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Added Postgres support.

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This commit is contained in:
lwark
2024-07-25 08:41:44 -05:00
parent 54e1e55804
commit 4bc5e08ac6
32 changed files with 579 additions and 1030 deletions
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2
src/submissions/backend/db/__init__.py
View File

@@ -17,7 +17,7 @@ def set_sqlite_pragma(dbapi_connection, connection_record):
connection_record (_type_): _description_
"""
cursor = dbapi_connection.cursor()
cursor.execute("PRAGMA foreign_keys=ON")
# cursor.execute("PRAGMA foreign_keys=ON")
cursor.close()

23
src/submissions/backend/db/models/__init__.py
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@@ -3,12 +3,13 @@ Contains all models for sqlalchemy
"""
from __future__ import annotations
import sys, logging
from sqlalchemy import Column, INTEGER, String, JSON
from sqlalchemy import Column, INTEGER, String, JSON, inspect
from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session
from sqlalchemy.ext.declarative import declared_attr
from sqlalchemy.exc import ArgumentError
from typing import Any, List
from pathlib import Path
from tools import report_result
# Load testing environment
if 'pytest' in sys.modules:
@@ -90,7 +91,7 @@ class BaseClass(Base):
Returns:
dict | list | str: Output of key:value dict or single (list, str) desired variable
"""
"""
dicto = dict(singles=['id'])
output = {}
for k, v in dicto.items():
@@ -110,7 +111,7 @@ class BaseClass(Base):
Returns:
Any | List[Any]: Result of query execution.
"""
"""
return cls.execute_query(**kwargs)
@classmethod
@@ -152,38 +153,43 @@ class BaseClass(Base):
case _:
return query.limit(limit).all()
@report_result
def save(self):
"""
Add the object to the database and commit
"""
# logger.debug(f"Saving object: {pformat(self.__dict__)}")
report = Report()
try:
self.__database_session__.add(self)
self.__database_session__.commit()
# self.__database_session__.merge(self)
except Exception as e:
logger.critical(f"Problem saving object: {e}")
self.__database_session__.rollback()
report.add_result(Result(msg=f"Problem saving object {e}", status="Critical"))
return report
class ConfigItem(BaseClass):
"""
Key:JSON objects to store config settings in database.
"""
"""
id = Column(INTEGER, primary_key=True)
key = Column(String(32)) #: Name of the configuration item.
value = Column(JSON) #: Value associated with the config item.
key = Column(String(32)) #: Name of the configuration item.
value = Column(JSON) #: Value associated with the config item.
def __repr__(self):
return f"ConfigItem({self.key} : {self.value})"
@classmethod
def get_config_items(cls, *args) -> ConfigItem|List[ConfigItem]:
def get_config_items(cls, *args) -> ConfigItem | List[ConfigItem]:
"""
Get desired config items from database
Returns:
ConfigItem|List[ConfigItem]: Config item(s)
"""
"""
config_items = cls.__database_session__.query(cls).all()
config_items = [item for item in config_items if item.key in args]
if len(args) == 1:
@@ -196,4 +202,5 @@ from .controls import *
from .organizations import *
from .kits import *
from .submissions import *
BasicSubmission.reagents.creator = lambda reg: SubmissionReagentAssociation(reagent=reg)

2
src/submissions/backend/db/models/kits.py
View File

@@ -1532,7 +1532,7 @@ class Process(BaseClass):
query = cls.__database_session__.query(cls)
match name:
case str():
logger.debug(f"Lookup Process with name str {name}")
# logger.debug(f"Lookup Process with name str {name}")
query = query.filter(cls.name == name)
limit = 1
case _:

