).all()
from .controls import *
# import order must go: orgs, kit, subs due to circular import issues
from .organizations import *

24
src/submissions/backend/db/models/controls.py
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@@ -43,7 +43,7 @@ class ControlType(BaseClass):
Returns:
ControlType | List[ControlType]: Single result if the limit = 1, else a list.
"""
"""
query = cls.__database_session__.query(cls)
match name:
case str():
@@ -83,7 +83,7 @@ class ControlType(BaseClass):
Returns:
List[ControlType]: Control types that have targets
"""
"""
return [item for item in cls.query() if item.targets != []]
@classmethod
@@ -93,7 +93,7 @@ class ControlType(BaseClass):
Returns:
Pattern: Constructed pattern
"""
"""
strings = list(set([item.name.split("-")[0] for item in cls.get_positive_control_types()]))
return re.compile(rf"(^{'|^'.join(strings)})-.*", flags=re.IGNORECASE)
@@ -175,19 +175,19 @@ class Control(BaseClass):
output = []
# logger.debug("load json string for mode (i.e. contains, matches, kraken2)")
try:
# data = json.loads(getattr(self, mode))
data = self.__getattribute__(mode)
except TypeError:
data = {}
logger.debug(f"Length of data: {len(data)}")
# logger.debug("dict keys are genera of bacteria, e.g. 'Streptococcus'")
for genus in data:
_dict = {}
_dict['name'] = self.name
_dict['submitted_date'] = self.submitted_date
_dict['genus'] = genus
_dict = dict(
name=self.name,
submitted_date=self.submitted_date,
genus=genus,
target='Target' if genus.strip("*") in self.controltype.targets else "Off-target"
)
# logger.debug("get Target or Off-target of genus")
_dict['target'] = 'Target' if genus.strip("*") in self.controltype.targets else "Off-target"
# logger.debug("set 'contains_hashes', etc for genus")
for key in data[genus]:
_dict[key] = data[genus][key]
@@ -247,13 +247,13 @@ class Control(BaseClass):
case _:
pass
# by date range
if start_date != None and end_date == None:
if start_date is not None and end_date is None:
logger.warning(f"Start date with no end date, using today.")
end_date = date.today()
if end_date != None and start_date == None:
if end_date is not None and start_date is None:
logger.warning(f"End date with no start date, using Jan 1, 2023")
start_date = date(2023, 1, 1)
if start_date != None:
if start_date is not None:
match start_date:
case date():
# logger.debug(f"Lookup control by start date({start_date})")

717
src/submissions/backend/db/models/kits.py
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File diff suppressed because it is too large Load Diff

50
src/submissions/tools.py
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@@ -2,6 +2,8 @@
Contains miscellaenous functions used by both frontend and backend.
'''
from __future__ import annotations
import json
from pathlib import Path
import numpy as np
import logging, re, yaml, sys, os, stat, platform, getpass, inspect, csv
@@ -10,7 +12,7 @@ from jinja2 import Environment, FileSystemLoader
from logging import handlers
from pathlib import Path
from sqlalchemy.orm import Session
from sqlalchemy import create_engine
from sqlalchemy import create_engine, text
from pydantic import field_validator, BaseModel, Field
from pydantic_settings import BaseSettings, SettingsConfigDict
from typing import Any, Tuple, Literal, List
@@ -137,7 +139,7 @@ def get_first_blank_df_row(df:pd.DataFrame) -> int:
# Settings
class Settings(BaseSettings):
class Settings(BaseSettings, extra="allow"):
"""
Pydantic model to hold settings
@@ -147,21 +149,26 @@ class Settings(BaseSettings):
"""
directory_path: Path
database_path: Path|str|None = None
backup_path: Path
super_users: list|None = None
power_users: list|None = None
rerun_regex: str
backup_path: Path|str|None = None
# super_users: list|None = None
# power_users: list|None = None
# rerun_regex: str
submission_types: dict|None = None
database_session: Session|None = None
package: Any|None = None
model_config = SettingsConfigDict(env_file_encoding='utf-8')
@field_validator('backup_path')
@field_validator('backup_path', mode="before")
@classmethod
def set_backup_path(cls, value):
if isinstance(value, str):
value = Path(value)
def set_backup_path(cls, value, values):
match value:
case str():
value = Path(value)
case None:
value = values.data['directory_path'].joinpath("Database backups")
if not value.exists():
value.mkdir(parents=True)
# metadata.backup_path = value
return value
@@ -177,11 +184,14 @@ class Settings(BaseSettings):
@field_validator('database_path', mode="before")
@classmethod
def ensure_database_exists(cls, value):
def ensure_database_exists(cls, value, values):
if value == ":memory:":
return value
if isinstance(value, str):
value = Path(value)
match value:
case str():
value = Path(value)
case None:
value = values.data['directory_path'].joinpath("submissions.db")
if value.exists():
return value
else:
@@ -225,6 +235,20 @@ class Settings(BaseSettings):
if value == None:
return package
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
# self.set_from_db(db_path=kwargs['database_path'])
def set_from_db(self, db_path:Path):
session = Session(create_engine(f"sqlite:///{db_path}"))
config_items = session.execute(text("SELECT * FROM _configitem")).all()
session.close()
config_items = {item[1]:json.loads(item[2]) for item in config_items}
for k, v in config_items.items():
if not hasattr(self, k):
self.__setattr__(k, v)
def get_config(settings_path: Path|str|None=None) -> Settings:
"""
Get configuration settings from path or default if blank.