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