50
src/submissions/backend/db/models/submissions.py
View File

@@ -23,7 +23,7 @@ import pandas as pd
from openpyxl import Workbook
from openpyxl.worksheet.worksheet import Worksheet
from openpyxl.drawing.image import Image as OpenpyxlImage
from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr
from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report
from datetime import datetime, date
from typing import List, Any, Tuple, Literal
from dateutil.parser import parse
@@ -691,7 +691,8 @@ class BasicSubmission(BaseClass):
Args:
input_dict (dict): Input sample dictionary
xl (pd.ExcelFile): original xl workbook, used for child classes mostly
xl (Workbook): original xl workbook, used for child classes mostly
custom_fields: Dictionary of locations, ranges, etc to be used by this function
Returns:
dict: Updated sample dictionary
@@ -739,6 +740,7 @@ class BasicSubmission(BaseClass):
input_excel (Workbook): initial workbook.
info (dict | None, optional): dictionary of additional info. Defaults to None.
backup (bool, optional): Whether this is part of a backup operation. Defaults to False.
custom_fields: Dictionary of locations, ranges, etc to be used by this function
Returns:
Workbook: Updated workbook
@@ -1046,14 +1048,16 @@ class BasicSubmission(BaseClass):
"""
code = 0
msg = ""
report = Report()
disallowed = ["id"]
if kwargs == {}:
raise ValueError("Need to narrow down query or the first available instance will be returned.")
for key in kwargs.keys():
if key in disallowed:
raise ValueError(
f"{key} is not allowed as a query argument as it could lead to creation of duplicate objects. Use .query() instead.")
instance = cls.query(submission_type=submission_type, limit=1, **kwargs)
sanitized_kwargs = {k: v for k, v in kwargs.items() if k not in disallowed}
# for key in kwargs.keys():
# if key in disallowed:
# raise ValueError(
# f"{key} is not allowed as a query argument as it could lead to creation of duplicate objects. Use .query() instead.")
instance = cls.query(submission_type=submission_type, limit=1, **sanitized_kwargs)
# logger.debug(f"Retrieved instance: {instance}")
if instance is None:
used_class = cls.find_polymorphic_subclass(attrs=kwargs, polymorphic_identity=submission_type)
@@ -1070,7 +1074,8 @@ class BasicSubmission(BaseClass):
else:
code = 1
msg = "This submission already exists.\nWould you like to overwrite?"
return instance, code, msg
report.add_result(Result(msg=msg, code=code))
return instance, report
# Custom context events for the ui
@@ -1135,7 +1140,7 @@ class BasicSubmission(BaseClass):
# logger.debug(widg)
widg.setParent(None)
pyd = self.to_pydantic(backup=True)
form = pyd.to_form(parent=obj)
form = pyd.to_form(parent=obj, disable=['rsl_plate_num'])
obj.app.table_widget.formwidget.layout().addWidget(form)
def add_comment(self, obj):
@@ -1352,13 +1357,29 @@ class Wastewater(BasicSubmission):
Args:
input_dict (dict): Input sample dictionary
xl (Workbook): xl (Workbook): original xl workbook, used for child classes mostly.
custom_fields: Dictionary of locations, ranges, etc to be used by this function
Returns:
dict: Updated sample dictionary
"""
input_dict = super().custom_info_parser(input_dict)
logger.debug(f"Input dict: {pformat(input_dict)}")
if xl is not None:
input_dict['csv'] = xl["Copy to import file"]
try:
input_dict['csv'] = xl["Copy to import file"]
except KeyError as e:
logger.error(e)
try:
match input_dict['rsl_plate_num']:
case dict():
input_dict['csv'] = xl[input_dict['rsl_plate_num']['value']]
case str():
input_dict['csv'] = xl[input_dict['rsl_plate_num']]
case _:
pass
except Exception as e:
logger.error(f"Error handling couldn't get csv due to: {e}")
return input_dict
@classmethod
@@ -1604,11 +1625,12 @@ class WastewaterArtic(BasicSubmission):
Args:
input_dict (dict): Input sample dictionary
xl (pd.ExcelFile): original xl workbook, used for child classes mostly
custom_fields: Dictionary of locations, ranges, etc to be used by this function
Returns:
dict: Updated sample dictionary
"""
# TODO: Clean up and move range start/stops to db somehow.
from backend.validators import RSLNamer
input_dict = super().custom_info_parser(input_dict)
egel_section = custom_fields['egel_results']
ws = xl[egel_section['sheet']]
@@ -1621,12 +1643,11 @@ class WastewaterArtic(BasicSubmission):
source_plates_section = custom_fields['source_plates']
ws = xl[source_plates_section['sheet']]
data = [dict(plate=ws.cell(row=ii, column=source_plates_section['plate_column']).value, starting_sample=ws.cell(row=ii, column=source_plates_section['starting_sample_column']).value) for ii in
range(source_plates_section['start_row'], source_plates_section['end_row'])]
range(source_plates_section['start_row'], source_plates_section['end_row']+1)]
for datum in data:
if datum['plate'] in ["None", None, ""]:
continue
else:
from backend.validators import RSLNamer
datum['plate'] = RSLNamer(filename=datum['plate'], sub_type="Wastewater").parsed_name
input_dict['source_plates'] = data
return input_dict
@@ -1820,6 +1841,7 @@ class WastewaterArtic(BasicSubmission):
input_excel (Workbook): initial workbook.
info (dict | None, optional): dictionary of additional info. Defaults to None.
backup (bool, optional): Whether this is part of a backup operation. Defaults to False.
custom_fields: Dictionary of locations, ranges, etc to be used by this function
Returns:
Workbook: Updated workbook
@@ -2798,7 +2820,7 @@ class WastewaterArticAssociation(SubmissionSampleAssociation):
DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
"""
id = Column(INTEGER, ForeignKey("_submissionsampleassociation.id"), primary_key=True)
source_plate = Column(String(16))
source_plate = Column(String(32))
source_plate_number = Column(INTEGER)
source_well = Column(String(8))
ct = Column(String(8)) #: AKA ct for N1