Pre code cleanup
This commit is contained in:
lwark
@@ -167,10 +167,10 @@ class BasicSubmission(BaseClass):
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dicto = dict(
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details_ignore=['excluded', 'reagents', 'samples',
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'extraction_info', 'comment', 'barcode',
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'platemap', 'export_map', 'equipment', 'tips'],
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'platemap', 'export_map', 'equipment', 'tips', 'custom'],
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# NOTE: Fields not placed in ui form
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form_ignore=['reagents', 'ctx', 'id', 'cost', 'extraction_info', 'signed_by', 'comment', 'namer',
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'submission_object', "tips", 'contact_phone'] + recover,
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'submission_object', "tips", 'contact_phone', 'custom'] + recover,
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# NOTE: Fields not placed in ui form to be moved to pydantic
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form_recover=recover
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)
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@@ -347,12 +347,14 @@ class BasicSubmission(BaseClass):
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logger.error(f"Error setting tips: {e}")
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tips = None
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cost_centre = self.cost_centre
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custom = self.custom
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else:
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reagents = None
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samples = None
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equipment = None
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tips = None
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cost_centre = None
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custom = None
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# logger.debug("Getting comments")
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try:
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comments = self.comment
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@@ -381,6 +383,7 @@ class BasicSubmission(BaseClass):
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# logger.debug(f"Setting contact to: {contact} of type: {type(contact)}")
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output["contact"] = contact
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output["contact_phone"] = contact_phone
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output["custom"] = custom
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return output
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def calculate_column_count(self) -> int:
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@@ -549,26 +552,29 @@ class BasicSubmission(BaseClass):
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case "ctx" | "csv" | "filepath" | "equipment":
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return
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case item if item in self.jsons():
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# logger.debug(f"Setting JSON attribute.")
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existing = self.__getattribute__(key)
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if value is None or value in ['', 'null']:
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logger.error(f"No value given, not setting.")
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return
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if existing is None:
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existing = []
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if value in existing:
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logger.warning("Value already exists. Preventing duplicate addition.")
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return
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else:
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if isinstance(value, list):
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existing += value
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else:
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if value is not None:
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if key == "custom":
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existing = value
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match value:
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case list():
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# logger.debug(f"Setting JSON attribute.")
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existing = self.__getattribute__(key)
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if value is None or value in ['', 'null']:
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logger.error(f"No value given, not setting.")
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return
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if existing is None:
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existing = []
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if value in existing:
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logger.warning("Value already exists. Preventing duplicate addition.")
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return
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else:
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if isinstance(value, list):
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existing += value
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else:
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existing.append(value)
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if value is not None:
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if key == "custom":
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existing = value
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else:
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existing.append(value)
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case _:
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existing = value
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self.__setattr__(key, existing)
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flag_modified(self, key)
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return
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@@ -749,9 +755,8 @@ class BasicSubmission(BaseClass):
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# logger.debug(f"Input dict: {input_dict}")
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# logger.debug(f"Custom fields: {custom_fields}")
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input_dict['custom'] = {}
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for k,v in custom_fields.items():
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logger.debug(f"Attempting custom parse of {k}: {v}")
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for k, v in custom_fields.items():
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# logger.debug(f"Attempting custom parse of {k}: {v}")
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match v['type']:
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case "exempt":
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continue
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@@ -766,8 +771,9 @@ class BasicSubmission(BaseClass):
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if v['start_column'] != v['end_column']:
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v['end_column'] = v['end_column'] + 1
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for ii in range(v['start_row'], v['end_row']):
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for jj in range(v['start_column'], v['end_column']+1):
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input_dict['custom'][k].append(dict(value=ws.cell(row=ii, column=jj).value, row=ii, column=jj))
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for jj in range(v['start_column'], v['end_column'] + 1):
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input_dict['custom'][k].append(
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dict(value=ws.cell(row=ii, column=jj).value, row=ii, column=jj))
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return input_dict
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@classmethod
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@@ -819,7 +825,7 @@ class BasicSubmission(BaseClass):
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logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} autofill")
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logger.debug(f"Input dict: {info}")
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logger.debug(f"Custom fields: {custom_fields}")
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for k,v in custom_fields.items():
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for k, v in custom_fields.items():
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try:
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assert v['type'] in ['exempt', 'range', 'cell']
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except (AssertionError, KeyError):
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@@ -1170,6 +1176,7 @@ class BasicSubmission(BaseClass):
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if "submitted_date" not in kwargs.keys():
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instance.submitted_date = date.today()
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else:
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logger.warning(f"Found existing instance: {instance}, asking to overwrite.")
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code = 1
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msg = "This submission already exists.\nWould you like to overwrite?"
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report.add_result(Result(msg=msg, code=code))
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@@ -1659,7 +1666,8 @@ class Wastewater(BasicSubmission):
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continue
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copy = dict(submitter_id=sample['submitter_id'], row=row, column=column)
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well_24.append(copy)
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input_dict['origin_plate'] = [item for item in DocxWriter.create_plate_map(sample_list=well_24, rows=4, columns=6)]
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input_dict['origin_plate'] = [item for item in
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DocxWriter.create_plate_map(sample_list=well_24, rows=4, columns=6)]
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return input_dict
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@@ -1728,14 +1736,22 @@ class WastewaterArtic(BasicSubmission):
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ws = wb[info_dict['sheet']]
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img_loader = SheetImageLoader(ws)
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for ii in range(info_dict['start_row'], info_dict['end_row'] + 1):
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logger.debug(f"Checking row: {ii}")
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# logger.debug(f"Checking row: {ii}")
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for jj in range(info_dict['start_column'], info_dict['end_column'] + 1):
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# logger.debug(f"Checking column: {jj}")
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cell_str = f"{row_map[jj]}{ii}"
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if img_loader.image_in(cell_str):
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return img_loader.get(cell_str)
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try:
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return img_loader.get(cell_str)
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except ValueError as e:
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logger.error(f"Could not open image from cell: {cell_str} due to {e}")
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return None
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return None
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input_dict = super().custom_info_parser(input_dict)
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input_dict['submission_type'] = dict(value="Wastewater Artic", missing=False)
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logger.debug(f"Custom fields: {custom_fields}")
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egel_section = custom_fields['egel_controls']
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ws = xl[egel_section['sheet']]
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